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At the moment DNA Sequence Assembler is cited in almost 900 articles, at a rate of about 0.9 citations per day.

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DNA Sequence Assembler was cited in the following articles

  • Tomas Cermak, Z.K., Roman Hobza, Andrea Koblizkova, Alex Widmer, Jiri Macas, Boris Vyskot and Eduard Kejnovsky (2008) Survey of repetitive sequences in Silene latifolia with respect to their distribution on sex chromosomes Chromosome Research 16: 961-976.
  • Vatsala, T.M., Raj, S.M., and Manimaran, A. (2008) A pilot-scale study of biohydrogen production from distillery effluent using defined bacterial co-culture. International Journal of Hydrogen Energy 33: 5404-5415.
  • Worm, P., Fermoso, F.G., Lens, P.N.L., and Plugge, C.M. (2009) Decreased activity of a propionate degrading community in a UASB reactor fed with synthetic medium without molybdenum, tungsten and selenium. Enzyme and Microbial Technology 45: 139-145.
  • Ajiboye, Remi M., Solberg, Owen D., Lee, Bryan M., Raphael, E., DebRoy, C., and Riley, Lee W. (2009) Global Spread of Mobile Antimicrobial Drug Resistance Determinants in Human and Animal Escherichia coli and Salmonella Strains Causing Community-Acquired Infections. Clinical Infectious Diseases 49: 365-371.
  • Ami, E.B., Yuval, B., and Jurkevitch, E. (2009) Manipulation of the microbiota of mass-reared Mediterranean fruit flies Ceratitis capitata (Diptera: Tephritidae) improves sterile male sexual performance. ISME J.
  • Behrens, S., Azizian, M.F., McMurdie, P.J., Sabalowsky, A., Dolan, M.E., Semprini, L., and Spormann, A.M. (2008) Monitoring Abundance and Expression of "Dehalococcoides" Species Chloroethene-Reductive Dehalogenases in a Tetrachloroethene-Dechlorinating Flow Column. Applied and Environmental Microbiology 74: 5695-5703.
  • Falk, M.W., Song, K.-G., Matiasek, M.G., and Wuertz, S. (2009) Microbial community dynamics in replicate membrane bioreactors - Natural reproducible fluctuations. Water Research 43: 842-852.
  • Gaëtan, B., Thomas Le, C., Danielle, A., Philippe, V., and Georges, B. (2009) Diversity of culturable marine filamentous fungi from deep-sea hydrothermal vents. Environmental Microbiology 11: 1588-1600.
  • Guay, J.-F., Boudreault, S., Michaud, D., and Cloutier, C. (2009) Impact of environmental stress on aphid clonal resistance to parasitoids: Role of Hamiltonella defensa bacterial symbiosis in association with a new facultative symbiont of the pea aphid. Journal of Insect Physiology 55: 919-926.
  • Kröber, M., Bekel, T., Diaz, N.N., Goesmann, A., Jaenicke, S., Krause, L. et al. (2009) Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing. Journal of Biotechnology 142: 38-49.
  • María-Eugenia Guazzaroni, A.B., Peter N. Golyshin, Manuel Ferrer (2009) Metagenomics as a new technological tool to gain scientific knowledge. World Journal of Microbiology and Biotechnology 25: 945-954.
  • Musat, F., and Widdel, F. (2008) Anaerobic degradation of benzene by a marine sulfate-reducing enrichment culture, and cell hybridization of the dominant phylotype. Environmental Microbiology 10: 10-19.
  • Musat, F., Galushko, A., Jacob, J., Widdel, F., Kube, M., Reinhardt, R. et al. (2009) Anaerobic degradation of naphthalene and 2-methylnaphthalene by strains of marine sulfate-reducing bacteria. Environmental Microbiology 11: 209-219.
  • Nayak, S.N., Balaji, J., Upadhyaya, H.D., Hash, C.T., Kishor, P.B.K., Chattopadhyay, D. et al. (2009) Isolation and sequence analysis of DREB2A homologues in three cereal and two legume species. Plant Science 177: 460-467.
  • Pillai, M.R., Hariharan, R., Janki Mohan, B., Lakshmi, S., Chiplunkar, S.V., Patkar, M. et al. (2009) Molecular variants of HPV-16 associated with cervical cancer in Indian population. International Journal of Cancer 125: 91-103.
  • Ram Kumar Pandian, S., Deepak, V., Kalishwaralal, K., Muniyandi, J., Rameshkumar, N., and Gurunathan, S. (2009a) Synthesis of PHB nanoparticles from optimized medium utilizing dairy industrial waste using Brevibacterium casei SRKP2: A green chemistry approach. Colloids and Surfaces B: Biointerfaces 74: 266-273.
  • Ram Kumar Pandian, S., Deepak, V., Kalishwaralal, K., Rameshkumar, N., Jeyaraj, M., and Gurunathan, S. (2009b) Optimization and fed-batch production of PHB utilizing dairy waste and sea water as nutrient sources by Bacillus megaterium SRKP-3. Bioresource Technology 101: 705-711.
  • Sampaio, S.C.F., Gomes, T.A.T., Pichon, C., du Merle, L., Guadagnini, S., Abe, C.M. et al. (2009) The Flagella of an Atypical Enteropathogenic Escherichia coli Strain Are Required for Efficient Interaction with and Stimulation of Interleukin-8 Production by Enterocytes In Vitro. Infection and Immunity 77: 4406-4413.
  • Adiputra, Y. T., et al. (2011). "Genetic relationship of milkfish (Chanos chanos) from Indonesia, the Philippines and Taiwan using mitochondrial cytochrome b sequences." Journal of Applied Ichthyology 27(4): 1100-1103.
  • Amacher, J., et al. (2009). "Molecular approach to determine contributions of the protist community to particle flux." Deep Sea Research Part I: Oceanographic Research Papers 56(12): 2206-2215.
  • Basile, M. A., et al. (2010). "The effect of the surface charge of hydrogel supports on thermophilic biohydrogen production." Bioresource Technology 101(12): 4386-4394.
  • Ben Khalifa, M. and H. Fakhfakh (2011). "Note Detection of 16S rDNA of ‘Candidatus Phytoplasma mali’ in plum decline in Tunisia." Canadian Journal of Plant Pathology 33(3): 332-336.
  • Berlin, S., et al. (2010). "High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus</i&gt." BMC Genomics 11(1): 1-14.
  • Bienapfl, J. C., et al. (2011). "Specific molecular detection of Phytophthora sojae using conventional and real-time PCR." Fungal Biology 115(8): 733-740.
  • Blaskó, B., et al. (2009). "Linkage analysis of the C4A/C4B copy number variation and polymorphisms of the adjacent steroid 21-hydroxylase gene in a healthy population." Molecular Immunology 46(13): 2623-2629.
  • Blomconfidence scoreist, M., et al. (2012). "Chlamydia psittaci in Swedish wetland birds: A risk to zoonotic infection?" Avian Diseases: null-null.
  • Amatulli, M., et al. "Conventional and real-time PCR for the identification of Fusarium fujikuroi and Fusarium proliferatum from diseased rice tissues and seeds." European Journal of Plant Pathology: 1-8.
  • Amatulli, M. T., et al. (2010). "Molecular identification of Fusarium spp. associated with bakanae disease of rice in Italy and assessment of their pathogenicity." Plant Pathology 59(5): 839-844.
  • Cardenas, A., et al. (2012). "Shifts in bacterial communities of two caribbean reef-building coral species affected by white plague disease." ISME J 6(3): 502-512.
  • Carrillo-Reyes, J., et al. (2012). "Different start-up strategies to enhance biohydrogen production from cheese whey in UASB reactors." International Journal of Hydrogen Energy 37(7): 5591-5601.
  • Cervantes, F. J., et al. (2011). "Anaerobic degradation of benzene by enriched consortia with humic acids as terminal electron acceptors." Journal of Hazardous Materials 195(0): 201-207.
  • Christelová, P., et al. (2011). "A multi gene sequence-based phylogeny of the Musaceae (banana) family." BMC Evolutionary Biology 11(1): 1-13.
  • Allue-Guardia, A., et al. (2011). "Bacteriophage-encoding cytolethal distending toxin type V gene induced from nonclinical Escherichia coli isolates." Infect Immun 79(8): 3262-3272.
    Cytolethal distending toxin (Cdt) is produced by a variety of pathogenic bacteria, including pathogenic serotypes of Shiga toxin-producing Escherichia coli (STEC). The Cdt family comprises five variants (Cdt-I to Cdt-V) encoded by three genes located within the chromosome or plasmids or, in the case of Cdt-I, within bacteriophages. In this study, we evaluated the occurrence of the cdt gene in a collection of 140 environmental STEC isolates. cdt was detected in 12.1% of strains, of which five strains carried inducible bacteriophages containing the Cdt-V variant. Two Cdt-V phages of the Siphoviridae morphology lysogenized Shigella sonnei, generating two lysogens: a single Cdt phage lysogen and a double lysogen, containing a Cdt phage and an Stx phage, both from the wild-type strain. The rates of induction of Cdt phages were evaluated by quantitative PCR, and spontaneous induction of Cdt-V phage was observed, whereas induction of Stx phage in the double lysogen was mitomycin C dependent. The Cdt distending effect was observed in HeLa cells inoculated with the supernatant of the Cdt-V phage lysogen. A ClaI fragment containing the cdt-V gene of one phage was cloned, and sequencing confirmed the presence of Cdt-V, as well as a fragment downstream from the cdt homolog to gpA, encoding a replication protein of bacteriophage P2. Evaluation of Cdt-V phages in nonclinical water samples showed densities of 10(2) to 10(9) gene copies in 100 ml, suggesting the high prevalence of Cdt phages in nonclinical environments.
  • Antony, R., et al. (2012). "Diversity and physiology of culturable bacteria associated with a coastal Antarctic ice core." Microbiological Research 167(6): 372-380.
    Microbiological studies of polar ice at different depths may provide important comparisons, as they preserve records of microbial cells and past climate. In this study, we examined bacterial abundance, diversity and glaciochemical composition from three depths of an ice core from coastal Dronning Maud Land, East Antarctica. Higher bacterial abundance corresponded with high in situ sea-salt Na+ and dust concentration, suggesting that bacteria might have been transported and deposited into ice along with dust particles and marine aerosols. Fourteen bacterial isolates belonging to the genera Methylobacterium, Brevundimonas, Paenibacillus, Bacillus and Micrococcus were retrieved. Frequent isolation of similar bacterial genera from different cold environments suggests that they possess features that enable survival and metabolism for extended periods of time at sub-zero temperatures. The highest number and diversity of recoverable bacteria was obtained from 49 m depth corresponding to 1926 AD and consisted of bacteria from 4 different genera whereas at 11 m (1989 AD) and 33 m (1953 AD) samples only species belonging to the genera Bacillus was recovered. Among the Bacillus species, Bacillus aryabhattai which has been reported only from the upper stratosphere, was isolated and is the first record from the Earth's surface. Methylobacterium was the most dominant genera at 49 m depth and its prevalence is attributable to a combination of high in situ methanesulfonate concentration, specialized metabolism and environmental hardiness of Methylobacterium. Some of the isolated bacteria were found to respire and grow using methanesulfonate, suggesting that they may utilize this substrate to sustain growth in ice. In addition, NO3? (2.93–3.69 ?M), NH4+ (1.45–3.90 ?M) and PO43? (0.01–0.75 ?M) present in the ice could be potential sources fueling bacterial metabolism in this environment. It could be deduced from the study that variation in bacterial abundance and diversity was probably associated with the prevailing in situ conditions in ice.
  • Azziz, G., et al. (2012). "Abundance, diversity and prospecting of culturable phosphate solubilizing bacteria on soils under crop–pasture rotations in a no-tillage regime in Uruguay." Applied Soil Ecology 61(0): 320-326.
    Phosphate solubilizing bacteria (PSB) abundance and diversity were examined during two consecutive years, 2007 and 2008, in a crop/pasture rotation experiment in Uruguay. The study site comprised five treatments with different soil use intensity under a no-tillage regime. In the first year of sampling, abundance of PSB was significantly higher in natural prairie (NP) and permanent pasture (PP) than in continuous cropping (CC); rotation treatments harbored populations that did not differ significantly from those in the others. The percentage of PSB relative to total heterotrophic bacteria ranged between 0.18% and 13.13%. PSB diversity also showed statistical differences among treatments, with PP populations more diverse than those present in CC. In the second year sampled no differences were found in PSB abundance or diversity. Two hundred and fifty PSB were isolated in 2007 and classified according to their phosphate solubilization activity in vitro. Twelve of these isolates showing the greatest solubilization activity were selected for 16S rDNA sequencing. Ten isolates presumably belong to the genus Pseudomonas and two isolates showed high similarity with members of the genera Burkholderia and Acinetobacter.
  • Bartoš, J., et al. (2011). "Genetic mapping of DArT markers in the Festuca – Lolium complex and their use in freezing tolerance association analysis." TAG Theoretical and Applied Genetics 122(6): 1133-1147.
    Species belonging to the Festuca – Lolium complex are important forage and turf species and as such, have been studied intensively. However, their out-crossing nature and limited availability of molecular markers make genetic studies difficult. Here, we report on saturation of F. pratensis and L. multiflorum genetic maps using Diversity Array Technology (DArT) markers and the DArTFest array.The 530 and 149 DArT markers were placed on genetic maps of L. multiflorum and F. pratensis , respectively, with overlap of 20 markers, which mapped in both species. The markers were sequenced and comparative sequence analysis was performed between L. multiflorum , rice and Brachypodium . The utility of the DArTFest array was then tested on a Festulolium population FuRs0357 in an integrated analysis using the DArT marker map positions to study associations between markers and freezing tolerance. Ninety six markers were significantly associated with freezing tolerance and five of these markers were genetically mapped to chromosomes 2, 4 and 7. Three genomic loci associated with freezing tolerance in the FuRs0357 population co-localized with chromosome segments and QTLs previously indentified to be associated with freezing tolerance. The present work clearly confirms the potential of the DArTFest array in genetic studies of the Festuca–Lolium complex. The annotated DArTFest array resources could accelerate further studies and improvement of desired traits in Festuca–Lolium species.
  • Blomconfidence scoreist, M., et al. (2012). "Chlamydia psittaci in birds of prey, Sweden." Infect Ecol Epidemiol 2.
    BACKGROUND: Chlamydia psittaci is an intracellular bacterium primarily causing respiratory diseases in birds but may also be transmitted to other animals, including humans. The prevalence of the pathogen in wild birds in Sweden is largely unknown. METHODS: DNA was extracted from cloacae swabs and screened for C. psittaci by using a 23S rRNA gene PCR assay. Partial 16S rRNA and ompA gene fragments were sequence determined and phylogenies were analysed by the neighbour-joining method. RESULTS AND CONCLUSION: The C. psittaci prevalence was 1.3% in 319 Peregrine Falcons and White-tailed Sea Eagles, vulnerable top-predators in Sweden. 16S rRNA and ompA gene analysis showed that novel Chlamydia species, as well as novel C. psittaci strains, are to be found among wild birds.
  • BOGERT, V. D., et al. (2011). Microarray Analysis and Barcoded Pyrosequencing Provide Consistent Microbial Profiles Depending on the Source of Human Intestinal Samples. Washington, DC, ETATS-UNIS, American Society for Microbiology.
    Large-scale and in-depth characterization of the intestinal microbiota necessitates application of high-throughput 16S rRNA gene-based technologies, such as barcoded pyrosequencing and phylogenetic microarray analysis. In this study, the two techniques were compared and contrasted for analysis of the bacterial composition in three fecal and three small intestinal samples from human individuals. As PCR remains a crucial step in sample preparation for both techniques, different forward primers were used for amplification to assess their impact on microbial profiling results. An average of 7,944 pyrosequences, spanning the V1 and V2 region of 16S rRNA genes, was obtained per sample. Although primer choice in barcoded pyrosequencing did not affect species richness and diversity estimates, detection of Actinobacteria strongly depended on the selected primer. Microbial profiles obtained by pyrosequencing and phylogenetic microarray analysis (HITChip) correlated strongly for fecal and ileal lumen samples but were less concordant for ileostomy effluent. Quantitative PCR was employed to investigate the deviations in profiling between pyrosequencing and HITChip analysis. Since cloning and sequencing of random 16S rRNA genes from ileostomy effluent confirmed the presence of novel intestinal phylotypes detected by pyrosequencing, especially those belonging to the Veillonella group, the divergence between pyrosequencing and the HITChip is likely due to the relatively low number of available 16S rRNA gene sequences of small intestinal origin in the DNA databases that were used for HITChip probe design. Overall, this study demonstrated that equivalent biological conclusions are obtained by high-throughput profiling of microbial communities, independent of technology or primer choice.
  • Cabral, T. S., et al. (2012). "Abrachium, a new genus in the Clathraceae, and Itajahya reassessed." Mycotaxon 119(1): 419-429.
  • Christensen, E. G., et al. (2011). "Sublethal triclosan exposure decreases susceptibility to gentamicin and other aminoglycosides in Listeria monocytogenes." Antimicrob Agents Chemother 55(9): 4064-4071.
    The human food-borne pathogen Listeria monocytogenes is capable of persisting in food processing plants despite cleaning and sanitation and is likely exposed to sublethal biocide concentrations. This could potentially affect susceptibility of the bacterium to biocides and other antimicrobial agents. The purpose of the present study was to determine if sublethal biocide concentrations affected antibiotic susceptibility in L. monocytogenes. Exposure of L. monocytogenes strains EGD and N53-1 to sublethal concentrations of Incimaxx DES (containing peroxy acids and hydrogen peroxide) and Triquart Super (containing quaternary ammonium compound) in four consecutive cultures did not alter the frequency of antibiotic-tolerant isolates, as determined by plating on 2x the MIC for a range of antibiotics. Exposure of eight strains of L. monocytogenes to 1 and 4 mug/ml triclosan did not alter triclosan sensitivity. However, all eight strains became resistant to gentamicin (up to 16-fold increase in MIC) after exposure to sublethal triclosan concentrations. Gentamicin-resistant isolates of strains N53-1 and 4446 were also resistant to other aminoglycosides, such as kanamycin, streptomycin, and tobramycin. Gentamicin resistance remained at a high level also after five subcultures without triclosan or gentamicin. Aminoglycoside resistance can be caused by mutations in the target site, the 16S rRNA gene. However, such mutations were not detected in the N53-1-resistant isolates. A combination of gentamicin and ampicillin is commonly used in listeriosis treatment. The triclosan-induced resistance is, hence, of great concern. Further investigations are needed to determine the molecular mechanisms underlying the effect of triclosan.
  • Christerson, L., et al. (2012). "Chlamydia trachomatis strains show specific clustering for men who have sex with men compared to heterosexual transmission in Sweden, the Netherlands and the United States." J Clin Microbiol.
    High-resolution genotyping of Chlamydia trachomatis improves characterization of strains infecting different patient groups and sexual networks. In this study multilocus-sequence typing (MLST) and ompA sequence determination was used for analysis of C. trachomatis strains from 203 men who have sex with men (MSM) from Sweden, the Netherlands and the United States. Obtained results were compared with data from 153 heterosexual women from Sweden and the Netherlands. The overlap in MLST/ompA-profiles between MSM from Sweden and the Netherlands was 68%, while the overlap between heterosexuals from these countries was only 18%. The distribution of genotypes in MSM from the United States was less similar to the European countries, with respectively 45% and 46% overlap with MSM in Sweden and the Netherlands. Minimum spanning tree analysis of MLST/ompA sequence types identified two large clusters that contained almost exclusively MSM and comprised 74% of all MSM samples. Three other clusters were predominated by samples from women, but also contained MSM specimens. Of 19 detected variants of the MLST target CT144, three variants were highly associated with MSM. Our study supports both the hypothesis of tissue tropism as well as epidemiological network structures as explanations to linkage between specific genetic variants and sexual orientation.
  • Christerson, L. and B. Herrmann (2012). Guidelines for High-Resolution Genotyping of Chlamydia trachomatis Using Multilocus Sequence Analysis Diagnosis of Sexually Transmitted Diseases. C. R. MacKenzie and B. Henrich, Humana Press. 903: 51-64.
  • Darissa, O., et al. (2010). "Optimized approaches for the sequence determination of double-stranded RNA templates." Journal of Virological Methods 169(2): 397-403.
  • Direito, S. O. L., et al. (2011). "A wide variety of putative extremophiles and large beta-diversity at the Mars Desert Research Station (Utah)." International Journal of Astrobiology 10(Special Issue 03): 191-207.
    Humankind's innate curiosity makes us wonder whether life is or was present on other planetary bodies such as Mars. The EuroGeoMars 2009 campaign was organized at the Mars Desert Research Station (MDRS) to perform multidisciplinary astrobiology research. MDRS in southeast Utah is situated in a cold arid desert with mineralogy and erosion processes comparable to those on Mars. Insight into the microbial community composition of this terrestrial Mars analogue provides essential information for the search for life on Mars: including sampling and life detection methodology optimization and what kind of organisms to expect. Soil samples were collected from different locations. Culture-independent molecular analyses directed at ribosomal RNA genes revealed the presence of all three domains of life (Archaea, Bacteria and Eukarya), but these were not detected in all samples. Spiking experiments revealed that this appears to relate to low DNA recovery, due to adsorption or degradation. Bacteria were most frequently detected and showed high alpha- and beta-diversity. Members of the Actinobacteria, Proteobacteria, Bacteroidetes and Gemmatimonadetes phyla were found in the majority of samples. Archaea alpha- and beta-diversity was very low. For Eukarya, a diverse range of organisms was identified, such as fungi, green algae and several phyla of Protozoa. Phylogenetic analysis revealed an extraordinary variety of putative extremophiles, mainly Bacteria but also Archaea and Eukarya. These comprised radioresistant, endolithic, chasmolithic, xerophilic, hypolithic, thermophilic, thermoacidophilic, psychrophilic, halophilic, haloalkaliphilic and alkaliphilic micro-organisms. Overall, our data revealed large difference in occurrence and diversity over short distances, indicating the need for high-sampling frequency at similar sites. DNA extraction methods need to be optimized to improve extraction efficiencies.
  • Divya, B., et al. (2011). "16S rRNA-based bacterial diversity in the organic-rich sediments underlying oxygen-deficient waters of the eastern Arabian Sea." World Journal of Microbiology and Biotechnology 27(12): 2821-2833.
  • Elbir, H., et al. (2010). "Ovine clone ST1464: a predominant genotype of Staphylococcus aureus subsp. anaerobius isolated from sheep in Sudan." J Infect Dev Ctries 4(4): 235-238.
    BACKGROUND: The aim of the present study was to examine the phenotypic and genotypic relatedness of 17 Staphylococcus aureus subsp. anaerobius isolates recovered from sheep abscesses in Khartoum state, Sudan, during the period 2007-2008. METHODOLOGY: This sample was characterised using antibiogram typing, biochemical typing with the commercial PhenePlate system (PhP-CS) and multilocus sequence typing (MLST). RESULTS: Low levels of resistance were noted to the 11 antimicrobial agents tested. All the isolates corresponded to a single PhP type, and to a single, novel, multilocus sequence type, designated ST1464. CONCLUSION: These results demonstrate that the vast majority of cases of sheep abscess disease in Khartoum state are caused by a single novel clone of S. aureus subsp. anaerobius.
  • Emmerich, M., et al. (2012). "Abundance, distribution, and activity of Fe(II)-oxidizing and Fe(III)-reducing microorganisms in hypersaline sediments of Lake Kasin, southern Russia." Appl Environ Microbiol 78(12): 4386-4399.
    The extreme osmotic conditions prevailing in hypersaline environments result in decreasing metabolic diversity with increasing salinity. Various microbial metabolisms have been shown to occur even at high salinity, including photosynthesis as well as sulfate and nitrate reduction. However, information about anaerobic microbial iron metabolism in hypersaline environments is scarce. We studied the phylogenetic diversity, distribution, and metabolic activity of iron(II)-oxidizing and iron(III)-reducing Bacteria and Archaea in pH-neutral, iron-rich salt lake sediments (Lake Kasin, southern Russia; salinity, 348.6 g liter(-1)) using a combination of culture-dependent and -independent techniques. 16S rRNA gene clone libraries for Bacteria and Archaea revealed a microbial community composition typical for hypersaline sediments. Most-probable-number counts confirmed the presence of 4.26 x 10(2) to 8.32 x 10(3) iron(II)-oxidizing Bacteria and 4.16 x 10(2) to 2.13 x 10(3) iron(III)-reducing microorganisms per gram dry sediment. Microbial iron(III) reduction was detected in the presence of 5 M NaCl, extending the natural habitat boundaries for this important microbial process. Quantitative real-time PCR showed that 16S rRNA gene copy numbers of total Bacteria, total Archaea, and species dominating the iron(III)-reducing enrichment cultures (relatives of Halobaculum gomorrense, Desulfosporosinus lacus, and members of the Bacilli) were highest in an iron oxide-rich sediment layer. Combined with the presented geochemical and mineralogical data, our findings suggest the presence of an active microbial iron cycle at salt concentrations close to the solubility limit of NaCl.
  • Galindo, R. C., et al. (2012). "Gene expression profile suggests that pigs (Sus scrofa) are susceptible to Anaplasma phagocytophilum but control infection." Parasit Vectors 5(1): 181.
    ABSTRACT: BACKGROUND: Anaplasma phagocytophilum infects a wide variety of hosts and causes granulocytic anaplasmosis in humans, horses and dogs and tick-borne fever in ruminants. Infection with A. phagocytophilum results in the modification of host gene expression and immune response. The objective of this research was to characterize gene expression in pigs (Sus scrofa) naturally and experimentally infected with A. phagocytophilum trying to identify mechanisms that help to explain low infection prevalence in this species. RESULTS: For gene expression analysis in naturally infected pigs, microarray hybridization was used. The expression of differentially expressed immune response genes was analyzed by real-time RT-PCR in naturally and experimentally infected pigs. Results suggested that A. phagocytophilum infection affected cytoskeleton rearrangement and increased both innate and adaptive immune responses by up regulation of interleukin 1 receptor accessory protein-like 1 (IL1RAPL1), T-cell receptor alpha chain (TCR-alpha), thrombospondin 4 (TSP-4) and Gap junction protein alpha 1 (GJA1) genes. Higher serum levels of IL-1 beta, IL-8 and TNF-alpha in infected pigs when compared to controls supported data obtained at the mRNA level. CONCLUSIONS: These results suggested that pigs are susceptible to A. phagocytophilum but control infection, particularly through activation of innate immune responses, phagocytosis and autophagy. This fact may account for the low infection prevalence detected in pigs in some regions and thus their low or no impact as a reservoir host for this pathogen. These results advanced our understanding of the molecular mechanisms at the host-pathogen interface and suggested a role for newly reported genes in the protection of pigs against A. phagocytophilum.
  • Gao, J., et al. (2012). A Chinese patient with acquired partial lipodystrophy caused by a novel mutation with LMNB2 gene. Journal of Pediatric Endocrinology and Metabolism. 25: 375.
  • Gujaria, N., et al. (2011). "Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea ( Cicer arietinum L.)." TAG Theoretical and Applied Genetics 122(8): 1577-1589.
    A transcript map has been constructed by the development and integration of genic molecular markers (GMMs) including single nucleotide polymorphism (SNP), genic microsatellite or simple sequence repeat (SSR) and intron spanning region (ISR)-based markers, on an inter-specific mapping population of chickpea, the third food legume crop of the world and the first food legume crop of India. For SNP discovery through allele re-sequencing, primer pairs were designed for 688 genes/expressed sequence tags (ESTs) of chickpea and 657 genes/ESTs of closely related species of chickpea. High-quality sequence data obtained for 220 candidate genic regions on 2–20 genotypes representing 9 Cicer species provided 1,893 SNPs with an average frequency of 1/35.83 bp and 0.34 PIC (polymorphism information content) value. On an average 2.9 haplotypes were present in 220 candidate genic regions with an average haplotype diversity of 0.6326. SNP2CAPS analysis of 220 sequence alignments, as mentioned above, provided a total of 192 CAPS candidates. Experimental analysis of these 192 CAPS candidates together with 87 CAPS candidates identified earlier through in silico mining of ESTs provided scorable amplification in 173 (62.01%) cases of which predicted assays were validated in 143 (82.66%) cases (CGMM). Alignments of chickpea unigenes with Medicago truncatula genome were used to develop 121 intron spanning region (CISR) markers of which 87 yielded scorable products. In addition, optimization of 77 EST-derived SSR (ICCeM) markers provided 51 scorable markers. Screening of easily assayable 281 markers including 143 CGMMs, 87 CISRs and 51 ICCeMs on 5 parental genotypes of three mapping populations identified 104 polymorphic markers including 90 markers on the inter-specific mapping population. Sixty-two of these GMMs together with 218 earlier published markers (including 64 GMM loci) and 20 other unpublished markers could be integrated into this genetic map. A genetic map developed here, therefore, has a total of 300 loci including 126 GMM loci and spans 766.56 cM, with an average inter-marker distance of 2.55 cM. In summary, this is the first report on the development of large-scale genic markers including development of easily assayable markers and a transcript map of chickpea. These resources should be useful not only for genome analysis and genetics and breeding applications of chickpea, but also for comparative legume genomics.
  • Haines, W. P. and D. Rubinoff (2012). "Molecular phylogenetics of the moth genus Omiodes Guenée (Crambidae: Spilomelinae), and the origins of the Hawaiian lineage." Molecular Phylogenetics and Evolution 65(1): 305-316.
    The moth genus Omiodes (Crambidae) comprises about 80 species and has a circumtropical distribution, with the type species, O. humeralis, occurring in Central America. In Hawaii, there are 23 native species currently placed in Omiodes, but this classification has been disputed, and they were previously placed in various other genera. We used molecular phylogenetic analyses to assess the monophyly of Omiodes as a whole, and specifically of the Hawaiian species, as well as their geographic origins and possible ancestral host plants. Mitochondrial (COI) and nuclear (wingless, EF1?, CAD, and RPS5) DNA was sequenced for Omiodes from Hawaii, South America, and Australasia, along with many other putative outgroup spilomeline genera. Phylogenies were estimated using maximum likelihood and Bayesian inference, and various taxon and character datasets. With the exception of two paleotropical species (O. basalticalis and O. odontosticta, whose placement was unresolved) all Hawaiian, paleotropical and neotropical Omiodes, including the type species, fell within a well-supported, monophyletic clade. Although the center of diversity for Omiodes is in the Neotropics, its center of origin was ambiguous, due to poor resolution of the basal splits between paleotropical and neotropical Omiodes. Very low genetic divergence within the Hawaiian Omiodes suggests a relatively recent colonization of the Hawaiian Islands. Phylogenies constructed using all codon positions were poorly resolved at intergeneric levels, and did not reveal a sister taxon for Omiodes, but phylogenies constructed using only first and second codon positions suggested a close relationship with Cnaphalocrocis. The monophyly of several other spilomeline genera is also discussed.
  • Harimalala, M., et al. "A novel cassava-infecting begomovirus from Madagascar: cassava mosaic Madagascar virus." Archives of Virology: 1-4.
  • Harishankar, A., et al. (2012). "Phylogenetic comparison of exonic US4, US7 and UL44 regions of clinical herpes simplex virus type 1 isolates showed lack of association between their anatomic sites of infection and genotypic/sub genotypic classification." Virology Journal 9(1): 65.
    BACKGROUND:HSV-1 genome is a mosaic of recombinants. Clinical Herpes simplex virus -1 (HSV1) isolates were already genotyped as A, B and C types based on nucleotide variations at Unique Short (US) 4 (gG) and US 7 (gI) regions through phylogeny. Analysis of Glycoprotein C (gC) exon present on the Unique Long (UL) region had also revealed the existence of different genotypes. Glycoprotein C is mainly involved in initial viral attachment to heparan sulphate on host cell surface facilitating the virus's binding and penetration into cell. As the amount of heparan sulphate on the host cell surface varies according to the cell type, it is plausible that different genotypes bind differentially to cell types. Hence, this study was framed to determine the existence of novel genotypes/sub genotypes in the US or UL regions which could associate with clinical entities.RESULTS:All the twenty five isolates analyzed in this study were of genotype A as per their gG gene sequences. In case of gI gene, 16 out of 25 were found to be type A and the remaining nine were type B putative intergenic recombinants. Intragenic recombinations were also encountered in both the US genes, with gG possessing novel subgenotypes, arbitrarily designated A1 and A2. The 9 type B isolates of gI genes also branched out into 2 clades due to genetic variations. Glycoprotein C of UL region had two distinct genotypic clades alpha and beta, whose topological distribution was significantly different from that of the US region. Neither the US nor UL regions, however, showed any preference among the genotypes to a specific anatomic site of infection. Even the non synonymous variations identified in the functional domain of gC, were not confined to a particular genotype/clinical entity.CONCLUSION:The analyses of the US and UL regions of the HSV-1 genome showed the existence of variegated genotypes in these two regions. In contrary to the documented literature, in which Asian strains were concluded as more conserved than European ones, our study showed the existence of a higher degree of variability among Indian strains. However, the identified novel genotypes and subgenotypes were not found associated with clinical entities.
  • Hegler, F., et al. (2012). "Influence of seasonal and geochemical changes on iron geomicrobiology of an iron-carbonate mineral water spring." Appl Environ Microbiol.
    The Fuschna spring in the Swiss Alps (Engadin) is a bicarbonate-iron(II)-rich, pH-neutral mineral water spring that is dominated visually by dark-green microbial mats at the side of the flow channel and orange iron(III)(oxyhydr)oxides in the flow channel. Gradients of O(2), dissolved iron(II), and bicarbonate establish in the water. Our goals were to identify the dominating biogeochemical processes and to determine to which extent changing geochemical conditions along the flowpath and seasonal changes influence mineral identity, crystallinity and microbial diversity. Geochemical analysis showed microoxic water at the spring outlet which became fully oxygenated within 2.3 m downstream. XRD and Mossbauer spectroscopy revealed calcite (CaCO(3)) and ferrihydrite (Fe(OH)(3)) as the dominant minerals which increased in crystallinity with increasing distance from the spring outlet. DGGE banding pattern cluster analysis revealed that the microbial community composition shifted mainly with seasons and to a lesser extent along the flow path. 16S rRNA gene sequence analysis showed that microbial communities differ between flow channel and flanking microbial mat. Microbial community analysis in combination with MPN analyses and qPCR showed that the mat was dominated by cyanobacteria, the channel by microaerophilic Fe(II)-oxidizers (1.97x10(7)+/-4.36x10(6) 16S rRNA gene copies g(-1) using Gallionella-specific qPCR primers), while high numbers of Fe(III)-reducers (10(9) cells/g) were identified both in the mat and the flow channel. Phototrophic and nitrate-reducing Fe(II)-oxidizers were present as well - although in lower numbers (10(3)-10(4) cells/g). In summary our data suggests that mainly seasonal changes caused microbial community shifts while geochemical gradients along the flow path influenced mineral crystallinity.
  • Hermet, A., et al. (2012). "Molecular systematics in the genus Mucor with special regards to species encountered in cheese." Fungal Biology 116(6): 692-705.
    The genus Mucor, a member of the order Mucorales, comprises different species encountered in cheeses. Although fungi play a fundamental role in cheese manufacturing and ripening, the taxonomy of many fungal species found in cheese is poorly defined; indeed, this is the case for Mucor spp. In the present study, we assessed the phylogenetic relationships among 70 Mucor strains, including 36 cheese isolates, by using a five gene phylogenetic approach combined with morphological analyses. Overall, at least six species of Mucor were identified among the cheese isolates including a possible new taxon. The present study also suggests that the genus Mucor comprises undescribed taxa and needs to be properly defined.
  • Jensen, J. S. (2012). Protocol for the Detection of Mycoplasma genitalium by PCR from Clinical Specimens and Subsequent Detection of Macrolide Resistance-Mediating Mutations in Region V of the 23S rRNA Gene
    Diagnosis of Sexually Transmitted Diseases. C. R. MacKenzie and B. Henrich, Humana Press. 903: 129-139.
  • Kamenetzky, L., et al. (2010). "Genomic analysis of wild tomato introgressions determining metabolism- and yield-associated traits." Plant Physiol 152(4): 1772-1786.
    With the aim of determining the genetic basis of metabolic regulation in tomato fruit, we constructed a detailed physical map of genomic regions spanning previously described metabolic quantitative trait loci of a Solanum pennellii introgression line population. Two genomic libraries from S. pennellii were screened with 104 colocated markers from five selected genomic regions, and a total of 614 bacterial artificial chromosome (BAC)/cosmids were identified as seed clones. Integration of sequence data with the genetic and physical maps of Solanum lycopersicum facilitated the anchoring of 374 of these BAC/cosmid clones. The analysis of this information resulted in a genome-wide map of a nondomesticated plant species and covers 10% of the physical distance of the selected regions corresponding to approximately 1% of the wild tomato genome. Comparative analyses revealed that S. pennellii and domesticated tomato genomes can be considered as largely colinear. A total of 1,238,705 bp from both BAC/cosmid ends and nine large insert clones were sequenced, annotated, and functionally categorized. The sequence data allowed the evaluation of the level of polymorphism between the wild and cultivated tomato species. An exhaustive microsynteny analysis allowed us to estimate the divergence date of S. pennellii and S. lycopersicum at 2.7 million years ago. The combined results serve as a reference for comparative studies both at the macrosyntenic and microsyntenic levels. They also provide a valuable tool for fine-mapping of quantitative trait loci in tomato. Furthermore, they will contribute to a deeper understanding of the regulatory factors underpinning metabolism and hence defining crop chemical composition.
  • Kirkel, D., et al. (2010). "Asymptomatic factor VII deficiency: gene analysis and structure-function relationships." Blood Coagulation & Fibrinolysis 21(1): 91-94 10.1097/MBC.1090b1013e328331e328708.
    Factor VII Padua is a variant form of factor VII deficiency characterized by a prolongation of the prothrombin time (PT), when the assay is performed using rabbit brain thromboplastin. The PT is normal when performed using either human or ox brain thromboplastin reagents, or a recombinant human tissue factor-based thromboplastin. We report a case of an African-American woman with asymptomatic factor VII deficiency, who had a prolonged PT and factor VII activity levels of 5-8% using rabbit brain thromboplastin, but a normal PT and factor VII activity levels when measured using recombinant human brain thromboplastin or tissue factor. The amino acid substitution (R304Q), which gives rise to factor VII Padua, was found in our patient, making this only the fourth African-American case described to date with this mutation. Our report emphasizes the importance of identifying this benign form of factor VII deficiency in order to avoid unnecessary exposure of patients to treatment with either plasma-derived products or recombinant activated factor VII. (C) 2010 Lippincott Williams & Wilkins, Inc.
  • Koczura, R., et al. "Association between the Presence of Class 1 Integrons, Virulence Genes, and Phylogenetic Groups of Escherichia coli Isolates from River Water." Microbial Ecology: 1-7.
  • Koizumi, N., et al. (2012). "Thirty-two polymorphic microsatellite loci of the mysid crustacean Mesopodopsis tenuipes." Conservation Genetics Resources 4(1): 55-58.
  • Koizumi, N., et al. "Development and characterization of 29 polymorphic microsatellite loci for Esomus metallicus." Conservation Genetics Resources: 1-4.
  • Koizumi, N., et al. "Isolation and characterization of 40 polymorphic microsatellite markers from Parambassis siamensis." Conservation Genetics Resources: 1-5.
  • Koizumi, N., et al. (2012). "Development and characterization of 23 polymorphic microsatellite markers for Sympetrum frequens." Conservation Genetics Resources 4(1): 67-70.
  • Koizumi, N., et al. (2011). "Isolation and characterization of 21 polymorphic microsatellite loci in the Japanese dace ( Tribolodon hakonensis )." Conservation Genetics Resources 3(3): 565-567.
  • Kopecký, D., et al. (2011). "Genomic constitution of Festuca  ×  Lolium hybrids revealed by the DArTFest array." TAG Theoretical and Applied Genetics 122(2): 355-363.
  • Kulkarni, S. S., et al. (2011). Mutation Analysis of the LDL Receptor Gene in Indian Families with Familial Hypercholesterolemia.
    Objective: Familial Hypercholesterolemia (FH) is a metabolic disorder inherited as an autosomal dominant trait characterized by an increased plasma low-density lipoprotein (LDL) level. The disease is caused by several different mutations in the LDL receptor (LDLR) gene. Several mutations have been reported in this gene in patients from several ethnic groups. Early identification of individuals carrying the defective gene could be useful in reducing the risk of atherosclerosis and myocardial infraction by the available therapeutic methods. The techniques available for determining the number of the functional LDLR molecules are difficult to carry out and expensive. Our study presents mutation analysis of the LDLR gene in 24 Indian families with FH. Material & Methods: Peripheral blood samples were obtained form individuals after taking informed consent on the condition that each of these individuals had at least one first-degree relative affected with FH. Genomic DNA was isolated, exon-specific intronic primers were designed and used to amplify DNA samples from individuals.PCR products were directly subjected to automated DNA sequencing to detect the mutations. Along with the affected individuals, ten ethnically matched controls were also analyzed to determine the presence of the same mutations. Patients with Nephrotic Syndrome admitted to hospital were excluded from the study. Results: All the 24 patients had total cholesterol level above 300 mg/dl and LDL cholesterol level above 200mg/dl. Sequence analysis of the LDL receptor (LDLR) gene showed 3 novel mutations which have never been reported elsewhere. In exon 10 we reported g.29372_29373insC, which was found in all the 24 patients and was missence mutation coding for C (cysteine) instead of V (valine). Conclusion: Our study reported 3 novel mutations in 24 Indian families. These novel mutations are predicted to produce change in the amino acid and thus leading to the conformational changes in the structure of LDLR protein. Change in the LDLR protein makes the LDL receptor unable to transport the cholesterol in to the cell and hence cholesterol starts accumulating in the blood stream and leads to FH. Key Words: Familial Hypercholesterolemia; Mutation analysis; LDL Receptor gene DOI: Asian Journal of Medical Sciences 2 (2011) 82-86
  • Larkin, B. G., et al. (2012). "Foliar nutrients shape fungal endophyte communities in Western white pine (Pinus monticola) with implications for white-tailed deer herbivory." Fungal Ecology 5(2): 252-260.
  • Liu, J.-h., et al. (2012). "Variations of human papillomavirus type 58 E6, E7, L1 genes and long control region in strains from women with cervical lesions in Liaoning province, China." Infection, Genetics and Evolution 12(7): 1466-1472.
    Infection with certain types of human papillomaviruses (HPVs) is a risk factor for the development of cervical cancer. HPV type 58 (HPV 58) is prevalent among Chinese women. The intratype sequence variants differ in oncogenic potential and their prevalences vary across geographic regions. The objective of this study was to analyze the variations of HPV 58 E6, E7, L1 genes and long control region (LCR) in a large samples collected from northeastern Chinese women with cervical lesions. A total of 2938 cervical samples were collected and tested for HPV type using a chip hybridization assay. The E6, E7, L1 genes and LCR of HPV 58 strains were amplified and the amplicons were subjected to direct nucleotide sequencing for variation identification. A total of 235 specimens were HPV 58 positive. High proportions of HPV 58 E6 (83.8%), E7 (76.7%), L1 (90.8%) genes and LCR (91.4%) variants were identified in strains from Chinese women. The most frequently observed variations were C307T (52.4%) in E6, T744G (74.9%) in E7, A6014C (56.9%) in L1 genes and C7266T, A7714G (55.2%) in LCR. For the E6 gene, nine nucleotide variations were identified. Among them, the A140G (T11A), A184C (E25D), G266C (V53L) and A313G were novel variations. Sequencing of the E7 gene revealed four typical nucleotide changes: G761A (G63D), G694A (G41R), T803C (V77A) and T744G. In the L1 gene, 39 nucleotide variations and 13 amino acid substitutions were identified. Among these mutations, 21 variations are reported here for the first time. Lineage A of HPV 58 was found in 142 of 174 strains (81.6%). The most prevalent HPV 58 variants in Chinese northeastern women belongs to lineage A. Novel variations in E6 and L1 genes were also reported. These findings provide new data regarding E6 and L1 gene variations of HPV 58 from women in northeast China.
  • Liu, T., et al. (2012). "Gut bacteria profiles of Mus musculus at the phylum and family levels are influenced by saturation of dietary fatty acids." Anaerobe 18(3): 331-337.
  • Long, Y.-S., et al. (2011). "Human transcription factor genes involved in neuronal development tend to have high GC content and CpG elements in the proximal promoter region." Journal of Genetics and Genomics 38(4): 157-163.
    Transcription factors (TFs) play critical roles in the development of the nervous system, but the transcriptional regulatory mechanisms of these genes are poorly understood. Here we analyzed 5-kb of the 5? flanking genomic DNA sequences of 41 TF genes involved in neuronal development. The results showed that the TF genes tend to have higher GC contents in the proximal region and most of the TF genes have at least one proximal GC-rich (GC content > 60%) promoter with a CpG island. The promoter distribution analysis showed that the GC-poor promoters were sporadically distributed within the 5-kb flanking genomic sequence (FGS); however, more than half (37 of 70) of the GC-rich promoters were located in the proximal region between nucleotides ?1 and ?500. Luciferase assays showed that partial GC-rich promoters increased gene expression in SH-SY5Y cells and that CpG methylation repressed the promoter activity. This study suggests a potential general mechanism for regulation of TF expression.
  • Mann, J., et al. (2010). "Screening and selection of fungi for bioremediation of olive mill wastewater." World Journal of Microbiology and Biotechnology 26(3): 567-571.
  • Maurice, S., et al. (2011). "Improved molecular methods to characterise Serpula lacrymans and other Basidiomycetes involved in wood decay." Journal of Microbiological Methods 84(2): 208-215.
  • MCLAUGHLIN, et al. (2011). Detection of Helicobacter in the fecal material of the endangered Yangtze finless porpoise Neophocaena phocaenoides asiaeorientalis. Oldendorf, ALLEMAGNE, Inter-Research.
    In animals, infection by the Epsilonproteobacteria Helicobacter spp. and H. cetorum is widespread. It has been suggested that H. cetorum may cause gastritis in cetaceans. The aim of our study was to investigate the presence of Helicobacter spp. in the fecal material of the endangered Yangtze finless porpoise Neophocaena phocaenoides asiaeorientalis. The fecal material of 12 porpoises living in the wild in Poyang Lake and 1 porpoise living in captivity at the Wuhan Baiji Dolphinarium were examined by PCR for the presence of Helicobacter spp. The fecal material of 8 of 12 wild porpoises and the captive porpoise were positive for Helicobacter spp. as determined by PCR using Helicobacter-specific primers, which target the 16S rRNA gene. A 16S rRNA clone library was then prepared from 1 sample isolated from a female porpoise living in the wild. DNA sequence analysis from 3 of the clones showed 98 to 99 % identity to the H. cetorum 16S rRNA gene. These results demonstrate the prevalence of Helicobacter spp. and H. cetorum in endangered freshwater finless porpoises.
  • Michaelidou, U., et al. (2011). "Microbial communities and electrochemical performance of titanium-based anodic electrodes in a microbial fuel cell." Appl Environ Microbiol 77(3): 1069-1075.
    Four types of titanium (Ti)-based electrodes were tested in the same microbial fuel cell (MFC) anodic compartment. Their electrochemical performances and the dominant microbial communities of the electrode biofilms were compared. The electrodes were identical in shape, macroscopic surface area, and core material but differed in either surface coating (Pt- or Ta-coated metal composites) or surface texture (smooth or rough). The MFC was inoculated with electrochemically active, neutrophilic microorganisms that had been enriched in the anodic compartments of acetate-fed MFCs over a period of 4 years. The original inoculum consisted of bioreactor sludge samples amended with Geobacter sulfurreducens strain PCA. Overall, the Pt- and Ta-coated Ti bioanodes (electrode-biofilm association) showed higher current production than the uncoated Ti bioanodes. Analyses of extracted DNA of the anodic liquid and the Pt- and Ta-coated Ti electrode biofilms indicated differences in the dominant bacterial communities. Biofilm formation on the uncoated electrodes was poor and insufficient for further analyses. Bioanode samples from the Pt- and Ta-coated Ti electrodes incubated with Fe(III) and acetate showed several Fe(III)-reducing bacteria, of which selected species were dominant, on the surface of the electrodes. In contrast, nitrate-enriched samples showed less diversity, and the enriched strains were not dominant on the electrode surface. Isolated Fe(III)-reducing strains were phylogenetically related, but not all identical, to Geobacter sulfurreducens strain PCA. Other bacterial species were also detected in the system, such as a Propionicimonas-related species that was dominant in the anodic liquid and Pseudomonas-, Clostridium-, Desulfovibrio-, Azospira-, and Aeromonas-related species.
  • Mokracka, J., et al. (2012). "Integrons, ?-lactamase and qnr genes in multidrug resistant clinical isolates of Proteus mirabilis and P. vulgaris." APMIS: n/a-n/a.
  • Mokracka, J., et al. (2012). "Multiresistant Enterobacteriaceae with class 1 and class 2 integrons in a municipal wastewater treatment plant." Water Research 46(10): 3353-3363.
    In this study, 1832 strains of the family Enterobacteriaceae were isolated from different stages of a municipal wastewater treatment plant, of which 221 (12.1%) were intI-positive. Among them 61.5% originated from raw sewage, 12.7% from aeration tank and 25.8% from the final effluent. All of the intI-positive strains were multiresistant, i.e. resistant to at least three unrelated antimicrobials. Although there were no significant differences in resistance range, defined as the number of antimicrobial classes to which an isolate was resistant, between strains isolated from different stages of wastewater treatment, for five ?-lactams the percentage of resistant isolates was the highest in final effluent, which may reflect a selective pressure the bacteria are exposed to, and the possible route of dissemination of ?-lactam resistant strains to the corresponding river. The sizes of the variable part of integrons ranged from 0.18 to 3.0 kbp and contained up to four incorporated gene cassettes. Sequence analysis identified over 30 different gene cassettes, including 24 conferring resistance to antibiotics. The highest number of different gene cassettes was found in bacteria isolated from the final effluent. The gene cassettes were arranged in 26 different resistance cassette arrays; the most often were dfrA1-aadA1, aadA1, dfrA17-aadA5 and dfrA12-orfF-aadA2. Regarding the diversity of resistance genes and the number of multiresistant bacteria in the final effluent, we concluded that municipal sewage may serve as a reservoir of integron-embedded antibiotic resistance genes.
  • Mokracka, J., et al. (2012). "Transferable integrons of Gram-negative bacteria isolated from the gut of a wild boar in the buffer zone of a national park." Annals of Microbiology 62(2): 877-880.
  • Mokracka, J., et al. (2011). "Resistance patterns and integron cassette arrays of Enterobacter cloacae complex strains of human origin." J Med Microbiol 60(Pt 6): 737-743.
    The aim of this research was to analyse the resistance patterns and characterize the distribution and genetic content of resistance integrons within Enterobacter cloacae complex strains originating from hospitalized patients. The strains were included in the E. cloacae complex study following sequence analysis of the hsp60 gene. The determination of resistance towards eight classes of antimicrobials was followed by PCR detection of integrons and analyses of the size and sequences of their variable parts. The majority of 69 clinical strains of the E. cloacae complex were identified as Enterobacter hormaechei. They were isolated from a variety of samples, including urine, wounds, blood and stools. The remaining isolates belonged to E. cloacae clusters III and IV, E. cloacae subsp. cloacae and Enterobacter kobei. Fifty-two isolates (75.4 %) were resistant to more than three unrelated antibiotics. The resistance for each antibiotic, except imipenem, was significantly associated with the presence of integrons. Class 1 integrons were detected in 55 % of isolates: 63.3 % of 'E. hormaechei subsp. steigerwaltii', 50 % of E. cloacae cluster III, 40 % of 'E. hormaechei subsp. oharae', 33 % belonging to E. cloacae cluster IV and 20 % of 'E. hormaechei subsp. hormaechei' were intI1-positive. All of the integrons were located on transferable genetic elements. The transferred resistance primarily included that to aminoglycosides, ticarcillin, piperacillin, sulfamethoxazole, trimethoprim and tetracycline. Sequence analysis of the variable regions of integrons identified two groups of genes: those encoding aminoglycoside adenylotransferases responsible for resistance to aminoglycosides, and dfr cassettes conferring resistance to trimethoprim. Integrons of the E. cloacae complex showed limited variability of genes encoding resistance to therapeutics and were stable in structure with the following cassette arrays: dfrA12-orfF-aadA2, aadB-aadA2, dfrA1-aadA1 and aacA4-aadA1. Hospital-dependent differences in type and arrays of gene cassettes were observed, which seemed to be conserved and not liable to changes.
  • Mokracka, J., et al. "Increased frequency of integrons and ?-lactamase-coding genes among extraintestinal Escherichia coli isolated with a 7-year interval." Antonie Van Leeuwenhoek: 1-12.
    We analyzed the level of antimicrobial resistance, and the presence of integrons and ?-lactamase-coding genes in 69 clinically relevant Escherichia coli strains originating from extraintestinal infections isolated in 1999–2001 and 2008–2010. Comparison of the two groups showed significant differences in drug resistance frequency, and the presence of integron and ?-lactamase-coding genes. The frequency of resistance to all antimicrobials beside imipenem, streptomycin, piperacillin/tazobactam, and sulfamethoxazole increased significantly, especially towards aminoglycosides, ?-lactams and fluoroquinolones. Similarly, we noticed an increase in the number of strains with integrons from 31.6 to 80.7 %. The presence of integrase genes was associated with elevated frequency of resistance to each antimicrobial tested besides imipenem, piperacillin/tazobactam and ceftazidime. The presence of integrons was also associated with multidrug resistance phenotype. The genetic content of integrons comprised genes determining resistance toward aminoglycosides, sulfonamides and trimethoprim. Moreover, we noticed a significant increase in the frequency of bla CTX-M ?-lactamases, with appearance of bla CTX-M-15 variant and newer plasmid-encoded ?-lactamases like CMY-15 and DHA. The emergence of strains resistant to several classes of antimicrobials and carrying integrons, ESBL and AmpC ?-lactamase-coding genes may predict the spread of isolates with limited treatment options.
  • Montoya, L., et al. (2011). "The Sulfate-Rich and Extreme Saline Sediment of the Ephemeral Tirez Lagoon: A Biotope for Acetoclastic Sulfate-Reducing Bacteria and Hydrogenotrophic Methanogenic Archaea." International Journal of Microbiology 2011.
  • Moraru, C., et al. (2010). "GeneFISH – an in situ technique for linking gene presence and cell identity in environmental microorganisms." Environmental Microbiology 12(11): 3057-3073.
    Our knowledge concerning the metabolic potentials of as yet to be cultured microorganisms has increased tremendously with the advance of sequencing technologies and the consequent discoveries of novel genes. On the other hand, it is often difficult to reliably assign a particular gene to a phylogenetic clade, because these sequences are usually found on genomic fragments that carry no direct marker of cell identity, such as rRNA genes. Therefore, the aim of the present study was to develop geneFISH – a protocol for linking gene presence with cell identity in environmental samples, the signals of which can be visualized at a single cell level. This protocol combines rRNA-targeted catalysed reporter deposition – fluorescence in situ hybridization and in situ gene detection. To test the protocol, it was applied to seawater samples from the Benguela upwelling system. For gene detection, a polynucleotide probe mix was used, which was designed based on crenarchaeotal amoA clone libraries prepared from each seawater sample. Each probe in the mix was selected to bind to targets with up to 5% mismatches. To determine the hybridization parameters, the Tm of probes, targets and hybrids was estimated based on theoretical calculations and in vitro measurements. It was shown that at least 30%, but potentially the majority of the Crenarchaeota present in these samples harboured the amoA gene and were therefore likely to be catalysing the oxidation of ammonia.
  • Muhle, H., et al. (2010). "Role of GRM4 in idiopathic generalized epilepsies analysed by genetic association and sequence analysis." Epilepsy Research 89(2–3): 319-326.
  • Muñoz, G., et al. (2011). "Effects of porcine MC4R and LEPR polymorphisms, gender and Duroc sire line on economic traits in Duroc × Iberian crossbred pigs." Meat Science 88(1): 169-173.
  • MY, V. T., et al. (2011). The Emergence of Rotavirus G12 and the Prevalence of Enteric Viruses in Hospitalized Pediatric Diarrheal Patients in Southern Vietnam. Deerfield, IL, ETATS-UNIS, The American Society of Tropical Medecine and Hygiene.
    Diarrhea is a major cause of childhood morbidity and mortality in developing countries, and the majority of infections are of viral etiology. We aimed to compare the etiological prevalence of the major enteric viruses in an urban and a rural setting in southern Vietnam. We simultaneously screened fecal specimens from 362 children in Ho Chi Minh City and Dong Thap province that were hospitalized with acute diarrhea over a 1-month-long period for four viral gastrointestinal pathogens. Rotavirus was the most common pathogen identified, but there was a differential prevalence of rotavirus and norovirus between the urban and rural locations. Furthermore, rotavirus genotyping and phylogenetic analysis again differentiated the genotypes by the sampling location. Our data show a disproportional distribution of enteric viral pathogens in urban and rural locations, and we provide evidence of continual importation of new rotavirus strains into southern Vietnam and report the emergence of rotavirus genotype G12.
  • Nakano, T. (2012). "A new sexannulate species of Orobdella (Hirudinida, Arhynchobdellida, Orobdellidae) from Yakushima Island, Japan." Zookeys(181): 79-93.
    A new sexannulate species of the genus Orobdella Oka, 1895, Orobdella mononokesp. n., is described on the basis of five specimens collected from Yakushima Island, Japan. Orobdella mononokesp. n. differs from other sexannulate Orobdella species in its possessing the following combination of characters: dorsal surface bicolor in life, I-XIII, XXVII and caudal sucker grayish purple, XIV-XXVI amber, male gonopore at XI c11/c12, female gonopore at XIII b2, 8 + 1/2 between gonopores, tubular but bulbous at junction with crop gastroporal duct, epididymides in XV-XIX, and atrial cornua ovate. Phylogenetic analyses using nuclear 18S rDNA and histone H3, and mitochondrial COI, tRNA(Cys), tRNA(Met), 12S rDNA, tRNA(Val) and 16S rDNA markers show that Orobdella mononokesp. n. is closely related to Orobdella esulcata Nakano, 2010 from Kyushu, Japan, and two species, Orobdella dolichopharynx Nakano, 2011 and Orobdella shimadae Nakano, 2011, from the Ryukyu Archipelago, Japan.
  • Nakano, T. (2012). "A new species of Orobdella (Hirudinida, Arhynchobdellida, Gastrostomobdellidae) and redescription of Orobdella kawakatsuorum from Hokkaido, Japan with the phylogenetic position of the new species." Zookeys(169): 9-30.
    A new quadrannulate Orobdella Oka, 1895 species, Orobdella koikeisp. n., is described on the basis of six specimens collected from Hokkaido, Japan. In addition, an emended description of quadrannulate Orobdella kawakatsuorum Richardson, 1975 is also provided. Orobdella koikei differs from other quadrannulate species of Orobdella in possessing the following combination of characters: color dorsally brown, IV uniannulate, male gonopore at XI b6, gastropore and female gonopore at XIII a1, 1/2 + 4 + 1/2 between gonopores, XXV triannulate, tubular but bulbous at junctions with gastropore and crop gastroporal duct, epididymides in XVII to XIX, and atrial cornua ovate. The phylogenetic position of the newly described species is estimated using mitochondrial COI, tRNA(Cys), tRNA(Met), 12S rDNA, tRNA(Val) and 16S rDNA markers. Orobdella koikei is a sister taxon of Orobdella kakawatsuorum according to the molecular phylogenetic analyses.
  • Nakano, T., et al. (2012). "Phylogenetic position of gastrostomobdellid leeches (Hirudinida, Arhynchobdellida, Erpobdelliformes) and a new family for the genus Orobdella." Zoologica Scripta 41(2): 177-185.
  • Navarro-Noya, Y. E., et al. (2010). "Bacterial communities associated with the rhizosphere of pioneer plants (Bahia xylopoda and Viguiera linearis) growing on heavy metals-contaminated soils." Antonie Van Leeuwenhoek 97(4): 335-349.
    In this study, the bacterial communities associated with the rhizospheres of pioneer plants Bahia xylopoda and Viguiera linearis were explored. These plants grow on silver mine tailings with high concentration of heavy metals in Zacatecas, Mexico. Metagenomic DNAs from rhizosphere and bulk soil were extracted to perform a denaturing gradient gel electrophoresis analysis (DGGE) and to construct 16S rRNA gene libraries. A moderate bacterial diversity and twelve major phylogenetic groups including Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Chloroflexi, Firmicutes, Verrucomicrobia, Nitrospirae and Actinobacteria phyla, and divisions TM7, OP10 and OD1 were recognized in the rhizospheres. Only 25.5% from the phylotypes were common in the rhizosphere libraries and the most abundant groups were members of the phyla Acidobacteria and Betaproteobacteria (Thiobacillus spp., Nitrosomonadaceae). The most abundant groups in bulk soil library were Acidobacteria and Actinobacteria, and no common phylotypes were shared with the rhizosphere libraries. Many of the clones detected were related with chemolithotrophic and sulfur-oxidizing bacteria, characteristic of an environment with a high concentration of heavy metal-sulfur complexes, and lacking carbon and organic energy sources.
  • Panphut, W., et al. (2011). "A novel integrase-containing element may interact with Laem-Singh virus (LSNV) to cause slow growth in giant tiger shrimp." BMC Veterinary Research 7(1): 1-15.
    Background From 2001-2003 monodon slow growth syndrome (MSGS) caused severe economic losses for Thai shrimp farmers who cultivated the native, giant tiger shrimp, and this led them to adopt exotic stocks of the domesticated whiteleg shrimp as the species of cultivation choice, despite the higher value of giant tiger shrimp. In 2008, newly discovered Laem-Singh virus (LSNV) was proposed as a necessary but insufficient cause of MSGS, and this stimulated the search for the additional component cause(s) of MSGS in the hope that discovery would lead to preventative measures that could revive cultivation of the higher value native shrimp species. Results Using a universal shotgun cloning protocol, a novel RNA, integrase-containing element (ICE) was found in giant tiger shrimp from MSGS ponds (GenBank accession number FJ498866). In situ hybridization probes and RT-PCR tests revealed that ICE and Laem-Singh virus (LSNV) occurred together in lymphoid organs (LO) of shrimp from MSGS ponds but not in shrimp from normal ponds. Tissue homogenates of shrimp from MSGS ponds yielded a fraction that gave positive RT-PCR reactions for both ICE and LSNV and showed viral-like particles by transmission electron microscopy (TEM). Bioassays of this fraction with juvenile giant tiger shrimp resulted in retarded growth with gross signs of MSGS, and in situ hybridization assays revealed ICE and LSNV together in LO, eyes and gills. Viral-like particles similar to those seen in tissue extracts from natural infections were also seen by TEM. Conclusions ICE and LSNV were found together only in shrimp from MSGS ponds and only in shrimp showing gross signs of MSGS after injection with a preparation containing ICE and LSNV. ICE was never found in the absence of LSNV although LSNV was sometimes found in normal shrimp in the absence of ICE. The results suggest that ICE and LSNV may act together as component causes of MSGS, but this cannot be proven conclusively without single and combined bioassays using purified preparations of both ICE and LSNV. Despite this ambiguity, it is recommended in the interim that ICE be added to the agents such as LSNV already listed for exclusion from domesticated stocks of the black tiger shrimp.
  • Peng, Q., et al. (2012). "Mitogenomic analysis of the genus Pseudois: Evidence of adaptive evolution of morphological variation in the ATP synthase genes." Mitochondrion 12(5): 500-505.
  • Poli, A., et al. (2012). "Molecular characterization of Fusarium oxysporum f.sp. cichorii pathogenic on chicory ( Cichorium intybus )." Phytoparasitica 40(4): 383-391.
  • Rathnasingh, C., et al. (2009). "Development and evaluation of efficient recombinant Escherichia coli strains for the production of 3-hydroxypropionic acid from glycerol." Biotechnology and Bioengineering 104(4): 729-739.
  • Ray, A., et al. (2012). "Sequence Analysis of Kaposi Sarcoma–Associated Herpesvirus (KSHV) MicroRNAs in Patients with Multicentric Castleman Disease and KSHV-Associated Inflammatory Cytokine Syndrome." Journal of Infectious Diseases 205(11): 1665-1676.
    Background Kaposi sarcoma–associated herpesvirus (KSHV) encodes 12 pre-microRNAs that yield 25 mature microRNAs. We previously reported phylogenetic analysis of the microRNA-coding region of KSHV from Kaposi sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman disease (MCD) patients. We observed a high level of conservation for most sequences but also a divergent cluster of 5 KSHV sequences, including 2 from MCD patients.Methods KSHV microRNA sequences from 23 MCD patients and 7 patients with a newly described KSHV-associated inflammatory cytokine syndrome (KICS) were examined by amplification, cloning, and sequencing of a 646-bp fragment of K12/T0.7 encoding microRNA-K12-10 and microRNA-K12-12 and a 2.8-kbp fragment containing the remaining 10 pre-microRNAs.Results Phylogenetic analysis showed a distinct variant cluster consisting exclusively of MCD and KICS patients in all trees. Pearson ?2 analysis revealed that 40 single-nucleotide polymorphisms (SNPs) at various loci were significantly associated with MCD and KICS risk. Cluster analysis of these SNPs generated several combinations of 3 SNPs as putative indicators of MCD and KICS risk.Conclusions These findings show that MCD and KICS patients frequently have unusual KSHV microRNA sequences and suggest an association between the observed sequence variation and risk of MCD and KICS.
  • Ray, A., et al. (2012). "Sequence Analysis of KSHV microRNAs in patients with Multicentric Castleman Disease and KSHV-associated Inflammatory Cytokine Syndrome." Journal of Infectious Diseases.
    Background Kaposi sarcoma-associated herpesvirus (KSHV) encodes 12 pre-microRNAs which yield 25 mature microRNAs. We previously reported phylogenetic analysis of the microRNA-coding region of KSHV from Kaposi sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman disease (MCD) patients. We observed a high level of conservation for most sequences, but also a divergent cluster of 5 KSHV sequences including 2 from MCD patients [1].Method KSHV microRNA sequences from 23 MCD patients and 7 patients with a newly described KSHV-associated inflammatory cytokine syndrome (KICS) were examined by amplification, cloning, and sequencing of a 646-bp fragment of K12/T0.7 encoding miRNA-K12-10 and miRNA-K12-12 and a 2.8-kbp fragment containing the remaining 10 pre-microRNAs.Results Phylogenetic analysis showed a distinct variant cluster consisting exclusively of MCD and KICS patients in all trees. Pearson’s chi-squared analysis revealed 40 single nucleotide polymorphisms (SNPs) at various loci were significantly associated with MCD and KICS risk. Cluster analysis of these SNPs generated several combinations of three SNPs as putative indicators of MCD and KICS risk.Conclusion These findings show that MCD and KICS patients frequently have unusual KSHV microRNA sequences and suggest an association between the observed sequence variation and risk of MCD and KICS.
  • Romano, I., et al. (2010). "Thermoanaerobacterium thermostercus sp. nov., a new anaerobic thermophilic hydrogen-producing bacterium from buffalo-dung." Extremophiles 14(2): 233-240.
  • Salcher, M. M., et al. (2011). "Seasonal bloom dynamics and ecophysiology of the freshwater sister clade of SAR11 bacteria /`that rule the waves/' (LD12)." ISME J 5(8): 1242-1252.
  • Sánchez-Andrea, I., et al. "Screening of anaerobic activities in sediments of an acidic environment: Tinto River." Extremophiles: 1-11.
  • Sarwar Azam, V. T., Pradeep Ruperao, Trushar Shah, Jayashree Balaji, BhanuPrakash Amindala, Andrew D. Farmer, David J. Studholme, Gregory D. May, David Edwards, Jonathan D. G. Jones and Rajeev K. Varshney (2012). "Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome." AMERICAN JOURNAL OF BOTANY 99(2): 186-192.
  • Saxena, R., et al. (2011). "Single feature polymorphisms (SFPs) for drought tolerance in pigeonpea ( Cajanus spp.)." Functional & Integrative Genomics 11(4): 651-657.
  • Scott, J. L., et al. (2010). "The evolutionary origins of ritualized acoustic signals in caterpillars." Nat Commun 1: 4.
  • Sharma, S., et al. (2011). "Genome-wide association studies of adolescent idiopathic scoliosis suggest candidate susceptibility genes." Human Molecular Genetics 20(7): 1456-1466.
    Adolescent idiopathic scoliosis (AIS) is an unexplained and common spinal deformity seen in otherwise healthy children. Its pathophysiology is poorly understood despite intensive investigation. Although genetic underpinnings are clear, replicated susceptibility loci that could provide insight into etiology have not been forthcoming. To address these issues, we performed genome-wide association studies (GWAS) of ∼327 000 single nucleotide polymorphisms (SNPs) in 419 AIS families. We found strongest evidence of association with chromosome 3p26.3 SNPs in the proximity of the CHL1 gene. We genotyped additional chromosome 3p26.3 SNPs and tested replication in two follow-up case-control cohorts, obtaining strongest results when all three cohorts were combined, but these were not confirmed in a separate GWAS. CHL1 is of interest, as it encodes an axon guidance protein related to Robo3. Mutations in the Robo3 protein cause orizontal gaze palsy with progressive scoliosis (HGPPS), a rare disease marked by severe scoliosis. Other top associations in our GWAS were with SNPs in the DSCAM gene encoding an axon guidance protein in the same structural class with Chl1 and Robo3. We additionally found AIS associations with loci in CNTNAP2, supporting a previous study linking this gene with AIS. Cntnap2 is also of functional interest, as it interacts directly with L1 and Robo class proteins and participates in axon pathfinding. Our results suggest the relevance of axon guidance pathways in AIS susceptibility, although these findings require further study, particularly given the apparent genetic heterogeneity in this disease.
  • SRINIVASAN, K., et al. (2011). Molecular Characterization Through Igs Sequencing Of Formae Speciales Of Fusarium Oxysporum Pathogenic On Lamb’s Lettuce.
    Twenty-nine strains of Fusarium oxysporum isolated from wilted lamb’s lettuce plants ( Valerianella olitoria ) along with eight ATCC reference strains were examined for differences in the nucleotide sequences of the ribosomal DNA (rDNA) intergenic spacer (IGS) region, which is about 2.5 kb long in these strains. A phylogenetic (neighbour-joining) analysis was performed on the strains and identified four phylogenetic groups, I, II, III, and IV. Most F. oxysporum isolates recovered from wilted lamb’s lettuce plants cultivated in northern Italy clustered in group I and were very similar to F. oxysporum f. sp. raphani . All the isolates, including the 8 control strains, were tested for pathogenicity on lamb’s lettuce cv. Trophy cultivated in the glasshouse. Most isolates from northern Italy were pathogenic on lamb’s lettuce, displaying varying degrees of virulence, and their IGS sequence were similar to the forma specialis raphani . However, four isolates were not pathogenic on lamb’s lettuce. Among the control strains, six showed moderate virulence; these belonged to the formae speciales raphani and conglutinans ; and two, belonging to the forma specialis matthioli (ATCC16602 and ATCC16603) were not pathogenic on lamb’s lettuce. In conclusion, analysis of the IGS sequences indicated that the isolates studied had different origins, and that phylogeny and pathogenicity were related; non-pathogenic isolates differed genetically from isolates that were poorly, moderately or highly virulent. To the best of our knowledge, this is the first report on the differences between formae speciales of F. oxysporum on lamb’s lettuce plants as determined by IGS sequence analysis.
  • Stram, Y., et al. (2011). "Multiple invasions of O1 FMDV serotype into Israel revealed by genetic analysis of VP1 genes of Israeli's isolates from 1989 to 2007." Veterinary Microbiology 147(3–4): 398-402.
  • Sun, Z., et al. (2012). "Variant Lineages of Human Papillomavirus Type 18 in Northeast China Populations Characterized by Sequence Analysis of E6, E7, and L1 Regions." International Journal of Gynecological Cancer 22(6): 930-936 910.1097/IGC.1090b1013e318253a318994.
    Introduction: In cervical cancer, human papillomavirus (HPV) 18 is predominantly related to adenocarcinomas. Variant lineages of HPV type 16 have been well characterized, whereas the knowledge about HPV 18 variants is limited in Northeast China. Methods: To identify prevalent and novel HPV 18 variants in Northeast China, the E6, E7, and L1 genes of HPV 18 from patients with cervical lesion were amplified and sequenced, and intratypic variants were analyzed by comparing to the known phylogenetic branches. Results: The HPV-18 E6 variants of our studied strains belong to 2 main branches: Asian-American (AA) variants in 81.5% and European (E) variants in 18.5%. Strains with variations of C287G, T482C, and C519A in E6 and C751T in E7 were novel variants. All the L1 genes of the analyzed HPV 18 strains had 4 C-G transversions at nucleotide positions of 5701, 6460, 6625, and 6842 and one G-A transition at position 5503. Moreover, strains with L1 nucleotide variations of A5920T, A6431T, and G6987A leading to amino acid substitutions of A164V, Q334P/H, and D520N are novel variants. Conclusions: Based on the E6 gene, the prevalent HPV 18 in Northeast China was AA and E variants. Besides some common variations reported before, some new variations in the E6, E7, and L1 genes were found. Data about the novel variations found in the L1 gene of HPV 18 variants may be helpful to design the diagnostic reagents and vaccine for naturally infected HPV 18 in Northeast China.
  • Sun, Z., et al. (2011). "Genetic Diversity of HPV-16 E6, E7, and L1 Genes in Women With Cervical Lesions in Liaoning Province, China." International Journal of Gynecological Cancer 21(3): 551-558 510.1097/IGC.1090b1013e3182112023.
    Introduction: High-risk human papillomaviruses (HPVs) play a cardinal role in the etiology of cervical cancer. The most prevalent type, HPV-16, shows intratypic sequence variants that are known to differ in oncogenic potential and geographic distribution. Intratype variations in oncogenic E6/E7 and capsid L1 proteins of HPV-16 are associated with risk of viral persistence and progression. Methods: This study was designed to analyze sequence variations in E6, E7, and L1 genes of HPV-16 in patients with cervical lesion to identify the most prevalent and novel HPV-16 variants in northern China. Results: Our results showed that HPV-16 variants with respect to E6 and E7 were high prevalence of the Asian lineage: 48.3% and 51.4%, respectively. Sequences of the E6 gene revealed 4 amino acid changes of variants D25E and L83V, with 48.3% (69/143) and 11.2% (16/143), respectively, and variants H78Y and E113D in this study. The results also showed the prevalence of 4 hot spots of E7 nucleotide variations leading to N29H, N29S, and 2 silent variations, nucleotide G666A and nucleotide T846C, with 4.2% (6/142), 43% (61/142), 32.4% (46/142), and 43% (61/142), respectively. The following L1 variations were found in this study: L103F, P104K, P104Y, P104S, D105G, P106S, N108P, F109V, C172S, H228D, and T292A. It was also found that 448S was inserted and 465D was deleted in the L1 amino acid sequences of all the samples. No significant relationship between HPV-16 variants and high-grade lesions was found. Conclusions: The study provides some new data on the genetic diversity of HPV-16, which may help to understand the oncogenic potential of the virus and design the diagnosis reagents and vaccine of HPV in China. Furthermore, in-depth studies are needed to determine the clinical and biological effects of these variants.
  • Taulé, C., et al. (2012). "The contribution of nitrogen fixation to sugarcane ( Saccharum officinarum L.), and the identification and characterization of part of the associated diazotrophic bacterial community." Plant and Soil 356(1): 35-49.
    Background and aims Rhizospheric, epiphytic and endophytic bacteria are associated with several non-legumes, colonizing their surface and inner tissues. Many of these bacteria are beneficial to their hosts, and are collectively termed plant growth-promoting rhizobacteria (PGPR). Recent interest has focused particularly upon PGPR that are endophytic (i.e. PGPE), and which have been reported to be associated with important crops such as rice, wheat and sugarcane. Different mechanisms are involved in bacteria-induced plant growth promotion (PGP), including biological nitrogen fixation (BNF), mineral solubilization, production of phytohormones and pathogen biocontrol. In Uruguay, sugarcane ( Saccharum officinarum L.) is considered a strategic multipurpose crop, used for bioenergy, feed, sugar and bioethanol production. The aim of this work was to estimate the BNF contribution to Uruguayan sugarcane cultivars, as well as to identify and characterize the (culturable) putatively endophytic diazotrophic bacteria associated with these varieties. Methods and results Results using the 15 N-dilution technique have shown that these sugarcane varieties obtain significant inputs of N from BNF (34.8–58.8% Ndfa). In parallel, a collection of 598 isolates of potentially endophytic diazotrophs was obtained from surface-sterilized stems using standard isolation techniques, and nifH + isolates from these were the subject of further studies. The bacteria were shown to belong to several genera, including Pseudomonas , Stenotrophomonas , Xanthomonas , Acinetobacter, Rhanella, Enterobacter , Pantoea , Shinella , Agrobacterium and Achromobacter . Additionally, some PGP features were studied in 35 selected isolates. The data obtained in this study represent the initial steps in a program aimed at determining the mechanisms of PGP of non-legume crops in Uruguay (such as sugarcane) with potentially beneficial plant-associated bacteria.
  • Taule, C., et al. (2012). "New betaproteobacterial Rhizobium strains able to efficiently nodulate Parapiptadenia rigida (Benth.) Brenan." Appl Environ Microbiol 78(6): 1692-1700.
    Among the leguminous trees native to Uruguay, Parapiptadenia rigida (Angico), a Mimosoideae legume, is one of the most promising species for agroforestry. Like many other legumes, it is able to establish symbiotic associations with rhizobia and belongs to the group known as nitrogen-fixing trees, which are major components of agroforestry systems. Information about rhizobial symbionts for this genus is scarce, and thus, the aim of this work was to identify and characterize rhizobia associated with P. rigida. A collection of Angico-nodulating isolates was obtained, and 47 isolates were selected for genetic studies. According to enterobacterial repetitive intergenic consensus PCR patterns and restriction fragment length polymorphism analysis of their nifH and 16S rRNA genes, the isolates could be grouped into seven genotypes, including the genera Burkholderia, Cupriavidus, and Rhizobium, among which the Burkholderia genotypes were the predominant group. Phylogenetic studies of nifH, nodA, and nodC sequences from the Burkholderia and the Cupriavidus isolates indicated a close relationship of these genes with those from betaproteobacterial rhizobia (beta-rhizobia) rather than from alphaproteobacterial rhizobia (alpha-rhizobia). In addition, nodulation assays with representative isolates showed that while the Cupriavidus isolates were able to effectively nodulate Mimosa pudica, the Burkholderia isolates produced white and ineffective nodules on this host.
  • Temkiv, T. Š., et al. (2012). "The microbial diversity of a storm cloud as assessed by hailstones." FEMS Microbiology Ecology 81(3): 684-695.
    Being an extreme environment, the atmosphere may act as a selective barrier for bacterial dispersal, where only most robust organisms survive. By remaining viable during atmospheric transport, these cells affect the patterns of microbial distribution and modify the chemical composition of the atmosphere. The species evenness and richness, and the community composition of a storm cloud were studied applying cultivation-dependent and cultivation-independent techniques to a collection of hailstones. In toto 231 OTUs were identified, and the total species richness was estimated to be about 1800 OTUs. The diversity indices – species richness and evenness – suggest a functionally stable community, capable of resisting environmental stress. A broad substrate spectrum of the isolates with epiphytic origin (genus Methylobacterium) implied opportunistic ecologic strategy with high growth rates and fast growth responses. These may grow in situ despite their short residence times in cloud droplets. In addition, epiphytic isolates utilized many atmospheric organic compounds, including a variety of carboxylic acids. In summary, the highly diverse bacterial community, within which the opportunistic bacteria may be particularly important in terms of atmospheric chemistry, is likely to remain functional under stressful conditions. Overall our study adds important details to the growing evidence of active microbial life in clouds.
  • Tinta, T., et al. (2012). "Jellyfish modulate bacterial dynamic and community structure." PLoS One 7(6): e39274.
    Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into possible changes in bacterial population dynamics and nutrient pathways following jellyfish blooms which have important implications for ecology of coastal waters.
  • Trm?i?, A., et al. (2011). "Complete nisin A gene cluster from Lactococcus lactis M78 (HM219853) — obtaining the nucleic acid sequence and comparing it to other published nisin sequences." Genes & Genomics 33(3): 217-221.
  • Verna, C., et al. (2010). "High symbiont diversity in the bone-eating worm Osedax mucofloris from shallow whale-falls in the North Atlantic." Environmental Microbiology 12(8): 2355-2370.
    Osedax worms are whale-fall specialists that infiltrate whale bones with their root tissues. These are filled with endosymbiotic bacteria hypothesized to provide their hosts with nutrition by extracting organic compounds from the whale bones. We investigated the diversity and distribution of symbiotic bacteria in Osedax mucofloris from shallow-water whale-falls in the North Atlantic using comparative 16S rRNA sequence analysis and fluorescence in situ hybridization (FISH). We observed a higher diversity of endosymbionts than previously described from other Osedax species. Endosymbiont sequences fell into eight phylogenetically distinct clusters (with 91.4–98.9% similarity between clusters), and considerable microdiversity within clusters (99.5–99.7% similarity) was observed. Statistical tests revealed a highly significant effect of the host individual on endosymbiont diversity and distribution, with 68% of the variability between clusters and 40% of the variability within clusters explained by this effect. FISH analyses showed that most host individuals were dominated by endosymbionts from a single cluster, with endosymbionts from less abundant clusters generally confined to peripheral root tissues. The observed diversity and distribution patterns indicate that the endosymbionts are transmitted horizontally from the environment with repeated infection events occurring as the host root tissues grow into the whale bones.
  • Wallménius, K., et al. (2012). "Prevalence of Rickettsia spp., Anaplasma phagocytophilum, and Coxiella burnetii in adult Ixodes ricinus ticks from 29 study areas in central and southern Sweden." Ticks and Tick-borne Diseases 3(2): 100-106.
  • Warren, A. E., et al. (2011). "Genotypic and phenotypic variation in Pseudomonas aeruginosa reveals signatures of secondary infection and mutator activity in certain cystic fibrosis patients with chronic lung infections." Infect Immun 79(12): 4802-4818.
    Evolutionary adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung is limited by genetic variation, which depends on rates of horizontal gene transfer and mutation supply. Because each may increase following secondary infection or mutator emergence, we sought to ascertain the incidence of secondary infection and genetic variability in populations containing or lacking mutators. Forty-nine strains collected over 3 years from 16 patients were phenotyped for antibiotic resistance and mutator status and were genotyped by repetitive-sequence PCR (rep-PCR), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST). Though phenotypic and genetic polymorphisms were widespread and clustered more strongly within than between longitudinal series, their distribution revealed instances of secondary infection. Sequence data, however, indicated that interlineage recombination predated initial strain isolation. Mutator series were more likely to be multiply antibiotic resistant, but not necessarily more variable in their nucleotide sequences, than nonmutators. One mutator and one nonmutator series were sequenced at mismatch repair loci and analyzed for gene content using DNA microarrays. Both were wild type with respect to mutL, but mutators carried an 8-bp mutS deletion causing a frameshift mutation. Both series lacked 126 genes encoding pilins, siderophores, and virulence factors whose inactivation has been linked to adaptation during chronic infection. Mutators exhibited loss of severalfold more genes having functions related to mobile elements, motility, and attachment. A 105-kb, 86-gene deletion was observed in one nonmutator that resulted in loss of virulence factors related to pyoverdine synthesis and elements of the multidrug efflux regulon. Diminished DNA repair activity may facilitate but not be absolutely required for rapid evolutionary change.
  • WYNGAERT, V. D., et al. (2011). Quantitative dominance of seasonally persistent filamentous cyanobacteria (Planktothrix rubescens) in the microbial assemblages of a temperate lake. Waco, TX, ETATS-UNIS, American Society of Limnology and Oceanography.
    The spatiotemporal changes in abundance and biomass of heterotrophic bacteria, of three major bacterial phylogenetic groups, and of picocyanobacteria in the upper 20 m of a deep prealpine lake (Lake Zurich, Switzerland) were monitored during a seasonally persistent bloom of the toxigenic filamentous cyanobacterium Planktothrix rubescens. In addition, bacterial 16S ribosomal deoxyribonucleic acid (rDNA) sequences were collected at one instance from the bloom layer and from waters above and below this zone. P. rubescens comprised up to 70% of particulate organic carbon during summer stratification and autumnal mixis and thus by far exceeded the total biomass both of other phytoplankton and of prokaryotes. A strong negative correlation was found between the estimated basin-wide biomass of P. rubescens and of heterotrophic bacteria, and there was different spatial niche preference of filamentous vs. picocyanobacteria. Only members of the Cytophaga-Flavobacterium lineage of Bacteroidetes showed an increasing tendency of association with the P. rubescens population, in particular at the onset of autumnal mixing. Although the filamentous cyanobacterium was the dominant primary producer throughout the year, it did not seem to be a carbon source for heterotrophic bacteria at all. We conclude that P. rubescens represents a powerful competitor of autotrophic and heterotrophic prokaryotes, likely due to both its specific physiological (photoheterotrophic) properties and its protection against zooplankton grazing. This competitiveness might be regarded as another reason for its mass occurrence in numerous lakes of the Northern hemisphere.
  • Zhao, S., et al. (2012). "Molecular phylogeny of major lineages of the avian family Phasianidae inferred from complete mitochondrial genome sequences." Journal of Natural History 46(11-12): 757-767.
  • Alba ZAREMSKI, S. P., Massimo MANNUCCI, Louis GASTONGUAY, Gaétan LE FLOCH (2011). "Molecular diagnosis by PCR-DHPLC technique of wood-decay fungi in historical buildings in Italy." PRO LIGNO 7 no. 4: 92-97.
    Wood inhabiting fungi cause real problems in the preservation of wooden surfaces and are responsible for the deterioration of cultural heritage. The identification of fungi based on morphological characteristics is still a topical issue. Nevertheless, they are limited for characterization and identification on an intraspecific level and even sometimes on an interspecific level. It is not always evident and thus many fungi remain unnamed or confused. The objective of this study was to circumvent these limitations by using a new molecular approach allowing fungal detection and identification in historic buildings in Italy. Fungal colonization was assessed by using PCR amplification and amplicons separation by Denaturing High Performance Liquid Chromatography. Due to its high sensitivity, the PCR-DHPLC technique was optimised to profile fungal communities in wood decay as well as ubiquitous contaminants.
  • Amy, A. H. J. P. P. S. (2011). "Identification of nitrifying bacteria contained in a commercial inoculant using molecular biology techniques."
    Nitrifying bacteria play an important role in aquatic and terrestrial environments through the nitrogen cycle. Nitrification, one of the processes of the nitrogen cycle, refers to the oxidation of ammonia to nitrate. This process requires two types of chemoautotrophic bacteria, ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB). These bacteria are essential in maintaining an optimal environment for plants and aquatic organisms, such as fish. Current applications of nitrifiers include: inoculants for aquariums, biofertilizers, and nitrogen removal in wastewater treatment plants. This study wants to identify a consortium of nitrifers that can be used to produce sufficient nitrate for plants in a hydroponic system. Previous studies have shown that Fritz-zyme turbostart 700, a commercial freshwater inoculant has had success in a semi-hydroponic system, zeoponics. Our lab’s preliminary data has shown that Fritz-zyme contains more than the specific nitrifying bacteria. In order to create the optimal consortium, it would be mandatory that we know exactly what bacteria we are working with. Using 16s rDNA universal primers and PGEM-T easy vector cloning kit, this study will amplify the 16s rDNA present in different enrichment samples and clone it into the PGEM-T easy vector E. coli plasmid. The cloned plasmids are transformed into competent E. coli cells and sequenced to identify the bacteria present in each sample. This study will determine whether the current enrichment techniques being used are sufficient to eliminate the heterotrophic and sporeforming bacteria present in the original Fritz-zyme.
  • Asmara, C. A. L. S. H. K. W. (2011). "Identification and characterization of Salmonella typhi isolates from Southwest Sumba District, East Nusa Tenggara based on 16S rRNA gene sequences." Biodiversitas 12: 1-6.
    The incidence rate of typhoid fever in the Southwest Sumba District, East Nusa Tenggara was approximately about 725/100,000. In spite of such rate, there was not much known-yet about the molecular epidemiology of the disease. Thus, having accurate data and a strong discriminatory ability was crucial to scrutinize the molecular epidemiology of S. typhi with a molecular phylogenetic approach based on 16S rRNA gene sequences. Sixteen isolates representative of S. typhi from different geographical regions in Southwest Sumba District along with the reference strain S. typhi NCTC 786 had been identified and characterised based on 16S rRNA gene sequences using PCR amplification and sequencing. The 16S rRNA sequences data were aligned with the corresponding available S. typhi sequences retrieved from the NCBI database by using CLUSTAL X software. Phylogenetic trees were generated with PHYLIP software package. Molecular phylogenetic analysis indicated that all the isolates belong to S. typhi species were suggested by their relativity with the type strain of S. typhi ATCC19430T. It was also found that the isolates which belong to S. typhi species formed several different centers of diversity within the 16S rRNA gene tree. Each clade consisted of the strains from different geographical places in the District. Thus, to conclude the inquiry, there was evident inter-geographical spread of the strains and it tended to spread further into more remote areas in the District.
  • Davis, C. a. E., Timothy (2009). "An Examination of Speciation, Extinction, and Evolutionary Relationships in Plants from Two Continents." Student Summer Scholars 34.
  • Fernandez, V. I. (2009). "Molecular identity of cyanobionts and mycobionts in Peltigera membranacea."
    Cyanobacteria of the genus Nostoc are widespread in nature and occur both in a freeliving state as wall as in symbiotic associations, most prominently with fungi in lichens and leguminous plans. A molecular phylogentic approach was used to investigate whether specific types of Nostoc associate with different samples of lichenizing Peltigera fungi or whether fungal spores from different lichens species can associate with one or several widespread strains of symbiotic Nostoc. The phylogenetic analysis was conducted on 16S ribosomal RNA genes from symbiotic strains of Nostoc and the Internal Transcribed Spacer (ITS) sequences of fungal rDNA. Samples of the lichen Peltigera membranacea were identified and collected from different places in Iceland, mainly around Reykjavik between 2008-2009. The prokaryotic 16S ribosomal RNA gene and the eukaryotic Internal Transcribed Spacer rDNA region fragments were amplified by the polymerase chain reaction from DNA extracted directly from the collected lichens, and sequenced directly. DNA extracted from lichen apothecia was also used for the ITS study. The result confirmed that 16S ribosomal RNA gene sequences were identical between lichen specimens in Iceland but not in other geographical areas such as Canada and U.S.A. The initial result from ITS sequences revealed heterogeneity in the mycobiont population of Peltigera membranacea in Iceland. But, still it needs mote thorough ITS analysis to confirm this.
  • Fu, Y. Z. L. H. B. "Research on DNA Cryptography."
    DNA Cryptography is based on biological problems: in theory, a DNA computer will not only has the same computing power as a modern computer but will also have a potency and function which traditional computers cannot match. First, DNA chains have a very large scale of parallelism, and its computing speed could reach 1 billion times per second; second, the DNA molecule - as a carrier of data - has a large capacity. It seems that one trillion bits of binary data can be stored in one cubic decimetre of a DNA solution; third, a DNA molecular computer has low power consumption, only equal to one-billionth of a traditional computer.
  • Hardbower, D. M. (2011). "The Temporal Dynamics of the Bacterial Communities in Lake Matoaka, an Eutrophic, Freshwater Lake."
    Little is known about microbial dynamics in freshwater ecosystems, particularly compared to marine systems. The taxonomy of many freshwater bacterial lineages has been determined, but the drivers of community composition dynamics have yet to be clearly determined. Given that community composition determines which important processes occur and the rate at which they occur, an increased understanding of the drivers of community composition change is necessary. The purpose of this study was to and to track changes in the profile of the bacterial species in Lake Matoaka, an eutrophic, freshwater lake, in response to the primary seasonal, environmental and biological drivers. Surface water samples were collected monthly over an 18 month period, along with environmental data (temp, pH, nutrients (P and N), chl-a). Viral and bacterial abundances were determined using epifluorescence microscopy. DNA was extracted from bacterial cells captured on a 0.22 ?m filter and bacterial community profiles were generated using terminal restriction fragment length polymorphism (tRFLP). Profiles were compared by converting chromatograms to binary matrices based on the presences or absence of peaks. Pearson correlations and a BioEnv analysis were used to identify relationships between viral and bacterial abundance, viral and bacterial community composition and environmental factors. Bacterial communities were also characterized by sequencing of 16S rRNA clone libraries from two months, June 2009 and December 2009 (summer and winter), within the sample period. Distribution of T-RFs across the 18-month sampling period was analyzed by constructing cluster dendrograms, which suggested that there is no quantifiable seasonal/temporal trend in bacterial community composition. The only significant relationships revealed by correlation analysis were between bacterial and viral abundance, viral abundance and temperature, and bacterial abundance and temperature. BioEnv analysis indicated that the only environmental factor with any explanatory power in accounting for community composition change was temperature. However, inspection of dendrograms revealed that this relationship is not strictly linear and sample months do not cluster neatly based on temperature fluctuations. Moreover, viral and bacterial community compositions were determined to be very tightly linked by a Mantel test. 16S Clone libraries revealed that several dominant phyla were present within the lake, the foremost of these being Proteobacteria, consistent with the findings of previous freshwater studies. The distribution of genera varied between the two seasons. The bacterial assemblage of Lake Matoaka appears to be composed of acore of Proteobacteria that are consistently present, with a variable component that changes significantly over the annual cycle. While temperature was identified as having moderate explanatory power, a clear driver for community composition change was not determined. Future studies should include other biological and environmental factors, such as protozoan grazing and dissolved organic carbon. Future studies should also include a survey of the dynamics of community composition over several lakes of highly similar characteristics in order to clearly define drivers of bacterial communitycomposition change in freshwater ecosystems.
  • Jessica Amacher, S. N., Charles Baysinger, Michael Lomas "The contribution of protists to particle flux at the Bermuda Atlantic time-series study."
    The importance of small planktonic organisms in downward particle flux has been postulated in numerous studies, but because cells contained in particle trap material are difficult to identify with traditional methods, few direct observations exist. Clone libraries of small subunit ribosomal RNA (SSU RNA) genes now allow us to determine the relative contributions of different taxa to particle flux. Here we present results from a selection of water column and 150 m particle trap samples from a two year molecular time-series at the Bermuda Atlantic Time-series Study (BATS). Samples were selected from the winter– spring bloom periods in 2009 and 2010, and also from October 2008 and July 2009, which were selected for cloning and sequencing. Temperature, chlorophyll, particulate organic carbon flux, and denaturing gradient gel electrophoresis data were used to identify unusual events in the upper water column. Our results indicate that protist taxa contribute to flux at a rate proportional to their abundance in the water column. Dinoflagellate and marine alveolate SSU RNA sequences made up the greatest fraction of both the water column and trap libraries. Diatom SSU RNA sequences were present in several samples, but were not abundant. Only one time point was available in which diatom sequences were detected in both the water column and trap libraries. In this case their relative abundance in the trap library was found to be roughly proportional to that of the water column libraries. SSU RNA sequences matching to taxonomic groups known to include small-sized cells, for example the prasinophyte genera Bathycoccus, Micromonas and Ostreococcus, were detected in a greater proportion in trap material than in the corresponding water column samples. In one sample from the late winter bloom, prasinophyte sequences accounted for up to 4.5% of water column libraries and 13% of the trap library. Additionally, group-specific qPCR for Mamiellales provided the first quantitative estimates of the percent contribution of a group of small-sized taxa to POC flux. Our results indicate a flux of Mamiellales ranging from 0.002 to 0.47 mgC m-2 d-1, contributing up to 5.7% of total POC flux.
  • N Zondo, T. M. a. K. K. "A culture-dependent investigation of heavy-metal resistant bacteria in acid mine drainage with the potential for bioremediation."
    The extreme conditions of low pH and elevated concentrations of toxic heavy metals in acid mine drainage (AMD) have created an ecological niche for acidophilic and metallophilic microorganisms that could find application in various biotechnological strategies. The microbial diversity present in AMD contaminated water from the West Rand Basin in Gauteng, South Africa was investigated to identify potential microorganisms for exploitation in bioremediation and biosensing. A culture-dependent study was performed to isolate and characterize metallophilic bacteria and determine their minimum inhibitory concentrations (MICs) to various heavy metals. Five bacterial genera were identified using 16S rDNA sequencing: Bacillus, Microbacterium, Pantoea, Massilia and Micrococcus, in addition to an uncultured strain. Bacteria were isolated on media supplemented with cobalt (Co), nickel (Ni) and lead (Pb) with MICs ranging from 175 ppm, 100 – 300 ppm and 1700 ppm, respectively. Genera identified in this study have previously been reported to show resistance to different heavy metals and could find application in bioremediation while their genetic elements responsible for heavy metal-resistance can be exploited in the design of an in situ biosensor for monitoring of AMD contamination.
  • Olivier Chakirou, A. V., Teodora C. Carsai, Valentin A. Bâlteanu, Viorica Cosier (2012). "Aspects regarding the molecular characterisation of the Romanian Shepherd dog breeds." Animal Biology & Animal Husbandry 4(1): 28-31.
    There are four shepherd dog breeds at the present time in Romania: the Bucovina Shepherd dog, the Carpathian Shepherd dog, the Mioritic Shepherd dog and the Corb Shepherd dog. The first three breeds have been provisory homologated by the F.C.I. The Corb Shepherd dog breed is only recognized in Romania. In this article we present the steps we have performed in order to obtain the mitochondrial DNA nucleotide sequences for several individuals belonging to the three homologated Romanian dog breeds, in order to be used for later phylogenetic studies.
  • Pablo R. Hardoim, R. N., Angela Sessitsch, Leo S. van Overbeek, Jan D. van Elsas "Enterobacter oryziphilus sp. nov. and Enterobacter oryzendophyticus sp. nov., isolated from the endosphere of rice roots."
    Six Gram-negative, facultatively anaerobic, non-spore-forming, nitrogen-fixing, rod-shaped isolates were obtained from the root endosphere of rice grown at the IRRI and investigated in a polyphasic taxonomic study. Comparative 16S rRNA and rpoB gene sequence analyses allocated the isolates within the family Enterobacteriaceae, with Enterobacter radicincitans, E. arachidis and E. cowanii as the closest relatives. On the basis of the phylogenetic analyses, DNA–DNA hybridization data and unique biochemical characteristics, the isolates were shown to belong to the genus of Enterobacter, and were distinguishable into distinct groups that represent two novel species. These two species can be differentiated from each other and their nearest neighbours by the following characteristics: utilization of adonitol, D-arabitol, m-inositol, L-aspartic acid, D-melibiose, D-raffinose, decarboxylation of ornithine and positive methyl red test. Both species revealed PGP activities as well as adaptation to the host plant.
  • Piepenbring, T. A. H. M. (2011). "Biodiversity of Asterina species on Neotropical host plants: new species and records from Panama." Mycologia 103 no. 6: 1284-1301.
    Two new species of the genus Asterina are described from living leaves collected in provinces Chiriquí and Bocas del Toro in western Panama. Asterina alloplecti on Alloplectus ichtyoderma (Gesneriaceae) differs from other Asterina on Gesneriaceae by its stalked appressoria and host relationship. Asterina compsoneurae on Compsoneura sprucei (Myristicaceae) can be distinguished from other members of Asterina on Myristicaceae by its larger ascomata, larger, prominently spinose ascospores and host relationship. New records for Panama are Asterina corallopoda from a new host plant species (Solanum trizygum, Solanaceae), A. diplopoda, A. ekmanii from a new host plant species (Gonzalagunia rudis, Rubiaceae), A. siphocampyli from a new host plant genus and species (Burmeistera vulgaris, Campanulaceae) and A. styracina from a new host-plant species (Styrax argenteus, Styracaceae). This study increases the number of species of Asterina known for Panama from 12 to 19 and the number of Asterinaceae from 14 to 21. Asterina corallopoda, A. diplopoda, A. ekmanii, A. siphocampyli and A. styracina are illustrated for the first time. A phylogeny inferred from the analysis of LSU rDNA sequences of species of Asterina is presented. The diversity and host-plant patterns of known Neotropical species of Asterina are discussed.
  • Schroeder, W. H. W. a. D. (2010). "Aquatic viral ecology." MAVE 14: 134–144.
    By unraveling the genetic code of viruses, genome sequencing offers a new era for aquatic virus ecology giving access to ecological function of viruses on an unprecedented scale. Although this chapter starts with the suggestion to that virus genome sequencing should be conducted professionally if financially feasible, we essentially try and guide the reader through some of the procedures that will direct a novice through a genome sequencing project. Arguably, the most important recommendation is to start with as high purity virus nucleic acid as possible. We use the adage, junk in equals junk out. Once sequence information is obtained, there is plenty of free, user-friendly software available to help build, annotate, and then compare sequence data. Acquiring metadata is another important aspect that is not often considered when embarking on a genome project. A new initiative by the Genomic Standards Consortium has introduced Minimum Information about a Genome Sequence (MIGS) that allows standardization of the way the data are collected to make it useful for downstream post-genomic analyses. Most viruses sequenced to date have produced surprises, and there is more to come from the other 10 viruses still to be sequenced. This chapter focuses on sequencing purified virus isolates rather than virus metagenomes.
  • Silvieus, K. B. D. S. "DNA Barcoding of Quercus sp. at Pierce Cedar Creek Institute Using the matK Gene."
    When identifying different species in the field or in a laboratory, morphological characteristics are often used. These distinguishable characteristics can be very similar among different species which can make the identification process very difficult. Another way to denote different species is through a DNA barcoding method. Similar to items in a store that have a universal product code (UPC), DNA barcoding is a short genetic sequence that identifies an individual organism as a member of a particular species. The species examined were Quercus sp. (oaks); 71 samples of the 8 different species growing at Pierce Cedar Creek were collected for DNA extraction. The samples were all preserved into herbarium specimens and DNA was extracted from all of them. The extracted DNA was then amplified using PCR and gel electrophoresis methods. The successful amplified DNA was then sequenced using the gel slab method and the capillary method. Successful sequences came from the capillary method of sequencing and these samples were then analyzed using computer software to obtain a base pair reading of the sequence code. The seven sequences that were analyzed had no variations in their base pairs supporting the idea that they are of the same species, Quercus rubra.
  • YILMAZ, Ç. (2008). "Systolic architectures for sequence alignment operations ".
    In this work, new and optimized algorithms and application specific processors based on these algorithms to perform sequence alignment operations, which is one of the basic operations in bioinformatics are designed. In this work, systolic architectures are developed to implement pairwise and multiple sequence alignment operations. Proposed hardware methods develop hardwares implemented on ASIC and FPGA platforms at the rate of over one hundred per cent. The designs proposed in this work provides performance gain up to 189,92% when it is implemented on FPGA. Therefore, it is provided to other research branches in bioinformatics to analyse larger amount of data in smaller time periods.
  • Zhang, Y. Z. B. F. X. (2012). "DNA cryptography based on DNA Fragment assembly." Information Science and Digital Content Technology (ICIDT), 2012 8th International Conference on 1: 179 - 182.
    In this paper, the authors introduce the background of DNA cryptography, and briefly describe the features of DNA molecular, key bio-technologies and related software. And then the authors study the difficult biological problem which is the key and basic part in designing of DNA encryption, and put forward our own difficult problem which is that it is difficult to assembly when overlaps are destroyed and prove its difficulty with examples. After analysis of encoding of DNA and mechanism of symmetric encryption, the authors design a symmetric system using the technology of DNA digital coding and DNA fragment assembly. The security analysis proves that the scheme has high confidential strength.
  • Nikolaos Alachiotis, E. V., Pavlos Pavlidis, Alexandros Stamatakis (2012). "ChromatoGate: A Tool for Detecting Base Mis-Calls in Multiple Sequence Alignments by Semi-Automatic Chromatogram Inspection."
    Automated DNA sequencers generate chromatograms that contain raw sequencing data. They also generate data that translates the chromatograms into molecular sequences ofA, C, G, T, or N(unde-termined) characters. Since chromatogram translation programs frequently introduce errors, a manual inspection of the generated sequence data is often required. Traditionally, users inspect every base call in a sequence, assess the quality of the corresponding chromatogram peak, and decide whether the base call is accurate or not. As sequence numbers and lengths increase, visual inspection and manual correc-tion of chromatograms and corresponding sequences on a per-peak and per-nucleotide basis becomes an error-prone, time-consuming, and tedious process. We introduce ChromatoGate (CG), a open-source software that facilitates, accelerates, and partially automates the inspection of chromatograms and the detection of respective sequencing errors for bi-directional sequencing runs. A fully automated error correction algorithm has not been implemented in ChromatoGate to provide users full control over the error correction process. Initially, the program scans a given multiple sequence alignment (MSA) for potential sequencing errors, assuming that each polymorphic site in the alignment may be attributed to a sequencing error with a certain probability. The guided MSA assembly procedure in ChromatoGate detects chromatogram peaks of all characters in an alignment that lead to polymorphic sites, given a user-defined threshold. The threshold value represents the sensitivity of the sequencing error detection mechanism. After this pre-filtering, the user only needs to inspect a small number of peaks in every chromatogram to correct sequencing errors. Finally, we show that correcting sequencing errors is important, because population genetic and phylogenetic inferences can be misled by MSAs with uncorrected mis-calls. Our experiments indicate that estimates of population mutation rates can be affected two- to three-fold by uncorrected errors. Raw sequence data from automated sequencers contain base mis-calls which need to be corrected in MSAs prior to conducting further analyses, because such mis-calls can mislead downstream analyses. ChromatoGate facilitates and substantially accelerates the inspection and correction of sequencing mis-calls. The process of minimizing sequencing errors during MSA assembly is simplified by identifying only a small fraction of chromatogram peaks that require furtherinspection.
  • Santhosh J Eapen, O. R. a. A. C. "Sequence Alignment."
    A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acids or nucleotides. Multiple sequence alignment also refers to the process of aligning such a sequence set. Because three or more sequences of biologically relevant length can be difficult and are almost always time-consuming to align by hand, computational algorithms are used to produce and analyze the alignments. MSAs require more sophisticated methodologies than pairwise alignment because they are more computationally complex. Most multiple sequence alignment programs use heuristic methods rather than global optimization because identifying the optimal alignment between more than a few sequences of moderate length is prohibitively computationally expensive.
  • Christerson, L. U. U., Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Bacteriology) (2011). "
    High Resolution Genotyping of Chlamydia trachomatis."
    Chlamydia trachomatis is an obligate intracellular bacterium of major human health concern, causing urogential chlamydia infections, lymphogranuloma venereum (LGV) and trachoma. Chlamydia is one of the most common sexually transmitted infections worldwide and can cause infertility.
    In the first four papers described herein we used a high resolution multilocus sequence typing (MLST) system to investigate the epidemiology of C. trachomatis, and showed that MLST is superior to conventional ompA genotyping with respect to resolution. In the fifth paper we simplified the methodology by developing and validating a multilocus typing (MLT) DNA microarray based on the MLST system.
    In more detail, MLST analysis of consecutive specimens from 2006 in Örebro County in Sweden, and comparison to specimens from 1999-2000, showed that the new variant C. trachomatis (nvCT) is monoclonal and likely has appeared in recent years.
    MLST analysis of LGV specimens from men who have sex with men (MSM) showed that the increase of LGV in Europe in the last decade indeed was a clonal outbreak, contrary to the USA where LGV might have been present all along.
    In the third paper, clinical symptoms could not be correlated with the MLST genotypes, suggesting, together with the combined results of all previous studies, that bacterial factors, if important, need to be understood in the context of host factors.
    MLST analysis of specimens from a high incidence C. trachomatis area in North Norway revealed interesting epidemiological details concerning unusual genetic variants, the nvCT and MSM, but found no significant difference in genetic diversity compared to two other geographic areas in Norway.
    Lastly, we developed a MLT array that provides high resolution while being rapid and cost-effective, which makes it an interesting alternative for C. trachomatis genotyping.
    In conclusion, the MLST system and the MLT array have proven to be useful tools and should now be applied in further investigations to improve our understanding of C. trachomatis epidemiology.
  • Dr. M. Anandaraj, D. J. K. G., P. R. Rahul, A. Chandrasekar, Dr. Santosh J. Eapen, Dr. Prasath (2011). "National training on "Allele Mining" ." Laboratory manual: 2-64.
    Any molecular biology work is basically done using the genetic material of an organism, either DNA or RNA. Thus the isolation of a good quality DNA/RNA is essential to the success/failure of any experiment. The main role of DNA molecules is the long-term storage of information in the form of triplet codons containing the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Ribonucleic acids (RNA) are crucial molecules in the “central dogma of life” and perform vital functions in both structural and functional roles. RNA molecules form the bridge between the stable genetic information contained within DNA and enzymes and proteins that carry out much of the metabolism within the cell. Many of the sites of protein synthesis, the ribosomes within the cell, are composed of these ribonucleic acids as tRNA molecules that deliver the amino acid building blocks to the ribosomes. Of all the RNA species, the nucleic acid intermediate, messenger RNA, is a desirable source of material to biologists, since this reflects much of, what ultimately, is translated into enzymes and proteins. High quality RNA is the starting material to study the qualitative and quantitative changes in mRNA expression, in- vitro translation, RNase protection assay, reverse transcriptase - polymerase chain reaction (RT-PCR) and cloning. The gene specific primers can be designed based on sequence information available at the NCBI database and can be used for the isolation of genes using RT-PCR.
  • Jillian M. Petersen, C. W., Caroline Verna, Katrin Knittel and Nicole Dubilier (2012). "Origins and Evolutionary Flexibility of Chemosynthetic Symbionts From Deep-Sea Animals." Biol. Bull 223, no 1: 123-137.
    Bathymodiolin mussels dominate hydrothermal vent and cold seep communities worldwide. Symbiotic associations with chemosynthetic sulfur- and methane-oxidizing bacteria that provide for their nutrition are the key to their ecological and evolutionary success. The current paradigm is that these symbioses evolved from two free-living ancestors, one methane-oxidizing and one sulfur-oxidizing bacterium. In contrast to previous studies, our phylogenetic analyses of the bathymodiolin symbionts show that both the sulfur and the methane oxidizers fall into multiple clades interspersed with free-living bacteria, many of which were discovered recently in metagenomes from marine oxygen minimum zones. We therefore hypothesize that symbioses between bathymodiolin mussels and free-living sulfur- and methane-oxidizing bacteria evolved multiple times in convergent evolution. Furthermore, by 16S rRNA sequencing and fluorescence in situ hybridization, we show that close relatives of the bathymodiolin symbionts occur on hosts belonging to different animal phyla: Raricirrus beryli, a terebellid polychaete from a whale-fall, and a poecilosclerid sponge from a cold seep. The host range within the bathymodiolin symbionts is therefore greater than previously recognized, confirming the remarkable flexibility of these symbiotic associations.
  • Nestor G. Basso, Carmen A. Úbeda, Maria M. Bunge & Liza B. Martinazzo (2011). "A new genus of neobatrachian frog from southern Patagonian forests, Argentina and Chile." Magnolia Press.
    In 1975 Lynch named a new species of frog based on two specimens from Puerto Eden, Wellington Island, southern Chile, tentatively allocated to the genus Telmatobius . Telmatobius grandisonae Lynch was later included by the same author in his genus Atelognathus. Based on a reappraisal of the type material and the description of the internal and external morphology, karyotype, tadpole mo rphology and molecular evidence from recentl y discovered specimens collected at Lago del Desierto, southern Argentina, we describe the monotypic genus Chaltenobatrachus, with Telmatobius grandisonae (Lynch) serving as the type species. Chaltenobatrachus differs from Atelognathus mainly in having a uniform bright green dorsal coloration, with brown to reddish warts; orange iris with gold spots; fingers with interdigital membrane; frontoparietals well developed; small nasals;well ossified sphenethmoid; anteriorly expanded homosternum; skin of tadpole transparent; oral disc with protruding anterior and lateral papillae; diploid number 2n = 32 chromosomes. The genetic distances between Chaltenobatrachus and Atelognathus meet or exceed most othe r intergeneric comparisons.
  • Obornik, M. (2009). "Identification and Diagnostics of Entomopathogenic Protozoa." Insect Pathogens: Molecular Approaches and Techniques: 101-123.
    Molecular methods allow us to recognize and identify target organisms from a variety of environments including laboratory cultures, host tissues or environmental samples, through a detection of specific molecular markers. Ascending progress in the field of molecular evolution during last 15 years greatly influenced high-order taxonomy. It has been shown that the proposed kingdom Protozoa comprising unicellular heterotrophic eukaryotes is polyphyletic in its nature and its taxonomic relevance is no longer sustainable.
  • Piccini, C., et al. (2011). "Genetic and eco-physiological differences of South American Cylindrospermopsis raciborskii isolates support the hypothesis of multiple ecotypes." Harmful Algae 10(6): 644-653.
    The global distribution of the toxic cyanobacterium Cylindrospermopsis raciborskii has recently increased, and it has now been identified in tropical, subtropical and temperate freshwater bodies. The mechanisms underlying its success and expansion are still unknown. Several hypotheses have been proposed, including climate change, natural selection and physiological tolerance to different environmental conditions. In this study, we determined the phenotypic and genotypic characteristics of two recently isolated South American strains of C. raciborskii obtained from Uruguay. We analyzed the morphology, growth preferences, tolerance to low temperature (14 °C) and toxin production of the strains and performed phylogenetic analyses based on the ITS and nifH gene sequences. Both isolates showed significantly different morphology and growth behavior under different light intensities and phosphate supply. When genetic differences were assessed by BOX PCR, cluster analyses revealed that they could also be distinguished genotypically and were clearly distinct from C. raciborskii isolated from other continents. Phylogenetic analysis showed that the Uruguayan strains were closely affiliated to other C. raciborskii isolated from the Americas, especially to those from Brazil. Similar to previous studies, we found three solid clusters (Africa-Australia, Europe and America) according to the geographical origin of the isolates. Interestingly, based on nifH sequences, subclusters were identified in American populations indicating an early spread of the species within the continent. We propose that phenotypic and genetic variability of C. raciborskii populations is linked to the existence of different ecotypes whose success is subject to the local environmental conditions.
  • Reyhaneh Darsouei , J. K., Mehdi Modarres Avval "A Comparison of DNA Barcoding with Classic Method in Diagnosis Five of Aphid Species on Pome Fruit Trees in Mashhad
    " Iranian Journal of Plant Protection Science 42(2).
    Aphids are among important agricultural pests. The pest's evolutionary tendency towards a loss of taxonomically useful characteristics, as well as morphological plasticity due to host type and as a result of environmental factors, make a morphological identification of aphids difficult, whereas exact identification is indispensable for managment of these pests. Thus, modern identification methods could help in managing these pests. In this study conducted during 2008-2010 on trees in pome fruit orchards in Mashhad region of Iran, classic method accompanied with DNA barcoding was employed for an identification of aphid pests. Aphis pomi, Dysaphis afiinis, D. plantaginea, Nearctaphis bakeri and Allocotaphis quaestionis were collected from apple, quince and pear trees, A. quaestionis being reported for the first time from Iran. DNA barcoding was provided for cox1 gene in these species and phylogenetic relationship investigated among the collected species as well as other species within the family. DNA barcoding confirmed the morphological identification. Results of molecular data were compatible with morphological characteristics and classic grouping, separating the studied species as based on genus and tribe. This is the first data gathered about aphid characterization in Iran while applying DNA barcoding. The results of this study indicate that cox1 sequence could be useful in aphids' identification and recognition of their internal relationships.
  • Rosen, A. L. U., Department of Clinical and Experimental Medicine) (2010). "Development of pharmacogenetic tests and improvement of autosomal ancestry DNA test (Utveckling av farmakogenetiska test och forbattring av autosomalt ursprungstest)."
    This master thesis was performed at the personal genomics company DNA-Guide Europa AB. The goal was to create DNA tests for drug response and to update the already existing DNA test for autosomal ancestry.
    The DNA tests for drug response: The objective of this part of the master thesis was to create individual DNA test for response to each drug within different groups of medicines. The tests were meant to interest private customers. DNA-Guide uses a microarray technique for the DNA-analysis and this delimited the choice of SNPs. Inserts, deletions, repeats and copies of a whole gene can be difficult to implement on the microarray chip. The SNPs and studies used as a base for the tests had to fulfil several criteria. The studies must be large enough to prove that the association between the genotype and the response to the drug is valid among Europeans, since it's the clientele of the company. The found association must also be strong enough to be of interest for a DNA test at DNA-Guide.
    If the SNPs could be implemented on the microarray chip a customer report was created about the possible results. The report had the same structure and design as those for the existing DNA tests at DNA-Guide. The work resulted in DNA tests and reports for medicines within the seven groups of medicines; anticoagulants, medicine against high cholesterol, blood pressure lowering medicine, asthma inhalers, antidepressants, birth-control pills and antiretroviral drugs.
    The DNA test for autosomal ancestry: The purpose of the update was to enhance to customers understanding of their results and the construction of the test. The update resulted in a description of how the used algorithm processes the results (from the DNA analysis) and a guide to interpret the results of the test.
    Conclusions: Both the DNA tests for drug response and the updated DNA test for autosomal ancestry can add value for the customers at DNA-Guide. The DNA tests for drug response can offer an explanation to why a medicine does not have an effect or reveal if the customer has higher risk of adverse effects. Even though recommendations for dosage or treatment could not be provided in almost all of the created DNA tests, being aware of the higher risk can be the first step to avoid adverse effects. The update of the DNA test report for autosomal ancestry resulted in a better description of the algorithm and limitations of the test, which can enhance the customers’ understanding of their results.
  • Tamas Geczy, M. L. P., Said El Kazzouli, Dina M. Sigano, Ji-Hye Kang, Christopher J. Valle, Julia Selezneva, Wonhee Woo, Noemi Kedei, Nancy E. Lewin, Susan H. Garfield, Langston Lim, Poonam Mannan, Victor E. Marquez and Peter M. Blumberg (2012). "Molecular Basis for Failure of "Atypical" C1 Domain of Vav1 to Bind Diacylglycerol/Phorbol Ester." The Journal of Biological Chemistry 287.
    C1 domains, the recognition motif of the second messenger diacylglycerol and of the phorbol esters, are classified as typical (ligand-responsive) or atypical (not ligand-responsive). The C1 domain of Vav1, a guanine nucleotide exchange factor, plays a critical role in regulation of Vav activity through stabilization of the Dbl homology domain, which is responsible for exchange activity of Vav. Although the C1 domain of Vav1 is classified as atypical, it retains a binding pocket geometry homologous to that of the typical C1 domains of PKCs. This study clarifies the basis for its failure to bind ligands. Substituting Vav1-specific residues into the C1b domain of PKC?, we identified five crucial residues (Glu9, Glu10, Thr11, Thr24, and Tyr26) along the rim of the binding cleft that weaken binding potency in a cumulative fashion. Reciprocally, replacing these incompatible residues in the Vav1 C1 domain with the corresponding residues from PKC? C1b (?C1b) conferred high potency for phorbol ester binding. Computer modeling predicts that these unique residues in Vav1 increase the hydrophilicity of the rim of the binding pocket, impairing membrane association and thereby preventing formation of the ternary C1-ligand-membrane binding complex. The initial design of diacylglycerol-lactones to exploit these Vav1 unique residues showed enhanced selectivity for C1 domains incorporating these residues, suggesting a strategy for the development of ligands targeting Vav1.
  • Basilua Kanza, J. P., E. El Fahime, et al. (2012). "Pyrethroid, DDT and malathion resistance in the malaria vector Anopheles gambiae from the Democratic Republic of Congo." Transactions of The Royal Society of Tropical Medicine and Hygiene.
    Background Malaria remains the most important parasitic disease in sub-Saharan Africa. We investigated the extent of resistance in the malaria vector Anopheles gambiae from the Democratic Republic of Congo (DRC) to three classes of insecticide approved by WHO for indoor residual spraying.Method Standard WHO bioassays were performed on adult Anopheles mosquitoes reared in the laboratory from larvae collected from different sites. Molecular techniques were used for species identification and to identify knockdown resistance (kdr) and acetylcholinesterase (ace-1R) mutations in individual mosquitoes.Results Only A. gambiae s.s., the nominal member of the A. gambiae species complex, was found. Bioassays showed phenotypic resistance to the main insecticides used in the region, notably pyrethroids (deltamethrin, permethrin, lambda-cyhalothrin), an organochlorine (DDT) and an organophosphate (malathion). The L1014F kdr allele, often associated with resistance to pyrethroids and DDT, was detected in samples from all collection sites at varying frequencies. No ace-1R resistance alleles (associated with organophosphate and carbamate resistance) were detected.Conclusions These data can be used to inform a resistance management strategy that requires comprehensive information concerning malaria vector species composition in the areas of interest, and their susceptibility to the insecticides proposed for their control.
  • Dahle, S. "Phylogenetic analysis of the genus Paratanytarsus (Diptera: Chironomidae)."
    The non-biting midges (Chironomidae) are among of the most successful insects in freshwater systems and often dominate in abundance and species richness. The genus Paratanytarsus contains species from all biogeographic regions except tropical Africa, 19 species are known from Europe. Previous molecular work has suggested the presence of undescribed species within some species groups, in addition the monophyly of the genus has been questioned. In this study four nuclear molecular markers, CAD1, CAD4, PGD and AATS1 are utilized in order to reconstruct the evolutionary history of the genus. Samples identified to 16 different species have been collected at locations in Northern Europe, Arctic Canada and Australia. The results of the phylogenetic analysis supports the monophyly of the genus, while considerable intraspesific variation is revealed within several species. Material identified to P. austriacus/hyperboreus is found to group into four separated genetic clusters, two of which appear to be undescribed cryptic species based on currently used morphological characters. Canadian P. dissimilis and P. tenuis ends up paraphyletic with respect to European samples and might represent new Nearctic species. The Australian taxa came out well-embedded in the tree without any close relatives. It is hypothesized that bipolar migrations has occurred in the history of the genus.
  • Deng, T., C. Kim, et al. (2013). "Zhengyia shennongensis: A new bulbiliferous genus and species of the nettle family (Urticaceae) from central China exhibiting parallel evolution of the bulbil trait." Taxon 62(1): 89-99.
    Zhengyia shennongensis is described here as a new genus and species of the nettle family (Urticaceae) from Hubei province, central China. The phylogenetic position of Z. shennongensis is determined using DNA sequences of nuclear ribosomal ITS and three plastid regions (rbcL, psbA-trnH, trnL-F). Zhengyia shennongensis is readily distinguished from the related genera Urtica, Hesperocnide, and Laportea in the tribe Urticeae by its seed (oblong-globose or subglobose and not compressed achenes, surface densely covered with nipple-shaped protuberances) and stipule morphology (large leaf-like stipules with auriculate and amplexicaulous base and united with stem). Phylogenetic evidence indicates that Zhengyia is a distinct group related to Urtica (including Hesperocnide) species and Laportea cuspidata in tribe Urticeae. The bulbiliferous species of the tribe (L. bulbifera, L. cuspidata, Z. shennongensis) do not form a clade. This result indicates that the bulbil trait evolved in parallel within Urticeae. Our findings highlight the importance of shady and moist habitats in promoting species diversification and the parallel evolution of morphological traits that are likely to be adaptive.
  • Jaekel, U., N. Musat, et al. (2012). "Anaerobic degradation of propane and butane by sulfate-reducing bacteria enriched from marine hydrocarbon cold seeps." ISME J.
    The short-chain, non-methane hydrocarbons propane and butane can contribute significantly to the carbon and sulfur cycles in marine environments affected by oil or natural gas seepage. In the present study, we enriched and identified novel propane and butane-degrading sulfate reducers from marine oil and gas cold seeps in the Gulf of Mexico and Hydrate Ridge. The enrichment cultures obtained were able to degrade simultaneously propane and butane, but not other gaseous alkanes. They were cold-adapted, showing highest sulfate-reduction rates between 16 and 20?°C. Analysis of 16S rRNA gene libraries, followed by whole-cell hybridizations with sequence-specific oligonucleotide probes showed that each enrichment culture was dominated by a unique phylotype affiliated with the Desulfosarcina-Desulfococcus cluster within the Deltaproteobacteria. These phylotypes formed a distinct phylogenetic cluster of propane and butane degraders, including sequences from environments associated with hydrocarbon seeps. Incubations with 13C-labeled substrates, hybridizations with sequence-specific probes and nanoSIMS analyses showed that cells of the dominant phylotypes were the first to become enriched in 13C, demonstrating that they were directly involved in hydrocarbon degradation. Furthermore, using the nanoSIMS data, carbon assimilation rates were calculated for the dominant cells in each enrichment culture.
  • Koizumi, N., S. Morioka, et al. (2013). "Characterization of twenty-four polymorphic microsatellite loci of Rasbora borapetensis." Conservation Genetics Resources: 1-3.
    Twenty-four microsatellite loci were isolated and characterized from the genome of Rasbora borapetensis. Flanking polymerase chain reaction primers were designed and used to amplify these loci in 32 individuals. All loci were polymorphic with allele numbers ranging from 2 to 27, observed heterozygosity from 0.031 to 1.000 and expected heterozygosity from 0.031 to 0.965. All loci conformed to the Hardy–Weinberg equilibrium and no evidence of null alleles was observed. Pairwise comparisons between alleles did not detect any linkage disequilibrium. The high level of polymorphisms observed in these microsatellite loci will enhance future investigations on the genetic differentiation and structure of populations of Rasbora borapetensis.
  • Muhle, H., I. Helbig, et al. "The role of SLC2A1 in early onset and childhood absence epilepsies." Epilepsy Research(0).
    Summary Early Onset Absence Epilepsy constitutes an Idiopathic Generalized Epilepsy with absences starting before the age of four years. Mutations in SLC2A1, encoding the glucose transporter, account for approximately 10% of EOAE cases. The role of SLC2A1 mutations in absence epilepsies with a later onset has not been assessed. We found two mutation carriers in 26 EOAE patients, while no mutations were found in 124 probands affected by CAE or JAE.
  • Nahar, S., M. Afrad, et al. (2013). "A novel norovirus recombinant strain GII.4/GII.21 in Bangladesh, 2011." Virus Genes: 1-4.
    We identified a novel inter-genotype recombinant norovirus strain, Dhaka85/2011/BGD, collected from a stool specimen of a nine-month-old infant who was hospitalized with diarrhea. Molecular investigation and phylogenetic analysis classified its RNA polymerase gene as GII.4-like, which commonly circulates in humans. The capsid gene was classified as GII.21-like, most likely originated from water. The discovery of this novel strain is an illustration of the enormous diversity among the norovirus strains, especially in developing countries and has important implications for future vaccine strategies.
  • Roth, A. L. and N. D. Hanson (2012). "Rapid Detection and Statistical Differentiation of KPC Gene Variants in Gram-negative Pathogens Using High Resolution Melting and ScreenClust Analysis." Journal of Clinical Microbiology.
    In the United States, production of the KPC β-lactamase is an important mechanism of carbapenem resistance in Gram-negative pathogens. Infections with KPC-producing organisms are associated with increased morbidity and mortality therefore, rapid detection of KPC-producing pathogens is critical in patient care and infection control. We developed a real-time PCR assay complemented with traditional high resolution melting (HRM) analysis as well as statistically-based genotyping using the Rotor-Gene ScreenClust HRM software to both detect the presence of blaKPC and differentiate between KPC-2-like and KPC-3-like alleles. One-hundred sixty-six clinical isolates of Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii with varying β-lactamase susceptibility patterns were tested in the validation of this assay, 66 of which were known to produce the KPC β-lactamase. The real-time PCR assay was able to detect the presence of blaKPC in all 66 of the clinical isolates (100% sensitivity and specificity); HRM analysis demonstrated that 26 had KPC-2-like melting peak temperatures while 40 had KPC-3-like melting peak temperatures. Sequencing of 21 amplified products confirmed the melt peak results with 9 isolates carrying blaKPC-2 and 12 isolates carrying blaKPC-3. This PCR/HRM assay can identify KPC-producing Gram-negative pathogens in as little as three hours after isolation of pure colonies, does not require post-PCR sample manipulation for HRM analysis, and ScreenClust analysis allows for easy interpretation into blaKPC-2-like and blaKPC-3-like alleles. Therefore, this assay is a rapid method to identify the presence of blaKPC enzymes in Gram-negative pathogens that can be easily integrated into busy clinical microbiology laboratories.
  • Staley, C., E. Chase, et al. (2013). "Detection and differentiation of Vibrio vulnificus and V.?sinaloensis in water and oysters of a Gulf of Mexico estuary." Environmental Microbiology 15(2): 623-633.
    Vibrio vulnificus is a potentially lethal human pathogen that occurs naturally in estuarine waters and shellfish. Vibrio vulnificus was quantified in water and oysters from Florida's Gulf Coast by plating on mCPC agar, enrichment and plating, and quantitative PCR (qPCR). Vibrio vulnificus was detected in 19%, 29%, and 97% of samples respectively by direct plating, qPCR, and enrichment. Only 8% of typical colonies from direct plating were confirmed by PCR for vvhA; others yielded no or atypically sized amplicons. Sequencing of the 16S rDNA of 16 vvhA-negative isolates with colony morphology typical of V.vulnificus identified 75% as V.sinaloensis. In vitro growth curves showed that V.sinaloensis grew more rapidly than V.vulnificus in seawater at temperatures ≤30°C. In contrast, the growth rate of V.vulnificus in alkaline peptone water was greater than that of V.sinaloensis, suggesting that these species can outcompete one another under conditions that are relevant to environmental parameters or regulatory monitoring regimes respectively. The virulence potential and ecology of V.sinaloensis are poorly understood; however, its phenotypic resemblance to V.vulnificus and the possibility that it could outcompete the pathogen in warm, estuarine waters argue for the need for a better understanding of this newly described Vibrio species.
  • Zimmer, B. L. (2012). "Quorum Sensing and Microbial Interactions in Coral Black Band Disease and Coral-Associated Bacteria." FIU Electronic Theses and Dissertations 781.
    The black band disease (BBD) microbial consortium often causes mortality of reef-building corals. Microbial chemical interactions (i.e., quorum sensing (QS) and antimicrobial production) may be involved in the BBD disease process. Culture filtrates (CFs) from over 150 bacterial isolates from BBD and the surface mucopolysaccharide layer (SML) of healthy and diseased corals were screened for acyl homoserine lactone (AHL) and Autoinducer-2 (AI-2) QS signals using bacterial reporter strains. AHLs were detected in all BBD mat samples and nine CFs. More than half of the CFs (~55%) tested positive for AI-2. Approximately 27% of growth challenges conducted among 19 isolates showed significant growth inhibition. These findings demonstrate that QS is actively occurring within the BBD microbial mat and that culturable bacteria from BBD and the coral SML are able to produce QS signals and antimicrobial compounds. This is the first study to identify AHL production in association with active coral disease.
  • Zhang, J., et al. (2011). "The impact of next-generation sequencing on genomics." Journal of Genetics and Genomics 38(3): 95-109.
    This article reviews basic concepts, general applications, and the potential impact of next-generation sequencing (NGS) technologies on genomics, with particular reference to currently available and possible future platforms and bioinformatics. NGS technologies have demonstrated the capacity to sequence DNA at unprecedented speed, thereby enabling previously unimaginable scientific achievements and novel biological applications. But, the massive data produced by NGS also presents a significant challenge for data storage, analyses, and management solutions. Advanced bioinformatic tools are essential for the successful application of NGS technology. As evidenced throughout this review, NGS technologies will have a striking impact on genomic research and the entire biological field. With its ability to tackle the unsolved challenges unconquered by previous genomic technologies, NGS is likely to unravel the complexity of the human genome in terms of genetic variations, some of which may be confined to susceptible loci for some common human conditions. The impact of NGS technologies on genomics will be far reaching and likely change the field for years to come.


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