PhD in Natural Sciences
Amongst my first scientific endeavours was the development of geneFISH - an in situ method for simultaneous rRNA and gene detection in environmental microorganisms, during my PhD with Rudolf Amann at the Max Planck Institute for Marine Microbiology, Bremen, Germany. The development of geneFISH represents an ongoing processes, which I continued during my first postdoc (also with Rudi Amann) and in which I'm still involved to the present day through a tight collaboration with the Amann group (including the PhD student Jimena Barrero Canosa). While still in Bremen, and, in collaboration with members of Matthew Sullivan's group (University of Arizona) - Elke Allers and Melissa Duhaime, I have worked on the development of phageFISH - a markedly improved geneFISH protocol tailored for the detection of intracellular and extracellular viruses in microorganisms.
Together with Rudolf Amann I have organized the workshop entitled “The 1st Bremen FISH camp”, which brought together world specialists in Fluorescence In Situ Hybridization in microorganisms for two intensive weeks of lab experiments and lectures. The event took place at the Max Planck Institute for Marine Microbiology, Bremen, in the time interval 14th to 24th of June, 2011. It was concluded with the publication of a special “Fluorescence In Situ Hybridization (FISH)” issue in Systematic and Applied Microbiology (Volume 35 No. 8 . 2012). During the workshop. the active involvement microscopy specialists from Carl Zeiss raised my interest in the potential applications of super-resolution microscopy techniques in environmental microbiology, through combination with Fluorescence In Situ Hybridization.
Working on phageFISH has opened to me the fascinating world of microbial viruses and presently, in the group of Ricardo Amils (Centre of Astrobiology, Madrid, Spain), I'm researching acidophilic viruses and their hosts.
Super-resolution microscopy in environmental microbiology
The application of super-resolution microscopy in the study of environmental microbes is only at the beginning. Initial experiments (see Moraru and Amann, 2012) which combined FISH with super-resolution microscopy has shown that, at least in pure cultures of Escherichia coli and Beggiatoa alba, rRNA targeted FISH combined with Structured Illumination Fluorescence Microscopy (SIM) and by direct Stochastical Optical Reconstruction Microscopy (dSTORM) can be used for sub-cellular localization of ribosomes. What's more, dSTORM allows generation of molecular density maps of the ribosomes, and, as such, holds many promises for the quantification of per cell ribosome numbers. Further experiments along these lines are in progress.
Single gene detection in microorganisms by Fluorescence In Situ Hybridization (FISH)
Development of geneFISH and of a probe design concept and software for polynucleotide probes
My work regarding geneFISH is focused on two major points: i) sensitivity, that is how to make the signal from single genes detectable and ii) specificity, that is how to design probes to address the high diversity of microbial genes in complex environmental samples.
To address the sensitivity, I have been using a signal amplification system that involves the recognition of Dig-labeled polynucleotide probes by HRP-labeled antibodies, and later, enzymatic deposition of many fluorescently labeled molecules in the hybridized cells by the HRP. This led to the development of the geneFISH protocol, which is described in detail in Moraru et. al, 2010. For more information and new developments on geneFISH, click here.
To address the specificity, I have moved from laboratory work to computer work, developing a concept and software (PolyPro) for polynucleotide probe design. The main concept recognizes the high allele diversity of microbial genes in environment samples, and proposes the use of polynucleotide probe mixes to target single genes. This concept is described in Moraru et. al, 2011. For more information and new developments on polynucleotide probe specificity, click here.
Development of bioinformatics software for polynucleotide probe design and sequence analysis
Beginning with April 2010 I am the Cofounder and comanager of BioSoft, Pitesti, Romania, a company specialized in the development of software for bioinformatics. Here my contribution is focused on the conceptual and algorithmic design of DNA Sequence Assembler and NextGen SFF/FastQ Workbench) bioinformatics software. DNA Baser Sequence Assembler is a program for sequence assembly and Single Nucleotide Point (SNP) mutation detection for sequences generated via Sanger sequecing, while SFF/FastQ Workbench is working with reads generated by pyrosequencing.
My extended CV can be found here.