Jean-Marie Rouillard

• PhD
• MYcroarray

Barton et al. raise several statistical concerns regarding our original analyses that highlight the challenge of inferring natural selection using ancient genomic data. We show here that these concerns have limited impact on our original conclusions. Specifically, we recover the same signature of enrichment for high FST values at the immune loci re...

Infectious diseases are among the strongest selective pressures driving human evolution1,2. This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis³. This pandemic devastated Afro-Eurasia, killing up...

Meiotic crossovers (COs) play a critical role in generating genetic variation and maintaining faithful segregation of homologous chromosomes during meiosis. We develop a haplotype-specific fluorescence in situ hybridization (FISH) technique that allows visualization of COs directly on metaphase chromosomes. Oligonucleotides (oligos) specific to chr...

Objectives In the 14th century AD, medieval Europe was severely affected by the Great European Famine as well as repeated bouts of disease, including the Black Death, causing major demographic shifts. This high volatility led to increased mobility and migration due to new labor and economic opportunities, as evidenced by documentary and stable isot...

Significance Whole-chromosome oligo-FISH paints using synthetic oligonucleotide libraries that can be amplified and labeled were generated for all 10 chromosomes of maize, facilitating chromosome studies with high sensitivity and specificity for genetically diverse lines. Applications include visualization of simple or complex chromosomal aberratio...

Development of a eukaryotic karyotype relies on identification of individual chromosomes in the species, which has been accomplished only in a limited... Developing the karyotype of a eukaryotic species relies on identification of individual chromosomes, which has been a major challenge for most nonmodel plant and animal species. We developed a nov...

Parallel detection approaches are of interest to many researchers interested in identifying multiple water and foodborne pathogens simultaneously. Availability and cost-effectiveness are two key factors determining the usefulness of such approaches for laboratories with limited resources. In this study, we developed and validated a high-density mic...

Smallpox holds a unique position in the history of medicine. It was the first disease for which a vaccine was developed and remains the only human disease eradicated by vaccination. Although there have been claims of smallpox in Egypt, India, and China dating back millennia [1–4], the timescale of emergence of the causative agent, variola virus (VA...

After evolving in Africa at the close of the Miocene, mammoths (Mammuthus sp.) spread through much of the northern hemisphere, diversifying morphologically as they entered various habitats. Paleontologically, these morphs are conventionally recognized as species. In Pleistocene North America alone, several mammoth species have been recognized, inha...

Among the fossils of hitherto unknown mammals that Darwin collected in South America between 1832 and 1833 during the Beagle expedition [1 • Fernicola J.C. • Vizcaíno S.F. • De Iuliis G. The fossil mammals collected by Charles Darwin in South America during his travels on board the HMS Beagle.Revist. Asoc. Geol. Argent. 2009; 64: 147-159 • Google...

Human cytogenetic applications rely on detecting the presence, position, and location of specific chromosomal regions within the nucleus as well as chromosomal abnormalities, mainly through the use of Fluorescent In Situ Hybridization (FISH). Conventionally, FISH probes have been generated from PCR amplification of genomic regions or BACs followed...

Custom-defined oligonucleotide collections have a broad range of applications in fields of synthetic biology, targeted sequencing, and cytogenetics. Also, they are used to encode information for technologies like RNA interference, protein engineering and DNA-encoded libraries. High-throughput parallel DNA synthesis technologies developed for the ma...

We report metrics from complete genome capture of nuclear DNA from extinct mammoths using biotinylated RNAs transcribed from an Asian elephant DNA extract. Enrichment of the nuclear genome ranged from 1.06- to 18.65-fold, to an apparent maximum threshold of ∼80% on-target. This projects an order of magnitude less costly complete genome sequencing f...

Yersinia pestis has caused at least three human plague pandemics. The second (Black Death, 14-17th centuries) and third (19-20th centuries) have been genetically characterised, but there is only a limited understanding of the first pandemic, the Plague of Justinian (6-8th centuries). To address this gap, we sequenced and analysed draft genomes of Y...

Oligonucleotide microarrays allow the production of complex custom oligonucleotide libraries for nucleic acid detection-based applications such as fluorescence in situ hybridization (FISH). We have developed a PCR-free method to make single-stranded DNA (ssDNA) fluorescent probes through an intermediate RNA library. A double-stranded oligonucleotid...

Sewage pollution remains the most significant source of human waterborne pathogens. This study describes the detection and characterization of human enteric viruses in community wastewaters using cell culture coupled with multiple target microarrays (with a total of 780 unique probes targeting 27 different groups of both DNA and RNA viruses) and po...

Targeted DNA enrichment through hybridization capture (EHC) is rapidly replacing PCR as the method of choice for enrichment prior to genomic resequencing. This is especially true in the case of ancient DNA (aDNA) from long-dead organisms, where targets tend to be highly fragmented and outnumbered by contaminant DNA. However, the behavior of EHC usi...

Antimicrobial peptides (AMPs) belong to a class of natural microbicidal molecules that have been receiving great attention for their lower propensity for inducing drug resistance, hence, their potential as alternative drugs to conventional antibiotics. By generating AMP libraries, one can study a large number of candidates for their activities simu...

Number of reads for each unique sequence generated by 454 GS Junior. All unique sequences with a full length coding region (>128 bp, peptide-coding region plus primer binding site) were plotted versus their corresponding number of reads for each MID group (a). A close-up look at the plot (b) reveals the break point at about 20 reads per sequence fo...

List of PLN-423 variants from 454 sequencing. (TXT)

Primer sequences used in this study. (PDF)

PLN-423 mutant library. (TXT)

Amino acid groups used for peptide library design. (PDF)

Fluorescence in situ hybridization (FISH) is a powerful tool to study chromosome structure, positioning, and gene expression on a cell-by-cell basis. We have developed Oligopaints [1], a PCR-based method for generating highly efficient FISH probes from complex DNA libraries. Our method can visualize genomic regions ranging in size from tens of kilo...

Exon 9 (421bp) was incorrectly predicted by aligning this snake transcript to other species transcripts. Mapping of reads from captured sample to the reference sequence reveals that exon 9 should be split into 4 distinct exons. 2. Uncover exact exon structure Figure shows delineation of exon 9 into 4 exons (orange) and discovery of novel intron seq...

A host of observations demonstrating the relationship between nuclear architecture and processes such as gene expression have led to a number of new technologies for interrogating chromosome positioning. Whereas some of these technologies reconstruct intermolecular interactions, others have enhanced our ability to visualize chromosomes in situ. Her...

Excessive use of antibiotics in human and animal health care for the treatment and prevention of bacterial infections led to a rapid increase in antibiotic-resistant pathogenic bacteria. Antimicrobial peptides (AMPs) belong to a class of natural microbicidal molecules with lower propensity for inducing drug resistance; hence, they present significa...

The design of microarrays is currently based on studies focusing on DNA hybridization reaction in bulk solution. However, the presence of a surface to which the probe strand is attached can make the solution-based approximations invalid, resulting in sub-optimum hybridization conditions. To determine the effect of surfaces on DNA duplex formation,...

Pooled short-hairpin RNA (shRNA) library screening is a powerful tool for identifying a set of genes in biological pathways that require stable expression to produce a desired phenotype. Massive parallel sequencing of half-hairpins has proven highly variable and has not given satisfactory results concerning the relative abundance of different shRNA...

E. coli EcNR1 genome reference sequence. E. coli EcNR1 is a derivative of E. coli K12 MG1655 containing a modified λ prophage integrated at the bioA/bioB locus. We created a reference genome sequence for E. coli EcNR1 by adding the above genetic modification to the E. coli K12 MG1655 reference sequence (NC_000913) obtained from the National Center...

acrAB and mdh functional assays. AcrAB-TolC efflux pump activity was measured via ethidium bromide (EtBr) accumulation in reconstructed single mutants and clonal isolates harbouring acrAB mutations from evolution end populations. Mid log phase cells were incubated with ethidium bromide and intracellular ethidium bromide was monitored via relative f...

Full mutation list. Full lists of SNP, indel, and SV mutations discovered in G3.2, G3.6, G3.266.7, and X3.5 with Illumina sequencing. Mutation positions are genomic coordinates in the E. coli EcNR1 reference sequence, gene descriptions are from the KEGG database, mutation frequency is defined as mutant reads divided by the total number of mapped re...

Tracing mutations found in endpoint populations through intermediate generations. We investigated the dynamics of genotypic adaptation in the G3 and X3 lineages by genotyping population samples from intermediate generations for selected mutations identified in the end point populations. Genotyping was conducted by screening whole-population cryopre...

qRT-PCR validation of gadA, fimI, fabA, and rfaJ gene expression changes. qRT-PCR was used to validate gene expression changes measured by DNA microarray. Target concentrations were determined by fitting the MAK2 PCR model to qRT-PCR data [31]. Expression levels were normalized to house keeping gene rpoD (sigma factor 70). (A) rpoD normalized expre...

Primers and oligos used in this study. Sequences of forward and reverse primers used for Sanger sequencing, allele specific PCR, qRT-PCR, and all other PCR reactions described in this study are listed. Sequences of oligonucleotides used for ssDNA mediated homologous recombination are also given.

Microarray Data and Analyses. Microarray data for gene expression study of G3.2 and the parent E. coli EcNR1 (WT) in 0% and 0.5% (w/v) isobutanol glucose minimal medium. Genes that responded to isobutanol most differently between G3.2 and WT are tabulated with p-values and transcription factors controlling them. Differentially expressed genes, p-va...

Isobutanol is a promising next-generation biofuel with demonstrated high yield microbial production, but the toxicity of this molecule reduces fermentation volumetric productivity and final titer. Organic solvent tolerance is a complex, multigenic phenotype that has been recalcitrant to rational engineering approaches. We apply experimental evoluti...

Advances in microbial engineering have led to the development of metabolic pathways for producing higher molecular weight alcohols as next-generation biofuels [1]. In particular, Escherichia coli has been successfully engineered to produce isobutanol in high yield (86% of theoretical maximum) from carbohydrates [1], and direct photosynthetic conver...

We designed an oligonucleotide microarray using probe sequences based upon a phylogenetic analysis of 16S rRNA genes recovered from members of the bacterial division Acidobacteria. A total of 42,194 oligonucleotide probes targeting members of the Acidobacteria division at multiple phylogenetic levels were included on a high-density microarray. Posi...

A conjugated polymer (CP) and molecular-beacon-based solid-state DNA sensing system is developed to achieve sensitive, label-free detection. A novel conjugated poly(oxadiazole) derivative exhibiting amine and thiol functional groups (POX-SH) is developed for unique chemical and photochemical stability and convenient solid-state on-chip DNA synthesi...

The conventional gene synthesis methods, chemical or PCR, usually require over 2 weeks because of the separate executions of the different procedures. An integrated microfluidic chip system is designed to reduce this processing time to only 2 days with much less reaction volumes, and experimental reagent and solvent requirements. This fast high thr...

We describe a new method to synthesize and amplify cDNA for gene expression profiling on oligonucleotide microarrays. Currently, two methods used to amplify targets are polymerase chain reaction (PCR) or T7 polymerase based in vitro transcription. Conventional PCR due to its non-linear nature is prone to bias in amplification of multiple templates....

The inevitable emergence of the bacterial resistance to conventional antibiotics is the driving force for the development of novel class of anti-infectives, such as Antimicrobial Peptides (AMPs). These peptides are considered as promising drug candidates to replace and/or supplement the existing antibiotics. The rapid increasing need for the potent...

OligoArrayDb is a comprehensive database containing pangenomic oligonucleotide microarray probe sets designed for most of the sequenced genomes that are not covered by commercial catalog arrays. The availability of probe sequences, associated with custom microarray fabrication services offered by many companies and cores presents the unequalled pos...

A series of uniquely stable oxadizole-containing conjugated polymer based microarrays and intercalating dye for a sensitive and selective label-free DNA detection were developed. Signal amplifying and self-signaling DNA microarray was prepared by means of covalent immobilization of POXI polymer on a glass substrate having isothiocyanato groups as a...

Pathogen detection tools with high reliability are needed for various applications, including food and water safety and clinical diagnostics. In this study, we designed and validated an in situ-synthesized biochip for detection of 12 microbial pathogens, including a suite of pathogens relevant to water safety. To enhance the reliability of presence...

A combination of PEG-based surface passivation techniques and spatially addressable SPPS (solid-phase peptide synthesis) was used to demonstrate a highly specific cell-peptide adhesion assay on a microfluidic platform. The surface of a silicon-glass microchip was modified to form a mixed self-assembled monolayer that presented PEG moieties interspe...

Compared with the well equipped arsenal of surface modification methods for flat surfaces, techniques that are applicable to curved, colloidal surfaces are still in their infancy. This technological gap exists because spin-coating techniques used in traditional photolithographic processes are not applicable to the curved surfaces of spherical objec...

No Abstract Peer Reviewed http://deepblue.lib.umich.edu/bitstream/2027.42/56086/1/4667_ftp.pdf

Dangling ends and surface-proximal tails of gene targets influence probe-target duplex formation and affect the signal intensity of probes on diagnostic microarrays. This phenomenon was evaluated using an oligonucleotide microarray containing 18-mer probes corresponding to the 16S rRNA genes of 10 waterborne pathogens and a number of synthetic and...

A versatile microreactor platform featuring a novel chemical-resistant microvalve array has been developed using combined silicon/polymer micromachining and a special polymer membrane transfer process. The basic valve unit in the array has a typical ‘transistor’ structure and a PDMS/parylene double-layer valve membrane. A robust multiplexing algori...

Two collections of oligonucleotides have been designed for preparing pangenomic human and mouse microarrays. A total of 148 993 and 121 703 oligonucleotides were designed against human and mouse transcripts. Quality scores were created in order to select 25 342 human and 24 109 mouse oligonucleotides. They correspond to: (i) a BLAST-specificity sco...

Nucleic acid hybridization serves as backbone for many high-throughput systems for detection, expression analysis, comparative genomics and re-sequencing. Specificity of hybridization between probes and intended targets is always critical. Approaches to ensure and evaluate specificity include use of mismatch probes, obtaining dissociation curves ra...

In a recent report, we have presented the layer-by-layer (LBL) assembly of a biomimetic nanostructured composite from Na(+)-montmorillonite clay nanosheets and poly(diallylmethylammonium chloride) (Tang, Z.; Kotov, N.; Magonov, S.; Ozturk, B. Nat. Mater. 2003, 2, 413). The structure, deformation mechanism, and mechanical properties of the material...

Development of parallel detection tools using microarrays is critically reviewed in view of the need for screening multiple microorganisms in a single test. Potential research needs with respect to probe design and specificity, validation, sample concentration, selective target enrichment and amplification, and data analysis are discussed. Data ill...

There is substantial interest in implementing a bioinformatics tool that allows the design of oligonucleotides to support the development of in vitro gene synthesis. Current protocols to make long synthetic DNA molecules rely on the in vitro assembly of a set of short oligonucleotides, either by ligase chain reaction (LCR) or by assembly PCR. Ideal...

Amplification within chromosome arm 11q involving the mixed-lineage leukemia gene (MLL) locus is a rare but recurrent aberration in acute myeloid leukemia and myelodysplastic syndrome (AML/MDS). We and others have observed that 11q amplifications in most AML/MDS cases have not been restricted to the chromosomal region surrounding the MLL gene. Ther...

Large DNA constructs of arbitrary sequences can currently be assembled with relative ease by joining short synthetic oligodeoxynucleotides (oligonucleotides). The ability to mass produce these synthetic genes readily will have a significant impact on research in biology and medicine. Presently, high-throughput gene synthesis is unlikely, due to the...

There is evidence that 8q amplification is associated with poor prognosis in hepatoblastoma. A previous comparative genomic hybridization analysis identified a critical region in chromosomal bands 8q11.2-q13. Using restriction landmark genomic scanning in combination with a virtual genome scan, we showed that this region is delineated by sequences...

There is a substantial interest in implementing bioinformatics technologies that allow the design of oligonucleotides to support the development of microarrays made from short synthetic DNA fragments spotted or in situ synthesized on slides. Ideally, such oligonucleotides should be totally specific to their respective targets to avoid any cross-hyb...

Gene amplification is an important mechanism of oncogene activation in various human cancers, including ovarian carcinomas (OvCas). We used restriction landmark genomic scanning (RLGS) to detect amplified DNA fragments in the genomes of 47 primary OvCas. Visual analysis of the RLGS gel images revealed several OvCa samples with spots of greater inte...

Tumor cells cultured in vitro are widely used to investigate the molecular biology of cancers and to evaluate responses to drugs and other agents. The full extent to which gene expression in cancer cells is modulated by extrinsic factors and by the microenvironment in which the cancer cells reside remains to be determined. Two cancer cell lines (A5...

In Saccharomyces cerevisiae, Rna14 protein is involved in both cleavage and polyadenylation of mRNA in the nucleus. Previous work has demonstrated that this protein is also localized in mitochondria. Moreover, all known rna14 mutants can be separated into two distinct classes: the poly(A)-negative class, which contains mutants that are deficient in...

OligoArray is a program that computes gene specific and secondary structure free oligonucleotides for genome-scale oligonucleotide microarray construction or other applications. Availability: The program code is distributed under the GNU General Public License and is freely available for non-profit use via request from the authors.

Restriction landmark genome scanning (RLGS) allows comparative analysis of several thousand DNA fragments in the genome and provides a means to identify CpG islands that are altered in tumor cells as a result of amplification, deletion, or methylation changes. We have developed a novel informatics tool, designated virtual genome scan (VGS), that ma...

The dawn of the post-genome era is leading to extraordinary opportunities in biomedicine. Our group has embarked on a major effort to integrate genomics, transcriptomics and proteomics for the profiling of tumor tissues, an approach we refer to as operomics. Our major goals are the molecular classification of tumors and the identification of marker...

The dawn of the post-genome era is leading to extraordinary opportunities in biomedicine. Our group has embarked on a major effort to integrate genomics, transcriptomics and proteomics for the profiling of tumor tissues, an approach we refer to as operomics. Our major goals are the molecular classification of tumors and the identification of marker...

ICF (immunodeficiency, centromeric region instability and facial anomalies) is a recessive disease caused by mutations in the DNA methyltransferase 3B gene ( DNMT3B ). Patients have immunodeficiency, chromosome 1 (Chr1) and Chr16 pericentromeric anomalies in mitogen-stimulated lymphocytes, a small decrease in overall genomic 5-methylcytosine levels...

q23 is a frequent site of gene amplification in breast cancer. Several lines of evidence suggest the presence of multiple amplicons on 17q23. To characterize distinct amplicons on 17q23 and localize putative oncogenes, we screened genes and expressed sequence tags ( ESTs ) in existing physical and radiation hybrid maps for amplification and overexp...

A new computational method for whole-genome analysis by in silico restriction mapping has been developed and has been evaluated by comparison with experimental restriction analysis of tumor DNA.

We have developed a comprehensive approach to identifying molecular changes in lung cancer that includes both genomic and proteomic analyses. The related effort has produced a large amount of data pertaining to gene expression at the RNA and protein levels. As a result, we have constructed a database that contains protein expression data on lung ca...

There is substantial interest in implementing technologies that allow comparisons of whole genomes of individuals and of tissues and cell populations. Restriction landmark genome scanning (RLGS) is a highly resolving gel-based technique in which several thousand fragments in genomic digests are visualized simultaneously and quantitatively analyzed....

RNA14 was identified as a gene involved in premessenger RNA cleavage and polyadenylation. These processing steps take place in the nucleus, but the Rna14p protein is distributed in both the nucleus and the cytoplasm. By subcellular fractionation, we show here that the cytoplasmic fraction is localised in the mitochondria. In order to understand the...

SSM4 was isolated as a suppressor ofrna14-1, a mutant involved in nuclear mRNA maturation. In order to isolate genes interacting withSSM4, we have searched for mutants that are syntheticlethal in association with anSSM4 deletion. Among the mutants obtained, one, namedsls1-1, shows apet − phenotype. We have cloned and sequenced this gene. It encodes...

Over the past decade, the advent of next-generation DNA sequencing technology has enabled genome sequences of model organisms. However, sequencing costs are still limiting the characterization of many other organism genomes. For many, transcriptome sequences are the only available data or can more easily be obtained. We highlight the use of MYbai...