2016 - Spring
Institute for Universal Biology Upcoming Events
BCXT/IUB Seminar Series at Noon in IGB Conference Center 612
Thursday, January 28 - Nam Duc Nguyen, BCXT- "A Novel Method for Microbial Forensics"
A multiple sequence alignment (MSA) is a hypothesis of the evolutionary relationships between different biological sequences. MSAs play a crucial role in answering questions about phylogeny estimation, positive selection, and remote protein homology detection. In my talk, I will present a novel technique for representing a MSA, and how this representation can be used to accurately align short reads to an existing alignment. I will present TIPP, a method that uses this technique to perform taxonomic classification and profiling of metagenomic reads. Finally, I will present applications of TIPP toward the problems of viral identification of short reads and host identification from metagenomic data.
Wednesday, February 3 - Fei He, Department of Bioengineering/BCXT - "Study the Developmental Plasticity Through meta-analysis of Gene Expression data"
Two thousand years ago in China, a person named ‘Yanzi’ argued that a delicious orange can taste like cardboard if it is grown on the other side of the river. We now know that the phenotype is caused by the interaction between gene and environment. Given the same genome, different phenotype can be induced under different environments. This developmental plasticity might mainly be caused by the gene expression plasticity. Currently, tens of thousands of gene expression profiling data are available for model species. Using those publicly available data, we inferred the expression plasticity (i.e. gene responsiveness to perturbation) for a model plant, Arabidopsis. Our initial results indicated the expression plasticity is a universal feature for plant genes. Genes involved in critical developmental regulations such as Hox TF show the lowest plasticity while genes interacting with environments such as photosystem show the highest plasticity. We are also analyzing the evolution of this feature using public transcriptome data including yeast, worm, fly, zebrafish, mouse and human. Based on our preliminary observation, we propose that expression plasticity may serve as a driving power for evolution. This is still an on-going project. I’d like to share my progress with all of you. In short, I am trying to answer some basic biological questions by mining public omics data.
Friday, February 19 - Yiran Dong, Department of Geology/BCXT - "Strategies Enable Filamentous Aquificales Microbial Communities to Thrive in Mammoth Hot Springs, Yellowstone National Park"
March 3, 2016 - Jinzi Deng, Department of Geology/BCXT - "Adaptation of Escherichia coli to Ciprofloxacin gradients in a porous microfluidic device"
Microorganisms in nature have evolved survival strategies to cope with a wide variety of environmental stresses, including steep gradients in temperature, pH, flow conditions, substrate availability and aqueous chemistry. Next-generation microfluidic devices now permit previously unattainable levels of control and reproducibility of these dynamic chemical environmental stresses. They also provide a consistently reliable real-time means to quantitatively track microbe abundance along a stress gradient. In the present study, newly designed and fabricated microfluidic devices with porous media have been utilized to determine the chemical stress fields that enhance adaptation and thus to test how E. coli bacterial communities adapt to antibiotic stresses. By applying antibiotic and nutrient into inlet channels adjacent to either side of the porous media inoculated with E. coli, a gradient of antibiotic was formed. Hydrogel barriers were selectively photo-polymerized in between of the inlet channels and the porous media to prevent convection in the porous media. Hence, chemical solute can only be transported through the hydrogel by diffusion, creating a reproducible antibiotic gradient over the porous media. The bacteria were also constrained by the hydrogel boundary barriers from escaping the porous media. Preliminary observations suggest that the number of E. coli cells increased over time in regions with lower ciprofloxacin concentration. In regions with higher antibiotic concentrations, cell number initially decreased and then fluctuated. The overall distribution of E. coli biomass in the porous media showed good correlation with the linear gradient of stress and nutrients at steady state. The area with the most abundant bacteria might be the most optimal environment in the system and might indicate the micro-chemical conditions which enhance survival and evolution. Future work will evaluate E. coli responses to other environmental stresses, including nutrient limitation and temperature change
Friday, Apri 1, 2016 ((Cancelled)) - Changyi Zhang, Department of Microbiology/BCXT - "Genome-wide analysis of Gene Function in the Hyperthermophilic Crenarchaeon Sulfolobus islandicus with Genetics and Genomics"
Sulfolobus islandicus, an aerobic hyperthermophilic crenarchaeon which grows optimally at 80°C and pH 2 in terrestrial solfataric springs distributes around the world, has been developed as a novel model microorganism to study the unique biology of Crenarchaea. Here, a comprehensive genome-scale analysis of gene function by transposon mutagenesis coupled with deep sequencing methodology has been developed successfully in S. islandicus. Three independent transposon insertion libraries with around 100,000 colonies in total were collected, sequenced and then mapped to the reference genome. As a result, about 90,000 unique insertions (reads >3) were identified, allowing us to classify about 17% of the genome (~460 genes) as possible essential genes. The differences noted between our data with those predictors of essentiality led to several surprisingly discoveries. For example, the reverse gyrase-encoding gene, which is considered as a hallmark of hyperthermophiles and a prerequisite for hyperthermophilic life, is dispensable for cell survival as a couple of transposon insertions were found. This result was further confirmed by a successful disruption of the reverse gyrase gene via reverse genetics, suggesting that S. islandicus does not require reverse gyrase. Our investigation of essentiality of every gene will serve as a valuable resource to reveal unexplored genetic determinants and the underlying mechanisms of various biological processes especially the DNA repair, replication and recombination in the S. islandicus.
Friday, April 15, 2016 - Dipti Nayak/BCXT - "CRISPR-Cas9 Mediated Genome Editing of the Methanogenic Archaeon Methanosarcina acetivorans C2A"
Methane is potent greenhouse gas that contributes significantly to global warming. Around 70% of the methane released in the Earth’s atmosphere is produced by methanogenic Archaea. These microorganisms produce methane as a byproduct of anaerobic respiration and can only grow on a limited number of carbon compounds. Strains belonging to the Methanosarcina species have emerged as preeminent model organisms for dissecting the genetics of methanogenesis as they are metabolically versatile relative to other methanogens, commonly found in diverse anaerobic environments, and genetically tractable. Despite the range of tools available for the genetic manipulation of Methanosarcina sp., mutant generation is a laborious and slow process that takes between 6-8 weeks under optimal conditions, and is a major bottleneck in the genetic analysis of methanogenesis in these strains.
In this talk, I outline the development of a new CRISPR-Cas9 based genetic tool for Methanosarcina acetivorans C2A and demonstrate that this technique can be used to efficiently introduce (multiple) mutations in 2-3 weeks. Two distinct inducible promoters were used to drive the expression of the Cas9 ORF from Streptococcus pyogenes and one or more single guide (sg) RNA on a low-copy plasmid in M. acetivorans C2A. No evidence of nonhomologous end joining (NHEJ) was detected and efficient homologous recombination mediated repair was observed when a repair template containing regions homologous to the target locus was also provided. More than 99% of colonies recovered contain the repair template at the target locus. Mutant recovery did not depend on the expression of Cas9 but was diminished when the sgRNA was induced. The size of the homology arms in the repair template and the distance of the repair template from the double strand break (DSB) point on the chromosome also influenced mutant recovery. Altogether, these results establish a new tool for rapid genetic manipulation of Methanosarcina strains.
2016 - Spring IGB Seminars at Noon in IGB Conference Center 612
Tuesday, February 23 - Professor Sergei Maslov, Institute for Genomic Biology Maslov Profile - "TBD"
Tuesday, April 5 - ((Pioneers Seminar)) Professor Julie Dunning Hotopp, University of Maryland Dunning Hotopp "Lateral Gene Transfer from Bacteria to Animals, Including Humans"
Lateral gene transfer (LGT) is the transfer of DNA between divergent species leading to mutations in the recipient genome. In 2007, we demonstrated that there are extensive amounts of Wolbachia endosymbiont DNA in the genomes of diverse arthropods and filarial nematodes. Since then, LGT is increasingly described as occurring from bacteria to animals, particularly from Wolbachia endosymbionts to their arthropod and nematode hosts. We have found that multiple copies of the Wolbachia genome are transferred into the Drosophila nuclear genome in three Drosophila ananassae lines. In one line, 2% of the nuclear genome is of bacterial origin, including 20% of the known material on a Drosophila autosome. Likewise, at least 115.4-kbp, or 10.6% of the total 1.08 Mbp Wolbachia genome in the nematode Brugia malayi has been transferred to its nematode host, including 227 Wolbachia genes and gene fragments. Complete open reading frames may have been transferred for 32 of these genes, with four transfers having evidence of life stage-specific regulation of transcription at levels similar to other nematode transcripts, raising the possibility that they might be functional. Based on our findings with these endosymbiont-host systems, we hypothesized that there could even be integration of bacterial DNA in human somatic cells. Using publicly available sequence data from the human genome project, the 1000 Genomes Project, and The Cancer Genome Atlas (TCGA), we have presented evidence that bacterial DNA integrates into the human somatic genome through an RNA intermediate and that such integrations are detected more frequently in (a) tumors than normal samples, (b) RNA than DNA samples, and (c) the mitochondrial genome than the nuclear genome.