Flt-1 (VEGFR-1) coordinates discrete stages of blood vessel formation

In developing blood vessel networks, the overall level of vessel branching often correlates with angiogenic sprout initiations, but in some pathological situations, increased sprout initiations paradoxically lead to reduced vessel branching and impaired vascular function. We examine the hypothesis that defects in the discrete stages of angiogenesis can uniquely contribute to vessel branching outcomes

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

Generation and Comparative Analyses of Genome-scale Metabolic Models for the Genus Shewanella using the Model SEED

The genus Shewanella consists of aquatic microorganisms that are distributed worldwide. Their features include respiratory and metabolic diversity as well as the ability to thrive in extreme environments. The study of Shewanella’s versatile metabolism can provide insights into the species’ capacity for biotechnology such as bioremediation and microbial fuel cells. The Model SEED (http://seed-viewer.theseed.org/models), a web-based resource for microbial genome analysis, was used to generate genome-scale metabolic models for sequenced Shewanella genomes. The draft metabolic model for S. oneidensis was curated, focusing on areas of metabolism that have not been well-curated in previous modeling efforts (e.g., anaerobic respiratory systems, lipopolysaccharide biosynthesis). The goals of this work are to 1) expand the coverage of metabolic diversity in databases used for metabolic modeling, 2) design and refine software tools to facilitate manual curation of metabolic models and 3) generate a complete S. oneidensis metabolic model that can be used with computational tools and high throughput experimental approaches to advance our understanding of the metabolic strategies and physiology of the genus Shewanella

Isolation and Characterization of Saccharomyces cerevisiae mutants defective in Unsaturated Fatty Acid Recognition

When dietary unsaturated fatty acids (UFAs) are present, cells down regulate expression of the enzyme ∆9 desaturase, encoded by OLE1, which is responsible for producing UFAs. A screen was designed to isolate mutants defective in recognition of the presence of UFAs, and the subsequent transcriptional regulation of the ∆9-desaturase. Using a reporter gene construct controlled by the OLE1 promoter, several mutants were identified and one mutant, KH2, was chosen for additional characterization. The mutation that renders KH2 incapable of molecular response to UFAs is a recessive trait due to a single mutation. While the reporter construct demonstrates that transcriptional regulation of OLE1 is defective, fatty acid analysis reveals normal regulation in response to UFA supplements, indicating that post-transcriptional regulation is intact. This implies that the mutation is not responsible for universal response to UFAs, but just transcriptional regulation. Further work to identify genes responsible for regulation of OLE1 was initiated through genomic library screening. Initial results identified a genomic fragment that returned KH2 phenotype to wildtype. However, examination of individual genes on that fragment revealed that one gene may be a suppressor, rather than the responsible for the authentic phenotype due to mutation. Additional work is ongoing to determine the identity of this suppressor. In addition, further library work will attempt to identify the authentic gene responsible for OLE1 regulation

Flt-1 (VEGFR-1) coordinates discrete stages of blood vessel formation

AIMS: In developing blood vessel networks, the overall level of vessel branching often correlates with angiogenic sprout initiations, but in some pathological situations, increased sprout initiations paradoxically lead to reduced vessel branching and impaired vascular function. We examine the hypothesis that defects in the discrete stages of angiogenesis can uniquely contribute to vessel branching outcomes. METHODS AND RESULTS: Time-lapse movies of mammalian blood vessel development were used to define and quantify the dynamics of angiogenic sprouting. We characterized the formation of new functional conduits by classifying discrete sequential stages—sprout initiation, extension, connection, and stability—that are differentially affected by manipulation of vascular endothelial growth factor-A (VEGF-A) signalling via genetic loss of the receptor flt-1 (vegfr1). In mouse embryonic stem cell-derived vessels genetically lacking flt-1, overall branching is significantly decreased while sprout initiations are significantly increased. Flt-1(−/−) mutant sprouts are less likely to retract, and they form increased numbers of connections with other vessels. However, loss of flt-1 also leads to vessel collapse, which reduces the number of new stable conduits. Computational simulations predict that loss of flt-1 results in ectopic Flk-1 signalling in connecting sprouts post-fusion, causing protrusion of cell processes into avascular gaps and collapse of branches. Thus, defects in stabilization of new vessel connections offset increased sprout initiations and connectivity in flt-1(−/−) vascular networks, with an overall outcome of reduced numbers of new conduits. CONCLUSIONS: These results show that VEGF-A signalling has stage-specific effects on vascular morphogenesis, and that understanding these effects on dynamic stages of angiogenesis and how they integrate to expand a vessel network may suggest new therapeutic strategies

Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

Students' participation in collaborative research should be recognised

Letter to the editor