- PhyloCSF
PhyloCSF is a widely used tool to identify evolutionary signatures of protein-coding regions using multispecies genome alignments. The PhyloCSF Candidate Coding Regions (PCCRs) are displayed as distinct blocks and follow strict protocol and are derived by pruning the PhyloCSF Regions list to generate the set of PCCRs which are high confidence.
- A cellular surveillance and defense system that delays aging phenotypes in C. elegans.
Aging is an important risk factor for disease and is accompanied by the decline of many physiological characteristics, including physical performance. One of the most powerful tests of physical ability in elderly humans is the short physical performance battery (SPPB) (Guralnik et al., 1994), an assessment of the maximum exercise capacity of lower extremities over a short period of time. A similar metric of maximum velocity (MV) in a short period (30s) is proposed as an equally informative measurement inC. elegans (Hahm et al., 2015). MV declines with age, correlates well with longevity, accurately reports movement ability, and importantly, is predictive of future longevity (Hahm et al., 2015).Here, we characterized the differences in gene expression between high MV group and low MV group of the same age in C. elegans. The genes related to nucleosomes and involved in regulatory processes, including transcriptional regulation (chromatin assembly, regulation of RNA metabolic process and regulation of transcription), and neuronal signaling (neurogenesis, axon guidance, and regulation of neurotransmitter levels) were up-regulated in low MV group compared to high MV group. In contrast, genes belonged to metabolic processes and mitochondria were down-regulated in low MV group compared to high MV group.
- A High-Content, Phenotypic Screen Identifies Fluorouridine as an Inhibitor of Pyoverdine Biosynthesis and Pseudomonas aeruginosa Virulence
Pseudomonas aeruginosa is an opportunistic pathogen that causes severe health problems. Despite intensive investigation, many aspects of microbial virulence remain poorly understood. We used a high-throughput, high-content, whole-organism, phenotypic screen to identify small molecules that inhibit P. aeruginosa virulence in C. elegans. Approximately half of the hits were known antimicrobials. A large number of hits were non-antimicrobial bioactive compounds, including the cancer chemotherapeutic 5-fluorouracil. We determined that 5-fluorouracil both transiently inhibits bacterial growth and reduces pyoverdine biosynthesis. Pyoverdine is a siderophore that regulates the expression of several virulence determinants and is critical for pathogenesis in mammals. We show that 5-fluorouridine, a downstream metabolite of 5-fluorouracil, is responsible for inhibiting pyoverdine biosynthesis. We also show that 5-fluorouridine, in contrast to 5-fluorouracil, is a genuine anti-virulent compound, with no bacteriostatic or bacteriocidal activity. To our knowledge, this is the first report utilizing a whole-organism screen to identify novel compounds with antivirulent properties effective against P. aeruginosa.
- Novel Immune Modulators Enhance Caenorhabditis elegans Resistance to Multiple Pathogens.
Traditional treatments for bacterial infection have focused upon directly inhibiting growth of the pathogen. However, an equally important determinant of infection outcome is the host defense response. We previously performed a high-throughput chemical screen to identify small molecules that rescued the nematode Caenorhabditis elegans from infection by Pseudomonas aeruginosa. Over 20 of the hits stimulated host defense gene expression. During in-depth studies of five such molecules using microarray analysis, bioinformatic clustering, and RNAi knockdown of candidate gene targets, we identified PMK-1/p38 MAPK and SKN-1/Nrf2 as two key pathways modulated by these hits. Interestingly, the molecules studied did not depend on a single pathway for ameliorating P. aeruginosa pathogenesis in liquid-based assay, but did rely on the PMK-1/p38 MAPK pathway during a colonization-based infection assay on agar. A subset of these molecules was also protective against Enterococcus faecalis and Staphylococcus aureus. In general, the compounds showed little toxicity against mammalian cells or worms, consistent with their identification in a phenotypic, high-content screen. These molecules possess significant potential for use as tools to study innate immune processes
- Bio-electrospraying the nematode Caenorhabditis elegans
Bio-electrospray, the direct jet-based cell handling apporach, is able to handle a wide range of cells. Studies at the genomic, genetic, and the physiological level have shown that, post-treatment, cellular integrity is unperturbed and a high percentage (>70%, compared to control) of cells remain viable. Although, these results are impressive, it may be argued that cell based systems are oversimplistic. This study utilizing a well characterised multicellular model organism, the non-parasitic nematode Caenorhabditis elegans. Nematodes were subjected to bio-electrosprays to demonstrate that bio-electrosprays can be safely applied to nematodes.
- Grape seed extracts-mediated lipid mobility in C. elegans
Oligomeric proanthocyanidins (OPCs) reduce triglycerides in the nematode C. elegans. Lipase was strongly inhibited in vitro accompanied by the reduction of total triglyceride storage capacity in vivo; Lipophilic staining was also attenuated in wild type worms and high-fat mutants exposed to OPCs. Apart from biochemical analyses, lipid metabolism was also genetically regulated, emphasizing the necessity to study underlying regulation mechanisms in intact animals. To gain a deeper insight into the potential gene targets of purified oligomeric proanthocyanidin trimer gallate (pOPC7), a binary microarray assay was carried out with wild type N2 populations continuously exposed to a bacterial diet with or without pOPC7.