Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans

Background Increasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the natural variation of this nematode species. Results Here we report on the identification of genomic differences between the reference strain N2 and the Hawaiian strain CB4856, one of the most genetically distant strains from N2. To identify both small- and large-scale genomic variations (GVs), we have sequenced the CB4856 genome using both Roche 454 (~400 bps single reads) and Illumina GA DNA sequencing methods (101 bps paired-end reads). Compared to previously described variants (available in WormBase), our effort uncovered twice as many single nucleotide variants (SNVs) and increased the number of small InDels almost 20-fold. Moreover, we identified and validated large insertions, most of which range from 150 bps to 1.2 kb in length in the CB4856 strain. Identified GVs had a widespread impact on protein-coding sequences, including 585 single-copy genes that have associated severe phenotypes of reduced viability in RNAi and genetics studies. Sixty of these genes are homologs of human genes associated with diseases. Furthermore, our work confirms previously identified GVs associated with differences in behavioural and biological traits between the N2 and CB4856 strains. Conclusions The identified GVs provide a rich resource for future studies that aim to explain the genetic basis for other trait differences between the N2 and CB4856 strains

PO-246 Effects of Different Methods of Precooling on Sub-maximal Intensity Exercise in Heat and High Humidity

Objective This study aimed to investigate the influence of using different precooling measures on the capacity of competition and the exercise performance in hot and humidity environment. The most effectual means of precooling will be recommended to help coaches and athletes to improve the ability and performance in training and matches Methods Ten male football (Rugby) players who came from the rugby team totally completed four experimental conditions in hot/humid conditions (38℃, 50% humidity). Initially, a 30-min precooling period consisting of either nothing to control (CONT, C); wearing cooling vest (4℃, V); ingesting of ice beverage (2.3 ml /kg of 4℃, I); or the mix method of combination of V and I (V+I, M). Following this, sub-maximal exercise (80% VO2max) of treadmill test occurred, until athletes exhausted Results The running distance of M and V and I have a significant increase (P≤0.05) than CONT. The peak oxygen uptake of exhaustion was no significant difference between each other. After exercise, the change rate of heart rate ratio of M compared with CONT has a very significant decrease (P≤0.01). The core temperature of M and CONT has a significant increase (P≤0.05) in comparison. The surface temperature of I and M and V comparison with CONT has a very significant increase (P≤0.01). When participants exhaust, the RPE of M in comparison with CONT had significantly lower (P≤0.05). The RPB and the rating of thermal sensation of each condition were no significant difference. After exercise, the blood lactic concentration of each ones was no significant difference Conclusions In hot and humidity condition, precooling has a promoting effect on the sub-maximal exercise. Precooling measures could improve the exercise performance and maintain the stability of functional status and physiology, especially the mix method. &nbsp

Precise Measurements of Branching Fractions for Ds+D_s^+ Meson Decays to Two Pseudoscalar Mesons

We measure the branching fractions for seven $D_{s}^{+}$ two-body decays to pseudo-scalar mesons, by analyzing data collected at $\sqrt{s}=4.178\sim4.226$ GeV with the BESIII detector at the BEPCII collider. The branching fractions are determined to be $\mathcal{B}(D_s^+\to K^+\eta^{\prime})=(2.68\pm0.17\pm0.17\pm0.08)\times10^{-3}$, $\mathcal{B}(D_s^+\to\eta^{\prime}\pi^+)=(37.8\pm0.4\pm2.1\pm1.2)\times10^{-3}$, $\mathcal{B}(D_s^+\to K^+\eta)=(1.62\pm0.10\pm0.03\pm0.05)\times10^{-3}$, $\mathcal{B}(D_s^+\to\eta\pi^+)=(17.41\pm0.18\pm0.27\pm0.54)\times10^{-3}$, $\mathcal{B}(D_s^+\to K^+K_S^0)=(15.02\pm0.10\pm0.27\pm0.47)\times10^{-3}$, $\mathcal{B}(D_s^+\to K_S^0\pi^+)=(1.109\pm0.034\pm0.023\pm0.035)\times10^{-3}$, $\mathcal{B}(D_s^+\to K^+\pi^0)=(0.748\pm0.049\pm0.018\pm0.023)\times10^{-3}$, where the first uncertainties are statistical, the second are systematic, and the third are from external input branching fraction of the normalization mode $D_s^+\to K^+K^-\pi^+$. Precision of our measurements is significantly improved compared with that of the current world average values

Genomic identification and functional characterization of essential genes in Caenorhabditis elegans

For over 30 years, researchers have taken advantage of genetic balancers and forward genetic screens to isolate lethal mutations, which have been studied to identify essential genes in C. elegans. Using traditional genetic methods, such as genetic mapping, complementation tests, and transgenic rescue assays, many essential genes have been successfully identified. However, to pinpoint a specific essential gene the involved experiments are usually labor intensive and time consuming. Nowadays, genetic methods combined with whole genome sequencing (WGS) and bioinformatics analysis provide an effective approach for the molecular identification of essential genes. In my thesis I successfully identified 64 new essential genes with 107 lethal mutations in genomic regions of C. elegans of around 14 Mb from Chromosome III(mid) and Chromosome V(left), by combining genetic mapping, Illumina sequencing, bioinformatics analyses, and experimental validation. Most of these genes have multiple recovered mutant alleles. Of these 64 genes 5 have new alleles identified, which had not been previously studied by RNA interference depletion. Furthermore, by investigating the locations of lethal missense mutations in essential genes, I have identified five novel protein functional domains. Functional characterization of the identified essential genes shows that most of them are enzymes, including helicases, tRNA synthetase, and kinases. There are also ribosomal proteins. Gene Ontology functional annotation also indicates that essential genes tend to execute enzyme and nucleic acid binding activities during fundamental processes, such as intracellular protein synthesis. Essential gene analysis shows that compared to non-essential genes, essential genes have fewer paralogs, and encode proteins that are in protein interaction hubs. Essential genes are also more abundantly and consistently expressed over all developmental stages than non-essential genes. All these essential genes traits in C. elegans are consistent with those of human disease genes. Unsurprisingly, most (90%) human orthologs of essential genes in this study are related to human diseases. Therefore, functional characterization of essential genes underlines their importance as proxies for understanding the biological functions of human disease genes

Genomic Identification and Functional Characterization of Essential Genes in Caenorhabditis elegans

Using combined genetic mapping, Illumina sequencing, bioinformatics analyses, and experimental validation, we identified 60 essential genes from 104 lethal mutations in two genomic regions of Caenorhabditis elegans totaling ∼14 Mb on chromosome III(mid) and chromosome V(left). Five of the 60 genes had not previously been shown to have lethal phenotypes by RNA interference depletion. By analyzing the regions around the lethal missense mutations, we identified four putative new protein functional domains. Furthermore, functional characterization of the identified essential genes shows that most are enzymes, including helicases, tRNA synthetases, and kinases in addition to ribosomal proteins. Gene Ontology analysis indicated that essential genes often encode for enzymes that conduct nucleic acid binding activities during fundamental processes, such as intracellular DNA replication, transcription, and translation. Analysis of essential gene shows that they have fewer paralogs, encode proteins that are in protein interaction hubs, and are highly expressed relative to nonessential genes. All these essential gene traits in C. elegans are consistent with those of human disease genes. Most human orthologs (90%) of the essential genes in this study are related to human diseases. Therefore, functional characterization of essential genes underlines their importance as proxies for understanding the biological functions of human disease genes

Spectrum of variations in dog-1/FANCJ and mdf-1/MAD1 defective Caenorhabditis elegans strains after long-term propagation

Background: Whole and partial chromosome losses or gains and structural chromosome changes are hallmarks of human tumors. Guanine-rich DNA, which has a potential to form a G-quadruplex (G4) structure, is particularly vulnerable to changes. In Caenorhabditis elegans, faithful transmission of G-rich DNA is ensured by the DOG-1/FANCJ deadbox helicase. Results: To identify a spectrum of mutations, after long-term propagation, we combined whole genome sequencing (WGS) and oligonucleotide array Comparative Genomic Hybridization (oaCGH) analysis of a C. elegans strain that was propagated, in the absence of DOG-1 and MDF-1/MAD1, for a total of 470 generations, with samples taken for long term storage (by freezing) in generations 170 and 270. We compared the genomes of F170 and F470 strains and identified 94 substitutions, 17 InDels, 3 duplications, and 139 deletions larger than 20 bp. These homozygous variants were predicted to impact 101 protein-coding genes. Phenotypic analysis of this strain revealed remarkable fitness recovery indicating that mutations, which have accumulated in the strain, are not only tolerated but also cooperate to achieve long-term population survival in the absence of DOG-1 and MDF-1. Furthermore, deletions larger than 20 bp were the only variants that frequently occurred in G-rich DNA. We showed that 126 of the possible 954 predicted monoG/C tracts, larger than 14 bp, were deleted in unc-46 mdf-1 such-4; dog-1 F470 (JNC170). Conclusions: Here, we identified variants that accumulated in C. elegans’ genome after long-term propagation in the absence of DOG-1 and MDF-1. We showed that DNA sequences, with G4-forming potential, are vulnerable to deletion-formation in this genetic background.Medical Genetics, Department ofMedicine, Faculty ofMolecular Medicine and Therapeutics, Centre forScience, Faculty ofZoology, Department ofNon UBCReviewedFacult