On some sequencing problems in finite groups

AbstractA finite group is called Z-sequenceable if its non-identity elements can be listed x1, x2, …, xn so that xixi+1 for i = 1, 2, …, n − 1. Various necessary and sufficient conditions are determined for such sequencings to exist. In particular, it is proved that if n ⩾ 3, then the symmetric group Sn is not Z-sequenceable

VEGF regulates local inhibitory complement proteins in the eye and kidney

10.1172/JCI86418Journal of Clinical Investigation1271199-21

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

Multi-ancestry study of blood lipid levels identifies four loci interacting with physical activity.

Many genetic loci affect circulating lipid levels, but it remains unknown whether lifestyle factors, such as physical activity, modify these genetic effects. To identify lipid loci interacting with physical activity, we performed genome-wide analyses of circulating HDL cholesterol, LDL cholesterol, and triglyceride levels in up to 120,979 individuals of European, African, Asian, Hispanic, and Brazilian ancestry, with follow-up of suggestive associations in an additional 131,012 individuals. We find four loci, in/near CLASP1, LHX1, SNTA1, and CNTNAP2, that are associated with circulating lipid levels through interaction with physical activity; higher levels of physical activity enhance the HDL cholesterol-increasing effects of the CLASP1, LHX1, and SNTA1 loci and attenuate the LDL cholesterol-increasing effect of the CNTNAP2 locus. The CLASP1, LHX1, and SNTA1 regions harbor genes linked to muscle function and lipid metabolism. Our results elucidate the role of physical activity interactions in the genetic contribution to blood lipid levels

Recent Region-wide Declines in Caribbean Reef Fish Abundance

Profound ecological changes are occurring on coral reefs throughout the tropics, with marked coral cover losses and concomitant algal increases, particularly in the Caribbean region. Historical declines in the abundance of large Caribbean reef fishes likely reflect centuries of overexploitation. However, effects of drastic recent degradation of reef habitats on reef fish assemblages have yet to be established. By using meta-analysis, we analyzed time series of reef fish density obtained from 48 studies that include 318 reefs across the Caribbean and span the time period 1955–2007. Our analyses show that overall reef fish density has been declining significantly for more than a decade, at rates that are consistent across all subregions of the Caribbean basin (2.7% to 6.0% loss per year) and in three of six trophic groups. Changes in fish density over the past half-century are modest relative to concurrent changes in benthic cover on Caribbean reefs. However, the recent significant decline in overall fish abundance and its consistency across several trophic groups and among both fished and nonfished species indicate that Caribbean fishes have begun to respond negatively to habitat degradation

Comparing introductory course planning among full-time and part-time faculty

Using data from a nationally representative survey of faculty teaching introductory college courses, this exploratory study compares course planning procedures of full-time and part-time faculty teaching courses in eight academic fields. The choice of variables examined was guided by a general model of course design developed from earlier studies of course planning. To control for discipline-related differences in faculty planning assumptions, separate analyses were conducted for the eight fields. No key differences were found between full-time and part-time faculty on the primary factors under investigation: substantive content-related influences on courses, strength of influence within the instructional environment, and planning steps and content arrangements faculty preferred.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43604/1/11162_2004_Article_BF00992618.pd

Genome-wide linkage screen for testicular germ cell tumour susceptibility loci

A family history of disease is a strong risk factor for testicular germ cell tumour (TGCT). In order to identify the location of putative TGCT susceptibility gene(s) we conducted a linkage search in 237 pedigrees with two or more cases of TGCT. One hundred and seventy-nine pedigrees were evaluated genome-wide with an average inter-marker distance of 10 cM. An additional 58 pedigrees were used to more intensively investigate several genomic regions of interest. Genetic linkage analysis was performed with the ALLEGRO software using two model-based parametric analyses and a non-parametric analysis. Six genomic regions on chromosomes 2p23, 3p12, 3q26, 12p13-q21, 18q21-q23 and Xq27 showed heterogeneity LOD (HLOD) scores of greater than 1, with a maximum HLOD of 1.94 at 3q26. Genome-wide simulation studies indicate that the observed number of HLOD peaks greater than one does not differ significantly from that expected by chance. A TGCT locus at Xq27 has been previously reported. Of the 237 pedigrees examined in this study, 66 were previously unstudied at Xq27, no evidence for linkage to this region was observed in this new pedigree set. Overall, the results indicate that no single major locus can account for the majority of the familial aggregation of TGCT, and suggests that multiple susceptibility loci with weak effects contribute to the diseas

The Shark Assemblage at French Frigate Shoals Atoll, Hawai‘i: Species Composition, Abundance and Habitat Use

Empirical data on the abundance and habitat preferences of coral reef top predators are needed to evaluate their ecological impacts and guide management decisions. We used longline surveys to quantify the shark assemblage at French Frigate Shoals (FFS) atoll from May to August 2009. Fishing effort consisted of 189 longline sets totaling 6,862 hook hours of soak time. A total of 221 sharks from 7 species were captured, among which Galapagos (Carcharhinus galapagensis, 36.2%), gray reef (Carcharhinus amblyrhynchos, 25.8%) and tiger (Galeocerdo cuvier, 20.4%) sharks were numerically dominant. A lack of blacktip reef sharks (Carcharhinus melanopterus) distinguished the FFS shark assemblage from those at many other atolls in the Indo-Pacific. Compared to prior underwater visual survey estimates, longline methods more accurately represented species abundance and composition for the majority of shark species. Sharks were significantly less abundant in the shallow lagoon than adjacent habitats. Recaptures of Galapagos sharks provided the first empirical estimate of population size for any Galapagos shark population. The overall recapture rate was 5.4%. Multiple closed population models were evaluated, with Chao Mh ranking best in model performance and yielding a population estimate of 668 sharks with 95% confidence intervals ranging from 289–1720. Low shark abundance in the shallow lagoon habitats suggests removal of a small number of sharks from the immediate vicinity of lagoonal islets may reduce short-term predation on endangered monk seal (Monachus schauinslandi) pups, but considerable fishing effort would be required to catch even a small number of sharks. Additional data on long-term movements and habitat use of sharks at FFS are required to better assess the likely ecological impacts of shark culling