Scaffolding and validation of bacterial genome assemblies using optical restriction maps

Motivation: New, high-throughput sequencing technologies have made it feasible to cheaply generate vast amounts of sequence information from a genome of interest. The computational reconstruction of the complete sequence of a genome is complicated by specific features of these new sequencing technologies, such as the short length of the sequencing reads and absence of mate-pair information. In this article we propose methods to overcome such limitations by incorporating information from optical restriction maps

A Vision for Ice Giant Exploration

From Voyager to a Vision for 2050: NASA and ESA have just completed a study of candidate missionsto Uranus and Neptune, the so-called ice giant planets. It is a Pre-Decadal Survey Study, meant to inform the next Planetary Science Decadal Survey about opportunities for missions launching in the 2020's and early 2030's. There have been no space flight missions to the ice giants since the Voyager 2 flybys of Uranus in 1986 and Neptune in 1989. This paper presents some conclusions of that study (hereafter referred to as The Study), and how the results feed into a vision for where planetary science can be in 2050. Reaching that vision will require investments in technology andground-based science in the 2020's, flight during the 2030's along with continued technological development of both ground- and space-based capabilities, and data analysis and additional flights in the 2040's. We first discuss why exploring the ice giants is important. We then summarize the science objectives identified by The Study, and our vision of the science goals for 2050. We then review some of the technologies needed to make this vision a reality

A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat

<p>Abstract</p> <p>Background</p> <p><it>Brachypodium distachyon </it>(<it>Brachypodium</it>) has been recognized as a new model species for comparative and functional genomics of cereal and bioenergy crops because it possesses many biological attributes desirable in a model, such as a small genome size, short stature, self-pollinating habit, and short generation cycle. To maximize the utility of <it>Brachypodiu</it>m as a model for basic and applied research it is necessary to develop genomic resources for it. A BAC-based physical map is one of them. A physical map will facilitate analysis of genome structure, comparative genomics, and assembly of the entire genome sequence.</p> <p>Results</p> <p>A total of 67,151 <it>Brachypodium </it>BAC clones were fingerprinted with the SNaPshot HICF fingerprinting method and a genome-wide physical map of the <it>Brachypodium </it>genome was constructed. The map consisted of 671 contigs and 2,161 clones remained as singletons. The contigs and singletons spanned 414 Mb. A total of 13,970 gene-related sequences were detected in the BAC end sequences (BES). These gene tags aligned 345 contigs with 336 Mb of rice genome sequence, showing that <it>Brachypodium </it>and rice genomes are generally highly colinear. Divergent regions were mainly in the rice centromeric regions. A dot-plot of <it>Brachypodium </it>contigs against the rice genome sequences revealed remnants of the whole-genome duplication caused by paleotetraploidy, which were previously found in rice and sorghum. <it>Brachypodium </it>contigs were anchored to the wheat deletion bin maps with the BES gene-tags, opening the door to <it>Brachypodium</it>-Triticeae comparative genomics.</p> <p>Conclusion</p> <p>The construction of the <it>Brachypodium </it>physical map, and its comparison with the rice genome sequence demonstrated the utility of the SNaPshot-HICF method in the construction of BAC-based physical maps. The map represents an important genomic resource for the completion of <it>Brachypodium </it>genome sequence and grass comparative genomics. A draft of the physical map and its comparisons with rice and wheat are available at <url>http://phymap.ucdavis.edu/brachypodium/</url>.</p

Interrelationships Between the Kinetics of VLDL Subspecies and HDL Catabolism in Abdominal Obesity: A Multicenter Tracer Kinetic Study

Context: Low plasma high-density lipoprotein (HDL) cholesterol is a major abnormality in abdominal obesity. This relates due to accelerated HDL catabolism, but the underlying mechanism requires further elucidation. The relationships between HDL catabolism and other variables that may be modified in abdominal obesity, such as very low-density lipoprotein (VLDL) subspecies (VLDL1, VLDL2) kinetics, liver fat, or visceral adiposity, remain to be investigated. Objectives: Our aim was to study the associations between HDL apolipoprotein (apo)-A-I fractional catabolic rate (FCR) and the kinetics of VLDL subspecies and estimates of liver and visceral and sc fat. Design: We carried out a multicenter in vivo kinetic study using stable isotopes (deuterated leucine and glycerol) in 62 individuals with abdominal obesity. Results: In a multivariate analysis, among the morphological and biological parameters that may predict apoA-I FCR, liver fat (beta = .400, P = .003), and VLDL1-apoB (beta = .307, P = .020) were independently associated with apoA-I FCR. In a multivariate analysis, among the kinetic parameters, VLDL1-triglycerides (TGs) indirect FCR (beta = .357, P = .001), VLDL1-TG production rate (beta = 0.213, P = .048), and apoA-II FCR (beta = .667, P < .0001) were independently associated with apoA-I FCR. After adjustment for VLDL1-TG production rate, liver fat was no more correlated with apoA-I FCR. No association between apoA-I FCR and visceral fat was observed. Conclusions: We show that VLDL1 is an important independent determinant of apoA-I FCR and more precisely that apoA-I FCR is independently associated with both catabolism and the production of VLDL1-TG. In addition, we show an association between liver fat and apoA-I FCR that is mostly mediated by VLDL1-TG production. These data indicate that, in abdominal obesity, dysfunctional VLDL1 metabolism is an important modulator of HDL apoA-I catabolism

Mechanisms of toxic action and structure-activity relationships for organochlorine and synthetic pyrethroid insecticides.

The mechanisms and sites of action of organochlorine (DDT-types and chlorinated alicyclics) and synthetic pyrethroid insecticides are presented with discussion of symptoms, physiological effects, and selectivity. The structural requirements for toxicity are assessed, and structure-activity relationships are considered for each subclass. Lipophilicity is important for all the groups because it facilitates delivery of these neurotoxicants to the site of action in the nerve. Steric factors including molecular volume, shape, and isomeric configuration greatly influence toxicity. Electronic parameters also have been demonstrated to affect biological activity in some of the groups of insecticides, e.g., Hammett's sigma and Taft's sigma * as indicators of electronegativity. New synthetic pyrethroids continue to be developed, with varied structures and different physicochemical and biological properties

Population-Level Effects of Human Papillomavirus Vaccination Programs on Infections with Nonvaccine Genotypes

We analyzed human papillomavirus (HPV) prevalences during prevaccination and postvaccination periods to consider possible changes in nonvaccine HPV genotypes after introduction of vaccines that confer protection against 2 high-risk types, HPV16 and HPV18. Our meta-analysis included 9 studies with data for 13,886 girls and women ≤19 years of age and 23,340 women 20–24 years of age. We found evidence of cross-protection for HPV31 among the younger age group after vaccine introduction but little evidence for reductions of HPV33 and HPV45. For the group this same age group, we also found slight increases in 2 nonvaccine high-risk HPV types (HPV39 and HPV52) and in 2 possible high-risk types (HPV53 and HPV73). However, results between age groups and vaccines used were inconsistent, and the increases had possible alternative explanations; consequently, these data provided no clear evidence for type replacement. Continued monitoring of these HPV genotypes is important

Ethics, politics and migration: Public debates on the free movement of Romanians and Bulgarians in the UK, 2006–2013

Public debates on immigration have become the subject of much concern, particularly in the UK. This article applies an ethical lens to assess changes in public debates over intra-EU migration in six UK national newspapers during 2006 and 2013. It finds an almost complete dominance of communitarian justifications, mainly based on welfare chauvinism, but a notable increase in security-related arguments and a decrease in economic nationalist ideas. Alternative cosmopolitan arguments about immigration go from rare to virtually absent. The discussion links these shifts to a failure of the UK centre-left to overcome historic difficulties in presenting a coherent narrative on immigration policy

The pharmaceutical use of permethrin: Sources and behavior during municipal sewage treatment

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ 2010 Springer Science+Business Media, LLC.Permethrin entered use in the 1970s as an insecticide in a wide range of applications, including agriculture, horticultural, and forestry, and has since been restricted. In the 21st century, the presence of permethrin in the aquatic environment has been attributed to its use as a human and veterinary pharmaceutical, in particular as a pedeculicide, in addition to other uses, such as a moth-proofing agent. However, as a consequence of its toxicity to fish, sources of permethrin and its fate and behavior during wastewater treatment are topics of concern. This study has established that high overall removal of permethrin (approximately 90%) was achieved during wastewater treatment and that this was strongly dependent on the extent of biological degradation in secondary treatment, with more limited subsequent removal in tertiary treatment processes. Sources of permethrin in the catchment matched well with measured values in crude sewage and indicated that domestic use accounted for more than half of the load to the treatment works. However, removal may not be consistent enough to achieve the environmental quality standards now being derived in many countries even where tertiary treatment processes are applied.United Utilities PL