Lattice QCD with mixed actions

We discuss some of the implications of simulating QCD when the action used for the sea quarks is different from that used for the valence quarks. We present exploratory results for the hadron mass spectrum and pseudoscalar meson decay constants using improved staggered sea quarks and HYP-smeared overlap valence quarks. We propose a method for matching the valence quark mass to the sea quark mass and demonstrate it on UKQCD clover data in the simpler case where the sea and valence actions are the same.Comment: 15 pages, 10 figures some minor modification to text and figures. Accepted for publicatio

Nucleon isovector structure functions in (2+1)-flavor QCD with domain wall fermions

We report on numerical lattice QCD calculations of some of the low moments of the nucleon structure functions. The calculations are carried out with gauge configurations generated by the RBC and UKQCD collaborations with (2+1)-flavors of dynamical domain wall fermions and the Iwasaki gauge action ($\beta = 2.13$). The inverse lattice spacing is $a^{-1} = 1.73$ GeV, and two spatial volumes of ((2.7{\rm fm})^3) and ((1.8 {\rm fm})^3) are used. The up and down quark masses are varied so the pion mass lies between 0.33 and 0.67 GeV while the strange mass is about 12 % heavier than the physical one. The structure function moments we present include fully non-perturbatively renormalized iso-vector quark momentum fraction, (_{u-d}), helicity fraction, (< x >_{\Delta u - \Delta d}), and transversity, (_{\delta u - \delta d}), as well as an unrenormalized twist-3 coefficient, (d_1). The ratio of the momentum to helicity fractions, (_{u-d}/_{\Delta u - \Delta d}), does not show dependence on the light quark mass and agrees well with the value obtained from experiment. Their respective absolute values, fully renormalized, show interesting trends toward their respective experimental values at the lightest quark mass. A prediction for the transversity, (0.7 _{\delta u -\delta d} < 1.1), in the (\bar{\rm MS}) scheme at 2 GeV is obtained. The twist-3 coefficient, (d_1), though yet to be renormalized, supports the perturbative Wandzura-Wilczek relation.Comment: 14 pages, 22 figures

Localization and chiral symmetry in 2+1 flavor domain wall QCD

We present results for the dependence of the residual mass of domain wall fermions (DWF) on the size of the fifth dimension and its relation to the density and localization properties of low-lying eigenvectors of the corresponding hermitian Wilson Dirac operator relevant to simulations of 2+1 flavor domain wall QCD. Using the DBW2 and Iwasaki gauge actions, we generate ensembles of configurations with a $16^3\times 32$ space-time volume and an extent of 8 in the fifth dimension for the sea quarks. We demonstrate the existence of a regime where the degree of locality, the size of chiral symmetry breaking and the rate of topology change can be acceptable for inverse lattice spacings $a^{-1} \ge 1.6$ GeV.Comment: 59 Pages, 23 figures, 1 MPG linke

Incretin mimetics as pharmacological tools to elucidate and as a new drug strategy to treat traumatic brain injury

Traumatic brain injury (TBI), either as an isolated injury or in conjunction with other injuries, is an increasingly common occurring event. An estimated 1.7 million injuries occur within the US each year and 10 million people are affected annually worldwide. Indeed, some one-third (30.5%) of all injury-related deaths in the U.S. are associated with TBI, which will soon outstrip many common diseases as the major cause of death and disability. Associated with a high morbidity and mortality, and no specific therapeutic treatment, TBI has become a pressing public health and medical problem. The highest incidence of TBI occurs among young adults (15 to 24 years age) as well as in the elderly (75 years and older) who are particularly vulnerable as injury, often associated with falls, carries an increased mortality and worse functional outcome following lower initial injury severity. Added to this, a new and growing form of TBI, blast injury, associated with the detonation of improvised explosive devices in the war theaters of Iraq and Afghanistan, are inflicting a wave of unique casualties of immediate impact to both military personnel and civilians, for which long-term consequences remain unknown and may potentially be catastrophic. The neuropathology underpinning head injury is becoming increasingly better understood. Depending on severity, TBI induces immediate neuropathological effects that for the mildest form may be transient but with increasing severity cause cumulative neural damage and degeneration. Even with mild TBI, which represents the majority of cases, a broad spectrum of neurological deficits, including cognitive impairments, can manifest that may significantly influence quality of life. In addition, TBI can act as a conduit to longer-term neurodegenerative disorders. Prior studies of glucagon-like peptide-1 (GLP-1) and long-acting GLP-1 receptor agonists have demonstrated neurotrophic/neuroprotective activities across a broad spectrum of cellular and animal models of chronic neurodegenerative (Alzheimer's and Parkinson's diseases) and acute cerebrovascular (stroke) disorders. In line with the commonality in mechanisms underpinning these disorders as well as TBI, the current article reviews this literature and recent studies assessing GLP-1 receptor agonists as a potential treatment strategy for mild to moderate TBI

Discovery of mating in the major African livestock pathogen Trypanosoma congolense

The protozoan parasite, Trypanosoma congolense, is one of the most economically important pathogens of livestock in Africa and, through its impact on cattle health and productivity, has a significant effect on human health and well being. Despite the importance of this parasite our knowledge of some of the fundamental biological processes is limited. For example, it is unknown whether mating takes place. In this paper we have taken a population genetics based approach to address this question. The availability of genome sequence of the parasite allowed us to identify polymorphic microsatellite markers, which were used to genotype T. congolense isolates from livestock in a discrete geographical area of The Gambia. The data showed a high level of diversity with a large number of distinct genotypes, but a deficit in heterozygotes. Further analysis identified cryptic genetic subdivision into four sub-populations. In one of these, parasite genotypic diversity could only be explained by the occurrence of frequent mating in T. congolense. These data are completely inconsistent with previous suggestions that the parasite expands asexually in the absence of mating. The discovery of mating in this species of trypanosome has significant consequences for the spread of critical traits, such as drug resistance, as well as for fundamental aspects of the biology and epidemiology of this neglected but economically important pathogen

Selenoprotein gene nomenclature

The human genome contains 25 genes coding for selenocysteine-containing proteins (selenoproteins). These proteins are involved in a variety of functions, most notably redox homeostasis. Selenoprotein enzymes with known functions are designated according to these functions: TXNRD1, TXNRD2, and TXNRD3 (thioredoxin reductases), GPX1, GPX2, GPX3, GPX4 and GPX6 (glutathione peroxidases), DIO1, DIO2, and DIO3 (iodothyronine deiodinases), MSRB1 (methionine-R-sulfoxide reductase 1) and SEPHS2 (selenophosphate synthetase 2). Selenoproteins without known functions have traditionally been denoted by SEL or SEP symbols. However, these symbols are sometimes ambiguous and conflict with the approved nomenclature for several other genes. Therefore, there is a need to implement a rational and coherent nomenclature system for selenoprotein-encoding genes. Our solution is to use the root symbol SELENO followed by a letter. This nomenclature applies to SELENOF (selenoprotein F, the 15 kDa selenoprotein, SEP15), SELENOH (selenoprotein H, SELH, C11orf31), SELENOI (selenoprotein I, SELI, EPT1), SELENOK (selenoprotein K, SELK), SELENOM (selenoprotein M, SELM), SELENON (selenoprotein N, SEPN1, SELN), SELENOO (selenoprotein O, SELO), SELENOP (selenoprotein P, SeP, SEPP1, SELP), SELENOS (selenoprotein S, SELS, SEPS1, VIMP), SELENOT (selenoprotein T, SELT), SELENOV (selenoprotein V, SELV) and SELENOW (selenoprotein W, SELW, SEPW1). This system, approved by the HUGO Gene Nomenclature Committee, also resolves conflicting, missing and ambiguous designations for selenoprotein genes and is applicable to selenoproteins across vertebrates

The Alaska Arctic Vegetation Archive (AVA-AK)

The Alaska Arctic Vegetation Archive (AVA-AK, GIVD-ID: NA-US-014) is a free, publically available database archive of vegetation-plot data from the Arctic tundra region of northern Alaska. The archive currently contains 24 datasets with 3,026 non-overlapping plots. Of these, 74% have geolocation data with 25-m or better precision. Species cover data and header data are stored in a Turboveg database. A standardized Pan Arctic Species List provides a consistent nomenclature for vascular plants, bryophytes, and lichens in the archive. A web-based online Alaska Arctic Geoecological Atlas (AGA-AK) allows viewing and downloading the species data in a variety of formats, and provides access to a wide variety of ancillary data. We conducted a preliminary cluster analysis of the first 16 datasets (1,613 plots) to examine how the spectrum of derived clusters is related to the suite of datasets, habitat types, and environmental gradients. Here, we present the contents of the archive, assess its strengths and weaknesses, and provide three supplementary files that include the data dictionary, a list of habitat types, an overview of the datasets, and details of the cluster analysis

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

Recent statistical analyses suggest that sequencing of pooled samples provides a cost effective approach to determine genome-wide population genetic parameters. Here we introduce PoPoolation, a toolbox specifically designed for the population genetic analysis of sequence data from pooled individuals. PoPoolation calculates estimates of θWatterson, θπ, and Tajima's D that account for the bias introduced by pooling and sequencing errors, as well as divergence between species. Results of genome-wide analyses can be graphically displayed in a sliding window plot. PoPoolation is written in Perl and R and it builds on commonly used data formats. Its source code can be downloaded from http://code.google.com/p/popoolation/. Furthermore, we evaluate the influence of mapping algorithms, sequencing errors, and read coverage on the accuracy of population genetic parameter estimates from pooled data

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

Genome-wide comparison of transcription factor binding between related Drosophila species highlights how sequence changes affect the biochemical events that underlie animal development

A Sex-Specific Metabolite Identified in a Marine Invertebrate Utilizing Phosphorus-31 Nuclear Magnetic Resonance

Hormone level differences are generally accepted as the primary cause for sexual dimorphism in animal and human development. Levels of low molecular weight metabolites also differ between men and women in circulating amino acids, lipids and carbohydrates and within brain tissue. While investigating the metabolism of blue crab tissues using Phosphorus-31 Nuclear Magnetic Resonance, we discovered that only the male blue crab (Callinectes sapidus) contained a phosphorus compound with a chemical shift well separated from the expected phosphate compounds. Spectra obtained from male gills were readily differentiated from female gill spectra. Analysis from six years of data from male and female crabs documented that the sex-specificity of this metabolite was normal for this species. Microscopic analysis of male and female gills found no differences in their gill anatomy or the presence of parasites or bacteria that might produce this phosphorus compound. Analysis of a rare gynandromorph blue crab (laterally, half male and half female) proved that this sex-specificity was an intrinsic biochemical process and was not caused by any variations in the diet or habitat of male versus female crabs. The existence of a sex-specific metabolite is a previously unrecognized, but potentially significant biochemical phenomenon. An entire enzyme system has been synthesized and activated only in one sex. Unless blue crabs are a unique species, sex-specific metabolites are likely to be present in other animals. Would the presence or absence of a sex-specific metabolite affect an animal's development, anatomy and biochemistry