The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes

<p>Abstract</p> <p>Background</p> <p>High quality annotation of the genes and transposable elements in complex genomes requires a human-curated integration of multiple sources of computational evidence. These evidences include results from a diversity of <it>ab initio </it>prediction programs as well as homology-based searches. Most of these programs operate on a single contiguous sequence at a time, and the results are generated in a diverse array of readable formats that must be translated to a standardized file format. These translated results must then be concatenated into a single source, and then presented in an integrated form for human curation.</p> <p>Results</p> <p>We have designed, implemented, and assessed a Perl-based workflow named DAWGPAWS for the generation of computational results for human curation of the genes and transposable elements in plant genomes. The use of DAWGPAWS was found to accelerate annotation of 80–200 kb wheat DNA inserts in bacterial artificial chromosome (BAC) vectors by approximately twenty-fold and to also significantly improve the quality of the annotation in terms of completeness and accuracy.</p> <p>Conclusion</p> <p>The DAWGPAWS genome annotation pipeline fills an important need in the annotation of plant genomes by generating computational evidences in a high throughput manner, translating these results to a common file format, and facilitating the human curation of these computational results. We have verified the value of DAWGPAWS by using this pipeline to annotate the genes and transposable elements in 220 BAC insertions from the hexaploid wheat genome (<it>Triticum aestivum </it>L.). DAWGPAWS can be applied to annotation efforts in other plant genomes with minor modifications of program-specific configuration files, and the modular design of the workflow facilitates integration into existing pipelines.</p

General and Localized corrosion of Austenitic and Borated Stainless Steels in Simulated Concentrated Ground Waters

Boron containing stainless steels are used in the nuclear industry for applications such as spent fuel storage, control rods and shielding. It was of interest to compare the corrosion resistance of three borated stainless steels with standard austenitic alloy materials such as type 304 and 316 stainless steels. Tests were conducted in three simulated concentrated ground waters at 90 C. Results show that the borated stainless were less resistant to corrosion than the witness austenitic materials. An acidic concentrated ground water was more aggressive than an alkaline concentrated ground water

Long Term Corrosion Potential and Corrosion Rate of Creviced Alloy 22 in Chloride Plus Nitrate Brines

Alloy 22 is a nickel base alloy highly resistant to all forms of corrosion. In conditions where tight crevices exist in hot chloride containing solutions and at anodic potentials, Alloy 22 may suffer crevice corrosion, a form of localized attack. The occurrence (or not) of crevice corrosion in a given environment (e.g. salt concentration and temperature), is governed by the values of the critical potential (E{sub crit}) for crevice corrosion and the corrosion potential (E{sub corr}) that the alloy may establish in the studied environment. If E{sub corr} is equal or higher than E{sub crit}, crevice corrosion may be expected. In addition, it is generally accepted that as Alloy 22 becomes passive in a certain environment, its E{sub corr} increases and its corrosion rate (CR) decreases. This paper discusses the evolution of E{sub corr} and corrosion rate (CR) of creviced Alloy 22 specimens in six different mixtures of sodium chloride (NaCl) and potassium nitrate (KNO{sub 3}) at 100 C. The effect of immersion time on the value of E{sub crit} was also determined. Two types of specimens were used, polished as-welded (ASW) and as-welded plus solution heat-treated (ASW+SHT). The latter contained the black annealing oxide film on the surface. Results show that, as the immersion time increases, E{sub corr} increased and the CR decreased. Even for highly concentrated brine solutions at 100 C the CR was &lt; 30 nm/year after more than 250 days immersion. Some of the exposed specimens (mainly the SHT specimens) suffered crevice corrosion at the open circuit potential in the naturally aerated brines. Immersion times of over 250 days did not reduce the resistance of Alloy 22 to localized corrosion

Flaxseed supplementation decreases methanogenic gene abundance in the rumen of dairy cows

The objective of this study was to investigate the effects of a flaxseed-supplemented diet on archaeal abundance and gene expression of methanogens in the rumen of dairy cows. In all, 11 non-lactating dairy cows were randomly divided into two groups: group A (five cows) and B (six cows). The two diets fed were: (1) the control diet, a conventional dry cow ration; and (2) the flaxseed-supplemented diet, the conventional dry cow ration adjusted with 12.16% ground flaxseed incorporated into the total mixed ration. A cross-over experiment was performed with the two groups of cows fed the two different diets for five 21-day periods, which included the first adaptation period followed by two treatment and two wash out periods. At the end of each feeding period, rumen fluid samples were collected via rumenocentesis and DNA was extracted. Quantitative PCR was utilized to analyze the gene abundance of 16S ribosomal RNA (16S rRNA) targeting the ruminal archaea population and the mcrA gene coding for methyl coenzyme-M reductase subunit A, a terminal enzyme in the methanogenesis pathway. Results demonstrated a 49% reduction of 16S rRNA and 50% reduction of mcrA gene abundances in the rumen of dairy cows fed the flaxseedsupplemented diet in comparison with those fed the control diet. This shows flaxseed supplementation effectively decreases the methanogenic population in the rumen. Future studies will focus on the mechanisms for such reduction in the rumen of dairy cattle, as well as the relationship between methanogenic gene expression and methane production.Keywords: Dairy cattle, Mcra, Methanogenic gene, Flaxsee

Getting it right when budgets are tight: Using optimal expansion pathways to prioritize responses to concentrated and mixed HIV epidemics.

BACKGROUND: Prioritizing investments across health interventions is complicated by the nonlinear relationship between intervention coverage and epidemiological outcomes. It can be difficult for countries to know which interventions to prioritize for greatest epidemiological impact, particularly when budgets are uncertain. METHODS: We examined four case studies of HIV epidemics in diverse settings, each with different characteristics. These case studies were based on public data available for Belarus, Peru, Togo, and Myanmar. The Optima HIV model and software package was used to estimate the optimal distribution of resources across interventions associated with a range of budget envelopes. We constructed "investment staircases", a useful tool for understanding investment priorities. These were used to estimate the best attainable cost-effectiveness of the response at each investment level. FINDINGS: We find that when budgets are very limited, the optimal HIV response consists of a smaller number of 'core' interventions. As budgets increase, those core interventions should first be scaled up, and then new interventions introduced. We estimate that the cost-effectiveness of HIV programming decreases as investment levels increase, but that the overall cost-effectiveness remains below GDP per capita. SIGNIFICANCE: It is important for HIV programming to respond effectively to the overall level of funding availability. The analytic tools presented here can help to guide program planners understand the most cost-effective HIV responses and plan for an uncertain future

Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains

<p>Abstract</p> <p>Background</p> <p>Many plant genomes are resistant to whole-genome assembly due to an abundance of repetitive sequence, leading to the development of gene-rich sequencing techniques. Two such techniques are hypomethylated partial restriction (HMPR) and methylation spanning linker libraries (MSLL). These libraries differ from other gene-rich datasets in having larger insert sizes, and the MSLL clones are designed to provide reads localized to "epigenetic boundaries" where methylation begins or ends.</p> <p>Results</p> <p>A large-scale study in maize generated 40,299 HMPR sequences and 80,723 MSLL sequences, including MSLL clones exceeding 100 kb. The paired end reads of MSLL and HMPR clones were shown to be effective in linking existing gene-rich sequences into scaffolds. In addition, it was shown that the MSLL clones can be used for anchoring these scaffolds to a BAC-based physical map. The MSLL end reads effectively identified epigenetic boundaries, as indicated by their preferential alignment to regions upstream and downstream from annotated genes. The ability to precisely map long stretches of fully methylated DNA sequence is a unique outcome of MSLL analysis, and was also shown to provide evidence for errors in gene identification. MSLL clones were observed to be significantly more repeat-rich in their interiors than in their end reads, confirming the correlation between methylation and retroelement content. Both MSLL and HMPR reads were found to be substantially gene-enriched, with the <it>Sal</it>I MSLL libraries being the most highly enriched (31% align to an EST contig), while the HMPR clones exhibited exceptional depletion of repetitive DNA (to ~11%). These two techniques were compared with other gene-enrichment methods, and shown to be complementary.</p> <p>Conclusion</p> <p>MSLL technology provides an unparalleled approach for mapping the epigenetic status of repetitive blocks and for identifying sequences mis-identified as genes. Although the types and natures of epigenetic boundaries are barely understood at this time, MSLL technology flags both approximate boundaries and methylated genes that deserve additional investigation. MSLL and HMPR sequences provide a valuable resource for maize genome annotation, and are a uniquely valuable complement to any plant genome sequencing project. In order to make these results fully accessible to the community, a web display was developed that shows the alignment of MSLL, HMPR, and other gene-rich sequences to the BACs; this display is continually updated with the latest ESTs and BAC sequences.</p

Anodic Behavior of Alloy 22 in High Nitrate Brines at Temperatures Higher than 100(degree)C

Alloy 22 (N06022) may be susceptible to crevice corrosion in chloride solutions. Nitrate acts as an inhibitor to crevice corrosion. Several papers have been published regarding the effect of nitrate on the corrosion resistance of Alloy 22 at temperatures 100 C and lower. However, very little is known about the behavior of this alloy in highly concentrated brines at temperatures above 100 C. In the current work, electrochemical tests have been carried out to explore the anodic behavior of Alloy 22 in high chloride high nitrate electrolytes at temperatures as high as 160 C at ambient atmospheres. Even though Alloy 22 may adopt corrosion potentials in the order of +0.5 V (in the saturated silver chloride scale), it does not suffer crevice corrosion if there is high nitrate in the solution. That is, the inhibitive effect of nitrate on crevice corrosion is active for temperatures higher than 100 C

Cost-per-diagnosis as a metric for monitoring cost effectiveness of HIV testing programmes in low income settings in southern Africa : health economic and modelling analysis

Introduction: As prevalence of undiagnosed HIV declines, it is unclear whether testing programmes will be cost effective. To guide their HIV testing programmes,countries require appropriatemetrics that can be measured. The cost-per-diagnosisis potentially a useful metric. Methods:We simulated a series of setting-scenarios for adult HIV epidemics and ART programmes typical of settings in southern Africa using an individual-based model and projected forward from 2018 under two policies: (i) a minimum package of “core” testing (i.e. testing in pregnant women, for diagnosis of symptoms, in sex workers, and in men coming forward for circumcision) is conducted, and (ii) “core” testing as above plus “additional-testing”, for which we specify different rates of testing and various degrees to which those with HIV are more likely to test than thosewithout HIV. We also considered a plausible range of unit test costs. The aim was to assess the relationship between cost-per-diagnosisand the incremental cost-effectiveness ratio(ICER) of the additional-testingpolicy. Discount rate 3%; costs in 2018 $US. Results:There was a strong graded relationship between the cost-per-diagnosisand the ICER. Overall, the ICERwas below$500 per-DALY-averted (the cost effectiveness threshold used in primary analysis) so long as thecost-per-diagnosiswas below $315. This thresholdcost-per-diagnosiswas similar according to epidemic and programmatic features including the prevalence of undiagnosed HIV, the HIV incidence and a measure of HIV programme quality (the proportion of HIV diagnosed people having a viral load <1000 copies/mL). However, restrictingto women, additional-testingdid not appear cost-effective even at acost-per-diagnosisof below$50, while restrictingto men additional-testingwas cost effective up to a cost-per-diagnosisof $585. Thethreshold cost for testing in men fell to$256 when the cost effectiveness threshold was $300instead of$500, and to $81 when considering a discount rate of 10% perannum.Conclusions:For testing programmesin low income settings in southern African there is an extremely strong relationship between the cost-per-diagnosisand the cost per DALY averted, indicating that the cost-per-diagnosiscan be used to monitor the cost effectiveness of testing programmes

Rumen Microorganisms Decrease Bioavailability of Inorganic Selenium Supplements

Despite the availability of selenium (Se)-enriched trace mineral supplements, we have observed low Se status in cattle and sheep offered traditional inorganic Se supplements. Reasons for this may include inadequate intake or low bioavailability of inorganic Se sources. The objective of this study was to determine whether rumen microorganisms (RMO) alter the bioavailability of Se sources commonly used in Se supplements. Rumen microorganisms were isolated from ewes (n = 4) and incubated ex vivo with no Se (control), with inorganic Na selenite or Na selenate, or with organic selenomethionine (SeMet). Total Se incorporated into RMO and the amount of elemental Se formed were determined under equivalent conditions. Incorporation of Se from Na selenite, Na selenate, or SeMet into RMO was measured as fold change compared with control (no added Se). Incorporation of Se into microbial mass was greater for SeMet (13.2-fold greater than no-Se control) compared with inorganic Se supplements (P = 0.02); no differences were observed between inorganic Na selenate (3.3-fold greater than no-Se control) and Na selenite (3.5-fold greater than no-Se control; P = 0.97). Formation of non-bioavailable, elemental Se was less for RMO incubated with SeMet compared with inorganic Se sources (P = 0.01); no differences were observed between Na selenate and Na selenite (P = 0.09). The clinical importance of these results is that the oral bioavailability of organic SeMet should be greater compared with inorganic Se sources because of greater RMO incorporation of Se and decreased formation of elemental Se by RMO.Keywords: Rumen microorganisms, Sheep, Selenium bioavailability, Ruminant, Selenium supplement