Convex Representation of Metabolic Networks with Michaelis-Menten Kinetics.

Polyhedral models of metabolic networks are computationally tractable and can predict some cellular functions. A longstanding challenge is incorporating metabolites without losing tractability. In this paper, we do so using a new second-order cone representation of the Michaelis-Menten kinetics. The resulting model consists of linear stoichiometric constraints alongside second-order cone constraints that couple the reaction fluxes to metabolite concentrations. We formulate several new problems around this model: conic flux balance analysis, which augments flux balance analysis with metabolite concentrations; dynamic conic flux balance analysis; and finding minimal cut sets of networks with both reactions and metabolites. Solving these problems yields information about both fluxes and metabolite concentrations. They are second-order cone or mixed-integer second-order cone programs, which, while not as tractable as their linear counterparts, can nonetheless be solved at practical scales using existing software.

We have to stand up for ourselves: Barriers to self-determination experienced by Black youth in the transition to adulthood.

Transition outcomes for Black youth with intellectual and developmental disabilities are especially dire, lagging even further behind already poor outcomes among their White peers. Self-determination is a key factor in predicting better outcomes, but it is unclear how self-determination is fostered or hindered within the transition process for Black youth and their families. This study used the DisCrit framework to analyze interview data from Black students with intellectual and developmental disabilities and their parents regarding self-determination and effective transition services. Analysis resulted in four major themes: historical undertones, proxies for racial bias, spacialization of racialization, and interest convergence. Implications for future research, policy, and practice are discussed.

The Association of Specific Dietary Patterns with Cardiometabolic Outcomes in Women with a History of Gestational Diabetes Mellitus: A Scoping Review.

Gestational diabetes mellitus is associated with a significantly increased risk of later type 2 diabetes (T2DM) and cardiovascular disease (CVD). Post-natal interventions aim to reduce this risk by addressing diet and lifestyle factors and frequently focus on restricting energy or macronutrient intake. With increased interest in the role of complete dietary patterns in the prevention of cardiometabolic disease, we sought to evaluate what is known about the role of dietary patterns in reducing cardiometabolic risk in women with previous GDM. A systematic search was conducted to identify studies relating to dietary pattern and cardiometabolic parameters in women with a history of GDM. The search criteria returned 6014 individual studies. In total, 71 full texts were reviewed, with 24 studies included in the final review. Eleven individual dietary patterns were identified, with the Alternative Health Eating Index (AHEI), Mediterranean diet (MD), and low glycaemic index (GI) as the most commonly featured dietary patterns. Relevant reported outcomes included incident T2DM and glucose tolerance parameters, as well as several cardiovascular risk factors. Dietary patterns which have previously been extensively demonstrated to reduce the risk of cardiovascular and metabolic disorders in the general population, including AHEI, MD, and DASH, were found to be associated with a reduction in the incidence of T2DM, hypertension, and additional risk factors for cardiometabolic disease in women with a history of GDM. Notable gaps in the literature were identified, including the relationship between dietary patterns and incident CVD, as well as the relationship between a low GI diet and the development of T2DM in this population.

"Birthday-Banding" as a Strategy to Moderate the Relative Age Effect: A Case Study Into the England Squash Talent Pathway.

The relative age effect (RAE) is almost pervasive throughout youth sports, whereby relatively older athletes are consistently overrepresented compared to their relatively younger peers. Although researchers regularly cite the need for sports programs to incorporate strategies to moderate the RAE, organizational structures often continue to adopt a one-dimensional (bi)annual-age group approach. In an effort to combat this issue, England Squash implemented a "birthday-banding" strategy in its talent pathway, whereby young athletes move up to their next age group on their birthday, with the aim to remove particular selection time points and fixed chronological bandings. Thus, the purpose of this study was to examine the potential effects of the birthday-banding strategy on birth quarter (BQ) distributions throughout the England Squash talent pathway. Three mixed-gender groups were populated and analyzed: (a) ASPIRE athletes (n = 250), (b) Development and Potential athletes (n = 52), and (c) Senior team and Academy athletes (n = 26). Chi-square analysis and odds ratios were used to test BQ distributions against national norms and between quartiles, respectively. Results reveal no significant difference between BQ distributions within all three groups (P > 0.05). In contrast to most studies examining the RAE within athlete development settings, there appears to be no RAE throughout the England Squash talent pathway. These findings suggest that the birthday-banding strategy may be a useful tool to moderate RAE in youth sports.

Allometry and Ecology of the Bilaterian Gut Microbiome.

Classical ecology provides principles for construction and function of biological communities, but to what extent these apply to the animal-associated microbiota is just beginning to be assessed. Here, we investigated the influence of several well-known ecological principles on animal-associated microbiota by characterizing gut microbial specimens from bilaterally symmetrical animals (Bilateria) ranging from flies to whales. A rigorously vetted sample set containing 265 specimens from 64 species was assembled. Bacterial lineages were characterized by 16S rRNA gene sequencing. Previously published samples were also compared, allowing analysis of over 1,098 samples in total. A restricted number of bacterial phyla was found to account for the great majority of gut colonists. Gut microbial composition was associated with host phylogeny and diet. We identified numerous gut bacterial 16S rRNA gene sequences that diverged deeply from previously studied taxa, identifying opportunities to discover new bacterial types. The number of bacterial lineages per gut sample was positively associated with animal mass, paralleling known species-area relationships from island biogeography and implicating body size as a determinant of community stability and niche complexity. Samples from larger animals harbored greater numbers of anaerobic communities, specifying a mechanism for generating more-complex microbial environments. Predictions for species/abundance relationships from models of neutral colonization did not match the data set, pointing to alternative mechanisms such as selection of specific colonists by environmental niche. Taken together, the data suggest that niche complexity increases with gut size and that niche selection forces dominate gut community construction.IMPORTANCE The intestinal microbiome of animals is essential for health, contributing to digestion of foods, proper immune development, inhibition of pathogen colonization, and catabolism of xenobiotic compounds. How these communities assemble and persist is just beginning to be investigated. Here we interrogated a set of gut samples from a wide range of animals to investigate the roles of selection and random processes in microbial community construction. We show that the numbers of bacterial species increased with the weight of host organisms, paralleling findings from studies of island biogeography. Communities in larger organisms tended to be more anaerobic, suggesting one mechanism for niche diversification. Nonselective processes enable specific predictions for community structure, but our samples did not match the predictions of the neutral model. Thus, these findings highlight the importance of niche selection in community construction and suggest mechanisms of niche diversification.

Using fine-scale spatial genetics of Norway rats to improve control efforts and reduce leptospirosis risk in urban slum environments.

The Norway rat (Rattus norvegicus) is a key pest species globally and responsible for seasonal outbreaks of the zoonotic bacterial disease leptospirosis in the tropics. The city of Salvador, Brazil, has seen recent and dramatic increases in human population residing in slums, where conditions foster high rat density and increasing leptospirosis infection rates. Intervention campaigns have been used to drastically reduce rat numbers. In planning these interventions, it is important to define the eradication units - the spatial scale at which rats constitute continuous populations and from where rats are likely recolonizing, post-intervention. To provide this information, we applied spatial genetic analyses to 706 rats collected across Salvador and genotyped at 16 microsatellite loci. We performed spatially explicit analyses and estimated migration levels to identify distinct genetic units and landscape features associated with genetic divergence at different spatial scales, ranging from valleys within a slum community to city-wide analyses. Clear genetic breaks exist between rats not only across Salvador but also between valleys of slums separated by <100 m-well within the dispersal capacity of rats. The genetic data indicate that valleys may be considered separate units and identified high-traffic roads as strong impediments to rat movement. Migration data suggest that most (71-90%) movement is contained within valleys, with no clear source population contributing to migrant rats. We use these data to recommend eradication units and discuss the importance of carrying out individual-based analyses at different spatial scales in urban landscapes.

A reconnaissance analysis of groundwater quality in the Eagle Ford shale region reveals two distinct bromide/chloride populations.

The extraction of oil and natural gas from unconventional shale formations has prompted a series of investigations to examine the quality of the groundwater in the overlying aquifers. Here we present a reconnaissance analysis of groundwater quality in the Eagle Ford region of southern Texas. These data reveal two distinct sample populations that are differentiable by bromide/chloride ratios. Elevated levels of fluoride, nitrate, sulfate, various metal ions, and the detection of exotic volatile organic compounds highlight a high bromide group of samples, which is geographically clustered, while encompassing multiple hydrogeological strata. Samples with bromide/chloride ratios representative of connate water displayed elevated levels of total organic carbon, while revealing the detection of alcohols and chlorinated compounds. These findings suggest that groundwater quality in the Western Gulf Basin is, for the most part, controlled by a series of natural processes; however, there is also evidence of episodic contamination events potentially attributed to unconventional oil and gas development or other anthropogenic activities. Collectively, this characterization of natural groundwater constituents and exogenous compounds will guide targeted remediation efforts and provides insight for agricultural entities, industrial operators, and rural communities that rely on groundwater in southern Texas.

Point source attribution of ambient contamination events near unconventional oil and gas development.

We present an analysis of ambient benzene, toluene, and xylene isomers in the Eagle Ford shale region of southern Texas. In situ air quality measurements using membrane inlet mobile mass spectrometry revealed ambient benzene and toluene concentrations as high as 1000 and 5000 parts-per-billion, respectively, originating from specific sub-processes on unconventional oil and gas well pad sites. The detection of highly variant contamination events attributable to natural gas flaring units, condensate tanks, compressor units, and hydrogen sulfide scavengers indicates that mechanical inefficiencies, and not necessarily the inherent nature of the extraction process as a whole, result in the release of these compounds into the environment. This awareness of ongoing contamination events contributes to an enhanced knowledge of ambient volatile organic compounds on a regional scale. While these reconnaissance measurements on their own do not fully characterize the fluctuations of ambient BTEX concentrations that likely exist in the atmosphere of the Eagle Ford Shale region, they do suggest that contamination events from unconventional oil and gas development can be monitored, controlled, and reduced.

A Two-Year Ecological Study of Norway Rats (Rattus norvegicus) in a Brazilian Urban Slum.

The Norway or brown rat (Rattus norvegicus) is among the most ubiquitous of rodents. However, the lack of studies describing Norway rat populations from tropical areas have limited our understanding regarding their demography and seasonal dynamics. In this study, we describe seasonal pattern in the abundance, reproductive parameters, and morphometrics of Norway rat populations in Salvador, Brazil. Rodents were trapped over four seasonal trapping periods (2013-2014) from three valleys. A total of 802 Norway rats were trapped over the course of the study over 7653 trap-nights. Norway rat abundance was high, but there was no significant differences between seasons. The reproductive parameters (e.g. frequency of pregnant and lactating females) did not show statistical differences between seasons. Female rats collected in the rainy season were heavier and older than females from the dry season. Salvador rats had a high incidence of pregnancy and birth rate (estimated birth rate of 79 young per year) compared to previous studies. The information generated is critical for the understanding of the ecology of Norway rat, the main reservoir of Leptospira in Salvador. However, future studies examining the effect of rodent control programs aimed at reducing populations, and determining rates of recovery, will further clarify our understanding of population dynamics.

Molecular Basis for the Selective Inhibition of Respiratory Syncytial Virus RNA Polymerase by 2'-Fluoro-4'-Chloromethyl-Cytidine Triphosphate.

Respiratory syncytial virus (RSV) causes severe lower respiratory tract infections, yet no vaccines or effective therapeutics are available. ALS-8176 is a first-in-class nucleoside analog prodrug effective in RSV-infected adult volunteers, and currently under evaluation in hospitalized infants. Here, we report the mechanism of inhibition and selectivity of ALS-8176 and its parent ALS-8112. ALS-8176 inhibited RSV replication in non-human primates, while ALS-8112 inhibited all strains of RSV in vitro and was specific for paramyxoviruses and rhabdoviruses. The antiviral effect of ALS-8112 was mediated by the intracellular formation of its 5'-triphosphate metabolite (ALS-8112-TP) inhibiting the viral RNA polymerase. ALS-8112 selected for resistance-associated mutations within the region of the L gene of RSV encoding the RNA polymerase. In biochemical assays, ALS-8112-TP was efficiently recognized by the recombinant RSV polymerase complex, causing chain termination of RNA synthesis. ALS-8112-TP did not inhibit polymerases from host or viruses unrelated to RSV such as hepatitis C virus (HCV), whereas structurally related molecules displayed dual RSV/HCV inhibition. The combination of molecular modeling and enzymatic analysis showed that both the 2'F and the 4'ClCH2 groups contributed to the selectivity of ALS-8112-TP. The lack of antiviral effect of ALS-8112-TP against HCV polymerase was caused by Asn291 that is well-conserved within positive-strand RNA viruses. This represents the first comparative study employing recombinant RSV and HCV polymerases to define the selectivity of clinically relevant nucleotide analogs. Understanding nucleotide selectivity towards distant viral RNA polymerases could not only be used to repurpose existing drugs against new viral infections, but also to design novel molecules.

A Comprehensive Analysis of Groundwater Quality in The Barnett Shale Region.

The exploration of unconventional shale energy reserves and the extensive use of hydraulic fracturing during well stimulation have raised concerns about the potential effects of unconventional oil and gas extraction (UOG) on the environment. Most accounts of groundwater contamination have focused primarily on the compositional analysis of dissolved gases to address whether UOG activities have had deleterious effects on overlying aquifers. Here, we present an analysis of 550 groundwater samples collected from private and public supply water wells drawing from aquifers overlying the Barnett shale formation of Texas. We detected multiple volatile organic carbon compounds throughout the region, including various alcohols, the BTEX family of compounds, and several chlorinated compounds. These data do not necessarily identify UOG activities as the source of contamination; however, they do provide a strong impetus for further monitoring and analysis of groundwater quality in this region as many of the compounds we detected are known to be associated with UOG techniques.

The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs.

Piwi-interacting RNAs (piRNAs) guide Piwi Argonautes to suppress transposon activity in animal gonads. Known piRNA populations are extremely complex, with millions of individual sequences present in a single organism. Despite this complexity, specific Piwi proteins incorporate piRNAs with distinct nucleotide- and transposon strand-biases (antisense or sense) of unknown origin. Here, we examined the contribution of structural domains in Piwi proteins toward defining these biases. We report the first crystal structure of the MID domain from a Piwi Argonaute and use docking experiments to show its ability to specify recognition of 5' uridine (1U-bias) of piRNAs. Mutational analyses reveal the importance of 5' end-recognition within the MID domain for piRNA biogenesis in vivo. Finally, domain-swapping experiments uncover an unexpected role for the MID-PIWI module of a Piwi protein in dictating the transposon strand-orientation of its bound piRNAs. Our work identifies structural features that allow distinguishing individual Piwi members during piRNA biogenesis.

Improved emollient use reduces atopic eczema symptoms and is cost neutral in infants: before-and-after evaluation of a multifaceted educational support programme.

BACKGROUND: Parents and carers of children with eczema often underuse emollient therapy, essential to repairing and protecting the defective skin barrier in atopic eczema. Educational interventions delivered by specialist dermatology nurses in hospital settings have been shown to improve emollient use and reduce symptoms of atopic eczema, but benefits of community-based interventions are uncertain. Support and information about appropriate care may often be inadequate for patients and carers in the community. METHODS: A multifaceted educational support programme was evaluated as a method of increasing emollient use and reducing atopic eczema in children. Support provided for parents and carers included an educational DVD, online daily diary and telephone helpline. The before and after study included 136 British children and their parents, providing baseline and 12 week follow-up data while receiving the programme. Measures included emollient use, POEM and PEST scores, and cost of care. RESULTS: Average emollient use increased by 87.6 g (95% CI: 81.9 to 119.5 g, p = 0.001) from baseline with the change being immediate and persistent. The POEM score reduced on average by 5.38 (95% CI: 4.36 to 6.41, p = 0.001), a 47% reduction from baseline. Similarly the PEST score reduced on average by 0.61 (95% CI: 0.47 to 0.75, p = 0.001), a 48% reduction from baseline. Sleep disturbance was reduced by 1.27 nights per week (95% CI: 0.85 to 1.68, p = 0.001) and parental feeling of control improved by 1.32 points (95% CI: 1.16 to 1.48, p = 0.001). From the NHS perspective, the programme was cost neutral overall within the study period. CONCLUSION: A community-based multifaceted educational support programme greatly increased emollient use, reducing symptoms of atopic eczema and general practitioner contacts, without increasing cost. Significant benefits may accrue to the families and carers of children with atopic eczema due to improved sleep patterns and greater feeling of control. PEST, a new simple measure of acute and remitting atopic eczema severity designed to help parents and children to monitor and manage eczema, merits further evaluation.