Using Ultra Performance Liquid Chromatography-Mass Spectrometric Based Metabolomics to Determine the Metabolic Differences due to Low Temperature or Genetic Mutation in \u3ci\u3eSalmonella enterica\u3c/i\u3e

Metabolomics aims to identify and quantify all of the small molecules within a cell. The relative concentrations of metabolites within cells grown under different experimental conditions, or different species, can be compared using pool size data. Exposing cellular cultures to isotopically labeled compounds allows the progress of metabolites through metabolic pathways to be tracked, known as flux. In the first experiment, the metabolic effects of exposure to lower than optimal temperatures in wild type Salmonella enterica, i.e. cold shock, were determined. The metabolites involved in glycolysis, the citric acid cycle, and the pentose phosphate pathway had less efficient labeling and smaller pool sizes at lower temperatures. Most of the amino acids detected showed less efficient labeling and larger pool sizes at lower temperatures, perhaps indicating that proteins were being broken down into amino acids. Alternatively, the less efficient labeling may be due to enzymes denaturing reducing the catalytic abilities of the cells, a slowdown in the rate of transcription or in the rate of translation. It is important to study cold shock in Salmonella enterica, at three temperatures in which contamination with the pathogen occurs, in order to see if there is a way to kill the pathogenic species more efficiently and limit the people who get ill from consuming Salmonella enterica from food contamination. The second experiment compared the purH mutant and the wild type strain of Salmonella enterica. The purH mutant had the gene that codes for the enzyme AICAR transformylase/IMP cyclohydrolase removed. AICAR is important to study since it is involved in many pathways in diverse organisms, activates AMP-activated protein kinase in mammals, which affects energy balance and the response to metabolic stress, and AICAR accumulation has been linked to an inhibition of the proliferation of cancer cells. Metabolites in glycolysis and the citric acid cycle were found to label less efficiently or have smaller pool sizes in the purH mutant, with the exceptions of those compounds involved in other pathways. The pentose phosphate pathway showed similar labeling patterns and larger pool sizes in the purH mutant, indicating that sugars may be going through the pathway

Conceptual Models for Integer Addition and Subtraction

In this article, we report the findings of a study conducted with 6 Grade 8 students in the United States. The students posed stories for open number sentences involving addition and subtraction of integers. We analysed the stories posed by the students to build models that describe the conceptual structures behind these posed stories – the conceptual models for integer addition and subtraction. These four conceptual models for thinking about and using integer addition and subtraction include Bookkeeping, Counterbalance, Relativity, and Translation, and are generated from the students’ posed stories. We also provide profiles of conceptual model use for two of the 6 students that describe how the students posed stories to accommodate conceptual model use, such as posing unconventional or unrealistic stories or changing the structure of the number sentences. The conceptual models and descriptions of how the students used them provide perspective into student thinking about integers and contexts, highlighting the mathematics of the students, and calling for a re-examination of contexts used in school mathematics

A quantitative study of neurochemically-defined populations of inhibitory interneurons in the superficial dorsal horn of the mouse spinal cord

Around a quarter of neurons in laminae I-II of the dorsal horn are inhibitory interneurons. These play an important role in modulating somatosensory information, including that perceived as pain or itch. Previous studies in rat identified four largely non-overlapping neurochemical populations among these cells, defined by expression of galanin, neuropeptide Y (NPY), neuronal nitric oxide synthase (nNOS) or parvalbumin. The galanin cells were subsequently shown to coexpress dynorphin. Several recent studies have used genetically-modified mice to investigate the function of different interneuron populations, and it is therefore important to determine whether the same pattern applies in mouse, and to estimate the relative sizes of these populations. We show that the neurochemical organisation of inhibitory interneurons in mouse superficial dorsal horn is similar to that in the rat, although a larger proportion of these neurons (33%) express NPY. Between them, these four populations account for ∼75% of inhibitory cells in laminae I-II. Since ∼25% of inhibitory interneurons in this region belong to a novel calretinin-expressing type, our results suggest that virtually all inhibitory interneurons in superficial dorsal horn can be assigned to one of these five neurochemical populations. Although our main focus was inhibitory neurons, we also identified a population of excitatory dynorphin-expressing cells in laminae I-II that are largely restricted to the medial part of the mid-lumbar dorsal horn, corresponding to glabrous skin territory. These findings are important for interpretation of studies using molecular-genetic techniques to manipulate the functions of interneuron populations to investigate their roles in somatosensory processing

Yes, The Government Should Tax Soft Drinks: Findings from a Citizens’ Jury in Australia

Taxation has been suggested as a possible preventive strategy to address the serious public health concern of childhood obesity. Understanding the public’s viewpoint on the potential role of taxation is vital to inform policy decisions if they are to be acceptable to the wider community. A Citizens’ Jury is a deliberative method for engaging the public in decision making and can assist in setting policy agendas. A Citizens’ Jury was conducted in Brisbane, Australia in May 2013 to answer the question: Is taxation on food and drinks an acceptable strategy to the public in order to reduce rates of childhood obesity? Citizens were randomly selected from the electoral roll and invited to participate. Thirteen members were purposively sampled from those expressing interest to broadly reflect the diversity of the Australian public. Over two days, participants were presented with evidence on the topic by experts, were able to question witnesses and deliberate on the evidence. The jurors unanimously supported taxation on sugar-sweetened drinks but generally did not support taxation on processed meats, snack foods and foods eaten/ purchased outside the home. They also supported taxation on snack foods on the condition that traffic light labelling was also introduced. Though they were not specifically asked to deliberate strategies outside of taxation, the jurors strongly recommended more nutritional information on all food packaging using the traffic light and teaspoon labelling systems for sugar, salt and fat content. The Citizens’ Jury suggests that the general public may support taxation on sugar-sweetened drinks to reduce rates of obesity in children. Regulatory reforms of taxation on sugar-sweetened drinks and improved labelling of nutritional information on product packaging were strongly supported by all members of the jury. These reforms should be considered by governments to prevent childhood obesity and the future burden on society from the consequences of obesity

Zooming in on the intracellular microbiome composition of bacterivorous <i>Acanthamoeba</i> isolates

Acanthamoeba, a free-living amoeba in water and soil, is an emerging pathogen causing severe eye infection known as Acanthamoeba keratitis. In its natural environment, Acanthamoeba performs a dual function as an environmental heterotrophic predator and host for a range of microorganisms that resist digestion. Our objective was to characterize the intracellular microorganisms of phylogenetically distinct Acanthamoeba spp. isolated in Australia and India through directly sequencing 16S rRNA amplicons from the amoebae. The presence of intracellular bacteria was further confirmed by in situ hybridization and electron microscopy. Among the 51 isolates assessed, 41% harboured intracellular bacteria which were clustered into four major phyla: Pseudomonadota (previously known as Proteobacteria), Bacteroidota (previously known as Bacteroidetes), Actinomycetota (previously known as Actinobacteria), and Bacillota (previously known as Firmicutes). The linear discriminate analysis effect size analysis identified distinct microbial abundance patterns among the sample types; Pseudomonas species was abundant in Australian corneal isolates (P &lt; 0.007), Enterobacteriales showed higher abundance in Indian corneal isolates (P &lt; 0.017), and Bacteroidota was abundant in Australian water isolates (P &lt; 0.019). The bacterial beta diversity of Acanthamoeba isolates from keratitis patients in India and Australia significantly differed (P &lt; 0.05), while alpha diversity did not vary based on the country of origin or source of isolation (P &gt; 0.05). More diverse intracellular bacteria were identified in water isolates as compared with clinical isolates. Confocal and electron microscopy confirmed the bacterial cells undergoing binary fission within the amoebal host, indicating the presence of viable bacteria. This study sheds light on the possibility of a sympatric lifestyle within Acanthamoeba, thereby emphasizing its crucial role as a bunker and carrier of potential human pathogens

High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs

<p>Abstract</p> <p>Background</p> <p>Allelic variation is the cornerstone of genetically determined differences in gene expression, gene product structure, physiology, and behavior. However, allelic variation, particularly cryptic (unknown or not annotated) variation, is problematic for follow up analyses. Polymorphisms result in a high incidence of false positive and false negative results in hybridization based analyses and hinder the identification of the true variation underlying genetically determined differences in physiology and behavior. Given the proliferation of mouse genetic models (e.g., knockout models, selectively bred lines, heterogeneous stocks derived from standard inbred strains and wild mice) and the wealth of gene expression microarray and phenotypic studies using genetic models, the impact of naturally-occurring polymorphisms on these data is critical. With the advent of next-generation, high-throughput sequencing, we are now in a position to determine to what extent polymorphisms are currently cryptic in such models and their impact on downstream analyses.</p> <p>Results</p> <p>We sequenced the two most commonly used inbred mouse strains, DBA/2J and C57BL/6J, across a region of chromosome 1 (171.6 – 174.6 megabases) using two next generation high-throughput sequencing platforms: Applied Biosystems (SOLiD) and Illumina (Genome Analyzer). Using the same templates on both platforms, we compared realignments and single nucleotide polymorphism (SNP) detection with an 80 fold average read depth across platforms and samples. While public datasets currently annotate 4,527 SNPs between the two strains in this interval, thorough high-throughput sequencing identified a total of 11,824 SNPs in the interval, including 7,663 new SNPs. Furthermore, we confirmed 40 missense SNPs and discovered 36 new missense SNPs.</p> <p>Conclusion</p> <p>Comparisons utilizing even two of the best characterized mouse genetic models, DBA/2J and C57BL/6J, indicate that more than half of naturally-occurring SNPs remain cryptic. The magnitude of this problem is compounded when using more divergent or poorly annotated genetic models. This warrants full genomic sequencing of the mouse strains used as genetic models.</p

Morquio A Syndrome-Associated Mutations: A Review of Alterations in the GALNS gene and a New Locus-Specific Database

Morquio A syndrome (mucopolysaccharidosis IVA) is an autosomal recessive disorder that results from deficient activity of the enzyme Nacetylgalactosamine-6-sulfatase (GALNS) due to alterations in the GALNS gene, which causes major skeletal and connective tissue abnormalities and effects on multiple organ systems. The GALNS alterations associated with Morquio A are numerous and heterogeneous, and new alterations are continuously identified. To aid detection and interpretation of GALNS alterations, from previously published research, we provide a comprehensive and upto-date listing of 277 unique GALNS alterations associated with Morquio A identified from 1,091 published GALNS alleles. In agreement with previous findings, most reported GALNS alterations are missense changes and even the most frequent alterations are relatively uncommon. We found that 48% of patients are assessed as homozygous for a GALNS alteration, 39% are assessed as heterozygous for two identified GALNS alterations, and in 13% of patients only one GALNS alteration is detected. We report here the creation of a locus-specific database for the GALNS gene (http://galns.mutdb.org/) that catalogs all reported alterations in GALNS to date. We highlight the challenges both in alteration detection and genotype– phenotype interpretation caused in part by the heterogeneity of GALNS alterations and provide recommendations for molecular testing of GALNS

Late Holocene climate anomaly concurrent with fire activity and ecosystem shifts in the eastern Australian Highlands

The alpine area of the Australian mainland is highly sensitive to climate and environmental change, and potentially vulnerable to ecosystem tipping points. Over the next two decades the Australian alpine region is predicted to experience temperature increases of at least 1 °C, coupled with a substantial decrease in snow cover. Extending the short instrumental record in these regions is imperative to put future change into context, and potentially provide analogues of warming. We reconstructed past temperatures, using a lipid biomarker palaeothermometer technique and mercury flux changes for the past 3500 years from the sediments of Club Lake, a high-altitude alpine tarn in the Snowy Mountains, southeastern Australia. Using a multi-proxy framework, including pollen and charcoal analyses, high-resolution geochemistry, and ancient microbial community composition, supported by high-resolution 210Pb and AMS 14C dating, we investigated local and regional ecological and environmental changes occurring in response to changes in temperature. We find the region experienced a general warming trend over the last 3500 years, with a pronounced climate anomaly occurring between 1000 and 1600 cal yrs. BP. Shifts in vegetation took place during this warm period, characterised by a decline in alpine species and an increase in open woodland taxa which co-occurred with an increase in regional fire activity. Given the narrow altitudinal band of Australian alpine vegetation, any future warming has the potential to result in the extinction of alpine species, including several endemic to the area, as treelines are driven to higher elevations. These findings suggest ongoing conservation efforts will be needed to protect the vulnerable alpine environments from the combined threats of climate changes, fire and invasive species.Zoë A. Thomas, Scott Mooney, Haidee Cadd, Andy Baker, Chris Turney, Larissa Schneider, Alan Hogg, Simon Haberle, Ken Green, Laura S. Weyrich, Vilma Pérez, Nicole E. Moore, Atun Zawadzki i, Sarah J. Kelloway, Stuart J. Kha

International collaborative study to assess cardiovascular risk and evaluate long-term health in cats with preclinical hypertrophic cardiomyopathy and apparently healthy cats:The REVEAL Study

Background: Hypertrophic cardiomyopathy is the most prevalent heart disorder in cats and principal cause of cardiovascular morbidity and mortality. Yet, the impact of preclinical disease is unresolved. Hypothesis/Objectives: Observational study to characterize cardiovascular morbidity and survival in cats with preclinical nonobstructive (HCM) and obstructive (HOCM) hypertrophic cardiomyopathy and in apparently healthy cats (AH). Animals: One thousand seven hundred and thirty client-owned cats (430 preclinical HCM; 578 preclinical HOCM; 722 AH). Methods: Retrospective multicenter, longitudinal, cohort study. Cats from 21 countries were followed through medical record review and owner or referring veterinarian interviews. Data were analyzed to compare long-term outcomes, incidence, and risk for congestive heart failure (CHF), arterial thromboembolism (ATE), and cardiovascular death. Results: During the study period, CHF, ATE, or both occurred in 30.5% and cardiovascular death in 27.9% of 1008 HCM/HOCM cats. Risk assessed at 1, 5, and 10 years after study entry was 7.0%/3.5%, 19.9%/9.7%, and 23.9%/11.3% for CHF/ATE, and 6.7%, 22.8%, and 28.3% for cardiovascular death, respectively. There were no statistically significant differences between HOCM compared with HCM for cardiovascular morbidity or mortality, time from diagnosis to development of morbidity, or cardiovascular survival. Cats that developed cardiovascular morbidity had short survival (mean \ub1 standard deviation, 1.3 \ub1 1.7 years). Overall, prolonged longevity was recorded in a minority of preclinical HCM/HOCM cats with 10% reaching 9-15 years. Conclusions and Clinical Importance: Preclinical HCM/HOCM is a global health problem of cats that carries substantial risk for CHF, ATE, and cardiovascular death. This finding underscores the need to identify therapies and monitoring strategies that decrease morbidity and mortality

Genome modeling system: A knowledge management platform for genomics

In this work, we present the Genome Modeling System (GMS), an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395) and matched lymphoblastoid line (HCC1395BL). These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms