Bioinformatics tools for analysing viral genomic data

The field of viral genomics and bioinformatics is experiencing a strong resurgence due to high-throughput sequencing (HTS) technology, which enables the rapid and cost-effective sequencing and subsequent assembly of large numbers of viral genomes. In addition, the unprecedented power of HTS technologies has enabled the analysis of intra-host viral diversity and quasispecies dynamics in relation to important biological questions on viral transmission, vaccine resistance and host jumping. HTS also enables the rapid identification of both known and potentially new viruses from field and clinical samples, thus adding new tools to the fields of viral discovery and metagenomics. Bioinformatics has been central to the rise of HTS applications because new algorithms and software tools are continually needed to process and analyse the large, complex datasets generated in this rapidly evolving area. In this paper, the authors give a brief overview of the main bioinformatics tools available for viral genomic research, with a particular emphasis on HTS technologies and their main applications. They summarise the major steps in various HTS analyses, starting with quality control of raw reads and encompassing activities ranging from consensus and de novo genome assembly to variant calling and metagenomics, as well as RNA sequencing

Writing for Comprehension: How does Writing Influence Informational Reading Comprehension in the Elementary Classroom?

This quantitative study was conducted through a school and university partnership. Data from benchmark reading assessments and writing rubrics were gathered over five weeks in a third-grade classroom in the rural mountains of the southeastern United States. Results indicate student growth in reading comprehension and writing. Findings confirm the positive correlation between reading and writing, which suggests integrating explicit reading and writing instruction supports students’ reading comprehension. Based on these findings, we suggest ways teachers can improve reading comprehension skills, blend reading and writing instruction, and pique student interest through an informational writing unit

Diabetes risk and amino acid profiles: cross-sectional and prospective analyses of ethnicity, amino acids and diabetes in a South Asian and European cohort from the SABRE (Southall And Brent REvisited) Study.

Aims/hypothesis: South Asian individuals have an increased risk of diabetes compared with Europeans that is unexplained by obesity and traditional or established metabolic measures. Circulating amino acids (AAs) may provide additional explanatory insights. In a unique cohort of European and South Asian men, we compared cross-sectional associations between AAs, metabolic and obesity traits, and longitudinal associations with incident diabetes. / Methods: Nuclear magnetic spectroscopy was used to measure the baseline (1988–1991) levels of nine AAs in serum samples from a British population-based cohort of 1,279 European and 1,007 South Asian non-diabetic men aged 40–69 years. Follow-up was complete for 19 years in 801 European and 643 South Asian participants. / Results: The serum concentrations of isoleucine, phenylalanine, tyrosine and alanine were significantly higher in South Asian men, while cross-sectional correlations of AAs with glycaemia and insulin resistance were similar in the two ethnic groups. However, most AAs were less strongly correlated with measures of obesity in the South Asian participants. Diabetes developed in 227 (35%) South Asian and 113 (14%) European men. Stronger adverse associations were observed between branched chain and aromatic AAs and incident diabetes in South Asian men. Tyrosine was a particularly strong predictor of incident diabetes in South Asian individuals, even after adjustment for metabolic risk factors, including obesity and insulin resistance (adjusted OR for a 1 SD increment, 1.47, 95% CI 1.17,1.85, p = 0.001) compared with Europeans (OR 1.10, 0.87, 1.39, p = 0.4; p = 0.045 for ethnicity × tyrosine interaction). / Conclusions/interpretation: Branched chain and aromatic AAs, particularly tyrosine, may be a focus for identifying novel aetiological mechanisms and potential treatment targets for diabetes in South Asian populations and may contribute to their excess risk of diabetes

Why HIV Positive Patients on Antiretroviral Treatment and/or Cotrimoxazole Prophylaxis Use Traditional Medicine: Perceptions of Health Workers, Traditional Healers and Patients: A Study in Two Provinces of South Africa

The study explored the perceptions, knowledge and attitudes of patients, health workers and traditional healers about the use of traditional medicine and Anti Retroviral Therapy (ART). The study explored the perceptions, knowledge and attitudes of patients, health workers and traditional healers about the use of traditional medicine and Anti Retroviral Therapy (ART), using an exploratory qualitative design in two provinces of South Africa: an urban township health facility in the Western Cape, and a rural district hospital in KwaZulu-Natal (KZN) with antennal HIV rate of 32% and 28%’respectively. In-depth interviews were conducted with 14 participants: six HIV patients on ART and using Traditional Medicine(TM), two doctors, two nurses and four traditional healers. Two focus group discussions - one at each site - were held with community health workers who work with HIV-positive patients (Western Cape [5] and in KZN [4]). Patient said to have used Traditional Healing Practices (THP) before they were diagnosed with HIV, and some who have been diagnosed with HIV continue using TM in conjunction with ART and/or Cotrimoxazole prophylaxis. Patients preferred not to disclose THP to health professionals because of lack of support and understanding. Patients utilize THP because of family expectations, privacy and confidentiality, especially when they have not disclosed their HIV status. Healthcare professionals had strong negative opinions about THP, especially for HIV-positive patients. Traditional healers supported the patient’s rationale for THP use. This study revealed a need to better understand factors involved in patients’ choosing to use THP concurrently with ART

Cellular Therapy for Fanconi Anemia: The Past, Present, and Future

Allogeneic hematopoietic cell transplantation (HCT) remains the only proven curative therapy for the hematologic manifestation of Fanconi anemia (FA). Over the past 2 decades, major advances have been made such that transplant outcomes have markedly improved. With the development of in vitro fertilization and preimplantation genetic diagnosis, HLA-matched sibling donor umbilical blood transplantation may be an option for more patients with FA. Recently, the use of pluripotent stem cells has been explored as a novel approach to model the hematopoietic developmental defects in FA, and to provide a potential source of autologous stem cells that can be genetically manipulated and used to generate corrected hematopoietic progenitors

Probing Distant Massive Black Holes with LISA

Idealized models are used to illustrate the potential of the Laser Interferometer Space Antenna (LISA) as a probe of the largely unknown population of cosmologically-distant Massive Black Holes (MBHs) and as a tool to measure their masses with unprecedented accuracy. The models suggest that LISA will most efficiently probe a MBH population of lower mass than the one found in bright quasars and nearby galactic nuclei. The mass spectrum of these MBHs could constrain formation scenarios for high-redshift, low-mass galaxies.Comment: 8 pages, 5 figures, accepted for publication in Class. Quant. Gravity (4th LISA Symposium Special Issue

Metagenomic approaches reveal differences in genetic diversity and relative abundance of nitrifying bacteria and archaea in contrasting soils

The abundance and phylogenetic diversity of functional genes involved in nitrification were assessed in Rothamsted soils under contrasting management regimes - permanent bare fallow, grassland and arable (wheat) cultivation maintained for more than 50 years. Metagenome and metatranscriptome analysis indicated that nitrite oxidizing bacteria (NOB) were more abundant than ammonia oxidizing archaea (AOA) and bacteria (AOB) in all soils. The most abundant AOA and AOB in the metagenomes were, respectively, Nitrososphaera and Ca. Nitrososcosmicus (family Nitrososphaeraceae) and Nitrosospira and Nitrosomonas (family Nitrosomonadaceae). The most abundant NOB were Nitrospira including the comammox species Nitrospira inopinata, Ca. N. nitrificans and Ca. N. nitrosa. Anammox bacteria were also detected. Nitrospira and the AOA Nitrososphaeraceae showed most transcriptional activity in arable soil. Similar numbers of sequences were assigned to the amoA genes of AOA and AOB, highest in the arable soil metagenome and metatranscriptome. The AOB amoA reads included those from comammox Nitrospira clades A and B, in addition to Nitrosomonadaceae. Nitrification potential assessed in soils amended or not with DCD (an inhibitor of AOB but not AOA) was highest in arable soils and lower in all soil microcosm assays containing DCD, indicating AOB were responsible for oxidizing ammonium fertilizer added to these soils

VALES: IV. Exploring the transition of star formation efficiencies between normal and starburst galaxies using APEX/SEPIA Band-5 and ALMA at low redshift

In this work we present new APEX/SEPIA Band-5 observations targeting the CO ($J=2\text{-}1$) emission line of 24 Herschel-detected galaxies at $z=0.1-0.2$. Combining this sample {with} our recent new Valpara\'iso ALMA Line Emission Survey (VALES), we investigate the star formation efficiencies (SFEs = SFR/$M_{\rm H_{2}}$) of galaxies at low redshift. We find the SFE of our sample bridges the gap between normal star-forming galaxies and Ultra-Luminous Infrared Galaxies (ULIRGs), which are thought to be triggered by different star formation modes. Considering the $\rm SFE'$ as the SFR and the $L'_{\rm CO}$ ratio, our data show a continuous and smooth increment as a function of infrared luminosity (or star formation rate) with a scatter about 0.5 dex, instead of a steep jump with a bimodal behaviour. This result is due to the use of a sample with a much larger range of sSFR/sSFR$_{\rm ms}$ using LIRGs, with luminosities covering the range between normal and ULIRGs. We conclude that the main parameters controlling the scatter of the SFE in star-forming galaxies are the systematic uncertainty of the $\alpha_{\rm CO}$ conversion factor, the gas fraction and physical size.Comment: 9pages, 7 figures, 1 table, accepted for publication in MNRA