Lycium strandveldense (Solanaceae), a new species from the western coast of South Africa

A new species, L. strandveldense, from the western coastal region of the Western and Northern Cape Provinces, is described and figured. L. strandveldense, which is functionally dioecious, resembles the bisexual L. afrum L., a species also found along the western coast. Because of the near similarity in leaf and floral characteristics, specimens of L. strandveldense have in the past been regarded as atypical forms of L. afrum. This new species is distinguished by its functionally dioecious habit, relatively short, narrowly oblong, bright green leaves instead of the long, linear, glaucous leaves of L. afrum, corolla dark purple instead of claret coloured, corolla tube shorter than in L. afrum, stamens of the male flowers slightly exserted from corolla mouth in contrast to the included stamens of L. afrum, and finally a smaller ellipsoid red berry instead of the large spherical black berry of L. afrum

Microbial metagenome of urinary tract infection.

Urine culture and microscopy techniques are used to profile the bacterial species present in urinary tract infections. To gain insight into the urinary flora, we analyzed clinical laboratory features and the microbial metagenome of 121 clean-catch urine samples. 16S rDNA gene signatures were successfully obtained for 116 participants, while metagenome sequencing data was successfully generated for samples from 49 participants. Although 16S rDNA sequencing was more sensitive, metagenome sequencing allowed for a more comprehensive and unbiased representation of the microbial flora, including eukarya and viral pathogens, and of bacterial virulence factors. Urine samples positive by metagenome sequencing contained a plethora of bacterial (median 41 genera/sample), eukarya (median 2 species/sample) and viral sequences (median 3 viruses/sample). Genomic analyses suggested cases of infection with potential pathogens that are often missed during routine urine culture due to species specific growth requirements. While conventional microbiological methods are inadequate to identify a large diversity of microbial species that are present in urine, genomic approaches appear to more comprehensively and quantitatively describe the urinary microbiome

Profound Perturbation of the Metabolome in Obesity Is Associated with Health Risk.

Obesity is a heterogeneous phenotype that is crudely measured by body mass index (BMI). There is a need for a more precise yet portable method of phenotyping and categorizing risk in large numbers of people with obesity to advance clinical care and drug development. Here, we used non-targeted metabolomics and whole-genome sequencing to identify metabolic and genetic signatures of obesity. We find that obesity results in profound perturbation of the metabolome; nearly a third of the assayed metabolites associated with changes in BMI. A metabolome signature identifies the healthy obese and lean individuals with abnormal metabolomes-these groups differ in health outcomes and underlying genetic risk. Specifically, an abnormal metabolome associated with a 2- to 5-fold increase in cardiovascular events when comparing individuals who were matched for BMI but had opposing metabolome signatures. Because metabolome profiling identifies clinically meaningful heterogeneity in obesity, this approach could help select patients for clinical trials

No major flaws in "Identification of individuals by trait prediction using whole-genome sequencing data"

In a recently published PNAS article, we studied the identifiability of genomic samples using machine learning methods [Lippert et al., 2017]. In a response, Erlich [2017] argued that our work contained major flaws. The main technical critique of Erlich [2017] builds on a simulation experiment that shows that our proposed algorithm, which uses only a genomic sample for identification, performed no better than a strategy that uses demographic variables. Below, we show why this comparison is misleading and provide a detailed discussion of the key critical points in our analyses that have been brought up in Erlich [2017] and in the media. Further, not only faces may be derived from DNA, but a wide range of phenotypes and demographic variables. In this light, the main contribution of Lippert et al. [2017] is an algorithm that identifies genomes of individuals by combining multiple DNA-based predictive models for a myriad of traits

Pharmacist-initiated management of antiretroviral therapy (PIMART)

We the undersigned, a collective of pharmacy researchers, practitioners and academics, call on the Minister to consider the following points in response to the input made by the South African Medical Association (SAMA) in relation to pharmacist-initiated management of antiretroviral therapy (PIMART), dated 9 September 2021. We wish to highlight the expertise of pharmacists in all matters relating to the design, production and use of quality, safe and affordable medicines. Furthermore, we need to stress the increasing importance of and role played by pharmacists in primary care teams, which has been further reinforced during the COVID-19 pandemic and subsequent vaccination efforts.http://www.samj.org.zamv2022Pharmacolog

Modification of forests by people means only 40% of remaining forests have high ecosystem integrity

Many global environmental agendas, including halting biodiversity loss, reversing land degradation, and limiting climate change, depend upon retaining forests with high ecological integrity, yet the scale and degree of forest modification remain poorly quantified and mapped. By integrating data on observed and inferred human pressures and an index of lost connectivity, we generate a globally consistent, continuous index of forest condition as determined by the degree of anthropogenic modification. Globally, only 17.4 million km2 of forest (40.5%) has high landscape-level integrity (mostly found in Canada, Russia, the Amazon, Central Africa, and New Guinea) and only 27% of this area is found in nationally designated protected areas. Of the forest inside protected areas, only 56% has high landscape-level integrity. Ambitious policies that prioritize the retention of forest integrity, especially in the most intact areas, are now urgently needed alongside current efforts aimed at halting deforestation and restoring the integrity of forests globally

Cancer Genome Sequencing and Its Implications for Personalized Cancer Vaccines

New DNA sequencing platforms have revolutionized human genome sequencing. The dramatic advances in genome sequencing technologies predict that the $1,000 genome will become a reality within the next few years. Applied to cancer, the availability of cancer genome sequences permits real-time decision-making with the potential to affect diagnosis, prognosis, and treatment, and has opened the door towards personalized medicine. A promising strategy is the identification of mutated tumor antigens, and the design of personalized cancer vaccines. Supporting this notion are preliminary analyses of the epitope landscape in breast cancer suggesting that individual tumors express significant numbers of novel antigens to the immune system that can be specifically targeted through cancer vaccines

Effects of 59Fe, 65Zn and of three soil types on dry matter yield, chemical composition and nitrogen fixation in Phaseolus vulgaris L. cv. carioca

The aim of this work was to study in greenhouse conditions the effects of two levels of iron and zinc on yield and chemical composition of common bean (Phaseolus vulgaris L.) and on atmospheric nitrogen fixation, in three soils, classified as Terra Roxa Estruturada (TRE), Latossol Vermelho Escuro (LVE), and Podzolico Vermelho Amarelo (PVA). The coefficient of utilization of these micronutrients by this crop and its distribution in above-ground parts and roots were also assessed. The rates for iron were 1.5 and 3.0 ppm, and for zinc, 2.5 and 5.0 ppm. It was applied 7.5 µCi of 59Fe/kg of soil with the lower rate of the stable iron, and 5.0 and 10.0 µCi of Zn/kg of soil in the pots corresponding to the lower and higher rate of the stable zinc, respectively. The plants were harveste at the age of 60 days and nitrogen, phosphorus, potassium, iron and zinc contents were determined. Immediately after harvest, symbiotic nitrogen fixation was assessed, using the acetylene reduction method. The detection of 59Fe and 65zn radioactivity were carried out on nitric percloric extract, by gamma ray spectrometry. The behavior of common bean presented high variation among the three soils, for all the variables. There was no influence of treatments of iron and zinc on dry matter of above ground part and root and also on the weight and number of nodules. The rate of 3.0 ppm of iron decreased the capacity of nodules to fix atmospheric nitrogen in relation to rate of 1.5 ppm, while the rate of 5.0 ppm of zinc increased this capacity, in relation to the rate of 2.5 ppm. There was significative effect of treatments on nitrogen, potassium and zinc contents in above ground part and on nitrogen and zinc contents in the root. The absorption of zinc from the fertilizer and the percentagem of zinc in the plant derived from fertilizer were diretly influenced by rate of zinc The higher coefficient of utilization of zinc from the fertilizer was 4.0%.No presente trabalho, conduzido em casa de vegetação, procuramos estudar os efeitos dos micronutrientes ferro e zinco na produção de materia seca, composição química do feijoeiro (Phaseolus vulgaris L.) e na fixação do nitrogênio atmosférico, em três solos, classificados como Terra Roxa Estruturada (TRE), Latossol Vermelho Escuro (LVE) e Podzólico Vermelho Amarelo (PVA). Procuramos também determinar os índices de aproveitamento destes micronutrientes pelo feijoeiro e sua distribuição na parte aérea e na raiz. O delineamento experimental foi um fatorial 3x7, sendo três solos e sete tratamentos por solo, com três repetições. Nos tratamentos, foram utilizados duas doses de ferro e duas doses de zinco em separado ou combinando as doses menores e maiores destes micronutrientes (Fe1Zn1, Fe2Zn2). As doses de ferro foram 1,5 e 3,0 ppm e as de zinco foram 2,5 e 5,0 ppm. Foram aplicados 7,5 µCi de 59Fe/kg de solo nos vasos correspondentes à dose menor de ferro e 5,0 e 10,0 µCi de 65Zn/kg de solo nos vasos correspondentes respectivamente à dose menor e maior de zinco. Todos os tratamentos receberam uma adubação básica. O comportamento do feijoeiro apresentou grande variação entre os três tipos de solos, para todas as variáveis. Não houve influência dos tratamentos de ferro e zinco na produção de parte aérea e raiz e nem no peso e numero dos nodulos. A dose de 3,0 ppm de ferro diminuiu a capacidade dos nódulos de fixarem nitrogênio atmosférico em relação à dose de 1,5 ppm enquanto que a dose de 5,0 ppm de zinco aumentou esta capacidade, em relação à dose de 2,5 ppm. Houve um efeito significativo dos tratamentos na concentração de nitrogênio, potássio, ferro e zinco na parte aérea e na concentração de nitrogênio, e zinco na raiz. A absorção de zinco dos fertilizantes e a percentagem do zinco na planta proveniente do adubo foram influenciadas diretamente pelas doses de zinco. O maior coeficiente de aproveitamento do zinco do adubo foi de 4,0%

Phylogenomic analysis of a 55.1 kb 19-gene dataset resolves a monophyletic Fusarium that includes the Fusarium solani Species Complex

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user¿s needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option availabl