DNA barcoding and molecular taxonomy of dark-footed forest shrew Myosorex cafer in the Eastern Cape and KwaZulu-Natal, South Africa

CITATION: Matamba, Emmanuel et al. 2020. DNA barcoding and molecular taxonomy of dark-footed forest shrew Myosorex cafer in the Eastern Cape and KwaZulu-Natal, South Africa. Vertebrate Zoology, 70(4):667, doi:10.26049/VZ70-4-2020-08.The original article is available at: https://www.researchgate.netThere is a paucity of molecular DNA barcoding informatics on the South African fauna, particularly on terrestrial small mammals. This study tested the utility of DNA barcoding in the dark-footed forest shrew (Myosorex cafer) from forested regions of the Eastern Cape and KwaZulu-Natal provinces of South Africa. Sampled forests included coastal scarp, dune forests and inland Afromontane mistbelt forests. Sequences of mtDNA cytochrome oxidase subunit I (COI, 623 bp), were generated for a total of 78 specimens representing Myosorex cafer (n = 72), Myosorex varius (n = 2), Crocidura cyanea (n = 2) and C. mariquensis (n = 2). Due to the fragmented nature of these forests, we also investigated the cranial morphology of Myosorex cafer, which is strictly confined to forests. Analyses of sequence data produced phylogenetic trees that were consistent with morphological identifications. Genetic data suggest that the movement of these animals between other forest types and the Amatole mistbelt forests has been restricted, as they are too far west of scarp forests to have been recolonized by them. This is the first study that supplies COI sequences of a South African Myosorex species, thus increasing the availability of DNA barcodes of South African small mammals on BOLD.Publisher's versio

Electron Tunneling through Pseudomonas aeruginosa Azurins on SAM Gold Electrodes

Robust voltammetric responses were obtained for wild-type and Y72F/H83Q/Q107H/Y108F azurins adsorbed on CH_3(CH_2)_nSH:HO(CH_2)_mSH (n=m=4,6,8,11; n=13,15 m=11) self-assembled monolayer (SAM) gold electrodes in acidic solution (pH 4.6) at high ionic strengths. Electron-transfer (ET) rates do not vary substantially with ionic strength, suggesting that the SAM methyl headgroup binds to azurin by hydrophobic interactions. The voltammetric responses for both proteins at higher pH values (>4.6 to 11) also were strong. A binding model in which the SAM hydroxyl headgroup interacts with the Asn47 carboxamide accounts for the relatively strong coupling to the copper center that can be inferred from the ET rates. Of particular interest is the finding that rate constants for electron tunneling through n = 8, 13 SAMs are higher at pH 11 than those at pH 4.6, possibly owing to enhanced coupling of the SAM to Asn 47 caused by deprotonation of nearby surface residues

Morphology and stable isotope analysis demonstrate different structuring of bat communities in rainforest and savannah habitats

Bats play important ecological roles in tropical systems, yet how these communities are structured is still poorly understood. Our study explores the structure of African bat communities using morphological characters to define the morphospace occupied by these bats and stable isotope analysis to define their dietary niche breadth. We compared two communities, one in rainforest (Liberia) and one in savannah (South Africa), and asked whether the greater richness in the rainforest was due to more species ‘packing’ into the same morphospace and trophic space than bats from the savannah, or some other arrangement. In the rainforest, bats occupied a larger area in morphospace and species packing was higher than in the savannah; although this difference disappeared when comparing insectivorous bats only. There were also differences in morphospace occupied by different foraging groups (aerial, edge, clutter and fruitbat). Stable isotope analysis revealed that the range of d13C values was almost double in rainforest than in savannah indicating a greater range of utilization of basal C3 and C4 resources in the former site, covering primary productivity from both these sources. The ranges in d15N, however, were similar between the two habitats suggesting a similar number of trophic levels. Niche breadth, as defined by either standard ellipse area or convex hull, was greater for the bat community in rainforest than in savannah, with all four foraging groups having larger niche breadths in the former than the latter. The higher inter-species morphospace and niche breadth in forest bats suggest that species packing is not necessarily competitive. By employing morphometrics and stable isotope analysis, we have shown that the rainforest bat community packs more species in morphospace and uses a larger niche breadth than the one in savannah.This work was financially supported in part by the National Research Foundation (NRF) of South Africa: the Sarchi Chair held by P.T. ArcelorMittal Liberia funded A.M.’s work at Mount Nimba.http://rsos.royalsocietypublishing.orgam2019Mammal Research InstituteZoology and Entomolog

Genetic information: important but not "exceptional"

Much legislation dealing with the uses of genetic information could be criticised for exceptionalising genetic information over other types of information personal to the individual. This paper contends that genetic exceptionalism clouds the issues, and precludes any real debate about the appropriate uses of genetic information. An alternative to “genetically exceptionalist” legislation is to “legislate for fairness”. This paper explores the “legislating for fairness” approach, and concludes that it demonstrates a fundamental misunderstanding of both how legislation is drafted, and how it is interpreted. The uncomfortable conclusion is this: policy-makers and legislators must tackle head-on the difficult policy questions concerning what should and should not be done with genetic information. Only by confronting this crucial issue will they achieve a workable legislative solution to the problems caused by genetic information

Decision making and experiences of young adults undergoing presymptomatic genetic testing for familial cancer: A longitudinal grounded theory study

Enabling informed choice is an essential component of care when offering young adults presymptomatic testing for a genetic condition. A systematic review on this topic revealed that many young adults grew up with little information regarding their genetic risk and that parents had applied pressure to them during the testing decision-making process. However, none of the studies retrieved were conducted in South European countries. To address this gap, we undertook a qualitative study based on grounded theory to explore the psychosocial implications of presymptomatic testing for hereditary cancer in Italian young adults aged 18-30 years. Interviews were conducted on three occasions: 1 month before counselling, and 2 weeks and 6 months after results. Data were coded and grouped under themes. A total of 42 interviews were conducted. Four themes emerged: knowledge, genetic counselling process, decision making and dealing with test results. Although participants grew up with little or no information about their genetic risk, none expressed regret at having the test at a young age. Pre-test counselling was appreciated as a source of information, rather than support for decision making. Decisions were often made autonomously and sometimes conflicted with parents' wishes. Participants reported no changes in health behaviours after testing. This evidence highlights the need for a comprehensive, longitudinal counselling process with appropriate timing and setting, which supports 'parent-to-offspring' risk communication first and decision making by young adults about presymptomatic testing and risk management afterwards. In conclusion, it is clear that counselling approaches for presymptomatic testing may require modification both for young adults and their parents. © 2017 European Society of Human Genetics

Presymptomatic genetic testing for hereditary cancer in young adults: a survey of young adults and parents

Presymptomatic testing for hereditary cancer syndromes should involve a considered choice. This may be particularly challenging when testing is undertaken in early adulthood. With the aim of exploring the psychosocial implications of presymptomatic testing for hereditary cancer in young adults and their parents, a cross-sectional survey was designed. Two questionnaires were developed (one for young adults who had considered presymptomatic testing, one for parents). Questionnaires were completed by 152 (65.2%) young adults and 42 (73.7%) parents. Data were analysed using descriptive statistics, inferential testing, and exploratory factor analysis and linear regression analysis. Young adults were told about their potential genetic risk at a mean age of 20 years; in most cases, information was given by a parent, often in an unplanned conversation. Although testing requests were usually made by young adults, the majority of parents felt they had control over the young adult’s decision and all felt their children should be tested. Results suggest that some young adults did not understand the implications of the genetic test but complied with parental pressure. Counselling approaches for presymptomatic testing may require modification both for young adults and their parents. Those offering testing need to be aware of the complex pressures that young adults can experience, which can influence their autonomous choices. It is therefore important to emphasise to both parents and young adults that, although testing can bring benefits in terms of surveillance and prevention, young adults have a choice

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN