Francis Wilson (1939–2022): Economist and mentor

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Fulufhelo Nelwamondo: NRF’s idealistic new leader

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Forest product harvesting in the Eastern Cape, South Africa : impacts on habitat structure

CITATION: Leaver, J. & Cherry, M. I. 2020. Forest product harvesting in the Eastern Cape, South Africa : impacts on habitat structure. South African Journal of Science, 116(9/10):7508, doi:10.17159/sajs.2020/7508.The original publication is available at https://sajs.co.zaThe Eastern Cape Province harbours 46% of South Africa’s remaining indigenous forest cover, and is one of the country’s poorest and least developed provinces. Forest resources thus represent a vital component of rural livelihoods in this region. Consequently, forest management policies aim to balance the needs of resource users with the ecological integrity of forest ecosystems. In a recent study, forest bird ranges were shown to have declined in the Eastern Cape over the past 20 years, despite increases in forest cover over the same time period, indicating that habitat degradation may be driving forest bird losses. Given that harvesting of forest products represents the primary human disturbance in forests in the Eastern Cape today, insight is needed regarding the link between resource use and habitat modification. We report on effects of harvesting of three key forest products – poles, timber and medicinal bark – on habitat structure at the ground, understorey and canopy layers in indigenous forests in the province. Harvest activities had considerable impacts on habitat structure, depending on the nature and extent of harvesting. Bark and timber harvesting resulted in canopy gaps, whereas pole harvesting reduced tree density, resulting in understorey gaps. Overall, harvest activities increased the frequency of canopy disturbance, and density of understorey layer foliage. Unsustainable bark harvesting practices increased the mortality rate of canopy trees, thereby increasing dead wood availability. By providing insight into human-mediated habitat modification in forests of the Eastern Cape, this study contributes to the development of ecologically informed sustainable resource management policies.https://sajs.co.za/article/view/7508Publisher's versio

Beyond just species: is Africa the most taxonomically diverse bird continent?

We analysed avian diversity in 8 similar-sized regions of Africa, and in an additional 16 regions spread across the world; half of these 24 regions were tropical and the other half were temperate. For each region, counts of species, genus, family and order were recorded rather than only a species count. We assert that this approach gives more accurate insights into diversity patterns, as we show that in relatively species-rich parts of the world species are on average taxonomically more similar to each other than in species-poor areas. Northwestern South America is the world's most species-rich region for birds, but we show that sub-Saharan Africa has greater diversity at higher taxonomic levels and is thus arguably the richest corner of the world for birds: the Mozambique–Zimbabwe region displays the highest diversity at the order level (with 30 orders), with all other sub-Saharan regions having between 27 and 29 orders each. Northern India is also extremely diverse (surprisingly so for a marginally temperate region) at all taxonomic levels below that of order. We hope that our study might generate further analyses of avian diversity beyond the species level

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

Are Cuckoos Maximizing Egg Mimicry by Selecting Host Individuals with Better Matching Egg Phenotypes?

Background: Avian brood parasites and their hosts are involved in complex offence-defense coevolutionary arms races. The most common pair of reciprocal adaptations in these systems is egg discrimination by hosts and egg mimicry by parasites. As mimicry improves, more advanced host adaptations evolve such as decreased intra- and increased interclutch variation in egg appearance to facilitate detection of parasitic eggs. As interclutch variation increases, parasites able to choose hosts matching best their own egg phenotype should be selected, but this requires that parasites know their own egg phenotype and select host nests correspondingly. Methodology/Principal Findings: We compared egg mimicry of common cuckoo Cuculus canorus eggs in naturally parasitized marsh warbler Acrocephalus palustris nests and their nearest unparasitized conspecific neighbors having similar laying dates and nest-site characteristics. Modeling of avian vision and image analyses revealed no evidence that cuckoos parasitize nests where their eggs better match the host eggs. Cuckoo eggs were as good mimics, in terms of background and spot color, background luminance, spotting pattern and egg size, of host eggs in the nests actually exploited as those in the neighboring unparasitized nests. Conclusions/Significance: We reviewed the evidence for brood parasites selecting better-matching host egg phenotypes from several relevant studies and argue that such selection probably cannot exist in host-parasite systems where hos

Imaging in situ breast carcinoma (with or without an invasive component) with technetium-99m pentavalent dimercaptosuccinic acid and technetium-99m 2-methoxy isobutyl isonitrile scintimammography

INTRODUCTION: The aim of the study was to retrospectively define specific features of the technetium-99m pentavalent dimercaptosuccinic acid ((99m)Tc-(V)DMSA) and technetium-99m 2-methoxy isobutyl isonitrile ((99m)Tc-Sestamibi [(99m)Tc-MIBI]) distribution in ductal breast carcinoma in situ and lobular breast carcinoma in situ (DCIS/LCIS), in relation to mammographic, histological and immunohistochemical parameters. MATERIALS AND METHODS: One hundred and two patients with suspicious palpation or mammographic findings were submitted preoperatively to scintimammography (a total of 72 patients with (99m)Tc-(V)DMSA and a total of 75 patients with (99m)Tc-Sestamibi, 45 patients receiving both radiotracers). Images were acquired at 10 min and 60 min, and were evaluated for a pattern of diffuse radiotracer accumulation. The tumor-to-background ratios were correlated (T-pair test) with mammographic, histological and immunohistochemical characteristics. RESULTS: Histology confirmed malignancy in 46/102 patients: 20/46 patients had DCIS/LCIS, with or without coexistent invasive lesions, and 26/46 patients had isolated invasive carcinomas. Diffuse (99m)Tc-(V)DMSA accumulation was noticed in 18/19 cases and (99m)Tc-Sestamibi in 6/13 DCIS/LCIS cases. Epithelial hyperplasia demonstrated a similar accumulation pattern. The sensitivity, specificity, accuracy, positive predictive value and negative predictive value for each tracer were calculated. Solely for (99m)Tc-(V)DMSA, the tumor-to-background ratio was significantly higher at 60 min than at 10 min and the diffuse uptake was significantly associated with suspicious microcalcifications, with the cell proliferation index ≥ 40% and with c-erbB-2 ≥ 10%. CONCLUSION: (99m)Tc-(V)DMSA showed high sensitivity and (99m)Tc-Sestamibi showed high specificity in detecting in situ breast carcinoma ((99m)Tc-(V)DMSA especially in cases with increased cell proliferation), and these radiotracers could provide clinicians with preoperative information not always obtainable by mammography

Structure-Guided Evolution of Potent and Selective CHK1 Inhibitors through Scaffold Morphing

Pyrazolopyridine inhibitors with low micromolar potency for CHK1 and good selectivity against CHK2 were previously identified by fragment-based screening. The optimization of the pyrazolopyridines to a series of potent and CHK1-selective isoquinolines demonstrates how fragment-growing and scaffold morphing strategies arising from a structure-based understanding of CHK1 inhibitor binding can be combined to successfully progress fragment-derived hit matter to compounds with activity in vivo. The challenges of improving CHK1 potency and selectivity, addressing synthetic tractability, and achieving novelty in the crowded kinase inhibitor chemical space were tackled by multiple scaffold morphing steps, which progressed through tricyclic pyrimido[2,3-b]azaindoles to N-(pyrazin-2-yl)pyrimidin-4-amines and ultimately to imidazo[4,5-c]pyridines and isoquinolines. A potent and highly selective isoquinoline CHK1 inhibitor (SAR-020106) was identified, which potentiated the efficacies of irinotecan and gemcitabine in SW620 human colon carcinoma xenografts in nude mice

Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate

Rates of evolution differ widely among proteins, but the causes and consequences of such differences remain under debate. With the advent of high-throughput functional genomics, it is now possible to rigorously assess the genomic correlates of protein evolutionary rate. However, dissecting the correlations among evolutionary rate and these genomic features remains a major challenge. Here, we use an integrated probabilistic modeling approach to study genomic correlates of protein evolutionary rate in Saccharomyces cerevisiae. We measure and rank degrees of association between (i) an approximate measure of protein evolutionary rate with high genome coverage, and (ii) a diverse list of protein properties (sequence, structural, functional, network, and phenotypic). We observe, among many statistically significant correlations, that slowly evolving proteins tend to be regulated by more transcription factors, deficient in predicted structural disorder, involved in characteristic biological functions (such as translation), biased in amino acid composition, and are generally more abundant, more essential, and enriched for interaction partners. Many of these results are in agreement with recent studies. In addition, we assess information contribution of different subsets of these protein properties in the task of predicting slowly evolving proteins. We employ a logistic regression model on binned data that is able to account for intercorrelation, non-linearity, and heterogeneity within features. Our model considers features both individually and in natural ensembles (“meta-features”) in order to assess joint information contribution and degree of contribution independence. Meta-features based on protein abundance and amino acid composition make strong, partially independent contributions to the task of predicting slowly evolving proteins; other meta-features make additional minor contributions. The combination of all meta-features yields predictions comparable to those based on paired species comparisons, and approaching the predictive limit of optimal lineage-insensitive features. Our integrated assessment framework can be readily extended to other correlational analyses at the genome scale

Mouse TRIP13/PCH2 Is Required for Recombination and Normal Higher-Order Chromosome Structure during Meiosis

Accurate chromosome segregation during meiosis requires that homologous chromosomes pair and become physically connected so that they can orient properly on the meiosis I spindle. These connections are formed by homologous recombination closely integrated with the development of meiosis-specific, higher-order chromosome structures. The yeast Pch2 protein has emerged as an important factor with roles in both recombination and chromosome structure formation, but recent analysis suggested that TRIP13, the mouse Pch2 ortholog, is not required for the same processes. Using distinct Trip13 alleles with moderate and severe impairment of TRIP13 function, we report here that TRIP13 is required for proper synaptonemal complex formation, such that autosomal bivalents in Trip13-deficient meiocytes frequently displayed pericentric synaptic forks and other defects. In males, TRIP13 is required for efficient synapsis of the sex chromosomes and for sex body formation. Furthermore, the numbers of crossovers and chiasmata are reduced in the absence of TRIP13, and their distribution along the chromosomes is altered, suggesting a role for TRIP13 in aspects of crossover formation and/or control. Recombination defects are evident very early in meiotic prophase, soon after DSB formation. These findings provide evidence for evolutionarily conserved functions for TRIP13/Pch2 in both recombination and formation of higher order chromosome structures, and they support the hypothesis that TRIP13/Pch2 participates in coordinating these key aspects of meiotic chromosome behavior