Thresholds for adding degraded tropical forest to the conservation estate

Logged and disturbed forests are often viewed as degraded and depauperate environments compared with primary forest. However, they are dynamic ecosystems1 that provide refugia for large amounts of biodiversity2,3, so we cannot afford to underestimate their conservation value4. Here we present empirically defined thresholds for categorizing the conservation value of logged forests, using one of the most comprehensive assessments of taxon responses to habitat degradation in any tropical forest environment. We analysed the impact of logging intensity on the individual occurrence patterns of 1,681 taxa belonging to 86 taxonomic orders and 126 functional groups in Sabah, Malaysia. Our results demonstrate the existence of two conservation-relevant thresholds. First, lightly logged forests (68%) of their biomass removed, and these are likely to require more expensive measures to recover their biodiversity value. Overall, our data confirm that primary forests are irreplaceable5, but they also reinforce the message that logged forests retain considerable conservation value that should not be overlooked

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Effect of installing columns from different solid waste materials on the soft clay bearing capacity

Soft clay deposits cause many problems due to low bearing capacity and high deformation. This paper presents the results of laboratory model tests for studying the improvement of soft clay-bearing capacity using two kinds of soil columns, the first is slag-cement dust columns and the second is bentonite column. Three columns from SCC (slag-cement dust columns) encased by Woven Geotextile are installed beneath a steel plate representing a footing. Four bentonite Columns (BC) encased with non-woven geotextile are installed around the steel plate at a distance of 1 B, where B is steel plate width. The research aims to assess the increase in the SCC length effect on clay-bearing capacity. A series of 4 experimental tests were performed. The results show that, the clay bearing capacity increased with the increase of column length because slag and bentonite can absorb the clay water content, leading to an increase clay shear strength. Floating columns gives better improvement than the end bearing columns. The slag partially replaced with cement dust is weak enough to transfer the total applied stress to a strong soil layer

Intraspecific and interspecific pre-adult competition on the neotropical region colonizer Zaprionus indianus (Diptera: Drosophilidae) under laboratory conditions Competição pré-adulta intra e interespecífica, em Zaprionus indianus (Diptera: Drosophilidae), espécie colonizadora da região neotropical, sob condições laboratoriais

This study analyzes the pre-adult interactions of Zaprionus indianus, a recently-introduced species in Brazil, with two others Drosophilidae under laboratory conditions. The effects of larval residues on the viability and on the developmental time of Z. indianus, Drosophila simulans and D. sturtevanti were used to evaluate pre-adult competitive interactions, conditioning the culture medium with larval residues. Pre-adult interactions between Z. indianus, D. sturtevanti and D. simulans may affect their relative abundance over time, since the viability of Z. indianus was negatively affected by residues of D. sturtevanti, and its residues reduced the viability of D. simulans and the developmental time of both D. simulans and D. sturtevanti.<br>Este estudo é uma análise das interações pré-adultas, sob condições laboratoriais, da mosca-do-figo Zaprionus indianus, espécie recentemente introduzida no Brasil, com dois outros drosofilídeos. A interferência de meio de cultura, acrescido de resíduos larvais, sobre a viabilidade e o tempo de desenvolvimento de Z. indianus, Drosophila simulans e D. sturtevanti foi utilizada para avaliar as interações competitivas pré-adultas. As interações pré-adultas entre Z. indianus, D. sturtevanti e D. simulans podem afetar sua abundância relativa ao longo do tempo, pois a viabilidade de Z. indianus foi negativamente afetada por resíduos de D. sturtevanti; os resíduos da mosca-do-figo reduziram a viabilidade de D. simulans e o tempo de desenvolvimento tanto de D. simulans como de D. sturtevanti

AHDC1 missense mutations in Xia-Gibbs syndrome

Xia-Gibbs syndrome (XGS; MIM: 615829) is a phenotypically heterogeneous neurodevelopmental disorder (NDD) caused by newly arising mutations in the AT-Hook DNA-Binding Motif-Containing 1 (AHDC1) gene that are predicted to lead to truncated AHDC1 protein synthesis. More than 270 individuals have been diagnosed with XGS worldwide. Despite the absence of an independent assay for AHDC1 protein function to corroborate potential functional consequences of rare variant genetic findings, there are also reports of individuals with XGS-like trait manifestations who have de novo missense AHDC1 mutations and who have been provided a molecular diagnosis of the disorder. To investigate a potential contribution of missense mutations to XGS, we mapped the missense mutations from 10 such individuals to the AHDC1 conserved protein domain structure and detailed the observed phenotypes. Five newly identified individuals were ascertained from a local XGS Registry, and an additional five were taken from external reports or databases, including one publication. Where clinical data were available, individuals with missense mutations all displayed phenotypes consistent with those observed in individuals with AHDC1 truncating mutations, including delayed motor milestones, intellectual disability (ID), hypotonia, and speech delay. A subset of the 10 reported missense mutations cluster in two regions of the AHDC1 protein with known conserved domains, likely representing functional motifs. Variants outside the clustered regions score lower for computational prediction of their likely damaging effects. Overall, de novo missense variants in AHDC1 are likely diagnostic of XGS when in silico analysis of their position relative to conserved regions is considered together with disease trait manifestations.Genetics of disease, diagnosis and treatmen

AHDC1 missense mutations in Xia-Gibbs syndrome

Xia-Gibbs syndrome (XGS; MIM: 615829) is a phenotypically heterogeneous neurodevelopmental disorder (NDD) caused by newly arising mutations in the AT-Hook DNA-Binding Motif-Containing 1 (AHDC1) gene that are predicted to lead to truncated AHDC1 protein synthesis. More than 270 individuals have been diagnosed with XGS worldwide. Despite the absence of an independent assay for AHDC1 protein function to corroborate potential functional consequences of rare variant genetic findings, there are also reports of individuals with XGS-like trait manifestations who have de novo missense AHDC1 mutations and who have been provided a molecular diagnosis of the disorder. To investigate a potential contribution of missense mutations to XGS, we mapped the missense mutations from 10 such individuals to the AHDC1 conserved protein domain structure and detailed the observed phenotypes. Five newly identified individuals were ascertained from a local XGS Registry, and an additional five were taken from external reports or databases, including one publication. Where clinical data were available, individuals with missense mutations all displayed phenotypes consistent with those observed in individuals with AHDC1 truncating mutations, including delayed motor milestones, intellectual disability (ID), hypotonia, and speech delay. A subset of the 10 reported missense mutations cluster in two regions of the AHDC1 protein with known conserved domains, likely representing functional motifs. Variants outside the clustered regions score lower for computational prediction of their likely damaging effects. Overall, de novo missense variants in AHDC1 are likely diagnostic of XGS when in silico analysis of their position relative to conserved regions is considered together with disease trait manifestations