Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation

Simple Summary Abigar cattle, native to southwestern Ethiopia's hot and humid environment, are recognized for their adaptability and vital contribution to local livelihoods and the livestock value chain. Investigating their genetic basis for adaptive traits is crucial for sustainable use. However, there is a paucity of studies on genomic diversity, population structure, and selection signatures of Abigar cattle. This study introduces the first whole-genome sequencing of Abigar cattle, revealing genes linked to heat tolerance, immune response, and stress resilience in tropical conditions. These findings offer essential genomic insights for future Abigar cattle breeding.Abstract Over time, indigenous cattle breeds have developed disease resistance, heat tolerance, and adaptability to harsh environments. Deciphering the genetic mechanisms underlying adaptive traits is crucial for their improvement and sustainable utilization. For the first time, we performed whole-genome sequencing to unveil the genomic diversity, population structure, and selection signatures of Abigar cattle living in a tropical environment. The population structure analysis revealed that Abigar cattle exhibit high nucleotide diversity and heterozygosity, with low runs of homozygosity and linkage disequilibrium, suggesting a genetic landscape less constrained by inbreeding and enriched by diversity. Using nucleotide diversity (Pi) and population differentiation (FST) selection scan methods, we identified 83 shared genes that are likely associated with tropical adaption. The functional annotation analysis revealed that some of these genes are potentially linked to heat tolerance (HOXC13, DNAJC18, and RXFP2), immune response (IRAK3, MZB1, and STING1), and oxidative stress response (SLC23A1). Given the wider spreading impacts of climate change on cattle production, understanding the genetic mechanisms of adaptation of local breeds becomes crucial to better respond to climate and environmental changes. In this context, our finding establishes a foundation for further research into the mechanisms underpinning cattle adaptation to tropical environments

Whole Genome Scan Uncovers Candidate Genes Related to Milk Production Traits in Barka Cattle

In this study, our primary aim was to explore the genomic landscape of Barka cattle, a breed recognized for high milk production in a semi-arid environment, by focusing on genes with known roles in milk production traits. We employed genome-wide analysis and three selective sweep detection methods (ZFST, theta pi ratio, and ZHp) to identify candidate genes associated with milk production and composition traits. Notably, ACAA1, P4HTM, and SLC4A4 were consistently identified by all methods. Functional annotation highlighted their roles in crucial biological processes such as fatty acid metabolism, mammary gland development, and milk protein synthesis. These findings contribute to understanding the genetic basis of milk production in Barka cattle, presenting opportunities for enhancing dairy cattle production in tropical climates. Further validation through genome-wide association studies and transcriptomic analyses is essential to fully exploit these candidate genes for selective breeding and genetic improvement in tropical dairy cattle

A role for human N-alpha acetyltransferase 30 (Naa30) in maintaining mitochondrial integrity

N-terminal acetylation (Nt-acetylation) by N-terminal acetyltransferases (NATs) is one of the most common protein modifications in eukaryotes. The NatC complex represents one of three major NATs of which the substrate profile remains largely unexplored. Here, we defined the in vivo human NatC Nt-acetylome on a proteome-wide scale by combining knockdown of its catalytic subunit Naa30 with positional proteomics. We identified 46 human NatC substrates, expanding our current knowledge on the substrate repertoire of NatC which now includes proteins harboring Met-Leu, Met-Ile, Met-Phe, Met-Trp, Met-Val, Met-Met, Met-His and Met-Lys N termini. Upon Naa30 depletion the expression levels of several organellar proteins were found reduced, in particular mitochondrial proteins, some of which were found to be NatC substrates. Interestingly, knockdown of Naa30 induced the loss of mitochondrial membrane potential and fragmentation of mitochondria. In conclusion, NatC N-tacetylates a large variety of proteins and is essential for mitochondrial integrity and function

EpiCass And CassavaNet4Dev Advanced Bioinformatics Workshop

EpiCass and CassavaNet4Dev are collaborative projects funded by the Swedish Research Council between the Swedish University of Agriculture (SLU) and the International Institute of Tropical Agriculture (IITA). The projects aim to investigate the influence of epigenetic changes on agricultural traits such as yield and virus resistance while also providing African students and researchers with advanced bioinformatics training and opportunities to participate in big data analysis events. The first advanced bioinformatics training workshop took place from May 16th to May 18th, 2022, followed by an online mini-symposium titled “Epigenetics and crop improvement” on May 19th. The symposium featured international speakers covering a wide range of topics related to plant epigenetics, cassava viral diseases, and cassava breeding strategies. A new online and on-site teaching model was developed for the three-day workshop to ensure maximum student participation across Western, Eastern, and Southern Africa. Initially planned in Nigeria, Kenya, Ethiopia, Tanzania, and Zambia, the workshop ultimately focused on Nigeria, Kenya, and Ethiopia due to a lack of qualified candidates in the other countries. Each classroom hosted 20 to 25 students, with at least one bioinformatician present for support. The classrooms were connected via video conferencing, whereas teachers located in different places in Africa and Europe joined the video stream to conduct teaching sessions. The workshop was divided into theoretical classes and hands-on sessions, where participants could run data analysis with support from online teachers and local bioinformaticians. To enable participants to run guided, CPU and RAM-intensive data analysis workflows and overcome local computing and internet access restrictions, a system of virtual machines (VMs) hosted in the cloud was developed. The teaching platform provided teaching and exercise materials to support the use of the VMs. Some students could not run heavy data analysis workflows due to unforeseen restrictions in the cloud. Currently, these issues have been solved and in the future all participants will have the opportunity to run the analysis steps independently in the cloud using the protocols hosted on the teaching platform

Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation

Over time, indigenous cattle breeds have developed disease resistance, heat tolerance, and adaptability to harsh environments. Deciphering the genetic mechanisms underlying adaptive traits is crucial for their improvement and sustainable utilization. For the first time, we performed whole-genome sequencing to unveil the genomic diversity, population structure, and selection signatures of Abigar cattle living in a tropical environment. The population structure analysis revealed that Abigar cattle exhibit high nucleotide diversity and heterozygosity, with low runs of homozygosity and linkage disequilibrium, suggesting a genetic landscape less constrained by inbreeding and enriched by diversity. Using nucleotide diversity (Pi) and population differentiation (FST) selection scan methods, we identified 83 shared genes that are likely associated with tropical adaption. The functional annotation analysis revealed that some of these genes are potentially linked to heat tolerance (HOXC13, DNAJC18, and RXFP2), immune response (IRAK3, MZB1, and STING1), and oxidative stress response (SLC23A1). Given the wider spreading impacts of climate change on cattle production, understanding the genetic mechanisms of adaptation of local breeds becomes crucial to better respond to climate and environmental changes. In this context, our finding establishes a foundation for further research into the mechanisms underpinning cattle adaptation to tropical environments.</p

Inhibition of T-tropic HIV Strains by Selective Antagonization of the Chemokine Receptor CXCR4

Bicyclams are a novel class of antiviral compounds that are highly potent and selective inhibitors of the replication of HIV-1 and HIV-2. Surprisingly, however, when the prototype compound AMD3100 was tested against M-tropic virus strains such as BaL, ADA, JR-CSF, and SF-162 in human peripheral blood mononuclear cells, the compound was completely inactive. Because of the specific and potent inhibitory effect of AMD3100 on T-tropic viruses, but not M-tropic viruses, it was verified that AMD3100 interacts with the CXC-chemokine receptor CXCR4, the main coreceptor used by T-tropic viruses. AMD3100 dose dependently inhibited the binding of a specific CXCR4 monoclonal antibody to SUP-T1 cells as measured by flow cytometry. It did not inhibit the binding of the biotinylated CC-chemokine macrophage inflammatory protein (MIP) 1α or MIP-1β, ligands for the chemokine receptor CCR5 (the main coreceptor for M-tropic viruses). In addition, AMD3100 completely blocked (a) the Ca2+ flux at 100 ng/ml in lymphocytic SUP-T1 and monocytic THP-1 cells, and (b) the chemotactic responses of THP-1 cells induced by stromal cell–derived factor 1α, the natural ligand for CXCR4. Finally, AMD3100 had no effect on the Ca2+ flux induced by the CC-chemokines MIP-1α, regulated on activation normal T cell expressed and secreted (RANTES; also a ligand for CCR5), or monocyte chemoattractant protein 3 (a ligand for CCR1 and CCR2b), nor was it able to induce Ca2+ fluxes by itself. The bicyclams are, to our knowledge, the first low molecular weight anti-HIV agents shown to act as potent and selective CXCR4 antagonists

Inhibition of activin-like kinase 4/5 attenuates cancer cachexia associated muscle wasting

Cancer mediated activation of the ActRIIB-ALK4/5 heterodimer by myostatin is strongly associated with muscle wasting. We investigated in vitro and in vivo the efficacy of ALK4/5 receptor blockers SB431542 and GW788388 in preventing muscle wasting, and explored synergy with IGF-I analogue LONG R3 (LR3) IGF-I. In vitro, C2C12 skeletal muscle cells were treated with vehicle, SB431542, GW788388 and LR3 IGF-I. A C26-CD2F1 cachexia model was used to induce cachexia in vivo. Mice were allocated as non-tumour bearing (NTB) or C26 tumour-bearing (C26 TB) vehicle control, treated with SB431542, LR3 IGF-I, SB431542 and LR3 IGF-I, or GW788388 (intraperitoneally or orally). In vitro, differentiation index and mean nuclei count increased using SB431542, GW788388, LR3 IGF-I. In vivo, GW788388 was superior to SB431542 in limiting loss of bodyweight, grip-strength and gastrocnemius weight. and downregulated Atrogin-1 expression comparable to NTB mice. LR3 IGF-I treatment limited loss of muscle mass, but at the expense of accelerated tumour growth. In conclusion, treatment with GW788388 prevented cancer cachexia, and downregulated associated ubiquitin ligase Atrogin-1

Community health workers for ART in sub-Saharan Africa: learning from experience – capitalizing on new opportunities

Low-income countries with high HIV/AIDS burdens in sub-Saharan Africa must deal with severe shortages of qualified human resources for health. This situation has triggered the renewed interest in community health workers, as they may play an important role in scaling-up antiretroviral treatment for HIV/AIDS by taking over a number of tasks from the professional health workers. Currently, a wide variety of community health workers are active in many antiretroviral treatment delivery sites

Unprecedented atmospheric ammonia concentrations detected in the high Arctic from the 2017 Canadian wildfires

Abstract From 17-22 August 2017 simultaneous enhancements of ammonia (NH3), carbon monoxide (CO), hydrogen cyanide (HCN), and ethane (C2H6) were detected from ground-based solar absorption Fourier transform infrared (FTIR) spectroscopic measurements at two high-Arctic sites: Eureka (80.05°N, 86.42°W) Nunavut, Canada and Thule (76.53°N, 68.74°W), Greenland. These enhancements were attributed to wildfires in British Columbia and the Northwest Territories of Canada using FLEXPART back-trajectories and fire locations from Moderate Resolution Imaging Spectroradiometer (MODIS) and found to be the greatest observed enhancements in more than a decade of measurements at Eureka (2006-2017) and Thule (1999-2017). Observations of gas-phase NH3 from these wildfires illustrates that boreal wildfires may be a considerable episodic source of NH3 in the summertime high Arctic. Comparisons of GEOS-Chem model simulations using the Global Fire Assimilation System (GFASv1.2) biomass burning emissions to FTIR measurements and Infrared Atmospheric Sounding Interferometer (IASI) measurements showed that the transport of wildfire emissions to the Arctic was underestimated in GEOS-Chem. However, GEOS-Chem simulations showed that these wildfires contributed to surface-layer NH3 and enhancements of 0.01-0.11 ppbv and 0.05-1.07 ppbv, respectively, over the Canadian Archipelago from 15-23 August 2017