Of the two cultivated species of allopolyploid cotton, Gossypium barbadense produces extra-long fibers for the production of superior textiles. We sequenced its genome (AD)2 and performed a comparative analysis. We identified three bursts of retrotransposons from 20 million years ago (Mya) and a genome-wide uneven pseudogenization peak at 11–20 Mya, which likely contributed to genomic divergences. Among the 2,483 genes preferentially expressed in fiber, a cell elongation regulator, PRE1, is strikingly At biased and fiber specific, echoing the A-genome origin of spinnable fiber. The expansion of the PRE members implies a genetic factor that underlies fiber elongation. Mature cotton fiber consists of nearly pure cellulose. G. barbadense and G. hirsutum contain 29 and 30 cellulose synthase (CesA) genes, respectively; whereas most of these genes (>25) are expressed in fiber, genes for secondary cell wall biosynthesis exhibited a delayed and higher degree of up-regulation in G. barbadense compared with G. hirsutum, conferring an extended elongation stage and highly active secondary wall deposition during extra-long fiber development. The rapid diversification of sesquiterpene synthase genes in the gossypol pathway exemplifies the chemical diversity of lineage-specific secondary metabolites. The G. barbadense genome advances our understanding of allopolyploidy, which will help improve cotton fiber quality.
Vitamin D deficiency is prevalent among pregnant Chinese women. Residing in areas with low ambient UVB levels increases the risk of vitamin D deficiency, especially for women experiencing advanced stages of gestation, for younger pregnant women and for women of Hui ethnicity; therefore, vitamin D supplementation and sensible sun exposure should be encouraged, especially in the winter months. Further studies must determine optimal vitamin D intake and sun exposure levels for maintaining sufficient vitamin D levels in pregnant Chinese women.
BackgroundDetermining patterns of HIV transmission is increasingly important for the most efficient use of modern prevention interventions. HIV phylogeny can provide a better understanding of the mechanisms underlying HIV transmission networks in communities.MethodsTo reconstruct the structure and dynamics of a local HIV/AIDS epidemic, the phylogenetic relatedness of HIV-1 subtype C env sequences obtained from 785 HIV-infected community residents in the northeastern sector of Mochudi, Botswana, during 2010–2013 was estimated. The genotyping coverage was estimated at 44%. Clusters were defined based on relatedness of HIV-1C env sequences and bootstrap support of splits.ResultsThe overall proportion of clustered HIV-1C env sequences was 19.1% (95% CI 17.5% to 20.8%). The proportion of clustered sequences from Mochudi was significantly higher than the proportion of non-Mochudi sequences that clustered, 27.0% vs. 14.7% (p = 5.8E-12; Fisher exact test). The majority of clustered Mochudi sequences (90.1%; 95% CI 85.1% to 93.6%) were found in the Mochudi-unique clusters. None of the sequences from Mochudi clustered with any of the 1,244 non-Botswana HIV-1C sequences. At least 83 distinct HIV-1C variants, or chains of HIV transmission, in Mochudi were enumerated, and their sequence signatures were reconstructed. Seven of 20 genotyped seroconverters were found in 7 distinct clusters.ConclusionsThe study provides essential characteristics of the HIV transmission network in a community in Botswana, suggests the importance of high sampling coverage, and highlights the need for broad HIV genotyping to determine the spread of community-unique and community-mixed viral variants circulating in local epidemics. The proposed methodology of cluster analysis enumerates circulating HIV variants and can work well for surveillance of HIV transmission networks. HIV genotyping at the community level can help to optimize and balance HIV prevention strategies in trials and combined intervention packages.
Background The heterogeneity of mesenchymal stem cells (MSCs) is poorly understood, thus limiting clinical application and basic research reproducibility. Advanced single‐cell RNA sequencing (scRNA‐seq) is a robust tool used to analyse for dissecting cellular heterogeneity. However, the comprehensive single‐cell atlas for human MSCs has not been achieved. Methods This study used massive parallel multiplexing scRNA‐seq to construct an atlas of > 130 000 single‐MSC transcriptomes across multiple tissues and donors to assess their heterogeneity. The most widely clinically utilised tissue resources for MSCs were collected, including normal bone marrow ( n = 3), adipose ( n = 3), umbilical cord ( n = 2), and dermis ( n = 3). Results Seven tissue‐specific and five conserved MSC subpopulations with distinct gene‐expression signatures were identified from multiple tissue origins based on the high‐quality data, which has not been achieved previously. This study showed that extracellular matrix (ECM) highly contributes to MSC heterogeneity. Notably, tissue‐specific MSC subpopulations were substantially heterogeneous on ECM‐associated immune regulation, antigen processing/presentation, and senescence, thus promoting inter‐donor and intra‐tissue heterogeneity. The variable dynamics of ECM‐associated genes had discrete trajectory patterns across multiple tissues. Additionally, the conserved and tissue‐specific transcriptomic‐regulons and protein‐protein interactions were identified, potentially representing common or tissue‐specific MSC functional roles. Furthermore, the umbilical‐cord‐specific subpopulation possessed advantages in immunosuppressive properties. Conclusion In summary, this work provides timely and great insights into MSC heterogeneity at multiple levels. This MSC atlas taxonomy also provides a comprehensive understanding of cellular heterogeneity, thus revealing the potential improvements in MSC‐based therapeutic efficacy.
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