Background: Predicting which species are likely to go extinct is perhaps one of the most fundamental yet challenging tasks for conservation biologists. This is particularly relevant for freshwater ecosystems which tend to have the highest proportion of species threatened with extinction. According to metapopulation theories, local extinction and colonization rates of freshwater subpopulations can depend on the degree of regional occupancy, notably due to rescue effects. However, relationships between extinction, colonization, regional occupancy and the spatial scales at which they operate are currently poorly known.
Methods: And Findings: We used a large dataset of freshwater fish annual censuses in 325 stream reaches to analyse how annual extinction/colonization rates of subpopulations depend on the regional occupancy of species. For this purpose, we modelled the regional occupancy of 34 fish species over the whole French river network and we tested how extinction/colonization rates could be predicted by regional occupancy described at five nested spatial scales. Results show that extinction and colonization rates depend on regional occupancy, revealing existence a rescue effect. We also find that these effects are scale dependent and their absolute contribution to colonization and extinction tends to decrease from river section to larger basin scales.
Conclusions: In terms of management, we show that regional occupancy quantification allows the evaluation of local species extinction/colonization dynamics and reduction of local extinction risks for freshwater fish species implies the preservation of suitable habitats at both local and drainage basin scales.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0084138 | PLOS |
Proc Natl Acad Sci U S A
January 2025
Center for Nutritional Sciences, Food Science and Human Nutrition Department, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL 32611.
Documented worldwide, impaired immunity is a cardinal signature resulting from loss of dietary zinc, an essential micronutrient. A steady supply of zinc to meet cellular requirements is regulated by an array of zinc transporters. Deletion of the transporter Zip14 (Slc39a14) in mice produced intestinal inflammation.
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Department of Urology Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, No. 136, Zhongshan 2nd Road, Yuzhong District, Chongqing, 400014, P.R. China.
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Binding of transcription factors (TFs) at gene regulatory elements controls cellular epigenetic state and gene expression. Current genome-wide chromatin profiling approaches have inherently limited resolution, complicating assessment of TF occupancy and co-occupancy, especially at individual alleles. In this work, we introduce Accessible Chromatin by Cytosine Editing Site Sequencing with ATAC-seq (ACCESS-ATAC), which harnesses a double-stranded DNA cytosine deaminase (Ddd) enzyme to stencil TF binding locations within accessible chromatin regions.
View Article and Find Full Text PDFJ Vis Exp
December 2024
Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center; Department of Gynecologic Oncology and Reproductive Medicine, University of Texas MD Anderson Cancer Center;
The CUT&RUN technique facilitates detection of protein-DNA interactions across the genome. Typical applications of CUT&RUN include profiling changes in histone tail modifications or mapping transcription factor chromatin occupancy. Widespread adoption of CUT&RUN is driven, in part, by technical advantages over conventional ChIP-seq that include lower cell input requirements, lower sequencing depth requirements, and increased sensitivity with reduced background signal due to a lack of cross-linking agents that otherwise mask antibody epitopes.
View Article and Find Full Text PDFSci China Life Sci
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Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
Inflammation is a driving force of hematopoietic stem cells (HSCs) aging, causing irreversible exhaustion of functional HSCs. However, the underlying mechanism of HSCs erosion by inflammatory insult remains poorly understood. Here, we find that transient LPS exposure primes aged HSCs to undergo accelerated differentiation at the expense of self-renewal, leading to depletion of HSCs.
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