Turning conflict into collaboration in managing commons: A case of Rupa Lake Watershed, Nepal

A growing body of literature on the commons has provided fascinating and intricate insights on how some local institutions have successfully managed to avoid a seemingly inevitable “tragedy of the commons” once popularized by Garrett Hardin. Primarily benefitting from the recent studies on the commonpool resources conducted by Elinor Ostrom and colleagues, polycentric selforganization and autonomy, rather than the direct state or market control over the commons, are often recognized as key features of the long enduring commons.However, these commons are quite diverse and the outcomes are often multiple and complex, accentuating the needs to differentiate among multiple commons outcomes. Furthermore, relatively under-reported are the cases where the degradation of common-pool resources are actually halted, and even restored. This study examines both the turbulent history of fishery mismanagement in Rupa Lake, Nepal and its reversal built around the participation, engagement and inclusiveness in the governance of its watershed. We find that Rupa Lake’s experience tells two stories. Reflecting Hardin’s dire forecast, the Rupa Lake watershed verged on collapse as population grew and seemingly selfish behaviorintensified under an open-access regime. But the users also found a way to rebound and reverse their course as they adopted a bottom-up approach to fishery management and established an innovative community institution, the ‘Rupa Lake Rehabilitation and Fishery Cooperative’, dedicated to the sustainable governance of the commons. This case highlights how one community at the threshold of ‘tragedy’ transformed itself by turning conflict into collaboration, which we hope contributes to the effort of better understanding multiple commons

Occupancy maps of 208 chromatin-associated proteins in one human cell type

Transcription factors are DNA-binding proteins that have key roles in gene regulation. Genome-wide occupancy maps of transcriptional regulators are important for understanding gene regulation and its effects on diverse biological processes. However, only a minority of the more than 1,600 transcription factors encoded in the human genome has been assayed. Here we present, as part of the ENCODE (Encyclopedia of DNA Elements) project, data and analyses from chromatin immunoprecipitation followed by high-throughput sequencing (ChIP–seq) experiments using the human HepG2 cell line for 208 chromatin-associated proteins (CAPs). These comprise 171 transcription factors and 37 transcriptional cofactors and chromatin regulator proteins, and represent nearly one-quarter of CAPs expressed in HepG2 cells. The binding profiles of these CAPs form major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalogue of DNA sequence motifs for transcription factors, and describe motifs that correspond to other transcription factors that are co-enriched with the primary ChIP target. For example, FOX family motifs are enriched in ChIP–seq peaks of 37 other CAPs. We show that motif content and occupancy patterns can distinguish between promoters and enhancers. This catalogue reveals high-occupancy target regions at which many CAPs associate, although each contains motifs for only a minority of the numerous associated transcription factors. These analyses provide a more complete overview of the gene regulatory networks that define this cell type, and demonstrate the usefulness of the large-scale production efforts of the ENCODE Consortium

Occupancy maps of 208 chromatin-associated proteins in one human cell type

Transcription factors are DNA-binding proteins that have key roles in gene regulation. Genome-wide occupancy maps of transcriptional regulators are important for understanding gene regulation and its effects on diverse biological processes. However, only a minority of the more than 1,600 transcription factors encoded in the human genome has been assayed. Here we present, as part of the ENCODE (Encyclopedia of DNA Elements) project, data and analyses from chromatin immunoprecipitation followed by high-throughput sequencing (ChIP–seq) experiments using the human HepG2 cell line for 208 chromatin-associated proteins (CAPs). These comprise 171 transcription factors and 37 transcriptional cofactors and chromatin regulator proteins, and represent nearly one-quarter of CAPs expressed in HepG2 cells. The binding profiles of these CAPs form major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalogue of DNA sequence motifs for transcription factors, and describe motifs that correspond to other transcription factors that are co-enriched with the primary ChIP target. For example, FOX family motifs are enriched in ChIP–seq peaks of 37 other CAPs. We show that motif content and occupancy patterns can distinguish between promoters and enhancers. This catalogue reveals high-occupancy target regions at which many CAPs associate, although each contains motifs for only a minority of the numerous associated transcription factors. These analyses provide a more complete overview of the gene regulatory networks that define this cell type, and demonstrate the usefulness of the large-scale production efforts of the ENCODE Consortium

Validation of Human Telomere Length Multi-Ancestry Meta-Analysis Association Signals Identifies POP5 and KBTBD6 as Human Telomere Length Regulation Genes

Genome-wide association studies (GWAS) have become well-powered to detect loci associated with telomere length. However, no prior work has validated genes nominated by GWAS to examine their role in telomere length regulation. We conducted a multi-ancestry meta-analysis of 211,369 individuals and identified five novel association signals. Enrichment analyses of chromatin state and cell-type heritability suggested that blood/immune cells are the most relevant cell type to examine telomere length association signals. We validated specific GWAS associations by overexpressing KBTBD6 or POP5 and demonstrated that both lengthened telomeres. CRISPR/Cas9 deletion of the predicted causal regions in K562 blood cells reduced expression of these genes, demonstrating that these loci are related to transcriptional regulation of KBTBD6 and POP5. Our results demonstrate the utility of telomere length GWAS in the identification of telomere length regulation mechanisms and validate KBTBD6 and POP5 as genes affecting telomere length regulation

Expanded encyclopaedias of DNA elements in the human and mouse genomes

All data are available on the ENCODE data portal: www.encodeproject. org. All code is available on GitHub from the links provided in the methods section. Code related to the Registry of cCREs can be found at https:// github.com/weng-lab/ENCODE-cCREs. Code related to SCREEN can be found at https://github.com/weng-lab/SCREEN.© The Author(s) 2020. The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.This work was supported by grants from the NIH under U01HG007019, U01HG007033, U01HG007036, U01HG007037, U41HG006992, U41HG006993, U41HG006994, U41HG006995, U41HG006996, U41HG006997, U41HG006998, U41HG006999, U41HG007000, U41HG007001, U41HG007002, U41HG007003, U54HG006991, U54HG006997, U54HG006998, U54HG007004, U54HG007005, U54HG007010 and UM1HG009442

Ethnopharmacological survey, Phytochemical screening and Antibacterial activity measurements of high altitude medicinal plants of Nepal: A bioprospecting approach

496-507The ethnopharmacological survey was undertaken to collect information about the use of seven most used medicinal plants, viz. Gentiana depressa D. Don, Rhododendron setosum D. Don , Rhodiola spp., Elsholtzia strobilifera (Benth.) Benth., Hedychium spicatum Sm., Eriophyton wallichii Benth., Rheum L. spp, in the region which is defined as a most potent area of high altitude medicinal plants by the Government of Nepal. The medical indication of each plant was reported on the basis of their uses by traditional healers and ethnic groups. Following the survey result, extraction of the samples was carried out by solvent extraction process in petroleum ether and cold methanol in view to compare their activity preliminarily. Phytochemical tests, cytotoxic effect (LC50) and zone of inhibition (ZOI) against 13 different bacteria and 5 different fungi indicated the medical value of these plants that supports their traditional uses. The results of this study reinforce bioprospecting of the plants as a potential and promising drug candidate for the future pharmacological industries

Turning conflict into collaboration in managing commons: A case of Rupa Lake Watershed, Nepal

A growing body of literature on the commons has provided fascinating and intricate insights on how some local institutions have successfully managed to avoid a seemingly inevitable “tragedy of the commons” once popularized by Garrett Hardin. Primarily benefitting from the recent studies on the commonpool resources conducted by Elinor Ostrom and colleagues, polycentric selforganization and autonomy, rather than the direct state or market control over the commons, are often recognized as key features of the long enduring commons.However, these commons are quite diverse and the outcomes are often multiple and complex, accentuating the needs to differentiate among multiple commons outcomes. Furthermore, relatively under-reported are the cases where the degradation of common-pool resources are actually halted, and even restored. This study examines both the turbulent history of fishery mismanagement in Rupa Lake, Nepal and its reversal built around the participation, engagement and inclusiveness in the governance of its watershed. We find that Rupa Lake’s experience tells two stories. Reflecting Hardin’s dire forecast, the Rupa Lake watershed verged on collapse as population grew and seemingly selfish behaviorintensified under an open-access regime. But the users also found a way to rebound and reverse their course as they adopted a bottom-up approach to fishery management and established an innovative community institution, the ‘Rupa Lake Rehabilitation and Fishery Cooperative’, dedicated to the sustainable governance of the commons. This case highlights how one community at the threshold of ‘tragedy’ transformed itself by turning conflict into collaboration, which we hope contributes to the effort of better understanding multiple commons

Transcriptional analysis of the multiple Sry genes and developmental program at the onset of testis differentiation in the rat.

BackgroundThe commonly used laboratory rat, Rattus norvegicus, is unique in having multiple Sry gene copies found on the Y chromosome, with different copies encoding amino acid variations that influence the resulting protein function. It is not clear which Sry genes are expressed at the onset of testis differentiation or how their expression correlates with that of other genes in testis-determination pathways.MethodsHere, two independent E11-E14 developmental RNAseq datasets show that multiple Sry genes are expressed at E12-E13.ResultsThe identified copies expressed during testis initiation include Sry4A, Sry1, and Sry3C, which are conserved in every strain of Rattus norvegicus with genomes sequenced to date.ConclusionsThis work represents a first step in defining the complex environment of rat testis differentiation that can open the door for generating sex reversal model systems using embryo manipulation techniques that have been available in the mouse but not the rat

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.

In the version of this article initially published, two members of the ENCODE Project Consortium were missing from the author list. Rizi Ai (Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA) and Shantao Li (Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA) are now included in the author list. These errors have been corrected in the online version of the article