bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of dependency and consumption pattern of different forest products by the forest fringe villages of Shivalik Himalaya, Uttarakhand, India
Authors: Jiju J.S. , Dasgupta Soumya , Kumar Amit , Gera Mohit 
Published: April 2021

AbstractForest are essential for human beings for the enormous services it gives for livelihood and subsistence in the developing countries. We estimated the consumption and extraction levels of three major forest products viz., timber, fuelwood, and fodder in 20 forest fringe villages of the Timli forest range of Uttarakhand, India. We used a questionnaire-based household-level survey to collect information on the household economy and dependence of 380 households selected through stratified random sampling. We estimated that 69% of the overall yearly timber consumption of 20 villages, which comes around 2750 cubic meters (cum), was extracted from the nearby forest. The average timber consumption was 0.52 ± 0.22 cum household-1year-1. We estimated the total annual fuelwood and fodder consumption to be 298913.89, and 204475 Quintal (Qt). The average fuelwood and fodder consumption were estimated to be 417.6 Quintal household-1year-1and 49 ± 9.1 Qt. household-1year-1. We did general linear regression analysis to assess major biophysical and socio-economic determinants of villages and households for dependency on timber, fuelwood, and fodder. We found that the population of the village, distance from forest, distance from market, and annual average income are the major determining factors for timber, fodder, and fuelwood demand of the villages. Extraction of timber and non-timber forest products was the primary cause of depletion of forest biomass and forest carbon emission. Conservation effective management strategies in collaboration with all the stakeholder departments are needed to conserve forest resources with minimum extraction pressure from forest fringe villages of the study area.HighlightsQuestionnaire based household level survey was done to assess extraction and consumption patter of fuelwood, fodder and timber in Shivalik range of Uttarakhand, India.Fuelwood and Timber consumption was found high compared to other studies in the low altitude areas.69% of total timber and 62% of the total fodder requirement met from the adjacent forest areas.Population of the village, distance from the forest and nearby market place, and annual average income were the major determinants of dependency of different forest products.
The genetic architecture underlying body-size traits plasticity over different temperatures and developmental stages inCaenorhabditis elegans
Authors: Maulana Muhammad I. , Riksen Joost A.G. , Snoek Basten L. , Kammenga Jan E. , Sterken Mark G. 
Published: April 2021

AbstractMost ectotherms obey the temperature-size rule, meaning they grow larger in a colder environment. This raises the question of how the interplay between genes and temperature affect the body size of ectotherms. Despite the growing body of literature on the physiological life-history and molecular genetic mechanism underlying the temperature-size rule, the overall genetic architecture orchestrating this complex phenotype is not yet fully understood. One approach to identify genetic regulators of complex phenotypes is Quantitative Trait Locus (QTL) mapping. Here, we explore the genetic architecture of body size phenotypes, and plasticity of body-size phenotypes in different temperatures usingCaenorhabditis elegansas a model ectotherm. We used 40 recombinant inbred lines (RILs) derived from N2 and CB4856, which were reared at four different temperatures (16°C, 20°C, 24°C, and 26°C) and measured at two developmental stages (L4 and adult). The animals were measured for body length, width at vulva, body volume, length/width ratio, and seven other body-size traits. The genetically diverse RILs varied in their body-size phenotypes with heritabilities ranging from 0.0 to 0.99. We detected 18 QTL underlying the body-size traits across all treatment combinations, with the majority clustering on Chromosome X. We hypothesize that the Chromosome X QTL could result from a known pleiotropic regulator –npr-1 –known to affect the body size ofC. elegansthrough behavioral changes. We also found five plasticity QTL of body-size which three of them colocalized with some body-size QTL at certain temperature. In conclusion, our findings shed more light on multiple loci affecting body size plasticity and the possibility of co-regulation of traits and traits plasticity by the same loci under different environment.
Homologs of circadian clock proteins impact the metabolic switch between light and dark growth in the cyanobacteriumSynechocystissp. PCC 6803
Authors: Scheurer Nina M. , Rajarathinam Yogeswari , Timm Stefan , Köbler Christin , Kopka Joachim , Hagemann Martin , Wilde Annegret 
Published: April 2021

AbstractThe putative circadian clock system of the facultative heterotrophic cyanobacterial strainSynechocystissp. PCC 6803 comprises the following three Kai-based systems: a KaiABC-based potential oscillator that is linked to the SasA-RpaA two-component output pathway and two additional KaiBC systems without a cognate KaiA component. Mutants lacking the genes encoding the KaiAB1C1 components or the response regulator RpaA show reduced growth in light/dark cycles and do not show heterotrophic growth in the dark. In the present study, the effect of these mutations on central metabolism was analyzed by targeted and nontargeted metabolite profiling. The strongest metabolic changes were observed in the dark in ΔrpaAand, to a lesser extent, in the ΔkaiAB1C1mutant. These observations included the overaccumulation of 2-phosphoglycolate, which correlated with the overaccumulation of the RbcL subunit in the mutants, and taken together, these data suggest enhanced RubisCO activity in the dark. The imbalanced carbon metabolism in the ΔrpaAmutant extended to the pyruvate family of amino acids, which showed increased accumulation in the dark. Hence, the deletion of the response regulatorrpaAhad a more pronounced effect on metabolism than the deletion of thekaigenes. The larger impact of therpaAmutation is in agreement with previous transcriptomic analyses and likely relates to a KaiAB1C1-independent function as a transcription factor. Collectively, our data demonstrate an important role of homologs of clock proteins inSynechocystisfor balanced carbon and nitrogen metabolism during light-to-dark transitions.
LIN37-DREAM Prevents DNA End Resection and Homologous Recombination at DNA Double Strand Breaks in Quiescent Cells
Authors: Chen Bo-Ruei , Wang Yinan , Tubbs Anthony T. , Zong Dali , Fowler Faith C. , Zolnerowich Nicholas , Wu Wei , Bennett Amelia , Chen Chun-Chin , Feng Wendy , Nussenzweig Andre , Tyler Jessica K. , Sleckman Barry P. 
Published: April 2021

AbstractDNA double strand break (DSB) repair by homologous recombination (HR) is thought to be restricted to the S- and G2- phases of the cell cycle in part due to 53BP1 antagonizing DNA end resection in G1-phase and non-cycling quiescent (G0) cells. Here, we show that LIN37, a component of the DREAM transcriptional repressor, functions in a 53BP1-independent manner to prevent DNA end resection and HR in G0cells. Loss of LIN37 leads to expression of HR proteins, including BRCA1, BRCA2, PALB2 and RAD51, and DNA end resection in G0cells even in the presence of 53BP1. In contrast to 53BP1-deficiency, DNA end resection in LIN37-deficient G0cells depends on BRCA1 and leads to RAD51 filament formation and HR. LIN37 is not required to protect DNA ends in cycling cells at G1-phase. Thus, LIN37 regulates a novel 53BP1-independent cell phase-specific DNA end protection pathway that functions uniquely in quiescent cells.
Human-derived alleles inSOSTandRUNX23′UTRs cause differential regulation in a bone cell-line model
Authors: Moriano Juan , Martínez-Gil Núria , Andirkó Alejandro , Balcells Susana , Grinberg Daniel , Boeckx Cedric 
Published: April 2021

AbstractThe inquiry into the phenotypic features that set apart human species, such as a light, gracile skeleton and a rounded skull characteristic ofHomo sapiens, can now benefit from the examination of ancient genomes. These have added a new layer of analysis allowing the identification of genetic differences between species like ours and our closest extinct relatives. Most of these genetic differences are non-coding changes with unknown functional consequences, and dissecting their putative regulatory effect remains challenging. Here we focus on the three prime untranslated regions (3’UTR), known to play a critical role in messenger RNA regulation and a plausible locus for divergent regulation betweenHomospecies. We report a set of genes with derived 3’UTR changes in either theHomo sapiensor the Neanderthal/Denisovan lineages and experimentally evaluate the impact of 3’UTR variants in four genes:E2F6,GLI3,RUNX2andSOST. We performed a luciferase reporter assay in a bone cell-line model and found a statistically significant difference for the 3’UTR variants ofSOST(Homo sapiens-derived) andRUNX2(Neanderthal/Denisovan-derived). The differential expression caused by these variants in our experimental model points to species differences in bone mineral density. Thus, this study adds insights into the functional effects of regulatory variants that emerged in recent human evolution.
Direct observation of aggregate-triggered selective autophagy
Authors: Janssen Anne F.J. , Korsten Giel , Nijenhuis Wilco , Katrukha Eugene A. , Kapitein Lukas C. 
Published: April 2021

ABSTRACTDegradation of aggregates by selective autophagy is important as damaged proteins may impose a threat to cellular homeostasis. Although the core components of the autophagy machinery are well-characterized, the spatiotemporal regulation of many selective autophagy processes, including aggrephagy, remains largely unexplored. Furthermore, because most live-cell imaging studies have so far focused on starvation-induced autophagy, little is known about the dynamics of aggrephagy. Here, we describe the development and application of the mKeima-PIM assay, which enables live-cell observation of autophagic turnover and degradation of inducible protein aggregates in conjunction with key autophagy players. This allowed us to quantify the relative timing and duration of different steps of aggrephagy and revealed the short-lived nature of the autophagosome. The assay furthermore showed the spatial distribution of omegasome formation, highlighting that autophagy initiation is directly instructed by the cargo. Moreover, we found that nascent autophagosomes mostly remain immobile until acidification occurs. Thus, our assay provides new insights into the spatiotemporal regulation and dynamics of aggrephagy.
Single Cell Chemical Proteomics (SCCP) Interrogates the Timing and Heterogeneity of Cancer Cell Commitment to Death
Authors: Végvári Ákos , Rodriguez Jimmy E , Zubarev Roman A 
Published: April 2021

AbstractChemical proteomics studies the effects of drugs upon cellular proteome. Due to the complexity and diversity of tumors, the response of cancer cells to drugs is also heterogeneous, and thus proteome analysis at single cell level is needed. Here we demonstrate that single cell proteomics techniques have become quantitative enough to tackle the drug effects on the target proteins, enabling single cell chemical proteomics (SCCP). Using SCCP, we studied here the time-resolved response of individual adenocarcinoma A549 cells to anticancer drugs methotrexate, camptothecin and tomudex, revealing the early emergence of cellular subpopulations committed and uncommitted to death. As a novel and useful approach to exploring the heterogeneous response to drugs of cancer cells, SCCP may prove to be a “killer application” for single cell proteomics.
Absolute quantification and single-cell dose-response of cytosolic siRNA delivery
Authors: Hedlund Hampus , Du Rietz Hampus , Johansson Johanna , Zedan Wahed , Huang Linfeng , Wallin Jonas , Wittrup Anders 
Published: April 2021

AbstractEndosomal escape and subsequent cytosolic delivery of small inhibitory RNA (siRNA) therapeutics is believed to be highly inefficient. Since, it has not been possible to quantify cytosolic amounts of delivered siRNA at therapeutic doses, determination of delivery bottlenecks and total efficiency has been difficult. Here, we present a confocal microscopy-based method to detect cytosolic delivery of fluorescently labelled siRNA during lipid-mediated delivery. This method enables detection and quantification of sub-nanomolar cytosolic siRNA release amounts from individual release events with measures of quantitation confidence for each event. Single-cell kinetics of siRNA-mediated knockdown in cells expressing destabilized eGFP unveiled a dose-response relationship with respect to knockdown induction, depth and duration in the range from several hundred to thousands of cytosolic siRNA molecules. Accurate quantification of cytosolic siRNA, and the establishment of the intracellular dose-response relationships, will aid the development and characterization of novel delivery strategies for nucleic acid therapeutics.
Host regulator PARP1 contributes to sex differences and immune responses in a mouse model of tuberculosis
Authors: Krug Stefanie , Ordonez Alvaro A. , Klunk Mariah , Kang Bong Gu , Jain Sanjay K. , Dawson Ted M. , Dawson Valina L. , Bishai William R. 
Published: April 2021

AbstractTuberculosis (TB) is a devastating infectious disease responsible for nearly 2 million deaths annually that has a poorly understood male bias. Elucidating the basis of this male bias may enable precision medicine interventions for TB treatment and prevention. Here, we identify the master regulator Poly(ADP-ribose) Polymerase 1 (PARP1) as a driver of TB sex differences. We found that infection withM. tuberculosis(M. tb) triggers robust PARP activation in mouse lungs, suggesting that PARP1 activation is a fundamental host response to TB. Remarkably, PARP1 deletion abolished known sex differences in TB cytokine responses and blunted the early induction of TNFα, IL-1ß, IFNγ, MCP-1, and IL-6, particularly in male mice. In contrast, PARP1 was required for IL-10 induction in male or female mice. PARP1 deletion was protective against TB in female mice, resulting in significantly prolonged survival and reduced bacterial burden, but impaired TB containment in male mice. Our findings indicate that PARP1 contributes to TB sex differences via sexually divergent immune regulation and uniquely enhances early proinflammatory responses in males that prove beneficial for TB containment.
Stem cell quiescence requires PRC2/PRC1-mediated mitochondrial checkpoint
Authors: Ishibashi JR , Taslim TH , Hussein AM , Brewer D , Liu S , Harper S , Nguyen B , Dang J , Chen A , Del Castillo D , Mathieu J , Ruohola-Baker H 
Published: April 2021

ABSTRACTBoth normal and tumorous stem cells can arrest cell division, avoid apoptosis, and then regenerate lost daughter cells following acute genotoxic insult. This protective, reversible proliferative arrest, known as “quiescence,” is still poorly understood. Here, we show that mTOR-regulated mitophagy is required for radiation insult-induced quiescence inDrosophilagermline stem cells (GSCs). In GSCs, depletion of mito-fission (Drp1) or mitophagy (Pink1 and Parkin) eliminates entry into quiescence, while depletion of mitochondrial biogenesis (PGC1α) or fusion (Mfn2) eliminates exit from quiescence. We also find that mitophagy-dependent quiescence is under epigenetic control; knockdown of Jarid2 (PRC2) or Pc or Sce (PRC1) stabilizes the mitochondria and locks GSCs out of quiescence, while knockdown of PRC2-specific demethylase, Utx, prevents re-accumulation of the mitochondria and locks GSCs in quiescence. These data suggest that mitochondrial number coordinates reversible quiescence. We further identify that the mechanism of quiescence in both GSCs and human induced pluripotent stem cells (iPSCs) relies on mitophagy to deplete the mitochondrial pool of CycE and limit cell cycle progression. This alternative method of G1/S regulation may present new opportunities for therapeutic purposes.
GC-biased gene conversion in X-Chromosome palindromes conserved in human, chimpanzee, and rhesus macaque
Authors: Jackson Emily K. , Bellott Daniel W. , Skaletsky Helen , Page David C. 
Published: April 2021

ABSTRACTGene conversion is GC-biased across a wide range of taxa. Large palindromes on mammalian sex chromosomes undergo frequent gene conversion that maintains arm-to-arm sequence identity greater than 99%, which may increase their susceptibility to the effects of GC-biased gene conversion. Here, we demonstrate a striking history of GC-biased gene conversion in 12 palindromes conserved on the X chromosomes of human, chimpanzee, and rhesus macaque. Primate X-chromosome palindrome arms have significantly higher GC content than flanking single-copy sequences. Nucleotide replacements that occurred in human and chimpanzee palindrome arms over the past 7 million years are one-and-a-half times as GC-rich than the ancestral bases they replaced. Using simulations, we show that our observed pattern of nucleotide replacements is consistent with GC-biased gene conversion with a magnitude of 70%, similar to previously reported values based on analyses of human meioses. However, GC-biased gene conversion explains only a fraction of the observed difference in GC content between palindrome arms and flanking sequence, suggesting that additional factors are required to explain elevated GC content in palindrome arms. This work supports a greater than 2:1 preference for GC bases over AT bases during gene conversion, and demonstrates that the evolution and composition of mammalian sex chromosome palindromes is strongly influenced by GC-biased gene conversion.
Dynamic conformational states of apo and cabozantinib bound TAM kinases to differentiate active-inactive kinetic models
Authors: Naresh Gatta K R S , Guruprasad Lalitha 
Published: April 2021

AbstractTyro3, Axl, Mer (TAM) receptor tyrosine kinases (RTKs) are overexpressed in several human cancers. Cabozantinib, a small molecule inhibitor constrains the activity of TAM kinases at nanomolar concentrations. The dynamic active and inactive conformations of kinases play a crucial role in inhibitor binding and the activation of intracellular downstream signalling pathways. The all atom molecular dynamics (MD) simulations at microsecond timescale and longer provide robust insights into the structural details of conformational alterations of proteins due to their role cellular metabolic activities and signaling pathways. In this current study we report microsecond molecular dynamics (MD) simulations of apo, cabozantinib complexed active and inactive TAM RTKs and analysed the post-MD trajectories using the principal component analysis (PCA). Markov State Models (MSM) and transition pathways from Perron-cluster cluster analysis. For consensus, the 1µs atomistic simulations with enhanced computational algorithms indicated us to treat tyrosine kinase family by overwhelming dynamic states existence when bound to kinase inhibitors. The dynamic mechanistic pathways intrinsic to the kinase activity and protein conformational landscape in the TAM kinases are revealed due to the alterations in the P-loop, αC-helix, activation loop and αF-helix that result in breaking the regulatory and catalytic spines. We deciphered the long lived kinetic transition states of distinct active and inactive structural models from MD simulations trajectories of TAM RTKs bound inhibitor complex that have not been revealed so far.
NrnA is a linear dinucleotide phosphodiesterase with limited function in cyclic dinucleotide metabolism inListeria monocytogenes
Authors: Gall Aaron R. , Siletti Cheta , Huynh TuAnh N. 
Published: April 2021

ABSTRACTListeria monocytogenesproduces both c-di-AMP and c-di-GMP to mediate many important cellular processes, but the levels of both nucleotides must be regulated. C-di-AMP accumulation attenuates virulence and diminishes stress response, and c-di-GMP accumulation impairs bacterial motility. An important regulatory mechanism to maintain c-di-AMP and c-di-GMP homeostasis is to hydrolyze them to the linear dinucleotides pApA and pGpG, respectively, but the fates of these hydrolytic products have not been examined inL. monocytogenes. We found that NrnA, a stand-alone DHH-DHHA1 phosphodiesterase, has a broad substrate range, but with a strong preference for linear dinucleotides over cyclic dinucleotides. Although NrnA exhibited detectable cyclic dinucleotide hydrolytic activities in vitro, NrnA had negligible effects on their levels in the bacterial cell, even in the absence of the c-di-AMP phosphodiesterases PdeA and PgpH. The ΔnrnAmutant had a mammalian cell infection defect that was fully restored byE. coliOrn. Together, our data indicate thatL. monocytogenesNrnA is functionally orthologous to Orn, and its preferred physiological substrates are most likely linear dinucleotides. Furthermore, our findings revealed that, unlike some other c-di-AMP and c-di-GMP-producing bacteria,L. monocytogenesdoes not employ their hydrolytic products to regulate their phosphodiesterases, at least at the pApA and pGpG levels in the ΔnrnAmutant. Finally, the ΔnrnAinfection defect was overcome by constitutive activation of PrfA, the master virulence regulator, suggesting that accumulated linear dinucleotides might inhibit the expression, stability, or function of PrfA-regulated virulence factors.IMPORTANCEListeria monocytogenesproduces both c-di-AMP and c-di-GMP, and encodes specific phosphodiesterases that degrade them into pApA and pGpG, respectively, but the metabolism of these products has not been characterized in this bacterium. We found thatL. monocytogenesharbors an NrnA homolog that degrades a broad range of nucleotides, but exhibits a strong biochemical and physiological preference for linear dinucleotides, including pApA and pGpG. Unlike in some other bacteria, these oligoribonucleotides do not appear to interfere with cyclic dinucleotide hydrolysis. The absence of NrnA is well tolerated byL. monocytogenesin broth cultures but impairs its ability to infect mammalian cells. These findings indicate a separation of cyclic dinucleotide signaling and oligoribonucleotide metabolism inL. monocytogenes.