bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive studies of Head Maralla, Punjab, Pakistan vegetation for ethnopharmacological and ethnobotanical uses and their elaboration through quantitative indices
Authors: Iqbal Muhammad Sajjad , Ali Muhammad Azhar , Akbar Muhammad , Hussain Syed Atiq , Arshad Noshia , Munir Saba , Masood Hajra , Zafar Samina , Ahmad Tahira , Shaheen Nazra , Mashooq Rizwana , Sajjad Hifsa , Zahoor Munaza , Bashir Faiza , Shahbaz Khizra , Arshad Hamna , Fatima Noor , Nasir Faiza , Hashmi Ayesha Javed , Chaudhary Sofia , Waqas Ahmad , Islam Muhammad 
Published: November 2020

AbstractHead Maralla is a non-recognized wetland with diversified flora that becomes focus of current studies. Whole plant or their parts are being used for treating various maladies and they are the integral part of livelihood in the area. Unique species includingOsmunda regalisis used for blood and renal diseases purifier. Wild plant resources are key to traditional ethnobotanical knowledge based practices and industrial applications. Current study reports Head Marala inhabitant’s interaction with these resources and identify priorities at species and habitat level for conservation. Four sites viz., River Tavi, Upstream Chenab, River Manawarwala Tavi and Bhalolpur were designated to record traditional knowledge through questionnaire and interviews during field trips. One hundred nineteen (119) plant species were identified belonging to 54 families, of which 87 species were of dicot, 12monocots, 05ferns, and 4 species of bryophytes. Fifty percent of the plant species were utilized as a whole for therapeutic purposes, followed by leaves which had more than 20% usage of total consumption. Ailments viz., urination (14%) followed by cough (8%), cold (7%), stomach (6%), asthma (6%), constipation (5%), laxative (5%), diarrhea (4%) etc., were associated with vegetation. Bronchial disorders, pneumonia, dyspepsia, anthelmintic and kidney stones, etc., were also among other diseases commonly cured by traditional knowledge. Fifteen percent of vegetation contributes as fodder species consumed by local community for livestock while almost 17% of local plants were utilized for industrial purposes like timber, fuel, furniture, wooden pots and sports goods. In conclusion the ecosystem of Head Maralla is a complex of aquatic, terrestrial and agricultural land that is located on climatic and geographical divides, which further add to botanical interest as included many wetland habitats with unique diversity of plants. It is suggested to devise comprehensive conservation strategies to safe indigenous knowledge in systematic way for comprehending ecological services.
DAF-18 is required for the age-dependent increase in DAF-16 activity inCaenorhabditis elegans
Authors: Carrasco Kali , Youngman Matthew J. 
Published: November 2020

ABSTRACTThe insulin/insulin-like growth factor signaling (IIS) pathway modulates growth, survival, and lifespan by regulating FOXO transcription factors. InCaenorhabditis elegans, IIS maintains DAF-16/FOXO in an inactive state unless animals are challenged by environmental stress. Recent evidence suggests that DAF-16 becomes activated as part of normal aging inC. elegans, yet the regulatory module responsible for this phenomenon is largely undefined. Embedded within IIS is phospholipid signaling in which PIP3produced by the PI3 kinase AGE-1 is an upstream event in DAF-16 inhibition. Countering AGE-1 is DAF-18, an ortholog of human PTEN phosphatase that dephosphorylates PIP3. Although it is required for normal lifespan inC. elegans, functional characterization of DAF-18 has primarily focused on its roles during development in the germline and neurons. In this study we asked whether DAF-18 plays a role in the age-dependent activation of DAF-16, and specifically in DAF-16-mediated immunity. Our data show that DAF-18 is expressed in multiple tissues during adulthood. We found that DAF-18 contributes to host defense in adult animals by functioning in the neurons and intestine, likely working through DAF-16 which acts in those same tissues to confer immunity. Supporting this possibility, DAF-18 was required for increased DAF-16 transcriptional activity during aging. Post-translational modifications including ubiquitination and sumoylation appear to be required for the function of DAF-18 during aging inC. elegans, indicating that strategies to modulate PTEN activity are evolutionarily conserved. Our results establish an important role for DAF-18 later in life and imply that it is a critical component of a neuroendocrine signaling circuit that governs the dynamic activity of DAF-16.
Analysis of SARS-CoV-2 spike glycosylation reveals shedding of a vaccine candidate
Authors: Brun Juliane , Vasiljevic Snežana , Gangadharan Bevin , Hensen Mario , Chandran Anu V. , Hill Michelle L. , Kiappes J.L. , Dwek Raymond A. , Alonzi Dominic S. , Struwe Weston B. , Zitzmann Nicole 
Published: November 2020

AbstractSevere acute respiratory syndrome coronavirus 2 is the causative pathogen of the COVID-19 pandemic which as of Nov 15, 2020 has claimed 1,319,946 lives worldwide. Vaccine development focuses on the viral trimeric spike glycoprotein as the main target of the humoral immune response. Viral spikes carry glycans that facilitate immune evasion by shielding specific protein epitopes from antibody neutralisation. Immunogen integrity is therefore important for glycoprotein-based vaccine candidates. Here we show how site-specific glycosylation differs between virus-derived spikes and spike proteins derived from a viral vectored SARS-CoV-2 vaccine candidate. We show that their distinctive cellular secretion pathways result in different protein glycosylation and secretion patterns, which may have implications for the resulting immune response and future vaccine design.
AStreptomyces venezuelaeCell-Free Toolkit for Synthetic Biology
Authors: Moore Simon J , Lai Hung-En , Chee Soo-Mei , Toh Ming , Coode Seth , Capel Patrick , Corre Christophe , de los Santos Emmanuel LC , Freemont Paul S 
Published: November 2020

AbstractProkaryotic cell-free coupled transcription-translation (TX-TL) systems are emerging as a powerful tool to examine natural product biosynthetic pathways in a test-tube. The key advantages of this approach are the reduced experimental timescales and controlled reaction conditions. In order to realise this potential, specialised cell-free systems in organisms enriched for biosynthetic gene clusters, with strong protein production and well-characterised synthetic biology tools, is essential. TheStreptomycesgenus is a major source of natural products. To study enzymes and pathways fromStreptomyces, we originally developed a homologousStreptomycescell-free system to provide a native protein folding environment, a high G+C (%) tRNA pool and an active background metabolism. However, our initial yields were low (36 μg/mL) and showed a high level of batch-to-batch variation. Here, we present an updated high-yield and robustStreptomycesTX-TL protocol, reaching up to yields of 266 μg/mL of expressed recombinant protein. To complement this, we rapidly characterise a range of DNA parts with different reporters, express high G+C (%) biosynthetic genes and demonstrate an initial proof of concept for combined transcription, translation and biosynthesis ofStreptomycesmetabolic pathways in a single ‘one-pot’ reaction.
Competition within low-density bacterial populations as an unexpected factor regulating carbon decomposition in bulk soil
Authors: Coche Alexandre , Babey Tristan , Rapaport Alain , Vieublé Gonod Laure , Garnier Patricia , Nunan Naoise , de Dreuzy Jean-Raynald 
Published: November 2020

AbstractBacterial decomposition of organic matter in soils is generally believed to be mainly controlled by the access bacteria have to their substrate. The influence of bacterial traits on this control has, however, received little attention. Here, we develop a bioreactive transport model to screen the interactive impacts of dispersion and bacterial traits on mineralization. We compare the model results with two sets of previously performed cm-scale soil-core experiments in which the mineralization of the pesticide 2,4-D was measured under well-controlled initial distributions and transport conditions. Bacterial dispersion away from the initial substrate location induced a significant increase in 2,4-D mineralization, revealing the existence of a regulation of mineralization by the bacterial decomposer density, in addition to the dilution of substrate. This regulation of degradation by density becomes dominant for bacteria with an efficient uptake of substrate at low substrate concentrations (a common feature of oligotrophs). The model output suggests that the distance between bacteria adapted to oligotrophic environments is a stronger regulator of degradation than the distance between these bacteria and the substrate initial location. Such oligotrophs, commonly found in soils, compete with each other for substrate even at remarkably low population densities. The ratio-dependent Contois growth model, which includes a density regulation in the expression of the uptake efficiency, provide a more versatile representation than the substrate-dependent Monod model in these conditions. In view of their strong interactions, bioreactive and transport processes cannot be handled independently but should be integrated, in particular when reactive processes of interest are carried out by oligotrophs.Abstract FigureHighlights-The impact of spatial distributions on decomposition depends on bacterial traits-Decomposition can be reduced by competition between bacteria even at low densities-Bacterial density regulation counterbalances substrate accessibility regulation-Regulation of decomposition by bacterial density is more acute for oligotrophs
Extracellular Matrix Remodeling Associated with Bleomycin-Induced Lung Injury Supports Pericyte-To-Myofibroblast Transition
Authors: Hannan Riley T. , Miller Andrew E. , Hung Ruei-Chun , Sano Catherine , Peirce Shayn M. , Barker Thomas H. 
Published: November 2020

AbstractOf the many origins of pulmonary myofibroblasts, microvascular pericytes are a known source. Prior literature has established the ability of pericytes to transition into myofibroblasts, but provide limited insight into molecular cues that drive this process during lung injury repair and fibrosis. Fibronectin and RGD-binding integrins have long been considered pro-fibrotic factors in myofibroblast biology, and here we test the hypothesis that these known myofibroblast cues coordinate pericyte-to-myofibroblast transitions. Specifically, we hypothesized that αvβ3 integrin engagement on fibronectin induces pericyte transition into myofibroblastic phenotypes in the murine bleomycin lung injury model. Myosin Heavy Chain 11 (Myh11)-CreERT2 lineage tracing in transgenic mice allows identification of cells of pericyte origin and provides a robust tool for isolating pericytes from tissues for further evaluation. We used this murine model to track and characterize pericyte behaviors during tissue repair. The majority of Myh11 lineage-positive cells are positive for the pericyte surface markers, PDGFRβ (55%) and CD146 (69%), and display typical pericyte morphology with spatial apposition to microvascular networks. After intratracheal bleomycin treatment of mice, Myh11 lineage-positive cells showed significantly increased contractile and secretory markers, as well as αv integrin expression. According to RNASeq measurements, many disease and tissue-remodeling genesets were upregulated in Myh11 lineage-positive cells in response to bleomycin-induced lung injury. In vitro, blocking αvβ3 binding through cyclo-RGDfK prevented expression of the myofibroblastic marker αSMA relative to controls. In response to RGD-containing provisional matrix proteins present in lung injury, pericytes may alter their integrin profile. This altered matrix-integrin axis contributes to pericyte-to-myofibroblastic transition and represents a possible therapeutic target for limiting the myofibroblastic burden in lung fibrosis.HighlightsPericyte lineage model enables study of transdifferentiating pericytesHigh dimensional flow cytometry used to characterize pulmonary stromal cellsPulmonary pericytes express matrix-remodeling genes and proteins in lung injuryMyofibroblasts derived from pericytes have active αvβ3 integrinIn vitro assay reveals necessity of RGD for pericyte transdifferentiation
Divergent profiles of fentanyl withdrawal and associated pain in mice and rats
Authors: Uddin Olivia , Jenne Carleigh , Fox Megan E. , Arakawa Keiko , Keller Asaf , Cramer Nathan 
Published: November 2020

AbstractOpioid abuse has devastating effects on patients, their families, and society. Withdrawal symptoms are severely unpleasant, prolonged, and frequently hinder recovery or lead to relapse. The sharp increase in abuse and overdoses arising from the illicit use of potent and rapidly-acting synthetic opioids, such as fentanyl, highlights the urgency of understanding the withdrawal mechanisms related to these drugs. Progress is impeded by inconsistent reports on opioid withdrawal in different preclinical models. Here, using rats and mice of both sexes, we quantified withdrawal behaviors during spontaneous and naloxone-precipitated withdrawal, following two weeks of intermittent fentanyl exposure. We found that both mice and rats lost weight during exposure and showed increased signs of distress during spontaneous and naloxone precipitated withdrawal. However, these species differed in their expression of withdrawal associated pain, a key contributor to relapse in humans. Spontaneous or ongoing pain was preferentially expressed in rats in both withdrawal conditions, while no change was observed in mice. In contrast, withdrawal associated thermal hyperalgesia was found only in mice. These data suggest that rats and mice diverge in how they experience withdrawal and which aspects of the human condition they most accurately model. These differences highlight each species’ strengths as model systems and can inform experimental design in studies of opioid withdrawal.
Genetic manipulation of the Brassicaceae smut fungusThecaphora thlaspeos
Authors: Plücker Lesley , Bösch Kristin , Geißl Lea , Hoffmann Philipp , Göhre Vera 
Published: November 2020

AbstractInvestigation of plant-microbe interactions greatly benefits from genetically tractable partners to address molecularly the virulence and defense mechanisms. The smut fungusUstilago maydisis a model pathogen in that sense: efficient homologous recombination and a small genome allow targeted modification. On the host side, maize is limiting with regard to rapid genetic alterations. By contrast, the model plantArabidopsis thalianais an excellent model with a vast amount of information and techniques as well as genetic resources. Here, we present a transformation protocol for the Brassicaceae smut fungusThecaphora thlaspeos. Using the well-established transformation of protoplasts, we generated the first reporter strains expressing fluorescent proteins to follow mating. As a proof-of-principle for homologous recombination, we deleted the pheromone receptorpra1. As expected, this mutant cannot mate. Further analysis will contribute to our understanding of the role of mating for infection biology in this novel model fungus. From now on, the genetic manipulation ofT. thlaspeos, which is able to colonize the model plantA. thaliana,provides us with a pathosystem, in which both partners are genetically amenable to study smut infection biology.
Mutations in the juxtamembrane segment of the cholesterol-binding site of APP alter its processing and promotes production of shorter, less toxic Aβ peptides
Authors: Hanbouch Linda , Schaack Béatrice , Kasri Amal , Fontaine Gaëlle , Gkanatsiou Eleni , Brinkmalm Gunnar , Portelius Erik , Blennow Kaj , Mourier Gilles , Gilles Nicolas , Millan Mark J , Marquer Catherine , Zetterberg Henrik , Boussicault Lydie , Potier Marie-Claude 
Published: November 2020

AbstractBackgroundThe brains of patients with Alzheimer’s disease (AD) reveal increased cellular membrane levels of cholesterol. Correspondingly, we previously showed that elevating levels of membrane cholesterol in neuronal cultures recapitulates early AD phenotypes including excessive cleavage of amyloid β (Aβ) peptides from the amyloid precursor protein (APP). Here we aimed to evaluate how the presence of a cholesterol-binding site (CBS) in the transmembrane and juxtamembrane regions of APP regulates its processing.MethodsWe generated seven single and two double APP mutants at amino acid positions 22, 26, 28, 29, 33, 39 of the Aβ sequence changing the charge and/or hydrophobicity of the targeted amino acids. HEK293T cells were transfected with APP constructs and secreted Aβ peptides were measured using ELISA and mass spectrometry (MS). APP processing in normal and high cholesterol condition, and endocytosis were assessed in stably expressing APPwtand APPK28AHEK293T clones. Finally, we measured the binding of synthetic peptides derived from the Aβ sequence to cholesterol-rich exosomes purified from control HEK293T cells.ResultsMost mutations triggered a reduction in the production of Aβ40 and Aβ42 peptides, whereas only juxtamembrane mutants resulted in the generation of shorter Aβ peptides. We confirmed by mass spectrometry this specific change in the profile of secreted Aβ peptides for the most characteristic APPK28Amutant. A transient increase of plasma membrane cholesterol enhanced the production of Aβ40 by APPWT, an effect absent with APPK28A. The enzymatic activity of α-, β- and γ-secretases remained unchanged in cells expressing APPK28A. Similarly, APPK28Asubcellular localization in early endosomes did not differ to APPWT. Finally, WT but not CBS mutant Aβ derived peptides bound to cholesterol-rich exosomes.ConclusionsTaken together, these data reveal a major role of the juxtamembrane region of APP in binding to cholesterol and accordingly in the regulation of APP processing. Binding of cholesterol to K28 could staple APP to the juxtamembrane region thereby permitting access to γ-secretase cleavage at positions 40-42. The APPK28 mutant would lie deeper in the membrane, facilitating the production of shorter Aβ peptides and unveiling this specific region as a novel target for reducing the production of toxic Aβ species.
Comparison of changes in electrical activity, in isolated andin vivohearts, induced by voluntary exercise in female rats
Authors: Stones Rachel , Drinkhill Mark , White Ed 
Published: November 2020

AbstractRegular mild exercise is recommended to the general population as beneficial to health. Regular exercise typically leads to structural and electrical remodelling of the heart but in human studies it is difficult to relate the extrinsic and intrinsic influences on intact hearts to changes seen at the single cell level. In this study we wished to test whether changes in electrical activity in intact hearts, in response to voluntary wheel running exercise training, were consistent with our previous observations in single cardiac myocytes and whether these changes resulted in altered susceptibility to arrhythmic stimuli.Female rats performed 5 weeks of voluntary wheel running. Implanted telemetry transmitters were used to measure electrocardiograms (ECGs) and determine heart rate variability (HRV) in conscious, unrestrained, trained (TRN) and sedentary (SED) animals. In isolated hearts, left ventricular epicardial monophasic action potentials (MAPs) were recorded and the responses to potentially arrhythmic interventions were assessed.Exercise training caused cardiac hypertrophy, as indexed by a significantly greater heart weight to body weight ratio. Consistent with previous measurements of action potential duration in single myocytes, MAPs were significantly longer at 50%, 75% and 90% repolarization. Arrhythmic susceptibility was not different between SED and TRN hearts. Trained animals displayed significantly altered HRV by week 5, in a manner consistent with reduced sympathetic tone, however resting ECG parameters, including those most associated with repolarisation duration, were unaltered. We conclude that intrinsic changes to cellular cardiac electrophysiology, induced by mild voluntary exercise, are not attenuated by the electronic loading that occurs in intact hearts. However,in vivo,extrinsic neuro-hormonal control of the heart may minimize the effects of intrinsic alterations in electrical activity.
Genetic variation at the species and population levels in the Rocky Mountain ridged mussel (Gonidea angulata)
Authors: Mock Karen E. , Walton James A. , Brownlee Steven F. R. , Mageroy Jon H. , Wilson Greg , Walker Ian R. 
Published: November 2020

AbstractFreshwater mussels in western North America are threatened by water diversions, climate change, loss of required host fish, and other factors, and have experienced marked decline in the past several decades. All four of the primary lineages (potentially species) of freshwater mussels in the western U.S. and Canada are widespread and have somewhat generalist host fish requirements. Of these lineages, perhaps the most poorly understood and of greatest conservation concern isGonidea angulata(Rocky Mountain ridged mussel).Gonideais a monotypic genus occurring only in the western continental U.S. and southern Canada. Here we describe the patterns of genetic variation across the species range, including several populations in the Okanagan Valley at the northern edge of the range. We detected only ten mitochondrial cytochrome oxidase I haplotypes, three of which ere commonly found across major hydrologic basins, and the remainder of which were basin-specific variants. Haplotypes differed by a maximum of 5 of 537 nucleotides. New microsatellite loci were developed forG. angulataas a part of this study. Data from these microsatellite loci indicated that the population in the Chehalis River, Washington, was distinct from other locations, and that the Okanagan lake population was somewhat diverged from the remaining populations in the Columbia River and Klamath Lake. Only low levels of inbreeding were detected, in contrast to previous findings inMargartifera falcata,suggesting that hermaphroditism is not common. The population with the least diversity, according to microsatellite data, was the northernmost known population in Okanagan Lake We discuss the biogeographic and conservation implications of our findings.
High resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies
Authors: Garrett Meghan E. , Galloway Jared , Chu Helen Y. , Itell Hannah L. , Stoddard Caitlin I. , Wolf Caitlin R. , Logue Jennifer K. , McDonald Dylan , Matsen Frederick A. , Overbaugh Julie 
Published: November 2020

SUMMARYDefining long-term protective immunity to SARS-CoV-2 is one of the most pressing questions of our time and will require a detailed understanding of potential ways this virus can evolve to escape immune protection. Immune protection will most likely be mediated by antibodies that bind to the viral entry protein, Spike (S). Here we used Phage-DMS, an approach that comprehensively interrogates the effect of all possible mutations on binding to a protein of interest, to define the profile of antibody escape to the SARS-CoV-2 S protein using COVID-19 convalescent plasma. Antibody binding was common in two regions: the fusion peptide and linker region upstream of the heptad repeat region 2. However, escape mutations were variable within these immunodominant regions. There was also individual variation in less commonly targeted epitopes. This study provides a granular view of potential antibody escape pathways and suggests there will be individual variation in antibody-mediated virus evolution.