bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct denitrifying phenotypes of predominant bacteria mould nitrous oxide metabolism in upland agricultural soils
Authors: Wu Qiaoyu , Ji Mengmeng , Yu Siyu , Li Ji , Wu Xiaogang , Ju Xiaotang , Liu Binbin , Zhang Xiaojun 
Published: March 2022

AbstractDenitrifying nitrous oxide (N2O) emissions in agroecosystems result from variations in microbial composition and soil properties. However, the microbial mechanisms of differential N2O emissions in agricultural soils are less understood. Microcosm experiments of two types of Chinese farmland soil were conducted with nitrate (250 mg/kg) and a combination of glucose (1000 mg/kg) and nitrate, and a case with no addition was used as the control. The results show that N2O accumulation in black soil (BF) was significantly higher than that in fluvo-aquic soil (FF) independent of carbon and nitrogen supply. The abundance of denitrifying genes was significantly higher in FF, but the ratios of genes responsible for N2O production (narG, nirS, and nirK) to the gene for N2O reduction (nosZ) did not significantly differ between the two soils. However, the soils showed obvious discrepancies in denitrifying bacterial communities. High accumulation of N2O was verified by the isolates of Rhodanobacter, which is predominant in BF due to its truncated denitrifying genes and lack of N2O reduction capacity. The dominance of complete denitrifiers such as Castellaniella in FF led to a rapid reduction in N2O and reduced N2O accumulation, as demonstrated when its corresponding isolate was inoculated into both studied soils. Therefore, the different phenotypes of N2O metabolism of the distinct denitrifiers maintained in the two soils caused their differing N2O accumulation. This knowledge could guide the regulation of the denitrifying bacterial community and the phenotypes of N2O metabolism in agricultural soils to reduce N2O emissions.
miR-329 and miR-495-mediated Prr7 downregulation is required for homeostatic synaptic depression in rat hippocampal neurons
Authors: Inouye Michiko O. , Colameo David , Ammann Irina , Schratt Gerhard 
Published: March 2022

AbstractHomeostatic synaptic depression (HSD) in excitatory neurons is a cell autonomous mechanism which protects excitatory neurons from over-excitation as a consequence of chronic increases in network activity. In this process, excitatory synapses are weakened and eventually eliminated, as evidenced by a reduction in synaptic AMPA receptor expression and dendritic spine loss. Originally considered a global, cell-wide mechanism, local forms of regulation, such as the local control of mRNA translation in dendrites, are being increasingly recognized in HSD. Yet, identification of excitatory proteins whose local regulation is required for HSD is still limited. Here, we show that Proline-rich protein 7/Transmembrane Adapter Protein 3 (Prr7) downregulation in dendrites of rat hippocampal neurons is necessary for HSD induced by chronic increase in network activity resulting from a blockade of inhibitory synaptic transmission by picrotoxin (PTX). We further identify two activity-regulated miRNAs, miR-329-3p and miR-495-3p, which inhibit Prr7 mRNA translation and are required for HSD. Moreover, we found that Prr7 knockdown reduces expression of the synaptic scaffolding protein SPAR, which is rescued by pharmacological inhibition of CDK5, indicating a role of Prr7 protein in the maintenance of excitatory synapses via protection of SPAR from degradation. Together, our findings highlight a novel HSD mechanism in which chronic activity leads to miR-329 and miR-495-mediated local Prr7 reduction upstream of the CDK5-SPAR pathway.
Parasite and pathogen prevalence in our closest animal companions is determined by accessibility of sanitation services
Authors: Chalkowski Kayleigh , Lepczyk Christopher A. , Wilson Alan E. , Valenta Kim , Sipley Breanna , Brownlee Joi , Morgan Abbey M. , Santos Scott R. , Willoughby Janna R. , Zohdy Sarah 
Published: March 2022

AbstractDespite the critical role parasites play in ecosystem functioning and their considerable influence on human society, little is known about their variations in abundance on a global scale. This gap in knowledge is amplified by a lack of holistic understanding on how the abundance of parasites of wildlife and humans varies across environmental and socioeconomic gradients, despite a need to integrate study of parasites across social and environmental spheres. Free-roaming companion animals (e.g., domestic cats (Felis catus) and dogs (Canis lupus familiaris)) share pathogens and have frequent contact with humans and wildlife. Thus, they are an effective model to understand how parasite and pathogen prevalence of humans and wildlife varies across environmental and socioeconomic gradients. Through a global systematic review and analysis of socioeconomic and environmental variables, including per capita GDP, income disparity, sanitation, biodiversity, island habitation, and latitude, we find that sanitation and island habitation best explained free-roaming companion animal parasite and pathogen prevalence. Sanitation was significantly associated with parasite and pathogen prevalence in free-roaming companion animals, such that for every 10% increase in the proportion of the human population with improved sanitation access, parasite and pathogen prevalence in free-roaming companion animals decreased by 12% (5-19%, 95% C.L.; p = 0.0023). Since companion animals share many parasites with humans and wildlife, these results suggest that actionable interventions to improve sanitation access could reduce parasite and pathogen exposure risks from companion animals to humans and wildlife.Significance StatementIn addition to playing a critical role in ecosystem functioning, parasites also influence human health, behavior, and society. Further, parasites are also impacted by human activities, as much as by ecological phenomena in natural environments. Despite these dualities, little is known about their variations in abundance on a global scale across environmental and socioeconomic gradients. Using free-roaming companion animals (e.g., domestic cats (Felis catus) and dogs (Canis lupus familiaris)) as a model system, we find that access to safely managed sanitation services is strongly associated with parasite and pathogen prevalence. This finding underscores improvements to sanitation as an actionable One Health intervention that could reduce parasite and pathogen exposure risks from companion animals to humans and wildlife.
Oil accumulation in leaves driven by a native promoter-gene fusion created using CRISPR/Cas9 mediated genomic deletion
Authors: Bhunia Rupam Kumar , Menard Guillaume , Eastmond Peter J. 
Published: March 2022

AbstractAchieving gain-of-function phenotypes without inserting foreign DNA is an important challenge for plant biotechnologists. Here we show that a gene can be brought under the control of a promoter from an upstream gene by deleting the intervening genomic sequence using dual-guide CRISPR/Cas9. We fuse the promoter of a non-essential photosynthesis-related gene to DIACYLGLYCEROL ACYLTRANSFERASE 2 (DGAT2) to drive oil biosynthesis in leaves of a lipase deficient sugar-dependent 1 mutant. DGAT2 expression is enhanced more than twenty-fold and the triacylglycerol content increases by around thirty-fold. This strategy offers a transgene-free route to engineering gain-of-function traits such as high lipid forage to increase the productivity and sustainability of ruminant farming.
Kaempferol over-accumulation in the flavonoid 3’ hydroxylase tt7 mutant disrupts seed coat outer integument differentiation and compromises seed longevity
Authors: Niñoles R , Arjona P. , Hashim A. , Bueso E. , Serrano R. , Molina I. , Gadea J 
Published: March 2022

SUMMARYSeeds slowly accumulate damage during storage, which ultimately results in germination failure. The seed coat is the barrier between the embryo and the external environment, and its composition is critical for seed longevity. Flavonols accumulates in the outer integument, but the effect of altering flavonol composition on outer integument development has not been explored.Genetic, biochemical, ultrastructural and transcriptomics assays on a battery of loss-of-function mutants in the flavonoid biosynthesis pathway were used to study the effect of altered flavonoid composition in seed development and seed longevity.Controlled deterioration assays indicate that loss-of-function of the flavonoid 3’ hydroxylase TT7 gene dramatically affects seed longevity and seed development. Seed outer integument differentiation is compromised from nine days after pollination in tt7 seeds, with a defective suberine layer and incomplete degradation of seed-coat starch. These distinctive phenotypes are not shared by other mutants showing also altered flavonoid composition. Double-mutant analysis indicate that over-accumulation of kaempferol is the primary cause of the observed phenotypes. Expression analysis suggest that the tt7 flavonoid pattern affects transcriptional and non-transcriptional levels of regulation.The increase of kaempferols in the seed coat influences seed development. This positions TT7 as an essential player modulating seed coat development and seed longevity.
Myosin essential light chain 1sa decelerates actin and thin filament gliding on β-myosin molecules
Authors: Osten Jennifer , Mohebbi Maral , Uta Petra , Matinmehr Faramarz , Wang Tianbang , Kraft Theresia , Amrute-Nayak Mamta , Scholz Tim 
Published: March 2022

AbstractThe β-myosin heavy chain expressed in ventricular myocardium and the myosin heavy chain (MyHC) in slow-twitch skeletal soleus muscle type-I fibers are both encoded by MYH7. Thus, these myosin molecules are deemed equivalent. However, some reports suggested variations in the light chain composition between soleus and ventricular myosin, which could influence functional parameters such as maximum velocity of shortening. To test for functional differences of the actin gliding velocity on immobilized myosin molecules we made use of the in vitro motility assay.We found that ventricular myosin moved actin filaments with approx. 0.9 μm/s significantly faster than soleus myosin (0.3 μm/s). Unregulated actin filaments are not the native interaction partner of myosin and are believed to slow down movement. Yet, using native thin filaments purified from soleus or ventricular tissue, the gliding velocity of soleus and ventricular myosin remained significantly different. When comparing the light chain composition of ventricular and soleus β-myosin a difference became evident. Soleus myosin contains not only the “ventricular” essential light chain (ELC) MLC1sb/v, but also an additional longer and more positively charged MLC1sa. Moreover, we revealed that on a single muscle fiber level, a higher relative content of MLC1sa was associated with significantly slower actin gliding.We conclude that the ELC MLC1sa decelerates gliding velocity presumably by a decreased dissociation rate from actin associated with a higher actin affinity compared to MLC1sb/v. Such ELC/actin interactions might also be relevant in vivo as differences between soleus and ventricular myosin persisted when native thin filaments were used.SummaryCompared to the “ventricular” essential myosin light chain MLC1sb/v, the longer and more positively charged MLC1sa present in slow-twitch soleus muscle fibers decelerates actin filament gliding on β-myosin molecules presumably by a decreased dissociation rate from actin filaments.
Biodiversity effects on seedling biomass growth are modulated by light environment across functional groups
Authors: Anujan Krishna , Shabnam Alisha , Ali Irfan , Kumar G Ashok , Sankaran Mahesh , Krishnadas Meghna , Naeem Shahid 
Published: March 2022

AbstractTree biodiversity has the potential to ensure consistency in the functioning of forest ecosystems, not just over space, but over long-timescales by maintaining composition through recruitment. However, for continued buffering in the face of global environmental change, the sensitivity of biodiversity-ecosystem functioning relationships to heterogeneous environments needs to be understood.Seedling recruitment in carbon-rich tropical forests is a result of biotic and abiotic drivers but their combined outcomes at the community-level remain poorly understood. Although biodiversity in seedling communities can potentially increase their growth and biomass accumulation, abiotic drivers like light can alter this effect through divergent effects on constituent species and functional groups. In forests with high baseline heterogeneity in microclimates, these processes can enhance or constrain regeneration.We tested the effects and interactions between species richness and canopy cover on the growth of seedling communities consisting of tropical broad-leaved evergreen and deciduous forest species using a fully crossed manipulated experiment in the Andaman Islands, India and compared these with field observations from a long-term forest plot in the same landscape.We show that in the critical seedling establishment phase, species richness and light increase community biomass independently. Accounting for variation across species, individual species on average accumulated more biomass in communities with both higher light and higher diversity.We also show that overyielding in species rich communities fits expectations from a model of complementarity with non-random overyielding than selection or spatial insurance effects.Synthesis Taken together, our results show that the potential for biodiversity to increase ecosystem functioning in seedling communities is modulated by light. Further understanding on the interaction of biodiversity with multiple abiotic drivers and their effect on regeneration dynamics is crucial for predicting future ecosystem functioning.
Remodeled Connexin 43 hemichannels alter cardiac excitability and promote arrhythmias
Authors: Lillo Mauricio A. , Muñoz Manuel F. , Gaul-Muller Kelli , Shirokova Natalia , Xie Lai-Hua , Fraidenraich Diego , Contreras Jorge E. 
Published: March 2022

ABSTRACTConnexin-43 (Cx43) is the most abundant protein forming gap junction channels (GJCs) in cardiac ventricles. In multiple cardiac pathologies, including hypertrophy and heart failure, Cx43 is found remodeled at the lateral side of the intercalated discs of ventricular cardiomyocytes. Remodeling of Cx43 has been long linked to spontaneous ventricular arrhythmia, yet the mechanisms by which arrhythmias develop are still debated. Using a model of a dystrophic cardiomyopathy, we previously showed that remodeled Cx43 function as aberrant hemichannels (non-forming GJCs) that alter cardiomyocyte excitability and, consequently, promote arrhythmias. Here, we aim to evaluate if opening of remodeled Cx43 can serve as a general mechanism to alter cardiac excitability independent of cellular dysfunction associated with a particular cardiomyopathy. To address this issue, we used a genetically modified Cx43 knock-in mouse (S3A) that promotes cardiac remodeling of Cx43 protein without apparent cardiac dysfunction. Importantly, when S3A mice were subjected to cardiac stress using the β-adrenergic agonist isoproterenol (Iso), they displayed acute and severe arrhythmias, which were not observed in WT mice. Pre-treatment of S3A mice with the Cx43 hemichannel blocker, Gap19, prevented Iso-induced abnormal electrocardiographic behavior. At the cellular level, when compared with WT, Iso-treated S3A cardiomyocytes showed increased membrane permeability and greater plasma membrane depolarization, which subsequently leads to triggered activity. These cellular dysfunctions were also prevented by Cx43 hemichannel blockers. Our results support the notion that opening of remodeled Cx43 hemichannels, regardless of the type of cardiomyopathy, is sufficient to mediate cardiac stress-induced arrhythmogenicity.
Probing function in ligand-gated ion channels without measuring ion transport
Authors: Godellas Nicole E. , Grosman Claudio 
Published: March 2022

ABSTRACTAlthough the functional properties of ion channels are most accurately assessed using electrophysiological approaches, a number of experimental situations call for alternative methods. Here, working on members of the pentameric ligand-gated ion-channel (pLGIC) superfamily, we focused on the practical implementation of, and the interpretation of results from, equilibrium-type ligand-binding assays. Ligand-binding studies of pLGICs are—by no means—new, but the lack of uniformity in published protocols, large disparities between the results obtained for a given parameter by different groups, and a general disregard for constraints placed on the experimental observations by simple theoretical considerations suggested that a thorough analysis of this classic technique was in order. To this end, we present a detailed practical and theoretical study of this type of assay using radiolabeled α-bungarotoxin, unlabeled small-molecule cholinergic ligands, the human homomeric α7-AChR, and extensive calculations in the framework of a realistic five-binding-site reaction scheme. Furthermore, we show examples of the practical application of this method to tackle two long-standing questions in the field: whether ligand-binding affinities are sensitive to binding-site occupancy, and whether mutations to amino-acid residues in the transmembrane domain can affect the channel’s affinities for ligands that bind to the extracellular domain.
ezQTL: A Web Platform for Interactive Visualization and Colocalization of Quantitative Trait Loci and GWAS
Authors: Zhang Tongwu , Klein Alyssa , Sang Jian , Choi Jiyeon , Brown Kevin M 
Published: March 2022

AbstractGenome-wide association studies (GWASs) have identified thousands of genomic loci associated with complex diseases and traits, including cancer. The vast majority of common trait-associated variants identified via GWAS fall in non-coding regions of the genome, posing a challenge in elucidating the causal variants, genes, and mechanisms involved. Expression quantitative trait locus (eQTL) and other molecular QTL studies have been valuable resources in identifying candidate causal genes from GWAS loci through statistical colocalization methods. While QTL colocalization is becoming a standard analysis in post-GWAS investigation, an easy web tool for users to perform formal colocalization analyses with either user-provided or public GWAS and eQTL datasets has been lacking. Here, we present ezQTL, a web-based bioinformatic application to interactively visualize and analyze genetic association data such as GWAS and molecular QTLs under different linkage disequilibrium (LD) patterns (1000 Genomes Project, UK Biobank, or user-provided data). This application allows users to perform data quality control for variants matched between different datasets, LD visualization, and two-trait colocalization analyses using two state-of-the-art methodologies (eCAVIAR and HyPrColoc), including batch processing. ezQTL is a free and publicly available cross-platform web tool, which can be accessed online at https://analysistools.cancer.gov/ezqtl.
Inter-microscope comparability of dental microwear texture data obtained from different optical profilometers
Authors: Winkler Daniela E. , Kubo Mugino O. 
Published: March 2022

AbstractDental microwear texture analysis has become a well-established approach for dietary inference and reconstruction of mammals and other tetrapods, both extant and extinct. As the amount of available data grows immensely, researchers could benefit from combining data gathered by others to perform meta-analyses. However, different devices used to capture three-dimensional surface scans for DMTA are known to produce variation even when measuring the same surface. Here we compare DMTA data of 36 guinea pigs that received different diets in a controlled feeding experiment, measured on a confocal disc-scanning and a confocal laser-scanning microscope. We are testing different pre-analysis filtering protocols to mitigate differences. We find inter-microscopes and filter-related differences for the majority of analysed 41 DMTA parameters. Certain microscope-specific filter routines resulted in less differences than other pre-analysis protocols. We further identify DMTA parameters which were stable regardless of microscope or pre-analysis treatment. Overall, the results obtained on both microscopes show the same dietary differentiation between guinea pig feeding groups, which supports that DMTA is a suitable method to obtain repeatable, objective dietary inferences. We finally propose a roadmap to enhance data exchange and inter-lab comparability and collaboration in the future.
Cultural adaptation of the person-centered maternity care scale at governmental health facilities in Cambodia
Authors: Naito Yuko Takahashi , Fukuzawa Rieko , Afulani Patience A. , Kim Rattana , Aiga Hirotsugu 
Published: March 2022

AbstractBackgroundIn Cambodia, the importance of valuing women’s childbirth experiences in improving quality of care has been understudied. This is largely because of absence of reliable Khmer tools for measuring women’s intrapartum care experiences. Generally, cross-cultural development of those tools often involves translation from a source language into a target language. Yet, few earlier studies considered Cambodian cultural context. Thus, we developed the Cambodian version of the Person-Centered Maternity Care (PCMC) scale, by culturally adapting its original to Cambodian context for ensuring cultural equivalence and content validity.MethodsThree rounds of cognitive interviewing with 20 early postpartum women were conducted at two governmental health facilities in Cambodia. Cognitive interviewing was composed of structured questionnaire pretesting and qualitative probing. The issues identified in the process of transcribing and translating audio-recorded cognitive interviews were iteratively discussed among study team members, and further analyzed.ResultsA total of 14 issues related to cultural adaptations were identified in the 31 translated questions for the Cambodian version of the PCMC scale. Our study identified three key findings: (i) discrepancies between the WHO recommendations on intrapartum care and Cambodian field realities; (ii) discrepancies in recognition on PCMC between national experts and local women; and (iii) challenges in correctly collecting and interpreting less-educated women’s views on intrapartum care.ConclusionNot only women’s verbal data but also their non-verbal data and cultural contexts should be comprehensively counted, when reflecting Cambodian women’s intrapartum practice realities in the translated version. This is the first study that attempted to develop the tool for measuring Cambodian women’s experiences during childbirth, by addressing cross-cultural issues.
Stem cell regulators control a G1 duration gradient in the plant root meristem
Authors: Echevarria Clara , Desvoyes Bénédicte , Marconi Marco , Franco-Zorrila José Manuel , Lee Laura , Umeda Masaaki , Sablowski Robert , Birnbaum Kenneth D. , Wabnik Krzysztof , Gutierrez Crisanto 
Published: March 2022

AbstractIn meristems, where new plant organs initiate, key stem cell regulators have been identified, but their link to cell cycle progression remains unclear. Here, we show that the root meristem has a positional gradient of G1 duration that ranges from ∼2 h near the meristem boundary to more than 20 h in stem cells and early derivatives. Mutants in the PLETHORA (PLT) genes shortened G1 length and flattened its gradient. Computer modeling of an incoherent feed-forward loop (IFFL) predicted the inference of a negative regulatory pathway. We propose that PLT genes play opposing roles, maintaining meristem and stem cell activity and inhibiting G1 progression through the CDK inhibitor KRP5, a PLT target, and RBR1. This establishes a previously undescribed proximal-distal feature of the root meristem in which a G1 duration gradient is shaped by stem cell and meristem maintenance regulators.