bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards Stewardship of Wild Species and Their Domesticated Counterparts: A Case Study in Northern Wild Rice (Zizania palustrisL.)
Authors: McGilp Lillian , Haas Matthew W. , Shao Mingqin , Millas Reneth , Castell-Miller Claudia , Kern Anthony J. , Shannon Laura M. , Kimball Jennifer A. 
Published: August 2022

AbstractNorthern Wild Rice (NWR;Zizania palustrisL.) is an aquatic, annual grass with significant ecological, cultural, and economic importance to the Great Lakes region of North America. In this study, we assembled and genotyped a diverse collection of 839 NWR individuals using genotyping-by-sequencing (GBS) and obtained 5,955 single-nucleotide polymorphisms (SNPs). Our collection consisted of samples from 12 wild NWR populations collected across Minnesota and Western Wisconsin, some of which were collected over two time points; a representative collection of cultivated NWR varieties and breeding populations; and aZizania aquaticaoutgroup. Using these data, we characterized the genetic diversity, relatedness, and population structure of this broad collection of NWR genotypes. We found that wild populations of NWR clustered primarily by their geographical location, with some clustering patterns likely influenced by historical ecosystem management. Cultivated populations were genetically distinct from wild populations, suggesting limited gene flow between the semi-domesticated crop and its wild counterparts. The first genome-wide scans of putative selection events in cultivated NWR suggest that the crop is undergoing heavy selection pressure for traits conducive to irrigated paddy conditions. Overall, this study presents a large set of SNP markers for use in NWR genetic studies and provides new insights into the gene flow, history, and complexity of wild and cultivated populations of NWR.
Alignment-free microbiome-based classification of fresh produce safety and quality
Authors: Liao Chao , Wang Luxin , Quon Gerald 
Published: August 2022

AbstractSmall samples sizes and loss of up to 50-70% of sequencing data during the data denoising step of preprocessing can limit the statistical power of fresh produce microbiome analyses and prevent detection of important bacterial species associated with produce contamination or quality reduction. Here, we explored an alignment-free analysis strategy using k-mer hashes to identify DNA signatures predictive of produce safety and produce quality, and compared it against the amplicon sequence variant (ASV) strategy that uses a typical denoising step. Random forests (RF)-based classifiers for fresh produce safety and quality using 7-mer hash datasets had significantly higher classification accuracy than those using the ASV datasets. We also demonstrated that the proposed combination of integrating multiple datasets and leveraging an alignment-free 7-mer hash strategy leads to better classification performance for fresh produce safety and quality. Results generated from this study lay the foundation for future studies that wish and need to incorporate and/or compare different microbiome sequencing datasets for the application of machine learning in the area of microbial safety and quality of food.
A molecular switch modulates assembly and host factor binding of the HIV-1 capsid
Authors: Schirra Randall T. , dos Santos Nayara F. B. , Zadrozny Kaneil K. , Kucharska Iga , Ganser-Pornillos Barbie K. , Pornillos Owen 
Published: August 2022

AbstractUpon entry into a new host cell, the HIV-1 capsid performs multiple essential functions, which include shielding the genome from innate immune sensors1, promoting reverse transcription2 and transporting the core from the entry site at the plasma membrane to the integration site inside the nucleus3,4. The HIV-1 capsid is a fullerene cone made of hexamers and pentamers of the viral CA protein5,6. The two types of capsomers are quasi-equivalent, with the same structural elements mediating distinct inter-subunit contacts. In other studied quasi-equivalent viruses, the capacity of genetically identical subunits to form hexamers and pentamers is conferred by molecular switches. Such a switch has not been previously found in retroviral CA proteins. Here, we report cryoEM structures of the HIV-1 CA pentamer within assembled in vitro capsids at nominal resolutions of 2.4-3.4 Å. Comparison with the hexamer identified an internal loop that adopts distinct conformations, 310 helix in the pentamer and random coil in the hexamer. Designed manipulations of the coil/helix configuration allowed us to control pentamer and hexamer formation in a predictable manner, thus proving its function as a molecular switch. Importantly, the switch controls not only fullerene cone assembly, but also the capsid’s capacity to bind post-entry host factors that are critical for viral replication. Furthermore, the switch forms part of the binding site of the new ultra-potent HIV-1 inhibitor, lenacapavir. These studies reveal that a critical assembly element also controls the post-assembly functions of the capsid, and provide new insights on capsid inhibition and uncoating.
HIV-1 GAG SPECIFICITY FOR PIP2-CONTAINING MEMBRANES MIGHT BE DRIVEN BY MACROMOLECULAR ELECTRIC PROPERTIES RATHER THAN MOLECULAR AFFINITIES
Authors: Socas L. B. P. , Ambroggio E. E. 
Published: August 2022

AbstractThe HIV-1 assembly occurs at the plasma membrane, where the GAG polyprotein plays a crucial role. The GAG-membrane association is directed by the matrix domain (MA), which is myristoylated and has a highly basic region that interacts with the anionic lipids. Several evidence suggests that the presence of phosphatidylinositol-(4,5)-bisphosphate (PIP2) highly influence this binding. In addition, MA also interacts with nucleic acids, which is proposed to be important for the specificity of GAG for PIP2-containing membranes. It is proposed that RNA could have a chaperone function when interacting with the MA domain, preventing GAG from associating with unspecific lipid interfaces. Here, we study the interaction of MA with monolayer and bilayer membrane systems, focused on the specificity for PIP2 and on the possible effects of a GAG N-terminal peptide to impair the binding for either RNA or membrane. We found that RNA decreases the kinetics of the protein association with lipid monolayers but without any effect on the selectivity for PIP2. Interestingly, for bilayer systems, this selectivity increases in presence of both the peptide and RNA, even for highly negative charged compositions, where MA by itself doesn’t discriminate between membranes with or without PIP2. Therefore, we propose that the specificity of MA for PIP2-membranes might be related to the electrostatic properties of both membrane and protein local environments, rather than a simple difference in molecular affinities. This scenario gives a new understanding of the regulation mechanism with a macromolecular view instead of considering molecular interactions within a ligand-receptor model.ImportanceHIV-1 virions are formed at the PM of infected cells through a direct interaction of the viral GAG protein with lipids. This is a finely regulated process governed by the GAG N-terminal matrix domain, MA. Here, we obtained compelling evidence on how this process depends on the local dielectric environments of both, the membrane and MA. Using bio-membrane mimicking systems, we found how MA myristoylation is involved in the interfacial absorption and anchoring of the protein, where the interaction with RNA negatively regulates this process but in a lesser extent when traces of the PIP2 lipid are present. Additionally, an N-terminal GAG-derived peptide competes with MA for the nucleic acid binding and impair the protein-membrane interaction when PIP2 is absent. All these data allowed us to propose a model for MA association with lipid interfaces and how it depends on oligonucleotide binding, lipid composition and competing peptide presence.
Mouse population genetics phenocopies heterogeneity of human Chd8 haploinsufficiency
Authors: Tabbaa Manal , Knoll Allison , Levitt Pat 
Published: August 2022

AbstractPreclinical models of neurodevelopmental disorders typically use single inbred strains which fail to capture human genetic and symptom heterogeneity that is common clinically. We tested if systematically modeling human genetic diversity in mouse genetic reference panels would recapitulate population and individual differences in responses to a syndromic mutation in the high-confidence autism risk gene, CHD8. Trait disruptions mimicked those seen in human populations, including high penetrance of macrocephaly and disrupted behavior, but with robust strain and sex differences. For every trait, some strains exhibited a range of large effect size disruptions, sometimes in opposite directions, and remarkably others expressed resilience. Thus, systematically introducing genetic diversity into mouse models of neurodevelopmental disorders provides a better framework for discovering individual differences in symptom etiologies and improved treatments.One-Sentence SummaryAutism trait heterogeneity due to a syndromic gene mutation is recapitulated in mice by incorporating genetic diversity.
Ion Mobility for Unknown Metabolite Identification: Hope or Hype?
Authors: Asef Carter K. , Rainey Markace , Garcia Brianna M. , Gouveia Goncalo J. , Shaver Amanda O. , Leach Franklin E. , Morse Allison M. , Edison Arthur S. , McIntyre Lauren M. , Fernández Facundo M. 
Published: August 2022

ABSTRACTIon mobility (IM) spectrometry provides semi-orthogonal data to mass spectrometry (MS), showing promise for identifying unknown metabolites in complex non-targeted metabolomics datasets. While current literature has showcased IM-MS for identifying unknowns under near ideal circumstances, less work has been conducted to evaluate the performance of this approach in metabolomics studies involving highly complex samples with difficult matrices. Here, we present a workflow incorporating de novo molecular formula annotation and MS/MS structure elucidation using SIRIUS 4 with experimental IM collision cross-section (CCS) measurements and machine learning CCS predictions to identify differential unknown metabolites in mutant strains of Caenorhabditis elegans. For many of those ion features this workflow enabled the successful filtering of candidate structures generated by in silico MS/MS predictions, though in some cases annotations were challenged by significant hurdles in instrumentation performance and data analysis. While for 37% of differential features we were able to successfully collect both MS/MS and CCS data, fewer than half of these features benefited from a reduction in the number of possible candidate structures using CCS filtering due to poor matching of the machine learning training sets, limited accuracy of experimental and predicted CCS values, and lack of candidate structures resulting from the MS/MS data. When using a CCS error cutoff of ±3%, an average 28% of candidate structures could be successfully filtered. Herein, we identify and describe the bottlenecks and limitations associated with the identification of unknowns in non-targeted metabolomics using IM-MS to focus and provide insight on areas requiring further improvement.
Targeting neuroinflammation with Abscisic Acid reduces pain sensitivity in females and hyperactivity in males of an ADHD mice model
Authors: Meseguer-Beltrán Maria , Sánchez-Sarasúa Sandra , Landry Marc , Kerekes Nóra , Sánchez-Pérez Ana María 
Published: August 2022

ABSTRACTAimsAttention deficit/hyperactivity disorder (ADHD) is a neurodevelopmental syndrome characterized by dopaminergic dysfunction. In this study, we aimed to demonstrate the link between dopaminergic deficit and neuroinflammation underlying ADHD symptoms.Subjects and TreatmentWe used a validated ADHD mice model, that involves perinatal 6-OHDA lesion. Animals were treated with 20mg/L (drinking water) of Abscisic acid (ABA) for one month. We tested behaviour (learning and memory, anxiety, social interactions, and pain) in both females and male mice, in all eight groups (control and lesioned, with/without ABA). Postmortem, we analyzed microglia morphology and Ape1 expression in specific brain areas related to the descending pain inhibitory pathway.ResultsIn females, dopaminergic deficit increased pain sensitivity, but not hyperactivity, in contrast to males. This behaviour was associated with inflammatory microglia and lower Ape1 levels in the anterior cingulate cortex (ACC) and posterior insula cortex (IC). ABA treatment reduced inflammation and alleviated pain. In males, ABA reduced hyperactivity, but had no significant effect on inflammation.ConclusionsThis is the first study proving a sex-dependent association between dopamine dysfunction and inflammation in specific brain areas, leading to different behavior outcomes in a mouse model of ADHD. These findings provide new clues for potential treatments.
Single-cell transcriptomic profiling in inherited retinal degeneration reveals distinct metabolic pathways in rod and cone photoreceptors
Authors: Chen Yiyi , Dong Yujie , Yan Jie , Wang Lan , Yu Shirley , Jiao Kangwei , Paquet-Durand François 
Published: August 2022

AbstractThe cellular mechanisms underlying hereditary photoreceptor degeneration are still poorly understood. The aim of this study was to systematically map the transcriptional changes that occur in the degenerating mouse retina at the single cell level. To this end, we employed single cell RNA-sequencing (scRNA-seq) and retinal degeneration-1 (rd1) mice to profile the impact of the disease mutation on the diverse retinal cell types during early post-natal development. The transcriptome data allowed to annotate 43,979 individual cells grouped into 20 distinct retinal cell types. We further characterized cluster-specific metabolic and biological changes in individual cell types. Our results highlight Ca2+-signaling as relevant to hereditary photoreceptor degeneration. Though metabolic reprogramming in retina, known as ‘Warburg effect’, has been documented, further metabolic changes were noticed in rd1 mice. Such metabolic changes in rd1 mutation was likely regulated through mitogen-activated protein kinase (MAPK) pathway. By combining single-cell transcriptomes and immunofluorescence staining, our study revealed cell type-specific changes in gene expression, as well as interplay between Ca2+ induced cell death and metabolic pathways.
Multiple polarity kinases inhibit phase separation of F-BAR protein Cdc15 and antagonize cytokinetic ring assembly in fission yeast
Authors: Bhattacharjee Rahul , Hall Aaron , Mangione MariaSanta C. , Igarashi Maya G. , Roberts-Galbraith Rachel H. , Chen Jun-Song , Vavylonis Dimitrios , Gould Kathleen L. 
Published: August 2022

AbstractThe F-BAR protein Cdc15 is essential for cytokinesis in Schizosaccharomyces pombe and it plays a key role in attaching the cytokinetic ring (CR) to the plasma membrane. Cdc15’s abilities to bind to the membrane and oligomerize via its F-BAR domain are inhibited by phosphorylation of its intrinsically disordered region (IDR). Multiple cell polarity kinases regulate Cdc15 IDR phosphostate, and of these the DYRK kinase Pom1 phosphorylation sites on Cdc15 have been shown in vivo to prevent CR formation at cell tips. Here, we compared the ability of Pom1 to control of Cdc15 phosphostate and cortical localization to that of other Cdc15 kinases: Kin1, Pck1, and Shk1. We identified distinct but overlapping cohorts of Cdc15 phosphorylation sites targeted by each kinase, and the number of sites correlated with each kinases’ abilities to influence Cdc15 PM localization. Coarse-grained simulations predicted that cumulative IDR phosphorylation moves the IDRs of a dimer apart and toward the F-BAR tips. Further, simulations indicated that the overall negative charge of phosphorylation masks positively charged amino acids necessary for F-BAR oligomerization and membrane interaction. Finally, simulations suggested that dephosphorylated Cdc15 undergoes phase separation driven by IDR interactions. Indeed, dephosphorylated but not phosphorylated Cdc15 undergoes liquid-liquid phase separation to form droplets in vitro that recruit Cdc15 binding partners. In cells, Cdc15 phosphomutants also formed PM-bound condensates that recruit other CR components. Together, we propose that a threshold of Cdc15 phosphorylation by assorted kinases prevents Cdc15 condensation on the PM and antagonizes CR assembly.
The exploration in the size of scientific collaboration team using kernel density estimation
Authors: An Ran , Shan Wei 
Published: August 2022

PurposeScientific collaboration is becoming a common pattern in the social organization of knowledge production. The paper tries to figure out the relationship between scientific collaboration team size and scientific output.Design/methodology/approachBased on ESI database from year 2009–2019, the paper describes changes of collaboration team size from one author to more than 10 authors in 22 disciplines. Kernel density estimation and multidimensional kernel density estimation method are used to calculate optimal collaboration team size and appropriate collaboration team size in 22 disciplines. As bandwidth is one of the major issues in construction of kernel density estimation, the paper uses five different algorithms to calculate bandwidth. The method with the lowest mean absolute percentage error is chosen. Robustness test is conducted based on different sets of data.FindingsThe results show that scientific collaboration becomes more widely and deeply. As time goes by, collaboration team size is becoming larger and larger. Natural science disciplines have larger collaboration team size and faster growth rate than social science disciplines. Considering both qualitative and quantitative measures, the paper proves the universality of optimal and appropriate scientific collaboration team size among 22 disciplines and calculates the specific number.Originality/valueThe paper tries to investigate the law of scientific collaboration team size variation and provide a full picture of evolution of collaboration team size among 22 disciplines in 10 years. The paper first applies distribution method to figure out the relationship between scientific collaboration team size and scientific output and provides optimal collaboration team size and appropriate collaboration team size.
Disparate changes of living standard in China: perspective from Engel's coefficient
Authors: Xie Qingxin , Yi Fujin , Tian Xu 
Published: August 2022

PurposeThis paper aims to investigate the changes in living standard among families with different socio-economic status in China with the use of Engel's Coefficient. The authors develop a decomposition methodology to figure out the driving forces behind changes in Engel's Coefficient, and investigate how dramatic economic growth, volatile food price and rapid nutrition transition affect living standard among different families.Design/methodology/approachThe authors propose a statistical method to decompose the changes in living standard measured by Engel's Coefficient into structure effect, price effect, quantity effect and income effect. Using the China Health and Nutrition Survey data between 2000 and 2011, the authors estimate these four effects by employing a decomposition method.FindingsResults show that Engel's Coefficient in China decreased by 8.7 percentage points (hereafter “pp”) during 2000–2011, where structure effect leads to 0.2 pp increase, price effect results in 17.7 pp increase, quantity effect brings about 12.4 pp decline and income effect contributes to 14.2 pp decline. Results indicate that rising food prices are the main obstacle to improve households' living standard. Typically, poor and rural families' living standard is more vulnerable to the rise in food prices, and they benefit less from income growth.Originality/valueThis study proposes a decomposition method to investigate the determinants of change in Engel's Coefficient, which provides a deeper understanding of how economic growth, food price change and nutrition transition affect people's living standard in different socio-economic groups in developing countries. This study also provides valuable insights on how to achieve common prosperity from the perspective of consumption upgrading.
The intermittent institutional innovation and China's economic fluctuations: a calibrated model and a dynamic analysis
Authors: Sun Ninghua , Zeng Lei 
Published: August 2022

PurposeChina's economic transition is essentially the process of China's institutional changes. During the changes, the appearance of institutional innovation is not regular; instead, it is intermittent and random. The purpose of this paper is to show that the fitful appearance of institutional innovation is the root of China's economic growth and fluctuations.Design/methodology/approachThis paper constructs a real business cycle (RBC) model introducing the institutional factor expressed in the quantitative form under the dynamic stochastic general equilibrium (DSGE) framework by measuring China's institutional changes quantitatively.FindingsBy comparing the characteristics of the actual economic data with those of the simulated economic data, we find that this RBC model can explain 94.44%, 66.07%, 23.46%, 21.03% and 15.45% of the cyclical fluctuations in output, investment, labor, consumption and capital, respectively.Originality/valueThe impulse response analysis finds that the institutional shocks have a relatively long duration, lasting about 30 years, and decline slowly over time, while technological shocks decline relatively fast, lasting approximately ten years.
“Getting stuck in”: body work and physical capital in non-traditional occupations
Authors: Murphy Caroline , O'Meara Aoife 
Published: August 2022

PurposeDrawing on Bourdieu's conceptualisation of physical capital, this article explores the experiences of male and female employees in non-traditional occupations where body work is an integral part of the role. Specifically, the authors examine how being an underrepresented gender in this context impacts the experience of work, including challenges faced and perceptions for future opportunities in the role.Design/methodology/approachThe research is based on two in-depth case studies undertaken in the social care and security/door work sector. Semi-structured interviews were conducted with male social care workers and female security workers in the night-time hospitality sector. Management representatives were also interviewed in each case. The interviews examined how the nature of the work in these roles impacted on the underrepresented gender's perceptions of various aspects of their working lives.FindingsThe findings illustrate how many of the challenges associated with non-traditional occupations are experienced differently in body work roles, either being amplified or instead presenting opportunities for the role holder with implications for the day-to-day and longer-term experience of work. The findings illustrate how the actions and behaviour of management and colleagues can exacerbate the extent to which underrepresented gender feel accepted within their role and organisation.Practical implicationsOrganisational decision makers need to be aware of the importance of reviewing practices regarding hiring, promotion and the allocation of tasks and duties for non-traditional role holders engaged in body work.Originality/valueThe article contributes to understandings of “body work” and physical capital in non-traditional occupations, illustrating how gender-based assumptions can restrict individuals in these roles to a greater extent than in other forms of work where the body is salient to the performance of the role.