bluuebunny/crossref_metadata_2025_split huggingface dataset:
Moderate DNA methylation changes associated with nitrogen remobilization and leaf senescence in Arabidopsis
Authors: Vatov Emil , Zentgraf Ulrike , Ludewig Uwe 
Published: September 2021

SummaryThe lifespan of plants and tissues is restricted by environmental and genetic components. Following the transition to reproductive growth, leaf senescence ceases cellular life in monocarpic plants to remobilize nutrients to storage organs.We observed altered leaf to seed ratios, faster senescence progression and enhanced nitrogen remobilization from the leaves in two methylation mutants (ros1 and the triple dmr1/2 cmt3 knockout).DNA methylation in wild type Col-0 leaves initially moderately declined with progressing leaf senescence, predominantly in the CG context, while the ultimate phase of leaf discoloration was associated with moderate de novo methylation of cytosines, primarily in the CHH context.Relatively few differentially methylated regions, including one in the ROS1 promoter linked to the down-regulation of ROS1, were present, but these were unrelated to known senescence-associated genes.Differential methylation patterns were identified in transcription factor binding sites, such as the W-boxes that are targeted by WRKYs, which impaired transcription factor binding when methylated in vitro.Mutants that are defective in DNA methylation showed distinct nitrogen remobilization, which was associated with altered patterns of leaf senescence progression. But moderate methylome changes during leaf senescence were not specifically associated with up-regulated genes during senescence.
APPRIS principal isoforms and MANE Select transcripts in clinical variant interpretation
Authors: Pozo Fernando , Rodriguez Jose Manuel , Vazquez Jesus , Tress Michael L. 
Published: September 2021

AbstractMost coding genes are able to generate multiple alternatively spliced transcripts. Determining which of these transcript variants produces the main protein isoform, and which of a gene’s multiple splice variants are functionally important, is crucial in comparative genomics and essential for clinical variant interpretation.Here we show that the principal isoforms chosen by APPRIS and the MANE Select variants provide the best approximations of the main cellular protein isoforms. Principal isoforms are predicted from conservation and from protein features, and MANE transcripts are chosen from the consensus between teams of expert manual curators. APPRIS principal isoforms coincide in over 94% of coding genes with MANE Select transcripts and the two methods are particularly discriminating when they agree on the main splice variant. Where the two methods agree, the splice variants coincide with the main isoform detected in proteomics experiments in 98.2% of genes with multiple protein isoforms.We also find that almost all ClinVar pathogenic mutations map to MANE Select or APPRIS principal isoforms. Where APPRIS and MANE agree on the main isoform, 99.93% of validated pathogenic variants map to principal rather than alternative exons. MANE Plus Clinical transcripts cover most validated pathogenic mutations in alternative coding exons. TRIFID functional importance scores are particularly useful for distinguishing clinically important alternative isoforms: the highest scoring TRIFID isoforms are more than 300 times more likely to have validated pathogenic mutations.We find that APPRIS, MANE and TRIFID are important for determining the biological relevance of splice isoforms and should be an essential part of clinical variant interpretation.
Herbivorous fish of Sinai marine protected areas (Gulf of Aqaba): Structure baseline for potential thermal stress impact management
Authors: El-Haddad Khaled M. , Ali Abdel-Hamid A. M. , Abdel-Rahman Mohammed S. , Mohammed Saad Z. , Abdel-Gawad Fagr Kh. , Guerriero Giulia , Temraz Tarek A. 
Published: September 2021

AbstractHerbivorous reef fishes are critically important for maintaining the health and resilience of coral reefs. In the Egyptian Gulf of Aqaba (GoA), many of these herbivores are important fishery targets, however, little is known about their biomass and size structure patterns. Here, we conduct a large-scale (∼250 km of coastline) assessment of the status of herbivorous fish populations on 30 reef sites from eight coastal regions in the GoA. These regions are subjected to three levels of fishing and protection, ranging from almost no fishing (No-take, NT), and moderately fished (via Gear-restriction, GR) to heavily fished (Open-access, OA). We found that the NT fishery reserve was the most effective in maintaining herbivorous fish richness, body-size, and biomass across all functional groups, though numerical density was not. Total herbivore biomass was 4.3 and 2.8 times higher on NT reefs and GR reefs respectively than on OA reefs. Among GoA regions, only Ras Mohammed and Sharm El-Sheikh (unfished), and Nabq (moderately fished) met the global mean herbivore biomass target of ∼30 kg/500 m2. Our work also highlights three important results regarding the impacts of fishing and fisheries management on herbivorous fish populations: (i) size structure was heavily skewed toward smaller individuals, with fishes less than (20 cm) accounting for 81.1% of the population in heavily fished OA reefs vs. 52.8% at unfished NT reefs, (ii) biomass of larger herbivore individuals (>35 cm) accounted for less than 1% of the total biomass in OA reefs vs. 37% at NT reefs, and (iii) large-bodied target species, Cetoscarus bicolor, Naso unicorn, and Kyphosus spp., accounting for 15.9% of the total biomass at NT reefs on average, while they were virtually absent from OA reefs. Collectively, these findings suggest that many principal fishery species in the central-northern regions of the GoA have been overexploited, which in turn can lead to reef degradation. Therefore, there is an urgent need to develop a participatory management approach and enforce restrictions on destructive fishing gear in order to promote recovery of herbivore biomass.HighlightsLarge-scale assessment of the status of herbivorous fishes in the northern Red Sea.Comparison of herbivorous fish assemblages across three levels of fishing pressure.Large-bodied herbivore species were either rare or absent at heavily fished reefs.Loss of these key herbivores may boost algal dominance, thus diminish reef functionality.Promoting local community participation in the fishery management process.
Inhibitory hippocampo-septal projection controls locomotion and exploratory behavior
Authors: Chen Yuh-Tarng , Guo Jun , Xu Wei 
Published: September 2021

AbstractAlthough the hippocampus is generally considered a cognitive center for spatial representation, learning and memory, increasing evidence supports its roles in regulation of locomotion. However, the neuronal mechanisms of hippocampal regulation of locomotion and exploratory behavior remain unclear. Here we found that the inhibitory hippocampo-septal projection bi-directionally controls locomotion speed of mice. Pharmacogenetic activation of these septum-projecting interneurons decreased locomotion and exploratory behavior. Similarly, activation of the hippocampus-originated inhibitory terminal in the medial septum reduced locomotion. On the other hand, inhibition of the hippocampus-originated inhibitory terminal increased locomotion. The locomotion-regulative roles were specific to the septal projecting interneurons as activation of hippocampal interneurons projecting to the retrosplenial cortex did not change animal locomotion. Therefore, this study reveals a specific long-range inhibitory output from the hippocampus in the regulation of animal locomotion.
Evolution of antigen-specific follicular helper T cell transcriptional programs across effector function and through to memory
Authors: Robinson Amanda M. , Higgins Brett W. , Shuparski Andrew G. , Miller Karen B. , McHeyzer-Williams Louise J. , McHeyzer-Williams Michael G. 
Published: September 2021

AbstractUnderstanding how follicular helper T cells (TFH) regulate the specialization, maturation, and differentiation of adaptive B cell immunity is crucial for developing durable high-affinity immune protection. Using indexed-single cell molecular strategies, we reveal a skewed intra-clonal assortment of higher affinity TCR and the distinct molecular programming of the localized TFH compartment compared to emigrant conventional effector TH(ETH) cells. We find a temporal shift in BCR class switch which permits identification of inflammatory and anti-inflammatory modules of transcriptional programming that subspecialize TFH function before and during the germinal center (GC) reaction. Late collapse of this local primary GC reaction reveals a persistent post-GC TFH population which discloses a putative memory TFH program. These studies define specialized antigen-specific TFH transcriptional programs that progressively direct class-specific evolution of high-affinity B cell immunity and uncover the transcriptional program of a memory TFH population as the regulators of antigen recall.Graphical AbstractSummaryDistinct inflammatory and anti-inflammatory antigen-specific TFH transcriptional programs regulate class-specific B cell maturation.Highlights- Skewed intra-clonal assortment of high affinity TCR into the TFH compartment- Significant temporal delay in anti-inflammatory IgG1 production- Inflammatory and anti-inflammatory transcriptional modules subspecialize TFH- Late GC collapse reveals a persisting post-GC putative memory TFH compartment
Antigen identification and high-throughput interaction mapping by reprogramming viral entry
Authors: Dobson Connor S. , Reich Anna N. , Gaglione Stephanie , Smith Blake E. , Kim Ellen J. , Dong Jiayi , Ronsard Larance , Okonkwo Vintus , Lingwood Daniel , Dougan Michael , Dougan Stephanie K. , Birnbaum Michael E. 
Published: September 2021

AbstractDeciphering immune recognition is critical for understanding a broad range of diseases and for the development of effective vaccines and immunotherapies. Efforts to do so are limited by a lack of technologies capable of simultaneously capturing the complexity of adaptive immune receptor repertoires and the landscape of potential antigens. To address this, we present RAPTR (Receptor-Antigen Pairing by Targeted Retroviruses). RAPTR combines viral pseudotyping and molecular engineering approaches to enable one-pot library on library interaction screens by displaying antigens on the surface of lentiviruses and encoding their identity in the viral genome. Antigen-specific viral infection of cells allows readout of both antigen and receptor identities via single-cell sequencing. The resulting system is modular, scalable, and compatible with any cell type, making it easily implemented. These techniques provide a suite of new tools for targeted viral entry, molecular engineering, and interaction screens with broad potential applications.
Using AlphaFold to predict the impact of single mutations on protein stability and function
Authors: Pak Marina A. , Markhieva Karina A. , Novikova Mariia S. , Petrov Dmitry S. , Vorobyev Ilya S. , Maksimova Ekaterina S. , Kondrashov Fyodor A. , Ivankov Dmitry N. 
Published: September 2021

AbstractAlphaFold changed the field of structural biology by achieving three-dimensional (3D) structure prediction from protein sequence at experimental quality. The astounding success even led to claims that the protein folding problem is “solved”. However, protein folding problem is more than just structure prediction from sequence. Presently, it is unknown if the AlphaFold-triggered revolution could help to solve other problems related to protein folding. Here we assay the ability of AlphaFold to predict the impact of single mutations on protein stability (ΔΔG) and function. To study the question we extracted metrics from AlphaFold predictions before and after single mutation in a protein and correlated the predicted change with the experimentally known ΔΔG values. Additionally, we correlated the AlphaFold predictions on the impact of a single mutation on structure with a large scale dataset of single mutations in GFP with the experimentally assayed levels of fluorescence. We found a very weak or no correlation between AlphaFold output metrics and change of protein stability or fluorescence. Our results imply that AlphaFold cannot be immediately applied to other problems or applications in protein folding.
Genome-wide mapping implicates R-loops in lineage-specific processes and formation of DNA break hotspots in neural stem/progenitor cells
Authors: Thongthip Supawat , Carlson Annika , Crossley Madzia P. , Schwer Bjoern 
Published: September 2021

ABSTRACTRecent work has revealed classes of recurrent DNA double-strand breaks (DSBs) in neural stem/progenitor cells, including transcription-associated, promoter-proximal breaks and recurrent DSB clusters in late-replicating, long neural genes. However, the mechanistic factors promoting these different classes of DSBs in neural stem/progenitor cells are not understood. Here, we elucidated the genome-wide landscape of DNA:RNA hybrid structures called “R-loops” in primary neural stem/progenitor cells in order to assess their contribution to the different classes of DNA break “hotspots”. We report that R-loops in neural stem/progenitor cells are associated primarily with transcribed regions that replicate early and genes that show GC skew in their promoter region. Surprisingly, the majority of genes with recurrent DSB clusters in long, neural genes does not show substantial R-loop accumulation. We implicate R-loops in promoter-proximal DNA break formation in highly transcribed, early replicating regions and conclude that R-loops are not a driver of recurrent double-strand break cluster formation in most long, neural genes. Together, our study provides an understanding of how R-loops may contribute to DNA break hotspots and affect lineage-specific processes in neural stem/progenitor cells.
small RNA can move long distances through plant vasculature to influence gene expression in shoot apical meristems
Authors: Minow Mark A. A. , Coneva Viktoriya , Lesy Victoria , Misyura Max , Colasanti Joseph 
Published: September 2021

AbstractIn plants, small RNA (sRNA) can regulate gene expression via post transcriptional gene silencing (PTGS) or through RNA-directed DNA methylation (RdDM) leading to transcriptional gene silencing (TGS). sRNA is mobile throughout the plant, with movement occurring short distances from cell-to-cell as well as long distances through the vasculature via phloem trafficking. The range of long-distance sRNA mediated signaling from the vasculature to the shoot apical meristem (SAM) is not clear. To investigate this, two independent transgenic approaches were used to examine trafficking of phloem-expressed sRNA to the SAM in Arabidopsis thaliana. First, the phloem companion-cell specific promoter SUC2 was used to drive expression of an inverted repeat complementary to FLOWERING LOCUS D (FD), a flowering time regulator expressed exclusively in the SAM. In a separate experiment, the SUC2 promoter was used to express an artificial microRNA (aMiR) designed to target a synthetic CLAVATA3 (CLV3) target in the SAM stem cells. Both systems provide evidence of a phloem-to-SAM sRNA communication axis connecting distal regions of the plant to the stem cells of the SAM, which ultimately gives rise to all shoot tissues, including gametes. Thus, phloem-to-SAM sRNA movement defines an important link between sRNA expressed in distal regions of the plant and the growing shoot. Importantly, phloem-to-SAM sRNA trafficking may allow somatic sRNA to direct SAM RdDM, fixing transient sRNA expression events into stable epigenetic changes.
Arabidopsis iron superoxide dismutase 1 protects against methyl viologen-induced oxidative stress in a copper-dependent manner
Authors: Melicher Pavol , Dvořák Petr , Krasylenko Yuliya , Shapiguzov Alexey , Kangasjärvi Jaakko , Šamaj Jozef , Takáč Tomáš 
Published: September 2021

AbstractIron superoxide dismutase 1 (FSD1) was recently characterized as a plastidial, cytoplasmic, and nuclear superoxide dismutase with osmoprotective and antioxidative functions. However, its role in oxidative stress tolerance is not well understood. Here, we characterized the role of FSD1 in response to methyl viologen (MV)-induced oxidative stress in Arabidopsis thaliana. The findings demonstrated that the antioxidative function of FSD1 depends on the availability of Cu2+ in growth media. Prolonged MV exposure led to a decreased accumulation rate of superoxide, higher levels of hydrogen peroxide production, and higher protein carbonylation in the fsd1 mutants and transgenic plants lacking a plastidial pool of FSD1, compared to the wild type. MV led to a rapid increase in FSD1 activity, followed by a decrease. Chloroplastic localization of FSD1 is necessary for these changes. Proteomic analysis showed that the sensitivity of the fsd1 mutants coincided with decreased abundance of ferredoxin and light PSII harvesting complex proteins, with altered levels of signaling proteins. Collectively, the study provides evidence for the conditional antioxidative function of FSD1 and its possible role in signaling.
The importance of region of origin and geographical labeling for tea consumers: the moderating effect of traditional tea processing method and tea prices
Authors: Wang Tung-Sheng , Liang Austin Rong-Da , Ko Chia-Chun , Lin Jie-Heng 
Published: September 2021

PurposeThe objective of this study is to investigate the impact of geographical labeling (GL) and place of origin on consumers' perceived tea quality and purchase intention, as well as to analyze the moderating effects of traditional tea processing methods and the price of tea.Design/methodology/approachThis study conducts two experiments by combining a simulated scenario with a questionnaire; overall, 383 and 678 valid samples were collected, respectively.Findings(1) The existence of GL is extremely important and will give consumers the perception of higher tea quality resulting in higher purchase intention. The tea’s production method and geographic location are strongly correlated. Thus, whether the tea is produced with traditional methods has a moderating effect on the place of origin, GL, and consumer response in study 1. (3) Different tea pricing has a moderating effect on the place of origin/GL and consumer response in study 2.Originality/valueThis study demonstrates the relationship between consumers' perception of tea GL, and their response helps to identify the difference between Eastern and Western tea culture, which can be used to help promote and market tea leaves. Multiple clues show a complementary effect between the place of origin and the GL on tea packaging. In addition, perception of the tea craftsmanship from the place of origin (long-term) and the price manipulation (short-term) have a moderating effect, which can be used to improve tea marketing design in academia and in practice.
Inventory decision-making biases: a review and suggestions for future research
Authors: Yamini S. , Gajanand M.S. 
Published: September 2021

PurposeThe paper provides a comprehensive overview of the biases in inventory decisions, under the umbrella of behavioural operations, considering research findings that used experimental methods. Research in this field has gained traction but, to the best of our knowledge, review articles that summarize these research findings are scarce. Hence, there is a need to synthesize the anomalies and biases reported in inventory decision-making literature to gain a more integrated understanding.Design/methodology/approachThis study reviews themes relevant to inventory and behavioural operations management from the articles published in recognized top-tier journals during the period between 2000 and 2020 with an aim to build a classification framework. Further, using a systematic review procedure, the relevant research studies are divided into sub-sections and appropriate search strategies are adopted to pleat more information on inventory ordering biases.FindingsThis study presents a classification framework by highlighting the factors influencing the biases in inventory decisions and describes the effects of utility preferences on the decision-making behaviour. It highlights the inventory ordering pattern under unconventional settings and also for different supply chain settings. This systematic review helps in identifying the research gap and in giving directions for future researchers.Originality/valueThe study presents a systematic review and detailed analysis of the research in inventory decision making through a behavioural lens. The study shows a clear direction of progress over the years, and implies new directions for looking beyond placing orders and for moving towards a more integrated approach while making supply chain decisions. It will be useful for researchers and practitioners working on newsvendor decisions, supply chain contracts, behavioural economics, behavioural operations management, bounded rationality theory and experimental economics.
Use of social networks in stock investment
Authors: Lei Shan , Ramos Salazar Leslie 
Published: September 2021

PurposeDrawing on the literature regarding the social network and stock investment, this paper aims to focus on the use of the social network on stock ownership decisions at individual levels. This paper also attempts to shed light on potential mediators of the relationship between the social network and stock ownership.Design/methodology/approachTo determine the relationship between stock ownership and using the social network, logistic regression was used. In order to isolate the effect of using hs on stock ownership, a decomposing method was adopted.FindingsThe findings provide evidence of the positive contribution of the use of social networks in stock ownership. Personal characteristics, such as household net worth, homeownership, education level and risk tolerance, may play a vital role in influencing individuals' decisions regarding stock investment. In addition, this study contributes to our understanding of income's mediating role in stock investment decisions.Originality/valueFirst, the authors contribute theoretically by drawing from the assumptions of social networking contagion theory, social influence theory, and social capital theory. Second, we explored potential mediators of the relationship between the social network and stock ownership. Third, this study complements the literature in incorporating the social network in business, financial professionals to be exact.