bluuebunny/crossref_metadata_2025_split huggingface dataset:
The superior salinity tolerance of wheat cultivar Shanrong No. 3 cannot be attributed to elevated Ta-sro1 poly(ADP-ribose) polymerase activity
Authors: Vogt Sarah , Feijs Karla , Hosch Sebastian , De Masi Raffaella , Lintermann Ruth , Loll Bernhard , Wirthmueller Lennart 
Published: October 2021

SummarySaline soils limit the production of important staple crops such as wheat, particularly in arid and semiarid regions. Salt tolerance is a multi-gene trait and this complicates breeding of wheat varieties that deliver high yields under saline soil conditions. Notably, the elevated salinity tolerance of wheat cultivar Shanrong No. 3 (SR3) has been linked to a specific proteoform of the wheat SIMILAR TO RCD1 ONE (SRO1) protein that was created in an asymmetric genome hybridization with tall wheat grass. The two amino acid polymorphisms of the Ta-sro1 proteoform enhance the poly(ADP-ribose) polymerase (PARP) activity of the protein suggesting that altered poly-ADP-ribosylation of unknown substrate proteins or nucleic acids underlie the elevated salinity tolerance of cultivar SR3. To elucidate the molecular basis for the elevated PARP activity of the Ta-sro1 proteoform we solved a crystal structure of the catalytic PARP domain. Surprisingly, the structure revealed that the postulated binding site for the co-substrate NAD+ substantially differs from the structurally conserved NAD+ binding sites of canonical PARP enzymes. Consistently, we find that Ta-sro1 does not bind NAD+ and lacks ADP-ribosyltransferase activity. Therefore, although the structure revealed that one of the polymorphic amino acids is located close to the proposed active site, the elevated salinity tolerance of cultivar SR3 cannot be explained by altered ADP-ribosyltransferase activity of Ta-sro1.
Highly efficient generation of canker resistant sweet orange enabled by an improved CRISPR/Cas9 system
Authors: Huang Xiaoen , Wang Nian 
Published: October 2021

SummarySweet orange (Citrus sinensis) is the most economically important species for the citrus industry. However, it is susceptible to many diseases including citrus bacterial canker caused by Xanthomonas citri subsp. citri (Xcc) that triggers devastating effects on citrus production. Conventional breeding has not met the challenge to improve disease resistance of sweet orange due to the long juvenility and other limitations. CRISPR-mediated genome editing has shown promising potentials for genetic improvements of plants. Generation of biallelic/homozygous mutants remains difficult for sweet orange due to low transformation rate, existence of heterozygous alleles for target genes and low biallelic editing efficacy using the CRISPR technology. Here, we report improvements in the CRISPR/Cas9 system for citrus gene editing. Based on the improvements we made previously (dicot codon optimized Cas9, tRNA for multiplexing, a modified sgRNA scaffold with high efficiency, CsU6 to drive sgRNA expression), we further improved our CRISPR/Cas9 system by choosing superior promoters (CmYLCV or CsUbi promoter) to drive Cas9 and optimizing culture temperature. This system was able to generate a biallelic mutation rate of up to 89% for Carrizo citrange and 79% for Hamlin sweet orange. Consequently, this system was used to generate canker resistant Hamlin sweet orange by mutating the effector binding element (EBE) of canker susceptibility gene CsLOB1, which is required for causing canker symptoms by Xcc. Six biallelic Hamlin sweet orange mutant lines in the EBE were generated. The biallelic mutants are resistant to Xcc. Biallelic mutation of the EBE region abolishes the induction of CsLOB1 by Xcc. This study represents a significant improvement in sweet orange gene editing efficacy and generating disease resistant varieties via CRISPR-mediated genome editing. This improvement in citrus genome editing makes genetic studies and manipulations of sweet orange more feasible.
Transcriptome profiling of the ventral pallidum reveals a role for pallido-thalamic neurons in cocaine reward
Authors: Engeln Michel , Fox Megan E. , Chandra Ramesh , Choi Eric Y. , Nam Hyungwoo , Qadir Houman , Thomas Shavin S. , Rhodes Victoria M. , Turner Makeda D. , Herman Rae J. , Calarco Cali A. , Lobo Mary Kay 
Published: October 2021

AbstractPsychostimulant exposure alters the activity of ventral pallidum (VP) projection-neurons. However, the molecular underpinnings of these circuit dysfunctions are unclear. We used RNA- sequencing to reveal alterations in the transcriptional landscape of the VP that are induced by cocaine self-administration in mice. We then probed gene expression in select VP neuronal subpopulations to isolate a circuit associated with cocaine intake. Finally, we used both overexpression and CRISPR-mediated knockdown to test the role of a gene target on cocaine- mediated behaviors as well as dendritic spine density. Our results showed that a large proportion (55%) of genes associated with structural plasticity were changed 24 hours following cocaine intake. Among them, the transcription factor Nr4a1 (Nuclear receptor subfamily 4, group A, member 1, or Nur77) showed high expression levels. We found that the VP to mediodorsal thalamus (VP→MDT) projection neurons specifically were recapitulating this increase in Nr4a1 expression. Overexpressing Nr4a1 in VP→MDT neurons enhanced drug-seeking and drug- induced reinstatement, while Nr4a1 knock down prevented self-administration acquisition and subsequent cocaine-mediated behaviors. Moreover, we showed that Nr4a1 negatively regulated spine dynamics in this specific cell subpopulation. Together, our study identifies for the first time the transcriptional mechanisms occurring in VP in drug exposure. Our study provides further understanding on the role of Nr4a1 in cocaine-related behaviors and identifies the crucial role of the VP→MDT circuit in drug intake and relapse-like behaviors.
Natural variation further increases resilience of sorghum bred for chronically drought-prone environments
Authors: Dong Hongxu , Birhan Techale , Abajebel Nezif , Wakjira Misganu , Mitiku Tesfaye , Lemke Cornelia , Vadez Vincent , Paterson Andrew H. , Bantte Kassahun 
Published: October 2021

AbstractClimate-change-associated shifts in rainfall distribution together with a looming worldwide water crisis make drought resilience of central importance to food security. Even for relatively drought resilient crops such as sorghum, moisture stress is nonetheless one of the major constraints for production. Here, we explore the potential to use natural genetic variation to build on the inherent drought tolerance of an elite cultivar (Teshale) bred for Ethiopian conditions including chronic drought, evaluating a backcross nested-association mapping (BC-NAM) population using 12 diverse founder lines crossed with Teshale under three drought-prone environments in Ethiopia. All twelve populations averaged higher head exsertion and lower leaf senescence than the recurrent parent in the two highest-stress environments, reflecting new drought resilience mechanisms from the donors. A total of 154 QTLs were detected for eight drought responsive traits – the validity of these were supported in that 100 (64.9%) overlapped with QTLs previously detected for the same traits, concentrated in regions previously associated with ‘stay-green’ traits as well as the flowering regulator Ma6 and drought resistant gene P5CS2. Allele effects show that some favorable alleles are already present in the Ethiopian cultivar, however the exotic donors offer rich scope for increasing drought resilience. Using model-selected SNPs associated with eight traits in this study and three in a companion study, phenotypic prediction accuracies for grain yield were equivalent to genome-wide SNPs and were significantly better than random SNPs, indicating that these studied traits are predictive of sorghum grain yield. Rich scope for improving drought resilience even in cultivars bred for drought-prone regions, together with phenotypic prediction accuracy for grain yield, provides a foundation to enhance food security in drought-prone areas like the African Sahel.
Spatiotemporal solidification of α-synuclein inside the liquid droplets
Authors: Ray Soumik , Chatterjee Debdeep , Mukherjee Semanti , Patel Komal , Mahato Jaladhar , Kadam Sangram , Krishnan Rakesh , Sawner Ajay Singh , Poudyal Manisha , Krishnamoorthy G , Chowdhury Arindam , Padinhateeri Ranjith , Maji Samir K. 
Published: October 2021

ABSTRACTLiquid-liquid phase separation (LLPS) and subsequent liquid-to-solid transition is implicated in membraneless organelles formation as well as disease associated protein aggregation. However, how liquid-to-solid transition is initiated inside a liquid droplet remains unclear. Here, using studies at single droplet resolution, we show that liquid-to-solid transition of α-synuclein (α-Syn) liquid droplets is associated with significant changes in the local microenvironment as well as secondary structure of the protein, which is prominently observed at the center of the liquid droplets. With the ageing of liquid droplets, the “structured” core at the center gradually expands and propagates over entire droplets. Further, during droplet fusion, smaller, homogeneous droplets progressively dissolve and supply proteins to the larger, heterogeneous droplets containing solid-like core at their center. The present study will significantly help to understand the physical mechanism of LLPS and liquid-to-solid transition in biological compartmentalization as well as in protein aggregation associated with human neurodegenerative disorders.Abstract Figure
Lysosome docking to Omegasomes and ER-connected Phagophores Occurs During DNAJB12 and GABARAP-Dependent Selective Autophagy of Misfolded P23H-Rhodopsin
Authors: Kennedy Andrew , Ren Hong Yu , Madden Victoria J. , Cyr Douglas M. 
Published: October 2021

AbstractWe report on how the ER-associated-autophagy pathway (ERAA) delivers P23H-rhodopsin (P23H-R) to the lysosome. P23H-R accumulates in an ERAD-resistant conformation that is stabilized by DNAJB12 and Hsp70. P23H-R, DNAJB12, and FIP200 co-localize in discrete foci that punctuate the rim of omegasome rings coated by WIPI1. P23H-R tubules thread through the wall of WIPI1 rings into their central cavity. Transfer of P23H-R from ER-connected phagophores to lysosomes requires GABARAP, and is associated with the transient docking of lysosomes to WIPI1 rings. Instances of lysosomes docking to WIPI1 foci are constitutive, and increase 250% upon P23H-R expression. After departure from WIPI1 rings, new patches of P23H-R are seen in the membranes of lysosomes. The absence of GABARAP prevents transfer of P23H-R from phagophores to lysosomes without interfering with docking. These data identify lysosome docking to omegasomes as an important step in the DNAJB12 and GABARAP-dependent autophagic disposal of dominantly toxic P23H-R.
Who takes care of the kids at when? Sex differences in avian parental care
Authors: Wang Daiping , Zhang Wenyuan , Richter Xiang-Yi Li 
Published: October 2021

AbstractParental care in birds consists of many elaborate forms, including nest building, incubation, and offspring provision, but we still do not know how much each parent contributes to the different forms. Furthermore, the variations, relationships, and potential drivers of sex differentiation in providing care across different care stages remain largely unknown. Here, we surveyed species in birds and uncovered remarkable differences in the sex role patterns across different care forms. This result implied that parental care should not be treated as a unitary trait but as a composite of integrated features with great variations. Further analyses revealed moderate correlations of the sex roles between care forms, indicating the existence of shared intrinsic drivers. We tested the effects of sexual selection, certainty of paternity, predation risk, and offspring’s life history traits in driving sex role variations. Results showed that species with strong sexual selection on males or uncertainty of paternity tend to have female-biased care.
A tiger in the Upper Midwest: Surveillance and genetic data support the introduction and establishment of Aedes albopictus in Iowa, USA
Authors: Hall David R. , Tokarz Ryan E. , Field Eleanor N. , Smith Ryan C. 
Published: October 2021

AbstractAedes albopictus is a competent vector of several arboviruses that has spread throughout the United States over the last three decades after it was initially detected in Texas in 1985. With the emergence of Zika virus in the Americas in 2015-2016 and an increased need to better understand the current distributions of Ae. albopictus in the US, we initiated surveillance efforts to determine the abundance of invasive Aedes species in Iowa. Here, we describe the resulting surveillance efforts from 2016-2020 in which we detect stable and persistent populations of Aedes albopictus in three Iowa counties. Based on temporal patterns in abundance and genetic analysis of mitochondrial DNA haplotypes between years, our data support that populations of Ae. albopictus are overwintering and have likely become established in the state. In addition, the localization of Ae. albopictus predominantly in areas of urbanization and noticeable absence in rural areas suggests that these ecological factors may represent potential barriers to their further spread and contribute to overwintering success. Together, these data document the establishment of Ae. albopictus in Iowa and their expansion into the Upper Midwest, where freezing winter temperatures were previously believed to limit their spread. With increasing globalization, urbanization, and rising temperatures associated with global warming, the range of invasive arthropod vectors, such as Ae. albopictus, is expected to only further expand, creating increased risks for vector-borne disease.
Engineering A Fluorescent Protein Color Switch Using Entropy-driven Beta Strand Exchange
Authors: John Anna M. , Sekhon Harsimranjit , Ha Jeung-Hoi , Loh Stewart N. 
Published: October 2021

ABSTRACTProtein conformational switches are widely used in biosensing. They are typically composed of an input domain (which binds a target ligand) fused to an output domain (which generates an optical readout). A central challenge in designing such switches is to develop mechanisms for coupling the input and output signals via conformational change. Here, we create a biosensor in which binding-induced folding of the input domain drives a conformational shift in the output domain that results in a 6-fold green-to-yellow ratiometric fluorescence change in vitro, and a 35-fold intensiometric fluorescence increase in cultured cells. The input domain consists of circularly permuted FK506 binding protein (cpFKBP) that folds upon binding its target ligand (FK506 or rapamycin). cpFKBP folding induces the output domain, an engineered GFP variant, to replace one of its β-strands (containing T203 and specifying green fluorescence) with a duplicate β-strand (containing Y203 and specifying yellow fluorescence) in an intramolecular exchange reaction. This mechanism employs the loop-closure entropy principle, embodied by folding of the partially disordered cpFKBP domain, to couple ligand binding to the GFP color shift. This proof-of-concept design has the advantages of full genetic encodability, ratiometric or intensiometric response, and potential for modularity. The latter attribute is enabled by circular permutation of the input domain.
The Formation of a Stable Sliding Clamp Discriminates MSH2-MSH3 and MSH2-MSH6 Mismatch Interaction
Authors: Britton Brooke M. , London James A. , Martin-Lopez Juana , Jones Nathan D. , Liu Jiaquan , Lee Jong-Bong , Fishel Richard 
Published: October 2021

ABSTRACTMutS homologs (MSH) are highly conserved core components of DNA mismatch repair (MMR). Mismatch recognition provokes ATP-binding by MSH proteins that drives a conformational transition from a short-lived lesion-searching clamp to an extremely stable sliding clamp on the DNA. Once on DNA the MSH sliding clamps provide a platform for the assembly of MMR strand-specific excision components beginning with the highly conserved MutL homologs (MLH/PMS). Previous studies with short mismatch-containing oligonucleotides revealed an MSH ATP hydrolysis (ATPase) cycle that included mismatch recognition, the formation of an ATP-bound sliding clamp and dissociation from the end of a mismatched DNA that ultimately recovers the mismatch binding conformation. We found that ATP-bound MSH complexes on blocked-end or very long DNA are extremely stable under a range of ionic conditions. These observations underpinned the development of a high-throughput fluorescence resonance energy transfer (FRET) system capable of clearly distinguishing between HsMSH2-HsMSH3 and HsMSH2-HsMSH6 activities that is suitable for chemical inhibitor screens.
Gravity interpretation for the Bethe Ansatz expansion of the
N=4
SYM index
Authors: Aharony Ofer , Benini Francesco , Mamroud Ohad , Milan Elisa 
Published: October 2021

The superconformal index of the N=4 SU(N) supersymmetric Yang-Mills theory counts the 1/16-BPS (Bogomol’nyi-Prasad-Sommerfield) states in this theory, and has been used via the AdS/CFT correspondence to count black hole microstates of 1/16-BPS black holes. On one hand, this index may be related to the Euclidean partition function of the theory on S3×S1 with complex chemical potentials, which maps by the AdS/CFT correspondence to a sum over Euclidean gravity solutions. On the other hand, the index may be expressed as a sum over solutions to Bethe Ansatz (BA) equations. We show that the solutions to the BA equations that are known to have a good large N limit, for the case of equal chemical potentials for the two angular momenta, have a one-to-one mapping to (complex) Euclidean black hole solutions on the gravity side. This mapping captures both the leading contribution from the classical gravity action (of order N2), as well as nonperturbative corrections in 1/N, which on the gravity side are related to wrapped D3-branes. Some of the BA solutions map to orbifolds of the standard Euclidean black hole solutions (which obey exactly the same boundary conditions as the other solutions). there are many more gravitational solutions than Bethe Ansatz solutions, but we show that, by considering the nonperturbative effects, the extra solutions are ruled out, leading to a precise match between the solutions on both sides.

Published by the American Physical Society
2021
An ARIMA-based study of bibliometric index prediction
Authors: Song Yanhui , Cao Jiayi 
Published: October 2021

PurposeThe purpose of this paper is to predict bibliometric indicators based on ARIMA models and to study the short-term trends of bibliometric indicators.Design/methodology/approachThis paper establishes a non-stationary time series ARIMA (p, d, q) model for forecasting based on the bibliometric index data of 13 journals in the library intelligence category selected from the Chinese Social Sciences Citation Index (CSSCI) as the data source database for the period 1998–2018, and uses ACF and PACF methods for parameter estimation to predict the development trend of the bibliometric index in the next 5 years. The predicted model was also subjected to error analysis.FindingsARIMA models are feasible for predicting bibliometric indicators. The model predicted the trend of the four bibliometric indicators in the next 5 years, in which the number of publications showed a decreasing trend and the H-value, average citations and citations showed an increasing trend. Error analysis of the model data showed that the average absolute percentage error of the four bibliometric indicators was within 5%, indicating that the model predicted well.Research limitations/implicationsThis study has some limitations. 13 Chinese journals were selected in the field of Library and Information Science as the research objects. However, the scope of research based on bibliometric indicators of Chinese journals is relatively small and cannot represent the evolution trend of the entire discipline. Therefore, in the future, the authors will select different fields and different sources for further research.Originality/valueThis study predicts the trend changes of bibliometric indicators in the next 5 years to understand the trend of bibliometric indicators, which is beneficial for further in-depth research. At the same time, it provides a new and effective method for predicting bibliometric indicators.
Co-worker support, voluntary turnover intention and knowledge withholding among IT specialists: the mediating role of affective organizational commitment
Authors: Kmieciak Roman 
Published: October 2021

PurposeThe purpose of this paper is to assess the effect of co-worker support on horizontal knowledge withholding and voluntary turnover intention among IT specialists. The study also explores the mediating role of affective organizational commitment.Design/methodology/approachThe data are drawn from 118 IT specialists from a Polish software company. The model is tested through partial least squares path modeling.FindingsThe results revealed that the negative effect of co-worker support on voluntary turnover intention is fully mediated by organizational affective commitment. Contrary to expectations, co-worker support is not significantly negatively related to horizontal knowledge withholding.Research limitations/implicationsThe cross-sectional data, self-reports and small sample size are limitations of this study. The respondents were a relatively homogenous group of employees, so the generalizability of results to other employees and industries is limited.Practical implicationsTo increase affective organizational commitment and reduce voluntary turnover intention among IT specialists, managers should create the conditions to enhance co-worker support.Originality/valueThis research clarifies the role of affective organizational commitment, which has proven to be a bridge linking co-worker support and voluntary turnover intention. Moreover, this research investigates the previously unexplored effect of co-worker support on horizontal knowledge withholding.