bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Wide Characterization, Identification And Expression Analysis OfErfGene Family In Cotton
Authors: Zafar Muhammad Mubashar , Rehman Abdul , Razzaq Abdul , Parvaiz Aqsa , Mustafa Ghulam , Mo Huijuan , Youlu Yuan , Shakeel Amir , Ren Maozhi 
Published: December 2020

AbstractERFis a subfamily ofAP2/EREBPsuperfamily, contained single AP2 domain. The overexpression ofERFgenes steered to abiotic stress tolerance and pathogen resistance in transgenic plants. Here, a genome-wide analysis ofERFgene family within two diploid species (G. arboreum & G. raimondii) and two tetraploid species (G. barbadense, G. hirsutum) was performed. A total of 118, 120, 213, 220 genes contained sequence single AP2 domain were identified inG. arboreum,G. raimondii,G. barbadenseandG. hirsutumrespectively. The identified genes were unevenly distributed across 13/26 chromosomes of A and D genomes of cotton. Genome comparison revealed that segmental duplication may have played crucial roles in the expansion of the cottonERFgene family, and tandem duplication also played a minor role. Analysis of RNA-Seq data indicated that cottonERFgene expression levels varied across different tissues and in response to different abiotic stress. Overall, our results could provide valuable information for better understanding the evolution of cottonERFgenes and lays a foundation for future investigation in cotton.
Artificial Antigen Presenting Cells for Detection and Desensitisation of Auto-reactive T cells Associated with Type 1 Diabetes
Authors: Artzy-Schnirman Arbel , Abu-Shah Enas , Chandrawati Rona , Altman Efrat , Yusuf Norkhairin , Wang Shih-Ting , Ramos Jose , Hansel Catherine S. , Haus-Cohen Maya , Dahan Rony , Arif Sefina , Dustin Michael L. , Peakman Mark , Reiter Yoram , Stevens Molly M. 
Published: December 2020

AbstractAutoimmune diseases and in particular type 1 diabetes rely heavily on treatments that target the symptoms rather than prevent the underlying disease. One of the barriers to better therapeutic strategies is the inability to detect and efficiently target rare autoreactive T-cell populations that are major drivers of these conditions. Here, we develop a unique artificial antigen presenting cell (aAPC) system from biocompatible polymer particles that allows specific encapsulation of bioactive ingredients. Using our aAPC we demonstrate that we are able to detect rare autoreactive CD4 populations in human patients and using mouse models we demonstrate that our particles are able to induce desensitization in the autoreactive population. This system provides a promising tool that can be used in the prevention of autoimmunity before disease onset.
Genomic profiling of cancerous patients identifies FPR2 as an alternative immunotherapeutic target in glioblastoma multiforme
Authors: Yang Yuqing , Sun Ting , Qiu Chuchen , Chen Dongjing , Wu You 
Published: December 2020

ABSTRACTBackgroundGlioblastoma multiforme (GBM) is a type of high-grade brain tumor known for its proliferative, invasive property, and low survival rate. Recently, with the advancement in therapeutics for tumors such as targeted therapy, individual cancer-specific biomarkers could be recognized as targets for curative purposes. This study identified six differentially expressed genes that have shown significant implications in clinical field, including FPR2, VEGFA, SERPINA1, SOX2, PBK, and ITGB3. FPR2 was of the same protein family with FPR1, and the latter has been repeatedly reported to promote motility and invasiveness of multiple tumor forms.MethodsThe gene expression profiling of 40 GBM samples and five normal samples from the TCGA database were comprehensively analyzed. The differentially expressed genes (DEGs) were identified using R package and screened by enrichment analysis and examination of protein–protein interaction networks, in order to further explore the functions of DEGs with the highest association with clinical traits and to find hub genes. A qRT-PCR and Western blots were conducted to verify the results of this study.ResultsOur investigation showed that FPR2, VEGFA, SERPINA1, SOX2, PBK, and ITGB3 were significantly up-regulated in GBM primary tumor compared to the control group. Functional enrichment analysis of the DEGs demonstrated that biological functions related to immune systems, cell division and cell cycle were significantly increased, which were closely related to tumor progression and development. Downstream construction of PPI network analysis indicated that FPR2 was a hub gene involved in high level of interaction with CR3 and VEGFA, which played a key role in inflammatory pathways and cellular dysfunction.ConclusionFPR2, VEGFA, SERPINA1, SOX2, PBK, and ITGB3 were significantly over-expressed in primary tumor samples of GBM patients and were involved in cellular functions and pathways contributing to tumor progression. Out of these six pivotal genes, we intensively focused on FPR2, and our analysis and experimental data both suggested its efficacy as a potential biomarker, serving as an alternative immunotherapeutic target for glioblastoma multiforme.
Curvature of the retroviral capsid assembly is modulated by a molecular switch
Authors: Thames Tyrone , Bryer Alexander J , Qiao Xin , Jeon Jaekyun , Weed Ryan , Janicki Kaylie , Hu Bingwen , Gor’kov Peter L. , Hung Ivan , Gan Zhehong , Perilla Juan R , Chen Bo 
Published: December 2020

AbstractDuring the maturation step, the capsid proteins (CAs) of a retrovirus assemble into polymorphic capsids, whose acute curvature is largely determined by insertion of 12 pentamers into the hexameric lattice. Despite years of intensive research, it remains elusive how the CA switches its conformation between the quasi-equivalent pentameric and hexameric assemblies to generate the acute curvature in the capsid. Here we report the high-resolution structural model of the RSV CA T=1 capsid. By comparing with our prior model of the RSV CA tubular assembly consisting entirely of hexameric lattices, we identify that a dozen of residues are the key to dictate the incorporation of acute curvatures in the capsid assembly. They undergo large torsion angle changes, which result a 34° rotation of the C-terminal domain relative to its N-terminal domain around the flexible interdomain linker, without substantial changes of either the conformation of individual domains or the assembly contact interfaces.
Standardization of inducer-activated broad host range expression modules: Debugging and refactoring an alkane-responsive AlkS/PalkBdevice
Authors: Arce-Rodríguez Alejandro , Benedetti Ilaria , Silva-Rocha Rafael , de Lorenzo Víctor 
Published: December 2020

ABSTRACTAlthough inducible heterologous expression systems have been available since the birth of recombinant DNA technology, the diversity of devices and genetic architectures of the corresponding vectors have often resulted in a lack of reproducibility and interoperability. In an effort to increase predictability of expression of genes of interest in a variety of possible bacterial hosts we propose a composition standard for debugging and reassembling all regulatory parts that participate in the performance of such devices. As a case study we address then-octane and dicyclopropyl ketone (DCPK)-induciblePalkBpromoter of the alkane biodegradation pOCT plasmid ofPseudomonas putida. The standardized expression module consisted of an editedalkSregulatory gene that is divergently expressed and separated ofPalkBby a synthetic DNA buffer sequence. The native DNA sequence of the structuralalkSgene was modified to alleviate the catabolite repression exerted by some carbon and nitrogen sources through the Crc/Hfq complex of some hosts. ThePalkBpromoter along with thealkSvariants were then formatted as SEVA (Standard European Vector Architecture) cargoes and their activity parameters inP. putidadetermined with GFP and luminiscent reporters. The thereby refactored system showed improvements in various features desirable in conditional expression modules: inducibility, capacity, noise reduction and on/off ratio. When applied to other promoter/regulator pairs, the compositional standard thereby implemented in the AlkS/PalkBmodule will enable more complex genetic programming in non-model bacteria.
Activation of cGAS/STING pathway upon paramyxovirus infection
Authors: Iampietro Mathieu , Dumont Claire , Mathieu Cyrille , Spanier Julia , Robert Jonathan , Charpenay Aude , Dupichaud Sébastien , Dhondt Kévin P. , Aurine Noémie , Pelissier Rodolphe , Ferren Marion , Mély Stéphane , Gerlier Denis , Kalinke Ulrich , Horvat Branka 
Published: December 2020

SUMMARYDuring inflammatory diseases, cancer and infection, the cGAS/STING pathway is known to recognize foreign or self-DNA in the cytosol and activate an innate immune response. Here, we report that negative-strand RNA paramyxoviruses, Nipah virus (NiV) and Measles virus (MeV), can also trigger the cGAS/STING axis. While mice deficient for MyD88, TRIF and MAVS still moderately control NiV infection when compared to WT mice, additional STING deficiency resulted in 100% lethality, suggesting synergistic roles of these pathways in host protection. Moreover, deletion of cGAS or STING resulted in decreased type-I interferon production with enhanced paramyxoviral infection in both human and murine cells. Finally, the phosphorylation and ubiquitination of STING, observed during viral infections, confirmed the activation of cGAS/STING pathway by NiV and MeV. Our data suggest that cGAS/STING activation is critical in controlling paramyxovirus infection, and possibly represent attractive targets to develop countermeasures against severe disease induced by these pathogens.
Systematic evaluation of chromosome conformation capture assays
Authors: Oksuz Betul Akgol , Yang Liyan , Abraham Sameer , Venev Sergey V. , Krietenstein Nils , Parsi Krishna Mohan , Ozadam Hakan , Oomen Marlies E. , Nand Ankita , Mao Hui , Genga Ryan MJ , Maehr Rene , Rando Oliver J. , Mirny Leonid A. , Gibcus Johan Harmen , Dekker Job 
Published: December 2020

AbstractChromosome conformation capture (3C)-based assays are used to map chromatin interactions genome-wide. Quantitative analyses of chromatin interaction maps can lead to insights into the spatial organization of chromosomes and the mechanisms by which they fold. A number of protocols such as in situ Hi-C and Micro-C are now widely used and these differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of experimental parameters of 3C-based protocols. We find that different protocols capture different 3D genome features with different efficiencies. First, the use of cross-linkers such as DSG in addition to formaldehyde improves signal-to-noise allowing detection of thousands of additional loops and strengthens the compartment signal. Second, fragmenting chromatin to the level of nucleosomes using MNase allows detection of more loops. On the other hand, protocols that generate larger multi-kb fragments produce stronger compartmentalization signals. We confirmed our results for multiple cell types and cell cycle stages. We find that cell type-specific quantitative differences in chromosome folding are not detected or underestimated by some protocols. Based on these insights we developed Hi-C 3.0, a single protocol that can be used to both efficiently detect chromatin loops and to quantify compartmentalization. Finally, this study produced ultra-deeply sequenced reference interaction maps using conventional Hi-C, Micro-C and Hi-C 3.0 for commonly used cell lines in the 4D Nucleome Project.
Road salt compromises functional morphology of larval gills in populations of an amphibian
Authors: Szeligowski Richard V. , Scanley Jules A. , Broadbridge Christine C. , Brady Steven P. 
Published: December 2020

AbstractThroughout much of the world, winter deicing practices have led to secondary salinization of freshwater habitats, where numerous taxa are vulnerable to elevated salinity. Many amphibians are of particular concern because of their permeable skin and reliance on small ponds and pools, where salinity levels can be high. The early life-history stages of amphibians that develop in these habitats are especially sensitive to salt exposure. Larvae developing in salt-polluted environments must osmoregulate through ion exchange in gills. While salt-induced changes to the physiology of ion exchange in amphibian gills is generally understood, functionally relevant changes in gill morphology remain poorly described. Yet the structure of gills should be an important component affecting their ionoregulatory capacity, for instance in terms available surface area. Larval amphibian gills also play critical roles in gas exchange and foraging. Thus, changes in gill morphology due to salt pollution potentially affect not only osmoregulation, but also respiration and feeding. Here, we used a chronic exposure experiment to quantify the effect of salinity on larval gill morphology in populations of the wood frog (Rana sylvatica). We measured a suite of morphological traits on gill tufts, where ionoregulation and gas exchange occur, and on gill filters, which are used in feeding. Larvae raised in high salinity conditions had gill tufts with lower surface area to volume ratio, while epithelial cells on these tufts were less circular but occurred at higher densities. Gill filters showed increased spacing, which can potentially reduce their efficiency in filtering food particles. Together, these changes seem likely to diminish the ionoregulatory and respiratory capacity of gill tufts, and compromise feeding functionality of gill filters. Thus, a singular change in the aquatic environment from a widespread pollutant has the potential to generate a suite of consequences via changes in gill morphology. Critically, this suite of negative effects is likely most detrimental in salinized environments, where ionoregulatory demands are higher, which in turn should increase respiratory demands along with energy acquisition demands through foraging.Summary StatementChronic road salt exposure alters the functional morphology of gills in larval amphibians, potentially compromising osmoregulation, feeding, and respiration.
Enhancing bioreactor arrays for automated measurements and reactive control with ReacSight
Authors: Bertaux François , Sosa-Carrillo Sebastián , Fraisse Achille , Aditya Chetan , Furstenheim Mariela , Batt Gregory 
Published: December 2020

AbstractNew small-scale, low-cost bioreactors provide researchers with exquisite control of environmental parameters of microbial cultures over long durations, allowing them to perform sophisticated, high-quality quantitative experiments that are particularly useful in systems biology, synthetic biology and bioengineering. However, existing setups are limited in their automated measurement capabilities, primarily because sensitive and specific measurements require bulky, expensive, stand-alone instruments. Here, we present ReacSight, a generic and flexible strategy to enhance bioreactor arrays for automated measurements and reactive experiment control. On the hardware side, ReacSight leverages a pipetting robot for sample collection, handling and loading. On the software side, ReacSight provides a versatile instrument control architecture and a generic event system for reactive experiment control. ReacSight is ideally suited to integrate open-source, open-hardware components but can also accommodate closed-source, GUI-only components (e.g. cytometers). We use ReacSight to assemble a platform for cytometry-based characterization and reactive optogenetic control of parallel yeast continuous cultures. Using a dedicated bioreactor array, we showcase its capabilities on three applications. First, we achieve parallel real-time control of gene expression with light in different bioreactors. Second, we explore the impact of nutrient scarcity on fitness and cellular stress using well-controlled, high-information content competition assays. Third, we exploit nutrient scarcity to achieve dynamic control over the composition of a two-strain consortium. To illustrate the genericity of ReacSight, we also assemble an equivalent platform using the optogenetic-ready, open-hardware and commercially available Chi.Bio bioreactors.
Deciphering colchicine like actions of clerodin in terms of microtubule destabilization based mitotic abnormalities, G2/M-phase arrest, and plant polyploidy
Authors: Roy Sujit , Kundu Lalit Mohan , Roy Gobinda Chandra , Barman Manabendu , Chakraborty Tista , Ghosh Poulomi , Das Ria , Tripathy Debabrata , Singh Nanda , Banerjee Sagnik , Bhattacharjee Atanu , Pal Amit , Chatterjee Anupam , Ray Sanjib 
Published: December 2020

AbstractClerodin (C24H34O7), a clerodane diterpenoid, is a bitter principle ofClerodendrum viscosum. The present study aimed to decipher colchicine-like actions of clerodin in terms of microtubule destabilization based mitotic abnormalities, G2-M arrest, and plant polyploidy. Purified clerodin showed increased metaphase frequency in Human Peripheral Blood Lymphocytes (HPBLs), Human Embryonic Kidney cells (HEK-293), andAllium ceparoot apical meristem cells. Both squashed slide of the onion root tip and flow cytometric analysis of radish protoplast revealed a significantly increased frequency of polyploid cells. Flow cytometric analysis showed an increase in frequencies of G2-M in MCF-7 cells from 6.10 to 16.25% after clerodin (200μg/mL) treatment for 24 h. Confocal microscopy imaging of tubulin in clerodin-treated MCF-7 cells revealed microtubule destabilization. Molecular docking and LIGPLOT analysis indicate that clerodin interact in the colchicine binding site, including, single hydrogen bond with Asn 101 of α-tubulin. In summary, our experimental data revealed that clerodin has metaphase arresting, microtubule destabilization, and polyploidy inducing ability similar to colchicine. Molecular docking analysis revealed for the first time that clerodin and colchicine interact at the common site of tubulin residue indicating a common mechanism of action. The results also indicate similar cytotoxic potentialities of both clerodin and colchicine even though they belong to different chemical groups. Thus, clerodin may be used in place of colchicine as a plant polyploidy inducing agent in plant breeding programs in Agriculture.
The effect of corporate social responsibility (CSR) on shareholder value: evidence from the 9/11 terrorist attack
Authors: Ongsakul Viput , Jiraporn Pornsit , Tong Shenghui , Treepongkaruna Sirimon 
Published: December 2020

Purpose
This paper aims to explore the effect of corporate social responsibility (CSR) on shareholder value using the stock market reactions to a terrorist attack. This paper exploits the September 11 terrorist attack as an unanticipated exogenous shock that reduced shareholder wealth suddenly and unexpectedly. Based on the risk-mitigation hypothesis, the argument is that more socially responsible firms should suffer less negative market reactions.

Design/methodology/approach
This paper uses the standard event study methodology to estimate the stock market reactions to the 9/11 terrorist attack. Then, the study executes a cross-section analysis to determine whether CSR offers any protection in the presence of a sudden negative shock. Additional analysis includes propensity score matching, instrumental-variable analysis and using Oster’s (2019) method for testing coefficient stability.

Findings
The results show that the negative stock market reactions to the shock are significantly alleviated for firms with strong social responsibility. A rise in CSR by one standard deviation improves the market reactions by 22.56% of the average decline. This is consistent with the prediction of the risk mitigation hypothesis, where CSR spawns moral capital or goodwill that functions as an insurance-like defense in case of an adverse event.

Research limitations/implications
The study focuses on short-term market reactions because this method is more likely to show a causal effect. Future research may investigate long-term effects.

Originality/value
While prior research has investigated the effect of CSR on firm value, it has been challenging to establish causality. The approach is more likely to show causality as it is based on a sudden and unanticipated negative shock. This paper also uses several methods to reduce endogeneity, making it more likely that the results show causality, rather than merely an association.
Distribution of amoebal endosymbiotic environmental chlamydia Neochlamydia S13 via amoebal cytokinesis
Authors: Okude Miho , Matsuo Junji , Yamazaki Tomohiro , Saito Kentaro , Furuta Yoshikazu , Nakamura Shinji , Thapa Jeewan , Okubo Torahiko , Higashi Hideaki , Yamaguchi Hiroyuki 
Published: December 2020

AbstractWe previously isolated a symbiotic environmental amoeba, harboring an environmental chlamydia, Neochlamydia S13. Interestingly, this bacterium failed to survive outside of host cells and was immediately digested inside other amoebae, indicating bacterial distribution via cytokinesis. This may provide a model for understanding organelle development and chlamydial pathogenesis and evolution; therefore, we assessed our hypothesis of Neochlamydia S13 distribution via cytokinesis by comparative analysis with other environmental Chlamydiae (Protochlamydia R18 and Parachlamydia Bn9). Dual staining with 4′,6‐diamidino‐2‐phenylindole and phalloidin revealed that the progeny of Neochlamydia S13 and Protochlamydia R18 existed in both daughter cells with a contractile ring on the verge of separation. However, in contrast to other environmental Chlamydiae, little Neochlamydia S13 16S ribosomal DNA was amplified from the culture supernatant. Interestingly, Neochlamydia S13 failed to infect aposymbiotic amoebae, indicating an intimate interaction with the host cells. Furthermore, its infectious rates in cultures expanded from a single amoeba were always maintained at 100%, indicating distribution via cytokinesis. We concluded that unlike other environmental Chlamydiae, Neochlamydia S13 has a unique ability to divide its progeny only via host amoebal cytokinesis. This may be a suitable model to elucidate the mechanism of cell organelle distribution and of chlamydial pathogenesis and evolution.
Organ‐preserving procedures as an option for treatment of patients with pancreatic neuroendocrine tumours
Authors: Kriger Andrey G. , Berelavichus Stanislav V. , Kaldarov Ayrat R. , Gorin David S. , Raevskaya Marianna B. , Kazennov Vladimir V. , Zekster Vita Y. , Panteleev Vladimir I. 
Published: December 2020

AbstractObjectivePancreatic neuroendocrine tumour (pNET) is a rare type of tumour with different malignant potential. Nowadays there is no universal approach for treatment of small and benign‐looking pNETs throughout the world.MethodsThere were 137 patients with pNETs surgically treated in our department between 2007 and 2017. Most of them were female ‐ 96 cases with median age 42 years old. Organ‐preserving procedures (OP) were performed in 44 (32%) cases and were compared with standard procedures 93 (68%) cases.ResultsMain intraoperative characteristics were comparable in groups. There was significantly less estimated blood loss volume in the OP group: less than 1 dL. Postoperative length of stay and drainage placement time were less in the OP group. There were less pancreatic fistulas and no delayed gastric empties in the OP group. 90‐day postoperative mortality rate was the same in both groups: four cases of severe postoperative pancreatitis with acute respiratory distress syndrome.ConclusionAs the “wait‐and‐see” policy can be not useful due to uncontrolled disease progression, choice of organ‐preserving treatment first can become the first line of decision taking in small benign pNETs. Our experience shows that organ‐preserving treatment is more comfortable for the surgeon and for the patient. However, it is not the universal position. The long‐term survival data still has to be estimated.