bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Pathophysiology of Cardiac Injury and Cardiac Microthrombi in Fatal COVID-19: Insights from Clinico-histopathologic and Single Nuclei RNA Sequencing Analyses
Authors: Fukuma Nobuaki , Hulke Michelle L. , Brener Michael I. , Golob Stephanie , Zilinyi Robert , Zhou Zhipeng , Tzimas Christos , Russo Ilaria , McGroder Claire , Pfeiffer Ryan , Chong Alexander , Zhang Geping , Burkhoff Daniel , Leon Martin B. , Maurer Mathew , Moses Jeffrey W. , Uhlemann Anne-Catrin , Hibshoosh Hanina , Uriel Nir , Szabolcs Matthias J. , Redfors Björn , Marboe Charles C. , Baldwin Matthew R. , Tucker Nathan R. , Tsai Emily J.
Published: July 2021

Cardiac injury is associated with critical COVID-19, yet its etiology remains debated. To elucidate the pathogenic mechanisms of COVID-19-associated cardiac injury, we conducted a single-center prospective cohort study of 69 COVID-19 decedents. Of six cardiac histopathologic features, microthrombi was the most commonly detected (n=48, 70%). We tested associations of cardiac microthrombi with biomarkers of inflammation, cardiac injury, and fibrinolysis and with in-hospital antiplatelet therapy, therapeutic anticoagulation, and corticosteroid treatment, while adjusting for multiple clinical factors, including COVID-19 therapies. Higher peak ESR and CRP during hospitalization were independently associated with higher odds of microthrombi. Using single nuclei RNA-sequence analysis, we discovered an enrichment of pro-thrombotic/anti-fibrinolytic, extracellular matrix remodeling, and immune-potentiating signaling amongst cardiac fibroblasts in microthrombi-positive COVID-19 hearts relative to microthrombi-negative COVID-19. Non-COVID-19 non-failing hearts were used as reference controls. Our cumulative findings identify the specific transcriptomic changes in cardiac fibroblasts as salient features of COVID-19-associated cardiac microthrombi.
Deep learning-based segmentation of high-resolution computed tomography image data outperforms commonly used automatic bone segmentation methods
Authors: Patton Daniella M. , Henning Emilie N. , Goulet Rob W. , Carroll Sean K. , Bigelow Erin M.R. , Provencher Benjamin , Piché Nicolas , Marsh Mike , Jepsen Karl J. , Bredbenner Todd L.
Published: July 2021

Segmenting bone from background is required to quantify bone architecture in computed tomography (CT) image data. A deep learning approach using convolutional neural networks (CNN) is a promising alternative method for automatic segmentation. The study objectives were to evaluate the performance of CNNs in automatic segmentation of human vertebral body (micro-CT) and femoral neck (nano-CT) data and to investigate the performance of CNNs to segment data across scanners.

Scans of human L1 vertebral bodies (microCT [North Star Imaging], n=28, 53μm3) and femoral necks (nano-CT [GE], n=28, 27μm3) were used for evaluation. Six slices were selected for each scan and then manually segmented to create ground truth masks (Dragonfly 4.0, ORS). Two-dimensional U-Net CNNs were trained in Dragonfly 4.0 with images of the [FN] femoral necks only, [VB] vertebral bodies only, and [F+V] combined CT data. Global (i.e., Otsu and Yen) and local (i.e., Otsu r = 100) thresholding methods were applied to each dataset. Segmentation performance was evaluated using the Dice coefficient, a similarity metric of overlap. Kruskal-Wallis and Tukey-Kramer post-hoc tests were used to test for significant differences in the accuracy of segmentation methods.

The FN U-Net had significantly higher Dice coefficients (i.e., better performance) than the global (Otsu: p=0.001; Yen: p=0.001) and local (Otsu [r=100]: p=0.001) thresholding methods and the VB U-Net (p=0.001) but there was no significant difference in model performance compared to the FN + VB U-net (p=0.783) on femoral neck image data. The VB U-net had significantly higher Dice coefficients than the global and local Otsu (p=0.001 for both) and FN U-Net (p=0.001) but not compared to the Yen (p=0.462) threshold or FN + VB U-net (p=0.783) on vertebral body image data.

The results demonstrate that the U-net architecture outperforms common thresholding methods. Further, a network trained with bone data from a different system (i.e., different image acquisition parameters and voxel size) and a different anatomical site can perform well on unseen data. Finally, a network trained with combined datasets performed well on both datasets, indicating that a network can feasibly be trained with multiple datasets and perform well on varied image data.
Gliding motility of a uranium tolerant Bacteroidetes bacterium Chryseobacterium sp. strain PMSZPI: Insights into the architecture of spreading colonies
Authors: Khare Devanshi , Chandwadkar Pallavi , Acharya Celin
Published: July 2021

Uranium tolerant soil bacterium Chryseobacterium sp. strain PMSZPI moved over solid agar surfaces by gliding motility thereby forming spreading colonies which is a hallmark of members of Bacteroidetes phylum. PMSZPI genome harbored orthologs of all the gld and spr genes considered as core bacteroidetes gliding motility genes of which gldK, gldL, gldM, and gldN were co-transcribed. Here, we present the intriguing interplay between gliding motility and cellular organization in PMSZPI spreading colonies. While nutrient deficiency enhanced colony spreading, high agar concentrations and presence of motility inhibitor like 5-hydroxyindole reduced the spreading. A detailed in situ structural analysis of spreading colonies revealed closely packed cells forming multiple layers at center of colony while the edges showed clusters of cells periodically arranged in hexagonal lattices interconnected with each other. The cell migration within the colony was visualized as branched structures wherein the cells were buried within extracellular matrix giving rise to ‘fern’ like patterns. PMSZPI colonies exhibited strong iridescence that showed correlation with gliding motility. Presence of uranium reduced motility and iridescence and induced biofilm formation. This is a first report of gliding motility and iridescence in a bacterium from uranium enriched environment that could be of significant interest from an ecological perspective.

Originality-Significance Statement

This work provides the first description of the gliding motility and iridescence or structural coloration in a Bacteroidetes soil bacterium from uranium enriched environment. The periodic arrangement of the cell population in the spreading colonies achieved through gliding motility resulted in bright structural coloration of the colonies when illuminated. The study describes the exogenous factors including nutrition, substrate, presence of uranium influencing the motility and iridescence of the bacterium. The highly organized cell population in the gliding and iridescent bacterium may have conferred survival advantage in metal/uranium enriched ecosystem.
Evolution of binding preferences among whole-genome duplicated transcription factors
Authors: Gera Tamar , Jonas Felix , More Roye , Barkai Naama
Published: July 2021

Throughout evolution, new transcription factors (TFs) emerge by gene duplication, promoting growth and rewiring of transcriptional networks. How TF duplicates diverge is known for only a few studied cases. To provide a genome-scale view, we considered the 35% of budding yeast TFs, classified as whole-genome duplication (WGD)-retained paralogs. Using high-resolution profiling, we find that ~60% of paralogs evolved differential binding preferences. We show that this divergence results primarily from variations outside the DNA binding domains (DBDs), while DBD preferences remain largely conserved. Analysis of non-WGD orthologs revealed that ancestral preferences are unevenly split between duplicates, while new targets are acquired preferentially by the least conserved paralog (biased sub/neo-functionalization). Dimer-forming paralogs evolved mostly one-sided dependency, while other paralogs interacted through low-magnitude DNA-binding competition that minimized paralog interference. We discuss the implications of our findings for the evolutionary design of transcriptional networks.
Can AlphaFold2 predict protein-peptide complex structures accurately?
Authors: Ko Junsu , Lee Juyong
Published: July 2021

Abstract

In this preprint, we investigated whether AlphaFold2, AF2, can predict protein-peptide complex structures only with sequence information. We modeled the structures of 203 protein-peptide complexes from the PepBDB DB and 183 from the PepSet. The structures were modeling with concatenated sequences of receptors and peptides via poly-glycine linker. We found that for more than half of the test cases, AF2 predicted the bound structures of peptides with good accuracy, Cα-RMSD of a peptide < 3.0 Å. For about 40% of cases, the peptide structures were modeled with an accuracy of Cα-RMSD < 2.0 Å. Our benchmark results clearly show that AF2 has a great potential to be applied to various higher-order structure prediction tasks.
CD8+ T-Cell Metabolic Rewiring Defined by Single-Cell RNA-Sequencing Identifies a Critical Role of ASNS Expression Dynamics in T-Cell Differentiation
Authors: Fernández-García Juan , Franco Fabien , Parik Sweta , Pane Antonino A. , Broekaert Dorien , van Elsen Joke , Vermeire Ines , van Brussel Thomas , Schepers Rogier , Modave Elodie , Karakach Tobias K. , Carmeliet Peter , Lambrechts Diether , Ho Ping-Chih , Fendt Sarah-Maria
Published: July 2021

Cytotoxic T cells dynamically rewire their metabolism during the course of an immune response. While T-cell metabolism has been extensively studied at phenotypic endpoints of activation and differentiation, the underlying dynamics remain largely elusive. Here, we leverage on single-cell RNA-sequencing (scRNA-seq) measurements of in vitro activated and differentiated CD8+ T cells cultured in physiological media to resolve these metabolic dynamics. We find that our scRNA-seq analysis identifies most metabolic changes previously defined in in vivo experiments, such as a rewiring from an oxidative to an anabolism-promoting metabolic program during activation to an effector state, which is later reverted upon memory polarization. Importantly, our scRNA-seq data further provide a dynamic description of these changes. In this sense, our data predict a differential time-dependent reliance of CD8+ T cells on the synthesis versus uptake of various non-essential amino acids during T-cell activation, which we corroborate with additional functional in vitro experiments. We further exploit our scRNA-seq data to identify metabolic genes that could potentially dictate the outcome of T-cell differentiation, by ranking them based on their expression dynamics. Among the highest-ranked hits, we find asparagine synthetase (Asns), whose expression sharply peaks for effector CD8+ T cells and further decays towards memory polarization. We then confirm that these in vitro Asns expression dynamics are representative of an in vivo situation in a mouse model of viral infection. Moreover, we find that disrupting these expression dynamics in vitro, by depleting asparagine from the culture media, delays central-memory polarization. Accordingly, we find that preventing the decay of ASNS by stable overexpression at the protein level in vivo leads to a significant increase in effector CD8+ T-cell expansion, and a concomitant decrease in central-memory formation, in a mouse model of viral infection. This shows that ASNS expression dynamics dictate the fate of CD8+ T-cell differentiation. In conclusion, we provide a resource of dynamic expression changes during CD8+ T-cell activation and differentiation that is expected to increase our understanding of the dynamic metabolic requirements of T cells progressing along the immune response cascade.
Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition
Authors: Hoffmann Ute A. , Heyl Florian , Rogh Said N. , Wallner Thomas , Backofen Rolf , Hess Wolfgang R. , Steglich Claudia , Wilde Annegret
Published: July 2021

Ribonucleases are crucial enzymes in RNA metabolism and post-transcriptional regulatory processes in bacteria. Cyanobacteria encode the two essential ribonucleases RNase E and RNase J. Cyanobacterial RNase E is shorter than homologues in other groups of bacteria and lacks both the chloroplast-specific N-terminal extension as well as the C-terminal domain typical for RNase E of enterobacteria. In order to investigate the function of RNase E in the model cyanobacterium Synechocystis sp. PCC 6803, we engineered a temperature-sensitive RNase E mutant by introducing two site-specific mutations, I65F and spontaneously occurring V94A. This enabled us to perform RNA-seq after the transient inactivation of RNase E by a temperature shift (TIER-seq) and to map 1,472 RNase-E-dependent cleavage sites. We inferred a dominating cleavage signature consisting of an adenine at the -3 and a uridine at the +2 position within a single-stranded segment of the RNA. The data identified putative RNase-E-dependent instances of operon discoordination, mRNAs likely regulated jointly by RNase E and an sRNA, potential 3’ end-derived sRNAs and a dual-acting mechanism for the glutamine riboswitch. Our findings substantiate the pivotal role of RNase E in post-transcriptional regulation and suggest the redundant or concerted action of RNase E and RNase J in cyanobacteria.
Lytic transglycosylases mitigate periplasmic crowding by degrading soluble cell wall turnover products
Authors: Weaver Anna , Alvarez Laura , Rosch Kelly , Ahmed Asraa , Wang Garrett , VanNieuwenhze Michael , Cava Felipe , Dörr Tobias
Published: July 2021

The peptidoglycan cell wall is a predominant structure of bacteria, determining cell shape and supporting survival in diverse conditions. Peptidoglycan is dynamic and requires regulated synthesis of new material, remodeling, and turnover – or autolysis – of old material. Despite exploitation of peptidoglycan synthesis as an antibiotic target, we lack a fundamental understanding of how peptidoglycan synthesis and autolysis intersect to maintain the cell wall. Here, we uncover a critical physiological role for a widely misunderstood class of autolytic enzymes, lytic transglycosylases (LTGs). We demonstrate that LTG activity is essential to survival by contributing to periplasmic processes upstream and independent of peptidoglycan recycling. Defects accumulate in Vibrio cholerae LTG mutants due to generally inadequate LTG activity, rather than absence of specific enzymes, and essential LTG activities are likely independent of protein-protein interactions, as heterologous expression of a non-native LTG rescues growth of a conditionally LTG-null mutant. Lastly, we demonstrate that soluble, uncrosslinked, endopeptidase-dependent peptidoglycan chains, also detected in the wild-type, are enriched in LTG mutants, and that LTG mutants are hypersusceptible to the production of diverse periplasmic polymers. Collectively, our results suggest that LTGs prevent toxic crowding of the periplasm with synthesis-derived peptidoglycan polymers and contrary to prevailing models, that this autolytic function can be temporally separate from peptidoglycan synthesis.
Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans
Authors: Price Ian F. , Hertz Hannah L. , Pastore Benjamin , Wagner Jillian , Tang Wen
Published: July 2021

The germline produces gametes that transmit genetic and epigenetic information to the next generation. Maintenance of germ cells and development of gametes require germ granules—well-conserved membraneless and RNA-rich organelles. The composition of germ granules is elusive owing to their dynamic nature and their exclusive expression in the germline. Using C. elegans germ granule, called P granule, as a model system, we employed a proximity-based labeling method in combination with mass spectrometry to comprehensively define its protein components. This set of experiments identified over 200 proteins, many of which contain intrinsically disordered regions. An RNAi-based screen identified factors that are essential for P granule assembly, notably EGGD-1 and EGGD-2, two previously uncharacterized LOTUS-domain proteins. Loss of eggd-1 and eggd-2 results in separation of P granules from nuclear envelope, germline atrophy and reduced fertility. We show that intrinsically disordered regions of EGGD-1 are required to anchor EGGD-1 to the nuclear periphery while its LOTUS domains are required to promote perinuclear localization of P granules. Together, our work expands the repertoire of P granule constituents and provides new insights into the role of LOTUS-domain proteins in germ granule organization.
1,25(OH)2D3 attenuates hepatic insulin resistance in rats with streptozotocin-induced diabetes via antioxidation
Authors: Huang Guoyu , Ding Runrong , Zhang Yujing , Gao Jiaojiao , Xu Ze , Li Wenjie , Li Xing
Published: July 2021

Aim

This study was conducted to explore the mechanism by which 1,25(OH)2D3 ameliorates hepatic insulin resistance in rats with streptozotocin (STZ)-induced type 2 diabetes.

Methods

Sprague Dawley (SD) rats were randomly divided into five groups: normal, control, and 1,25(OH)2D3 administered at 0.075, 0.15, and 0.3 μg/kg/d. Tissue and blood samples were obtained from all five groups after 4 and 12 weeks of treatment. Morphological changes in the livers were observed with HE staining. The levels of fasting blood glucose (FBG), insulin, and lipids were determined using an automatic biochemistry analyzer. The levels of hepatic glycogen, superoxide dismutase (SOD), malondialdehyde (MDA), aspartate aminotransferase (AST), and alanine aminotransferase (ALT) were analyzed by spectrophotometry. Protein expression of AKT and GLUT2 was examined by western blotting.

Results

1,25(OH)2D3 treatment reduced the FBG content as well as hepatic MDA, AST, and ALT levels, improved the activity of SOD, and enhanced the expression of GLUT2 and AKT in diabetic rats. These findings suggest that 1,25(OH)2D3, exerts antioxidant effects and ameliorates insulin resistance in the liver.

Conclusion

1,25(OH)2D3 is a potential agent that could be used in the treatment of insulin resistance in the liver.
Antifungal activity ofConocephalum conicum(L) Dumort. (Marchantiophyta) againstFusarium oxysporumf. sp.lycopersici
Authors: Negi Kavita , Chaturvedi Preeti
Published: July 2021

Tomato, a high valuevegetable crop, suffers huge production losses in tropics due to a wilt disease caused byFusarium oxysporumf. sp.lycopersici. Present study was undertaken to find an effective biocontrol method to check fusarium wilt in order to curb the losses suffered by the crop growers. Organic extracts(acetone, methanol/ethanol) of thalloid bryophytes (Conocephalumconicum(L.) Dumort. andMarchantiapapillataRaddi subsp.grossibarba(Steph.) Bischl.)were tested againstF. oxysporumf. sp.lycopersiciusing disc diffusion and micro broth dilution assay.Methanol extract ofC.conicum(L.) Dumort. (CCDM) showed significantly high antifungal activity (85.5% mycelial inhibition; 31.25μg/mL MIC and 125μg/mL MFC).Potential of methanol extract was tested in a glasshouse experiment on tomato, which illustrated the efficacy of the plant extract to control the fusarial wilt. Morphological and ultrastructural alterationsin CCDM treated fusarium myceliawere observed in scanning electron microscopy. GC-MS analysis of CCDM extract showed the presence of51 constituents, and the dominant compounds werebis (bibenzyl), acyclic alkanes, fatty acids, sesquiterpenpoids and steroids. The study suggested thatC. conicumbeing an efficient source of Riccardin C like antifungal compounds provides a potent and eco-friendly alternative to conventional fungicides in vegetables.
B Cell Receptor Signaling Drives APOBEC3 Expression Via Direct Enhancer Regulation in Chronic Lymphocytic Leukemia B Cells
Authors: Wang Zhiquan , Yan Huihuang , Boysen Justin C. , Secreto Charla R. , Zhong Jian , Zhou Jiaqi , Gan Haiyun , Yu Chuanhe , Braggio Esteban , Slager Susan L. , Parikh Sameer A. , Kay Neil E.
Published: July 2021

Constitutively activated B cell receptor (BCR) signaling is a primary biological feature of chronic lymphocytic leukemia (CLL). The biological events controlled by BCR signaling in CLL are not fully understood and need investigation. To make inroads we obtained blood samples from CLL patients before and after Bruton’s tyrosine kinase inhibitors (BTKi) treatment and used them to study BCR signaling regulated genes. Here, by analysis of the chromatin states and gene expression profiles of CLL B cells from patients before and after BTKi ibrutinib treatment, we show that BTKi treatment leads to a decreased expression of APOBEC3 family genes in an enhancer regulation dependent manner. BTKi treatment reduces enrichment of enhancer markers (H3K4me1, H3K27ac) and chromatin accessibility at putative APOBEC3 enhancers. CRISPR-Cas9 directed deletion or inhibition of the putative APOBEC3 enhancers leads to reduced APOBEC3 expression. We further find that transcription factor NFATc1 couples BCR signaling with the APOBEC3 enhancer activity to control APOBEC3 expression. Importantly, enhancer regulated APOBEC3 expression contributes to replication stress in malignant B cells. We also demonstrate a novel mechanism for BTKi suppression of APOBEC3 expression via direct enhancer regulation in a NFATc1 dependent manner, implicating BCR signaling as a potential regulator of leukemic genomic instability.

Key points

BCR signaling pathway regulates APOBEC3 expression via direct enhancer regulation.

AOPEBC3 enhancers are involved in the process of DNA replication stress, implicating a potential role in B cell genomic instability and CLL evolution
Single-Cell Profiling of the Antigen-Specific Response to BNT162b2 SARS-CoV-2 RNA Vaccine
Authors: Kramer Kevin J. , Wilfong Erin M. , Voss Kelsey , Barone Sierra M. , Shiakolas Andrea R. , Raju Nagarajan , Roe Caroline E. , Suryadevara Naveenchandra , Walker Lauren , Wall Steven C. , Paulo Ariana , Schaefer Samuel , Dahunsi Debolanle , Westlake Camille S. , Crowe James E. , Carnahan Robert H. , Rathmell Jeffrey C. , Bonami Rachel H. , Georgiev Ivelin S. , Irish Jonathan M.
Published: July 2021

RNA-based vaccines against SARS-CoV-2 are critical to limiting COVID-19 severity and spread. Cellular mechanisms driving antigen-specific responses to these vaccines, however, remain uncertain. We used single-cell technologies to identify and characterized antigen-specific cells and antibody responses to the RNA vaccine BNT162b2 in longitudinal samples from a cohort of healthy donors. Mass cytometry and machine learning pinpointed a novel expanding, population of antigen-specific non-canonical memory CD4+and CD8+T cells. B cell sequencing suggested progression from IgM, with apparent cross-reactivity to endemic coronaviruses, to SARS-CoV-2-specific IgA and IgG memory B cells and plasmablasts. Responding lymphocyte populations correlated with eventual SARS-CoV-2 IgG and a donor lacking these cell populations failed to sustain SARS-CoV-2-specific antibodies and experienced breakthrough infection. These integrated proteomic and genomic platforms reveal an antigen-specific cellular basis of RNA vaccine-based immunity.

ONE SENTENCE SUMMARY

Single-cell profiling reveals the cellular basis of the antigen-specific response to the BNT162b2 SARS-CoV-2 RNA vaccine.
The transcriptional corepressor CTBP-1 acts with the SOX family transcription factor EGL-13 to maintain AIA interneuron cell identity in C. elegans
Authors: Saul Josh , Hirose Takashi , Robert Horvitz H.
Published: July 2021

Cell identity is characterized by a distinct combination of gene expression, cell morphology and cellular function established as progenitor cells divide and differentiate. Following establishment, cell identities can be unstable and require active and continuous maintenance throughout the remaining life of a cell. Mechanisms underlying the maintenance of cell identities are incompletely understood. Here we show that the gene ctbp-1, which encodes the transcriptional corepressor C-terminal binding protein-1 (CTBP-1), is essential for the maintenance of the identities of the two AIA interneurons in the nematode Caenorhabditis elegans. ctbp-1 is not required for the establishment of the AIA cell fate but rather functions cell-autonomously and can act in later larval stage and adult worms to maintain proper AIA gene expression, morphology and function. From a screen for suppressors of the ctbp-1 mutant phenotype, we identified the gene egl-13, which encodes a SOX family transcription factor. We found that egl-13 regulates AIA function and aspects of AIA gene expression, but not AIA morphology. We conclude that the CTBP-1 protein maintains AIA cell identity in part by utilizing EGL-13 to repress transcriptional activity in the AIAs. More generally, we propose that transcriptional corepressors like CTBP-1 might be critical factors in the maintenance of cell identities, harnessing the DNA-binding specificity of transcription factors like EGL-13 to selectively regulate gene expression in a cell-specific manner.
BRET-based self-cleaving biosensors for SARS-CoV-2 3CLpro Inhibitor Discovery
Authors: Hou Ningke , Peng Chen , Zhang Lijing , Zhu Yuyao , Hu Qi
Published: July 2021

The 3C-like protease (3CLpro) of SARS-CoV-2 is an attractive drug target for developing antivirals against SARS-CoV-2. A few small molecule inhibitors of 3CLpro are in clinical trials for COVID-19 treatments and more inhibitors are being developed. One limiting factor for 3CLpro inhibitors development is that the cellular activities of such inhibitors have to be evaluated in a Biosafety Level 3 (BSL-3) or BSL-4 laboratory. Here, we design genetically encoded biosensors that can be used in BSL-2 laboratories to set up cell-based assays for 3CLpro inhibitor discovery. The biosensors were constructed by linking a green fluorescent protein (GFP2) to the N-terminus and a Renilla luciferase (RLuc8) to the C-terminus of SARS-CoV-2 3CLpro, with the linkers derived from the cleavage sequences of 3CLpro. After over-expression of the biosensors in HEK293 cells, 3CLpro can be released from GFP2 and RLuc by self-cleavage, resulting in a decrease of the bioluminescence resonance energy transfer (BRET) signal. Using one of these biosensors, pBRET-10, we evaluated the cellular activities of several 3CLpro inhibitors. These inhibitors restored the BRET signal by blocking the proteolysis of pBRET-10, and their relative activities measured using pBRET-10 were consistent with their anti-SARS-CoV-2 activities reported previously. We conclude that the biosensor pBRET-10 is a useful tool for SARS-CoV-2 3CLpro inhibitor discovery. Furthermore, our strategy can be used to design biosensors for other viral proteases that share the same activation mechanism as 3CLpro, such as HIV protease PR and HCV protease NS3.

Highlights

Sensitive cell-based biosensors for 3CLpro inhibitor discovery in BSL-2 laboratories.

The BRET-based self-cleaving biosensors mimic the in vivo autoproteolytic activation of 3CLpro.

Similar biosensors can be designed for other self-cleaving proteases, such as HIV protease PR and HCV protease NS3.
A non-functional copy of the salmonid sex determining gene (sdY) is responsible for the “apparent” XY females in Chinook salmon, Oncorhynchus tshawytscha
Authors: Bertho Sylvain , Herpin Amaury , Jouanno Elodie , Yano Ayaka , Bobe Julien , Parrinello Hugues , Journot Laurent , Guyomard René , Muller Thomas , Swanson Penny , McKinney Garrett , Williamson Kevin , Meek Mariah , Schartl Manfred , Guiguen Yann
Published: July 2021

Many salmonids have a male heterogametic (XX/XY) sex determination system, and they are supposed to have a conserved master sex determining gene (sdY), that interacts at the protein level with Foxl2 leading to the blockage of the synergistic induction of Foxl2 and Nr5a1 of the cyp19a1a promoter. However, this hypothesis of a conserved master sex determining role of sdY in salmonids is still challenged by a few exceptions, one of them being the presence of some naturally occurring “apparent” XY Chinook salmon females. Here we show that XY Chinook salmon females have a sdY gene (sdY-N183), which has one missense mutation leading to a substitution of a conserved isoleucine to an asparagine (SdY I183N). In contrast, Chinook salmon males have both a non-mutated sdY-I183 gene and the missense mutation sdY-N183 gene. The 3D model of SdY-N183 predicts that the I183N hydrophobic to hydrophilic amino acid change leads to a local modification of the β-sandwich structure of SdY. Using in vitro cell transfection assays we found that SdY-N183, like SdY-I183, is preferentially localized in the cytoplasm. However, compared to SdY-I183, SdY-N183 is more prone to degradation, its nuclear translocation by Foxl2 is reduced and SdY-N183 is unable to significantly repress the synergistic Foxl2/Nr5a1 induction of the cyp19a1a promoter. Altogether our results suggest that the sdY-N183 gene of XY Chinook females is a non-functional gene and that SdY-N183 is no longer able to promote testicular differentiation by impairing the synthesis of estrogens in the early differentiating gonads of wild Chinook salmon XY females.
First-principles investigation of V-doping effects on Fe3Cr4C3 carbide in hypereutectic Fe–Cr–C hardfacing coating
Authors: Shi Zhijun , Shao Wei , Xing Xiaolei , Ren Xuejun , Zhou Yefei , Yang Qingxiang
Published: July 2021

The mechanical property improvement of M
7C3 carbides in hypereutectic Fe–Cr–C hardfacing coating is required for its widespread application and longer service life. Vanadium is a frequently used alloying element, while the effects of V doping on the stability and tensile properties of M
7C3 carbide have been rarely reported. In this article, the formation enthalpy, structural stability, anisotropic tensile properties and electronic structure of V-doped M
7C3 (Fe3Cr4C3) carbide were calculated by the first-principles method. The mechanism by which the tensile property of Fe3Cr4C3 carbide can be improved by V-atom doping is discussed. The results show that the formation enthalpy (−0.24 eV/atom) of Fe3Cr3VC3 carbide is lower than that (0.48 eV/atom) of Fe3Cr4C3 carbide, which indicates that the formation of Fe3Cr3VC3 carbide is more facile. The absence of an imaginary frequency in the phonon dispersion spectra reveals that the Fe3Cr3VC3 carbide model is stable. Compared with Fe3Cr4C3 carbide, the tensile strength of Fe3Cr3VC3 carbide in the (0001) crystal face is increased from 44.42 to 48.46 GPa and that in the (1111) crystal face is also increased, from 28.99 to 34.19 GPa. The reasons that the tensile property of Fe3Cr4C3 can be improved by V doping are the electron redistribution and the formation of stronger bonds in Fe3Cr3VC3 carbide.
Crystal structure of copper perchlorophthalocyanine analysed by 3D electron diffraction
Authors: Gorelik Tatiana E. , Habermehl Stefan , Shubin Aleksandr A. , Gruene Tim , Yoshida Kaname , Oleynikov Peter , Kaiser Ute , Schmidt Martin U.
Published: July 2021

Copper perchlorophthalocyanine (CuPcCl16, CuC32N8Cl16, Pigment Green 7) is one of the commercially most important green pigments. The compound is a nanocrystalline fully insoluble powder. Its crystal structure was first addressed by electron diffraction in 1972 [Uyeda et al. (1972). J. Appl. Phys.
43, 5181–5189]. Despite the commercial importance of the compound, the crystal structure remained undetermined until now. Using a special vacuum sublimation technique, micron-sized crystals could be obtained. Three-dimensional electron diffraction (3D ED) data were collected in two ways: (i) in static geometry using a combined stage-tilt/beam-tilt collection scheme and (ii) in continuous rotation mode. Both types of data allowed the crystal structure to be solved by direct methods. The structure was refined kinematically with anisotropic displacement parameters for all atoms. Due to the pronounced crystal mosaicity, a dynamic refinement was not feasible. The unit-cell parameters were verified by Rietveld refinement from powder X-ray diffraction data. The crystal structure was validated by many-body dispersion density functional theory (DFT) calculations. CuPcCl16 crystallizes in the space group C2/m (Z = 2), with the molecules arranged in layers. The structure agrees with that proposed in 1972.
Structures of the Plasmodium falciparum heat-shock protein 70-x ATPase domain in complex with chemical fragments identify conserved and unique binding sites
Authors: Mohamad Nada , O'Donoghue Ailsa , Kantsadi Anastassia L. , Vakonakis Ioannis
Published: July 2021

Plasmodium falciparum invades erythrocytes and extensively modifies them in a manner that increases the virulence of this malaria parasite. A single heat-shock 70 kDa-type chaperone, PfHsp70-x, is among the parasite proteins exported to the host cell. PfHsp70-x assists in the formation of a key protein complex that underpins parasite virulence and supports parasite growth during febrile episodes. Previous work resolved the crystallographic structures of the PfHsp70-x ATPase and substrate-binding domains, and showed them to be highly similar to those of their human counterparts. Here, 233 chemical fragments were screened for binding to the PfHsp70-x ATPase domain, resulting in three crystallographic structures of this domain in complex with ligands. Two binding sites were identified, with most ligands binding proximal to the ATPase nucleotide-binding pocket. Although amino acids participating in direct ligand interactions are conserved between the parasite and human erythrocytic chaperones, one nonconserved residue is also present near the ligand. This work suggests that PfHsp70-x features binding sites that may be exploitable by small-molecule ligands towards the specific inhibition of the parasite chaperone.
Resilience of Islamic cryptocurrency markets to Covid-19 shocks and the Federal Reserve policy
Authors: Mnif Emna , Jarboui Anis
Published: July 2021

Purpose

After the COVID-19 outbreak, the Federal Reserve has undertaken several monetary policies to alleviate the pandemic consequences on the stock markets leading to a misunderstanding on the cryptocurrency market response. This paper aims to evaluate the effects of the Federal Reserve monetary policy on the Islamic and conventional cryptocurrency dynamics during the COVID-19 pandemic. We, specifically, examine the associate bubbles and feedbacks effects.

Design/methodology/approach

This paper developed a novel methodology that detects market bubbles using the statistical indicators defined by Psychological (PSY) tests. It also investigated the effect of the Federal Open Market Committee (FOMC) announcements on conventional and Islamic cryptocurrencies compatible with Islamic laws “Shari’ah” by using the event-driven regression.

Findings

The empirical results show that the FOMC announcements have a positive significant effect after one day of the event and a negative effect before two days of the announcement on the conventional cryptocurrency markets. However, the reaction of Islamic cryptocurrencies to these events is not significant except for Hello Gold after one day of the announcement. Besides, the Hello Gold and X8X cryptocurrencies present no bubbles during this period. However, Bitcoin and Ethereum markets have short-lived bubbles.

Research limitations/implications

The main contribution of this study is the investigation of the response and vulnerability to pandemic shocks of a new category of cryptocurrencies backed by tangible assets. This work has practical implications as it provides new insights into trading opportunities and market reactions.

Originality/value

To our knowledge, this work is the first study that compares the response of Islamic and conventional cryptocurrency markets to FOMC announcements during the COVID-19 pandemic and examines the presence of bubbles in these markets. Besides, the originality of this work is derived from the novelty of the data employed and the method used (PSY tests) in this study.
The moderation effect of work engagement on entrepreneurial attitude and organizational commitment: evidence from Thailand’s entry-level employees during the COVID-19 pandemic
Authors: Boonsiritomachai Waranpong , Sud-On Ploy
Published: July 2021

Purpose

Past research has convincingly shown that the more entrepreneurial employees are, the more likely they are to leave the organization and start their own enterprise. Therefore, the purpose of this paper is to understand how entrepreneurial employees can be retained in organizations by examining the relationships between work engagement, organizational commitment and entrepreneurial attitude among entry-level employees.

Design/methodology/approach

Covariance-based structural equation modeling is used to test the hypothesized relationships by using a survey of 416 employees.

Findings

The results of the study indicate that an entrepreneurial attitude significantly and positively contributes to work engagement, although it can divert employee attention regarding the level of commitment. Interestingly, the study findings show that employees will commit to an organization if they have engaged with the company, even if they have a highly entrepreneurial attitude.

Practical implications

This study’s findings are beneficial in understanding the concept of an entrepreneurial attitude and its impact on an organization. For firms to concurrently promote entrepreneurial characteristics and employee commitment, policy and staff practices must ensure the appropriate level of work engagement.

Originality/value

This study proposes new distal antecedent and consequence constructs of the engagement theory related to entrepreneurial attitude orientation and establishes the important link between these constructs with work engagement. The findings originally point to the role of work engagement in maintaining entrepreneurial employees and its effect on organizational commitment.
A half-bridge IGBT drive and protection circuit in dielectric barrier discharge power supply
Authors: Wang Xingquan , Lu Xiuyuan , Chen Wei , Wang Fengpeng , Huang Jun , Liu Lingli , Li Mengchao , Lin Kui
Published: July 2021

Purpose

This paper aims to improve the general circuit of driving and protection based on insulated gate bipolar transistor (IGBT) in dielectric barrier discharge power supply by designing a novel half-bridge inverter circuit with discrete components.

Design/methodology/approach

With one SG3524 chip, the structure based on discrete components is used to design the IGBT drive circuit. The driving waveform is isolated and sent out by photo-coupler 6N137. The protection circuit is realized by Hall sensor directly detecting the main circuit current, supplemented by a few components, including diodes, resistors, capacitors and triodes. It improves the reliability of the protection circuit.

Findings

In the driving circuit, the phase difference of signals from two channels are 180°. Moreover, when the duty cycle is set at 40%, it can ensure sufficient pulse width modulation response time. In the protection circuit, when over-current occurs, an intermittent output signal is automatically sent out. Furthermore, the over-current response time can be controlled independently. The peak voltage can be adjusted continuously from 0 to 30 kV with its frequency from 8 to 25 kHz and the power output up to 150 W.

Originality/value

The novel circuit of driving and protection makes not only its structure simpler and easier to be realized but also key parameters, such as frequency, the duty cycle and the driving voltage, continuously adjustable. Moreover, the power supply is suitable for other discharges such as corona discharge and jet discharge.
Longitudinal associations between soft skills, education and labour market outcomes: evidence from a survey of young Australians
Authors: Forrest Cameron J. , Swanton Tasman
Published: July 2021

Purpose

The purpose of this paper is to develop a measure of soft skills suitable for use in a large survey of Australian adolescents.

Design/methodology/approach

A survey was conducted with N = 4,704 Australians aged 15–19 over 2 years. Principal components analysis was performed on 14 self-report items, followed by generalised linear mixed modelling predicting education- and employment-related outcomes.

Findings

Self-reported problem solving, creativity, teamwork and verbal communication were alternately associated with later high school performance, hourly wage and employment status. These effects persisted when controlling for demographics and prior academic achievement.

Originality/value

Existing measures have been limited by their length or focus on specific skills or industries. The presented measures are short, domain-general, measure multiple skills simultaneously, and are suitable for a wide range of research contexts.
Factors influencing Bumiputera contractors' acceptance of the contractor's all risk takāful product
Authors: Ibrahim Mohd Azizi , Mat Nor Alias , Raja Hisham Raja Rizal Iskandar
Published: July 2021

Purpose

This research aims to investigate the factors that can influence Bumiputera contractors’ acceptance of the Contractor’s All Risks (CAR) takāful (Islamic insurance) product using the theory of reasoned action (TRA).

Design/methodology/approach

Using the method of quantitative surveys, 414 questionnaires were collected from targeted Bumiputera contractors in Malaysia (grade G1 to grade G7), except in Sabah and Sarawak, that are registered with the Construction Industry Development Board (CIDB) and are also members of Persatuan Kontraktor Melayu Malaysia (PKMM). The data was analysed using the partial least squares structural equation modeling (PLS-SEM) technique.

Findings

The findings from the PLS-SEM analysis show that attitude, subjective norm, religiosity and awareness have a positive relationship with Bumiputera contractors’ acceptance of the CAR takāful product. Religiosity appeared to be the most significant factor influencing Bumiputera contractors’ acceptance of the CAR takāful product.

Research limitations/implications

The respondents in this study only comprised Bumiputera contractors in Peninsular Malaysia, excluding those from Sabah and Sarawak. Therefore, it is not possible to generalise the findings to a broader population.

Practical implications

Takāful operators and their sales and marketing departments need to act proactively in promoting the benefits of investing in CAR takāful that follows Sharīʾah (Islamic law) rules and principles. They should create mechanisms to market CAR takāful better, thus accelerating its acceptance rate among contractors.

Originality/value

The paper uses the proposed extended TRA model, which includes the variables of religiosity and awareness in the TRA model. These variables were successfully integrated in the model, and the findings show that they have significantly contributed to the acceptance of the CAR takāful product among Bumiputera contractors.
Examining the influence of mindfulness on organizational role stress (ORS): a monitor acceptance theory perspective
Authors: Warrier Uma , Foropon Cyril , Chehimi Melinda
Published: July 2021

Purpose

The purpose of this paper is to examine the influence of mindfulness on organizational role stress (ORS) based on the Monitor Acceptance Theory (MAT) perspective.

Design/methodology/approach

This study is based on a cross-sectional data analysis collected from 137 employees working at an Indian IT organization located in Bangalore (India). ORS and MAAS scales have been used for measuring ORS and mindfulness, respectively.

Findings

Overall, the study findings have indicated a negative relationship (r = −0.588) between mindfulness (M) and ORS. First, both personal inadequacy (PI) and self-role distance (SRD) are found to be predominantly impacted by M, whereas both role erosion (RE) and role overload (RO) appear to be less affected by mindfulness. Second, SRD appears to be the highest ORS sub-dimension among IT employees. Third, building on the extant literature, it can be inferred that “no one size fits all”, ORS is both organization and context specific.

Originality/value

This study pioneers to establish empirical evidence between M and ORS. Training employees on M can help in effectively handling ORS.
Environmentally specific transformational leadership and green product development performance: the role of a green HRM system
Authors: Yan Jiaqi , Hu Wenan
Published: July 2021

Purpose

Green product development is a pivotal way to achieve environmental sustainability. The purpose of this paper is to theorize and empirically test how environmentally specific leadership enhances the green product development performance from the perspective of the HRM system. In this regard, the authors investigate the mediating role of the strength of the HRM system to change with regard to the relationship between environmentally specific leadership and green product development performance. For a substantial explanation of the boundary condition, the authors investigate the moderating role of the green HRM on the relationship between environmentally specific transformational leadership and the strength of the HRM system.

Design/methodology/approach

Based on climate strength theory, the authors use the three-wave survey data from 362 top or middle managers in the new energy industry of China. This study uses hierarchical linear regression and bootstrapping method to analyze the mediated moderation effect.

Findings

Results confirm a positive effect of environmentally specific leadership and the strength of the HRM system on green product development performance. The authors also found the mediation effect of the strength of the HRM system and the moderation effect of green HRM are all significant.

Originality/value

This study integrates the perspectives of both content-focused HRM and process-focused HRM and demonstrates why leadership and the HRM system could jointly enhance green product development performance in Asia.
Measuring an employer brand: a study towards valid scale development (as a second-order factor of a structural model)
Authors: Shrivastava Navin Kumar , Shukla Arvind Virendranath
Published: July 2021

Purpose

The study aims to conceptualise, develop and validates a scale to measure an employer brand(ing) (EB) based on the opinion of existing and potential employees.

Design/methodology/approach

A total of 431 student-respondents from B-Schools across India were surveyed in a cross-sectional study using a 70-item scale generated through literature review and expert interviews. Through exploratory factor analysis, six EB dimensions were derived. These were further validated using confirmatory factor analysis on data of 120 employees of the power sector.

Findings

A new 20-item EB scale- “EmBran” covers six dimensions of EB, namely, good human resource (HR) practices, business impression and work conditions, financial compensation, work-life balance, passive culture and standard HR policy. The paper posits EB as a second-order factor determined by six first-order factors.

Practical implications

The EB scale can be used by talent acquisition teams to derive meaningful insights into designing a policy for hiring and attracting young talent. It, thus, makes a significant contribution towards talent management. The scale also provides researchers with a fresh conceptualisation of the concept of the EB.

Originality/value

This study is unique as it considers the opinions of both existing and potential employees. Additionally, dimensions of passive culture and business impression and working conditions, emerged in the study.