bluuebunny/crossref_metadata_2025 huggingface dataset:
Wolbachia action in the sperm produces developmentally deferred chromosome segregation defects during the Drosophila mid-blastula transition
Authors: Warecki Brandt , Titen Simon , Alam Mohammad , Vega Giovanni , Lemseffer Nassim , Hug Karen , Sullivan William
Published: June 2022

Wolbachia, a vertically transmitted endosymbiont infecting many insects, spreads rapidly through uninfected populations by a mechanism known as Cytoplasmic Incompatibility (CI). In CI, embryos from crosses between Wolbachia-infected males and uninfected females fail to develop due to the immediate action of Wolbachia-produced factors in the first zygotic division. In contrast, viable progeny are produced when the female parent is infected. Here, we find ∼1/3 of embryos from CI crosses in Drosophila simulans develop normally beyond the first and subsequent pre-blastoderm divisions. Developing CI-derived embryos then exhibit chromosome segregation errors during the mid-blastula transition and gastrulation. Single embryo PCR and whole genome sequencing reveal a large percentage of the developed CI-derived embryos bypass the first division defect. Using fluorescence in situ hybridization, we find increased chromosome segregation errors in gastrulating CI-derived embryos that had avoided the first division defect. Thus, Wolbachia in the sperm induces independent immediate and developmentally deferred defects. Like the initial immediate defect, the delayed defect is rescued through crosses to infected females.
Distraction and cognitive control independently impact parietal and prefrontal response to pain
Authors: Silvestrini Nicolas , Corradi-Dell’Acqua Corrado
Published: June 2022

Previous studies found that distracting someone through a challenging activity leads to hypoalgesia, an effect mediated by parietal and prefrontal processes. Other studies suggest that challenging activities affect the ability to regulate one’s aching experiences, due to partially-common neural substrate between cognitive control and pain at the level the medial prefrontal cortex. We investigated effects of distraction and cognitive control on pain by delivering noxious stimulations during or after a Stroop paradigm (requiring high cognitive load) or a neutral condition. We found less intense and unpleasant subjective pain ratings during (compared to after) task execution. This hypoalgesia was associated with enhanced activity at the level of the dorsolateral prefrontal cortex and the posterior parietal cortex, which also showed negative connectivity with the insula. Furthermore, multivariate pattern analysis revealed that distraction altered the neural response to pain, by making it more similar to that associated with previous Stroop tasks. All these effects were independent of the nature of the task which, instead, led to a localized neural modulation around the anterior cingulate cortex. Overall, our study underscores the role played by two facets of human executive functions, which exert independent influence in the neural response of pain.
SEMA: Antigen B-cell conformational epitope prediction using deep transfer learning
Authors: Shashkova Tatiana I. , Umerenkov Dmitriy , Salnikov Mikhail , Strashnov Pavel V. , Konstantinova Alina V. , Lebed Ivan , Shcherbinin Dmitrii N. , Asatryan Marina N. , Kardymon Olga L. , Ivanisenko Nikita V.
Published: June 2022

One of the primary tasks in vaccine design and development of immunotherapeutic drugs is to predict conformational B-cell epitopes corresponding to primary antibody binding sites within the antigen tertiary structure. To date, multiple approaches have been developed to address this issue. However, for a wide range of antigens their accuracy is limited. In this paper, we applied the transfer learning approach using pretrained deep learning models to develop a model that predicts conformational B-cell epitopes based on the primary antigen sequence and tertiary structure. A pretrained protein language model, ESM-1b, and an inverse folding model, ESM-IF1, were fine-tuned to quantitatively predict antibody-antigen interaction features and distinguish between epitope and non-epitope residues. The resulting model called SEMA demonstrated the best performance on an independent test set with ROC AUC of 0.76 compared to peer-reviewed tools. We show that SEMA can quantitatively rank the immunodominant regions within the RBD domain of SARS-CoV-2. SEMA is available at https://github.com/AIRI-Institute/SEMAi and the web-interface http://sema.airi.net.
A universal pipeline for the alignment of electrode tracks with slice histology and electrophysiological data
Authors: Montijn Jorrit S. , Heimel J. Alexander
Published: June 2022

Modern electrophysiological experiments in neuroscience typically measure the activity of hundreds of neurons across multiple brain regions. Each recorded neuron has to be assigned its correct area of origin, which can be estimated using histological reconstructions of electrode tracks. However, this approach has a limited accuracy with which the probe position can be determined. While some tools exist to assist in this process in mice, such tools are scarce for other species, such as rats or macaques. Moreover, even in mice, a more reliable brain area assignment may be achieved by using spiking response properties to delineate area boundaries along the recording probe. Here we present the Universal Probe Finder, which provides multi-species support for reconstructing a probe’s brain area per spike-sorted cluster or recording site. It can use various data formats and can calculate neuronal responsiveness to experimental interventions with only event times and spike times to provide further neurophysiological markers that simplify and improve the reliability of assigning brain areas to neurons. The program can be downloaded here: https://github.com/JorritMontijn/UniversalProbeFinder.
Anaerobic methane oxidizing archaea offset sediment methane concentrations in Arctic thermokarst lagoons
Authors: Yang Sizhong , Anthony Sara E. , Jenrich Maren , In ‘t Zandt Michiel H. , Strauss Jens , Overduin Pier Paul , Grosse Guido , Angelopoulos Michael , Biskaborn Boris K. , Grigoriev Mikhail N. , Wagner Dirk , Knoblauch Christian , Jaeschke Andrea , Rethemeyer Janet , Kallmeyer Jens , Liebner Susanne
Published: June 2022

Thermokarst lagoons represent the transition state from a freshwater lacustrine to a marine environment, and receive little attention regarding their role for greenhouse gas production and release in Arctic permafrost landscapes. We studied the fate of methane (CH4) in sediments of a thermokarst lagoon in comparison to two thermokarst lakes on the Bykovsky Peninsula in northeastern Siberia through the analysis of sediment CH4concentrations and isotopic signature, methane-cycling microbial taxa, sediment geochemistry, and lipid biomarkers. We specifically assessed whether sulfate-driven anaerobic methane oxidation (S-AOM) through anaerobic methanotrophic archaea (ANMEs), common in marine sediments with constant supply of sulfate and methane, establish after thermokarst lagoon development and whether sulfate-driven ANMEs consequently oxidize CH4that would be emitted to the water column under thermokarst lake conditions. The marine-influenced lagoon environment had fundamentally different methane-cycling microbial communities and metabolic pathways compared to the freshwater lakes, suggesting a substantial reshaping of microbial and carbon dynamics during lagoon formation. Anaerobic sulfate-reducing ANME-2a/2b methanotrophs dominated the sulfate-rich sediments of the lagoon despite its known seasonal alternation between brackish and freshwater inflow. CH4concentrations in the freshwater-influenced sediments averaged 1.34±0.98 µmol g−1, with highly depleted δ13C-CH4values ranging from -89‰ to -70‰. In contrast, the sulfate-affected upper 300 cm of the lagoon exhibited low average CH4concentrations of 0.011±0.005 µmol g−1with comparatively enriched δ13C-CH4values of -54‰ to -37‰ pointing to substantial methane oxidation. Non-competitive methylotrophic methanogens dominated the methanogenic community of the lakes and the lagoon, independent of porewater chemistry and depth. This potentially contributed to the high CH4concentrations observed in all sulfate-poor sediments. Our study shows that S-AOM in lagoon sediments can effectively reduce sediment CH4concentrations and we conclude that thermokarst lake to lagoon transitions have the potential to mitigate terrestrial methane fluxes before thermokarst lakes fully transition to a marine environment.
Retinal metabolism: Evidence for uncoupling of glycolysis and oxidative phosphorylation via Cori-, Cahill-, and mini-Krebs-cycle
Authors: Chen Yiyi , Zizmare Laimdota , Calbiague Victor , Wang Lan , Yu Shirley , Herberg Friedrich W. , Schmachtenberg Oliver , Paquet-Durand François , Trautwein Christoph
Published: June 2022

The retina consumes massive amounts of energy, yet its metabolism and substrate exploitation remain poorly understood. Here, we used a murine explant model to manipulate retinal energy metabolism under entirely controlled conditions and utilized1H-NMR spectroscopy-based metabolomics, in situenzyme detection, and cell viability readouts to uncover the pathways of retinal energy production. Our experimental manipulations resulted in varying degrees of photoreceptor degeneration, while the inner retina and retinal pigment epithelium were essentially unaffected. This selective vulnerability of photoreceptors suggested very specific adaptations in their energy metabolism. Rod photoreceptors were found to rely strongly on oxidative phosphorylation, but only mildly on glycolysis. Conversely, cone photoreceptors were dependent on glycolysis but insensitive to electron transport chain decoupling. Importantly, photoreceptors appeared to uncouple glycolytic and Krebs-cycle metabolism via three different pathways: 1) the mini-Krebs-cycle, fueled by glutamine and branched-chain amino acids, generating N-acetylaspartate; 2) the alanine-generating Cahill-cycle; 3) the lactate-releasing Cori-cycle. Moreover, the metabolomic data indicated a shuttling of taurine and hypotaurine between the retinal pigment epithelium and photoreceptors, likely resulting in an additional net transfer of reducing power to photoreceptors. These findings expand our understanding of retinal physiology and pathology and shed new light on neuronal energy homeostasis and the pathogenesis of neurodegenerative diseases.Graphical abstract

Retinal photoreceptors employ both glucose and glutamate as fuels. While rod photoreceptors rely strongly on oxidative phosphorylation and the N-acetylaspartate producing mini-Krebs-cycle, cone photoreceptors rely on the lactate-producing Cori cycle and the oxidative, alanine producing Cahill cycle.

Highlights

The retina utilizes a complex energy switchboard consisting of the Krebs cycle, mini-Krebs cycle, Cahill cycle, and Cori cycle.

Mini-Krebs cycle runs more efficiently than ‘full’ Krebs cycle.

Alanine transaminase decouples glycolysis from the Krebs cycle.

Lactate, alanine, and N-acetylaspartate are distinctive energetic pathway signatures.
Bilateral JNK activation is a hallmark of interface contractility and promotes elimination of aberrant cells
Authors: Prasad Deepti , Illek Katharina , Fischer Friedericke , Holstein Kathrin , Classen Anne-Kathrin
Published: June 2022

Tissue-intrinsic defence mechanisms eliminate aberrant cells from epithelia and thereby maintain the health of developing tissues or adult organisms. ‘Interface contractility’ comprises one such distinct mechanism that specifically guards against aberrant cells, which undergo inappropriate cell fate and differentiation programs. The cellular mechanisms which facilitate detection and elimination of these aberrant cells are currently unknown. We find that in Drosophila imaginal discs, interface contractility is associated with bilateral JNK activation at the clonal interface of wild type and aberrant cells. Bilateral JNK activation is unique to interface contractility and is not observed in other tissue-intrinsic defence mechanisms, such as cell-cell competition. We find that JNK is activated cell-autonomously by either of the contacting cell types and drives apoptotic elimination of cells at clonal interfaces. Ultimately, JNK interface signalling provides a collective tissue-level mechanism, which ensures elimination of aberrant, misspecified cells that cannot be identified by cell fitness criteria, as in cell-cell competition. Importantly, oncogenic Ras activates interface contractility but evades apoptotic elimination by bilateral JNK activation. Combined, our work establishes bilateral JNK interface signalling and interface apoptosis as a new hallmark of interface contractility, and it highlights how oncogenic mutations evade tumour suppressor function encoded by this tissue-intrinsic surveillance system.
Comprehensive Analysis of CRISPR Base Editing Outcomes for Multimeric Protein
Authors: Kabra Meha , Moosajee Mariya , Newby Gregory A. , Molugu Kaivalya , Saha Krishanu , Liu David R. , Pattnaik Bikash R.
Published: June 2022

Point mutations in the KCNJ13 gene cause an autosomal recessive, childhood blindness, Leber congenital amaurosis (LCA16) due to a loss-of-function Kir7.1 channel. In the present study, we investigated the etiology of LCA16 caused by a KCNJ13 missense mutation (c.431T>C, p.Leu144Pro) and explored the activity of two cytosine base editors mRNAs (CBEs, BE4max-WTCas9, and evoCDA-SpCas9-NG) as a proof-of-concept therapeutic option. We observed the KCNJ13-related retinopathy phenotype in patients harboring L144P mutation. Our in-silico prediction and in vitro validation demonstrated that L144P mutation affects the channel function. We observed high on-target efficiency in the CBEs treated L144P mutant gene expressing HEK-293 cells. Strikingly, our evaluation of base editing efficacy using electrophysiology showed negligible channel function. We found that the editing bystander ‘Cs’ in the protospacer region led to a missense change (L143F) in evoCDA edited cells and only silent changes in BE4max edited cells. Upon investigation of the effect of the synonymous codon, our extended analysis revealed distortion of mRNA structure, altered half-life, and/or low abundance of the cognate tRNA. We propose that KCNJ13-L144P mutation or other genes that share similar genetic complexity may be challenging to correct with the current generation of CRISPR base editors, and a combinational therapy using CRISPR base editors with a tighter editing window and requisite cognate-tRNA supplementation could be an alternative therapeutic approach to restore Kir7.1 channel function in LCA16 patients. Other options for hard-to-rescue alleles could employ homology-directed repair using CRISPR/Cas9 nucleases, Prime editing, and AAV-mediated gene augmentation.
Ex vivoExpansion Potential of Murine Hematopoietic Stem Cells: A Rare Property Only Partially Predicted by Phenotype
Authors: Zhang Qinyu , Olofzon Rasmus , Konturek-Ciesla Anna , Yuan Ouyang , Bryder David
Published: June 2022

The scarcity of hematopoietic stem cells (HSCs) restricts their use in both clinical settings and experimental research. Here, we examined a recently developed method for expanding rigorously purified murine HSCsex vivo.After three weeks of culture, only 0.1% of cells exhibited the input HSC phenotype, but these accounted for almost all functional long-term HSC activity. Input HSCs displayed varying potential forex vivoself-renewal, with alternative outcomes revealed by single cell multimodal RNA- and ATAC-seq profiling. While most HSC progeny offered only transientin vivoreconstitution, these cells efficiently rescued mice from lethal myeloablation. The amplification of functional HSC activity allowed for long-term multilineage engraftment in unconditioned hosts that associated with a return of HSCs to quiescence. Thereby, our findings identify several key considerations forex vivoHSC expansion, with major implications also for assessment of normal HSC activity.

Key point:Ex vivoself-renewal is an intrinsic property of rare candidate HSCs, with implications for assessments of HSC activity by transplantation.
Trim69 is a microtubule regulator that acts as a pantropic viral inhibitor
Authors: Song Yuxin , Nguyen Xuan-Nhi , Kumar Anuj , da Silva Claire , Picard Léa , Etienne Lucie , Cimarelli Andrea
Published: June 2022

To identify novel cellular modulators of HIV-1 infection in IFN-stimulated myeloid cells, we have carried out a screen that combines functional and evolutionary analyses in THP-1-PMA cells that led us to the Tripartite Motif Protein 69 (Trim69), a poorly studied member of the Trim family of innate immunity regulators. Trim69 inhibits HIV-1, primate lentiviruses and the negative and positive-strand RNA viruses VSV and SARS-CoV2, overall indicating it is a broad-spectrum antiviral factor. Trim69 binds directly to microtubules and its antiviral activity is intimately linked to its ability to promote the accumulation of stable MTs, a specialized subset of microtubules. By analyzing the behavior of primary blood cells, we provide evidence that a program of MT stabilization is commonly observed in response to IFN-I in cells of the myeloid lineage and Trim69 is the key factor behind this program.

Overall, our study identifies Trim69 as the first antiviral innate defense factor that regulates the properties of microtubules to limit viral spread, highlighting the possibility that the cytoskeleton may be a novel unappreciated fighting ground in the host-pathogen interactions that underlie viral infections.
Exercise preserves fitness capacity during aging through AMPK and mitochondrial dynamics
Authors: Campos Juliane Cruz , Marchesi Bozi Luiz Henrique , Traa Annika , van der Bliek Alexander M , Van Raamsdonk Jeremy M. , Blackwell T. Keith , Ferreira Julio Cesar Batista
Published: June 2022

Exercise is a nonpharmacological intervention that improves health during aging, and a valuable tool in the diagnostics of aging-related diseases. In muscle, exercise transiently alters mitochondrial functionality and metabolism. Mitochondrial fission and fusion are critical effectors of mitochondrial plasticity, which allows a fine-tuned regulation of organelle connectiveness, size and function. Here we have investigated the role of mitochondrial dynamics during exercise in the genetically tractable modelCaenorhabditis elegans. We show that in body wall muscle a single exercise session induces a cycle of mitochondrial fragmentation followed by fusion after a recovery period, and that daily exercise sessions delay the mitochondrial fragmentation and fitness capacity decline that occur with aging. The plasticity of this mitochondrial dynamics cycle is essential for fitness capacity and its enhancement by exercise training. Surprisingly, among longevity-promoting mechanisms we analyzed, constitutive activation of AMPK uniquely preserves fitness capacity during aging. As with exercise training, this benefit of AMPK is abolished by impairment of mitochondrial fission or fusion. AMPK is also required for fitness capacity to be enhanced by exercise, with our findings together suggesting that exercise enhances muscle function through AMPK regulation of mitochondrial dynamics. Our results indicate that mitochondrial connectivity and the mitochondrial dynamics cycle are essential for maintaining fitness capacity and exercise responsiveness during aging, and suggest that AMPK activation may recapitulate some exercise benefits. Targeting mechanisms to optimize mitochondrial fission and fusion balance, as well as AMPK activation, may represent promising strategies for promoting muscle function during aging.

Significance Statement

Exercise is a powerful anti-aging intervention. In muscle exercise remodels mitochondrial metabolism and connectiveness, but the role of mitochondrial dynamics in exercise responsiveness has remained poorly understood. Working inCaenorhabditis elegans, we find that the mitochondrial dynamics cycle of fission and fusion is critical for fitness capacity, that exercise delays an aging-associated decline in mitochondrial connectiveness and fitness capacity, and that the mitochondrial dynamics cycle is required for the latter benefit. AMPK, which regulates mitochondrial dynamics, is needed for exercise to maintain fitness capacity with age and can recapitulate this exercise benefit. Our data identify the mitochondrial dynamics cycle as an essential mediator of exercise responsiveness, and an entry point for interventions to maintain muscle function during aging.
Regeneration and Developmental Enhancers Are Differentially Compatible with Minimal Promoters
Authors: Begeman Ian J. , Emery Benjamin , Kurth Andrew , Kang Junsu
Published: June 2022

Enhancers and promoters are cis-regulatory elements that control gene expression. Enhancers are activated in a cell type-, tissue-, and condition-specific manner to stimulate promoter function and transcription. Zebrafish have emerged as a powerful animal model for examining the activities of enhancers derived from various species through transgenic enhancer assays, in which an enhancer is coupled with a minimal promoter. However, the efficiency of minimal promoters and their compatibility with multiple developmental and regeneration enhancers have not been systematically tested in zebrafish. Thus, we assessed the efficiency of six minimal promoters and comprehensively interrogated the compatibility of the promoters with developmental and regeneration enhancers. We found that the fos minimal promoter and Drosophila synthetic core promoter (DSCP) yielded high rates of leaky expression that may complicate the interpretation of enhancer assays. Notably, the adenovirus E1b promoter, the zebrafish lepb 0.8-kb (P0.8) and lepb 2-kb (P2) promoters, and a new zebrafish synthetic promoter (ZSP) that combines elements of the E1b and P0.8 promoters drove little or no ectopic expression, making them suitable for transgenic assays. We also found significant differences in compatibility among specific combinations of promoters and enhancers, indicating the importance of promoters as key regulatory elements determining the specificity of gene expression. Our study provides guidelines for transgenic enhancer assays in zebrafish to aid in the discovery of functional enhancers regulating development and regeneration.
Adenosine Reduces Sinoatrial Node Cell AP Firing Rate by uncoupling its Membrane and Calcium Clocks
Authors: Wirth Ashley N. , Tsutsui Kenta , Maltsev Victor A. , Lakatta Edward G.
Published: June 2022

Abstract

The spontaneous action potential (AP) firing rate of sinoatrial nodal cells (SANC) is regulated by a system of intracellular Ca2+ and membrane ion current clocks driven by Ca2+-calmodulin-activated adenylyl cyclase-protein kinase A (PKA) signaling. The mean AP cycle length (APCL) and APCL variability inform on the effectiveness of clock coupling. Endogenous ATP metabolite adenosine (ado) binds to adenosine receptors that couple to Gi protein-coupled receptors, reducing spontaneous AP firing rate via Gβγ signaling that activates an membrane-clock outward current, IKACh. Ado also inhibits adenylyl cyclase activity via Giα signaling, impacting cAMP-mediated PKA-dependent protein phosphorylation and intracellular Ca2+ cycling. We hypothesize that in addition to IKAdo activation, ado signaling impacts Ca2+ via Giα signaling and that both effects reduce AP firing rate by reducing the effectiveness of the Ca2+ and membrane clock coupling. To this end, we measured Ca2+ and membrane potential characteristics in enzymatically isolated single rabbit SANC. 10 µM ado substantially increased both the mean APCL (on average by 43%, n=10) and AP beat-to-beat variability from 5.1±1.7% to 7.2±2.0% (n=10) measured via membrane potential and 5.0±2.2 to 10.6±5.9 (n=40) measured via Ca2+ (assessed as the coefficient of variability, CV=SD/mean). These effects were mediated by hyperpolarization of the maximum diastolic membrane potential (membrane clock effect) and suppression of diastolic spontaneous, local Ca2+ releases (LCRs) (Ca2+ clock effect): as LCR size distributions shifted from larger to smaller values, the time of LCR occurrence during diastolic depolarization (LCR period) became prolonged, and the ensemble LCR Ca2+ signal became reduced. The tight linear relationship of coupling between LCR period to the APCL in the presence of ado “drifted” upward and leftward, i.e. for a given LCR period, APCL was prolonged, becoming non-linear indicating clock uncoupling. An extreme case of uncoupling occurred at higher ado concentrations (>100 µM): small stochastic LCRs of the Ca2+ clock failed to self-organize and synchronize to the membrane clock, thus creating a failed attempt to generate an AP resulting in arrhythmia and cessation of AP firing. Thus, the effects of ado to activate Gβγ and IKACh, Ado and to activate Giα, suppressing adenylyl cyclase activity, both contribute to the ado-induced increase in the mean APCL and APCL variability by reducing the fidelity of clock coupling and AP firing rate.
Direct Force Measurement and Loading on Developing Tissues in Intact Avian Embryos
Authors: Chan Chon U , Xiong Fengzhu , Michaut Arthur , Vidigueira Joana M. N. , Pourquie Olivier , Mahadevan L.
Published: June 2022

Developmental morphogenesis is driven by tissue stresses acting on tissue rheology. Direct measurements of forces in small tissues (100μm-1mm)in situsuch as in early embryos require high spatial precision and minimal invasiveness. Here we report tissue force microscopy (TiFM) integrating a vertical cantilever probe and live imaging to enable close-loop control of mechanical loading in early chicken embryos. By testing previously qualitatively characterized force-producing tissues in the elongating body axis, we show that TiFM quantitatively captures stress dynamics with high sensitivity. TiFM also provides the capacity of applying a stable, minimally-invasive and physiologically relevant load to drive tissue deformation, which alters morphogenetic progression and cell movements. Together, TiFM addresses a key technological gap in tissue force measurement and manipulation in small developing embryos, and promises to contribute to the quantitative understanding of complex multi-tissue mechanics during development.
Probing the biophysical constraints of SARS-CoV-2 spike N-terminal domain using deep mutational scanning
Authors: Ouyang Wenhao O. , Tan Timothy J.C. , Lei Ruipeng , Song Ge , Kieffer Collin , Andrabi Raiees , Matreyek Kenneth A. , Wu Nicholas C.
Published: June 2022

Increasing the expression level of the SARS-CoV-2 spike (S) protein has been critical for COVID-19 vaccine development. While previous efforts largely focused on engineering the receptor-binding domain (RBD) and the S2 subunit, the N-terminal domain (NTD) has been long overlooked due to the limited understanding of its biophysical constraints. In this study, the effects of thousands of NTD single mutations on S protein expression were quantified by deep mutational scanning. Our results revealed that in terms of S protein expression, the mutational tolerability of NTD residues was inversely correlated with their proximity to the RBD and S2. We also identified NTD mutations at the interdomain interface that increased S protein expression without altering its antigenicity. Overall, this study not only advances the understanding of the biophysical constraints of the NTD, but also provides invaluable insights into S-based immunogen design.
Structure of the GOLD-domain seven-transmembrane helix protein family member TMEM87A
Authors: Hoel Christopher M. , Zhang Lin , Brohawn Stephen G.
Published: June 2022

TMEM87s are eukaryotic transmembrane proteins with two members (TMEM87A and TMEM87B) in humans. TMEM87s have proposed roles in protein transport to and from the Golgi, as mechanosensitive ion channels, and in developmental signaling. TMEM87 disruption has been implicated in cancers and developmental disorders. To better understand TMEM87 structure and function, we determined a cryo-EM structure of human TMEM87A in lipid nanodiscs. TMEM87A consists of a Golgi-dynamics (GOLD) domain atop a membrane spanning seven-transmembrane helix domain with a large cavity open to solution and the membrane outer leaflet. Structural and functional analyses suggest TMEM87A may not function as an ion channel or G-protein coupled receptor. We find TMEM87A shares its characteristic domain arrangement with seven other proteins in humans; three that had been identified as evolutionary related (TMEM87B, GPR107, and GPR108) and four previously unrecognized homologs (GPR180, TMEM145, TMEM181, and WLS)). Among these structurally related GOLD domain seven-transmembrane helix (GOST) proteins, WLS is best characterized as a membrane trafficking and secretion chaperone for lipidated Wnt signaling proteins. We find key structural determinants for WLS function are conserved in TMEM87A. We propose TMEM87A and structurally homologous GOST proteins could serve a common role in trafficking membrane-associated cargo.
Humanized mice bearing CRISPR/Cas9 Disruption of Signal Transducer and Activator of Transcription 1 (STAT1) to Model Primary Immunodeficiency
Authors: Aron Jennifer L. , Thauland Timothy , Khan Humza , Butte Manish J.
Published: June 2022

Background

The search for a single, pathogenic genetic variant in a patient suspected to have a monogenic inborn error of immunity (IEI) often reveals a multitude of rare variants of unknown significance (VUS). Distinguishing which VUS is disease-causing versus the irrelevant, rare variants from the genetic background is slow and difficult. Advances in gene editing technology, particularly CRISPR/Cas9, promise to accelerate the timeline for the development of single-variant animal models, thus affording an experimental system for validating new genes and their variants.

Objective

We sought to demonstrate a proof-of-concept of using CRISPR/Cas9 in human hematopoietic stem cells (hHSC) to develop of humanized mice bearing a hematopoietic deficiency in signal transducer and activator 1 (STAT1).

Methods

Using CRISPR/Cas9, we introduced indels into the STAT1 gene of hHSCs and implanted them into immunodeficient mice. The reconstituted immune systems were assessed by flow cytometry.

Results

Mice transplanted with cells edited to eliminate STAT1 developed human immune systems with diverse cell phenotypes. Lymphocytes from these reconstituted mice showed low expression of STAT1 protein and diminished phosphorylation of STAT1 in response to interferon stimulation. These data mirror the impaired, but not abolished, response to interferons seen in human partial STAT1 deficiency. CRISPR/Cas9 genome editing techniques can be used to rapidly and inexpensively create functional, humanized models of primary immune deficiencies.
Corner flows induced by surfactant-producing bacteria Bacillus subtilis and Pseudomonas fluorescens
Authors: Li Yuan , Sanfilippo Joe , Kearns Daniel , Yang Judy Q.
Published: June 2022

Mechanistic understanding of bacterial spreading in soil is critical to control pathogenic contamination of groundwater and soil as well as design bioremediation projects. However, our understanding is currently limited by the lack of direct bacterial imaging in soil conditions. Here, we overcome this limitation by directly observing the spread of bacterial solution in a transparent chamber with varying corner angles designed to replicate soil-like conditions. We show that two common soil bacteria, Bacillus subtilis and Pseudomonas fluorescens, generate flows along sharp corners (< 60°) by producing surfactants that turn nonwetting solid surfaces into wetting surfaces. We further show that a surfactant-deficient mutant of B. subtilis cannot generate corner flows along sharp corners, confirming that the bacteria-generated corner flows require the production of bacterial surfactants. The speed of biosurfactant-induced corner flow at the sharp corner is about several millimeters per hour, similar to that of bacterial swarming, the fastest mode of known bacterial surface translocation. We further demonstrate that the bacteria-generated corner flow only occurs when the corner angle is less than a critical value, which can be predicted from the contact angle of the bacterial solution. Furthermore, we show that the corner flow has a maximum height due to the roundness or cutoff of corners. The mechanistic understanding and mathematical theories of bacterial spreading presented in this study will help improve predictions of bacterial spreading in soil, where corners are ubiquitous, and facilitate future designs of soil contamination mitigation and other bioremediation projects.

Importance

The spread of bacterial cells in soil regulates soil biogeochemical cycles, increases the possibility of soil and groundwater contamination, and controls the efficiency of many bacteria-based bioremediation projects. However, mechanistic understanding of bacterial spreading in soil remains incomplete due to a lack of direct or in-situ observations. Here, we simulate confined spaces of soil using a transparent material with similar hydrophobicity as hydrocarbon-covered soil and directly visualize the spread of two common soil bacteria, Bacillus subtilis and Pseudomonas fluorescens. We show that both bacteria can generate vertical flows along sharp corners of the transparent chamber. The velocity of the bacterial corner flow is several millimeters per hour. We further demonstrate that the corner flow was generated by bacteria-produced bio-surfactants, which are soap-like chemicals and turn nonwetting solid surfaces into wetting surfaces. Our results will help improve predictions of bacterial spreading in soil and facilitate designs of soil-related bioremediation projects.
How knowledge sharing encourages innovative work behavior through occupational self-efficacy? The moderating role of entrepreneurial leadership
Authors: Islam Talat , Zahra Iram , Rehman Saif Ur , Jamil Saqib
Published: June 2022

Purpose

Innovation has become a necessity for the information technology (IT) sector, especially during COVID-19 pandemic. Therefore, this study aims to investigate how knowledge sharing affects employees’ innovative work behavior (IWB). Specifically, the study examined occupational self-efficacy (as mediating mechanism) and entrepreneurial leadership (as boundary condition) to encourage IWB.

Design/methodology/approach

The study used social media platforms to collect data from 270 employees working in the IT sector through “google forms” on convenience basis between March and August, 2021. The study applied structural equation modeling in two stages to examine the measurement model (for uni-dimensionality) and the structural model (for hypotheses testing).

Findings

The study noted that knowledge sharing positively affects employees’ IWB and occupational self-efficacy positively explains this association. In addition, employees’ perception of entrepreneurial leadership strengthens the association between knowledge sharing and IWB.

Research limitations/implications

The study collected data from a developing country during COVID-19 by using a cross-sectional design that may restrict causality. However, the findings suggest the management not only encourages knowledge sharing environment but also engages employees in various training that motivate them to experiment with new ideas and techniques.

Originality/value

This study extends the existing literature on knowledge sharing and IWB by exploring occupational self-efficacy as mediating mechanism and entrepreneurial leadership as a boundary condition.
Parameter estimation for grey system models: gradient matching versus integral matching
Authors: Wei Baolei , Xie Naiming , Yang L.U.
Published: June 2022

Purpose

The cumulative sum (Cusum) operator, also referred to as accumulating generation operator, is the fundamental of grey system models and proves to be successful in various real-world applications. This paper aims to uncover the advantages of the Cusum operator from a parameter estimation perspective, i.e. comparing integral matching with classical gradient matching.

Design/methodology/approach

Grey system models are represented as a state space form to investigate the effect of measurement errors on estimation performance; subsequently, gradient matching and integral matching are respectively formulated to estimate parameters from noisy observations and, then, their quantitative relationships are established by using matrix computation tricks.

Findings

Extensive simulations, which are conducted on both linear and non-linear models under different sample size and noise level combinations, show that integral matching is superior to gradient matching, and, also the former is less sensitive to measurement error.

Originality/value

This paper explains why the Cusum operator is widely utilized in grey system models, thereby further solidifying the mathematical fundamentals of grey system models.
Yin-Yang balancing: a novel way of managing firms’ entrepreneurial orientation paradoxes
Authors: Pauluzzo Rubens
Published: June 2022

Purpose

This paper investigates how to embrace an “either/and” logic, borrowed from the Yin-Yang epistemological system, to provide a different perspective to the entrepreneurial orientation (EO) research and reframe its paradoxes and dilemmas.

Design/methodology/approach

The study adopts the duality map for paradox management, a tool designed to recognize and measure the threshold as a range within which opposite elements can be properly balanced for a healthy tension, to show that the apparently contradictory poles of the EO construct can co-exist within the same organization depending on specific situations, contexts and time.

Findings

By using duality maps as working models, the study shows that, in real life, the apparently contradictory poles of the EO construct co-exist in a healthy tension within the same organization and are managed in a constant process of dynamic balancing over time.

Research limitations/implications

The present paper contributes to the EO research by providing a different perspective to the EO concept, thus filling the gap on how to go beyond the traditional polarized (“either/or”) paradigm that has dominated the EO literature since its origins.

Originality/value

EO is dominated by a polarized view that sees opposites as sharp dichotomies. However, the complexity and variability of today’s interconnected world are pushing scholars to move from this hegemonic Western perspective by adopting different cultural and philosophical approaches able to balance the inherent duality of the EO concept.
Examining the impact of India–USA free trade agreement on agriculture sector: an ex-ante partial equilibrium analysis
Authors: Jain Neha , Kumar Sandeep
Published: June 2022

Purpose

The purpose of the paper is to explore the economic repercussions of potential India–USA free trade agreement (FTA) on the trade of agricultural commodities at HS 2-digit level.

Design/methodology/approach

The analysis is undertaken by assuming tariff reduction in a phased manner using the World Integrated Trade Solutions (WITS)-SMART partial equilibrium model to identify the trade creation and trade diversion effects.

Findings

Overall results show that both the trading partners gain from the proposed FTA. Trade creation dominates over trade diversion in India's analysis.

Practical implications

An FTA between India and the USA could be an essential step toward more liberal trade regimes and provide enormous economic benefits to both countries. Government of both the countries should support deeper integration. This will create more job opportunities and generate prosperity in both economies.

Originality/value

There are numerous studies conducted on evaluating the impact of FTAs ratified between countries. But there are limited studies which evaluate the impact of the proposed India–USA FTA on the economies of both trading partners specifically on the agriculture sector.
Women entrepreneurs’ persistence at the time of the COVID-19 pandemic: a decision-making perspective
Authors: Nouri Pouria
Published: June 2022

Purpose

Decision-making is of utmost importance for entrepreneurs. One of the most important entrepreneurial decisions is the decision to persist, which under certain circumstances such as a high level of adversity may seal the fate of entrepreneurs’ businesses. Nevertheless, the main antecedents of the decision to persist among entrepreneurs have remained understudied. This dearth of research is more obvious with respect to women entrepreneurs, especially in developing countries. To address this gap, this paper aims to explore the main antecedents of the decision to persist among women entrepreneurs.

Design/methodology/approach

By adopting a narrative approach, data were collected through a combination of semi-structured and in-depth questions with a sample of Iranian women entrepreneurs founding and running small businesses offering services in a variety of sectors and analysed by narrative data analysis.

Findings

According to the findings, the pandemic-emanated uncertainty, personal attachment to one’s venture as well as the reluctance of being blamed by one’s family, and the fear of the unknown future were the main drivers of the decision to persist among the entrepreneurs.

Originality/value

This paper offers two novel contributions to the extant literature. This paper is a pioneer not only in exploring entrepreneurs’ decisions during the COVID-19 pandemic but also in studying the decision to persist in the context of the developing nations.
The impact of local government economic development programs on city-level entrepreneurial activity: evidence from Southern California
Authors: Asencio Hugo D. , Prager Fynnwin , Martínez José N. , Tamura John
Published: June 2022

Purpose

This paper examines the relationship between government economic development programming and entrepreneurial activity, by examining evidence in Southern California cities. While numerous studies explore this relationship between government institutions and entrepreneurship at the level of countries and states, significant questions remain at the level of city government, and the influence of local government economic development programs on city-level entrepreneurial activity.

Design/methodology/approach

This paper uses regression analysis of data from all 215 Southern California cities to decompose the complex relationships between economic development programming and different types of entrepreneurial activity.

Findings

Results suggest startups are attracted to cities with higher crime rates, more diversity, and older populations, yet not those with higher levels of economic development programming. There is evidence that some types of economic development programming may influence entrepreneurship, especially for the level of minority-owned businesses.

Originality/value

The paper makes three important contributions to the literature. First, it is among the first to use local (city-level) entrepreneurship as an outcome variable to measure the effect of government economic development programming. Many scholars have instead chosen to look at outcomes relating to general economic growth (e.g. new jobs) rather than outcomes specific to local entrepreneurship. Second, it explores city-wide entrepreneurial activity with respect to numerous measures, such as start-ups, minority and female ownership, and self-employment. Third, it examines the potential influence of economic development programming, both on aggregate and decomposed into economic development program clusters.
Sources of bias in death determination: A research note articulating the need to include systemic sources of biases along with cognitive ones as impacting mortality data
Authors: Neuilly Melanie‐Angela
Published: June 2022

There are structural and organizational factors that impact how and what mortality data are collected. There are individual decision‐making processes and implicit cognitive biases that influence how and what mortality data are collected. Yet there seems to be a disconnect between how and why these two broad sources of bias may collide and how both need to be understood in order to be able to approach solutions aimed at strengthening the accuracy of mortality data. Using results from a mixed‐method, long‐term research project at four medicolegal offices in two countries, France and the United States, this research note proposes that truly understanding the sources of implicit cognitive bias in forensic pathologists and other medicolegal actors requires knowledge of legal, cultural, and organizational structures that shape medicolegal systems and in turn constrain individual actors' decision‐making processes. The goal is to advocate for multilevel and multi‐methods approaches to propose systemic solutions to the issue of implicit cognitive biases in forensic pathologists and other medicolegal actors' decision‐making processes. For this purpose, the author outlines a series of specific issues to be integrated in future research.
The Press and Pulse of Climate Change: Extreme Events in the Colorado River Basin
Authors: McCoy Amy L. , Jacobs Katharine L. , Vano Julie A. , Wilson J. Keaton , Martin Season , Pendergrass Angeline G. , Cifelli Rob
Published: June 2022

Extremes in temperature and precipitation are associated with damaging floods, prolonged drought, destructive wildfires, agricultural challenges, compromised human health, vulnerable infrastructure, and threatened ecosystems and species. Often, the steady and progressive trends (or presses) of rising global temperature are the central focus in how climate impacts are described. However, observations of extreme weather events (or pulses) increasingly show that the intensity, duration and/or frequency of acute events are also changing, resulting in greater impacts on communities and the environment. Describing how the influence of extreme events may shape water management in the Colorado River Basin in clear terms is critical to sound future planning and efforts to manage risk. Three scenario planning workshops in 2019 and 2020 were held as part of a Colorado River Conversations series, identifying potential impacts from multiple intersecting extreme events. Water managers identified climate‐related events of concern in the Colorado River Basin that necessitate greater attention and adaptive responses. To support efforts to include consideration of climate‐change‐driven extremes in water management and planning, we explore the current state of knowledge at the confluence of long‐term climate shifts and extreme weather in the Colorado River Basin related to the events of concern that were identified by scenario planning participants.