bluuebunny/crossref_metadata_2025 huggingface dataset:
Delving into human α1,4-galactosyltransferase acceptor specificity: the role of enzyme dimerization
Authors: Mikołajczyk Krzysztof , Wróblewski Karol , Kmiecik Sebastian
Published: March 2024

Human α1,4-galactosyltransferase (A4galt), a Golgi apparatus-resident GT, synthesizes Gb3 glycosphingolipid (GSL) and P1 glycotope on glycoproteins (GPs), which are receptors for Shiga toxin types 1 and 2. Despite the significant role of A4galt in glycosylation processes, the molecular mechanisms underlying its varied acceptor specificities remain poorly understood. Here, we attempted to elucidate A4galt specificity towards GSLs and GPs by exploring its interaction with GTs with various acceptor specificities, GP-specific β1,4-galactosyltransferase 1 (B4galt1) and GSL-specific β1,4-galactosyltransferase isoenzymes 5 and 6 (B4galt5 and B4galt6). Using a novel NanoBiT assay, we found that A4galt can form homodimers and heterodimers with B4galt1 and B4galt5 in two cell lines, human embryonic kidney cells (HEK293) and Chinese hamster ovary cells (CHO-Lec2). We found that A4galt-B4galts heterodimers preferred N-terminally tagged interactions, while in A4galt homodimers, the favored localization of the fused tag depended on the cell line used. Furthermore, by employing AlphaFold for state-of-the-art structural prediction, we analyzed the interactions and structures of these enzyme complexes. Our analysis highlighted that the A4galt-B4galt5 heterodimer exhibited the highest prediction confidence, indicating a significant role of A4galt heterodimerization in determining enzyme specificity toward GSLs and GPs. These findings enhance our knowledge of A4galt acceptor specificity and may contribute to a better comprehension of pathomechanisms of the Shiga toxin-related diseases.
A PTER-dependent pathway of taurine metabolism linked to energy balance
Authors: Wei Wei , Lyu Xuchao , Markhard Andrew L. , Fu Sipei , Mardjuki Rachel E. , Cavanagh Peter E. , Zeng Xianfeng , Rajniak Jakub , Lu Nannan , Xiao Shuke , Zhao Meng , Dolores Moya-Garzon Maria , Truong Steven D. , Chou Jonathan Chiu-Chun , Wat Lianna W. , Chidambaranathan-Reghupaty Saranya , Coassolo Laetitia , Xu Duo , Shen Fangfang , Huang Wentao , Ramirez Cuauhtemoc B. , Jang Cholsoon , Svensson Katrin J. , Fischbach Michael A , Long Jonathan Z.
Published: March 2024

Taurine is a conditionally essential micronutrient and one of the most abundant amino acids in humans1–3. In endogenous taurine metabolism, dedicated enzymes are involved in biosynthesis of taurine from cysteine as well as the downstream derivatization of taurine into secondary taurine metabolites4,5. One such taurine metabolite is N-acetyltaurine6. Levels of N-acetyltaurine are dynamically regulated by diverse physiologic perturbations that alter taurine and/or acetate flux, including endurance exercise7, nutritional taurine supplementation8, and alcohol consumption6,9. While taurine N-acetyltransferase activity has been previously detected in mammalian cells6,7, the molecular identity of this enzyme, and the physiologic relevance of N-acetyltaurine, have remained unknown. Here we show that the orphan body mass index-associated enzyme PTER (phosphotriesterase-related)10is the principal mammalian taurine N-acetyltransferase/hydrolase. In vitro, recombinant PTER catalyzes bidirectional taurine N-acetylation with free acetate as well as the reverse N-acetyltaurine hydrolysis reaction. Genetic ablation of PTER in mice results in complete loss of tissue taurine N-acetyltransferase/hydrolysis activities and systemic elevation of N-acetyltaurine levels. Upon stimuli that increase taurine levels, PTER-KO mice exhibit lower body weight, reduced adiposity, and improved glucose homeostasis. These phenotypes are recapitulated by administration of N-acetyltaurine to wild-type mice. Lastly, the anorexigenic and anti-obesity effects of N-acetyltaurine require functional GFRAL receptors. Together, these data uncover enzymatic control of a previously enigmatic pathway of secondary taurine metabolism linked to energy balance.
Anatomy of a pest control failure: Introgression of cytochrome P450 337B3 alleles from invasive old-world bollworm into native corn earworm (Lepidoptera: Noctuidae)
Authors: Nufer Marissa I. , Coates Brad S. , Abel Craig A. , O’Neill Patrick , McCracken Morgan , Jain Devendra , Pierce Calvin A. , Glover James , Towles Tyler , Reddy Gadi VP , Perera Omaththage P.
Published: March 2024

The establishment of invasive species populations can threaten the ecological balance in naïve habitats and impact agricultural production practices.Helicoverpa armigera(old-world bollworm, OWBW) andH. zea(corn earworm, CEW) were geographically separated prior to the 2013 report of OWBW invasion into South America. Introgression of OWBW-specific cytochrome P450 337B3 (CYP337B3) gene into CEW was repeatedly detected across South America and the Caribbean. Two hybrids were documented from Texas in 2019. In this study, screening insects collected in Olathe, Colorado, USA, where a failure of pyrethroids to control CEW damage to conventional sweetcorn in 2023 detected 28.6% of insects with the OWBW-specific CYP337B3 marker. Nucleotide sequencing of the CYP337B3 gene identified 73.1 and 26.9% of insects carried CYP337B3v2 and CYP337B3v6 alleles, respectively and 0.15 overall frequency of CYP337B3 alleles. Based on prior data for distinct phylogeographic origins of CYP337B3v2 and v6 alleles, our results indicate Olathe samples were derived from two different introductions; An uncertain source of the v6 allele that was initially reported in West Africa and possibly South American or Caribbean origin of the globally distributed v2 allele. One of the 1618 individuals screened also carried a ribosomal RNA internal transcribed spacer 1 (ITS1) derived from OWBW. Local selection pressures at the Olathe location imposed by repeated pyrethroid exposures are likely attributed to the prevalence of CYP337B3, where control practices hasten the accumulation of phenotypic resistance by adaptive introgression. Pyrethroid and other resistance factors carried by invasive OWBW may continue to impact CEW management tactics across the Americas.
Diversification of an emerging bacterial plant pathogen; insights from the global spread ofXanthomonas euvesicatoriapv.perforans
Authors: Timilsina Sujan , Iruegas-Bocardo Fernanda , Jibrin Mustafa O. , Sharma Anuj , Subedi Aastha , Kaur Amandeep , Minsavage Gerald V. , Huguet-Tapia Jose , Klein-Gordon Jeannie , Adhikari Pragya , Adhikari Tika B. , Cirvilleri Gabriella , de la Barrera Laura Belen Tapia , Bernal Eduardo , Creswell Tom C. , Tien Doan Thi Kieu , Coutinho Teresa A. , Egel Daniel S. , Félix-Gastélum Rubén , Francis David M. , Kebede Misrak , Ivey Melanie Lewis , Louws Frank J. , Luo Laixin , Maynard Elizabeth T. , Miller Sally A. , Thu Nga Nguyen Thi , Osdaghi Ebrahim , Quezado-Duval Alice M. , Roach Rebecca , Rotondo Francesca , Ruhl Gail E. , Shutt Vou M. , Thummabenjapone Petcharat , Trueman Cheryl , Roberts Pamela D. , Jones Jeffrey B. , Vallad Gary E. , Goss Erica M.
Published: March 2024

Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution.Xanthomonas euvesicatoriapv.perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a model for understanding diversification of recently emerged bacterial plant pathogens. AlthoughXephas been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinctXeppopulations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization ofXopeffector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of theXeppangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.
The cytoplasmic tail of myelin protein zero induces morphological changes in lipid membranes
Authors: Krokengen Oda C. , Touma Christine , Mularski Anna , Sutinen Aleksi , Dunkel Ryan , Ytterdal Marie , Raasakka Arne , Mertens Haydyn D.T. , Simonsen Adam Cohen , Kursula Petri
Published: March 2024

The major myelin protein expressed by the peripheral nervous system Schwann cells is protein zero (P0), representing 50% of the total protein content in myelin. This 30-kDa integral membrane protein consists of an immunoglobulin (Ig)-like domain, a transmembrane helix, and a 69-residue C-terminal cytoplasmic tail (P0ct). The basic residues in P0ct contribute to the tight packing of the myelin lipid bilayers, and alterations in the tail affect how P0 functions as an adhesion molecule necessary for the stability of compact myelin. Several neurodegenerative neuropathies are related to P0, including the more common Charcot-Marie-Tooth disease (CMT) and Dejerine-Sottas syndrome (DSS), but also rare cases of motor and sensory polyneuropathy. We find that high P0ct concentrations affect the membrane properties of bicelles and induce a lamellar-to-inverted hexagonal phase transition, which causes the bicelles to fuse into long, protein-containing filament-like structures. These structures likely reflect the formation of semi-crystalline lipid domains of potential relevance for myelination. Not only is P0ct important for stacking lipid membranes, but time-lapse fluorescence microscopy shows that it might affect membrane properties during myelination. We further describe recombinant production and low-resolution structural characterization of full-length human P0. Our findings shed light on P0ct effects on membrane properties, and with successful purification of full-length P0, we have new tools to studyin vitrothe role P0 has in myelin formation and maintenance.
MOSAIC: a highly efficient, one-step recombineering approach to plasmid editing and diversification
Authors: van den Brink Marijn , Althuis Timotheus Y. , Danelon Christophe , Claassens Nico J.
Published: March 2024

The editing of plasmids and construction of plasmid libraries is paramount to the engineering of desired functionalities in synthetic biology. Typically, plasmids with targeted mutations are produced through time– and resource-consuming DNA amplification and/or cloning steps. In this study, we establish MOSAIC, a highly efficient protocol for the editing of plasmids and generation of combinatorial plasmid libraries. This quick protocol employs the efficient single-stranded DNA annealing protein (SSAP) CspRecT to incorporate (libraries of) DNA oligos harboring the desired mutations into a target plasmid inE. coli.In addition to up to 90% single-target plasmid editing efficiency, we demonstrate that MOSAIC enables the generation of a combinatorial plasmid library spanning four different target regions on a plasmid, in a single transformation. Lastly, we integrated a user-friendly validation pipeline using Nanopore sequencing reads, requiring minimal computational experience. We anticipate that MOSAIC will provide researchers with a simple, rapid and resource-effective method to edit plasmids or generate large, diverse plasmid libraries for a wide range ofin vivoorin vitroapplications in molecular and synthetic biology.

Abstract Figure

GRAPHICAL ABSTRACT
Aeromonas hydrophilaCobQ is a new type of NAD+- and Zn2+-independent protein lysine deacetylase
Authors: Wang Yuqian , Wang Guibin , Zhang Lishan , Cai Qilan , Lin Meizhen , Huang Dongping , Xie Yuyue , Lin Wenxiong , Lin Xiangmin
Published: March 2024

Protein N−-lysine acetylation (Kac) modifications play crucial roles in diverse physiological and pathological functions in cells. In prokaryotic cells, there are only two types of lysine deacetylases (KDACs) that are Zn2+- or NAD+-dependent. In this study, we reported a protein, AhCobQ, inAeromonas hydrophilaATCC 7966 that presents NAD+- and Zn2+-independent KDAC activity. Furthermore, its KDAC activity is located in an unidentified domain (from 195–245 aa). Interestingly, AhCobQ has no homology with current known KDACs, and no homologous protein was found in eukaryotic cells. A protein substrate analysis showed that AhCobQ has specific protein substrates in common with other known KDACs, indicating that these KDACs can dynamically co-regulate the states of Kac proteins. Microbiological methods employed in this study affirmed AhCobQ’s positive regulation of isocitrate dehydrogenase (ICD) enzymatic activity at the K388 site, implicating AhCobQ in the modulation of bacterial enzymatic activities. In summary, our findings present compelling evidence that AhCobQ represents a distinctive type of KDAC with significant roles in bacterial biological functions.

The lack of exploration of new lysine acetylases and deacetylases (KDACs) and their protein substrates in prokaryotic cells has become a bottleneck in the functional study of lysine acetylation modifications. In this study, we reported a novel Zn2+- and NAD+-independent KDAC protein, AhCobQ, inAeromonas hydrophila. Interestingly, this protein does not share homology with current known KDACs, and its KDAC activity is located in an unknown domain for which a homologous protein cannot be found in eukaryotic cells. The following analysis showed that AhCobQ affected the enzymatic activity and protein-protein interaction ability of its protein substrates. In summary, these results extended our understanding of the regulatory mechanism of bacterial lysine acetylation modifications.

Highlights

AhCobQ is an NAD+- and Zn2+-independent protein lysine deacetylase.

There are no proteins homologous to AhCobQ in eukaryotes.

The deacetylase activity of AhCobQ is located in an unknown domain.

AhCobQ has specific protein substrates and substrates in common with other lysine deacetylases.

AhCobQ positively regulates the enzymatic activity of isocitrate dehydrogenase at its K388 site.
Interactions betweenPseudomonas aeruginosaand six opportunistic pathogens cover a broad spectrum from mutualism to antagonism
Authors: Laffont Clémentine , Wechsler Tobias , Kümmerli Rolf
Published: March 2024

Bacterial infections often involve more than one pathogen. While it is known that polymicrobial infections can impact disease outcomes, we have a poor understanding about how pathogens affect each other’s behaviour and fitness. Here, we used a microscopy approach to explore interactions betweenPseudomonas aeruginosaand six opportunistic human pathogens that often co-occur in polymicrobial infections:Acinetobacter baumannii,Burkholderia cenocepacia,Escherichia coli,Enterococcus faecium,Klebsiella pneumoniae, andStaphylococcus aureus.When following growing micro-colonies on agarose pads over time, we observed a broad spectrum of species-specific ecological interactions, ranging from mutualism to antagonism. For example,P. aeruginosaengaged in a mutually beneficial interaction withE. faeciumbut suffered from antagonism byE. coliandK. pneumoniae. While we found little evidence for active directional growth towards or away from cohabitants, we observed that certain species increased growth in double layers in co-cultures and that physical forces due to fast colony expansion had a major impact on fitness and interaction patterns. Overall, our work provides an atlas of pathogen interactions, potentially useful to understand species dynamics in polymicrobial infections. We discuss possible mechanisms driving pathogen interactions and offer predictions of how the different ecological interactions could affect virulence.
Adaptive evolution of sesquiterpene deoxyphomenone in mycoparasitism byHansfordia pulvinataassociated with horizontal gene transfer fromAspergillusspecies
Authors: Maeda Kazuya , Sumita Takuya , Nishi Oumi , Sushida Hirotoshi , Higashi Yumiko , Nakagawa Hiroyuki , Suzuki Tomoko , Iwao Eishin , Fanani Much Zaenal , Nishiya Yoshiaki , Iida Yuichiro
Published: March 2024

Leaf mold caused by the ascomycete fungusCladosporium fulvumis a devastating disease of tomato plants. The mycoparasitic fungusHansfordia pulvinatais an effective biocontrol agent that parasitizesC. fulvumhyphae on leaves and secretes 13-deoxyphomenone, an eremophilane-type sesquiterpene, which was also identified as a sporulation-inducing factor inAspergillus oryzae. Here, we identified deoxyphomenone biosynthesis (DPH) gene clusters conserved in bothH. pulvinataandAspergillussectionFlaviincludingA. oryzaeandA. flavus. Functional disruption ofDPH1orthologous genes encoding sesquiterpene cyclase inH. pulvinata,A. oryzaeand its close relativeA. flavusrevealed that deoxyphomenone inH. pulvinatahad exogenic antifungal activity against the host fungusC. fulvumand controlled endogenic sporulation inAspergillusspecies. Deoxyphomenone also inhibited mycelial growth ofC. fulvumand the non-host tomato pathogenPseudocercospora fuligena. CompleteDPHclusters, highly similar to those inH. pulvinata, were exclusive toAspergillussectionFlavi, while species in otherAspergillussections contained fragmentedDPHclusters. A comparative genomics analysis revealed that theseDPHgene clusters share a common origin and are horizontally transferred across large taxonomic distances from an ancestor ofAspergillustoH. pulvinata. Our results suggest that, after horizontal transfer,H. pulvinatamaintained theDPHcluster as the inhibitory effect of deoxyphomenone on spore germination and mycelial growth contributed to its mycoparasitism on the host fungusC. fulvum.
Mar1, an HMG-box protein, regulatesn-alkane adsorption and cell morphology of the dimorphic yeastYarrowia lipolytica
Authors: Kimura-Ishimaru Chiaki , Liang Simiao , Matsuse Katsuro , Iwama Ryo , Sato Kenta , Watanabe Natsuhito , Tezaki Satoshi , Horiuchi Hiroyuki , Fukuda Ryouichi
Published: March 2024

The dimorphic yeastYarrowia lipolyticapossesses an excellent ability to utilizen-alkane as a sole carbon and energy source. Although there are detailed studies on the enzymes that catalyze the reactions in the metabolic processes ofn-alkane inY. lipolytica, the molecular mechanism underlying the incorporation ofn-alkane into the cells remains to be elucidated. BecauseY. lipolyticaadsorbsn-alkane, we postulated thatY. lipolyticaincorporatesn-alkane through direct interaction with it. We isolated and characterized mutants defective in adsorption ton-hexadecane. One of the mutants harbored a nonsense mutation inMAR1(Morphology andn-alkaneAdsorptionRegulator) encoding a protein containing a high mobility group box. The deletion mutant ofMAR1exhibited defects in adsorption ton-hexadecane and filamentous growth on solid media, whereas the strain that overexpressedMAR1exhibited hyperfilamentous growth. Fluorescence microscopic observations suggested that Mar1 localizes in the nucleus. RNA-seq analysis revealed the alteration of the transcript levels of several genes, including those encoding transcription factors and cell surface proteins, by the deletion ofMAR1. These findings suggest thatMAR1is involved in the transcriptional regulation of the genes required forn-alkane adsorption and cell morphology transition.

IMPORTANCE

Y. lipolytica, a dimorphic yeast capable of assimilatingn-alkane as a carbon and energy source, has been extensively studied as a promising host for bioconversion ofn-alkane into useful chemicals and bioremediation of soil and water contaminated by petroleum. While the metabolic pathway ofn-alkane in this yeast and the enzymes involved in this pathway have been well-characterized, the molecular mechanism to incorporaten-alkane into the cells is yet to be fully understood. Due to the ability ofY. lipolyticato adsorbs ton-alkane, it has been hypothesized thatY. lipolyticaincorporatesn-alkane through direct interaction with it. In this study, we identified a gene,MAR1, which plays a crucial role in the transcriptional regulation of the genes necessary for the adsorption ton-alkane and the transition of the cell morphology inY. lipolytica. Our findings provide valuable insights that could lead to advanced applications ofY. lipolyticainn-alkane bioconversion and bioremediation.
Synthetic genome modules designed for programmable silencing of functions and chromosomes
Authors: Lu Xinyu , Shaw William M , Sutradhar Anima , Stracquadanio Giovanni , Ellis Tom
Published: March 2024

Unlike in bacteria, eukaryotes rarely cluster sets of genes in their genomes according to function, instead having most genes spread randomly across different chromosomes and loci. However, with the advent of genome engineering, synthetic co-location of genes that together encode a cell function has now become possible. Here, using Saccharomyces cerevisiae we demonstrate the feasibility of reorganising a set of yeast genes encoding a cell function, tryptophan biosynthesis, into a synthetic genome module by deleting these genes and their regulatory elements from their native genomic loci while in parallel reconstructing them into gene cluster format by synthetic DNA assembly. As part of synthetic module design, loxPsym sequences recognised by Cre recombinase are placed between all module genes, and we leverage these for a novel master regulation system we call dCreSIR. Using dCreSIR we externally control silencing of synthetic modules by targeted binding of chromatin recruiters to loxPsym sites and this leads to inhibition of local transcription. We further show that dCreSIR can go beyond modules and be used to specifically downregulate expression across an entire synthetic yeast chromosome containing loxPsym sites. Together, our work offers insights into yeast genome organisation and establishes new principles and tools for the future design and construction of modular synthetic yeast genomes.
Predicting microbial growth conditions from amino acid composition
Authors: Barnum Tyler P. , Crits-Christoph Alexander , Molla Michael , Carini Paul , Lee Henry H. , Ostrov Nili
Published: March 2024

The ability to grow a microbe in the laboratory enables reproducible study and engineering of its genetics. Unfortunately, the majority of microbes in the tree of life remain uncultivated because of the effort required to identify culturing conditions. Predictions of viable growth conditions to guide experimental testing would be highly desirable. While carbon and energy sources can be computationally predicted with annotated genes, it is harder to predict other requirements for growth such as oxygen, temperature, salinity, and pH. Here, we developed genome-based computational models capable of predicting oxygen tolerance (92% balanced accuracy), optimum temperature (R2=0.73), salinity (R2=0.81) and pH (R2=0.48) for novel taxonomic microbial families without requiring functional gene annotations. Using growth conditions and genome sequences of 15,596 bacteria and archaea, we found that amino acid frequencies are predictive of growth requirements. As little as two amino acids can predict oxygen tolerance with 88% balanced accuracy. Using cellular localization of proteins to compute amino acid frequencies improved prediction of pH (R2 increase of 0.36). Because these models do not rely on the presence or absence of specific genes, they can be applied to incomplete genomes, requiring as little as 10% completeness. We applied our models to predict growth requirements for all 85,205 species of sequenced bacteria and archaea and found that uncultivated species are enriched in thermophiles, anaerobes, and acidophiles. Finally, we applied our models to 3,349 environmental samples with metagenome-assembled genomes and showed that individual microbes within a community have differing growth requirements. This work guides identification of growth constraints for laboratory cultivation of diverse microbes.
Characterization of novel role for Rab27B in autophagy regulation in colorectal cancer
Authors: Afroz Sahida , Preet Ranjan , Vishwakarma Vikalp , Evans Andrew E. , Dixon Dan A.
Published: March 2024

Introduction

Autophagy is a dynamic, multi-step process that cells use to degrade damaged, abnormal, and potentially harmful cellular substances. While autophagy is maintained at a basal level in all cells, it is activated at a higher level in many cancer cells and promotes tumor growth, anti-tumor immune response, and resistance to cancer therapy. As a result, autophagy is increasingly being recognized to have an important role in cancer progression and emerging as a potential target for cancer therapy. We recently discovered that small GTPase Rab27B, a known regulator of vesicle trafficking and exosome secretion, is also involved in the autophagy process.

Methods

Rab27B was knocked out using CRISPR/Cas9 in CRC cell line HCT116. Western blotting, Immunofluorescence, MTT assay, spheroid formation assay, soft agar assay and xenograft studies were performed to analyze the effects of Rab27B deletion on CRC cells.

Results

CRISPR/Cas9 deletion or siRNA knockdown of Rab27B in colorectal cancer cells (CRC) showed an abnormal accumulation of autophagy vesicles. Additionally, we observed a significant increase in the autophagy markers LC3-II and p62 by immunocytochemistry and western blot analysis, suggesting a defect in the autophagy flux process. Lysotracker and mCherry-EGFP-LC3 fusion construct indicate an impairment in autophagosome and lysosome fusion when Rab27B is silenced. This defect was rescued by full-length and constitutively active GTP mutant of Rab27B. As autophagy has been shown to have a pro-survival role in tumor growth and stress response, we hypothesized that the observed defects in autophagy flux resulting from Rab27B loss would cause reduced stress response and tumor growth. Indeed, Rab27B knockout reduced cell viability in response to starvation and a 94% reduction in soft agar colony formation. Rab27B deletion also prevented spheroid formationin vitro.Finally, to analyze the effect of Rab27B deletion in tumor formationin vivo, we performed a xenograft study with wildtype and Rab27B knockout CRC cells, resulting in a dramatic loss of tumor growth (p<0.0001) in the KO cells.

Conclusions

Together, our results demonstrate a new role of Rab27B in the autophagy trafficking process in CRC. Future studies will focus on investigating the mechanism of how Rab27B functions in the autophagy pathway and whether Rab27B can be targeted as a potential therapeutic strategy for CRC.
Discovery of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach
Authors: Merten Eric M. , Sears John D. , Leisner Tina M. , Hardy Paul B. , Ghoshal Anirban , Hossain Mohammad Anwar , Asressu Kesatebrhan Haile , Brown Peter J. , Stashko Michael A. , Herring Laura , Mordant Angie L. , Webb Thomas S. , Mills Christine A. , Barker Natalie K. , Streblow Zachary J. , Perveen Sumera , Arrowsmith Cheryl , Arnold Jamie J. , Cameron Craig E , Streblow Daniel N. , Moorman Nathaniel J. , Heise Mark , Willson Timothy M. , Popov Konstantin , Pearce Kenneth H.
Published: March 2024

Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has been responsible for numerous large-scale outbreaks in the last twenty years. Currently, there are no FDA-approved therapeutics for any alphavirus infection. CHIKV non-structural protein 2 (nsP2), which contains a cysteine protease domain, is essential for viral replication, making it an attractive target for a drug discovery campaign. Here, we optimized a CHIKV nsP2 protease (nsP2pro) biochemical assay for the screening of a 6,120-compound cysteine-directed covalent fragment library. Using a 50% inhibition threshold, we identified 153 hits (2.5% hit rate). In dose-response follow up, RA-0002034, a covalent fragment that contains a vinyl sulfone warhead, inhibited CHIKV nsP2pro with an IC50of 58 ± 17 nM, and further analysis with time-dependent inhibition studies yielded a kinact/KIof 6.4 x 103M-1s-1. LC-MS/MS analysis determined that RA-0002034 covalently modified the catalytic cysteine in a site-specific manner. Additionally, RA-0002034 showed no significant off-target reactivity against a panel of cysteine proteases. In addition to the potent biochemical inhibition of CHIKV nsP2pro activity and exceptional selectivity, RA-0002034 was tested in cellular models of alphavirus infection and effectively inhibited viral replication of both CHIKV and related alphaviruses. This study highlights the discovery and characterization of the chemical probe RA-0002034 as a promising hit compound from covalent fragment-based screening for development toward a CHIKV or pan-alphavirus therapeutic.

Significance Statement

Chikungunya virus is one of the most prominent and widespread alphaviruses and has caused explosive outbreaks of arthritic disease. Currently, there are no FDA-approved drugs to treat disease caused by chikungunya virus or any other alphavirus-caused infection. Here, we report the discovery of a covalent small molecule inhibitor of chikungunya virus nsP2 protease activity and viral replication of four diverse alphaviruses. This finding highlights the utility of covalent fragment screening for inhibitor discovery and represents a starting point towards the development of alphavirus therapeutics targeting nsP2 protease.
Does relationship conflict reduce novel idea communication through perceived leader openness? Power distance orientation as a moderator
Authors: Tsai Ming-Hong
Published: March 2024

Purpose

This paper aims to investigate why followers have low perceptions of leader openness and thus feel reluctant to communicate novel ideas by examining leader–follower relationship conflict (i.e. interpersonal incompatibility) and a follower’s power distance orientation (i.e. an acceptance of uneven power distribution in organizations) as antecedents.

Design/methodology/approach

The research administrators conducted a three-wave work behavior survey in Study 1, a laboratory experiment in Study 2, and an online experiment in Study 3.

Findings

The results demonstrated that leader–follower relationship conflict reduced followers’ perceptions of leader openness. However, the negative impact of relationship conflict became non-significant when followers have high power distance orientations (i.e. an acceptance of uneven power distribution in organizations). The findings also showed an indirect interaction effect of leader–follower relationship conflict and followers’ power distance orientation on the followers’ communication of novel ideas through the followers’ perceptions of leader openness.

Originality/value

The research suggests that followers with higher power distance orientations are more likely to communicate novel ideas consistently because their relationship conflicts with their leaders do not negatively influence their perceptions of leader openness. Although researchers traditionally view cultures with a high level of power distance value as an obstacle to employee creativity, the present study reveals the benefits of an individual-level power distance orientation.
Identification of key bottlenecks in human rights-based approach to family planning among HIV-infected women in a resource-restricted setting of Nepal
Authors: Dhungana Govinda Prasad , Bhatta Dwij Raj , Zhang Wei-Hong
Published: March 2024

Purpose

Family planning (FP) services through the lens of human rights are not well known in Nepal. This study aims to assess Family Planning 2020: Rights and Empowerment Principles for Family Planning and identify factors affecting contraceptive use among HIV-infected women living in rural Far Western Nepal.

Design/methodology/approach

This study conducted a cross-sectional survey using self-designed proforma. To assess the association between contraceptive use and independent variables, this study calculated adjusted odd ratio (AOR) with 95% confidence interval (CI) using statistical package for social sciences (SPSS) V.20.

Findings

Only 37.8% of participants had access to full range of contraceptive methods, and only 57.5% of participants received proper counseling. Agency/autonomy, transparency/accountability and voice/participation were practiced by 43.7%, 23.4% and 19.7% of participants, respectively. Husband’s support (AOR = 4.263; 95% CI: 1.640–11.086), availability of FP services in their locality (AOR = 2.497; 95% CI: 1.311–4.754), employment (AOR = 3.499; 95% CI: 1.186–10.328) and postpartum period (AOR = 0.103; 95% CI: 0.023–0.475) were significantly associated with contraceptive use.

Research limitations/implications

Health-care providers’ and program managers’ perspectives were not examined.

Practical implications

Findings of this study will be useful for making strategic plan on human rights-based approach to FP.

Social implications

Expanding access to contraceptive information and services and strengthening autonomy, accountability and participation are key to human rights-based approach to FP.

Originality/value

This study identified that inadequate counselling, nonavailability of full range of contraceptive methods, low level of autonomy, accountability and participation were key bottlenecks in fulfilling human rights-based approach to FP.
The spillover effect of export on total factor productivity of enterprises: panel data approach in Vietnam
Authors: Nguyen Anh Tuyet , Hoang Vu Hiep , Le Phuong Thao , Nguyen Thi Thanh Huyen , Pham Thi Thanh Van
Published: March 2024

Purpose

This study addresses the empirical results of the spillover effect with export as the primary economic activity that enhances local businesses' total factor productivity (TFP). A learning mechanism is expected to be generated and used as the basis for the policy implication.

Design/methodology/approach

This study adopted the Cobb–Douglas function and multiple estimation approaches, including the generalized method of moments, the Olley–Pakes and the Levinsohn–Petrin estimation techniques. The findings were estimated based on the panel data of a Vietnamese local businesses survey conducted by the General Statistics Office of Vietnam (GSO) from 2010 to 2019.

Findings

The results showed that the highest TFP belongs to the businesses in the Southeast region, the Mekong Delta region, the mining industry and the foreign-invested enterprises. The lowest impacted TFP are businesses in the Northwest region and agricultural, forestry and fishery sectors. In addition, the estimated results also show that the positive spillover effect on TFP is shown through forward and backward linkage. The negative spillover effect is expressed through the backward and horizontal channels.

Research limitations/implications

This study offers original empirical evidence on the learning mechanisms via which exports contribute to productivity improvement in a developing Asian economy, so making a valuable contribution to the existing academic literature in this domain. The findings of this research make a valuable contribution to the advancement of understanding on the many ways via which spillover effects manifest such as horizontal, forward, backward and supplied-backward linkage.

Practical implications

The study's findings indicate that it is advisable for governments to give priority to the development and improvement of forward and supply chain linkages between exporters and local suppliers. This approach is recommended in order to optimize the advantages derived from export spillovers. At the organizational level, it is imperative for enterprises to strengthen their technological and managerial skills in order to efficiently incorporate knowledge spillovers that originate from overseas partners and trade counterparts.

Originality/value

This study sheds new evidence on the export spillover effect on productivity in emerging economies, with Vietnam as the case study. The paper contributes to the research's originality by adopting novel methodological aspects to estimate local businesses' impact on total factor productivity.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-05-2023-0373
DARLOS: a lightweight dual-arm robotic live-line operation system for autonomous high-voltage distribution grid maintenance
Authors: Wang Zhiqiang
Published: March 2024

Purpose

This paper aims to present a novel lightweight distribution grid operating robot system with focus on lightweight and multi-functionality, aiming for autonomous and live-line maintenance operations.

Design/methodology/approach

A ground-up redesign of the dual-arm robotic system with 12-DoF is applied for substantial weight reduction; a dual-mode operating control framework is proposed, with vision-guided autonomous operation embedded with real-time manual teleoperation controlling both manipulators simultaneously; a quick-swap tooling system is developed to conduct multi-functional operation tasks. A prototype robotic system is constructed and validated in a series of operational experiments in an emulated environment both indoors and outdoors.

Findings

The overall weight of the system is successfully brought down to under 150 kg, making it suitable for the majority of vehicle-mounted aerial work platforms, and it can be flexibly and quickly deployed in population dense areas with narrow streets. The system equips with two dexterous robotic manipulators and up to six interchangeable tools, and a vision system for AI-based autonomous operations. A quick-change tooling system ensures the robot to change tools on-the-go without human intervention.

Originality/value

The resulting dual-arm robotic live-line operation system robotic system could be compact and lightweight enough to be deployed on a wide range of available aerial working platforms with high mobility and efficiency. The robot could both conduct routine operation tasks fully autonomously without human direct operation and be manually operated when required. The quick-swap tooling system enables lightweight and durable interchangeability of multiple end-effector tools, enabling future expansion of operating capabilities across different tasks and operating scenarios.
Learning to safeguard: exploring adult safeguarding officers' readiness for online learning and their perceptions of a blended learning safeguarding training programme
Authors: McDaid Bridget
Published: March 2024

Purpose

This paper aims to present commentary on adult safeguarding designated officers’ (nominated senior staff members in the Health Service Executive and its funded services) in Ireland readiness for online learning and their perception of the blended approach used in their training and considers the implications of this for practice.

Design/methodology/approach

In total, 233 designated officers were surveyed. A self-administered online survey comprising of two instruments was used. The questionnaire combines two previously validated tools measuring readiness for online learning and perceptions of blended learning. Minor modifications were made to account for local circumstance and language. Demographic questions relevant to the survey population were added. The response rate was 49%.

Findings

Designated officers regarded specified competencies for online learning as important to very important with highest importance placed in time management. Designated officers expressed they were confident to very confident in their ability to accomplish all competencies in online learning. The highest confidence was in the technical competencies. Designated officers are demonstrating high readiness for online learning. Designated officers reported positively on online contributions and on blended learning workload. The scores indicate positive perceptions of the blended learning experience. Responses to an open-ended question were largely positive with some suggestions for improvement made.

Practical implications

Findings have helped inform planning and development of the Health Service Executive’s adult safeguarding training for designated officers with changes made since this survey was undertaken.

Originality/value

To the best of the author’s knowledge, this is the first time a survey was undertaken of designated officers in Ireland with a view to improving safeguarding training. Recommendations for adaptions to the blended designated officer programme were proposed and subsequently accepted and implemented.
Looking back and beyond the complex dynamics of humanitarian operations
Authors: Cunha Luiza Ribeiro Alves , Leiras Adriana , Goncalves Paulo
Published: March 2024

Purpose

Due to the unknown location, size and timing of disasters, the rapid response required by humanitarian operations (HO) faces high uncertainty and limited time to raise funds. These harsh realities make HO challenging. This study aims to systematically capture the complex dynamic relationships between operations in humanitarian settings.

Design/methodology/approach

To achieve this goal, the authors undertook a systematic review of the extant academic literature linking HO to system dynamics (SD) simulation.

Findings

The research reviews 88 papers to propose a taxonomy of different topics covered in the literature; a framework represented through a causal loop diagram (CLD) to summarise the taxonomy, offering a view of operational activities and their linkages before and after disasters; and a research agenda for future research avenues.

Practical implications

As the authors provide an adequate representation of reality, the findings can help decision makers understand the problems faced in HO and make more effective decisions.

Originality/value

While other reviews on the application of SD in HO have focused on specific subjects, the current research presents a broad view, summarising the main results of a comprehensive CLD.
Assessing the mediating role of organizational justice between the responsible leadership and employee turnover intention in health-care sector
Authors: Khanam Zeba , Khan Zebran , Arwab Mohd , Khan Ariba
Published: March 2024

Purpose

The aim of this study is to investigate the extent to which organizational justice (OJ) mediates between responsible leadership (RL) and employee turnover intention (TI).

Design/methodology/approach

Both online and offline questionnaire was used to collect the data from 387 Indian health-care employees, and the data were analyzed using partial least squares structural equation modeling (PLS-SEM) with the help of SmartPLS 4.

Findings

The study’s findings demonstrated a significant positive association between RL and OJ and a negative association between OJ and employee TI. Furthermore, results also confirmed the mediating role of OJ between RI and TI.

Research limitations/implications

The generalizability of the study‘s data collection is limited because it is based on the responses of Indian health-care sector employees to an online and offline survey. The authors propose that the health-care sector uses RL as an approach that takes a broad view of the parties with a stake and focuses on creating fairness in acts and justice at the workplace to address the major issue of employee turnover.

Originality/value

This study expanded on previous research by demonstrating that the influence of responsible leadership on employee TI is mediated by OJ in the context of India’s health-care sector. It also contributes to the literature regarding RI, OJ and TI. The study also enriched the body of knowledge about using the PLS-SEM approach to predict employee TI.
Labor camps in Dubai: implications of courtyard regulations on daylight performance
Authors: Sheta Wael , El Hussainy Mariam , Abdelwahab Sahar
Published: March 2024

Purpose

The fundamental aim of the study is to investigate the implications of labor housing designs in Dubai, with a focus on courtyards and the governing building regulations, on daylight performance as an underlying factor impacting laborers’ indoor environmental quality. Several studies shed light on the subject of labor camps and labor migration in Dubai, but few have focused on the subject from the perspective of the environmental performance of these camps. A model that represents one of the labor camps was built using Rhinoceros 7.0 and Grasshopper software packages. Annual daylighting and glare simulations were carried out using the lighting modeling engine RADIANCE 5.0 in conjunction with the “ClimateStudio”.

Design/methodology/approach

The construction sector has emerged as a significant economic development driver, attracting a diverse labor force from a variety of countries to Dubai. As a result, Dubai authorities have implemented several measures to ensure the provision of suitable housing facilities for its labor force. These measures contribute to the reduction of energy costs in labor housing by encouraging the use of renewable energy. While several studies shed light on the subject of labor camps and labor migration in Dubai, few have focused on the subject from the perspective of the environmental performance of these camps.

Findings

The study provided statistical evidence that the current regulations governing courtyards in labor housing resulted in significant changes in daylight levels across different floor levels of the labor housing units. It is suggested that both 2:3 and 3:4 Court Width-to-Height ratios would further contribute to a more consistent daylight Illuminance with marginal statistical differences between floor levels (p > 0.05). The 3:4 ratio, on the other hand, offers a consistent distribution across all floor levels in the North and South with negligible variances, although weakly significant differences can be yet expected between the first and fourth floors in the East and West orientations (p < 0.05). The results of Annual Sunlight Exposure (ASE) suggest excessive solar incidence and a high probability of glare, which remains a problem that must be addressed under the governing building regulations.

Originality/value

This study could serve as a framework for analyzing and contrasting the findings of other studies on labor accommodation, notably in the Gulf Cooperation Council (GCC) countries. Such an approach has the potential to enhance living conditions in labor accommodations in Dubai and other areas. It is necessary to meet people' physical and psychological well-being while also addressing sustainability and regulatory compliance.