bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into the mechanism of mycelium transformation ofStreptomyces toxytriciniinto pellet
Authors: Kumar Punit , Khushboo  , Rajput Deepanshi , Dubey Kashyap Kumar 
Published: February 2023

AbstractFormation of the mycelial pellet in submerged cultivation ofStreptomycetesis unwanted in industrial fermentation processes as it imposes mass transfer limitations, changes in the rheology of a medium, and affects the production of secondary metabolites. Though detailed information is not available about the factors involved in regulating mycelial morphology but it is studied that culture conditions and genetic information of strain play a key role. Moreover, the proteomic study has revealed the involvement of low molecular weight proteins such as; DivIVA, FilP, ParA, Scy, and SsgA proteins in apical growth and branching of hyphae which results in the establishment of the mycelial network. The present study proposes the mechanism of pellet formation ofStreptomyces toxytricini(NRRL B-5426) with the help of microscopic and proteomic analysis. The microscopic analysis revealed that growing hyphae followed a certain organized path of growth and branching, which was further converted into the pellet, and proteomic analysis revealed the production of low molecular weight proteins, which possibly participate in the regulation of pellet morphology.
The difficulties of predicting evolutionary response to selection
Authors: Björklund Mats 
Published: February 2023

AbstractThere has been a long debate about the difficulties of predicting evolutionary change despite knowledge of selection and genetic variance. One reason might be the stochastic effects of sexual reproduction creating a variance of offspring genotypes and thus phenotypes. This was tested by means of an explicit genetic individual-based simulation with one trait determined by 50 loci. After 100 generations of weak fluctuating selection an experiment was performed where the optimum was displaced one standard deviation. The response and the predicted response were then compared for 100 populations. The simulation shows two things, first there is a considerable variation in response between populations. This was also found when the same population was replicated many times with the same selection. Second, using the individual-based estimates of genetic variance seriously overestimates the predicted response, while an approach using the variance of mean pair breeding values gave essentially unbiased predictions. However, in all cases there was a lack of precision. Hence, the “missing response” is, at least partly, due to an overestimation of predicted response and an inevitable variance around the predicted value.
Functional prediction of proteins from the human gut archaeome
Authors: Novikova Polina V. , Busi Susheel Bhanu , Probst Alexander J. , May Patrick , Wilmes Paul 
Published: February 2023

AbstractThe human gastrointestinal tract contains diverse microbial communities, including archaea. Among them,Methanobrevibacter smithiirepresents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as IBD and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation ofM. smithiiproteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut andM. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer betweenClostridiaspecies andM. smithii, which includessporulation stage V proteins AEand AD. Our study broadens the understanding of archaeal biology, particularlyM. smithii,and highlights the importance of considering both sequence and structure for the prediction of protein function.
SPI-1 virulence gene expression modulates motility ofSalmonellaTyphimurium in a proton motive force- and adhesins-dependent manner
Authors: Saleh Doaa Osama , Horstmann Julia A. , Giralt-Zúñiga María , Weber Willi , Durairaj Abilash Chakravarthy , Klotzsch Enrico , Strowig Till , Erhardt Marc 
Published: February 2023

AbstractBoth the bacterial flagellum and the evolutionary related injectisome encoded on theSalmonellapathogenicity island 1 (SPI-1) play crucial roles during the infection cycle ofSalmonellaspecies. The interplay of both is highlighted by the complex cross-regulation that includes transcriptional control of the flagellar master regulatory operonflhDCby HilD, the master regulator of SPI-1 gene expression. Contrary to the HilD-dependent activation of flagellar gene expression, we report here that activation of HilD resulted in a dramatic loss of motility, which was dependent on the presence of SPI-1. Single cell analyses revealed that HilD-activation results in a SPI-1-dependent induction of the stringent response and a pronounced decrease of proton motive force (PMF), while flagellation was not affected. We further found that activation of HilD enhanced the adhesion ofSalmonellato epithelial cells. A transcriptome analysis revealed a concomitant upregulation of several adhesin systems, which when overproduced, phenocopied the HilD-induced motility defect. We propose that a combination of SPI-1-dependent depletion of the PMF and upregulation of adhesins upon HilD-activation allows flagellatedSalmonellato rapidly modulate their motility during infection, thereby enabling efficient adhesion to host cells and delivery of effector proteins.
Computational modeling of DLBCL predicts response to BH3-mimetics
Authors: Cloete Ielyaas , Smith Victoria M. , Jackson Ross A. , Pepper Andrea , Pepper Chris , Vogler Meike , Dyer Martin J.S. , Mitchell Simon 
Published: February 2023

AbstractIn healthy cells, pro- and anti-apoptotic BCL2 family and BH3-only proteins are expressed in a delicate equilibrium. In contrast, this homeostasis is frequently perturbed in cancer cells due to the overexpression of anti-apoptotic BCL2 family proteins. Variability in the expression and sequestration of these proteins in Diffuse Large B cell Lymphoma (DLBCL) likely contributes to variability in response to BH3-mimetics. Successful deployment of BH3-mimetics in DLBCL requires reliable predictions of which lymphoma cells will respond. Here we show that a computational systems biology approach enables accurate prediction of the sensitivity of DLBCL cells to BH3-mimetics. We found that fractional killing of DLBCL, can be explained by cell-to-cell variability in the molecular abundances of signaling proteins. Importantly, by combining protein interaction data with a knowledge of genetic lesions in DLBCL cells, ourin silicomodels accurately predictin vitroresponse to BH3-mimetics. Furthermore, through virtual DLBCL cells we predict synergistic combinations of BH3-mimetics, which we then experimentally validated. These results show that computational systems biology models of apoptotic signaling, when constrained by experimental data, can facilitate the rational assignment of efficacious targeted inhibitors in B cell malignancies, paving the way for development of more personalized approaches to treatment.
CALCIUM-DEPENDENT PROTEIN KINASE32 regulates cellulose biosynthesis through post-translational modification of cellulose synthase
Authors: Xin Xiaoran , Wei Donghui , Lei Lei , Zheng Haiyan , Wallace Ian S. , Li Shundai , Gu Ying 
Published: February 2023

AbstractCellulose is an economically important source of food, paper, textiles, and biofuel. As an essential component of plant cell walls, cellulose is critical for plant cell growth. Despite its economic and biological significance, the regulation of cellulose biosynthesis is poorly understood. Phosphorylation and dephosphorylation of cellulose synthases (CESAs) were shown to impact the direction and velocity of cellulose synthase complexes (CSCs). Despite a high prevalence of phosphorylation sites in CESAs, the protein kinases that phosphorylate CESAs are largely unknown. Here, we demonstrate that CALCIUM-DEPENDENT PROTEIN KINASE32 (CPK32) regulates cellulose biosynthesisviaphosphorylation of CESA3. Phosphorylation of CESA3 is important for the motility and stability of CSCs. Hence, we uncovered a new function of CPKs that regulates cellulose biosynthesis and a novel mechanism by which phosphorylation regulates the stability of CSCs.
An integrative and multi-indicator approach for wildlife health applied to an endangered caribou herd
Authors: Aguilar Xavier Fernandez , Leclerc Lisa-Marie , Association Kugluktuk Angoniatit ,   Ekaluktutiak Hunters & Trappers Organization,   Olokhaktomiut Hunters & Trappers Committee, Mavrot Fabien , Roberto-Charron Amelie , Tomaselli Matilde , Mastromonaco Gabriela , Gunn Anne , Pruvot Mathieu , Rothenburger Jamie L. , Thanthrige-Don Niroshan , Jahromi Elham Zeini , Kutz Susan 
Published: February 2023

AbstractAssessing wildlife health in remote regions requires a multi-faceted approach that may include convenience samplings and the involvement of local communities. Combining data from hunted and captured caribou, we assessed the value of multiple indicators for understanding the health of the endangered Dolphin and Union caribou herd in Arctic Canada. We documented health determinants (infectious diseases and trace elements), processes (cortisol, pathology), and health outcomes (pregnancy and body condition). During a recent period of steep population decline our results suggested relatively good body condition and pregnancy rates and decreasing levels of stress, along with low adult cow survival. We identified multiple determinants of health as potential contributors to reduced survival, includingBrucellasuis biovar 4,Erysipelothrix rhusiopathiaeand lower hair trace minerals. This integrative approach that drew on multiple data sources has provided unprecedented knowledge on the health in this herd and highlights the value of documenting individual animal health to understand causes of wildlife declines.
The formation of an expanding memory representation in the hippocampus
Authors: Vaidya Sachin P. , Li Guanchun , Chitwood Raymond A. , Li Yiding , Magee Jeffrey C. 
Published: February 2023

AbstractHow brain networks connected by labile synapses store new information without catastrophically overwriting previous memories remains poorly understood1,2. To examine this, we tracked the same population of hippocampal CA1 place cells (PC) as mice learned a task for 7 days. We found evidence of memory formation as both the number of PCs maintaining a stable place field (PF) and the stability of individual PCs progressively increased across the week until most of the representation was composed of long-term stable PCs. The stable PCs disproportionately represented task-related learned information, were retrieved earlier within a behavioral session, and showed a strong correlation with behavioral performance. Both the initial formation of PCs and their retrieval on subsequent days was accompanied by prominent signs of behavioral timescale synaptic plasticity (BTSP), suggesting that even stable PCs were re-formed by synaptic plasticity each session. Further experimental evidence supported by a cascade-type state model indicates that CA1 PCs increase their stability each day they are active eventually forming a highly stable population. The results suggest that CA1 memory is implemented by an increase in the likelihood of new neuron-specific synaptic plasticity, as opposed to extensive long-term synaptic weight stabilization.
Integrates JA and ethylene signals in defense against brown spot disease: the role of NaWRKY70
Authors: Song Na , Wu Jinsong 
Published: February 2023

AbstractProduction of phytoalexins scopoletin and scopolin is regulated by jasmonate (JA) and ethylene signals inNicotianaspecies in response toAlternaria alternata, the necrotrophic fungal pathogen causing brown spot disease. However, how these two signals are coordinated to control this process remains unclear. Here, we found that levels of these two phytoalexins and transcripts of their key enzyme geneferuloyl-CoA 6’-hydroxylase 1(NaF6’H1) were synergistically induced in wild tobaccoN. attenuataby co-treatments of methyl jasmonate (MeJA) and ethephon, but were not altered by treatments with either MeJA or ethephon along. Through co-expression and functional analysis we identified NaWRKY70 as the key regulator for this synergistic induction. NaWRKY70 not only directly bound toNaF6’H1promoter and activated its expression but also served as a regulation node to integrate JA and ethylene signals. Acting like locks, NaJAZe1, NaJAZe2 and NaEBF2 interacted with NaWRKY70 separately to suppressNaF6’H1expression. Meanwhile, NaMYC2b and NaEIN3-like 1functioned as transcription regulators ofNaWRKY70and activated ofNaF6’H1expression by protein interaction with NaWRKY70. Finally, NaWRKY70 controlled JA-Ile production by binding and activating its biosynthetic genes. Thus, our data uncovers a novel but complicate regulation network of phytoalexins by two phytohormonal signals, and demonstrates that NaWRKY70 integrates both JA and ethylene signals through transcriptional regulation and protein interaction to regulate scopoletin and scopolin biosynthesis and plant resistance toA. alternata.
Physical contacts between sparse biofilms promote plasmid transfer and generate functional novelty
Authors: Ramoneda Josep , Ma Yinyin , Schmidt Julian , Manhart Michael , Angst Daniel C. , Johnson David R. 
Published: February 2023

AbstractThe horizontal transfer of plasmids is an important driver of microbial evolution, such as conferring antibiotic resistance (AR) to new genotypes. In biofilms, the abundance of cell-cell contacts promotes the frequent transfer of plasmids and their associated genes. In this study, we expand our knowledge about AR-encoding plasmids by investigating their transfer between discrete biofilms as the biofilms grow and physically collide with each other. Using an experimental system consisting of two fluorescently labelledPseudomonas stutzeristrains and anEscherichia colistrain, we show that biofilm collisions promote plasmid transfer along the collision boundaries. The extent of plasmid transfer depends on the plasmid loss probability, the plasmid transfer probability, and the relative growth rates of plasmid-free and plasmid-carrying cells. We further show that the proliferation of plasmids after biofilm collision depends on the spatial positionings of plasmid-carrying cells along the collision boundary, thus establishing a link between the large-scale spatial distribution of discrete biofilms and the small-scale spatial arrangement of cells within individual biofilms. Our study reveals that plasmid transfer during biofilm collisions is determined by spatial factors operating at different organizational levels and length scales, expanding our understanding of the fate of plasmid-encoded traits in microbial communities.
Investigations on SARS-CoV-2 and other coronaviruses in mink farms in France at the end of the first year of COVID-19 pandemic
Authors: Wasniewski Marine , Boué Franck , Richomme Céline , Simon-Lorière Etienne , Van der Werf Sylvie , Donati Flora , Enouf Vincent , Blanchard Yannick , Beven Véronique , Leperchois Estelle , Leterrier Bryce , Corbet Sandrine , Le Gouil Meriadeg , Monchatre-Leroy Elodie , Picard-Meyer Evelyne 
Published: February 2023

AbstractSoon after the beginning of the COVID-19 pandemic in early 2020, theBetacoronavirusSARS-CoV-2 infection of several mink farms breeding American minks (Neovison vison) for fur was detected in several countries of Europe. The risk of a new reservoir formation and of a reverse zoonosis from minks was then a major concern. The aim of this study was to investigate the four French mink farms for the circulation of SARS-CoV-2 at the end of 2020. The investigations took place during the slaughtering period thus facilitating different types of sampling (swabs and blood). In one of the four mink farms, 96.6% of serum samples were positive in SARS-CoV-2 ELISA coated with purified N protein recombinant antigen and 54 out of 162 (33%) pharyngo-tracheal swabs were positive by RT-qPCR. The genetic variability among 12 SARS-CoV-2 genomes sequenced in this farm indicated the co-circulation of several lineages at the time of sampling. All SARS-CoV-2 genomes detected were nested within the 20A clade (Nextclade), together with SARS-CoV-2 genomes from humans sampled at the same period. The percentage of SARS-CoV-2 seropositivity by ELISA varied between 0.5 and 1.2% in the three other farms. Interestingly, among these three farms, 11 pharyngo-tracheal swabs and 3 fecal pools from two farms were positive by end-point RT-PCR for anAlphacoronavirushighly similar to a mink coronavirus sequence observed in Danish farms in 2015. In addition, a minkCaliciviridaewas identified in one of the two positive farms forAlphacoronavirus. The clinical impact of these unapparent viral infections is not known. The co-infection of SARS-CoV-2 with other viruses in mink farms could contribute to explain the diversity of clinical symptoms noted in different infected farms in Europe. In addition, the co-circulation of anAlphacoronavirusand SARS-CoV-2 within a mink farm would increase potentially the risk of viral recombination between alpha and betacoronaviruses already suggested in wild and domestic animals, as well as in humans.Author summaryFrance is not a country of major mink fur production. Following the SARS-CoV-2 contamination of mink farms in Denmark and the Netherlands, the question arose for the four French farms.The investigation conducted at the same time in the four farms revealed the contamination of one of them by a variant different from the one circulating at the same time in Denmark and the Netherlands mink farms.Investigation of three other farms free of SARS-CoV-2 contamination revealed the circulation of other viruses including a mink Alphacoronavirus andCaliciviridae, which could modify the symptomatology of SARS-CoV-2 infection in minks.
Interpretations of healthy eating after a diagnosis of multiple sclerosis: a secondary qualitative analysis
Authors: Weiss Hannah , Russell Rebecca D. , Black Lucinda , Begley Andrea 
Published: February 2023

PurposeMultiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system that causes debilitating symptoms. Currently, there is insufficient evidence to recommend a special diet for people with MS to slow disease progression and reduce symptoms. Little is known about the dietary choices made by people with MS. This study aimed to explore the interpretations of healthy eating in people recently diagnosed with MS. Objectives were to investigate the types of changes in food choices and to describe the impact of making these changes.Design/methodology/approachA social constructionist approach applying qualitative secondary analysis of semi-structured interviews was conducted (n = 11). Interviews were transcribed, coded and analysed using a deductive approach.FindingsParticipants were mostly female (82%), mean age 47 years and mean time since diagnosis eight months. Four themes emerged from the data: (1) moving in the direction of the dietary guidelines, (2) modifying intake of dietary fat, (3) requiring mental effort and (4) needing input from a dietitian.Practical implicationsThe directions of food choices and the absence of dietetic input highlighted in this study suggest the need for evidence-based nutrition education that enables people with MS to tailor dietary guidelines according to their preferences.Originality/valueHow people interpret healthy eating advice and the impact on making food choice changes is useful for explaining dietary changes in MS. Special diets promoted for MS provide conflicting advice, and the lack of access to dietitians means that additional mental effort is required when interpreting healthy eating messages and diets.
The impact of big data analytics capability on green supply chain integration: an organizational information processing theory perspective
Authors: Shi Haiqing , Feng Taiwen , Zhu Zhanguo 
Published: February 2023

PurposeDespite big data analytics capability (BDAC) has received extensive attention, how and under what conditions BDAC influences green supply chain integration (GSCI) remains unclear. This study draws on organizational information processing theory to examine the mediating effect of supply chain visibility in the BDAC–GSCI link and the moderating effects of flexibility- and control-oriented culture.Design/methodology/approachThe authors examined the research model using two-waved survey data gathered from 317 Chinese firms. The authors employed hierarchical regression analysis and bootstrapping method to test hypotheses and assessed the robust of theoretical model using structural model.FindingsThe authors found that BDAC facilitates all three dimensions of GSCI. Supply visibility mediates the relationship between BDAC and all three dimensions of GSCI, whereas demand visibility only mediates the positive effects of BDAC on green internal and customer integration. In addition, control-oriented culture strengthens the positive impacts of BDAC on supply and demand visibility, while the moderating effects of flexibility-oriented culture are insignificant.Originality/valueThis research contributes to opening the “black box” of how BDAC affects GSCI and provides novel guidelines for firms enhancing the degree of GSCI.
Influence of mentoring and job security on expatriate voice
Authors: Zhuang Wen-Long , Chu Yu-Han , Yang Tsun-Lih , Chang Yu-Ming 
Published: February 2023

PurposeThe purpose of this paper is to investigate the influence of mentoring functions on expatriate voice in multinational enterprises and whether job security plays a mediating role in this relationship.Design/methodology/approachIn total, 300 questionnaires were distributed in this study. Of the 173 responses received, 8 invalid questionnaires were excluded and 165 valid questionnaires were analysed. The effective questionnaire recovery rate was 55.00%.FindingsThe results revealed that the stronger the psychosocial support function, the role modelling function and the career development provided by the mentor, the more would be the expatriate voice behaviour. Furthermore, the psychological support, role model characteristics and career development guidance affect the expatriate voice behaviour through the mediation of job security.Originality/valueFew studies have focussed on the influence of expatriate mentoring functions and job security on expatriate voice. Furthermore, whether the mentoring function affects the job security of expatriates is unknown. The objective of this study is to fill this gap in the literature.