bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bam complex associated proteins inEscherichia coliare functionally linked to peptidoglycan biosynthesis, membrane fluidity and DNA replication
Authors: Bryant Jack A. , Staunton Kara A. , Doherty Hannah M. , Alao Micheal B. , Ma Xuyu , Morcinek-Orłowska Joanna , Goodall Emily C. A. , Gray Jessica , Milner Mathew , Cole Jeffrey A. , de Cogan Felicity , Knowles Timothy J. , Glinkowska Monika , Moradigaravand Danesh , Henderson Ian R. , Banzhaf Manuel 
Published: July 2023

AbstractBiogenesis of the bacterial outer membrane is key to bacterial survival and antibiotic resistance. Central to this is the β-barrel assembly machine (Bam) complex and its associated chaperones, which are responsible for transport, folding and insertion of outer membrane proteins (OMPs). TheEscherichia coliBam complex is composed of two essential subunits, BamA and BamD, and three non-essential accessory lipoproteins, BamB, BamC and BamE. Optimal Bam function is further dependent on the non-essential periplasmic chaperones DegP, Skp and SurA. Despite intensive study, the specific function of these non-essential Bam-associated proteins remains unknown. Here, we analysed ΔbamB, ΔbamC, ΔbamE, ΔsurA, Δskpand ΔdegPknockout strains by phenotypic screening, conservation analysis and high-throughput genetics. We reveal that Bam complex activity is impacted by changes in outer membrane lipid composition and that enterobacterial common antigen is essential in the absence of the chaperone SurA. We also show components of peptidoglycan are conditionally essential with Bam accessory lipoproteins and that DNA replication control is perturbed in the absence of specific OMP assembly components. Together, our data indicates potential mechanisms for coordination of OMP biogenesis with other cellular growth processes such as LPS and peptidoglycan biogenesis, and DNA replication control.
The Cellular Underpinnings of the Human Cortical Connectome
Authors: Zhang Xi-Han , Anderson Kevin M. , Dong Hao-Ming , Chopra Sidhant , Dhamala Elvisha , Emani Prashant S. , Margulies Daniel , Holmes Avram J. 
Published: July 2023

SummaryThe functional properties of the human brain arise, in part, from the vast assortment of cell types that pattern the cortex. The cortical sheet can be broadly divided into distinct networks, which are further embedded into processing streams, or gradients, that extend from unimodal systems through higher-order association territories. Here, using transcriptional data from the Allen Human Brain Atlas, we demonstrate that imputed cell type distributions are spatially coupled to the functional organization of cortex, as estimated through fMRI. Cortical cellular profiles follow the macro-scale organization of the functional gradients as well as the associated large-scale networks. Distinct cellular fingerprints were evident across networks, and a classifier trained on post-mortem cell-type distributions was able to predict the functional network allegiance of cortical tissue samples. These data indicate that thein vivoorganization of the cortical sheet is reflected in the spatial variability of its cellular composition.
Synaptophysin Chaperones the Assembly of 12 SNAREpins under each Ready-Release Vesicle
Authors: Bera Manindra , Radhakrishnan Abhijith , Coleman Jeff , Sundaram Ramalingam Venkat Kalyana , Ramakrishnan Sathish , Pincet Frederic , Rothman James E. 
Published: July 2023

AbstractThe synaptic vesicle protein Synaptophysin has long been known to form a complex with the v-SNARE VAMP, but a more specific molecular function or mechanism of action in exocytosis has been lacking because gene knockouts have minimal effects. Utilizing fully-defined reconstitution and single-molecule measurements, we now report that Synaptophysin functions as a chaperone that determines the number of SNAREpins assembling between a ready-release vesicle and its target membrane bilayer. Specifically, Synaptophysin directs the assembly of 12 ± 1 SNAREpins under each docked vesicle, even in the face of an excess of SNARE proteins. The SNAREpins assemble in successive waves of 6 ± 1 and 5 ± 2 SNAREpins, respectively, tightly linked to oligomerization of and binding to the vesicle Ca++sensor Synaptotagmin. Templating of 12 SNAREpins by Synaptophysin is likely the direct result of its hexamer structure and its binding of VAMP2 dimers, both of which we demonstrate in detergent extracts and lipid bilayers.Significance StatementSynaptophysin is the most abundant protein and a unique constituent of synaptic vesicles, yet it has no known function, due to minimal genetic phenotypes and the lack of biochemical assays. Here, we directly establish using two independent methods that the synaptic vesicle protein Synaptophysin forms a hexameric complex containing 12 copies of the v-SNARE VAMP2. These v-SNAREs assemble into SNAREpins as ready-release vesicles are formed in a fully-defined cell-free system, and do so in two equal waves organized by oligomerization of the Ca++sensor Synaptotagmin. In the absence of Synaptophysin, two waves are also observed, but the number of SNAREpins in each varies widely. We suggest that a single Synaptophysin hexamer in each vesicle symmetrically organizes 6 pairs of peripheral and central SNAREpins, the latter being directly bound to the Synaptotagmin ring. This gives rise to the symmetrical ring-like arrangement of densities observed by cryo-EM tomography under each synaptic vesicle (1, 2).
Regulation of potassium homeostasis inCaulobacter crescentus
Authors: Quintero-Yanes Alex , Léger Loïc , Collignon Madeline , Mignon Julien , Mayard Aurélie , Michaux Catherine , Hallez Régis 
Published: July 2023

AbstractPotassium (K+) is an essential physiological element determining membrane potential, intracellular pH, osmotic/turgor pressure, and protein synthesis in cells. Nevertheless, K+homeostasis remains poorly studied in bacteria. Here we describe the regulation of potassium uptake systems in the oligotrophic α-proteobacteriumCaulobacter crescentusknown as a model for asymmetric cell division. We show thatC. crescentuscan grow in concentrations from the micromolar to the millimolar range by essentially using two K+transporters to maintain potassium homeostasis, the low affinity Kup and the high affinity Kdp uptake systems. When K+is not limiting, we found that thekupgene is essential whilekdpinactivation does not impact the growth. In contrast,kdpbecomes critical but not essential andkupdispensable for growth in K+-limited environments. However, in the absence ofkdp, mutations inkupwere selected to improve growth in K+-depleted conditions, likely by improving the affinity of Kup for K+. In addition, mutations in the KdpDE two-component system, which regulateskdpABCexpression, suggest that the inner membrane sensor regulatory component KdpD works as a kinase in early stages of growth and as a phosphatase to regulate transition into stationary phase. Our data also show that KdpE is not only phosphorylated by KdpD but also by another non-cognate histidine kinase. On top of this, we determined the KdpE-dependent and independent K+transcriptome and identified the direct targets of KdpE. Together, our work illustrates how an oligotrophic bacterium responds to fluctuation in K+availability.ImportancePotassium (K+) is a key metal ion involved in many essential cellular processes. Its transport and regulation have been mainly studied in the bacterial model speciesEscherichia coliandBacillus subtilis. Here we show that the oligotrophCaulobacter crescentuscan support growth at lower K+concentrations by mainly using two K+uptake systems, the low-affinity Kup and the high-affinity Kdp. Interestingly, in the absence of Kdp, point mutations in Kup was selected to increase affinity for K+, which improved growth in K+-depleted conditions. Using genome-wide approaches, we also determined the entire set of genes required forC crescentusto survive at low K+concentration as well as the full K+-dependent regulon. Finally, we found that the transcriptional regulation mediated by the KdpDE two-component system is unconventional since unlikeE. coli, the inner membrane sensor regulatory component KdpD works rather as a phosphatase on the phosphorylated response regulator KdpE∼P. To our knowledge, this is the first comprehensive study of K+homeostasis in bacteria.
Octocoral microbiomes vary substantially across environmental gradients in deep waters
Authors: Vohsen Samuel A. , Herrera Santiago 
Published: July 2023

AbstractCoral-associated microbiomes vary greatly between colonies and localities with functional consequences on the host. However, the full extent of variability across the ranges of most coral species remains unknown, especially in corals living in deep waters. Here we characterized the microbiomes of four octocoral species from mesophotic and deep-sea habitats in the northern Gulf of Mexico,Muricea pendula, Swiftia exserta, Callogorgia delta,andParamuricea biscayausing 16S metabarcoding. We tested for microbiome differentiation between and within species, examining the influence of the coral’s genotype and environmental factors that vary with depth (53-2224 m) and geographic location (over 680 m). Coral microbiomes were often dominated by amplicon sequence variants whose abundances varied across hosts’ ranges including corallicolids,Endozoicomonas, members of the Mollicutes, and the BD1-7 clade. Coral species, depth, and geographic location significantly affected diversity, microbial community composition, and the abundance of individual microbes. Differences in host genotype, bottom temperature, and surface primary productivity could explain part of the variation associated with depth and geographic location. Altogether, this work demonstrates that the microbiomes of corals vary substantially across their ranges with potential functional consequences, identifies important ecological drivers in mesophotic and deep-sea corals, and can inform restoration efforts.
Treated eave screens in combination with screened doors and windows, are more effective than untreated eave screens in a similar combination in reducing indoor and outdoorAnophelespopulations under semi-filed conditions in western Kenya
Authors: Abong’o Bernard , Agumba Silas , Moshi Vincent , Simwero Jacob , Otima Jane , Ochomo Eric 
Published: July 2023

AbstractIntroductionHuman habitats remain the main point of human-vector interaction leading to malaria transmission despite sustained use of insecticide treated nets (ITNs) and indoor residual spraying (IRS). Simple structural modifications involving screening of doors, windows and eaves have great potential for reducing indoor entry of mosquitoes and hence malaria transmission.MethodsFour huts, each constructed inside a semi-field structure, allowing the experimental release of mosquitoes at the Kenya Medical Research Institute (KEMRI), Kisumu research station were used in the study. Two huts had untreated eave and door screens and screened air cavities in place of windows in experiment 1 with the eave screen treated using Actellic® insecticide in experiment 2. The other two huts remained unscreened throughout the study. First filial (F1) generation ofAnopheles funestusfrom Siaya, F0 reared fromAn. arabiensislarvae collected from Ahero andAn. arabiensisDongola strain from the insectary were raised to 3-day old adults and used in experiments. Two hundred, 3-day old adults of each species were released in each semi-field structure at dusk and recaptured the following day at 0700hrs and at 0900 hours. A single volunteer slept in each hut under untreated bed net each night of the study. Recaptured mosquitoes were counted and recorded by collection location, either indoor or outdoor of each hut in the different semi-field structures.ResultsSignificantly fewerAn. arabiensisfrom Ahero [RR=0.10; (95%CI: 0.02-0.63); P<0.0145],An. arabiensisDongola strain [RR=0.11; (95%CI: 0.04 – 0.19); P<0.0001 andAn. funestusfrom Siaya [RR=0.10; (95%CI: 0.06-0.17); P<0.0001] were observed inside modified huts compared to unmodified ones. Treating of eave screen material with Actellic® 300CS significantly reduced the numbersAn. arabiensisfrom Ahero [RR=0.003; (95%CI: 0.00-0.03); P<0.0001] andAn. arabiensisDongola strain [RR=0.03; (95%CI: 0.02-0.05); P<0.0001] indoors of huts with treated eave screen compared to huts with untreated eave screens, while totally preventing entry ofAn. funestusindoors. These modifications cost <250usd/structure.Discussion and ConclusionThis article describes affordable and effective ways of reducing mosquito entry into the house by modifying the eaves, doors and windows. These modifications were highly effective in reducing indoor entry of mosquitoes. Additionally, treatment of eave screen material with an effective insecticide further reduces theAnophelespopulation in and around the screened huts under semi-field conditions and could greatly complement existing vector control efforts.
The killing of human gut commensalE. coliED1a by tetracycline is associated with severe ribosome dysfunction
Authors: Khusainov Iskander , Romanov Natalie , Goemans Camille , Turoňová Beata , Zimmerli Christian E. , Welsch Sonja , Langer Julian D. , Typas Athanasios , Beck Martin 
Published: July 2023

SUMMARYRibosomes translate the genetic code into proteins. Recent technical advances have facilitated in situ structural analyses of ribosome functional states inside eukaryotic cells and the minimal bacterium Mycoplasma. However, such analyses of Gram-negative bacteria are lacking, despite their ribosomes being major antimicrobial drug targets. Here we compare twoE. colistrains, a labE. coliK-12 and human gut isolateE. coliED1a, for which tetracycline exhibits bacteriostatic and bactericidal action, respectively. Thein situribosome structures upon tetracycline treatment show a virtually identical drug binding-site in both strains, yet the distribution of ribosomal complexes clearly differs. While K-12 retains ribosomes in a translation competent state, tRNAs are lost in the vast majority of ED1a ribosomes. A differential response is also reflected in proteome-wide abundance and thermal stability assessment. Our study underlines the need to include molecular analyses and to consider gut bacteria when addressing antibiotic mode of action.HIGHLIGHTS•Ribosome structures of gram-negative bacteria are analyzed in situ•Tetracyline is bactericidal to gut isolate despite identical ribosome structures•When antibiotic is bacteriostatic, ribosomal translation competent states are retained•When antibiotic is bactericidal, cells rapidly accumulate P-tRNAs-deficient ribosomesGRAPHICAL ABSTRACT
Proteomics analysis reveals a role forE. colipolyphosphate kinase in membrane structure and polymyxin resistance during starvation
Authors: Baijal Kanchi , Abramchuk Iryna , Herrera Carmen M. , Trent M. Stephen , Lavallée-Adam Mathieu , Downey Michael 
Published: July 2023

ABSTRACTPolyphosphates (polyP) are chains of inorganic phosphates that can reach over 1000 residues in length. InEscherichia coli, polyP is produced by the polyP kinase (PPK) and is thought to play a protective role during the response to cellular stress. However, the molecular pathways impacted by PPK activity and polyP accumulation remain poorly characterized. In this work we used label-free mass spectrometry to study the response of bacteria that cannot produce polyP (Δppk) during starvation to identify novel pathways regulated by PPK.In response to starvation, we found 92 proteins significantly differentially expressed between wild-type and Δppkmutant cells. Wild-type cells were enriched for proteins related to amino acid biosynthesis and transport, whileΔppkmutants were enriched for proteins related to translation and ribosome biogenesis, suggesting that without PPK, cells remain inappropriately primed for growth even in the absence of required building blocks.From our dataset, we were particularly interested in Arn and EptA proteins, which were downregulated in Δppkmutants compared to wild-type controls, because they play a role in lipid A modifications linked to polymyxin resistance. Using western blotting, we confirm differential expression of these and related proteins, and provide evidence that this mis-regulation in Δppkcells stems from a failure to induce the BasS/BasR two-component system during starvation. We also show that Δppkmutants unable to upregulate Arn and EptA expression lack the respective L-Ara4N and pEtN modifications on lipid A. In line with this observation, loss ofppkrestores polymyxin sensitivity in resistant strains carrying a constitutively activebasRallele.Overall, we show a new role for PPK in lipid A modification during starvation and provide a rationale for targeting PPK to sensitize bacteria towards polymyxin treatment. We further anticipate that our proteomics work will provide an important resource for researchers interested in the diverse pathways impacted by PPK.
Emerging themes in food tourism: a systematic literature review and research agenda
Authors: Sujood  , Ali Ruksar , Irfan Saba , Hamid Sheeba 
Published: July 2023

PurposeThe aim of this paper is to review and categorise the body of existing research in order to better understand the state of food tourism. The primary objective of this study is to identify emerging themes in the area of food tourism and to highlight the relationships among them.Design/methodology/approachThis research consists of a systematic literature review of academic articles from the Scopus and Web of Science databases.FindingsTen themes of Food Tourism emerged from the analysis, i.e. Food Tourism and Local Food, Food Tourism and Sustainability, Food Tourism and Economy, Food Tourism and Food waste management, Food Tourism and Culture, Food Tourism and Environment, Food Tourism and Information Technology, Food Tourism and COVID-19, Food Tourism and Post pandemic consumer trust and Food Tourism and Tourism and Hospitality sector.Research limitations/implicationsThis study elaborates on the theoretical pieces of evidence on the connection between food and tourism. Not only limited to food tourism, but this paper also contributes to the literature in the area of economy, sustainability, post-COVID-19, food waste management, environment and technological innovations in food tourism.Originality/valueThis study contributes to a deeper understanding of the topic at hand. The study begins by systematically examining the topic to offer a thorough and in-depth analysis of food tourism. There is not a single study which has covered these many themes of food tourism, which makes it an important contribution to the literature.
Tax and income inequality: evidence from Sub-Saharan Africa
Authors: Brown Theodora Aba Kwegyeba , Bokpin Godfred A. , Sarpong-Kumankoma Emmanuel 
Published: July 2023

PurposeThis study aims to determine how taxes can be used to bridge income inequality gap in sub-Saharan Africa (SSA).Design/methodology/approachA panel data set of 36 SSA countries was analysed using generalised method of moments.FindingsThe results suggest that an increase in direct taxes relative to indirect taxes has a positive significant impact on income inequality. This is mostly due to the progressive nature of direct taxes as compared to indirect taxes.Originality/valueThis research contributes to the scant literature on how specific tax components affect income inequality, especially in developing countries.
Senior entrepreneurship dynamics: Latin America perspective
Authors: Amorós José Ernesto , Leporati Marcelo , Torres-Marín Alfonso Jesús 
Published: July 2023

PurposeThe main objective of this research is to exploratorily analyse different factors that influence the decision of the senior population (+50 years) to engage in entrepreneurship activities in a group of Latin American countries. This study considers the motivations for entrepreneurship (opportunity and necessity) and the level of development of the countries.Design/methodology/approachThe authors used data from the Global Entrepreneurship Monitor (GEM) with a sample of 22,139 observations of senior individuals in seven Latin American countries surveyed between 2013 and 2017. The authors also used the Human Development Index to capture the relevance of the level of development. The authors employed a multilevel logistic regression model to test the study hypotheses.FindingsThe study results show that individual factors such as personal income, education and occupation have a significant influence on the probability of entrepreneurship of senior individuals. Related to contextual factors, the level of human development of a country has a negative influence mainly on opportunity-based entrepreneurs.Originality/valueBecause of the rapidly ageing population in Latin America, understanding senior entrepreneurs and their motivations is very relevant not only in terms of theoretical development but also for policy and practical implications, primarily those related to labour markets and social protection.
Examining the impact of the platform economy on Spain’s cultural destinations through the lens of free tours
Authors: Rivera-García Jorge , Fernández-Villarán Asunción , Pastor-Ruiz Ricardo 
Published: July 2023

Purpose
Free guided walking tours are one of the most successful tourism segments in the digital platform economy. It is beginning to be associated with negative impacts in some of the destinations where it is spreading rapidly. Although the platform economy is generating increasing academic interest, the free tour model remains largely unexplored area in the literature. This study aims to examine how such activity affects cultural destinations.

Design/methodology/approach
Focussing on the largest Free Tours platform operating in Spain, GuruWalk, the methodology used analyses its impact in six cultural destinations on two of the sustainability dimensions: the territorial dimension and the governance, through an exploratory study.

Findings
The findings help to understand the differences that such activity generates in each destination depending on the phase of its life cycle, and to implement, if necessary, corrective measures. The research confirms that the impacts differ according to the tourist destination’s maturity, concluding that such activity contributes to the increase of tourist agglomerations and the overcrowding of cultural destinations in their middle and mature life cycles. The findings highlighted the importance of the role of local governance on free tour activity.

Originality/value
The main contribution is the association of the impacts they produce (especially in terms of massification) with destination life cycle phases. There were no similar precedents with a spatial or territorial analysis to reliably demonstrate not only that this activity has an impact on the territory but also what type of impact is produced.