bluuebunny/crossref_metadata_2025_split huggingface dataset:
TurboID reveals the proxiomes of CGE1, VIPP1, and VIPP2 inChlamydomonas reinhardtii
Authors: Kreis Elena , König Katharina , Sommer Frederik , Schroda Michael 
Published: December 2022

AbstractInChlamydomonas reinhardtii, VIPP1 and VIPP2 play a role in the sensing and coping with membrane stress and in thylakoid membrane biogenesis. To gain more insight into these processes, we aimed to identify proteins interacting with VIPP1/2 in the chloroplast and chose proximity labeling (PL) for this purpose. We used the transient interaction between the nucleotide exchange factor CGE1 and stromal HSP70B as test system. While PL with APEX2 and BioID proved to be inefficient, TurboID resulted in significant biotinylationin vivo. TurboID-mediated PL with VIPP1/2 as baits under ambient and H2O2stress conditions confirmed known interactions of VIPP1 with VIPP2, HSP70B and CDJ2. Novel proteins in the VIPP1/2 interaction network can be grouped into proteins involved in the biogenesis of thylakoid membrane complexes and the regulation of photosynthetic electron transport. A third group comprises 11 proteins of unknown function whose genes are upregulated under chloroplast stress conditions. We named them VIPP PROXIMITY LABELING (VPL1-11). and confirmed the proximity of VIPP1 and VPL2 in a reciprocal experiment. Our results demonstrate the robustness of TurboID-mediated PL for studying protein interaction networks in the chloroplast ofChlamydomonasand pave the way for analyzing functions of VIPPs in thylakoid biogenesis and stress responses.
Targeted chromosomal barcoding establishes direct genotype-phenotype associations for antibiotic resistance inMycobacterium abscessus
Authors: Calvet-Seral Juan , Crespo-Yuste Estefanía , Mathys Vanessa , Rodriguez-Villalobos Hector , Ceyssens Pieter-Jan , Martin Anandi , Gonzalo-Asensio Jesús 
Published: December 2022

ABSTRACTA bedaquiline resistantMycobacterium abscessusisolate was sequenced and a candidate mutation in theatpEgene was identified as responsible for the antibiotic resistance phenotype. To establish a direct genotype-phenotype relationship of this D29A mutation, we developed a recombineering-based method consisting of the specific replacement of the desired mutation in the bacterial chromosome. As surrogate bacteria, we used twoM. abscessusantibiotic susceptible strains: ATCC19977, and the SL541 clinical isolate. The allelic exchange substrates used in recombineering carried either the sole D29A mutation, or a genetic barcode of silent mutations in codons flanking the D29A mutation. After selection of bedaquiline resistantM. abscessuscolonies, transformed with both substrates, we obtained equivalent numbers of recombinants. These resistant colonies were analyzed by allele-specific PCR, and Sanger sequencing, demonstrating that the presence of the genetic barcode is linked to the targeted incorporation of the desired mutation in its chromosomal location. All recombinants displayed the same minimal inhibitory concentration to bedaquiline than the original isolate, from which the D29A mutation was identified. Finally, to demonstrate the broad applicability of this method, we confirmed the association of bedaquiline resistance with theatpEA64P mutation, performed in independentM. abscessusstrains and by independent researchers.
Characterisation of neonatalStaphylococcus capitisNRCS-A isolates compared with non NRCS-AStaphylococcus capitisfrom neonates and adults
Authors: Felgate Heather , Sethi Dheeraj , Faust Kirstin , Kiy Cemsid , Härtel Christoph , Rupp Jan , Clifford Rebecca , Dean Rachel , Tremlett Catherine , Wain John , Langridge Gemma , Clarke Paul , Page Andrew , Webber Mark A 
Published: December 2022

AbstractStaphylococcus capitisis a frequent cause of Late-Onset Sepsis (LOS) in neonates admitted to Neonatal Intensive Care Units (NICU). The NRCS-A clone ofS. capitishas been isolated from NICUs globally although the reasons for the global success of this clone are not understood.We analysed a collection ofS. capitiscolonising babies admitted to two NICUs, one in the UK and one in Germany as well as corresponding pathological clinical isolates. Genome analysis identified 3 groups; non-NRCS-A isolates, NRCS-A isolates, and a group of ‘proto NRCS-A’ - isolates closely related to NRCS-A but not associated with neonatal infection. All bloodstream isolates belonged to the NRCS-A group and were indistinguishable from strains carried on the skin or in the gut. NRCS-A isolates showed increased tolerance to chlorhexidine and antibiotics relative to the otherS. capitisas well as enhanced ability to grow at higher pH values. Analysis of 138 pangenomes of the clades identified characteristicnsrandtarJgenes in the NRCS-A and proto groups with a CRISPR-cas system only seen in NRCS-A isolates which also showed enrichment of genes for metal acquisition and transport.We found evidence for transmission ofS. capitisNRCS-A within NICU, with related isolates shared between babies and multiple acquisitions by some babies. Our data show NRCS-A strains commonly colonise uninfected babies in NICU representing a potential reservoir for potential infection. This work provides more evidence that adaptation to survive in the gut and on skin facilitates spread of NRCS-A, and that metal acquisition and tolerance may be important to the biology of NRCS-A. Understanding how NRCS-A survives in NICUs can help develop infection control procedures against this clone.
Scavenger receptor endocytosis controls apical membrane morphogenesis in theDrosophilaairways
Authors: Pinheiro Ana S. , Tsarouhas Vasilios , Senti Kirsten , Arefin Badrul , Samakovlis Christos 
Published: December 2022

AbstractThe acquisition of distinct branch sizes and shapes is a central aspect in tubular organ morphogenesis and function. In theDrosophilaairway tree, the interplay of apical ECM components with the underlying membrane and cytoskeleton controls tube elongation, but the link between ECM composition with apical membrane morphogenesis and tube size regulation is elusive. Here, we characterized Emp (epithelial membrane protein), aDrosophilaCD36-homologue belonging to the scavenger receptor class B protein-family.empmutant embryos fail to internalize the luminal chitin deacetylases Serp and Verm at the final stages of airway maturation and die at hatching with liquid filled airways. Emp localizes in apical epithelial membranes and shows cargo selectivity for LDLr-domain containing proteins.empmutants also display over elongated tracheal tubes with increased levels of the apical proteins Crb, DE-cad and phosphorylated Src (p-Src). We show that Emp associates and organizes the βH-Spectrin cytoskeleton and is itself confined by apical F-actin bundles. Overexpression or loss of its cargo protein Serp lead to abnormal apical accumulations of Emp and perturbations in p-Src levels. We propose that during morphogenesis, Emp senses and responds to luminal cargo levels by initiating apical membrane endocytosis along the longitudinal tube axis and thereby restricts airway elongation.
Point-of-care peptide hormone production enabled by cell-free protein synthesis
Authors: DeWinter Madison A. , Thames Ariel Helms , Guerrero Laura , Kightlinger Weston , Karim Ashty S. , Jewett Michael C. 
Published: December 2022

AbstractIn resource-limited settings, it can be difficult to safely deliver sensitive biologic medicines to patients due to cold chain and infrastructure constraints. Point-of-care drug manufacturing could circumvent these challenges since medicines could be produced locally and used on-demand. Towards this vision, we combine cell-free protein synthesis (CFPS) and a 2-in-1 affinity purification and enzymatic cleavage scheme to develop a platform for point-of-care drug manufacturing. As a model, we use this platform to synthesize a panel of peptide hormones, an important class of medications that can be used to treat a wide variety of diseases including diabetes, osteoporosis, and growth disorders. With this approach, temperature-stable lyophilized CFPS reaction components can be rehydrated with DNA encoding a SUMOylated peptide hormone of interest when needed. Strep-Tactin®affinity purification and on-bead SUMO protease cleavage yields peptide hormones in their native form that are recognized by ELISA antibodies and that can bind their respective receptors. With further development to ensure proper biologic activity and patient safety, we envision this platform could be used to manufacture valuable peptide hormone drugs at the point-of-care in resource-limited settings.
Application of self-organizing maps to AFM-based viscoelastic characterization of breast cancer cell mechanics
Authors: Weber Andreas , Vivanco Maria dM. , Toca-Herrera José L. 
Published: December 2022

AbstractCell mechanical properties have been proposed as label free markers for diagnostic purposes in diseases such as cancer. Cancer cells show altered mechanical phenotypes compared to their healthy counterparts. Atomic Force Microscopy (AFM) is a widely utilized tool to study cell mechanics. These measurements often need skilful users, physical modelling of mechanical properties and expertise in data interpretation. Together with the need to perform many measurements for statistical significance and to probe wide enough areas in tissue structures, the application of machine learning and artificial neural network techniques to automatically classify AFM datasets has received interest recently. We propose the use of self-organizing maps (SOMs) as unsupervised artificial neural network applied to mechanical measurements performed via AFM on epithelial breast cancer cells treated with different substances that affect estrogen receptor signalling. We show changes in mechanical properties due to treatments, as estrogen softened the cells, while resveratrol led to an increase in cell stiffness and viscosity. These data were then used as input for SOMs. Our approach was able to distinguish between estrogen treated, control and resveratrol treated cells in an unsupervised manner. In addition, the maps enabled investigation of the relationship of the input variables.
Sexually Transmitted Infections among Key Populations in India: A Protocol for Systematic Review
Authors: Bhatta Mihir , Majumdar Agniva , Ghosh Utsha , Ghosh Piyali , Banerji Papiya , Aridoss Santhakumar , Royal Abhiske , Biswas Subrata , Venkatesh Bhumika Tumkur , Adhikary Rajatsuvra , Dutta Shanta 
Published: December 2022

AbstractBackgroundSexually transmitted infections (STIs) are one of the leading causes of health, and economic burdens in the developing world, leading to considerable morbidity, mortality, and stigma. The incidence and prevalence of the four curable STIs viz syphilis, gonorrhoea, chlamydia, and trichomoniasis vary remarkably across different geographical locations. In India, the prevalence of four curable STI among general populations is in between 0 to 3.9 per cent. However, it is assumed that STI prevalence is much higher among subpopulations practicing high-risk behaviour. Like men who have sex with men (MSM), transgender (TG), injecting drug users (IDU) and female sex worker (FSW).ObjectivesIn the present circumstances, a systematic review is necessary to integrate the available data from previously published peer-reviewed articles and published reports from several competent authorities to provide the prevalence and geographical distribution of the four curable STIs among the key population of India.MethodsAll available articles will be retrieved from PubMed, Google Scholar, Cochrane database, Scopus, Science Direct, and the Global Health network using the appropriate search terms. The data will be extracted through data extraction form as per PICOS (population, intervention, comparison, outcome, study design) framework. Risk of bias and quality assessment will be performed with the help of the Funnel plot and Newcastle - Ottawa Quality Assessment Scale.ConclusionThe future systematic review, which will be generated from the present protocol, may provide evidence of the prevalence and geographical distribution of the four curable STIs among the key population of India. The findings of the future systematic review will strengthen the existing surveillance system in India, to determine the above-mention STIs prevalence among key populations in India.Protocol registration numberInternational Prospective Register for Systematic Reviews (PROSPERO) number CRD42022346470
Psychosocial attributes of housing and their relationship with health among refugee and asylum-seeking populations in high-income countries: systematic review
Authors: Brake Tessa , Dudek Verena , Sauzet Odile , Razum Oliver 
Published: December 2022

AbstractIntroductionHousing as a social determinant of health should provide not only shelter, but also a feeling of home. We explored psychosocial pathways creating a sense of home and influencing the relationship between housing and health among asylum seekers and refugees (ASR) in high-income countries.MethodsWe performed a systematic review. To be included, studies had to be peer-reviewed, published between 1995 and 2022, and focus on housing and health of ASR in high-income countries. We conducted a narrative synthesis.Results32 studies met the inclusion criteria. The psychosocial attributes influencing health most often identified werecontrol, followed byexpressing status, satisfaction, anddemand. Most attributes overlap with material/physical attributes and have an impact on ASR’s mental health. They are closely interconnected with each other.ConclusionsPsychosocial attributes of housing play an important role in the health of ASR; they are closely associated with material/physical attributes. Therefore, future research on housing and health of ASR should routinely examine psychosocial attributes, but always in association with physical attributes. The connections between these attributes are complex and need to be further explored.PROSPERO registration numberCRD42021239495
The adherens junction proteins α-catenin, vinculin and VASP cooperate to promote actin assembly
Authors: Said Rayan , Wang Hong , Pernier Julien , Narassimprakash Hemalatha , Roméro Stéphane , Gautreau Alexis M. , Mège René-Marc , Le Clainche Christophe 
Published: December 2022

AbstractThe cohesion of tissues requires that cells establish cell-cell junctions. Cells contact each other by forming Arp2/3-dependent lamellipodia before they initiate the formation of cadherin-based adherens junctions (AJs). Maturing AJs then assemble actin under force though the formation of a mechanosensitive complex comprising the actin-binding proteins α-catenin, vinculin and VASP, which individually act on the nucleation, elongation and organisation of actin filaments in different ways. However, the activity of the ternary complex that these actin-regulatory proteins form has not been investigated due to the difficulty of assembling this complex in vitro in the absence of force. Here, we first designed mutants of these proteins that interact independently of force. We then studied their activity by combining actin polymerization kinetics in fluorescence spectroscopy with observation of single actin filaments in TIRF microscopy. Our results reveal how α-catenin, vinculin and VASP combine their activities in a complex to inhibit Arp2/3-mediated branching, stimulate the nucleation and elongation of linear actin filaments from profilin-actin and crosslink these filaments into bundles. These findings shed light on the molecular mechanisms by which actin regulators synergistically control the transition of actin architecture and dynamics that accompanies the formation and maturation of AJs.
Structural basis for substrate recruitment by AMBRA1 E3 ligase receptor
Authors: Liu Ming , Wang Yang , Teng Fei , Mai Xinyi , Wang Xi , Su Ming-Yuan , Stjepanovic Goran 
Published: December 2022

AbstractAMBRA1 is a tumor suppressor protein that functions as a substrate receptor of the ubiquitin conjugation system as part of autophagy and cell-cycle regulatory network. The highly intrinsic disorder of AMBRA1 has so far precluded its structural determination. To solve this problem, we analyzed the domain organization and dynamics of AMBRA1 using hydrogen deuterium exchange mass spectrometry (HDX-MS). High deuterium uptake indicates that AMBRA1 is a dynamic and largely unstructured protein, and can be stabilized upon interaction with DDB1, the adaptor of the Cullin4A/B E3 ligase complex. Here we present the cryo-EM structure of AMBRA1 in complex with DDB1 at 3 Å resolution. The structure shows that parts of N- and C-terminal structural regions in AMBRA1 fold together into the highly dynamic WD40 domain, and reveals how DDB1 engages with AMBRA1 to create a binding scaffold for substrate recruitment. AMBRA1 uses its N-terminal helix-loop-helix and WD40 domain to bind the double-propeller fold of DDB1, whereas different regions target the specific cellular substrates for ubiquitination. We also demonstrate that DDB1 binding-defective AMBRA1 mutants prevent ubiquitination of the substrate Cyclin D1in vitroand decreased number of autophagosomes in the cells. Together, these results provide structural insights into AMBRA1-ubiquitin ligase complex and suggests a mechanism by which the AMBRA1 acts as a hub involved in various physiological processes.
Integrated proteomics reveals the landscape of autophagy degradation in human neurons and autophagy receptors regulating neuronal activity
Authors: Zhou Xiaoting , Lee You-Kyung , Li Xianting , Kim Henry , Sanchez-Priego Carlos , Han Xian , Tan Haiyan , Zhou Suiping , Fu Yingxue , Purtell Kerry , Wang Qian , Holstein Gay , Tang Beisha , Peng Junmin , Yang Nan , Yue Zhenyu 
Published: December 2022

AbstractAutophagy is a catabolic and self-degradative process crucial for maintaining cellular homeostasis. Malfunctional autophagy is implicated in neurodevelopmental and neurodegenerative diseases. However, the exact role and targets of autophagy in human neurons remain elusive. Here we reported a systematic investigation of neuronal autophagy targets through integrated proteomics. Deep proteomic profiling of multiple autophagy-deficient lines of human induced neurons, mouse brains, and LC3-interactome uncovers a role of neuronal autophagy in targeting primarily endoplasmic reticulum (ER), mitochondria, endosome, Golgi apparatus, synaptic vesicle (SV) proteins, and cAMP-PKA pathway, for degradation. Tubular ER and specific SV proteins are significant autophagy cargos in the axons. Functional validation identified calumenin as an ER resident autophagy receptor and illuminated a role of autophagy in regulating PKA and neuronal activity through AKAP11-mediated degradation. Our study thus reveals the landscape of autophagy degradation in human neurons and offers molecular insight into mechanisms of neurological disorders linked to autophagy deficiency.HighlightIntegrated proteomics reveals the landscape of autophagy degradation in human neuronsAutophagy clears tubular ER and selective ER and synaptic vesicle proteins in neuronsCalumenin is an ER resident autophagy receptorAutophagy controls PKA pathway and neuronal activity through autophagy receptor AKAP11
Detecting and staging diabetic retinopathy in retinal images using multi-branch CNN
Authors: Kusakunniran Worapan , Karnjanapreechakorn Sarattha , Choopong Pitipol , Siriapisith Thanongchai , Tesavibul Nattaporn , Phasukkijwatana Nopasak , Prakhunhungsit Supalert , Boonsopon Sutasinee 
Published: December 2022

PurposeThis paper aims to propose a solution for detecting and grading diabetic retinopathy (DR) in retinal images using a convolutional neural network (CNN)-based approach. It could classify input retinal images into a normal class or an abnormal class, which would be further split into four stages of abnormalities automatically.Design/methodology/approachThe proposed solution is developed based on a newly proposed CNN architecture, namely, DeepRoot. It consists of one main branch, which is connected by two side branches. The main branch is responsible for the primary feature extractor of both high-level and low-level features of retinal images. Then, the side branches further extract more complex and detailed features from the features outputted from the main branch. They are designed to capture details of small traces of DR in retinal images, using modified zoom-in/zoom-out and attention layers.FindingsThe proposed method is trained, validated and tested on the Kaggle dataset. The regularization of the trained model is evaluated using unseen data samples, which were self-collected from a real scenario from a hospital. It achieves a promising performance with a sensitivity of 98.18% under the two classes scenario.Originality/valueThe new CNN-based architecture (i.e. DeepRoot) is introduced with the concept of a multi-branch network. It could assist in solving a problem of an unbalanced dataset, especially when there are common characteristics across different classes (i.e. four stages of DR). Different classes could be outputted at different depths of the network.
Factors forming consumer willingness to pay a premium for free-range eggs
Authors: Slack Neale J. , Sharma Shavneet , Cúg Juraj , Singh Gurmeet 
Published: December 2022

PurposeLittle is known about the external stimuli, which trigger a change in a consumer's cognitive and affective state and lead to a consumer's willingness to pay a premium price (WTPPP) behavioural response. This study aims to close this knowledge gap by providing insight into how a unique combination of antecedents affects consumer attitude toward purchasing free-range eggs and leads to a behavioural response, which is measured by consumer WTPPP for free-range eggs.Design/methodology/approachAn online questionnaire was developed, with data collected from 392 Australian consumers. This study employs confirmatory factor analysis (CFA) to examine the measurement model before testing the hypothesised relationships using covariance-based structural equation modelling (CB-SEM).FindingsThe study reveals that the tested customer perceived value (CPV) dimensions, animal welfare and source credibility are positive stimuli of consumer attitude towards purchasing free-range eggs, which subsequently promotes consumer WTPPP for free-range eggs.Research limitations/implicationsFindings drawn from Australian consumers may not be generalisable to consumers from disparate contexts, and stimuli beyond those tested may influence consumer attitude and WTPPP.Originality/valueThis is one of the first studies to use the stimulus–organism–response (SOR) theory to investigate and contribute to extant knowledge and understanding of consumer behaviour relating to free-range eggs and specifically of consumer attitude towards purchasing and WTPPP for free-range eggs. This study offers practical implications for free-range egg farmers, retailers and policymakers.