bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methylthio-alkane reductases use nitrogenase metalloclusters for carbon-sulfur bond cleavage
Authors: Lago-Maciel Ana , Soares Jéssica C. , Zarzycki Jan , Buchanan Charles J. , Reif-Trauttmansdorff Tristan , Schmidt Frederik V. , Lometto Stefano , Paczia Nicole , Schuller Jan M. , Hansen D. Flemming , Heller Gabriella T. , Prinz Simone , Hochberg Georg K. A. , Pierik Antonio J. , Rebelein Johannes G. 
Published: October 2024

AbstractMethylthio-alkane reductases convert methylated sulfur compounds to methanethiol and small hydrocarbons, a process with important environmental and biotechnological implications. These enzymes are classified as nitrogenase-like enzymes, despite lacking the ability to convert dinitrogen to ammonia, raising fundamental questions about the factors controlling their activity and specificity. Here, we present the first molecular structure of the methylthio-alkane reductase, which reveals large metalloclusters, including the P-cluster and the [Fe8S9C]-cluster, previously only found in nitrogenases. Our findings suggest that distinct metallocluster coordination, surroundings, and substrate channels, determine the activity of these related metalloenzymes. This study provides new insights into nitrogen fixation, sulfur-compound reduction, and hydrocarbon production. We also shed light on the evolutionary history of P-cluster and [Fe8S9C]-cluster-containing reductases emerging prior to nitrogenases.
CRISPR associated enzymes are mislocalized to the cytoplasm in iPSC-derived neurons resulting in KRAB-specific degradation
Authors: Cajka Gregory , Liu Matthew , Shalem Ophir 
Published: October 2024

AbstractThe use of CRISPR-associated enzymes in iPSC-derived neurons for precise gene targeting and high-throughput gene perturbation screens offers great potential but presents unique challenges compared to dividing cell lines. CRISPRi screens in iPSC-derived neurons and glia have already been successful in relating gene function to neurological phenotypes; however, loss of dCas9-KRAB expression after differentiation has been observed by many labs and has been largely ascribed to transgene silencing after differentiation. Here, we investigated the expression levels of different CRISPR enzymes in iPSC and Ngn2-derived neurons using piggybac delivery. We found that the commonly used dCas9-KRAB (using theKOX1domain) displayed dramatic reduction in protein expression levels following neuronal differentiation, yet surprisingly, nCas9 constructs retained comparable protein expression between iPSCs and neurons. We further found that CRISPR constructs, primarily relying on the SV40 Nuclear Localization Signal (NLS), fail to efficiently localize to the nuclei of neurons, despite having robust nuclear levels in iPSCs, leading to KRAB-specific cytoplasmic degradation. By adding a neuronal-specific NLS, we were able to correct neuronal nuclear localization and protein expression, confirming the contribution of mislocalization to the instability of dCas9-KRAB in neurons. As the lack of nuclear localization can have a profound impact on editing and gene perturbation efficiency, we suggest further investigation across both cultured and in-vivo postmitotic cell models.
Impact of methicillin resistance on virulence factor expression inStaphylococcus aureus: Insights from gene expression profiling
Authors: Gharsallah Charfeddine , Ferjani Asma , Ghariani Mouna , Ferjani Sana , Kanzari Lamia , Rehaiem Amel , Fakhfakh Ahmed , Boutiba Ben Boubaker Ilhem 
Published: October 2024

AbstractStaphylococcus aureusis a major human pathogen causing various clinical infections and a leading cause of morbidity and mortality worldwide. S. aureus infections are problematic due to frequent antibiotic resistance, especially to methicillin. This study investigated 30 unduplicated S. aureus strains from clinical samples to establish a link between methicillin resistance and virulence factors.We detected and determined expression levels of the mecA gene, virulence genes (spdC, spA, atlA), and the RNAIII regulator using qRT-PCR. All virulence genes and the RNAIII regulator were detected in all strains. Phenotypic results showed only three strains (10%) were methicillin-resistant, while 12 (40%) carried the mecA gene. mecA-positive strains exhibited high expression of adhesion factors (spA) and biofilm formation factors (atlA), but low expression of the RNAIII regulator. The regulator’s expression was negatively correlated with mecA gene expression. Using a multilayer association network, we found a correlation between phenotypic methicillin resistance expression and mecA gene transcription inS. aureusmecA+. UnderstandingS. aureusvirulence determinants will help develop anti-virulence strategies, especially given the lack of an anti-S. aureusvaccine and rising antibiotic resistance.HighlightsComplex interplay between methicillin resistance and virulence:Our study unveils a complex interplay between methicillin resistance and the expression of virulence genes in Staphylococcus aureus clinical isolates.Phenotypic and molecular correlation:Phenotypic resistance to methicillin was observed in only 10% of the isolates, whereas 40% carried themecAgene. Molecular analysis revealed distinct expression patterns, notably elevatedspAandatlAexpression, inmecA+strains.Negative correlation withRNAIII:Our findings indicate a negative correlation betweenRNAIIIregulator expression and themecAgene in the same strains, shedding light on their regulatory relationship.Multilayer association network:Utilizing a multilayer association network, we established a correlation between phenotypic methicillin resistance andmecAgene transcription inS. aureus mecA+strains.
Amino acid competition shapesAcinetobacter baumanniigut carriage
Authors: Ren Xiaomei , Clark R. Mason , Bansah Dziedzom A. , Varner Elizabeth N. , Tiffany Connor R. , Jaswal Kanchan , Geary John H. , Todd Olivia A. , Winkelman Jonathan D. , Friedman Elliot S. , Zemel Babette S. , Wu Gary D. , Zackular Joseph P. , DePas William H. , Behnsen Judith , Palmer Lauren D. 
Published: October 2024

SummaryAntimicrobial resistance is an urgent threat to human health. Asymptomatic colonization is often critical for persistence of antimicrobial-resistant pathogens. Gut colonization by the antimicrobial-resistant priority pathogenAcinetobacter baumanniiis associated with increased risk of clinical infection. Ecological factors shapingA. baumanniigut colonization remain unclear. Here we show thatA. baumanniiand other pathogenicAcinetobacterevolved to utilize the amino acid ornithine, a non- preferred carbon source.A. baumanniiutilizes ornithine to compete with the resident microbiota and persist in the gut in mice. Supplemental dietary ornithine promotes long-term fecal shedding ofA. baumannii. By contrast, supplementation of a preferred carbon source—monosodium glutamate (MSG)— abolishes the requirement forA. baumanniiornithine catabolism. Additionally, we report evidence for diet promotingA. baumanniigut carriage in humans. Together, these results highlight that evolution of ornithine catabolism allowsA. baumanniito compete with the microbiota in the gut, a reservoir for pathogen spread.
Microglia regulate GABAergic neurogenesis in prenatal human brain through IGF1
Authors: Yu Diankun , Jain Samhita , Wangzhou Andi , De Florencio Stacy , Zhu Beika , Kim Jae Yeon , Choi Jennifer Ja-Yoon , Paredes Mercedes F , Nowakowski Tomasz J , Huang Eric J , Piao Xianhua 
Published: October 2024

AbstractGABAergic neurons are an essential cellular component of neural circuits. Their abundance and diversity have enlarged significantly in the human brain, contributing to the expanded cognitive capacity of humans. However, the developmental mechanism of the extended production of GABAergic neurons in the human brain remains elusive. Here, we use single-cell transcriptomics, bioinformatics, and histological analyses to uncover microglial regulation of the sustained proliferation of GABAergic progenitors and neuroblasts in the human medial ganglionic eminence (hMGE). We show that insulin-like growth factor 1 (IGF1) and its receptor IGR1R as the top ligand-receptor pair underlying microglia-progenitor communication in the prenatal human brain. Using our newly developed neuroimmune hMGE organoids, which mimics hMGE cytoarchitecture and developmental trajectory, we demonstrate that microglia-derived IGF1 promotes progenitor proliferation and the production of GABAergic neurons. Conversely, IGF1-neutralizing antibodies andIGF1knockout human embryonic stem cells (hESC)-induced microglia (iMG) completely abolished iMG-mediated progenitor proliferation. Together, these findings reveal a previously unappreciated role of microglia-derived IGF1 in promoting proliferation of neural progenitors and the development of GABAergic neurons.
Factors Promoting Lipopolysaccharide Uptake by Synthetic Lipid Droplets
Authors: Arnob Assame , Gairola Anirudh , Clayton Hannah , Jayaraman Arul , Wu Hung-Jen 
Published: October 2024

ABSTRACTLipoproteins are essential in removing lipopolysaccharide (LPS) from blood during bacterial inflammation. The physicochemical properties of lipoproteins and environmental factors can impact LPS uptake. In this work, synthetic lipid droplets containing triglycerides, cholesterols, and phospholipids, were prepared to mimic lipoproteins. The physicochemical properties of these lipid droplets, such as charges, sizes, and lipid compositions, were altered to understand the underlying factors affecting LPS uptake. The amphiphilic LPS could spontaneously adsorb on the surface of lipid droplets without lipopolysaccharide binding protein (LBP); however, the presence of LBP can increase LPS uptake. The positively charged lipid droplets also enhance the uptake of negatively charged LPS. Most interestingly, the LPS uptake highly depends on the concentrations of Ca2+near the physiological conditions, but the impact of Mg2+ions was not significant. The increase of Ca2+ions can improve LPS uptake by lipid droplets; this result suggested that Ca2+may play an essential role in LPS clearance. Since septic shock patients typically suffer from hypocalcemia and low levels of lipoproteins, the supplementation of Ca2+ions along with synthetic lipoproteins may be a potential treatment for severe sepsis.
Cultivation conditions of leafy vegetables determine phyllosphere bacterial community structures and ultimately affect growth ofL. monocytogenespost-harvest
Authors: Culliney Paul , Schmalenberger Achim 
Published: October 2024

AbstractCultivation conditions including plant species, variety, cultivation method and seasonality are all at least co-factors of epiphytic growth ofL. monocytogenes.Meanwhile, phyllosphere associated bacteria were found to influence colonisation of invading pathogens. Thus, the main objective of this study was to determine whether cultivation conditions are factors in the development of the bacterial phyllosphere community on leafy vegetables which consequently influencesL. monocytogenesgrowth. Indeed, this study revealed that vegetable cultivation condition was a more influential determinant of phyllosphere development than plant species. Of the identified phyllosphere associated bacteria presence ofPseudomonadaceaehad a positive correlation withL. monocytogenespopulations on all tested produce. Yet,Pseudomonadaceaecontent appeared to be more important forL. monocytogenesgrowth on spinach F1 Trumpet. From day 7 to 9 of storage,Pseudomonadaceaeincreases on open field spinach F1 Trumpet were associated withL. monocytogenes’largest increase (0.94 log10cfu g-1), whereasPseudomonadaceaecontent decreased for polytunnel spinach F1 Trumpet and the correspondingL. monocytogenespopulations remained unchanged.Carnobacteriaceaewere present on spinach F1 Trumpet from polytunnel but not on other spinach produce with higher associatedL. monocytogenesgrowth.Pectobacteriaceae(genusDickeya) increased for spinach F1 Trumpet polytunnel but decreased for other spinach produce with lower associatedL. monocytogenesgrowth. Similarly, polytunnel rocket Esmee had an increasing relative abundance ofPectobacteriaceaewhereas it remained constant for polytunnel rocket Buzz. Compared to summer spinach F1 Trumpet produce, winter produce had significantly greaterStreptococcaceaecontent and was correlated with a decrease inL. monocytogenesgrowth. Finally, higher phyllosphere alpha diversity putatively limitedL. monocytogenesgrowth. Ultimately, this study revealed that cultivation conditions determine bacterial phyllosphere community structure which consequently influencesL. monocytogenesgrowth.
Identification and mitigation of blood’s interference with the antimicrobial activity of AgNbO3particles
Authors: Talebpour Cyrus , Fani Fereshteh , Ouellette Marc , Fairfax Marilynn , Alamdari Houshang , Salimnia Hossein 
Published: October 2024

AbstractThe detrimental impact of blood on the antimicrobial activity of AgNbO3particles was identified and investigated. It was observed that the impact is more severe in the case of lysed blood and also operates in the case of commonly used silver salt, AgNO3. The inhibition was shown to be due to hemoglobin, but unrelated to the heme moiety. In an attempt to find additives to mitigate the inhibitory effect of hemoglobin, iron ions and the chelating agent, K2EDTA, were selected as promising candidates. Including iron on the particles was shown to have a marginal effect, but supplying the medium with K2EDTA, an agent preventing clotting of blood samples, fully countered the deleterious impact of hemoglobin on AgNbO3activity. These findings may be relevant for adapting the silver compounds to applications such as wound dressings, where silver’s antimicrobial action would have to take place in a medium containing blood.
The role of MEGF10 in myoblast fusion and hypertrophic response to overload of skeletal muscle
Authors: Richardson Louise , Hughes Ruth , Johnson Colin A , Egginton Stuart , Peckham Michelle 
Published: October 2024

AbstractBiallelic mutations in multiple EGF domain protein 10 (MEGF10) gene cause EMARDD (early myopathy, areflexia, respiratory distress and dysphagia) in humans, a severe recessive myopathy, associated with reduced numbers of PAX7 positive satellite cells. To better understand the role of MEGF10 in satellite cells, we overexpressed human MEGF10 in mouseH-2kb-tsA58 myoblasts and found that it inhibited fusion. Addition of purified extracellular domains of human MEGF10, with (ECD) or without (EGF) the N-terminal EMI domain toH-2kb-tsA58 myoblasts, showed that the ECD was more effective at reducing myoblast adhesion and fusion by day 7 of differentiation, yet promoted adhesion of myoblasts to non-adhesive surfaces, highlighting the importance of the EMI domain in these behaviours. We additionally tested the role of Megf10in vivousing transgenic mice with reduced (Megf10+/-) or no (Megf10-/-) Megf10. We found that the extensor digitorum longus muscle had fewer Pax7 positive satellite cell nuclei and was less able to undergo hypertrophy in response to muscle overload concomitant with a lower level of satellite cell activation. Taken together, our data suggest that MEGF10 may promote satellite cell adhesion and survival and prevent premature fusion helping to explain its role in EMARDD.
Neutralizing human monoclonal antibodies that target the PcrV component of the Type III Secretion System ofPseudomonas aeruginosaact through distinct mechanisms
Authors: Desveaux Jean-Mathieu , Faudry Eric , Contreras-Martel Carlos , Cretin François , Dergan-Dylon Leonardo Sebastian , Amen Axelle , Bally Isabelle , Tardivy-Casemajor Victor , Chenavier Fabien , Fouquenet Delphine , Caspar Yvan , Attrée Ina , Dessen Andréa , Poignard Pascal 
Published: October 2024

ABSTRACTPseudomonas aeruginosais a major human opportunistic pathogen associated with a high incidence of multi-drug resistance. The antibody-based blockade ofP. aeruginosavirulence factors represents a promising alternative strategy to mitigate its infectivity. In this study, we employed single B cell sorting to isolate, from cystic fibrosis patients, human monoclonal antibodies (mAbs) targeting proteins from theP. aeruginosaType 3 Secretion System (T3SS) and characterized a panel of mAbs directed at PscF and PcrV. Among those, two mAbs, P5B3 and P3D6, that bind to the injectisome tip protein PcrV, exhibited T3SS blocking activity. We solved the crystal structure of the P3D6 Fab-PcrV complex, which revealed that the Ab binds to the C-terminal region of PcrV. Further, we compared the T3SS-blocking activity of three PcrV-targeting mAbs, including two from previous independent studies, using two distinct assays to evaluate pore formation and toxin injection. We conducted a mechanistic and structural analysis of their modes of action through modeling based on the known structure of a functional homolog, SipD fromSalmonella typhimurium. The analysis suggests that anti-PcrV mAbs may act through different mechanisms, ranging from preventing PcrV oligomerization to disrupting PcrV’s scaffolding function, thereby inhibiting the assembly and function of the translocon pore. Our findings provide additional evidence that T3SS-targeting Abs, some capable of inhibiting virulence, are elicited inP. aeruginosa-infected patients. The results offer deeper insights into PcrV recognition by mAbs and their associated mechanisms of action, helping to identify which Abs are more likely to be therapeutically useful based on their mode of action and potency. This paves the way for developing effective alternatives to traditional antibiotics in the fight against this resilient pathogen.
In-SituStructure and Topography of AMPA Receptor Scaffolding Complexes Visualized by CryoET
Authors: Held Richard G. , Liang Jiahao , Esquivies Luis , Khan Yousuf A. , Wang Chuchu , Azubel Maia , Brunger Axel T. 
Published: October 2024

AbstractMost synapses in the brain transmit information by the presynaptic release of vesicular glutamate, driving postsynaptic depolarization through AMPA-type glutamate receptors (AMPARs). The nanometer-scale topography of synaptic AMPARs regulates response amplitude by controlling the number of receptors activated by synaptic vesicle fusion. The mechanisms controlling AMPAR topography and their interactions with postsynaptic scaffolding proteins are unclear, as is the spatial relationship between AMPARs and synaptic vesicles. Here, we used cryo-electron tomography to map the molecular topography of AMPARs and visualize theirin-situstructure. Clustered AMPARs form structured complexes with postsynaptic scaffolding proteins resolved by sub-tomogram averaging. Sub-synaptic topography mapping reveals the presence of AMPAR nanoclusters with exclusion zones beneath synaptic vesicles. Our molecular-resolution maps visualize the predominant information transfer path in the nervous system.
Operational excellence in online food delivery service: the role of food biosafety measures
Authors: Chinelato Flavia Braga , Hoyos Vallejo Carlos Arturo 
Published: October 2024

PurposeThis study explores how food biosafety measures (FBM), electronic service quality and product quality influence consumer satisfaction and loyalty in the online food delivery service (OFDS) sector. It also integrates the technology acceptance model (TAM) and the theory of planned behaviour (TPB) to form a robust framework for assessing consumer behaviours and providing insights for this sector.Design/methodology/approachData from 877 Colombian urban consumers were collected. The proposed theoretical model was tested using structural equation modelling (SEM) in the SEMinR package of the R program (an open-source programming language).FindingsThe results reveal that food biosafety measures and product quality are the most essential factors for OFDS consumers. Besides, food biosafety measures strongly affect product and e-service quality, which in turn significantly and directly impact consumer satisfaction and loyalty. This means that it is necessary to consider both visible actions strongly related to product quality and invisible actions that highlight the role of e-service quality in ensuring operational excellence.Practical implicationsTo maintain customer satisfaction and loyalty, OFDS managers should consider first working with restaurants that practice high food biosafety measures so that the order leaves the restaurant in good condition. However, OFDS should maintain these measures to ensure operational excellence from the order on the platform until delivery to the end consumer.Originality/valueThis innovative study demonstrates how FBMs directly affect perceptions of service, product quality, satisfaction and loyalty. This goes beyond traditional findings suggesting that food biosafety measures' influence is only indirect and mediated by satisfaction.
Teacher noticing within the context of lesson study: a systematic review and prospective trends
Authors: Yun Hange , Zhang Qiaoping , Cao Wei , Zhang Xiaolei 
Published: October 2024

PurposeTeacher noticing is a critical aspect of teaching competence that has garnered significant scholarly attention. This systematic review aims to comprehensively analyze the integration of teacher noticing into lesson study, exploring how different stages of lesson study influence the development of teacher noticing.Design/methodology/approachThis article systematically reviews 15 empirical studies on teacher noticing within the context of lesson study, focusing on research design, subjects, methods, theoretical frameworks and the specific impact of different stages of lesson study on teacher noticing.FindingsThe review reveals a geographical concentration of studies in Western countries, particularly in the United States, with a relative scarcity of research in East Asian contexts. Most studies focus on pre-service teachers, employ qualitative methods and are grounded in Van Es’s (2011) Learning to Notice framework. The findings indicate that different stages of lesson study significantly influence teacher noticing, particularly in the planning, teaching and reflection stages, where shifts in focus and depth of noticing are evident.Research limitations/implicationsThis paper explores how various lesson study stages impact teacher noticing development. It offers future research directions and calls for more cross-cultural studies. Certain activities within classroom research may restrict attention development, particularly when these activities fail to encourage in-depth cognitive analysis across all stages sufficiently. Future research should explore how to avoid these limitations in the classroom research process and design more effective strategies to support deep observation and analysis by teachers at each stage. In the reflection stage of classroom research, certain factors may restrict the focus on student thinking.Practical implicationsBy synthesizing the existing research into a comprehensive narrative, we provide an essential foundation for future studies on teacher noticing within lesson study contexts. This work not only charts the historical development of the field but also encourages more profound and actionable research engagement with the nuanced processes of teacher observation and reflection during lesson studies.Originality/valueThis paper explores how various lesson study stages impact teacher noticing development. It offers future research directions and calls for more cross-cultural studies and a combination of quantitative and qualitative methods to fully understand the effects of lesson studies on teacher noticing.