bluuebunny/crossref_metadata_2025_split huggingface dataset:
APEX2 proximity labeling of RNA in bacteria
Authors: Yassine Hadi , Schrader Jared M. 
Published: September 2024

SummaryRapid spatially controlled methods are needed to investigate RNA localization in bacterial cells. APEX2 proximity labeling was shown to be adaptable to rapid RNA labeling in eukaryotic cells, and through the fusion of APEX2 to different proteins targeted to different subcellular locations, has been useful to identify RNA localization in these cells. Therefore, we adapted APEX2 proximity labeling of RNA to bacterial cells by generating an APEX2 fusion to the RNase E gene, which is necessary and sufficient for BR-body formation. APEX2 fusion is minimally perturbative and RNA can be rapidly labeled on the sub-minute timescale with Alkyne-Phenol, outpacing the rapid speed of mRNA decay in bacteria. Alkyne-Phenol provides flexibility in the overall downstream application with copper catalyzed click-chemistry for downstream applications, such as fluorescent dyeazides or biotin-azides for purification. Altogether, APEX2 proximity labeling of RNA provides a useful method for studying RNA localization in bacteria.MotivationStudies over the past several years have shown that distinct RNAs can be targeted to subcellular locations in bacterial cells. The ability to investigate localized RNAs in bacteria is currently limited to imaging-based approaches or to laborious procedures to isolate ribonucleoprotein complexes by grad-seq, HITS-CLIP, or Rloc-seq. However, a major challenge in studying mRNA localization in bacterial cells is that bacterial mRNAs typically last for only a few minutes in the cell, while experiments to investigate their localization or interaction partners can take much longer. Therefore, rapid methods of studying RNA localization are needed to bridge this technical challenge.Highlights□APEX2 proximity labeling can be applied to RNA in bacteria□APEX2 RNA labeling reactions occur on the sub-minute timescale.□APEX2 workflow requires less material and time than current methods.□Alkyne-Phenol APEX2 substrate provides flexibility with click-chemistry.
Systematic genome-guided discovery of antagonistic interactions between archaea and bacteria
Authors: Strock Romain , Soo Valerie WC , Hocher Antoine , Warnecke Tobias 
Published: September 2024

ABSTRACTThe social life of archaea is poorly understood. In particular, even though competition and conflict are common themes in microbial communities, there is scant evidence documenting antagonistic interactions between archaea and their abundant prokaryotic brethren: bacteria. Do archaea specifically target bacteria for destruction? If so, what molecular weaponry do they use? Here, we present an approach to infer antagonistic interactions between archaea and bacteria from genome sequence. We show that a large and diverse set of archaea encode peptidoglycan hydrolases, enzymes that recognize and cleave a structure – peptidoglycan – that is a ubiquitous component of bacterial cell walls but absent from archaea. We predict the bacterial targets of archaeal peptidoglycan hydrolases using a structural homology approach and demonstrate that the predicted target bacteria tend to inhabit a similar niche to the archaeal producer, indicative of ecologically relevant interactions. Using a heterologous expression system, we demonstrate that two peptidoglycan hydrolases from the halophilic archaeaonHalogranum salariumB-1 kill the halophilic bacteriumHalalkalibacterium halodurans,a predicted target, and do so in a manner consistent with peptidoglycan hydrolase activity. Our results suggest that, even though the tools and rules of engagement remain largely unknown, archaeal-bacterial conflicts are likely common, and we present a roadmap for the discovery of additional antagonistic interactions between these two domains of life. Our work has implications for understanding mixed microbial communities that include archaea and suggests that archaea might represent a large untapped reservoir of novel antibacterials.
DNA replication dynamics are associated with genome composition inPlasmodiumspecies
Authors: Totañes Francis Isidore Garcia , Chapman Sarah E. , Rai Subash Kumar , Jones Mathew J. K. , Boemo Michael A. , Merrick Catherine J. 
Published: September 2024

ABSTRACTPlasmodiumspecies have variable genome compositions: many have an A/T-content of at least 80% while others are similar in composition to human cells. Here, we made a direct comparison of DNA replication dynamics in twoPlasmodiumspecies whose genomes differ by ∼20% A/T-content. This yielded fundamental insights into how DNA composition may affect replication. The highly A/T-biased genome ofP. falciparumshowed unusual replication dynamics that were not observed in the more balancedP. knowlesi– which had dynamics more like those of human cell lines. We observed that replication forks moved 50% slower inP. falciparumthan inP. knowlesi.InP. falciparum, replication forks slowed down over the course of S-phase whereas inP. knowlesi, fork speed increased as in human cells. Furthermore, in bothP. knowlesiand human cells, replication forks were strikingly slowed by sequences of particularly high A/T-bias, but inP. falciparum, although replication forks were inherently slow, they were not particularly slow in such biased sequences. Thus, the replisome ofP. falciparummay have evolved alongside its extremely biased genome, making it unusually robust to sequence bias. Since several antimalarial drugs act to stall DNA replication, this study may have implications for the effectiveness of, and development of, antimalarial therapies.
Craters on the melanoma surface facilitate tumor-immune interactions and demonstrate pathologic response to checkpoint blockade in humans
Authors: Ludin Aya , Stirtz Georgia L. , Tal Asaf , Nirmal Ajit J. , Besson Naomi , Jones Stephanie M. , Pfaff Kathleen L. , Manos Michael , Liu Sophia , Barrera Irving , Gong Qiyu , Rodrigues Cecilia Pessoa , Sahu Aditi , Jerison Elizabeth , Alessi Joao V. , Ricciuti Biagio , Richardson Douglas S. , Weiss Jodi D. , Moreau Hadley M. , Stanhope Meredith E. , Afeyan Alexander B. , Sefton James , McCall Wyatt D. , Formato Emily , Yang Song , Zhou Yi , Hoytema van Konijnenburg David P. , Cole Hannah L. , Cordova Miguel , Deng Liang , Rajadhyaksha Milind , Quake Stephen R. , Awad Mark M. , Chen Fei , Sorger Peter K. , Hodi F. Stephen , Rodig Scott J. , Murphy George F. , Zon Leonard I. 
Published: September 2024

SummaryImmunotherapy leads to cancer eradication despite the tumor’s immunosuppressive environment. Here, we used extended long-term in-vivo imaging and high-resolution spatial transcriptomics of endogenous melanoma in zebrafish, and multiplex imaging of human melanoma, to identify domains that facilitate immune response during immunotherapy. We identified crater-shaped pockets at the margins of zebrafish and human melanoma, rich with beta-2 microglobulin (B2M) and antigen recognition molecules. The craters harbor the highest density of CD8+T cells in the tumor. In zebrafish, CD8+T cells formed prolonged interactions with melanoma cells within craters, characteristic of antigen recognition. Following immunostimulatory treatment, the craters enlarged and became the major site of activated CD8+T cell accumulation and tumor killing that was B2M dependent. In humans, craters predicted immune response to ICB therapy, showing response better than high T cell infiltration. This marks craters as potential new diagnostic tool for immunotherapy success and targets to enhance ICB response.
Glycoinformatic profiling of label-free intact heparan sulfate oligosaccharides
Authors: Maciej-Hulme Marissa L. , Kim Jandi , Roberts Elijah T. , Zhang Yiqing , van der Velden Anouk , den Braanker Dirk , Yanginlar Cansu , de Graaf Mark , Rabelink Ton , van den Berg Bernard , van Omen Ellen , Maas Rutger , van de Logt Anne-Els , Amster I. Jonathan , van der Vlag Johan 
Published: September 2024

AbstractHeparan sulfates (HS) are a group of heterogenous linear, sulfated polysaccharides that play a role in in health and many diseases including cancer, cardiovascular, and kidney diseases. The structural variety of HS has greatly challenged the development and utility of HS analytics, particularly for native structures, leaving a significant gap in HS technologies for clinical application. Mass spectrometry (MS)-based profiling with bioinformatics offers a top-down approach that can retain variety in large data sets. Using healthy human plasmas, we developed an MS glycoprofiling approach for native HS oligosaccharides, which retains the structural complexity of each individual HS chain and generates an HS ‘index’ (or Heparan-ome) for each patient. As a proof of concept, analysis of 56 plasma samples ranging from 6 groups of kidney disease patients revealed a new subset cluster (20%, 4/20) of membranous glomerulopathy (MG) patients with distinct HS profiles, highlighting the potential of HS glycoprofiling as a powerful new approach into clinical practice, which warrants future development into clinical diagnostics of kidney and other diseases.Graphical abstract
Cell attachment and tail contraction ofS. aureusphage phi812
Authors: Bíňovský Ján , Šiborová Marta , Nováček Jiří , Bárdy Pavol , Baška Roman , Škubník Karel , Botka Tibor , Benešík Martin , Pantůček Roman , Tripsianes Konstantinos , Plevka Pavel 
Published: September 2024

AbstractPhages with contractile tails employ elaborate strategies to penetrate bacterial cell walls and deliver their genomes into the host cytoplasm. Most tailed phages that have been structurally characterized to date infect Gram-negative bacteria, but those targeting Gram-positive bacteria, many of which are important human pathogens, are less well understood. Here, we show that the baseplate of phage phi812, which infects Gram-positive Staphylococcus aureus, is formed of a core, wedge modules, and baseplate arms carrying receptor-binding proteins type 1 and 2 and tripod complexes. Upon binding to the S. aureus cell wall, the symmetry of the baseplate transforms from threefold to sixfold. The conformational changes propagate from the outer edge to the core of the baseplate. The receptor-binding proteins re-orient to bind to the host cell. Subsequently, central spike proteins degrade teichoic acids. The conformational changes to the tripod complexes trigger the release of the central spike and weld proteins from the baseplate, which enables the hub proteins to cleave cell wall peptidoglycan and facilitate penetration of the tail tube tip through the cell membrane. Changes in the positions of baseplate arms are transmitted through wedge modules to tail sheath initiator proteins. The ring formed by the tail sheath initiator proteins expands in diameter and thus triggers the contraction of the tail sheath. The tail sheath of phi812, which can bend up to 90° in its native conformation, shortens from 200 to 96 nm, which pushes the tail tube 10-30 nm into the cytoplasm, depending on the local thickness of the S. aureus cell wall. Our results provide the foundation for engineering phi812 to target specific S. aureus strains.
Kinetic regulation of kinesin’s two motor domains coordinates its stepping along microtubules
Authors: Niitani Yamato , Matsuzaki Kohei , Jonsson Erik , Vale Ronald D. , Tomishige Michio 
Published: September 2024

ABSTRACTThe two identical motor domains (heads) of dimeric kinesin-1 move in a hand-over-hand process along a microtubule, coordinating their ATPase cycles such that each ATP hydrolysis is tightly coupled to a step and enabling the motor to take many steps without dissociating. The neck linker, a structural element that connects the two heads, has been shown to be essential for the head-head coordination; however, which kinetic step(s) in the chemomechanical cycle is “gated” by the neck linker remains unresolved. Here, we employed pre-steady state kinetics and single molecule assays to investigate how the neck linker conformation affects kinesin’s motility cycle. We show that the backward-pointing configuration of the neck linker in the front kinesin head confers higher affinity for microtubules, but does not change ATP binding and dissociation rates. In contrast, the forward-pointing configuration of the neck linker in the rear kinesin head decreases the ATP dissociation rate but has little effect on microtubule dissociation. In combination, these conformation-specific effects of the neck linker favor ATP hydrolysis and dissociation of the rear head prior to microtubule detachment of the front head, thereby providing a kinetic explanation for the coordinated walking mechanism of dimeric kinesin.
Clustering large-scale biomedical data to model dynamic accumulation processes in disease progression and anti-microbial resistance evolution
Authors: Dauda Kazeem A. , Aga Olav N. L. , Johnston Iain G. 
Published: September 2024

AbstractAccumulation modelling uses machine learning to discover the dynamics by which systems acquire discrete features over time. Many systems of biomedical interest show such dynamics: from bacteria acquiring resistances to sets of drugs, to patients acquiring symptoms during the course of progressive disease. Existing approaches for accumulation modelling are typically limited either in the number of features they consider or their ability to characterise interactions between these features – a limitation for the large-scale genetic and/or phenotypic datasets often found in modern biomedical applications. Here, we demonstrate how clustering can make such large-scale datasets tractable for powerful accumulation modelling approaches. Clustering resolves issues of sparsity and high dimensionality in datasets but complicates the intepretation of the inferred dynamics, especially if observations are not independent. Focussing on hypercubic hidden Markov models (HyperHMM), we introduce several approaches for interpreting, estimating, and bounding the results of the dynamics in these cases and show how biomedical insight can be gained in such cases. We demonstrate this ‘Cluster-based HyperHMM’ (CHyperHMM) pipeline for synthetic data, clinical data on disease progression in severe malaria, and genomic data for anti-microbial resistance evolution inKlebsiella pneumoniae, reflecting two global health threats.
Vibrational resonance in bichromatically excited diatomic molecules in a shifted molecular potential
Authors: Abamba O. G. , Kolebaje O. T. , Vincent U. E. , McClintock P. V. E. 
Published: September 2024

For bichromatically excited diatomic molecules modeled in a shifted Tietz-Wei molecular potential, we demonstrate the occurrence of vibrational resonance (VR) when a saddle-node (SN) bifurcation takes place and its nonoccurrence in the absence of an SN bifurcation. We have examined the VR phenomenon and its connection with SN bifurcation for eight diatomic molecules, namely, H2, N2, Cl2, I2, O2, HF, CO, and NO, consisting of homogeneous, heterogenous, and halogen molecules. We demonstrate that each of them vibrates at a distinct resonant frequency but with a spread in frequency. The high-frequency amplitude at which VR occurs corresponds to the SN-bifurcation point. We validate our analytic results by numerical simulations and show that the homonuclear halogens respond only weakly to bichromatic fields, which may perhaps be linked to their absence of SN bifurcation.

Published by the American Physical Society
2024
The impact of social network and resource endowment of smallholders on sustainable apple production
Authors: Cui Shilei , Pathera Donasius , Li Yajuan , Jiao Xiaoqiang 
Published: September 2024

PurposeSmallholders are essential in ensuring food security; however, smallholder-dominated food production often involves high resource-environmental costs. This study analyzed the factors that differentiate horticultural practices, willingness to adopt technology and social networks between optimized practices (OPT) and farmer practices (FP) to provide localized and systematic solutions for the sustainable apple production.Design/methodology/approachTo explore the approach of smallholder-dominated sustainable apple production, 257 apple producers in the Bohai Bay region, a major apple planting area in China, were investigated. Life cycle assessment (LCA), emergy analysis and social network analysis methods were used for evaluation.FindingsThe results showed that the net economic profit and emergy sustainability index (ESI) in OPT was 15.8 × 104 RMB·ha-1 and 1.2, respectively, which were 126.9 and 128.0% higher than FP. In contrast, greenhouse gas (GHG) emissions under OPT was 29.3% lower than those under FP. OPT has a higher percentage of adoption of scientific fertilizer application and water-saving irrigation technologies compared to FP. OPT has strong learning abilities, more social resources (such as technical training and sharing technical experience with others) and connections with stakeholders in the apple supply chain. Optimizing smallholders' social capital, willingness to adopt technology, behavioral willingness and technological awareness can promote sustainable apple production.Originality/valueConsidering the horticultural practices employed by smallholders in conjunction with their social networks, these factors contributed to the transition of smallholder-led apple production toward sustainability. The findings provided viable options and a theoretical basis for smallholder-dominated crop production to move toward sustainability, with significant implications for policymakers.
Do children study longer depending on their parents’ level of engagement? An analysis of factors related to Brazilian students’ engagement
Authors: Macana Esmeralda Correa , Mirolli Thamires Zaboto , Silva Ana Luíza Farage , Lazaretti Lauana Rossetto , Bianchi Lorenzo Luiz , Frio Gustavo Saraiva , França Marco Tulio Aniceto 
Published: September 2024

PurposeThe purpose of this article is to investigate factors related to the time students spent on remote activities during the coronavirus (COVID-19) pandemic in 2020. Specifically, it analyzes whether the school’s relationship with the family and the guardians’ support are associated with longer study times for children and youth.Design/methodology/approachThis was performed using an ordered logit model on data from two waves of the survey Remote Education in the Perspective of Students and Their Families (PENP) with a nationally and regionally representative sample of Brazilian public school students.FindingsResults show the importance of contact between the school and the family and, to a greater extent, the direct support of parents or guardians. The odds of learners spending more hours studying increase 36% when schools provide guidance for parents and guardians; in turn, when they provide support for students during activities, these odds increase 144%.Originality/valueMoreover, students spend more time doing school activities in the later years of elementary school, high school and when they attend a state school.
Mentoring research projects in the Croatian higher education document framework
Authors: Kušević Barbara 
Published: September 2024

PurposeApproaching mentoring from the theoretical tradition of continental pedagogy and contrasting it to the neoliberal organization of the academy, this paper aims to analyze how the Croatian higher education document framework constructs mentoring graduate and postgraduate students' research projects.Design/methodology/approachThe analysis of 50 national- and university-level documents, which were coded using an adapted strategy described by Saldaña (2014), was guided by the following research questions. 1. Which elements of the mentor’s activity in guiding the research projects of graduate and postgraduate students are addressed by the relevant Croatian higher education documents? 2. Which elements of the graduate and postgraduate students’ activity in conducting research projects are addressed? 3. Which structural dimensions of mentoring these research projects are addressed?FindingsThe results point to the construction of mentoring as a pedagogical relationship based on guidance, support and dialog and also signal the processes of quantification of education and responsibilization of individuals.Practical implicationsThe results can be used in the critical revision of the documents as well as in supporting mentors in their professional roles.Originality/valueThis is the first analysis of the Croatian higher education document framework focused on mentoring students’ research projects.
Antecedents of effectuation and causation in SMEs from emerging markets: the role of CEO temporal focus
Authors: Kozachenko Ekaterina , Shirokova Galina , Bodolica Virginia 
Published: September 2024

Purpose
Previous studies considered effectuation and causation as alternative decision-making strategies used by entrepreneurs to navigate uncertainty, having various individual- and firm-level antecedents. This study aims to broaden our understanding of individual-level antecedents by examining the role of Chief Executive Officer (CEO) temporal focus in decision-making processes in small and medium-sized enterprises (SMEs).

Design/methodology/approach
Based on a multiple case study research design, the authors empirically analyse 16 Russian SMEs to uncover how the CEO temporal focus relates to the choice of effectuation/causation strategies under uncertainty.

Findings
CEOs with past orientation tend to adopt causation, future-oriented CEOs adhere to effectuation, while present-focused CEOs rely on both decision-making strategies (i.e. ambidexterity). Prior crisis-related experience is the underlying mechanism behind the relationship between CEO temporal orientation and effectuation/causation strategies. The authors formulate several propositions that may be tested in future studies in the field.

Originality/value
The contribution of this study consists in uncovering a new individual-level antecedent of effectuation/causation under uncertainty (i.e. CEO temporal focus) and suggesting that prior crisis experience acts as a mechanism underlying this relationship. The authors advance the strategic leadership theory by underscoring the CEO’s role in decision-making processes in SMEs.
Impact of digital financial inclusion on economic growth: a study on Bangladesh
Authors: Rahman Syed Mohammad Khaled , Chowdhury Mohammad Ashraful Ferdous , Sristi Nabila Rezwana 
Published: September 2024

PurposeThe purpose of the study is to find out the impact of Digital Financial Inclusion (DFI) on economic growth [(Industrial Production Index (INDP)] of Bangladesh.Design/methodology/approachUsing the monthly data over the period 2018 M12 to 2021 M12, this study applied the Auto-regressive Distributed Lag (ARDL) model to assess the effect of DFI indicators on INDP. The secondary data was collected from the Bangladesh Bank and CEIC Global Economic Data.FindingsThe study found that the majority of DFI indicators are positively associated with INDP. From the short-run ARDL, it is seen that one unit positive increase in Point of Sales Transactions (POST) can increase the INDP by 0.055 units. From the long-run ARDL, it is seen that POST and e-commerce transactions (ECOMT) have a significant positive impact, while Automated Teller Machine Transactions (ATMT) have a significant negative effect on INDP. One unit increase in POST and ECOMT increases INDP by 0.13544 and 0.11611 units, respectively.Research limitations/implicationsDuring the era of the fourth industrial revolution, the findings will be beneficial for policymakers, financial technology service providers, manufacturers, consumers, corporations and investors as they pave the way for a more inclusive approach to financial transactions for economic growth.Originality/valueThe study’s novelty is that it explored the influential DFI indicators and shed light on both short-run and long-run relationships between the indicators and macro-economy from the context of a developing nation.Peer reviewThe peer review history for this article is available at: https://publons.com/publon/10.1108/IJSE-04-2023-0306