bluuebunny/crossref_metadata_2025_split huggingface dataset:
Demonstration of Bioplastic Production from CO2and Formate using the Reductive Glycine Pathway inE. coli
Authors: Fedorova Daria , Ben-Nissan Roee , Milshtein Eliya , Jona Ghil , Dezorella Nili , Feiguelman Gil , Fedorov Rostislav , Gomaa Aya , Lindner Ariel B. , Noor Elad , Milo Ron 
Published: December 2023

AbstractThere is a strong need to develop technologies that reduce anthropogenic pollution and the dependence on nonrenewable Earth resources. One way of doing so is by harnessing biological systems for replacing the production of fossil-fuel based goods with low-environmental-impact alternatives. Recently, progress was made in engineering the model organismE. colito grow using CO2and formate as its only carbon and energy sources using the reductive glycine pathway (rGlyP). Here, we use this engineered strain ofE. colias a host system for the production of polyhydroxybutyrate (PHB), a biologically derived and biodegradable plastic. We confirmed the production of PHB in this strain using Nile red fluorescent microscopy, transmission electron microscopy, and GC measurements. Since formate can be efficiently generated from CO2by electrochemical reduction using renewable energy sources, this study serves as a proof of concept for the emerging field of electro-bioproduction.
Multi-Modal Mass Spectrometry Identifies a Conserved Protective Epitope inS. pyogenesStreptolysin O
Authors: Tang Di , Gueto-Tettay Carlos , Hjortswang Elisabeth , Ströbaek Joel , Ekström Simon , Happonen Lotta , Malmström Lars , Malmström Johan 
Published: December 2023

AbstractAn important element of antibody-guided vaccine design is the use of neutralizing/opsonic monoclonal antibodies to define protective epitopes in their native three-dimensional conformation. Here, we demonstrate a multi-modal mass spectrometry-based strategy for in-depth characterization of antigen-antibody complexes to enable the identification of protective epitopes using the cytolytic exotoxin Streptolysin O (SLO) fromStreptococcus pyogenesas a showcase. We first discovered a monoclonal antibody with an undisclosed sequence capable of neutralizing SLO-mediated cytolysis. The amino acid sequence of both the antibody light and the heavy chain was determined using mass spectrometry-basedde novosequencing, followed by chemical crosslinking mass spectrometry to generate distance constraints between the antibody fragment antigen-binding region and SLO. Subsequent integrative computational modeling revealed a discontinuous epitope located in Domain 3 of SLO that was experimentally validated by hydrogen-deuterium exchange mass spectrometry and reverse-engineering of the targeted epitope. The results show that the antibody inhibits SLO-mediated cytolysis by binding to a discontinuous epitope in Domain 3, likely preventing oligomerization and subsequent secondary structure changes critical for pore-formation. The epitope is highly conserved across >98% of the characterizedS. pyogenesisolates, making it an attractive target for antibody-based therapy and vaccine design against severe streptococcal infections.
Evolutionary change is remarkably time-independent across scales
Authors: De Lisle Stephen P. , Svensson Erik I. 
Published: December 2023

AbstractApparent time-scaling of evolutionary rates presents a potential dilemma. Rates of molecular, phenotypic, and lineage diversification typically scale negatively with time interval, raising questions about the ecological and evolutionary processes driving this pattern. Here we explore the fact that much apparent temporal scaling is an inevitable outcome of plotting a ratio against its denominator. We show that this effect readily explains the qualitative existence of a negative scaling relationship across different types of evolutionary rates. Highly unlikely relationships between timescale and accumulated evolutionary change are required to produce anything other than negative rate-time relationships. Empirical rate-time scaling relationships reflect unscaled magnitudes of evolution that are either unrelated to time and/or vary in their relationship with time. Over 99% of variation in rate-time relationships across five datasets can be explained by time variation alone, and simulations suggest a range of rate-time scaling exponents can be generated by similar evolutionary processes. These results raise challenges in the interpretation of evolutionary rate-time relationships, and highlight segmented regression as one useful approach to understanding temporal variation in evolution. Time-independence of evolutionary change raises new questions about the factors that generate temporal consistency in evolution.
Isolation and electrochemical analysis of a facultative anaerobic electrogenic strainKlebsiellasp. SQ-1
Authors: Zhou Lei , Tang Tuoxian , Deng Dandan , Wang Yayue , Pei Dongli 
Published: December 2023

AbstractElectricigens decompose organic matter and convert stored chemical energy into electrical energy through extracellular electron transfer. They serve as significant biocatalysts for microbial fuel cells which have practical applications in green energy generation, effluent treatment, and bioremediation. A facultative anaerobic electrogenic strain SQ-1 is isolated from sludge in a biotechnology factory. The strain SQ-1 is a close relative ofKlebsiella variicola. Multilayered biofilms form on the surface of a carbon electrode after the isolated bacteria are inoculated into a microbial fuel cell device. This strain produces high current densities of 625 μA cm-2by using acetate as the carbon source in a three-electrode configuration. The electricity generation performance is also analyzed in a dual-chamber microbial fuel cell. It reaches a maximum power density of 560 mW m-2when the corresponding output voltage is 0.59 V. The facultative strain SQ-1 utilizes hydrous ferric oxide as an electron acceptor to perform extracellular electricigenic respiration in anaerobic conditions. Since facultative strains possess better properties than anaerobic strains,Klebsiellasp. SQ-1 may be a promising exoelectrogenic strain for applications in microbial electrochemistry.
Structural basis of the mechanism and inhibition of a human ceramide synthase
Authors: Pascoa Tomas C. , Pike Ashley C.W. , Tautermann Christofer S. , Chi Gamma , Traub Michael , Quigley Andrew , Chalk Rod , Štefanic Saša , Thamm Sven , Pautsch Alexander , Carpenter Elisabeth P. , Schnapp Gisela , Sauer David B. 
Published: December 2023

AbstractCeramides are bioactive sphingolipids that play pivotal roles in regulating cellular metabolism. Ceramides and dihydroceramides are synthesized by a family of six ceramide synthase enzymes (CerS), each with distinct specificity for the acyl-CoA substrate. Importantly, the acyl chain length plays a key role in determining the physiological function of ceramides, as well as their role in metabolic disease. Ceramide with an acyl chain length of 16 carbons (C16 ceramide) has been implicated in obesity, insulin resistance and liver disease, and the C16 ceramide-synthesizing CerS6 is regarded as an attractive drug target for obesity-associated disease. Despite their importance, the molecular mechanism underlying ceramide synthesis by CerS enzymes remains poorly understood. Here, we report cryo-electron microscopy structures of human CerS6, capturing covalent intermediate and product-bound states. These structures, together with biochemical characterization using intact protein and small molecule mass spectrometry, reveal that CerS catalysis proceeds via a ping-pong reaction mechanism involving a covalent acyl-enzyme intermediate. Notably, the product-bound structure was obtained upon reaction with the mycotoxin fumonisin B1, providing new insights into its inhibition of CerS. These results provide a framework for understanding the mechanisms of CerS function, selectivity, and inhibition, and open new directions for future drug discovery targeting the ceramide and sphingolipid pathways.
Diverse viruses infect nitrifying archaea and bacteria communities in soil
Authors: Lee Sungeun , Hazard Christina , Nicol Graeme W. 
Published: December 2023

AbstractSoil virus communities are diverse and dynamic but contributions to specific processes, such as nitrification, are largely uncharacterised. Chemolithoautotrophic nitrifiers perform this essential component of the nitrogen cycle and are established model groups for linking phylogeny, evolution and ecophysiology due to limited taxonomic and functional diversity. Ammonia-oxidising bacteria (AOB) dominate the first step of ammonia oxidation at high supply rates, with ammonia-oxidising archaea (AOA) and complete ammonia-oxidisingNitrospira(comammox) often active at lower supply rates or when AOB are inactive, and nitrite-oxidising bacteria (NOB) completing canonical nitrification. Here, the diversity and genome content of dsDNA viruses infecting different nitrifier groups were characterised afterin situenrichment via differential host inhibition, a selective approach that alleviates competition for non-inhibited populations to determine relative activity. Microcosms were incubated with urea to stimulate nitrification and amended with 1-octyne or 3,4-dimethylpyrazole phosphate (AOB inhibited), acetylene (all ammonia oxidisers inhibited), or no inhibitor (AOB stimulated), and virus-targeted metagenomes characterised using databases of host genomes, reference (pro)viruses and hallmark genes. Increases in the relative abundance of nitrifier host groups were consistent with predicted inhibition profiles and concomitant with increases in the relative abundance of their viruses, represented by 200 viral operational taxonomic units. These included 61 high-quality/complete virus genomes 35-173 kb in length and possessing minimal similarity to validated families. Most AOA viruses were placed within a unique lineage and viromes were enriched in AOA multicopper oxidase genes. These findings demonstrate that focussed incubation studies facilitate characterisation of host-virus interactions associated with specific functional processes.
Bridging the Gap in Cancer Cell Behavior Against Matrix Stiffening: Insights from a Trizonal Model
Authors: Torki Mohammad E. , Liu Fan , Xu Rongguang , Chen Yunfeng , Fredberg Jeffery , Chen Zi 
Published: December 2023

AbstractThe intricate interplay between actomyosin contractility and extracellular matrix (ECM) strain stiffening is pivotal in cancer invasion. Despite the admitted impact of such feedback, current models are inadequate in predicting the largely overlapping ranges of cell shapes and their corresponding motility levels at intermediate ranges of collagen density. To address this gap, we introduce a free energy-based, trizonal model for cell shape transition under ECM stiffening, which delineates two distinct and one overlapping motility zones entitled with their implications for cancer progression: a low-motility zone with minimal invasiveness, a high-motility zone indicative of significantly invasive cells, and a mesoregion which harbors cells at crossroads of both states. This model integrates critical factors influencing the bidirectional interaction between the cell and ECM, thereby offering a deeper grasp of cancer cell behavior. Our findings reveal that the combined effects of ECM strain stiffening and cellular contractility are key drivers of cell population heterogeneity and invasiveness. This model goes beyond existing paradigms by accurately determining the optimal cell elongation at matrix-driven steady-state equilibrium, factoring in collagen density, contractility density, stress polarization, membrane-cortical tension, and integrin dynamics through the lens of total free energy minimization. The model’s predictive capability is further validated against measured cell shapes from histological sections. Altogether, this research not only bridges a crucial knowledge gap, but also provides a robust computational framework for predicting and replicating cell shape transitions observed in human functional tissue assays, thereby enhancing our ability to understand and potentially combat cancer invasion.SignificanceECM stiffening is crucial in prompting metastatic phenotypes, with the interaction between cell contractility and ECM stiffening heavily influenced by cell motility level and reflected in distinct cell shapes [1–3]. This research introduces a free-energy-based model that, based on sound physics, not only distinguishes among different cell populations by their motility levels, but also truly replicates the recently observed trizonal cell response to ECM stiffness. This predictive model, validated by experiment, bridges a critical gap in our understanding of cellular dynamics in cancer progression, offering profound insight into the physical concepts driving these complex interactions. Thereupon, this work provides a powerful computational tool, potentially leading to new strategies in diagnosing and treating cancer by targeting specific cell behavioral traits and interactions within the tumor microenvironment.
Mitochondrial protein heterogeneity stems from the stochastic nature of co-translational protein targeting in cell senescence
Authors: Khan Abdul Haseeb , Patel Rutvik J. , Viana Matheus P. , Rafelski Susanne M. , Brown Aidan I. , Zid Brian M. , Tsuboi Tatsuhisa 
Published: December 2023

AbstractA decline in mitochondrial function is a hallmark of aging and neurodegenerative diseases. It has been proposed that changes in mitochondrial morphology, including fragmentation of the tubular mitochondrial network, can lead to mitochondrial dysfunction, yet the mechanism of this loss of function is unclear. Most proteins contained within mitochondria are nuclear-encoded and must be properly targeted to the mitochondria. Here, we report that sustained mRNA localization and co-translational protein delivery leads to a heterogeneous protein distribution across fragmented mitochondria. We find that age-induced mitochondrial fragmentation drives a substantial increase in protein expression noise across fragments. Using a translational kinetic and molecular diffusion model, we find that protein expression noise is explained by the nature of stochastic compartmentalization and that co-translational protein delivery is the main contributor to increased heterogeneity. We observed that cells primarily reduce the variability in protein distribution by utilizing mitochondrial fission-fusion processes rather than relying on the mitophagy pathway. Furthermore, we are able to reduce the heterogeneity of the protein distribution by inhibiting co-translational protein targeting. This research lays the framework for a better understanding of the detrimental impact of mitochondrial fragmentation on the physiology of cells in aging and disease.
University–industry linkages and agendas for future studies: a systematic literature review and bibliometric analysis
Authors: Amarathunga Buddhini , Khatibi Ali , Talib Zunirah Mohd 
Published: December 2023

PurposeThis study aims to theoretically and experimentally investigate the literature on university–industry linkages (UILs) through a systematic literature review and bibliometric analysis. Seven research questions were addressed in the present study: (1) descriptive characteristics of the literature on UIL, (2) trends of annual scientific publications on UIL, (3) the most relevant and high-impact sources on UIL, (4) the most globally cited articles on UIL, (5) the most relevant countries on UIL, (6) outcomes of Bradford's Law of Scattering and Lotka's Law of scientific productivity and (7) the trending research areas and avenues for future studies on UIL.Design/methodology/approach Systematic literature review and bibliometric analysis mapping techniques were applied to the present study to analyze 907 articles extracted from the Scopus database. Analysis tools used were Biblioshiny software and VOSviewer software.Findings Findings show that the UIL is a progressively growing discipline with a record of a 5.71% average annual growth rate in scientific production each year from 1970 to 2023. The United States, China and the United Kingdom were the most productive countries in the field of UIL in terms of total scientific production and citations. Academic entrepreneurship, industrial ecology, social network analysis, active learning, engineering education, health economics, public health, university–industry relationships, communication, causal layered analysis and competitiveness are the potential avenues for future researchers in the field of UIL based on the thematic map of keywords analysis.Originality/value This study contributes to the debate on UIL by offering a comprehensive literature review. The findings of the current study will benefit graduates, universities, industries and the community at large.
The a priori procedure (APP) for estimating median under skew normal settings with applications in economics and finance
Authors: Hu Liqun , Wang Tonghui , Trafimow David , Choy S.T. Boris , Chen Xiangfei , Wang Cong , Tong Tingting 
Published: December 2023

PurposeThe authors’ conclusions are based on mathematical derivations that are supported by computer simulations and three worked examples in applications of economics and finance. Finally, the authors provide a link to a computer program so that researchers can perform the analyses easily.Design/methodology/approachBased on a parameter estimation goal, the present work is concerned with determining the minimum sample size researchers should collect so their sample medians can be trusted as good estimates of corresponding population medians. The authors derive two solutions, using a normal approximation and an exact method.FindingsThe exact method provides more accurate answers than the normal approximation method. The authors show that the minimum sample size necessary for estimating the median using the exact method is substantially smaller than that using the normal approximation method. Therefore, researchers can use the exact method to enjoy a sample size savings.Originality/valueIn this paper, the a priori procedure is extended for estimating the population median under the skew normal settings. The mathematical derivation and with computer simulations of the exact method by using sample median to estimate the population median is new and a link to a free and user-friendly computer program is provided so researchers can make their own calculations.
Perceiving IT affordances through the lens of multi-identity goals in rural governance information system
Authors: Zhu Ziqi , Liu Yuan , Wei June , Li Xuan 
Published: December 2023

PurposeThis research aims to investigate the impact of the collaborative governance mechanism on the implementation of rural governance information systems in developing countries. By integrating institutional logic theory, affordance theory and social identity theory, the authors propose modeling grassroots officials' affordance perception process and exploring the importance of multi-identities’ information technology (IT) goals in affordance perception.Design/methodology/approachThrough an exploratory case study, the authors identified three affordances of rural governance information systems and investigated the mechanisms influencing the perception of these affordances among grassroots officials. Next, the authors established a research model and collected 490 valid questionnaires from grassroots officials in China and analyzed the data using structural equation modeling (SEM).FindingsThe authors' study challenges previous assumptions by integrating institutional logic, affordance and social identity theories. The authors establish a perceived affordance path for rural governance information systems, recognize substitute effects among technological affordances and extend the theory to explain social factors influencing IT perception. The authors' findings suggest providing technical training for grassroots officials to enhance IT capabilities, and governments should prioritize essential functionalities in rural governance information systems to optimize resources. Training on collaborative governance mechanisms can improve IT affordance perception, enhancing digital platform utilization in governance processes.Research limitations/implicationsThe study was conducted mainly in China, and therefore, the findings may not be universal to other developing countries. Researchers are therefore encouraged to test the proposal in locations with different rural cultures.Practical implicationsThe paper includes implications for the development of IT perception in rural governance, the development of affordance perception theory and studying the relationship between IT goals and affordance perception.Originality/valueOverall, this paper addresses the need to understand how grassroots officials perceive IT affordances in rural governance and study the relationship between multi-identities’ goals and affordance perception.
Earnings management in local governments under a soft control regime
Authors: Haugdal Ane , Kjærland Frode , Gårseth-Nesbakk Levi , Oust Are 
Published: December 2023

PurposeThis study explores whether hard regulatory control decreases the level of earnings management in local governments. The implementation of a new regulatory approach by Norwegian authorities provides the opportunity for an empirical study.Design/methodology/approachThe authors adopt a two-stage strategy to investigate the existence of earnings management, using the Jones (1991) and modified Jones (Dechow et al., 1995) models to construct a random-effects model.FindingsThe authors test the hypothesis that, given decentralisation of control, there will be an increase in opportunistic financial reporting. This study's findings suggest that this is not the case, thereby indicating that a soft control regime does not diminish discipline in municipalities.Practical implicationsThis study has practical implications for policymaking in the public sector. Its findings suggest that municipalities do not engage in more earnings management under a soft regulatory regime. Hence, other authorities should consider adopting a soft regulatory approach to controlling local governments and their financial reporting systems.Originality/valueThis study contributes to a growing body of literature regarding earnings management by local governments. The authors investigate a hypothesis previously untested in the literature by comparing the degree of earnings management under different regulatory control regimes.