bluuebunny/crossref_metadata_2025_split huggingface dataset:
The SWIB domain-containing DNA topoisomerase I ofChlamydia trachomatismediates DNA relaxation
Authors: Shen Li , Diggs Caitlynn , Ferdous Shomita , Santos Amanda , Wolf Neol , Terrebonne Andrew , Carvajal Luis Lorenzo , Zhong Guangming , Ouellette Scot P. , Tse-Dinh Yuk-Ching 
Published: December 2024

AbstractThe obligate intracellular bacterial pathogen,Chlamydia trachomatis(Ct), has a distinct DNA topoisomerase I (TopA) with a C-terminal domain (CTD) homologous to eukaryotic SWIB domains. Despite the lack of sequence similarity at the CTDs betweenC. trachomatisTopA (CtTopA) andEscherichia coliTopA (EcTopA), full-length CtTopA removed negative DNA supercoilsin vitroand complemented the growth defect of anE. coli topAmutant. We demonstrated that CtTopA is less processive in DNA relaxation than EcTopA in dose-response and time course studies. An antibody generated against the SWIB domain of CtTopA specifically recognized CtTopA but not EcTopA orMycobacterium tuberculosisTopA (MtTopA), consistent with the sequence differences in their CTDs. The endogenous CtTopA protein is expressed at a relatively high level during the middle and late developmental stages ofC. trachomatis. Conditional knockdown oftopAexpression using CRISPRi inC. trachomatisresulted in not only a developmental defect but also in the downregulation of genes linked to nucleotide acquisition from the host cells. Because SWIB-containing proteins are not found in prokaryotes beyondChlamydiaspp., these results imply a significant function for the SWIB-containing CtTopA in facilitating the energy metabolism ofC. trachomatisfor its unique intracellular growth.ImportanceC. trachomatis(Ct) is a medically important bacterial pathogen that is responsible for the most prevalent sexually transmitted bacterial infection. Bioinformatics, genetics, and biochemical analyses have established that the presence of a SWIB domain in CtTopA, a DNA topoisomerase I, is relevant to chlamydial physiology. Further defining the mechanisms of the C-terminal SWIB domain on the catalytic function of CtTopA in an intracellular pathogen is warranted for a more complete understanding of the interactions betweenC. trachomatisand its host cells.
Production of the cobalamin lower ligand, 5,6-dimethylbenzimidazole, by a diatom under cobalamin-deplete conditions
Authors: Gleason Anna K. , Bannon Catherine C. , Bertrand Erin M. 
Published: December 2024

AbstractCobalamin, or vitamin B12, is a micronutrient required by half of all surveyed phytoplankton but produced only by select bacteria and archaea. Cobalamin influences community composition and primary productivity in various regions of the ocean and has been shown to be a critical currency in microbial interactions. Many prokaryotes and some phytoplankton can salvage and remodel cobalamin-related compounds, e.g. cobinamides and/or pseudocobalamin, to generate cobalamin using the lower ligand 5,6-dimethylbenzimidazole (DMB). The sources of DMB remain poorly characterized but are currently attributed to prokaryotes alone. Here, we grew axenic cultures of a recently isolatedThalassiosiraceaediatom over a range of cobalamin concentrations (0, 0.75, 10, 100 pM). Then, using mass spectrometry, we quantified cobalamin and DMB in both particulate (cellular) and dissolved (media) phases. We found that this diatom is a facultative cobalamin consumer: it takes up cobalamin when available but can survive in its absence. Strikingly, under low cobalamin availability, we demonstrate that the diatom produces DMB. This highlights eukaryotic production as a source of the molecule and suggests that cobalamin remodeling by phytoplankton may be less dependent on prokaryotes than previously imagined. We detected DMB in the media during stationary phase, highlighting eukaryotic production of the molecule as a public good. We provide evidence that DMB is produced by this diatom as a mechanism to cope with low cobalamin availability, suggesting that even amongst organisms that don’t absolutely require it, cobalamin use has important consequences for fitness.Importance SectionCobalamin (vitamin B12) is a scarce micronutrient in the ocean that impacts the composition and activity of marine microbial communities. Microbes employ a range of strategies to cope with low cobalamin availability, including remodeling degraded cobalamin compounds into cobalamin if DMB, a critical component of cobalamin, is available. Here we show that a recently isolatedThalassiosiraceaediatom doesn’t need cobalamin to survive, but will take it up and use it when available. Additionally, the diatom produces DMB under low cobalamin conditions. DMB production was previously thought to be restricted to bacteria and archaea, so these results suggest cobalamin remodeling by phytoplankton is not as dependent on interactions with prokaryotes as previously imagined. This work also demonstrates that even organisms that don’t absolutely require cobalamin for survival have adopted metabolic strategies to cope with its absence, emphasizing the importance of this vitamin for phytoplankton metabolism.
Dynamic interplay between RNAN6-methyladenosine modification and porcine reproductive and respiratory syndrome virus infection
Authors: Wang Zi-Han , Li Jing , Ma Sai-Ya , Liu Meng-Xuan , Zhan Yu-Fei , Jin Feng , Liu Bing-Xin , Wang Wenjing , He Mei , Yang Yu-Chuan , Tang Yandong , Wang Peng , Zhang Wuchao , Tong Jie 
Published: December 2024

ABSTRACTN6-methyladenosine (m6A) has attracted significant attention for its role in various biological processes, including RNA stability, translation, and the immune response. Understanding the role of m6A in viral infections is crucial to deep the complex interaction between virus and host cells. Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is a significant pathogen affecting swine health worldwide. Here, we firstly identified the m6A peaks in the PRRSV genome by m6A RNA immunoprecipitation sequencing (m6A-seq). Seven m6A-enriched regions within the PRRSV genome were detected, with one located in the N protein-coding region and the others distributed across nonstructural protein-coding regions. Notably, the Nsp2-coding region contained the highest m6A peak, spanning approximately 178 nucleotides. Functional analyses demonstrated a positive correlation between m6A modification levels and PRRSV replication in porcine alveolar macrophages (PAMs), as modulating the expression of m6A methyltransferases and demethylases significantly influenced viral replication. Moreover, treatment with the universal methylation inhibitor 3-deazaadenosine (3-DAA) effectively suppressed PRRSV replication, suggesting its potential as a novel anti-PRRSV therapeutic. To further elucidate the role of m6A in PRRSV infection, we analyzed the m6A landscape in PAMs infected with pandemic and highly pathogenic PRRSV strains. Among the 4,677 transcripts exhibiting altered m6A modification levels, the MAPK14 gene as well as other genes in p38/MAPK signaling pathway potentially emerged as the preliminary targets of m6A-mediated epigenetic regulation during PRRSV infection. These findings provide new insights into the epigenetic mechanisms underlying PRRSV infection and may facilitate the development of targeted anti-PRRSV strategies and therapeutics.IMPORTANCEThe involvement of m6A in viral genome has broader implications for our understanding of virus evolution and pathogenicity. The ability of viruses to adapt to their hosts and exploit host cellular mechanisms is a critical factor in their success as pathogens. As m6A is a modification that can be manipulated by both host and virus, studying its role in viral infections may reveal new insights into viral evolution. Understanding how different viruses utilize m6A could inform strategies for developing antiviral therapies that target these interactions. Such therapies could disrupt the ability of viruses to exploit m6A modifications, potentially reducing their virulence and enhancing host defenses.
TurboID-based proximity labeling discovers ABCF2 as an adhesion receptor for the zoonotic pathogenPasteurella multocida
Authors: Wang Fei , Shang Yuyao , Chen Menghan , Wang Zhihao , Liu Hanyuan , Hua Lin , Li Wentao , Chen Huanchun , He Qigai , Wu Bin , Peng Zhong 
Published: December 2024

AbstractPasteurella multocidais a zoonotic pathogen that can cause fatal infections in both animals and humans. A significant number of putative adhesive factors have been predicted to contribute to the pathogenesis ofP. multocida, but their interactive proteins on host cells remain unclear. In this study, we experimentally verified the roles of three previously proposed proteins (PlpE, PtfA, Hsf-2) in the adherence ofP. multocida. Through turboID-based proximity labeling screening, we identified ATP-binding cassette sub-family F member 2 (ABCF2) as a host interactive protein for PlpE/PtfA/Hsf-2. Crucial amino acid residues in PlpE, PtfA, and/or Hsf-2 that are essential for interacting with ABCF2 included Asp-123 (PlpE), Lys-88 (PtfA), Asp-136 (PtfA), Ala-464 (Hsf-2), Glu-473 (Hsf-2), and Arg-489 (Hsf-2). Knocking down or knocking out ABCF2 significantly reduced the adherence and invasion ofP.multocidato host cells, while overexpression of ABCF2 markedly increased these effects. However, ABCF2 did not contribute to the adherence of other bacterial species such asKlebsiella pneumoniaeandBordetella bronchiseptica. Additionally, we demonstrated thatP. multocidainfection upregulated the expression of host ABCF2 by activating the p38 MAPK and NF-κB signaling pathways. Furthermore, we showed that ABCF2 was involved in theP. multocida-induced p53-dependent apoptotic signaling pathway. To the best of our knowledge, this is the first identification of ABCF2 as a host factor contributing to the adherence ofP. multocidaand only the second report of ABCF2’s involvement in bacterial pathogenesis.ImportanceP. multocidacan cause fatal infections in both animals and humans, yet the mechanisms related to its pathogenesis remain to be fully explored. In this study, we identified ABCF2 as a crucial host interactive protein for three adhesive proteins encoded byP. multocidaand experimentally verified its role in the adherence and invasion ofP. multocida. Furthermore, we elucidated howP. multocidamodulates ABCF2 during its infection and revealed p53-dependent apoptosis as a downstream effect of ABCF2 duringP. multocidainfection. Given the absence of reports on ABCF2 contributing to the pathogenesis ofP. multocidaand only one previous report on the involvement of ABCF2 in bacterial pathogenesis prior to this study, this research could be valuable for comprehending the interactions between bacteria and hosts during bacterial infections.
PqsE acts as an adaptor protein for the quorum-sensing transcription factor RhlR inPseudomonas aeruginosa
Authors: Tchadi Bilalay V. , Derringer Jesse J. , Detweiler Anna K. , Taylor Isabelle R. 
Published: December 2024

AbstractPseudomonas aeruginosais a human pathogen that poses a significant health threat. Pathogenic behaviors ofP. aeruginosaare under control of the bacterial cell-cell communication system known as quorum sensing (QS). One of the QS master regulators, RhlR, is a receptor/transcription factor that not only relies on binding of its canonical ligand, C4-homoserine lactone (HSL), but additionally requires a protein-protein interaction with the enzyme, PqsE. We constructed heterologous reporter strains inEscherichia colithat allow measurements of the reliance of RhlR on C4-HSL and/or PqsE-binding for the ability to activate transcription of three RhlR-regulated genes:rhlA(PqsE-independent),phzM(PqsE-dependent), andazeB(PqsE-suppressed). Analogous assays measuring activation of the three genes inP. aeruginosawere performed and the patterns observed correlated tightly with the heterologous reporter assays. These results indicate that binding of PqsE to RhlR is able to fine-tune RhlR transcription factor activity in a promoter-specific manner.ImportancePseudomonas aeruginosais an opportunistic human pathogen that can cause fatal infections. There exists an urgent need for new, effective antimicrobial agents to combatP. aeruginosa. The PqsE-RhlR protein-protein interaction is essential forP. aeruginosato be able to make toxins, form biofilms, and infect host organisms. In this study, we use both non-native models inE. coliand measurements of gene expression/toxin production inP. aeruginosato show that the PqsE-RhlR interaction enables fine-tuned gene expression and a heightened ability ofP. aeruginosato adapt to external conditions. These findings will be highly valuable as continued efforts are made to design inhibitors of the PqsE-RhlR interaction and test them as potential antimicrobial agents againstP. aeruginosainfections.
mRNArchitect: optimized design of mRNA sequences
Authors: Budzinska Magdalena A. , Leonard Theodore E. , Chang Rachel Y. , Chaudhary Natasha , Cheetham Seth W. , Mercer Timothy R. , Gunter Helen M. 
Published: December 2024

AbstractSummarymRNA design is the critical first step in the development of a new vaccine or therapy. The mRNA primary sequence is assembled from multiple elements, including the coding sequence of the target protein or gene, flanking untranslated regions that enhance translation, and the poly(A) tail, which improves mRNA stability. The coding sequence can also be optimized to improve translation and stability, and the depletion of uridines and double-stranded RNA secondary structures can reduce reactogenicity. Here, we introducemRNArchitect, a software toolkit to assist in the design of mRNA sequences according to user requirements.mRNArchitectcan rapidly assemble and optimize mRNA sequences based on criteria including GC content, secondary structure, codon optimization, and uridine depletion. The sequences generated bymRNArchitectcan also be readily synthesized into DNA templates, and have been validated across a variety of applications. We offermRNArchitectas an open-source software toolkit to help scientists design new mRNA medicines.Availability and implementationmRNArchitectis available via a web portal atwww.basefacility.org.au/software/and Github athttps://github.com/BaseUQ/mRNArchitect.mRNArchitectis open-source and freely available under MIT License.
The MpANT-auxin loop modulatesMarchantia polymorphadevelopment
Authors: Dipp-Alvarez Melissa , Lorenzo-Manzanarez J. Luis , Flores-Sandoval Eduardo , Méndez-Álvarez Domingo , Espinal-Centeno Annie , León-Ruiz Jesús , Olvera-Martínez Fernando , Bowman John L. , Arteaga-Vázquez Mario A. , Cruz-Ramírez Alfredo 
Published: December 2024

AbstractAINTEGUMENTA-LIKE/PLETHORA(APB)genes are considered part of the ancestral developmental toolkit in land plants. InArabidopsis thaliana, these transcription factors are induced by auxin and are primarily expressed in tissues with actively dividing cells, where they play essential roles in organ development.Marchantia polymorpha, a liverwort that diverged fromA. thalianaearly in embryophyte evolution, possesses a singleAPBortholog, MpAINTEGUMENTA(MpANT), encoded in its genome. In this study, we aimed to characterize the function of MpANT. Analysis of a transcriptional fusion line indicates that MpANTis predominantly expressed in the meristematic region. We report that the MpANTpromoter region contains severalcis-acting Auxin Responsive Elements (AREs) and demonstrate that its expression, which occurs predominantly in meristematic regions, is significantly altered by addition of exogenous auxin and inhibition of auxin transport. These findings indicate that MpANTacts downstream of Auxin Response Factors (ARFs) and auxin signaling. Analyses of loss- and gain-of-function MpANTalleles highlight the importance of this transcription factor in meristem maintenance and cell proliferation. Additionally, we found that MpANTacts upstream of the auxin transporter MpPIN1by influencing auxin distribution. Taken together, our findings reveal a feedforward regulatory loop involving auxin, MpANT, and MpPIN1that is important for Marchantia development.
Linguistic networks uncover grammatical constraints of protein sentences comprised of domain-based words
Authors: Shimpi Adrian A. , Naegle Kristen M. 
Published: December 2024

AbstractEvolution has developed a set of principles that determine feasible domain combinations analogous to grammar within natural languages. Treating domains as words and proteins as sentences, made up of words, we apply a linguistic approach to represent the human proteome as an n-gram network. Combining this with network theory and application, we explore the functional language and rules of the human proteome. Additionally, we explored subnetwork languages by focusing on reversible post-translational modifications (PTMs) systems that follow a reader-writer-eraser paradigm. We find that PTM systems appear to sample grammar rules near the onset of the system expansion, but then convergently evolve towards similar grammar rules, which stabilize during the post-metazoan switch. For example, reader and writer domains are typically tightly connected through shared n-grams, but eraser domains are almost always loosely or completely disconnected from readers and writers. Additionally, after grammar fixation, domains with verb-like properties, such as writers and erasers, never appear – consistent with the idea of natural grammar that leads to clarity and limits futile enzymatic cycles. Then, given how some cancer fusion genes represent the possibility for the emergence of novel language, we investigate how cancer fusion genes alter the human proteome n-gram network. We find most cancer fusion genes follow existing grammar rules. Collectively, these results suggest that n-gram based analysis of proteomes is a complement to the more direct protein-protein interaction networks. N-grams can capture abstract functional connections in a more fully described manner, limited only by the definition of domains within the proteome and not by the combinatorial challenge of capturing all protein interaction connections.
Physical consequences of Lindbladian invariance transformations
Authors: de Almeida Yohan Vianna , Nicacio Fernando , Santos Marcelo F. 
Published: December 2024

On its own, the invariance properties of Markovian master equations have mostly played a mathematical or computational role in the evaluation of quantum open system dynamics. Because all forms of the equation lead to the same time evolution for the state of the system, the fixation of a particular form has only gained physical meaning when correlated with additional information such as in the evolution of quantum trajectories or the study of decoherence-free subspaces. Here, we show that these symmetry transformations can be exploited, on their own, to optimize practical physical tasks. In particular, we present a general formulation showing how they can be used to change the measurable values of physical quantities regarding the exchange of energy and/or information with the environment. We also analyze examples of optimization in quantum thermodynamics and, finally, discuss practical implementations in terms of quantum trajectories.

Published by the American Physical Society
2024
Psychological capital and the entrepreneurial performance of migrant workers: intermediary role of entrepreneurial opportunity identification
Authors: Ma Hongyu , Zhang Yongmei Carol , Topolansky Barbe Federico Guillermo , Stuart Mark 
Published: December 2024

PurposeThere is a pressing need for research on the difference in entrepreneurial performance influenced by the integration of migrant workers’ psychological capital and entrepreneurial opportunity identification. In addition, there is limited research on the association of entrepreneurial performance with different dimensions of psychological capital and how these dimensions affect the entrepreneurial performance of migrant workers. This research will partially address this gap in knowledge by assessing the influence of psychological capital and entrepreneurial opportunity identification on the entrepreneurial performance of migrant workers in China.Design/methodology/approachThis paper conducts a theoretical analysis of psychological capital, entrepreneurial opportunity identification and entrepreneurial performance and proposes a theoretical model of entrepreneurial opportunity identification acting as the intermediary role between psychological capital and the entrepreneurial performance of migrant workers. Based on the data collected from 899 rural households in Shaanxi Province, a structural equation model and a bootstrap method are used to verify the association between psychological capital, entrepreneurial opportunity identification and entrepreneurial performance.FindingsBoth entrepreneurial opportunity identification and psychological capital are conducive to the improvement of entrepreneurial performance. However, the entrepreneurial opportunity identification is found to exert a more significant impact on the entrepreneurial performance of migrant workers than psychological capital does. Findings have also revealed that the intermediary role of entrepreneurial opportunity identification is more prominent in the relationship between adventure and innovation and the entrepreneurial performance of migrant workers than that of self-confidence and optimism and entrepreneurial performance of migrant workers.Originality/valueBased on the results of empirical analysis, the paper proposes corresponding policy recommendations for guiding migrant workers to capitalize on their psychological capital, identify entrepreneurial opportunities, weigh up entrepreneurial risks and ultimately improve their entrepreneurial performance.
Full-cycle grids numerical simulation of the performance for newly developed micro turbine engine
Authors: Zhang Tianhe , Wu Lihong , Li Zheng , Liu Shewen 
Published: December 2024

Purpose
The purpose of this research is to investigate the feasibility of using the components series connection (CSC) method to predict the performance of a newly developed micro turbine engine (MTE) under rated operating condition.

Design/methodology/approach
The main research object is the MTE with known factory performance parameters, and the finite element method is used to discretize its main components into a full-cycle grid and then simulate it in the computational fluid dynamics method under rated operating condition using the CSC method. Finally, compare the results obtained by numerical simulations with the factory design parameters of the MTE.

Findings
The performance and flow field of MTE and each component were simulated and obtained. Compared with the factory design parameters, the errors are acceptable, with the outlet average total temperature and thrust exhibiting errors of 1.4% and 7.6%, respectively.

Practical implications
This paper introduces a faster and more convenient method for simulating the performance of MTE components and the entire engine while also making the simulations more realistic. The method was used to analyze the performance of the components and the whole engine of a newly developed MTE.

Originality/value
This research validates the feasibility of evaluating the overall performance of the MTE using the CSC method and provides a new method to solve performance calculations for MTE under any known working conditions.