bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examining the Biophysical Properties of the Inner Membrane of Gram-Negative ESKAPE Pathogens
Authors: Gazerani Golbarg , Piercey Lesley R. , Reema Syeda , Wilson Katie A. 
Published: August 2024

AbstractThe World Health Organization has identified multidrug-resistant bacteria as a serious global health threat. Gram-negative bacteria are particularly prone to antibiotic resistance, and their high rate of antibiotic resistance has been suggested to be related to the complex structure of their cell membrane. The outer membrane of Gram-negative bacteria contains lipopolysaccharides that protect the bacteria against threats such as antibiotics, while the inner membrane houses 20-30% of the bacterial cellular proteins. Given the cell membrane’s critical role in bacterial survival, antibiotics targeting the cell membrane have been proposed to combat bacterial infections. However, a deeper understanding of the biophysical properties of the bacterial cell membrane is crucial for developing effective and specific antibiotics. In this study, Martini coarse-grain molecular dynamics simulations were used to investigate the interplay between membrane composition and biophysical properties of the inner membrane across four pathogenic bacterial species:Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter cloacae, andEscherichia coli. The simulations indicate the impact of species-specific membrane composition on dictating the overall membrane properties. Specifically, cardiolipin concentration in the inner membrane is a key factor influencing the membrane features. Model membranes with varying concentrations of bacterial lipids (phosphatidylglycerol, phosphatidylethanolamine, and cardiolipin) further support the significant role of cardiolipin in determining the membrane biophysical properties. The bacterial inner membrane models developed in this work pave the way for future simulations of bacterial membrane proteins and for simulations investigating novel strategies aimed at disrupting the bacterial membrane to treat antibiotic-resistant infections.
The pro-tumoral and anti-tumoral roles of EphA4 on T regulatory cells and tumor associated macrophages during HNSCC tumor progression
Authors: Corbo Sophia , Nguyen Diemmy , Bhatia Shilpa , Darragh Laurel B. , Abdelazeem Khalid N.M. , Court Benjamin Van , Olimpo Nicholas A. , Gadwa Jacob , Yu Justin , Hodgson Chloe , Samedi Von , Garcia Enrique Sanz , Siu Lillian , Saviola Anthony , Heasley Lynn E. , Knitz Michael W. , Pasquale Elena B. , Karam Sana D. 
Published: August 2024

AbstractHead and Neck Squamous Cell Carcinoma (HNSCC) is a deadly cancer with poor response to targeted therapy, largely driven by an immunosuppressive tumor microenvironment (TME). Here we examine the immune-modulatory role of the receptor tyrosine kinase EphA4 in HNSCC progression. Within the TME, EphA4 is primarily expressed on regulatory T cells (Tregs) and macrophages. In contrast ephrinB2, an activating ligand of EphA4, is expressed in tumor blood vessels. Using genetically engineered mouse models, we show that EphA4 expressed in Tregs promotes tumor growth, whereas EphA4 expressed in monocytes inhibits tumor growth. In contrast, ephrinB2 knockout in blood vessels reduces both intratumoral Tregs and macrophages. A novel specific EphA4 inhibitor, APY-d3-PEG4, reverses the accelerated tumor growth we had previously reported with EphB4 cancer cell knockout. EphA4 knockout in macrophages not only enhanced their differentiation into M2 macrophage but also increased Treg suppressive activity. APY-d3-PEG4 reversed the accelerated growth seen in the EphA4 knockout of monocytes but conferred no additional benefit when EphA4 was knocked out on Tregs. Underscoring an EphA4-mediated interplay between Tregs and macrophages, we found that knockout of EphA4 in Tregs not only decreases their activation but also reduces tumor infiltration of pro-tumoral M2 macrophages. These data identify Tregs as a primary target of APY-d3-PEG4 and suggest a role for Tregs in regulating macrophage conversion. These data also support the possible anti-cancer therapeutic value of bispecific peptides or antibodies capable of promoting EphA4 blockade in Tregs but not macrophages.SignificanceEphA4 in regulatory T cells has a pro-tumoral effect while EphA4 in macrophages plays an anti-tumoral role underscoring the necessity of developing biologically rational therapeutics.
One step 4x and 12x 3D-ExM: robust super-resolution microscopy in cell biology
Authors: Norman Roshan X , Chen Yu-Chia , Recchia Emma E , Loi Jonathan , Rosemarie Quincy , Lesko Sydney L , Patel Smit , Sherer Nathan , Takaku Motoki , Burkard Mark E , Suzuki Aussie 
Published: August 2024

AbstractSuper-resolution microscopy has become an indispensable tool across diverse research fields, offering unprecedented insights into biological architectures with nanometer scale resolution. Compared to traditional nanometer-scale imaging methods such as electron microscopy, super-resolution microscopy offers several advantages, including the simultaneous labeling of multiple target biomolecules with high specificity and simpler sample preparation, making it accessible to most researchers. In this study, we introduce two optimized methods of super-resolution imaging: 4-fold and 12-fold 3D-isotropic and preserved Expansion Microscopy (4x and 12x 3D-ExM). 3D-ExM is a straightforward expansion microscopy method featuring a single-step process, providing robust and reproducible 3D isotropic expansion for both 2D and 3D cell culture models. With standard confocal microscopy, 12x 3D-ExM achieves a lateral resolution of under 30 nm, enabling the visualization of nanoscale structures, including chromosomes, kinetochores, nuclear pore complexes, and Epstein-Barr virus particles. These results demonstrate that 3D-ExM provides cost-effective and user-friendly super-resolution microscopy, making it highly suitable for a wide range of cell biology research, including studies on cellular and chromatin architectures.
The conserved ATPase PCH-2 controls the number and distribution of crossovers by antagonizing their formation inC. elegans
Authors: Patel Bhumil , Grobler Maryke , Herrera Alberto , Logari Elias , Ortiz Valery , Bhalla Needhi 
Published: August 2024

AbstractMeiotic crossover recombination is essential for both accurate chromosome segregation and the generation of new haplotypes for natural selection to act upon. This requirement is known as crossover assurance and is one example of crossover control. While the conserved role of the ATPase, PCH-2, during meiotic prophase has been enigmatic, a universal phenotype whenpch-2or its orthologs are mutated is a change in the number and distribution of meiotic crossovers. Here, we show that PCH-2 controls the number and distribution of crossovers by antagonizing their formation. This antagonism produces different effects at different stages of meiotic prophase: early in meiotic prophase, PCH-2 prevents double strand breaks from becoming crossover-eligible intermediates, limiting crossover formation at sites of initial double strand break formation and homolog interactions. Later in meiotic prophase, PCH-2 winnows the number of crossover-eligible intermediates, contributing to the designation of crossovers and ultimately, crossover assurance. We also demonstrate that PCH-2 accomplishes this regulation through the meiotic HORMAD, HIM-3. Our data strongly support a model in which PCH-2’s conserved role is to remodel meiotic HORMADs throughout meiotic prophase to destabilize crossover-eligible precursors, coordinate meiotic recombination with synapsis, and contribute to the progressive implementation of meiotic recombination, guaranteeing crossover control.
Discovery and description of gammanonin: a widely distributed natural product from Gammaproteobacteria
Authors: Costa Jonas H , Adams Eva E , Johnston Chad W 
Published: August 2024

AbstractAntibiotics are essential for modern medicine, but their use drives the evolution of antimicrobial resistance (AMR) that limits the long-term efficacy of any one drug. To keep pace with AMR and preserve our ability to treat bacterial infections, it is essential that we identify antibiotics with new structures and targets that are not affected by clinical resistance. Historically, most developmental candidates for antibiotics have come from microbial natural products, as they feature chemical structures and biological activities that have been honed over millions of years of evolution. Unfortunately, as classical bioactivity screens for natural product discovery are blind to the pharmacological properties of their hits, they often identify molecules with functional groups that limit their utility as drugs. One prominent example is actinonin, an inhibitor of bacterial peptide deformylase (PDF) whose activity is dependent on a hydroxamate moiety associated with toxicityin vivo. The abundance of bacterial genomes now presents an opportunity for target-based natural product discovery, where biosynthetic pathways can be mined for molecules that possess desired activities but lack toxic moieties. Here, we use bioinformatics to lead a chemotype-sensitive, target-based search for natural product inhibitors of bacterial PDF that lacks the conserved and problematic metal chelating group. We describe the discovery, heterologous expression, biosynthesis, total synthesis, and activity of the molecule gammanonin: an apparent actinonin homologue from Gammaproteobacteria. Moving forward, we hope this chemotype and target-driven methodology will help to expedite the discovery of new leads for antibiotic development.
PMS2 has both pro-mutagenic and anti-mutagenic effects on repeat instability in the Repeat Expansion Diseases
Authors: Walker Alexandra , Jimenez Diego Antonio , Usdin Karen , Zhao Xiaonan 
Published: August 2024

AbstractGenome Wide Association studies (GWAS) have implicated PMS2 as a modifier of somatic expansion in Huntington’s disease (HD), one of >45 known Repeat Expansion Diseases (REDs). PMS2 is a subunit of the MutLα complex, a major component of the mismatch repair (MMR) system, a repair pathway that is involved in the generation of expansions in many different REDs. However, while MLH3, a subunit of a second MutL complex, MutLγ, is required for all expansions, PMS2 has been shown to protect against expansion in some model systems but to drive expansion in others. To better understand PMS2’s behavior, we have compared the effect of the loss of PMS2 in different tissues of an HD mouse model (CAG/CTG repeats) and a mouse model for the Fragile X-related disorders (FXDs), disorders that result from a CGG/CCG repeat expansion. Mice heterozygous forPms2show increased expansions in most expansion-prone tissues in both disease models. However, inPms2null mice expansions of both repeats increased in some tissues but decreased in others. Thus, the previously reported differences in the effects of PMS2 in different model systems do not reflect fundamentally different roles played by PMS2 in different REDs, but rather the paradoxical effects of PMS2 in different cellular contexts. These findings have important implications not only for the mechanism of expansion and the development of therapeutic approaches to reduce the pathology generated by repeat expansion, but also for our understanding of normal MMR.
Human-specific features of cerebellar astrocytes and Purkinje cells: an anatomical comparison with mice and macaques
Authors: Hercher Christa , Ellerbeck Kristin , Toutée Louise , Ye Xinyu , Mpai Refilwe , Davoli Maria Antonietta , Watt Alanna J. , Murai Keith K. , Turecki Gustavo , Mechawar Naguib 
Published: August 2024

AbstractLittle is known about the morphological diversity and distribution of cerebellar astrocytes in the human brain and how or if these features differ from those of cerebellar astrocytes in species used to model human illnesses. To address this, we performed a comparative post-mortem examination of cerebellar astrocytes and Purkinje cells (PCs) in healthy humans, macaques, and mice using microscopy-based techniques. Visualizing with canonical astrocyte markers glial fibrillary acidic protein (GFAP) and aldehyde dehydrogenase-1 family member L1 (ALDH1L1), we mapped astrocytes within a complete cerebellar hemisphere. Astrocytes were observed to be differentially distributed across the cerebellar layers, displayed overall increases in area coverages with evolution, and showed features uniquely hominoid. Stereological quantifications in 3 functionally distinct cerebellar lobules demonstrated opposing trends for the canonical astrocyte markers across species with ALDH1L1+ astrocytes increasing with evolution and GFAP+ astrocytes decreasing. PC analyses revealed that while humans have the lowest PC densities, their cell body sizes were the largest with more ALDH1L1 immunoreactive astrocytes surrounding. Notably, the cognitive lobule crus I displayed the highest ratio of Bergmann glia to PC in all species. These findings align with the growing literature for astrocyte and PC heterogeneity and suggest cerebellar astrocyte and PC divergence both within and across species, possibly indicative of a role for these cells in higher-order cerebellar processing.
Cryo-ET of actin cytoskeleton and membrane structure in lamellipodia formation using optogenetics
Authors: Inaba Hironori , Imasaki Tsuyoshi , Aoyama Kazuhiro , Yoshihara Shogo , Takazaki Hiroko , Kato Takayuki , Goto Hidemasa , Mitsuoka Kaoru , Nitta Ryo , Nakata Takao 
Published: August 2024

SummaryLamellipodia are sheet-like protrusions essential for migration and endocytosis, yet the ultrastructure of the actin cytoskeleton during lamellipodia formation remains underexplored. Here, we combined the optogenetic tool PA-Rac1 with cryo-ET to enable ultrastructural analysis of newly formed lamellipodia. We successfully visualized lamellipodia at various extension stages, representing phases of their formation. In minor extensions, several unbundled actin filaments formed “Minor protrusions” at the leading edge. For moderately extended lamellipodia, cross-linked actin filaments formed small filopodia-like structures, termed “mini filopodia.” In fully extended lamellipodia, filopodia matured at multiple points, and cross-linked actin filaments running nearly parallel to the leading edge increased throughout the lamellipodia. These observations suggest that actin polymerization begins in specific plasma membrane regions, forming mini filopodia that either mature into full filopodia or detach from the leading edge to form parallel filaments. This actin turnover likely drives lamellipodial protrusion, providing new insights into actin dynamics and cell migration.
MIRO1 controls energy production and proliferation of smooth muscle cells
Authors: Qian Lan , Koval Olha M. , Endoni Benney T. , Juhr Denise , Stein Colleen S. , Allamargot Chantal , Lin Li-Hsien , Guo Deng-Fu , Rahmouni Kamal , Boudreau Ryan L. , Streeter Jennifer , Thiel William H. , Grumbach Isabella M. 
Published: August 2024

ABSTRACTBackgroundThe outer mitochondrial Rho GTPase 1, MIRO1, mediates mitochondrial motility within cells, but implications for vascular smooth muscle cell (VSMC) physiology and its roles invascular diseases, such as neointima formation following vascular injury are widely unknown.MethodsAn in vivo model of selective Miro1 deletion in VSMCs was generated, and the animals were subjected to carotid artery ligation. The molecular mechanisms relevant to VSMC proliferation were then explored in explanted VSMCs by imaging mitochondrial positioning and cristae structure and assessing the effects on ATP production, metabolic function and interactions with components of the electron transport chain (ETC).ResultsMIRO1 was robustly expressed in VSMCs within human atherosclerotic plaques and promoted VSMC proliferation and neointima formation in mice by blocking cell-cycle progression at G1/S, mitochondrial positioning, and PDGF-induced ATP production and respiration; overexpression of a MIRO1 mutant lacking the EF hands that are required for mitochondrial mobility did not fully rescue these effects. At the ultrastructural level, Miro1 deletion distorted the mitochondrial cristae and reduced the formation of super complexes and the activity of ETC complex I.ConclusionsMitochondrial motility is essential for VSMC proliferation and relies on MIRO1. The EF-hands of MIRO1 regulate the intracellular positioning of mitochondria. Additionally, the absence of MIRO1 leads to distorted mitochondrial cristae and reduced ATP generation. Our findings demonstrate that motility is linked to mitochondrial ATP production. We elucidated two unrecognized mechanisms through which MIRO1 influences cell proliferation by modulating mitochondria: first, by managing mitochondrial placement via Ca2+-dependent EF hands, and second, by affecting cristae structure and ATP synthesis.
ANO1 expression is associated with male survival in lung squamous cell carcinoma
Authors: Afolabi Oluwadamilare I. 
Published: August 2024

AbstractLung cancer is the leading cause of cancer deaths, with lung squamous cell carcinoma (LUSC) accounting for a substantial proportion of cases. LUSC exhibits significant variability in patient outcomes, influenced by clinicopathological factors such as stage, age, and sex, with men exhibiting higher rates of incidence and poorer outcomes compared to women. Therefore, prognosis modeling and customized approaches to LUSC therapy require the characterization of the biological mechanisms that differentiate tumors and patient outcomes across sexes. Using data from The Cancer Genome Atlas (TCGA), this study characterized gene expression patterns that distinguish male and female LUSC. Specifically, differential expression, survival, and Cox regression analyses assessed the prognostic value of ANO1 (Anoctamin 1) expression and methylation in LUSC. Analyses uncovered a significant overexpression of ANO1 in a subset of male LUSC tumors compared to a much lower expression in normal lung and female LUSC tumors. High ANO1 expression was associated with poor survival outcomes in male subjects. High ANO1 gene body methylation mirrored gene expression and was similarly associated with poor survival outcomes. ANO1’s prognostic value remained significant in a multivariate Cox regression analysis, establishing it as an independent prognostic biomarker. ANO1’s marked sex-specific differences in expression and prognostic value indicate its role in the sex disparity of LUSC survival, highlighting its potential as a biomarker and a target for sex-specific customized therapies.
PDPN/CLEC-2 axis modulates megakaryocyte subtypes in a hematopoietic stem cell-regulating megakaryocyte-dominant manner
Authors: Nara Rikuto , Notoh Hinako , Sasaki Tomoyuki , Tsukiji Nagaharu , Kamata Ayuka , Suzuki Nobuaki , Suzuki Atsuo , Okamoto Shuichi , Kanematsu Takeshi , Suzuki Naruko , Katsumi Akira , Kojima Tetsuhito , Suzuki-Inoue Katsue , Matsushita Tadashi , Tamura Shogo 
Published: August 2024

AbstractIntroductionMegakaryocytes are classified into several subtypes including LSP1-positive immune-skewed, MYLK4-positive hematopoietic stem cell (HSC)-regulating, and BMAL1-positive platelet-producing megakaryocytes. Podoplanin (PDPN)-expressing stromal cells generate a microenvironment that promotes megakaryopoiesis in the bone marrow. In this context, PDPN interacts with C-type lectin-like receptor-2 (CLEC-2) on megakaryocyte progenitors, which induces megakaryocyte proliferation. However, the megakaryocyte subtypes developed by the regulation of the PDPN/CLEC-2 axis have not yet been elucidated.Materials and MethodsWe established an immortalized bone marrow PDPN-expressing stromal cell line and a PDPN-knockout line (PDPN WT and KO feeder cells, respectively). Bone marrow hematopoietic progenitors were committed to megakaryocytes in co-culture with PDPN WT or KO feeder cells. The number and ploidy of megakaryocytes, resultant platelets, and the polarization of megakaryocyte subtypes were investigated.ResultsThe number of megakaryocytes was significantly increased in the co-culture with PDPN WT feeder cells compared to that with PDPN KO feeder cells. The megakaryocytes on the PDPN WT and KO feeders showed their main ploidy at 16N∼32N and 8N∼16N, respectively. The number of platelets decreased in the co-culture with the PDPN WT feeder compared to those in the co-culture with the PDPN KO feeder. Megakaryocyte subtypes were immunocytochemically detected inin vitrodifferentiated CD41-positive megakaryocytes. For each megakaryocyte subtype, the percentage of MYLK4-positive megakaryocytes significantly increased and the percentage of BMAL1-positive megakaryocytes significantly decreased when co-cultured with the PDPN WT feeder.ConclusionThe PDPN/CLEC-2 axis modulates megakaryocyte subtype differentiation, with a predominance of HSC-regulating megakaryocytes.
Breaking the glass ceiling in banking: the impact of female directors, digitalization, and income diversification on financial stability
Authors: Tariq Waqas , Chen Yinfei , Tariq Adeel , Torkkeli Marko 
Published: August 2024

Purpose
This study aims to analyze the impact of board gender diversity (BGD) on a bank’s financial stability. Moreover, it also examines whether digitalization and income diversification act as mediators (individual and serial) in this relationship.

Design/methodology/approach
Hypotheses were tested using data from Pakistan’s banking sector financial statements from 2017 to 2021. A two-step analytical approach was used: panel regression in STATA for initial hypothesis examination, followed by mediation analyses using bootstrapping in SPSS. In addition, mixed-effect ML regression was conducted to verify causation and ensure robust findings.

Findings
Results demonstrate that BGD, digitalization and income diversification are positively associated with higher financial stability. Moreover, as hypothesized, both digitalization and income diversification individually and sequentially mediate the relationship between BGD and banks’ financial stability.

Research limitations/implications
It is important to acknowledge the study’s limited five-year timeframe. Further investigation is needed to determine the optimal board compositions, especially considering the study’s inclusion of up to 25% female directors on boards.

Practical implications
Policymakers and top management should prioritize increasing the number of female directors on boards for diversity. Banks that involve female directors can benefit from the synergies between gender diversity and digitization, along with the unique perspectives these women offer. This cooperative dynamic enables banks to explore and capitalize on innovative income diversification opportunities, enter new markets and ensure financial stability.

Social implications
Research findings emphasize promotion of gender equality and meritocracy through increased female director representation. This fosters a more inclusive and cooperative decision-making culture, benefiting individual banks and setting a model for other sectors. Ultimately, it contributes to greater social acceptance of women executives.

Originality/value
The study reveals a novel mechanism, emphasizing the revolutionary impact of active female directors in tandem with digitalization, amplifying chances for income diversification and accelerating increased bank viability.