bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid and Quantitative Functional Interrogation of Human Enhancer Variant Activity in Live Mice
Authors: Hollingsworth Ethan W. , Liu Taryn A. , Jacinto Sandra H. , Chen Cindy X. , Alcantara Joshua A. , Kvon Evgeny Z. 
Published: December 2023

AbstractFunctional analysis of non-coding variants associated with human congenital disorders remains challenging due to the lack of efficientin vivomodels. Here we introduce dual-enSERT, a robust Cas9-based two-color fluorescent reporter system which enables rapid, quantitative comparison of enhancer allele activities in live mice of any genetic background. We use this new technology to examine and measure the gain- and loss-of-function effects of enhancer variants linked to limb polydactyly, autism, and craniofacial malformation. By combining dual-enSERT with single-cell transcriptomics, we characterize variant enhancer alleles at cellular resolution, thereby implicating candidate molecular pathways in pathogenic enhancer misregulation. We further show that independent, polydactyly-linked enhancer variants lead to ectopic expression in the same cell populations, indicating shared genetic mechanisms underlying non-coding variant pathogenesis. Finally, we streamline dual-enSERT for analysis in F0 animals by placing both reporters on the same transgene separated by a synthetic insulator. Dual-enSERT allows researchers to go from identifying candidate enhancer variants to analysis of comparative enhancer activity in live embryos in under two weeks.
Targeting PrfA from Listeria monocytogenes: a computational drug repurposing approach
Authors: Arias Moreno Xabier 
Published: December 2023

ABSTRACTHumans can develop listeriosis by ingestion of foods contaminated withListeria monocytogenes,an opportunistic gram-positive ubiquitous bacterium. Whilst the non-invasive form of listeriosis may be asymptomatic or cause mild flu-like symptoms, the invasive form of listeriosis is life-threatening and is associated with high hospitalization and fatality rates. Current antibiotic-based therapies are still effective against listeriosis. However, multi-drug resistantListeria monocytogenesstrains have already been identified, which represents a new risk in the treatment of invasive listeriosis. Therefore, it is increasingly urgent to identify new compounds that do not target the conventional biochemical pathways disrupted by current antibiotics. Positive Regulatory Factor A (PrfA) is a well-studied transcriptional factor inListeria monocytogenesthat is responsible for activating a plethora of virulence factors. Targeting virulence factors is a promising strategy that is being considered to combat bacterial infections, hence targeting PrfA is both logical and attractive. In the present computational drug repurposing approach, a complete FDA-approved drugs dataset of more than 700 compounds was virtually screened by docking the drugs against the structure of PrfA. Three of the most promising top-scored FDA drug candidates were then simulated complexed to PrfA. Data from Molecular docking and Molecular Dynamics simulations suggest that Dutasteride and Solifenacin may bind PrfA, and as a result, might exhibit inhibitory activity againstListeria monocytogenes. The use of Dutasteride and Solifenacin is safe in humans since they have been used in the treatment of benign prostatic hyperplasia and androgenic alopecia, and urinary incontinence respectively for decades. Their unique chemical scaffolds may represent valuable starting points for the rapid development of disruptive novel listeria-specific drugs that will be soon needed to combat multi-drug resistantListeria monocytogenesstrains.
Free-floating Bacteria Transcriptionally Respond to Shear Flow
Authors: Ramachandran Ashwin , Stone Howard A. , Gitai Zemer 
Published: December 2023

AbstractPlanktonic (free-floating) cells are typically assumed to be oblivious to any flow that carries them. Here we discover that planktonic bacteria can sense flow to induce gene expression changes that are beneficial in flow. Specifically, planktonicP. aeruginosainduce shear-rate-dependent genes that promote growth in low oxygen environments. Untangling this mechanism revealed that in flow, motileP. aeruginosaspatially redistribute, leading to cell density changes that activate quorum sensing, which in turn enhances oxygen uptake rate. In diffusion-limited environments, including those commonly encountered by bacteria, flow-induced cell density gradients also independently generate oxygen gradients that alter gene expression. Mutants deficient in this newly-discovered flow sensing mechanism exhibit decreased fitness in flow, suggesting that this dynamic coupling of biological and mechanical processes can be physiologically significant.One-Sentence SummaryFree-floating bacteria integrate biological and mechanical responses to adaptively alter gene expression in flow environments
Skeletal Muscle Satellite Cells Co-Opt the Tenogenic GeneScleraxisto Instruct Regeneration
Authors: Bai Yun , Harvey Tyler , Bilyou Colin , Hu Minjie , Fan Chen-Ming 
Published: December 2023

AbstractSkeletal muscles connect bones and tendons for locomotion and posture. Understanding the regenerative processes of muscle, bone and tendon is of importance to basic research and clinical applications. Despite their interconnections, distinct transcription factors have been reported to orchestrate each tissue’s developmental and regenerative processes. Here we show thatScxexpression is not detectable in adult muscle stem cells (also known as satellite cells, SCs) during quiescence.Scxexpression begins in activated SCs and continues throughout regenerative myogenesis after injury. By SC-specificScxgene inactivation (ScxcKO), we show thatScxfunction is required for SC expansion/renewal and robust new myofiber formation after injury. We combined single-cell RNA-sequencing and CUT&RUN to identify direct Scx target genes during muscle regeneration. These target genes help explain the muscle regeneration defects of ScxcKO, and are not overlapping withScx-target genes identified in tendon development. Together with a recent finding of a subpopulation ofScx-expressing connective tissue fibroblasts with myogenic potential during early embryogenesis, we propose that regenerative and developmental myogenesis co-opt theScxgene via different mechanisms.
The Salmon Microbial Genome Atlas enables novel insights into bacteria-host interactions via functional mapping
Authors: de León Arturo Vera-Ponce , Hoetzinger Matthias , Hensen Tim , Gupta Shashank , Weston Bronson , Johnsen Sander M. , Rasmussen Jacob A. , Clausen Cecilie Grønlund , Pless Louisa , Veríssimo Ana Raquel Andrade , Rudi Knut , Snipen Lars , Karlsen Christian René , Limborg Morten T. , Bertilsson Stefan , Thiele Ines , Hvidsten Torgeir R. , Sandve Simen R. , Pope Phillip B. , La Rosa Sabina Leanti 
Published: December 2023

AbstractThe essential role of the gut microbiota for host health and nutrition is well established for many terrestrial animals, while its importance for fish and particularly Atlantic salmon is unclear. Here, we present the Salmon Microbial Genome Atlas (SMGA) originating from wild and farmed fish both in freshwater and seawater, and consisting of 211 high-quality bacterial genomes, recovered by cultivation (n=131) and gut metagenomics (n=80). Bacterial genomes were taxonomically assigned into 14 different orders, including 28 distinctive genera and 31 potentially novel species. Benchmarking the SMGA, we functionally characterized key populations in the salmon gut that were detectedin vivo. This included the ability to degrade diet-derived fibers and release vitamins and other exo-metabolites with known beneficial effects, which were validated byin vitrocultivation and untargeted metabolomics. Together, the SMGA enables high resolution functional insight into salmon gut microbiota with relevance for salmon nutrition and health.
The molecular principles underlying diverse functions of the SLC26 family of proteins
Authors: Takahashi Satoe , Homma Kazuaki 
Published: December 2023

ABSTRACTMammalian SLC26 proteins are membrane-based anion transporters that belong to the large SLC26/SulP family, and many of their variants are associated with hereditary diseases. Recent structural studies revealed a strikingly similar homodimeric molecular architecture for several SLC26 members, implying a shared molecular principle. Now a new question emerges as to how these structurally similar proteins execute diverse physiological functions. In this study we sought to identify the common vs. distinct molecular mechanism among the SLC26 proteins using both naturally occurring and artificial missense changes introduced to SLC26A4, SLC26A5, and SLC26A9. We found: (i) the basic residue at the anion binding site is essential for both anion antiport of SLC26A4 and motor functions of SLC26A5, and its conversion to a nonpolar residue is crucial but not sufficient for the fast uncoupled anion transport in SLC26A9; (ii) the conserved polar residues in the N- and C-terminal cytosolic domains are likely involved in dynamic hydrogen-bonding networks and are essential for anion antiport of SLC26A4 but not for motor (SLC26A5) and uncoupled anion transport (SLC26A9) functions; (iii) the hydrophobic interaction between each protomer’s last transmembrane helices, TM14, is not of functional significance in SLC26A9 but crucial for the functions of SLC26A4 and SLC26A5, likely contributing to optimally orient the axis of the relative movements of the core domain with respect to the gate domains within the cell membrane. These findings advance our understanding of the molecular mechanisms underlying the diverse physiological roles of the SLC26 family of proteins.
Evolutionary and Developmental Specialization of Foveal Cell Types in the Marmoset
Authors: Zhang Lin , Cavallini Martina , Wang Junqiang , Xin Ruiqi , Zhang Qiangge , Feng Guoping , Sanes Joshua R. , Peng Yi-Rong 
Published: December 2023

AbstractIn primates, high-acuity vision is mediated by the fovea, a small specialized central region of the retina. The fovea, unique to the anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, the extent of cellular similarity across anthropoid foveas and the molecular underpinnings of foveal maturation remain unclear. Here, we used high throughput single cell RNA sequencing to profile retinal cells of the common marmoset (Callithrix jacchus), an early divergent in anthropoid evolution from humans, apes, and macaques. We generated atlases of the marmoset fovea and peripheral retina for both neonates and adults. Our comparative analysis revealed that marmosets share almost all its foveal types with both humans and macaques, highlighting a conserved cellular structure among primate foveas. Furthermore, by tracing the developmental trajectory of cell types in the foveal and peripheral retina, we found distinct maturation paths for each. In-depth analysis of gene expression differences demonstrated that cone photoreceptors and Müller glia, among others, show the greatest molecular divergence between these two regions. Utilizing single-cell ATAC-seq and gene-regulatory network inference, we uncovered distinct transcriptional regulations differentiating foveal cones from their peripheral counterparts. Further analysis of predicted ligand-receptor interactions suggested a potential role for Müller glia in supporting the maturation of foveal cones. Together, these results provide valuable insights into foveal development, structure, and evolution.Significance statementThe sharpness of our eyesight hinges on a tiny retinal region known as the fovea. The fovea is pivotal for primate vision and is susceptible to diseases like age-related macular degeneration. We studied the fovea in the marmoset–a primate with ancient evolutionary ties. Our data illustrated the cellular and molecular composition of its fovea across different developmental ages. Our findings highlighted a profound cellular consistency among marmosets, humans, and macaques, emphasizing the value of marmosets in visual research and the study of visual diseases.
A super-resolution compatible workflow for highly multiplexed immunofluorescence of routinely processed kidney tissue
Authors: Siegerist Florian , Kitzel Svenja , Telli Nihal , Dikou Juan Saydou , Drenić Vedran , Chadjichristos Christos E. , Chatziantoniou Christos , Endlich Nicole 
Published: December 2023

AbstractDeep insights into the complex cellular and molecular changes occurring during different (patho-)physiological conditions are essential for understanding the interactions and regulation of different proteins. This understanding is crucial for both research and diagnostics. However, the effectiveness of conventional immunofluorescence, an effective tool for visualizing the spatial distribution of cells or proteins, is limited in complex tissues. This is mainly due to challenges such as the spectral overlap of fluorophore wavelengths, a limited range of antibody types, and the inherent variability of samples.Multiplex immunofluorescence imaging offers a solution to these limitations by enabling precise localization of proteins and identification of different cell types in a single tissue sample. In this study, we demonstrate the cyclic staining and de-staining of paraffin kidney sections, making it suitable for routine use and compatible with super-resolution microscopy for podocyte ultrastructural studies. We have further developed a computerized workflow for data processing which is accessible to all researchers through commercially available reagents and open-access image analysis codes.As a proof of principle, we identified CDH2 as a marker for cellular lesions of sclerotic glomeruli in the nephrotoxic serum nephritis mouse model and cross-validated this finding with a human Nephroseq dataset indicating its translatability.In summary, our work represents a significant advance in multiplex imaging, which is crucial for understanding the localization of numerous proteins in a single FFPE kidney section and the compatibility with super-resolution microscopy to study ultrastructural changes of podocytes.
The novel bacterial effector proteinCbEPF1 mediates ER-LD membrane contacts to regulate host lipid droplet metabolism
Authors: Angara Rajendra Kumar , Sadi Arif , Gilk Stacey D. 
Published: December 2023

ABSTRACTEffective intracellular communication between cellular organelles is pivotal for maintaining cellular homeostasis. Tether proteins, which are responsible for establishing membrane contact sites between cell organelles, enable direct communication between organelles and ultimately influence organelle function and host cell homeostasis. While recent research has identified tether proteins in several bacterial pathogens, their functions have predominantly been associated with mediating inter-organelle communication specifically between the bacteria containing vacuole (BCV) and the host endoplasmic reticulum (ER). However, this study reveals a novel bacterial effector protein,CbEPF1, which acts as a molecular tether beyond the confines of the BCV and facilitates interactions between host cell organelles.Coxiella burnetii, an obligate intracellular bacterial pathogen, encodes the FFAT motif-containing proteinCbEPF1 which localizes to host lipid droplets (LDs).CbEPF1 establishes inter-organelle contact sites between host LDs and the ER through its interactions with VAP family proteins. Intriguingly,CbEPF1 modulates growth of host LDs in a FFAT motif-dependent manner. These findings highlight the potential for bacterial effector proteins to impact host cellular homeostasis by manipulating inter-organelle communication beyond conventional BCVs.
Longitudinal profiling of the pregnancy plasma proteome through organic solvent precipitation and nano LC-MS/MS
Authors: George A.L , Cook E , Smith G.C.S , Charnock-Jones D.S , O’Rahilly S , Reimann F , Gribble F.M , Kay R.G 
Published: December 2023

AbstractProteins secreted from maternal, fetal, and placental tissue are vital for processes like placental development, immunotolerance, and fetal growth, and are associated with pregnancy complications, necessitating predictive biomarkers. In this study, we introduce an acetonitrile-based precipitation coupled with solid-phase extraction that addresses limitations of current low throughput blood-based biomarker discovery workflows. Our method is efficient and cost-effective, and identified 433 protein groups, showing specific tissue associations and enrichment in reproductive tissues such as the placenta, breast, and endometrium. Significant alterations in proteins related to hormonal regulation, immune modulation, and placental development throughout gestation were observed. This approach offers comprehensive insights into the circulating pregnancy proteome, but also provides a scalable solution for larger studies for biomarker discovery in the context of pregnancy complications.TOC
Mechanism of connexin channel inhibition by mefloquine and 2-aminoethoxydiphenyl borate
Authors: Lavriha Pia , Han Yufei , Ding Xinyue , Qi Chao , Vaithia Anand , Korkhov Volodymyr M. 
Published: December 2023

AbstractGap junction intercellular communication (GJIC) between two adjacent cells involves direct exchange of cytosolic ions and small molecules via connexin gap junction channels (GJCs). Connexin GJCs have emerged as drug targets, with small molecule connexin inhibitors considered a viable therapeutic strategy in several diseases. The molecular mechanisms of GJC inhibition by known small molecule connexin inhibitors remain unknown, preventing the development of more potent and connexin-specific therapeutics. Here we show that two GJC inhibitors, mefloquine (MFQ) and 2-aminoethoxydiphenyl borate (2APB) bind to Cx32 and block dye permeation across Cx32 hemichannels (HCs) and GJCs. Cryo-EM analysis shows that 2APB binds to “site A”, close to the N-terminal gating helix of Cx32 GJC, restricting the entrance to the channel pore. In contrast, MFQ binds to a distinct “site M”, deeply buried within the pore. MFQ binding to this site modifies the electrostatic properties of Cx32 pore. Mutagenesis of V37, a key residue located in the site M, renders Cx32 HCs and GJCs insensitive to MFQ-mediated inhibition. Moreover, our cryo-EM analysis, mutagenesis and activity assays show that MFQ targets the M site in Cx43 GJC similarly to Cx32. Taken together, our results point to a conserved inhibitor binding site in connexin channels, opening a new route for development of specific drugs targeting connexins.One-Sentence SummaryInhibition of Cx32 and Cx43 channels via functionally relevant drug binding sites
Deepening the disciplinary cognition and constructing the theoretical system of socialist political economy with Chinese characteristics
Authors: Liu Can 
Published: December 2023

PurposeThe socialist political economy with Chinese characteristics is a systematic economic discipline, which theoretically summarises the socialist economic system and the path of economic development with Chinese characteristics. It is a systematic economic theory of adapting Marxism to the Chinese context. The theoretical system construction for the discipline of socialist political economy with Chinese characteristics is currently a major task.Design/methodology/approachFrom the perspective of disciplinary cognition, the theoretical system of the discipline of socialist political economy with Chinese characteristics includes the disciplinary attributes and connotations, theoretical basis, the origin of thoughts, major principles, logical starting point, main logic and problem-based study of major theoretical and practical issues.FindingsDeveloping the discipline and building the theoretical system of the socialist political economy with Chinese characteristics, several major principles should be adhered to, including building the socialist political economy with Chinese characteristics on the basis of historical materialism; building the theoretical paradigm of socialist political economy with Chinese characteristics around the analysis of production relations; adhering to the people-centred principle; taking common prosperity as the main logic of the socialist political economy with Chinese characteristics; studying the major theoretical and practical issues of building the socialism with Chinese characteristics in the new era based on problems; and reflecting the innovative development of the discipline in the textbook, The Socialist Political Economy with Chinese Characteristics.Originality/valueDisciplinary cognition involves the connotations, attributes, mission and development path of the discipline, which is related to how to construct the discipline system and is a significant part of the disciplinary construction.
Impostorization in the ivory tower: less discussed but more vexing than impostor syndrome
Authors: Gutiérrez Angélica S. , Cole Jean Lee 
Published: December 2023

PurposeGiven the lack of research on the lived experiences of racially minoritized women in academia, this paper provides primary accounts of their experience with impostorization. Impostorization refers to the policies, practices and seemingly innocuous interactions that make or intend to make individuals (i.e. women of color) question their intelligence, competence and sense of belonging.Design/methodology/approachTo explore experiences with impostorization and identify effective coping strategies to counter the debilitating effects of impostorization, 17 semi-structured interviews were conducted with women of color PhD students and faculty at universities throughout the USA and across disciplines.FindingsWhile impostor syndrome, which refers to feelings of inadequacy that individuals experience and a fear that they will be discovered as fraud, has garnered much attention, the present accounts suggest that the more vexing issue in academia is impostorization, not impostor syndrome. Forms of impostorization include microaggressions, grateful guest syndrome, invisibility and inclusion taxation.Originality/valueThe interviews reveal the implicit and explicit ways in which academia impostorizes racially minoritized women scholars and the coping strategies that they use to navigate and survive within academia. The accounts demonstrate the pernicious effects of labeling feelings of inadequacy and unbelonging as impostor syndrome rather than recognizing that the problem is impostorization. This is a call to change the narrative and go from a fix-the-individual to a fix-the-institution approach.