bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response to antibiotic treatment of bacterial vaginosis predicts the effectiveness of LACTIN-V (Lactobacillus crispatusCTV-05) in the prevention of recurrent disease
Authors: Hemmerling Anke , Wierzbicki Michael R. , Armstrong Eric , Cohen Craig R. 
Published: October 2023

ABSTRACTObjectivesLive biotherapeutic products (LBPs) containing vaginalLactobacillus crispatusare promising adjuvant treatments to prevent recurrent bacterial vaginosis (BV) but may depend on the success of initial antibiotic treatment.MethodsApost hocanalysis of data collected during the phase 2b LACTIN-V randomized control trial (L. crispatusCTV-05) explored the impact of clinical BV cure defined as Amsel criteria 0 of 3 (excluding pH, per 2019 FDA guidance) two days after completion of treatment with vaginal metronidazole gel on the effectiveness of an 11-week LACTIN-V dosing regimen to prevent BV recurrence by 12 and 24 weeks.ResultsAt enrollment, 88% of participants had achieved clinical BV cure. The effect of LACTIN-V on BV recurrence compared to placebo differed by initial clinical BV cure status (p=0.02 by 12 weeks, and p=0.08 by 24 weeks). The LACTIN-V to placebo risk ratio of BV recurrence by 12 weeks was 0.56 (CI: 0.35, 0.77) among participants with initial clinical BV cure, and 1.34 (CI: 0.47, 2.23) among participants without clinical BV cure. Among women receiving LACTIN-V, those who had achieved clinical BV cure at enrollment reached higher levels of detectableL. crispatusCTV-05 compared to women failing to achieve clinical BV cure.ConclusionLACTIN-V appears to only decrease BV recurrence in women with clinical cure of BV following antibiotic treatment. Future trials of LBPs should consider limiting enrollment to these women.
Rethinking animal attrition in preclinical research: expressing causal mechanisms of selection bias using directed acyclic graphs
Authors: Collazo Anja , Kuhn Hans-Georg , Kurth Tobias , Piccininni Marco , Rohmann Jessica L. 
Published: October 2023

AbstractAnimal attrition in preclinical experiments can introduce bias in the estimation of causal treatment effects, as surviving animals may not be representative of the entire study population. This can compromise the internal validity of the study, despite randomization at the outset. Directed Acyclic Graphs (DAGs) are commonly used tools to transparently visualize assumptions about the causal structure underlying observed data. By illustrating relationships between relevant variables, DAGs enable the detection of even less intuitive biases, and can thereby inform strategies for their mitigation. In this study, we present an illustrative causal model for preclinical stroke research, in which animal attrition induces a specific type of selection bias (i.e., collider stratification bias) due to the interplay of animal welfare, initial disease severity and negative side effects of treatment. Even when the treatment had no causal effect, our simulations revealed substantial bias across different scenarios. We show how researchers can potentially mitigate this bias in the analysis phase, even when only data from surviving animals are available, if knowledge of the underlying causal process that gave rise to the data is available. Collider stratification bias should be a concern in preclinical animal model studies with severe side effects and high post-randomization attrition.
Dual-Probe Activity-Based Protein Profiling Reveals Site-Specific Differences in Protein Binding of EGFR-Directed Drugs
Authors: van Bergen Wouter , Fiala Jan , Heck Albert J.R. , Baggelaar Marc P. 
Published: October 2023

AbstractComparative, dose-dependent analysis of interactions between small molecule drugs and their targets, as well as off-targets, in complex proteomes is crucial for selecting optimal drug candidates. The affinity of small molecules for targeted proteins is largely dictated by interactions between amino acid side chains and these drugs. Thus, studying drug-protein interactions at an amino acid resolution provides a comprehensive understanding of drug selectivity and efficacy. In this study, we further refined the site-specific activity-based protein profiling strategy, PhosID-ABPP, on a timsTOF HT mass spectrometer. This refinement enables dual dose-dependent competition of inhibitors within a single cellular proteome. Here, a comparative analysis of two activity-based probes (ABPs), developed to selectively target the epidermal growth factor receptor (EGFR), namely PF-06672131 and PF-6422899, facilitated the simultaneous identification of ABP-specific binding sites at a proteome-wide scale within a cellular proteome. Dose-dependent probe-binding preferences for proteinaceous cysteines, even at low nanomolar ABP concentrations, could be revealed. Notably, while both ABPs showed comparable affinities for the EGFR, PF-06672131 had a broader off-target reactivity profile. In contrast, PF-6422899 exhibited higher affinity for the ERBB2 receptor and bound to catalytic cysteines in several other enzymes, which is likely to disrupt their catalytic activity. Notably, PF-06672131 also effectively labeled ADP/ATP translocase proteins at a concentration of just 1 nanomolar. Additionally, analysis of different binding sites within the EGF receptor and the voltage-dependent anion channel 2 revealed secondary binding sites of both probes and provided insights into the binding poses of inhibitors on these proteins. Insights from the PhosID-ABPP analysis of these two ABPs serve as a valuable resource for understanding drug on– and off-target engagement in a dose– and site-specific manner.
Sub-retinal transplantation of human iPSC-derived retinal sheets: A promising approach for the treatment of macular degeneration
Authors: Barabino Andrea , Mellal Katia , Hamam Rimi , Polosa Anna , Griffith May , Bouchard Jean-François , Kalevar Ananda , Hanna Roy , Bernier Gilbert 
Published: October 2023

ABSTRACTRetinal degenerative diseases affect millions of people worldwide, and legal blindness is generally associated with the loss of cone photoreceptors located in the retina’s central region called the macula. Currently, there is no treatment to replace the macula. Addressing this unmet need, we employed control isogenic and hypoimmunogenic induced pluripotent stem cell (iPSC) lines to generate spontaneously polarized retinal sheets (RSs). They presented the advantage of facile customization and large-scale production, exhibiting a polarized 3D architecture within a 2D cell culture environment, thus readily adaptable for clinical applications. RSs were enriched in retinal progenitor and cone precursor cells, which could differentiate into mature S- and M/L-cones in long-term cultures. Single-cell RNA-seq analysis showed that RSs recapitulate the ontogeny of the developing human retina and are devoid of pluripotent stem cells. Isolation of neural rosettes for sub-retinal transplantation effectively eliminated unwanted cells such as RPE cells. In a porcine model of chemically induced retinal degeneration, grafts integrated the host retina and formed a new, yet immature, photoreceptor layer, exhibiting viability for up to 2 months. In one transplanted animal that met all criteria, including correct apicobasal orientation and seamless graft integration, functional and immunohistochemical assays suggest that grafts exhibited responsiveness to light stimuli and established putative synaptic connections with host bipolar neurons. This study underscores the potential and challenges of iPSC-derived RS for clinical applications while establishing the optimal methodology and conditions for RS transplantation, thus paving the path for future long-term functional investigations using RS grafts.
Colon cancer and cell transformation by clinicalSalmonellastrains are associated with bacterial virulence and intracellular fitness
Authors: Stévenin Virginie , Coipan Claudia E. , Duijster Janneke W. , van Elsland Daphne M. , Voogd Linda , van Hoek Angela H.A.M. , Wijnands Lucas M. , Jansen Lennert , Akkermans Jimmy J.L.L. , Neefjes-Borst Andra , Franz Eelco , Mughini-Gras Lapo , Neefjes Jacques 
Published: October 2023

SUMMARYNon-typhoidalSalmonella(NTS) are facultative intracellular pathogens that are associated epidemiologically and experimentally with colon cancer development. Yet, the driving factors ofSalmonella-induced cell transformation are mostly unknown. We compared 30 (case) NTS clinical strains isolated from patients who were diagnosed with colon cancer >1 year after NTS infection, versus 30 (control) strains from patients who did not develop colon cancer. While we observed diverse cell invasion and transformation efficiencies among the 60 NTS strains, case strains showed higher transformation efficiency than matching control strains. Genomic and transcriptomic analyses showed that transformation efficiency could not be attributed to specific genomic features, but was associated with gene expression, particularly metabolic genes and regulons. Moreover, high-transforming NTS strains display increased capacity to utilize various nutrient sources, including carbohydrates and amino acids, and grow significantly faster intracellularly than low-transforming NTS. Our results link NTS intracellular virulence to cancer promotion.Graphical abstractIn briefNon-typhoidalSalmonella(NTS) infections can promote cell transformation and colon cancer progression. Yet, little is known about the driving factors ofSalmonella-induced transformation. Stévenin et al. performed a multi-omic characterization of clinical NTS strains identified in a nation-wide epidemiological study as associated with colon cancer and revealed a link between bacterial virulence, intracellular fitness, and host cell transformation.Highlights- Cancer-associated clinical NTS generate more cell transformation than matching control NTS.- NTS transformation efficiency did not correlate with specific genetic features.- NTS transformation efficiency correlates with gene expression and bacterial metabolic needs.- High-transforming NTS display increased virulence and intracellular fitness.
High Resolution Biological and Physical Sampling Reveals Expression of Domoic Acid Biosynthetic Genes at Frontal Zones
Authors: Thukral Monica , Aron Allegra T. , Rabines Ariel J. , Petras Daniel , Preston Christina M. , Zheng Hong , Fussy Zoltan , James Chase , Ussler William , Lucas Andrew J. , Anderson Clarissa R. , Scholin Christopher A. , Dorrestein Pieter C. , Ryan John P. , Allen Andrew E. 
Published: October 2023

AbstractOcean microbes are the foundation of marine food webs, regulating carbon cycling and ecosystem dynamics. How they proliferate, die, move, and interact is regulated by physical, chemical, and biological factors that are dynamic and challenging to quantify in the natural environment. A significant limitation in many marine field studies is the inability to continuously sample the ever-changing ocean environment over space and time. In this study, we integrated spatiotemporal and multi-omic sample collection in an intensive sampling effort of phytoplankton ecology in Monterey Bay, California during the spring of 2021. Sampling methods coupled: (1) manual shipboard CTD sampling, (2) autonomous sampling using a Long-Range Autonomous Underwater Vehicle (LRAUV) equipped with an Environmental Sampling Processor (ESP), and (3) high-resolution physical measurements by an autonomous vertical profiler (Wirewalker). Sampling occurred as upwelling waned alongside declining domoic acid (DA) and low abundances of toxigenicPseudo-nitzschia. Conditions needed to spark a widespread and toxicPseudo-nitzschiabloom were absent, yet low-level DA was driven by similar mechanisms to those causing elevated DA. Three DA biosynthetic intermediate molecules were reported in the environment for the first time. Both shipboard and ESP sampling approaches identified DA biosynthetic gene expression at frontal zones. DA and expression ofdabA, the gene encoding the first committed step of DA biosynthesis, were higher in association with recently upwelled water that supplied nutrients for growth and DA biosynthesis. Detection of subtle variations indabgene expression in response to environmental variation provide a window into the ecological dynamics underpinning major toxic events.Graphical Abstract
Development and Characterization of the Mode-of-Action of Inhibitory and Agonist Peptides Targeting the Voltage-Gated Sodium Channel SCN1B/β1 Subunit
Authors: Williams Zachary J. , Alvarez-Laviada Anita , Hoagland Daniel , Jourdan L. Jane , Poelzing Steven , Gorelik Julia , Gourdie Robert G. 
Published: October 2023

ABSTRACTTreatment of cardiac arrhythmias by targeting ion channels is challenging, with safe and effective therapies remaining an unmet clinical need. Modeling and experimental studies have shown that a voltage-gated sodium channel (VGSC)-rich nanodomain at edge of the gap junction (GJ) called the perinexus could provide new mechanistic insights into normal and abnormal conduction of action potentials in the heart. We have reported that a 19 amino acid SCN1B (β1/β1B) mimetic peptide derived from the immunoglobulin domain of the VGSC subunit called βadp1 acutely disrupts β1-mediated adhesive interactions at cardiac perinexii, prompting arrhythmogenic changes during time courses of up to an hour. In the present study, we sought to gain further insight on βadp1 mode-of-action, as well as identifying new SCN1B (β1/β1B) mimetic peptides, with potential for inhibiting and/or promoting β1-mediated adhesion. This included studies of the effect of βadp1 and related peptides on SCN1B (β1/β1B) Regulated Intramembrane Proteolysis (RIP) - a signaling pathway that has been shown to effect gene transcription, including that of VGSC subunits. Using patch clamp to assay cell-cell contact-associated VGSC activity in cardiomyocytes, and electric cell substrate impedance sensing (ECIS) to assess intercellular adhesion in cells heterologously expressing β1, we find that inhibitory effects of βadp1 can persist for up to 5 hours. However, this acute inhibition is not sustained, with βadp1 effects on β1-mediated adhesion lost after 24 hours. We also determined that a short peptide (LQLEED) near the carboxyl-terminal portion of βadp1 inhibited adhesion in β1-expressing cells in a manner similar to βadp1. Paradoxically, dimeric peptides incorporating a repeat of the LQLEED sequence promoted intercellular adhesion at all time points studied over a 2-day time course. Inhibitory and agonistic peptides were found to effect β1 RIP, with βadp1increasing RIP continuously over 48 hours, whilst dimeric agonists acutely increased RIP at 6 hours post-treatment, but not thereafter. In the presence of DAPT, an inhibitor of RIP, the effects of βadp1 on ECIS-measured intercellular adhesion were lost, suggesting a relationship between RIP and inhibitory effects of the peptide. In sum, we identify novel SCN1B (β1/β1B) mimetic peptides with potential to inhibit and promote intercellular β1-mediated adhesion, possibly including by effects on β1 RIP, suggesting paths to development of anti-arrhythmic drugs targeting the perinexus.
The E3 ubiquitin ligase RNF216 contains a linear ubiquitin chain-determining-like domain that functions to regulate dendritic arborization and dendritic spine type in hippocampal neurons
Authors: Kadirvelu Jayashree , Jacobs Savannah E. , Liu Ruochuan , Charles Antoinette J. , Yin Jun , Mabb Angela M. 
Published: October 2023

AbstractOf the hundreds of E3 ligases found in the human genome, the RING-between RING (RBR) E3 ligase in the LUBAC (linear ubiquitin chain assembly complex) complex HOIP (HOIL-1-interacting protein or RNF31), contains a unique domain called LDD (linear ubiquitin chain determining domain). HOIP is the only E3 ligase known to form linear ubiquitin chains, which regulate inflammatory responses and cell death via activation of the NF-κB pathway. We identified an amino acid sequence within the RNF216 E3 ligase that shares homology to the LDD domain found in HOIP (R2-C). Here, we show that the R2-C domain of RNF216 promotes self-assembly of all ubiquitin chains, with a dominance for those assembled via K63-linkages. Deletion of the R2-C domain altered RNF216 localization, reduced dendritic complexity and changed the distribution of apical dendritic spine morphology types in primary hippocampal neurons. These changes were independent of the RNF216 RBR catalytic activity as expression of a catalytic inactive version of RNF216 had no effect. These data show that the R2-C domain of RNF216 diverges in ubiquitin assembly function from the LDD of HOIP and and functions independently of RNF216 catalytic activity to regulate dendrite development in neurons.
Failed reprogramming of transformed cells due to induction of apoptosis and senescence impairs tumor progression in lung cancer
Authors: Pedrosa Pablo , Zhang Zhenguang , Macias David , Ge Jianfeng , Denholm Mary , Dyas Anna , Nuñez-Quintela Victor , Estevez-Souto Valentin , Lado-Fernandez Patricia , Gonzalez Patricia , Gomez Maria , Martin Jose Ezequiel , Silva-Alvarez Sabela Da , Collado Manuel , Muñoz-Espín Daniel 
Published: October 2023

AbstractCell reprogramming to pluripotency applied to the study of cancer has identified transformation and pluripotency as two independent and incompatible cell fates. A detailed knowledge of the relationship between transformation and reprogramming could lead to the identification of new vulnerabilities and therapeutic targets in cancer. Here, we explore this interplay and find that OSKM expression limits tumor cell growth by inducing apoptosis and senescence. We identify Oct4 and Klf4 as the main individual reprogramming factors responsible for this effect. Mechanistically, the induction of cell cycle inhibitor p21 downstream of the reprogramming factors acts as mediator of cell death and senescence. Using a variety of in vivo systems, including allografts, orthotopic transplantation and KRAS-driven lung cancer mouse models, we demonstrate that OSKM expression impairs tumor growth and reduces tumor burden.
Dual antibacterial properties of copper coated nanotextured stainless steel
Authors: Tripathi Anuja , Park Jaeyoung , Pho Thomas , Champion Julie A. 
Published: October 2023

AbstractBacterial adhesion to stainless steel, an alloy commonly used in shared settings, numerous medical devices, and food and beverage sectors, can give rise to serious infections, ultimately leading to morbidity, mortality, and significant healthcare expenses. In this study, we have demonstrated Cu-coated nanotextured stainless steel (nSS) fabrication using electrochemical technique and its potential as an antibiotic-free biocidal surface against Gram-positive and negative bacteria. As nanotexture and Cu combine for dual methods of killing, this material should not contribute to drug resistant bacteria as antibiotic use does. Our approach involves applying a Cu coating on nanotextured stainless steel, resulting in a antibacterial activity within 30 minutes. We have performed comprehensive characterization of the surface revealing that the Cu coating consists of metallic Cu and oxidized states (Cu2+and Cu+). Cu-coated nSS induces a remarkable reduction of 97% in Gram-negativeEscherichia coliand 99% Gram-positiveStaphylococcus epidermidisbacteria. This material has potential to be used to create effective, scalable, and sustainable solutions to prevent bacterial infections caused by surface contamination without contributing to antibiotic resistance.Abstract Figure
Integrated Protocol of Protein Structure Modeling for Cryo-EM with Deep Learning and Structure Prediction
Authors: Terashi Genki , Wang Xiao , Prasad Devashish , Nakamura Tsukasa , Zhu Han , Kihara Daisuke 
Published: October 2023

AbstractStructure modeling from maps is an indispensable step for studying proteins and their complexes with cryogenic electron microscopy (cryo-EM). Although the resolution of determined cryo-EM maps has generally improved, there are still many cases where tracing protein main-chains is difficult, even in maps determined at a near atomic resolution. Here, we have developed a protein structure modeling method, called DeepMainmast, which employs deep learning to capture the local map features of amino acids and atoms to assist main-chain tracing. Moreover, since Alphafold2 demonstrates high accuracy in protein structure prediction, we have integrated complementary strengths of de novo density tracing using deep learning with Alphafold2’s structure modeling to achieve even higher accuracy than each method alone. Additionally, the protocol is able to accurately assign chain identity to the structure models of homo-multimers.
N-Acetylcysteine alters disease progression and increases Janus Kinase mutation frequency in a mouse model of precursor B cell acute lymphoblastic leukemia
Authors: Sams Mia P. , Iansavitchous James , Astridge Madeline , Rysan Heidi , Xu Li S. , Rodrigues de Oliveira Bruno , DeKoter Rodney P. 
Published: October 2023

AbstractB cell acute lymphoblastic leukemia (B-ALL) is the most prevalent type of cancer in young children and is associated with high levels of reactive oxygen species (ROS). The antioxidant N-acetylcysteine (NAC) was tested for its ability to alter disease progression in a mouse model of B-ALL. Mb1-CreΔPB mice have deletions in genes encoding PU.1 and Spi-B in B cells and develop B-ALL at 100% incidence. Treatment of Mb1-CreΔPB mice with NAC in drinking water significantly reduced the frequency of CD19+pre-B ALL cells infiltrating the thymus at 11 weeks of age. However, treatment with NAC did not reduce leukemia progression or increase survival by median 16 weeks of age. NAC significantly altered gene expression in leukemias in treated mice. Mice treated with NAC had increased frequencies of activating mutations in genes encoding Janus Kinases 1 and 3. In particular, frequencies ofJak3R653H mutations were increased in mice treated with NAC compared to control drinking water. NAC opposed oxidization of PTEN protein ROS in cultured leukemia cells. These results show that NAC alters leukemia progression in this mouse model, ultimately selecting for leukemias with highJak3R653H mutation frequencies.
Multi-pass, single-molecule nanopore reading of long protein strands with single-amino acid sensitivity
Authors: Motone Keisuke , Kontogiorgos-Heintz Daphne , Wee Jasmine , Kurihara Kyoko , Yang Sangbeom , Roote Gwendolin , Fang Yishu , Cardozo Nicolas , Nivala Jeff 
Published: October 2023

AbstractThe ability to sequence single protein molecules in their native, full-length form would enable a more comprehensive understanding of proteomic diversity. Current technologies, however, are limited in achieving this goal. Here, we establish a method for long-range, single-molecule reading of intact protein strands on a commercial nanopore sensor array. By using the ClpX unfoldase to ratchet proteins through a CsgG nanopore, we achieve single-amino acid level sensitivity, enabling sequencing of combinations of amino acid substitutions across long protein strands. For greater sequencing accuracy, we demonstrate the ability to reread individual protein molecules, spanning hundreds of amino acids in length, multiple times, and explore the potential for high accuracy protein barcode sequencing. Further, we develop a biophysical model that can simulate raw nanopore signalsa priori,based on amino acid volume and charge, enhancing the interpretation of raw signal data. Finally, we apply these methods to examine intact, folded protein domains for complete end-to-end analysis. These results provide proof-of-concept for a platform that has the potential to identify and characterize full-length proteoforms at single-molecule resolution.