bluuebunny/crossref_metadata_2025 huggingface dataset:
Machine learning predicts system-wide metabolic flux control in cyanobacteria
Authors: Kugler Amit , Stensjö Karin
Published: October 2023

Metabolic fluxes and their control mechanisms are fundamental in cellular metabolism, offering insights for the study of biological systems and biotechnological applications. However, quantitative and predictive understanding of controlling biochemical reactions in microbial cell factories, especially at the system level, is limited. In this work, we present ARCTICA, a computational framework that integrates constraint-based modelling with machine learning tools to address this challenge. Using the model cyanobacteriumSynechocystissp. PCC 6803 as chassis, we demonstrate that ARCTICA effectively simulates global-scale metabolic flux control. Key findings are that (i) the photosynthetic bioproduction is mainly governed by enzymes from the Calvin–Benson–Bassham (CBB) cycle, rather than by those involve in the biosynthesis of the end-product, (ii) the catalytic capacity of the CBB cycle limits the photosynthetic activity and downstream pathways and (iii) ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a major, but not the most, limiting step in the CBB cycle. Predicted metabolic reactions qualitatively align with prior experimental observations, validating our modelling approach. ARCTICA serves as a valuable pipeline for understanding cellular physiology and predicting rate-limiting steps in genome-scale metabolic networks, providing guidance for bioengineering of cyanobacteria.

Highlights

A workflow for flux control analysis inSynechocystissp. PCC 6803.

Machine learning with features derived from genome-scale metabolic modelling.

Identification of potential key reactions for metabolic adaptations and cell bioengineering.
TBL38 is an atypical homogalacturonan acetylesterase with a peculiar cell wall microdomain localization in Arabidopsis seed mucilage secretory cells
Authors: Dauphin Bastien G. , Ropartz David , Ranocha Philippe , Rouffle Maxime , Carton Camille , Ru Aurélie Le , Martinez Yves , Fourquaux Isabelle , Ollivier Simon , Mac-Bear Jessica , Trezel Pauline , Geairon Audrey , Jamet Elisabeth , Dunand Christophe , Pelloux Jérôme , Ralet Marie-Christine , Burlat Vincent
Published: October 2023

Plant cell walls are made of complex polysaccharidic/proteinaceous network whose biosynthesis and dynamics implicate several cell compartments and impact plant development. The synthesis and remodeling of homogalacturonan pectins is associated with multiple developmental processes ranging from growth to response to biotic/abiotic stress. It encompasses Golgi-localized methylation and acetylation and subsequent demethylation and deacetylation in the cell wall. In the last decade, our comprehension of plant polysaccharides acetylation has increased significantly thanks to the study of the TRICHOME BIREFRINGENCE-LIKE (TBL) protein family. TBLs are mostly described as Golgi-localized acetyltransferases specifically targeting diverse hemicelluloses or pectins. Varioustblmutants showed altered wall mechanical properties and dynamics. Here, we studyTBL38that is co-expressed withPECTIN METHYLESTERASE INHIBITOR6(PMEI6) andPEROXIDASE 36(PRX36) during the development of Arabidopsis seed mucilage secretory cells (MSCs). We demonstrate the atypical TBL38 cell wall localization restricted to the PMEI6/PRX36 MSC cell wall microdomain. Atbl38mutant displays an intriguing homogalacturonan immunological phenotype in this cell wall microdomain and in a MSC surface-enriched abrasion powder. This fraction was further characterized by mass spectrometry oligosaccharide profiling revealing an increased homogalacturonan acetylation phenotype. Finally, a recombinant TBL38 is shown to display pectin acetylesterase activityin vitro. These results indicate that TBL38 is an atypical cell wall-localized TBL that displays a homogalacturonan acetylesterase activity rather than a Golgi-localized acetyltransferase activity as observed in previously studied TBLs. TBL38 function during seed development is discussed.
Identification of new markers of angiogenic sprouting using transcriptomics: New role for RND3
Authors: Abbey Colette A , Duran Camille L , Chen Zhishi , Chen Yanping , Roy Sukanya , Coffell Ashley , Chakraborty Sanjukta , Wells Gregg B. , Chang Jiang , Bayless Kayla
Published: October 2023

Background: New blood vessel formation requires endothelial cells to transition from a quiescent to an invasive phenotype. Transcriptional changes are vital for this switch, but a comprehensive genome-wide approach focused exclusively on endothelial cell sprout initiation has not been reported. Approach and Results: Using a model of human endothelial cell sprout initiation, we developed a protocol to physically separate cells that initiate the process of new blood vessel formation (invading cells) from non-invading cells. We used this model to perform multiple transcriptomics analyses from multiple donors to monitor endothelial gene expression changes. Single-cell Population Analyses, single-cell Cluster Analyses, and bulk RNA sequencing were used to delineate transcriptomic changes in invading cells. The results revealed a 39 gene signature that was consistent with activation of signal transduction, morphogenesis, and immune responses. Many of the genes were previously shown to regulate angiogenesis, and include multiple tip cell markers. Upregulation of SNAI1, PTGS2, and JUNB protein expression was confirmed in invading cells, and silencing JunB and SNAI1 significantly reduced invasion responses. Separate studies investigated Rounding 3 (RND3), also known as RhoE, which has not yet been implicated in angiogenesis. Silencing RND3 reduced endothelial invasion distance as well as filopodia length, fitting with a pathfinding role for RND3 via regulation of filopodial extensions. Analysis of in vivo retinal angiogenesis in Rnd3 heterozygous mice confirmed a decrease in filopodial length compared to wild type littermates. Conclusion: Validation of multiple genes, including RND3, revealed a functional role for this gene signature early in the angiogenic process. This study expands the list of genes that are associated with the acquisition of a tip cell phenotype during endothelial cell sprout initiation.
Evaluating the use of GPT-3.5-turbo to provide clinical recommendations in the Emergency Department
Authors: Williams Christopher Y.K. , Miao Brenda Y. , Butte Atul J.
Published: October 2023

The release of GPT-3.5-turbo (ChatGPT) and other large language models (LLMs) has the potential to transform healthcare. However, existing research evaluating LLM performance on real-world clinical notes is limited. Here, we conduct a highly-powered study to determine whether GPT-3.5-turbo can provide clinical recommendations for three tasks (admission status, radiological investigation(s) request status, and antibiotic prescription status) using clinical notes from the Emergency Department. We randomly select 10,000 Emergency Department visits to evaluate the accuracy of zero-shot, GPT-3.5-turbo-generated clinical recommendations across four different prompting strategies. We find that GPT-3.5-turbo performs poorly compared to a resident physician, with accuracy scores 24% lower on average. GPT-3.5-turbo tended to be overly cautious in its recommendations, with high sensitivity at the cost of specificity. Our findings demonstrate that, while early evaluations of the clinical use of LLMs are promising, LLM performance must be significantly improved before their deployment as decision support systems for clinical recommendations and other complex tasks.
Parenting Self-Efficacy within the First Year Postpartum in Non-Birthing Parents: A Scoping Review Protocol
Authors: Dol Justine , Parker Jennifer A. , Chambers Christine T , Joy Phillip , Leahy-Warren Patricia , Dennis Cindy-Lee , Macdonald Marilyn , Hancock Kristy
Published: October 2023

Objective

The objective of this scoping review is to identify and analyze the literature on parenting self-efficacy in the non-birthing parent within the first year postpartum.

Introduction

Parenting self-efficacy is a parent’s confidence in their ability to organize and execute a set of tasks related raising children and providing them with protection and care in order to ensure their healthy development. To date, much of the work on parenting selfefficacy has focused on the birthing parent (e.g., mothers) excluding the non-birthing parent (e.g., fathers and LGBTQ+ parents).

Inclusion criteria

Studies that include participants that identify as the non-birthing parent (regardless of sex or gender) who have had an infant less than 12 months of age. Various self-efficacy outcomes related to parenting will be included, as well as sub-types of selfefficacy (e.g., chest/breastfeeding). No limitations based on context, geography, or parity will be applied. All qualitative and quantitative study designs will be included.

Methods

Databases to be searched will include MEDLINE, Embase, Web of Science, CINAHL, and PsycINFO with no time limitations applied. Title and abstracts and full text will be screened by two reviewers with disagreements solved with a third reviewer. The data extracted will include specific details about the population, study, methods, and outcomes. Data will be reported narratively and in tables, as appropriate.
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

Objectives

Live 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.

Methods

Apost 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.

Results

At 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.

Conclusion

LACTIN-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

Animal 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

Comparative, 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

Retinal 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

Non-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 abstract

In brief

Non-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

Ocean 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

Treatment 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

Of 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

Cell 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

Bacterial 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

Structure 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

B 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

The 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.
Loss of Grp170 results in catastrophic disruption of endoplasmic reticulum functions
Authors: Mann Melissa J. , Melendez-Suchi Chris , Sukhoplyasova Maria , Flory Ashley R. , Carson Irvine Mary , Iyer Anuradha R. , Vorndran Hannah , Guerriero Christopher J. , Brodsky Jeffrey L. , Hendershot Linda M. , Buck Teresa M.
Published: October 2023

GRP170, a product of theHyou1gene, is required for mouse embryonic development, and its ablation in kidney nephrons leads to renal failure. Unlike most chaperones, GRP170 is the lone member of its chaperone family in the ER lumen. However, the cellular requirement for GRP170, which both binds non-native proteins and acts as nucleotide exchange factor for BiP, is poorly understood. Here, we report on the isolation of embryonic fibroblasts from mice in which LoxP sites were engineered in theHyou1loci (Hyou1LoxP/LoxP). A doxycycline-regulated Cre recombinase was also stably introduced into these cells. Induction of Cre resulted in excision ofHyou1and depletion of Grp170 protein, culminating in apoptotic cell death. As Grp170 levels fell we observed increased steady-state binding of BiP to a client, slowed degradation of a misfolded BiP substrate, and BiP accumulation in NP40-insoluble fractions. Consistent with disrupted BiP functions, we observed reactivation of BiP storage pools and induction of the unfolded protein response (UPR) in futile attempts to provide compensatory increases in ER chaperones and folding enzymes. Together, these results provide insights into the cellular consequences of controlled Grp170 loss and insights into mutations in theHyou1locus and human disease.
Chemo-senolytic therapeutic potential against angiosarcoma
Authors: Wang Xuebing , Chung Claire Yik-Lok , Yoshioka Ai , Hashimoto Shinya , Jimbo Haruki , Tanizawa Hideki , Ohta Shinya , Fukumoto Takeshi , Noma Ken-ichi
Published: October 2023

Angiosarcoma is an aggressive soft-tissue sarcoma with a poor prognosis. Chemotherapy for this cancer typically employs paclitaxel, one of the taxanes (genotoxic drugs), although it has a limited effect due to chemoresistance for prolonged treatment. Here we examine a new angiosarcoma treatment approach that combines chemotherapeutic and senolytic agents. We first find that the chemotherapeutic drugs, cisplatin and paclitaxel, efficiently induce cellular senescence of angiosarcoma cells. Subsequent treatment with a senolytic agent, ABT-263, eliminates senescent cells through the activation of the apoptotic pathway. In addition, expression analysis indicates that senescence-associated secretory phenotype (SASP) genes are activated in senescent angiosarcoma cells and that ABT-263 treatment eliminates senescent cells expressing genes in the type-I interferon (IFN-I) pathway. Moreover, we show that cisplatin treatment alone requires a high dose to remove angiosarcoma cells, whereas a lower dose of cisplatin is sufficient to induce senescence, followed by the elimination of senescent cells by senolytic treatment. This study sheds light on a potential therapeutic strategy against angiosarcoma by combining a relatively low dose of cisplatin with the ABT-263 senolytic agent, which can help ease the deleterious side effects of chemotherapy.
Adverse mental health inpatient experiences: Qualitative systematic review of international literature and development of a conceptual framework
Authors: Hallett Nutmeg , Dickinson Rachel , Eneje Emachi , Dickens Geoffrey L.
Published: October 2023

Background

Trauma is increasingly linked to poor health outcomes. Adverse experiences in mental health inpatient settings can be traumatic and contribute to long-lasting negative effects like post-traumatic stress disorder. However, the full range of relevant experiences is often unaddressed in service design and delivery.

Aim

To describe the spectrum of negative experiences that people identify while they are inpatients in adult mental health services.

Method

A systematic literature review was conducted to identify qualitative studies that included people’s subjective negative reports of their inpatient admissions. CINAHL, MEDLINE and PsycINFO were searched from 2000 onwards, alongside a search of Google Scholar. The quality of studies was assessed using the Critical Appraisal Skills Programme qualitative checklist. Data were synthesised using the ‘best-fit’ framework synthesis approach. A patient and public involvement reference group contributed to the review.

Results

Studies (111) from 25 countries were included. Adverse mental health inpatient experiences can be conceptualised under three headings: the ecosystem (the physical environment and the resources available, and other people within or influential to that environment); systems (processes and transitions); and the individual (encroachments on autonomy and traumatisation).

Conclusions

Improved patient experience is associated with improved patient outcomes, and addressing negative experiences could significantly impact patient care. Mental health professionals should strive to create inpatient environments that are supportive, respectful, and safe for patients, which consideration of the adversity framework developed from this review can facilitate.
A Systematic Review: Cardiovascular effects of Systemic Sclerosis
Authors: Panchumarthi Dedeepya , Bathula Sasidhar Reddy , madam Sai Tapasvi , Nemani Raghu Ram Shanmukh , Panjiyar Binay Kumar
Published: October 2023

Systemic sclerosis is a connective autoimmune disorder characterized by the deposition of an extracellular matrix in the internal organs leading to fibrosis and damage to internal organs. Cardiovascular effects of systemic sclerosis include arrhythmias, coronary artery disease, valvular diseases, pericardial diseases, atherosclerosis, myocardial diseases. Thus it also has a fatal effect on the cardiovascular system making it significant to know its epidemiology, pathophysiology, screening techniques, and investigations which help in early diagnosis of the cardiac lesions of systemic sclerosis. Cardiovascular effects of systemic sclerosis is a multidisciplinary approach by a rheumatologist, cardiologist and radiologist. We reviewed 182 articles from renowned journals taken from google scholar and pubmed published between 2010 and 2023 of which 8 articles are focused for in depth review. This systematic review summarizes the effects of systemic sclerosis on cardiovascular system ranging from arrhythmias to pericardial diseases in brief including the pathogenesis, investigations and epidemiology.
The lung extracellular matrix protein landscape in severe early-onset and moderate chronic obstructive pulmonary disease
Authors: Joglekar M.M. , Bekker N.J. , Ngassie M.L. Koloko , Vonk J.M. , Borghuis T. , Reinders-Luinge M.A. , Bakker J. , Woldhuis R.R. , Pouwels S.D. , Melgert B.N. , Timens W. , Brandsma C.A. , Burgess J.K.
Published: October 2023

Extracellular matrix (ECM) remodeling has been implicated in the irreversible obstruction of airways and destruction of alveolar tissue in chronic obstructive pulmonary disease (COPD). Studies investigating differences in the lung ECM in COPD have mainly focused on some collagens and elastin, leaving an array of ECM components unexplored. We investigated the differences in the ECM landscape comparing severe-early onset (SEO-) COPD and moderate COPD to control lung tissue for collagen type I α chain 1 (COL1A1), COL6A1, COL6A2, COL14A1, fibulin 2 and 5 (FBLN2, FBLN5), latent transforming growth factor-beta binding protein 4 (LTBP4), lumican (LUM), versican (VCAN), decorin (DCN), and elastin (ELN) using image analysis and statistical modelling. Percentage area and/or mean intensity of expression of LUM in the parenchyma, and COL1A1, FBLN2, LTBP4, DCN, and VCAN in the airway walls, was proportionally lower in COPD compared to controls. Lowered levels of most ECM proteins were associated with decreasing FEV1measurements, indicating a relationship with disease severity. Furthermore, we identified six unique ECM signatures where LUM and COL6A1 in parenchyma and COL1A1, FBLN5, DCN, and VCAN in airway walls appear essential in reflecting the presence and severity of COPD. These signatures emphasize the need to examine groups of proteins to represent an overall difference in the ECM landscape in COPD, that are more likely to be related to functional effects, than individual proteins. Our study revealed differences in the lung ECM landscape between control and COPD and between SEO and moderate COPD signifying distinct pathological processes in the different subgroups.

NEW & NOTEWORTHY

Our study identified COPD-associated differences in the lung ECM composition. We highlight the compartmental differences in the ECM landscape in different subtypes of COPD. The most prominent differences were observed for severe-early onset COPD. Moreover, we identified unique ECM signatures that describe airway walls and parenchyma providing insight into the intertwined nature and complexity of ECM changes in COPD that together drive ECM remodeling and may contribute to disease pathogenesis.
ConfluentFUCCI for fully-automated analysis of cell-cycle progression in a highly dense collective of migrating cells
Authors: Goldstien Leo , Lavi Yael , Atia Lior
Published: October 2023

Understanding mechanisms underlying various physiological and pathological processes requires accurate and fully automated analysis of dense cell populations that collectively migrate, and specifically, relations between biophysical features and cell cycle progression aspects. A seminal tool that led to a leap in real-time study of cell cycle is the fluorescent ubiquitination-based cell cycle indicator (FUCCI). Here, we introduce ConfluentFUCCI, an open-source graphical user interface-based framework designed for fully automated analysis of cell cycle progression, cellular dynamics, and cellular morphology, in highly dense migrating cell collectives. Leveraging state-of-the-art tools, some incorporate deep learning, ConfluentFUCCI offers accurate nuclear segmentation and tracking using FUCCI tags, enabling comprehensive investigation of cell cycle progression at both the tissue and single-cell levels. We compare ConfluentFUCCI to the most recent relevant tool, showcasing its accuracy and efficiency in handling large datasets. Furthermore, we demonstrate the ability of ConfluentFUCCI to monitor cell cycle transitions, dynamics, and morphology within densely packed epithelial cell populations, enabling insights into mechanotransductive regulation of cell cycle progression. The presented tool provides a robust approach for investigating cell cycle-related phenomena in complex biological systems, offering potential applications in cancer research and other fields.
Streamlined generation of CRISPR/Cas9-mediated single-cell knockout clones in murine cell lines
Authors: Tobias Hub , Alex Cornean , Kellen Round , Thomas Fleming , Marc Freichel , Rebekka Medert
Published: October 2023

Clonal cell lines harbouring loss-of-function mutations in genes of interest are crucial for studying the cellular functions of the encoded proteins. Recent advances in genome engineering have converged on the CRISPR/Cas9 technology to quickly and reliably generate frameshift mutations in the target genes across various cell lines and species. Although high on-target cleavage efficiencies can be obtained reproducibly, screening and identifying clones with loss-of-function alleles remains a major bottleneck. Here, we describe a single sgRNA strategy to generate CRISPR/Cas9-mediated frameshift mutations in target genes of mammalian cell lines that can be easily and cost-effectively identified. Given the proliferation of workhorse cell lines such as HEK293 and N2a cells and the resulting clonal expansion of the cell type, our protocol can facilitate the isolation of knockout clonal cell lines and their genetic validation within a period of down to 3-4 weeks.
Factors affecting merchants' acceptance of P2P m-payments: a multigroup moderating effect of gender, age, and experience
Authors: Jean Pierre Sadrac , Mombeuil Claudel
Published: October 2023

Purpose

This paper hypothesized that perceived relative advantage and perceived compatibility would have a positive effect on merchants' intention to accept payments via P2P mobile payment services, while perceived financial risks and perceived costs would have a negative effect. The study also explored the differences in gender, age and experience.

Design/methodology/approach

The proposed model is based on the valence framework, where positive utility is represented by relative advantage and perceived compatibility, while negative utility is represented by perceived risks and perceived costs. The data for this study were collected from small business owners (merchants) at the largest public market in the Center Department of Mirebalais, Haiti, using a purposive sampling method.

Findings

The results of a structural equation modeling on a sample of 339 merchants only confirmed the effect of both perceived comparative advantage and perceived compatibility. Furthermore, the multigroup analysis revealed that the perceived comparative advantage is stronger for female merchants, older age groups and merchants who frequently used P2P m-payment for the transfer of remittances. Perceived compatibility is stronger for male merchants, younger age groups and merchants who occasionally used P2P m-payment for the transfer of remittances.

Originality/value

This study was conducted in the economic context of Haiti, where P2P m-payments are commonly used for transferring remittances. Since there are limited studies that examine P2P m-payment acceptance from the perspective of merchants, this study offers valuable insights.