bluuebunny/crossref_metadata_2025 huggingface dataset:
Building a model of sepsis: data integration unravels pathogenic mechanisms in severeP. aeruginosainfections
Authors: Messina Francesco , Rotondo Claudia , Ladeira Luiz , Properzi Michele , Dimartino Valentina , Riccitelli Benedetta , Staumont Bernard , Chilemi Giovanni , Geris Liesbet , Bocci Maria Grazia , Fontana Carla
Published: October 2024

Understanding how human hosts and bacterial pathogens interact with each other is essential to explaining the differences in severity and outcomes of systemic infectious diseases (sepsis). Such pathogens, likePseudomonas aeruginosa(PA), remain a major public health concern. In this work we present a data integration workflow to build a model of interaction betweenPAand its human host. The pathogenic mechanisms ofPAinfection are described through accurate mapping of protein-protein, and metabolite-protein direct interactions, betweenPAand human host, as well as a description of pathways activated in organs affected by severePAinfections.

In the first step, a literature review process was carried out based on previous experiences with virus-host interaction models. The collected Data was organized to build a conceptual model on multiple levels, providing a view of the relevant mechanisms involved in severe bacterial infections. All information aboutPAinfection was categorized into three main groups: a) conceptual information about pathogenesis; b) molecular interactions between bacterium and humans; and c) gene expression signatures and dysregulated pathways in severe infections. A dataset of 89PA– human interactions, involving 152 proteins/molecules (109 human proteins, 3 human molecules, 34PAproteins, and 5PAmolecules) was reviewed and annotated, providing a new perspective on thePA-host interaction to improve understanding of the host biological responses. Such data were complemented by transcriptomic data onPA-infected lung samples, highlighting overexpression of proinflammatory pathways as well as modulation of the activities ofPAon the host response in the lung.

Importance

The intricate interplay between host and microbial pathogens prompts us to use innovative data sources, combining omics data, clinical patient data, and pathogen features, through exploratory computational methods. A data curation process allowed us to put together a detailed description of the pathogenic mechanisms ofPAin the human host, connecting basic knowledge about clinical aspects, interactions between bacterial and host proteins, and pathways dysregulated duringPAinfection. The results of our work allowed us to start putting together a model ofPAinfection, defining specific steps inPAinfections and providing a significant step forward in understanding the deep interaction betweenPAand the human host in severe infections. This approach could be an effective way to predict specific clinical phenotypes in severe bacterial infections.
Resolving an unconventional non-photochemical quenching signature at the light-to-dark transition
Authors: Lam Lam , Patel-Tupper Dhruv , Lam Henry E. , Steen Collin J. , Ma Alexa , Ma Sophia A. , Leipertz Anna , Lee Tsung-Yen , Fleming Graham R. , Niyogi Krishna K.
Published: October 2024

Non-photochemical quenching (NPQ) protects photosynthetic organisms via diverse molecular players contributing at varying timescales. However, in the absence of one of the largest contributors to NPQ, energy-dependent quenching (qE), we observe an unusual but universal phenomenon: a transient increase in quenching in the dark following high light exposure. To mechanistically interrogate this light-to-dark (LtD) NPQ phenotype, we performed chlorophyll fluorescence lifetime snapshot measurements across a diverse array of Arabidopsis mutant backgrounds and chemical treatments. We found that the electrochemical gradient across the thylakoid membrane is essential for this phenomenon. Through analysis of higher-order Arabidopsis mutants, we also found that LtD NPQ is independent of the known forms of photoprotective NPQ, as well as the major and minor light-harvesting complexes (LHCII). Our results point to LtD NPQ as a photoinhibition (qI)-related, reaction center quenching with implications for photoprotection in fluctuating light.
In vivoProtective Efficacy of Emodin in Swiss Albino Mice Induced with Dalton Ascitic Lymphoma
Authors: Suluvoy Jagadish Kumar , Kolla Harish Babu , Joel Jesse , Balasubramanian Aavany
Published: October 2024

Lymphoma is a tumor that affects lymphoid tissues in the body. Treating lymphoma has become challenging because of the complexity of disease pathology, drug resistance mechanisms and side effects of existing chemo and radiation therapies. Treating cancers/tumors with plant based natural compounds is gaining interest recently because of their less toxicity profiles and efficiency in controlling the disease severity. Emodin is one such compound with such anti-cancer/tumor properties. It has immunosuppressive and anti-cancer properties through multiple ways. In this study, we have studied the therapeutic effect of emodin molecule in the DAL induced lymphoma, a well-established murine model to study and test the anti-lymphoma drugs. Our data has shown an outstanding therapeutic effect of emodin in controlling the lymphoma readouts in DAL induce Swiss Albino mice. These effects were studied in comparison with a standard drug molecule called methotrexate. Furthermore, thein-silicoanalysis has shown that emodin as a potential drug candidate for lymphoma based on the Lipinski’s rule of 5.
Comparative analysis of six adeno-associated viral vector serotypes in mouse inferior colliculus and cerebellum
Authors: Witteveen Isabelle , Balmer Timothy
Published: October 2024

Adeno-associated viral vector (AAV) serotypes vary in how effectively they express genes across different cell types and brain regions. Here we report a systematic comparison of the AAV serotypes 1, 2, 5, 8, 9, and the directed evolution derived AAVrg, in the inferior colliculus and cerebellum. The AAVs were identical apart from their different serotypes, each having a synapsin promotor and expressing GFP (AAV-hSyn-GFP). Identical titers and volumes were injected into the inferior colliculus and cerebellum of adult male and female mice and brains were sectioned and imaged 2 weeks later. Transduction efficacy, anterograde labeling of axonal projections, and retrograde labeling of somata, were characterized and compared across serotypes. Cell-type tropism was assessed by analyzing the morphology of the GFP-labeled neurons in the cerebellar cortex. In both the cerebellum and inferior colliculus, AAV1 expressed GFP in more cells, labeled a larger volume, and produced significantly brighter labeling than all other serotypes, indicating superior transgene expression. AAV1 labeled more Purkinje cells, unipolar brush cells, and molecular layer interneurons than the other serotypes, while AAV2 labeled a greater number of granule cells. These results provide guidelines for the use of AAVs as gene delivery tools in these regions.

Significance

AAVs have become ubiquitous gene expression tools in neuroscience research and are becoming more common in clinical settings. Naturally occurring and engineered serotypes have varying abilities to infect neurons and cause them to produce proteins of interest. The efficacy of AAV transduction in specific cell types depends on many factors and remains difficult to predict, so an empirical approach is often required to determine the best performing serotype in each population of cells. In the present study we show that AAV1 produces the highest expression in these two regions, labels the most axonal projections, and labels Purkinje cells and unipolar brush cells better than the other serotypes tested, while AAV2 labels granule cells most effectively.
Plasmid transmission dynamics and evolution of partner quality in a natural population of Rhizobium leguminosarum
Authors: Vereau Gorbitz David , Schwarz Chase , McMullen John G , Cerón-Romero Mario , Doyle Rebecca T. , Lau Jennifer A , Whitaker Rachel J , Vanderpool Carin K , Heath Katy
Published: October 2024

Many bacterial traits important to host-microbe symbiosis are determined by genes carried on extrachromosomal replicons such as plasmids, chromids, and integrative and conjugative elements. Multiple such replicons often coexist within a single cell and, due to horizontal mobility, have patterns of variation and evolutionary histories that are distinct from each other and from the bacterial chromosome. In nitrogen-fixing Rhizobium, genes carried on multiple plasmids make up almost 50% of the genome, are necessary for the formation of symbiosis, and underlie bacterial traits including host plant benefits. Thus the genomics and transmission of plasmids in Rhizobium underlie the ecology and evolution of this important model symbiont. Here we leverage a natural population of clover-associated Rhizobium in which partner quality has declined in response to long-term nitrogen fertilization. We use 62 novel, reference-quality genomes to characterize 257 replicons in the plasmidome and study their genomics and transmission patterns. We find that, of the four most frequent plasmid types, two (types II & III) have more stable size, larger core genomes, and track the chromosomal phylogeny (display more vertical transmission), while others (types I & IV – the symbiosis plasmid, or pSym) vary substantially in size, shared gene content, and have phylogenies consistent with frequent horizontal transmission. We also find differentiation in pSym subtypes driven by long-term nitrogen fertilization. Our results highlight the variation in plasmid transmission dynamics within a single symbiont and implicate plasmid horizontal transmission in the evolution of partner quality.
Ostial side branch stenosis in non-stenotic coronary segments: a characteristic finding in diabetes mellitus
Authors: Yamanaka Yasushi , Fujimori Yoshiharu , Hashimoto Satoshi , Kurihara Kazuto , Sasaki Tomoko , Yoshimura Masayuki , Takahashi Miki , Wakabayashi Tadamasa , Imai Taku
Published: October 2024

2.

Background

Ostial stenosis, a narrowing at the origin of coronary side branches, is commonly observed in branches diverging from stenotic coronary segments. However, it may also occur in branches diverging from non-stenotic segments, and the factors contributing to this phenomenon remain unclear.

Objectives

This study aimed to assess the incidence of ostial stenosis in coronary side branches diverging from non-stenotic segments and to identify associated risk factors.

Methods

We conducted a retrospective analysis of first-time, elective coronary angiograms (CAGs) from 884 patients. Side branches with a diameter larger than 2mm were included. Ostial stenosis was defined by two criteria: 1) the side branch diverged from a coronary segment with less than 25% diameter stenosis, and 2) the side branch exhibited ostial narrowing with more than 50% diameter stenosis. Clinical factors, including diabetes mellitus and lipid profiles, were assessed. Multivariate logistic regression was used to identify independent predictors of ostial stenosis.

Results

Of the 4,739 side branches analyzed, 508 (10.7%) exhibited ostial stenosis. Ostial stenosis was present in 285 (32.2%) patients. Patients with ostial stenosis had a significantly higher prevalence of diabetes mellitus (60.0% vs. 33.0%,p<0.00001) and lower high-density lipoprotein (HDL) cholesterol levels (48.5 ± 14.6 mg/dL vs. 52.0 ± 14.9 mg/dL,p<0.01) compared to those without stenosis. No significant differences were found in other clinical factors. Multivariate analysis identified diabetes mellitus as an independent predictor of ostial stenosis (odds ratio: 0.29, 95% CI: 0.20-0.43,p<0.0001).

Conclusions

Ostial stenosis in side branches diverging from non-stenotic coronary segments is significantly associated with diabetes mellitus. In diabetic patients, factors such as negative arterial remodeling, insulin resistance, and endothelial dysfunction likely play key roles in the development of this condition. These findings suggest that ostial stenosis could be an additional marker of advanced coronary artery disease in diabetes.
Elevated Liver Damage Biomarkers in Long COVID: A Systematic Review and Meta-Analysis
Authors: Almulla Abbas F. , Thipakorn Yanin , Zhang Yingqian , Maes Michael
Published: October 2024

Background

Long COVID (LC) presents with complex pathophysiology, affecting multiple organs and producing a range of symptoms, from neuropsychiatric disturbances to multi-organ dysfunction. Liver damage has emerged as a notable feature, yet no systematic review or meta-analysis has comprehensively evaluated the biomarkers confirming liver injury in LC patients.

Objective

The present study aims to examine blood-based biomarkers of liver damage in LC disease.

Methods

A search of PubMed, Google Scholar, SciFinder, and SCOPUS identified 61 eligible studies, including 7172 participants, with 3404 LC patients and 3768 controls.

Results

Our analysis identified a significant increase in the liver damage index among LC patients, with a moderate effect size (standardized mean difference, SMD = 0.553; confidence intervals; 95% CI: 0.305–0.760) compared to normal controls. Additionally, LC patients exhibited marked elevations in alanine aminotransferase (SMD = 0.615; 95% CI: 0.351;0.878), aspartate aminotransferase (SMD = 0.352; 95% CI: 0.068;0.637), gamma-glutamyl transferase (SMD = 0.969; 95% CI: 0.194;1.745), and lactate dehydrogenase (SMD = 0.666; 95% CI: 0.332;0.999) activities. Moreover, significant reductions were observed in total protein (SMD = -0.326; 95% CI: -0.631; -0.021) and increases in prothrombin time (SMD = 0.633; 95% CI: 0.077;1.189), ferritin (SMD = 0.437; 95% CI: 0.069;0.805), D-dimer (SMD = 0.359; 95% CI: 0.144;0.573). Further studies are needed to confirm reductions in platelet count and elevations in fibrinogen levels

Conclusion

This study suggests that LC is associated with persistent liver damage and coagulopathy, highlighting the need to incorporate liver injury into treatment strategies to reduce potential risks.
Outcomes of patients with calcific aortic valve disease according to the extent of cardiac damage
Authors: Moore Matthew K , Jones Gregory T , Whalley Gillian , Prendergast Bernard , Williams Michael J.A. , Coffey Sean
Published: October 2024

Abstract

Background

A staging system for aortic stenosis (AS) based upon the extent of cardiac damage has been proposed to better stratify risk and evaluate the benefit of aortic valve intervention (AVI), especially in those with moderate AS. We sought to evaluate the prognostic value of this staging system.

Methods

Data from initial clinically indicated echocardiograms performed between 2010 and 2018 in patients >18 years of age were extracted and linked to national outcome data. The combined primary outcome was mortality or hospitalization with heart failure.

Results

Amongst 24,699 patients, 513 and 920 had moderate and mild AS, respectively. In moderate AS, Stage 0 cardiac damage was present in 9.4%, Stage 1 in 53.7%, Stage 2 in 31.1%, Stage 3 in 3.2%, and Stage 4 in 2.6%. In mild AS, rates were 11.5%, 57.8%, 25.0%, 2.6%, and 3.0% for each consecutive stage. Increasing stage was associated with increased risk of the primary outcome in both moderate (HR 1.62/stage) and mild AS (HR 1.93/stage). After censoring at the time of AVI, increasing stage was also associated with mortality in moderate (HR 1.97/stage) and mild AS (HR 2.06/stage).

Conclusion

Stage of cardiac damage predicts prognosis in both moderate and mild AS to a similar extent. Outcomes may therefore not be fully related to the haemodynamic consequences of valve disease, and hence may not be entirely reversible after valve intervention. Revised management algorithms focusing on earlier intervention and novel treatment strategies targeting cardiac damage are needed to improve clinical outcomes in patients with AS.
Suppression ofaedes aegyptiby sterile insect technique on captiva island, florida, usa from 2020 to 2022
Authors: Morreale Rachel , Carvalho Danilo Oliveira , Stenhouse Steven , Bajonero Johanna , Pereira Rui , Hahn Daniel A , Lloyd Aaron , Hoel David F.
Published: October 2024

Aedes aegypti, an aggressive nuisance biter and the primary vector for numerous arboviruses, such as chikungunya, dengue, and Zika, presents significant control challenges due to its ability to thrive in urban environments, escapes insecticide treatment by using cryptic resting and oviposition sites, and development of resistance to chemical mosquito control products being used routinely. To test a new approach in their integrative mosquito management toolbox. From 2020 to 2022, the Lee County Mosquito Control District (LCMCD) employed the Sterile Insect Technique (SIT) to test a new approach in its integrated mosquito management toolbox, targeting the population suppression ofAe. aegyption Captiva Island, Florida. Over 24.1 million sterile males were released across three phases, covering up to 142 hectares. The study demonstrated a population reduction of up to 79% in wild adults and a 59% decline in egg densities in the primary intervention area. While population control was successful, an influx of wild females from untreated zones posed ongoing challenges to complete suppression in areas close to non-intervention areas. This supported a need for an area-wide integrated pest management (AW-IPM) approach. These results underscore SIT’s potential as a critical tool in integrated mosquito management strategies and emphasize practical application.
Multi-timescale neural adaptation underlying long-term musculoskeletal reorganization
Authors: Philipp Roland , Hara Yuki , Uchida Naoki , Ohta Naohito , Oya Tomomichi , Funato Tetsuro , Seki Kazuhiko
Published: October 2024

The central nervous system (CNS) can effectively control body movements despite environmental changes. While much is known about adaptation to external environmental changes, less is known about responses to internal bodily changes. This study investigates how the CNS adapts to long-term alterations in the musculoskeletal system using a tendon transfer model in non-human primates. We surgically relocated finger flexor and extensor muscles to examine how the CNS adapts its strategy for finger movement control by measuring muscle activities during grasping tasks. Two months post-surgery, the monkeys demonstrated significant recovery of grasping function despite the initial disruption. Our findings suggest a two-phase CNS adaptation process: an initial phase enabling function with the transferred muscles, followed by a later phase abolishing this enabled function and restoring a more efficient and “good enough” control strategy resembling the original. These results highlight a multi-phase CNS adaptation process with distinct time constants in response to sudden bodily changes, offering potential insights into understanding and treating movement disorders.

SIGNIFICANCE STATEMENT

This study demonstrates the remarkable ability of the CNS to adapt motor control to long-term internal changes, even after significant alterations to the musculoskeletal system. These findings expand our understanding of CNS plasticity and offer promising insights for enhancing rehabilitation following injuries or surgeries that disrupt body mechanics. By unraveling the mechanisms behind this long-term adaptation, targeted rehabilitation strategies to optimize motor recovery in patients with stroke, spinal cord injury, or musculoskeletal disorders can be developed, ultimately improving patient outcomes and quality of life.
Using readmers and hapmers in assessing phase switching after read error correction of Oxford Nanopore Sequences
Authors: Elbers Jean P. , Horner David , Löwenstern Tamara , Laccone Franco
Published: October 2024

Abstract

Methods for sequence error correction can improve sequence accuracy; however, there can be unintended errors added during error correction. One such example is phase switching, whereby sequences derived from genomes containing more than one parental copy have contributions from more than one parental haplotype. Such switches are mistakes that can confound downstream analyses especiallyde novogenome assembly. While DNA sequences do not possess words such as linguistic languages, one can partition a DNA sequence into word-like objects called k-mers. K-mers include pieces of DNA sequence of k length that can describe various properties of DNA sequences. With regard to phase switching, there are k-mers present in one parental haplotype not found in other(s). These so-called hapmers can represent inaccuracies in that parental haplotype’s assembly but also correct, unique DNA variation. Here we investigated the effect of DNA sequence error correction on phase switching at the sequence/read level. Using several error-correction methods, we find all methods tested are similar to raw, presumably, phase-switch-free Oxford Nanopore Technologies (ONT) sequences in the percentage of readmers (k-mers from the ONT sequences) matching one parental haplotype’s hapmers. This work demonstrates an efficient method to assess if an error-correction method has introduced phase switching implemented in the Julia programming language.
Sex and seasonal variations in melatonin suppression, and alerting response to light
Authors: Fazlali Fatemeh , Lazar Rafael , Yahya Faady , Stefani Oliver , Spitschan Manuel , Cajochen Christian
Published: October 2024

Light influences human physiology and behaviour by regulating circadian rhythms, melatonin secretion, and alertness. Previous research has reported sex differences in melatonin secretion and circadian rhythms, possibly related to women’s greater sensitivity to bright light. Other studies have suggested reduced photosensitivity and earlier circadian phases in summer than in winter in mid-latitude regions. This study explores the effects of sex, seasonality, and their combination on melatonin suppression and subjective sleepiness in response to moderate light exposure, considering prior light history and menstrual phases in females. We conducted a controlled, within-subject experiment with 48 healthy adults (18–35 years, 50% female) across different seasons. The study design included two 9-h laboratory sessions, with at least 5-day washout in between. Participants were exposed to dim and moderate light through a screen for 2 hours after their habitual bedtime. Female participants exhibited greater melatonin suppression (+4.69 %) but a lower alerting response (−6.00%) to moderate light compared to males. Both sexes demonstrated increased sensitivity to the NIF effects of light in winter, with stronger melatonin suppression (+18.05 %) and increased alertness (+7.60 %) compared to summer. While prior light history did not significantly impact melatonin suppression or alertness, it was associated with an earlier dim light melatonin onset (DLMO). Females during their luteal phase had earlier DLMO than those in their follicular phase. Our findings indicate an interaction between sex, seasonality, and light exposure in modulating melatonin suppression, emphasising the need for personalised light exposure recommendations according to individual biological and environmental contexts.
Development and Characterization of a 2D Porcine Colonic Organoid Model for Studying Intestinal Physiology and Barrier Function
Authors: Plenge Masina , Schnepel Nadine , Müsken Mathias , Rohde Judith , Goethe Ralph , Breves Gerhard , Mazzuoli-Weber Gemma , Benz Pascal
Published: October 2024

The porcine colon epithelium plays a crucial role in nutrient absorption, ion transport, and barrier function. However ethical concerns necessitate the development of alternatives to animal models for its study. The objective of this study was to develop and characterise a two-dimensional (2D)in vitromodel of porcine colonic organoids that closely mimics native colon tissue, thereby supporting in vitro research in gastrointestinal physiology, pathology, and pharmacology. Porcine colonic crypts were isolated and cultured in three-dimensional (3D) organoid systems, which were subsequently disaggregated to form 2D monolayers on transwell inserts. The integrity of the monolayers was evaluated through the measurement of transepithelial electrical resistance (TEER) and electron microscopy. The functional prerequisites of the model were evaluated through the measurement of the mRNA expression of key ion channels and transporters, using quantitative RT-PCR. Ussing chamber experiments were performed to verify physiological activity. The 2D monolayer displayed robust TEER values and retained structural characteristics, including microvilli and mucus-secreting goblet cells, comparable to those observed in native colon tissue. Gene expression analysis revealed no significant differences between the 2D organoid model and native tissue with regard to critical transporters. Ussing chamber experiments demonstrated physiological responses that were consistent with those observed in native colonic tissue. In conclusion, 2D porcine colonic organoid model can be recommended as an accurate representation of the physiological and functional attributes of the native colon epithelium. This model offers a valuable tool for investigating intestinal barrier properties, ion transport, and the pathophysiology of gastrointestinal diseases, while adhering to the 3R principles.
Combined Linkage Disequilibrium and Linkage Analysis (cLDLA): implementation of a powerful approach to identify the genetic basis of complex traits in a bioinformatics workflow
Authors: Upadhyay M. , Panchal A. , Medugorac I.
Published: October 2024

Identifying the relationship between the polymorphism segregating in a population and phenotypic differences of a trait observed between the individuals of a population is of major biological interest and represents the basis of forward genetics. Much of the traits of interest are influenced by several polymorphic genes and environmental conditions. Often the loci associated with such measurable traits are referred to as Quantitative trait loci. These loci are identified using several statistical approaches. One of them is combined linkage disequilibrium and linkage analysis (cLDLA). This approach, first proposed by Meuwissen and colleagues in 2002, is shown to be robust against population stratification/family structure and requires a relatively lower sample size compared to a genome-wide association study design. Previously, we have successfully used this approach in mapping several important traits in livestock such as identifying the genetic basis of polled condition in cattle and tail length in sheep. A cLDLA requires several complex computation processing and intermediary file conversion steps; for some of these steps no open-source tools are available. Therefore, running this analysis, manually, can prove challenging, tedious, or error-prone. We present, cldla, a bioinformatics workflow implemented in nextflow which takes the vcf file and phenotype file as inputs and implements all the downstream processing required for cLDLA. Additionally, it also has a separate workflow to estimate SNP-based heritability and features for interactive visualization of the results. The workflow is freely available at:https://github.com/Popgen48/cldla.
LIFERING, an E3 ligase, ubiquitinates the acyl-CoA dehydrogenase-like protein IBR3, and coordinates cell proliferation and death upon DNA damage
Authors: Kállai Brigitta M. , Németh Edit , Pettkó-Szandtner Aladár , Ahmad Zaki , Nagy Fruzsina , Bögre László , Magyar Zoltán , Mészáros Tamás , Horváth Beatrix M.
Published: October 2024

Plants rapidly respond to environmental changes to ensure an optimal balance between growth and survival with intact genome. Here, we show that a DNA damage response gene, which we namedLIFERING, is under the direct and independent regulation of ATM/ATR-SOG1 and RBR pathways. We demonstrate that LIFERING upon DNA damage plays an essential role in maintaining the balance between cell proliferation and cell death. Downstream of RBR, it is required to maintain proliferation, and in response to DNA damaging agents it initiates a cell death accompanied by rapid elongation and differentiation of the transit amplifying cells in the root meristem. LIFERING is a RING-between-RING E3 ligase; its ligase activity is dependent on the Cys392 residue located in the BRcat domain, responsible for the coordination of zinc ion binding. Using proximity labelling, we identified the acyl-CoA dehydrogenase-like protein IBR3, which is involved in the conversion of indole-3-butyric acid (IBA) to indole-3-acetic acid (IAA), as one of its targets. We provide evidence that IBR3 is ubiquitinated at several Lys residues in the presence of LIFERING. Our findings show that LIFERING rapidly responds to DNA damage and via ubiquitination of IBR3, is likely to be involved in the regulation of free-auxin level, indicating a link between DNA damage response and auxin regulation in the root.
Integrin alpha1 beta1 promotes interstitial fibrosis in a mouse model of polycystic kidney disease
Authors: Grenier C. , Lin I-H. , Peters DJM. , Pozzi A. , Lennon R. , Naylor RW.
Published: October 2024

Fibrosis is the cause of end-stage kidney failure in patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD). The molecular and cellular mechanisms involved in fibrosis are complex and anti-fibrotic therapies have so far failed to make an impact on patient welfare. Using unbiased proteomics analysis on thePkd1nl/nlmouse, we found that expression of the integrin α1 subunit is increased in this model of ADPKD. In human ADPKD tissue and two single cell RNA kidney disease datasets,ITGA1was also upregulated. To investigate the functional role of this integrin subunit in ADPKD, we generated aPkd1nl/nlItga1−/−mouse. We observed a significant reduction in kidney volume and kidney dysfunction in mice lacking the integrin α1 subunit. Kidneys fromPkd1nl/nlItga1−/−mice had smaller cysts and reduced interstitial expansion and tubular atrophy. Picrosirius red staining identified a restriction in collagen staining in the interstitium and the myofibroblast marker α smooth muscle actin was also downregulated. Myofibroblast cell proliferation was reduced inPkd1nl/nlItga1−/−mice and primary fibroblast cultures demonstrated an abrogated fibrogenic phenotype in integrin α1-depleted fibroblasts. These results highlight a previously unrecognised role for the integrin α1 subunit in kidney fibrosis.
Zika and Dengue Viruses Differentially Modulate Host mRNA Processing Factors Defining Its Virulence
Authors: Scholl Aaron , Gong Binsheng , Li Bingjie , Fatima Tahira , Tirrell Nikki , Karaiskos Spyros , Rios Maria , Xu Joshua , De Sandip
Published: October 2024

Rising global temperatures coupled with increasing international travel, and trade are contributing to spread of vectors such as ticks and mosquitoes, resulting in a surge of vector-borne flavivirus infection in human population. Furthermore, this increase in flavivirus infection pose threat to the safety of biologics such as cell and gene therapy products as human-derived materials are commonly used during manufacturing of these drug products. In this study, we conducted time-course transcriptomic and protein analyses to uncover the host molecular factors driving the virulence of Zika virus (ZIKV) and Dengue virus (DENV) in the context of host defense mechanisms, as these two viruses have caused the most recent and significant flavivirus outbreaks. Compared to DENV, ZIKV exhibited stronger virulence and cytopathic effects. RNA sequencing analysis revealed differential expression of various cellular factors, including RNA processing factors. Further investigation identified cell-type and time-dependent upregulation nonsense-mediated RNA decay (NMD), RNA degradation factors and nuclear pore complex (NPC) transcripts. Protein analysis showed that ZIKV, unlike DENV, degrades NMD factors in host cells, which along with mis-regulation of RNA degradation factors resulted in accumulation in host intronic transcripts as revealed by RNA-seq data. We also found that active nuclear transport is required for ZIKV replication, suggesting that therapeutic targeting of the NPC could potentially be effective in controlling ZIKV infection. Furthermore, from our findings we hypothesize that, ZIKV, but not DENV, drives early host cell cytopathy through targeted protein degradation. Current studies are underway to develop novel strategies to detect ZIKV, DENV and other flaviviruses in biologics based on transcriptomics and proteomics.

Teaser

Exploring the molecular basis of flavivirus virulence in host cells.
The representational geometry for naturalistic textures in macaque V1 and V2
Authors: Pavuluri Abhimanyu , Kohn Adam
Published: October 2024

Our understanding of visual cortical processing has relied primarily on studying the selectivity of individual neurons in different areas. A complementary approach is to study how the representational geometry of neuronal populations differs across areas. Though the geometry is derived from individual neuronal selectivity, it can reveal encoding strategies difficult to infer from single neuron responses. In addition, recent theoretical work has begun to relate distinct functional objectives to different representational geometries. To understand how the representational geometry changes across stages of processing, we measured neuronal population responses in primary visual cortex (V1) and area V2 of macaque monkeys to an ensemble of synthetic, naturalistic textures. Responses were lower dimensional in V2 than V1, and there was a better alignment of V2 population responses to different textures. The representational geometry in V2 afforded better discriminability between out-of-sample textures. We performed complementary analyses of standard convolutional network models, which did not replicate the representational geometry of cortex. We conclude that there is a shift in the representational geometry between V1 and V2, with the V2 representation exhibiting features of a low-dimensional, systematic encoding of different textures and of different instantiations of each texture. Our results suggest that comparisons of representational geometry can reveal important transformations that occur across successive stages of visual processing.
P23H rhodopsin aggregation in the ER causes synaptic protein imbalance in rod photoreceptors
Authors: Thompson Samantha L. , Crowder Sophie M. , Hekmatara Maryam , Sechrest Emily R. , Deng Wen-Tao , Robichaux Michael A.
Published: October 2024

Rod photoreceptor neurons in the retina detect scotopic light through the visual pigment rhodopsin (Rho) in their outer segments (OS). Efficient Rho trafficking to the OS through the inner rod compartments is critical for long-term rod health. Given the importance of protein trafficking to the OS, less is known about the trafficking of rod synaptic proteins. Furthermore, the subcellular impact of Rho mislocalization on rod synapses (i.e., “spherules”) has not been investigated. In this study we used super-resolution and electron microscopies, along with proteomics, to perform a subcellular analysis of Rho synaptic mislocalization in P23H-Rho-RFP mutant mice. We discovered that mutant P23H-Rho-RFP protein mislocalized in distinct ER aggregations within the spherule cytoplasm, which we confirmed with AAV overexpression. Additionally, we found synaptic protein abundance differences in P23H-Rho-RFP mice. By comparison, Rho mislocalized along the spherule plasma membrane in WT and rd10 mutant rods, in which there was no synaptic protein disruption. Throughout the study, we also identified a network of ER membranes within WT rod presynaptic spherules. Together, our findings indicate that photoreceptor synaptic proteins are sensitive to ER dysregulation.

Summary Statement

This study examines the impact of rhodopsin mislocalization on rod photoreceptor synaptic structures and synaptic protein levels using P23H rhodopsin and other retinitis pigmentosa mouse models.
A Practical and Safe Model of Nitrogen Mustard Injury in Cornea
Authors: Sandoval-Castellanos Ana M. , Ke Yao , Dam Tiffany M. , Maverakis Emanual , Mannis Mark J. , Wang Xiao-Jing , Zhao Min
Published: October 2024

Purpose

Sulfur mustard (SM) is an alkylating agent used in warfare and terrorism that inflicts devastating ocular injuries. Although the clinical symptoms are well described, the underlying mechanisms are not fully understood, hindering the development of effective treatments. One major roadblock is the lack of a suitable model due to the extremely hazardous nature of SM, which requires strict safety measures. As a safe and practical alternative, we report a novel model that uses mechlorethamine (nitrogen mustard) gel, an FDA-approved topical chemotherapeutic administered by patients at home. Here we demonstrate its suitability to induce mustard corneal injury in any laboratory.

Methods

Ex vivoporcine corneas were injured with mechlorethamine gel. Hematoxylin-eosin staining, and immunohistochemistry were performed to evaluate histopathology of SM-like corneal injuries: epithelium thickness and stromal separation, keratocyte and inflammatory cell counts, and expression of inflammation and fibrosis markers.

Results

This model showed the characteristic histopathology and expression of cyclooxygenase-2 (inflammation) and fibronectin-1 (fibrosis), which were consistent with other well-established SM-like corneal injury models.

Conclusion

Given its ease of implementation and safety, this mechlorethamine model could be used to study the full course of mustard corneal injuries. This model would greatly facilitate mustard injury research, shedding light on new knowledge that would increase our understanding of mustard ocular injuries while investigating novel therapeutics.

Translational relevance

this model will allow safe evaluation of SM-like corneal injuries within 24 hours, facilitating the identification of early/new molecules that might help to develop novel treatments which could be readily translated into the clinic.
Nicotinamide Metabolism Reprogramming Drives Reversible Senescence of Glioblastoma Cells
Authors: Narayanan Ashwin , Saurty-Seerunghen Mirca S , Michieletto Jessica , Delaunay Virgile , Bruneel Arnaud , Dupré Thierry , Ottolenghi Chris , Pontoizeau Clément , Ciccone Lucrezia , De La Vara Andreas , Idbaih Ahmed , Turchi Laurent , Virolle Thierry , Chneiweiss Hervé , Junier Marie-Pierre , El-Habr Elias A.
Published: October 2024

Recent studies show that metabolites, beyond their metabolic roles, can induce significant changes in cell behavior. Herein, we investigate the non-canonical role of nicotinamide (vitamin B3) on glioblastoma (GB) cell behavior. Nicotinamide induced senescence in GB cells, characterized by reduced proliferation, chromatin reorganization, increased DNA damage, enhanced beta-galactosidase activity, and decreased Lamin B1 expression. Nicotinamide-induced senescence was accompanied by an unexpected reprogramming of its metabolism, marked by simultaneous downregulated transcription of NNMT (nicotinamide N-methyltransferase) and NAMPT (nicotinamide phosphoribosyl-transferase). Nicotinamide effects on GB cells were mediated by decreased levels of SOX2. Consistently, analyses of patients’ single cell transcriptome datasets showed that GB cells with low NNMT and NAMPT expression levels were enriched in gene modules related to senescence. Remarkably, senescent GB cells retained tumor-forming abilityin vivo, albeit to a lesser extent compared to control cells. Further experiments at the single-cell level and transcriptomic analyses demonstrated that nicotinamide-induced senescence in GB cells is fully reversible. Overall, our findings identify a novel reversible senescent state in GB tumors and highlight the non-canonical role of NAM as a key driver of cancer cell plasticity.
A Longitudinal Analysis of Function Annotations of the Human Proteome Reveals Consistently High Biases
Authors: Phan An , Joshi Parnal , Kadelka Claus , Friedberg Iddo
Published: October 2024

The resources required to study gene function are limited, especially when considering the number of genes in the human genome and the complexity of their function. Therefore, genes are prioritized for experimental studies based on many different considerations, including, but not limited to, perceived biomedical importance, such as disease-associated genes, or the understanding of biological processes, such as cell signaling pathways. At the same time, most genes are not studied or are under-characterized, which hampers our understanding of their function and potential effects on human health and wellness. Understanding function annotation disparity is a necessary first step toward understanding how much functional knowledge is gained from the human genome, and toward guidelines for better targeting future studies of the genes in the human genome effectively. Here, we present a comprehensive longitudinal analysis of the human proteome utilizing data analysis tools from economics and information theory. Specifically, we view the human proteome as a population of proteins within a knowledge economy: we treat the quantified knowledge of the protein’s function as the analog of wealth and examine the distribution of information in a population of proteins in the proteome in the same manner distribution of wealth is studied in societies. Our results show a highly skewed distribution of information about human proteins over the last decade, in which the inequality in the annotations given to the proteins remains high. Additionally, we examine the correlation between the knowledge about protein function as captured in databases and the interest in proteins as reflected by mentions in the scientific literature. We show a large gap between knowledge and interest and dissect the factors leading to this gap. In conclusion, our study shows that research efforts should be redirected to less studied proteins to mitigate the disparity among human proteins both in databases and literature.
Development of an on-chip fluorescence anisotropy immunoassay for human C-peptide secretion reveals a general roadmap for tracer optimization
Authors: Wang Yufeng , Gulati Nitya , Regeenes Romario , Migliorini Adriana , Oake Amanda , Nostro Maria Cristina , Rocheleau Jonathan V.
Published: October 2024

Fluorescence anisotropy immunoassays (FAIAs) are widely used to quantify the concentration of target proteins based on competition with a tracer in binding a monoclonal antibody. We recently designed an FAIA to measure mouse C-peptide secretion from living islets in a continuous-flow microfluidic device (InsC-chip). To develop an assay for human C-peptide, our initial selection of antibody-tracer pairings revealed the need to optimize both the dynamic range and the binding kinetics to measure the assay on-chip effectively. Here, we present strategies for developing an on-chip FAIA using two different monoclonal antibodies to achieve both a large dynamic range and high temporal resolution. The two monoclonal antibodies (Ab1 & Ab2) to human C-peptide initially showed low dynamic range and slow kinetics, preventing them from being used in an on-chip assay. To shorten the time-to-reach equilibrium for Ab1, we reengineered the tracer based on a comparison between the human and mouse C-peptide sequences, resulting in > 30-fold shorter time-to-reach equilibrium. To increase the relatively small dynamic range for Ab2, we used partial epitope mapping and targeted point mutations to increase the dynamic range by 45%. Finally, we validated both FAIAs by measuring depolarization-induced insulin secretion from individual hESC-islets in our InsC-chip. These strategies provide a general roadmap for developing FAIAs with high sensitivity and sufficiently fast kinetics to be measured in continuous-flow microfluidic devices.
The Effect of Psychotherapy in the Management of Obesity: An umbrella review
Authors: Vasquez-Ponce Mariana , Gómez Óscar , González Ballesteros Luisa F. , Peralta-Reich Dina , Bermúdez-Gómez Julieta , Junco Juan David , Alba Maria Alejandra , Suarez-Ordoñez Luisa , Arana Nayeh , Ballesteros Eduardo , Mojica-Sierra Valeria , González Ballesteros Lina María
Published: October 2024

Objective

To assess the impact of psychotherapy on obesity treatment in outpatient settings.

Methods

The study targets adults with a BMI of 30 or higher, comparing psychotherapeutic interventions to usual care or no treatment. Key outcomes include weight loss, adverse events, depression, quality of life, and long-term BMI changes. Extensive database searches were conducted.

Results

Out of 1,334 articles reviewed, only 3 studies met the inclusion criteria, emphasizing the scarcity of relevant research. These studies primarily focused on behavioral and cognitive-behavioral strategies. Results showed that combining behavior therapy with diet/exercise led to greater weight loss than diet/exercise alone. Studies on cognitive therapy and general psychotherapy were less frequent and yielded weaker evidence. Despite varied methodologies, the findings suggest that behavioral therapy combined with dietary and exercise interventions offers improved outcomes, though more research is needed to strengthen these conclusions.

Conclusions

The study found that combining behavioral therapy with diet and exercise resulted in greater weight loss than diet and exercise alone. However, research on the impact of psychotherapy on obesity is limited, as only 3 studies met the inclusion criteria. Cognitive therapies and general psychotherapy provided weaker evidence. Therefore, further research is necessary to validate these findings and investigate alternative psychotherapeutic methods for treating obesity.
Metabolic analysis of sarcopenic muscle identifies positive modulators of longevity and healthspan inC. elegans
Authors: Jonk Steffi M , Nicol Alan , Chrysostomou Vicki , Lardner Emma , Yu Shu-Che , Stålhammar Gustav , Crowston Jonathan G , Tribble James R , Swoboda Peter , Williams Pete A
Published: October 2024

Sarcopenia is the age-related degeneration of skeletal muscle, resulting in loss of skeletal muscle tone, mass, and quality. Skeletal muscle is a source of systemic metabolites and macromolecules important for neuronal health, function and healthy neuronal aging. Age-related loss of skeletal muscle might result in decreased metabolite and macromolecule availability, resulting in reduced neuronal function or increased susceptibility to unhealthy aging and neurodegenerative diseases. We aimed to identify muscle metabolite candidates that regulate healthy aging. C57BL/6J mice were aged to young adult (4 months) and old age (25 months) and skeletal muscle was collected. Age related muscle loss was confirmed by reduced muscle mass, muscle fiber degeneration, reduced myosin intensity, in addition to a metabolic shift and increased DNA damage in skeletal muscle. Using a low molecular weight enriched metabolomics protocol, we assessed the metabolic profile of skeletal muscle from young adult and old mice and identified 20 metabolites that were significantly changed in aged muscle. These candidate metabolites were tested inC. elegansassays of lifespan, health span, muscle-, and mitochondrial morphology under normal and stressed conditions. We identified four candidate metabolites (beta-alanine, 4-guanidinobutanoic acid, 4-hydroxyproline, pantothenic acid) that when supplemented inC. elegansprovided robust gero- and mitochondrial protection. These candidates also affected life-, and health span inC. elegansmodels of amyotrophic lateral sclerosis and Duchenne muscular dystrophy. Our findings support that aging muscle can be used to identify novel metabolite modulators of lifespan and health and may show promise for future treatments of neurodegenerative and neuromuscular disorders.