bluuebunny/crossref_metadata_2025 huggingface dataset:
Diverse effects of fluorescent labels on alpha-synuclein condensate formation during liquid-liquid phase separation
Authors: Ziaunys Mantas , Sulskis Darius , Veiveris Dominykas , Sakalauskas Andrius , Mikalauskaite Kamile , Smirnovas Vytautas
Published: July 2024

Liquid-liquid phase separation is an emerging field of study, dedicated to understanding the mechanism and role of biomolecule assembly into membraneless organelles. One of the main methods employed in studying protein and nucleic acid droplet formation is fluorescence microscopy. Despite functioning as an excellent tool for monitoring biomolecule condensation, a few recent reports have presented possible drawbacks of using fluorescently labeled particles. It was observed that fluorescent tags could alter the process of protein liquid-liquid phase separation and even promote their aggregation. In this study, we examined the influence of three different protein labels on alpha-synuclein phase separationin vitroand determined that the changes in droplet formation were related to both the type, as well as concentration of the fluorescently tagged alpha-synuclein. Both protein-based labels (mCherry and eGFP) induced the formation of significantly larger droplets, while fluorescein-tagged alpha-synuclein generated an abundance of small condensates. The study also revealed that alpha-synuclein with protein-based labels could self-associate at much lower concentrations than its untagged counterpart, forming either large droplets or protein aggregates.
Pathogenicity is associated with population structure in a fungal pathogen of humans
Authors: Hatmaker E. Anne , Barber Amelia E. , Drott Milton T. , Sauters Thomas J. C. , Alastruey-Izquierdo Ana , Garcia-Hermoso Dea , Kurzai Oliver , Rokas Antonis
Published: July 2024

Aspergillus flavusis a clinically and agriculturally important saprotrophic fungus responsible for severe human infections and extensive crop losses. We analyzed genomic data from 250 (95 clinical and 155 environmental)A. flavusisolates from 9 countries, including 70 newly sequenced clinical isolates, to examine population and pan-genome structure and their relationship to pathogenicity. We identified fiveA. flavuspopulations, including a new population, D, corresponding to distinct clades in the genome-wide phylogeny. Strikingly, > 75% of clinical isolates were from population D. Accessory genes, including genes within biosynthetic gene clusters, were significantly more common in some populations but rare in others. Population D was enriched for genes associated with zinc ion binding, lipid metabolism, and certain types of hydrolase activity. In contrast to the major human pathogenAspergillus fumigatus,A. flavuspathogenicity in humans is strongly associated with population structure, making it a great system for investigating how population-specific genes contribute to pathogenicity.
Draft genome ofPalmaria palmataand intraspecific genetic variations in the North-East Atlantic
Authors: Rosignoli Serena , Inaba Masami , Schmid Matthias , McHale Marcus , Fort Antoine , Edwards Maeve D. , Mortensen Agnes Mols , Bartle Roy , Endal Arild , Baud Aurélien , Maggs Christine , Sulpice Ronan
Published: July 2024

The rhodophytePalmaria palmata(L.) Weber & Mohr is one of the target species of a growing European seaweed industry due to its high content of protein and essential amino acids which makes it suitable for human food, dietary supplements, and as salmon feed. However, the lack of a published nuclear genome limits phylogenetics analyses and gene function investigations which could help the development of a breeding programme.

We present the first draft genome ofP. palmatathat was obtained with PacBio HiFi long read sequencing with average coverage of 10×, consisting of an assembly of 1.05 Gb, N50=2.75Mb and BUSCO completeness of 72.1%. Additionally, a population study on the whole genome of 33P. palmataindividuals from across the Northern East Atlantic area found three main clusters consistent with their geographic distribution: (1) Denmark and Norway, (2) France and western Ireland, (3) Faroe Islands. All individuals from Northern Ireland share ancestry with western Ireland and Denmark, and some individuals from the Faroe Islands show admixture from Faroe, western Ireland and Northern Ireland. These results represent a fundamental step towards breeding and genetic studies to further explore the vastly unexploited economic potential ofPalmaria palmata.

Highlights

- We report the first draft genome ofPalmaria palmata, from PacBio HiFi long reads.

- The size of the genome, 1.05 Gb, is among the largest so far among the Rhodophyta.

- Busco completeness of 72.1% and contig N50 of 2.75 Mb indicate good quality.

- The genomes of 33 more individuals from North Atlantic Europe have been sequenced.

- Phylogenetic analysis found three clusters consistent with geographic distribution.
Nonergodicity and Simpson’s paradox in neurocognitive dynamics of cognitive control
Authors: Mistry Percy K. , Branigan Nicholas K. , Gao Zhiyao , Cai Weidong , Menon Vinod
Published: July 2024

Nonergodicity and Simpson’s paradox present significant, yet underappreciated challenges in neuroscience. Leveraging brain imaging and behavioral data from over 4,000 children and a Bayesian computational model of cognitive dynamics, we investigated brain-behavior relationships underlying cognitive control at both between-subjects and within-subjects levels. Strikingly, we observed a reversal of associations of inhibitory control brain activations with dynamic behavioral measures when comparing between-subjects and within-subjects analyses, revealing the nonergodic nature of these processes. This nonergodicity was pervasive throughout the brain but most pronounced in the salience network. Additionally, within-subjects analysis uncovered dissociated brain representations of reactive and proactive control processes, as well as distinct brain-behavior associations for individuals who adaptively versus maladaptively regulated cognitive control. Our findings offer insights into dynamic neural mechanisms of cognitive control during a critical developmental period. This work highlights the importance of embracing nonergodicity in human neuroscience, with implications for both theoretical understanding and applications to AI and psychopathology.
Main sequence of human luminance-evoked pupil dynamics
Authors: Coutinho Jonathan D , Huang Jeff , Lefèvre Philippe , Blohm Gunnar , Munoz Douglas P
Published: July 2024

Pupil responses are commonly used to provide insight into visual perception, autonomic control, cognition, and various brain disorders. However, making inferences from pupil data can be complicated by nonlinearities in pupil dynamics and variability within and across individuals, which challenge the assumptions of linearity or group level homogeneity required for common analysis methods. In this study, we evaluated luminance evoked pupil dynamics in young healthy adults (N=10, 5:5 M:F, ages 19-25) by identifying nonlinearities, variability, and conserved relationships across individuals to improve the ability to make inferences from pupil data. We found a nonlinear relationship between final pupil diameter and luminance, linearized by considering the logarithm of luminance. Peak diameter change and peak velocity were nonlinear functions of log-luminance for constriction but not dilation responses. Across participants, curve fit parameters characterizing pupil responses as a function of luminance were highly variable, yet there was an across-participant linear correlation between overall pupil size and pupil gain (i.e. diameter change per unit log-luminance change). In terms of within-participant trial-by-trial variability, participants showed greater variability in final pupil size compared to constriction peak diameter change as a function of log-luminance. Despite the variability in stimulus-response metrics within and across participants, we found that all participants showed a highly stereotyped “main sequence” relationship between peak diameter change and peak velocity (independent of luminance). The main sequence relationship can be used to inform models of the neural control of pupil dynamics and as an empirical analysis tool to evaluate variability and abnormalities in pupil behaviour.
Divide and conquer: Using RhizoVision Explorer to aggregate data from multiple root scans using image concatenation and statistical methods
Authors: Seethepalli Anand , Ottley Chanae , Childs Joanne , Cope Kevin , Fine Aubrey K. , Lagergren John , Iversen Colleen M. , Kalluri Udaya , York Larry M.
Published: July 2024

Roots are important in agricultural and natural systems for determining plant productivity and soil carbon inputs. The collection of root samples from the field and their subsequent cleaning and scanning in a water-filled tray ranging in size from 5 to 20 cm, followed by digital image analysis has been commonly used since the 1990s for measuring root length, volume, area, and diameter. However, one common issue has been neglected. Sometimes, the amount of roots for a sample is too much to fit into a single scanned image, so the sample is divided among several scans. There is no standard method to aggregate the root measurements across the scans of the same sample. Here, we describe and validate two methods for standardizing measurements across multiple scans: image concatenation and statistical aggregation. Both methods rely on standardizing file naming conventions to identify scans that belong to the same sample. Image concatenation refers to combining digital images into a single larger image while maintaining the original resolution. We developed a Python script that identifies which images belong to the same sample and returns a single, larger concatenated image for every set of images in a directory. These concatenated images (combining up to 10 scans) and the original images were processed with RhizoVision Explorer, a free and open-source software developed for estimating root traits from images, with the same settings. An R script was developed that can identify the rows of data belonging to the same sample in RhizoVision Explorer data files and apply correct statistical methods such as summation, weighted average by length, and average to the appropriate measurement types to return a single data row for each sample. These two methods were compared using example images from switchgrass, poplar, and various tree and ericaceous shrub species from a northern peatland and the Arctic. Overall, the new methods accomplished the goal of standardizing measurement aggregation. Most root measurements were nearly identical except median diameter, which can not be accurately computed by statistical aggregation. We believe the availability of these methods will be useful to the root biology community.
Esophageal epithelialIkkβdeletion promotes eosinophilic esophagitis in experimental allergy mouse model
Authors: Clevenger Margarette H , Wei Cenfu , Karami Adam L , Tsikretsis Lia E , Carlson Dustin A , Pandolfino John E , Gonsalves Nirmala , Winter Deborah R , Whelan Kelly A , Tétreault Marie-Pier
Published: July 2024

Background

Eosinophilic esophagitis (EoE) is a chronic T helper type 2 (Th2)-associated inflammatory disorder triggered by food allergens, resulting in esophageal dysfunction through edema, fibrosis, and tissue remodeling. The role of epithelial remodeling in EoE pathogenesis is critical but not fully understood.

Objective

To investigate the role of epithelial IKKβ/NFκB signaling in EoE pathogenesis using a mouse model with conditionalIkkβ knockout in esophageal epithelial cells (IkkβEEC-KO).

Methods

EoE was induced inIkkβEEC-KOmice through skin sensitization with MC903/Ovalbumin (OVA) followed by intraesophageal OVA challenge. Histological and transcriptional analyses were performed to assess EoE features. Single-cell RNA sequencing (scRNA-seq) was used to profile esophageal mucosal cell populations and gene expression changes.

Results

IkkβEEC-KO/EoE mice exhibited hallmark EoE features, including eosinophil infiltration, intraepithelial eosinophils, microabscesses, basal cell hyperplasia, and lamina propria remodeling. RNA-seq revealed significant alterations in IKKβ/NFκB signaling pathways, with decreased expression ofRELAand increased expression of IKKβ negative regulators. scRNA- seq analyses identified disrupted epithelial differentiation and barrier integrity, alongside increased type 2 immune responses and peptidase activity.

Conclusion

Our study demonstrates that loss of epithelial IKKβ signaling exacerbates EoE pathogenesis, highlighting the critical role of this pathway in maintaining epithelial homeostasis and preventing allergic inflammation. TheIkkβEEC-KO/EoE mouse model closely mirrors human EoE, providing a valuable tool for investigating disease mechanisms and therapeutic targets. This model can facilitate the development of strategies to prevent chronic inflammation and tissue remodeling in EoE.

Key Messages

Critical Role of Epithelial IKKβ/NFκB Signaling: Loss of this signaling exacerbates EoE, causing eosinophil infiltration, basal cell hyperplasia, and tissue remodeling, highlighting its importance in esophageal health.

Molecular Insights and Therapeutic Targets: scRNA-seq identified disrupted epithelial differentiation, barrier integrity, and enhanced type 2 immune responses, suggesting potential therapeutic targets for EoE.

Relevance of theIkkβEEC-KO/EoE Mouse Model: This model replicates human EoE features, making it a valuable tool for studying EoE mechanisms and testing treatments, which can drive the development of effective therapies.

Capsule Summary

This study reveals the crucial role of epithelial IKKβ/NFκB signaling in EoE, providing insights into disease mechanisms and potential therapeutic targets, highly relevant for advancing clinical management of EoE.
Early Lung Cancer Screening: A Comparative Study of CNN and Radiomics Models with Pulmonary Nodule Biologic Characterization
Authors: Gupta Mukund , Fandy Edbert Victor , Ghindani Krrish
Published: July 2024

Abstract

Lung cancer has become an increasingly prevalent disease, with an estimated 125,070 deaths in the United States alone in 2024 (5). To improve patient outcomes and assist doctors in differentiating between benign and malignant pulmonary nodules, this paper developed a Convolutional Neural Network (CNN) model for early binary detection of pulmonary nodules and assessed its effectiveness compared to other approaches. The CNN model showed an accuracy of 98.47%, while the radiomics-based SVM-LASSO model and the Lung-RADS system showed accuracies of 84.6% and 72.2% respectively. This demonstrates that the CNN model is significantly more effective for the early binary detection of pulmonary nodules than both the radiomics-based model and the Lung-RADS system. The paper also discusses the applications of Deep Learning in healthcare, concluding that although AI proves to be an effective method for early lung cancer detection, more research is needed to carefully assess the role and impact of AI in healthcare.
The single-berry metabolomic clock paradigm reveals new stages and metabolic switches during grapevine berry development
Authors: Tavernier Flora , Savoi Stefania , Torregrosa Laurent , Hugueney Philippe , Baltenweck Raymonde , Segura Vincent , Romieu Charles
Published: July 2024

Asynchronous development of berries causes metabolic chimerism in usual samples. We thus revisited the developmental changes in the metabolome of theVitis viniferasingle berries from anthesis to over-ripening.

A dataset of 9,256 ions obtained by non-targeted ultra-performance liquid chromatography coupled to high-resolution mass spectrometry was submitted to an analysis workflow combining classification and dimension reduction tools, to reveal the dynamics of metabolite composition without phenologicala priori.

This approach led to a metabolome-based definition of developmental stages, as well as the clustering of metabolites into 12 specific kinetic patterns. The single berry intrinsic metabolomic clock alleviates constitutive asynchronicity biases in the usual combination of phenological scales and observer clock. Such increase in temporal resolution enabled the identification of metabolite clusters annunciative of the onset of ripening since the herbaceous plateau. In particular, these clusters included transient lipidic changes and the start of ABA accumulation. We also highlighted a cluster of stilbenes that accumulate after sugar loading stops, during fruit shriveling.

This non-targeted approach enables a more precise and unbiased characterization of grapevine berry development through the metabolomic clock paradigm. The discovery of new metabolic milestones of berry development paves the way towards an unbiased assessment of berry physiological stages.
CDK4/6 inhibitors promote PARP1 degradation and act synergistically with PARP inhibitors in non-small cell lung cancer
Authors: Roggero Carlos M , Ghosh Anwesha B , Devineni Anvita , Ma Shihong , Blatt Eliot , Raj Ganesh V. , Yin Yi
Published: July 2024

Despite the widespread deregulation of CDK4/6 activity in non-small cell lung cancer (NSCLC), the clinical trials with CDK4/6 inhibitors (CDK4/6is) as a monotherapy have shown poor antitumor activity. However, our preclinical studies have revealed a significant potential for CDK4/6is to collaborate by influencing DNA damage repair pathways during radiotherapy. Given the considerable upregulation of PARP1 expression in NSCLC, we analyzed the efficacy of combined PARP and CDK4/6 inhibition in NSCLC models. Our findings demonstrate that CDK4/6is synergize with PARP inhibitors (PARPis) to inhibit the clonogenic growth of RB-proficient NSCLC models. This synergy is associated with increased accumulation of DNA damage, interrupted cell-cycle checkpoints, and enhanced apoptotic cell death. We showed that CDK4/6is mechanically promote PARP1 protein degradation, leading to decreased availability of DNA repair factors involved in homologous recombination and suppression of DNA repair competency. Furthermore, we showed that PARP trapping is required for this synergy. We then confirmed that combining PARPi and CDK4/6i blocked the growth of NSCLC xenografts in vivo and patient-derived explant models ex vivo. These findings reveal a previously uncharacterized impact of CDK4/6i on PARP1 levels in RB-proficient NSCLC models and the requirement of PARP trapping to render synergy between CDK4/6i and PARPi. Our research suggests that combining CDK4/6i with PARPi could be a promising therapeutic strategy for patients with RB-proficient NSCLC, potentially opening up new and more effective avenues for treatment.
The Virtual Parkinsonian Patient
Authors: Angiolelli Marianna , Depannemaecker Damien , Agouram Hasnae , Ŕegis Jean , Carron Romain , Woodman Marmaduke , Chiodo Letizia , Triebkorn Paul , Ziaeemehr Abolfazl , Hashemi Meysam , Eusebio Alexandre , Jirsa Viktor , Sorrentino Pierpaolo
Published: July 2024

Abstract

This study investigates the influence of the pharmacological nigrostriatal dopaminergic stimula-tion on the entire brain by analyzing EEG and deep electrodes, placed near the subthalamic nuclei, from 10 Parkinsonian patients, before (OFF) and after (ON) L-Dopa administration. We charac-terize large-scale brain dynamics as the spatio-temporal spreading of aperiodic bursts. We then simulate the effects of L-Dopa utilizing a novel neural-mass model that includes the local dopamine concentration. Whole-brain dynamics are simulated for different dopaminergic tones, generating predictions for the expected dynamics, to be compared with empirical EEG and deep electrode data. To this end, we invert the model and infer the most likely dopaminergic tone from empirical data, correctly identifying a higher Dopaminergic tone in the ON-state, and a lower dopaminergic tone in the OFF-state, for each patient. In conclusion, we successfully infer the dopaminergic tone by integrating anatomical and functional knowledge into physiological predictions, using solid ground truth to validate our findings.
A genome-wide association study in 10,000 individuals links plasma N-glycome to liver disease and anti-inflammatory proteins
Authors: Sharapov Sodbo , Timoshchuk Anna , Zaytseva Olga , Maslov Denis , Soplenkova Anna , Elgaeva Elizaveta E. , Tiys Evgeny S. , Mangino Massimo , Wittenbecher Clemens , Karssen Lennart , Timofeeva Maria , Nostaeva Arina , Vuckovic Frano , Trbojević-Akmačić Irena , Štambuk Tamara , Feoktistova Sofya , Potapova Nadezhda A. , Voroshilova Viktoria , Williams Frances , Primorac Dragan , Zundert Jan Van , Georges Michel , Suhre Karsten , Allegri Massimo , Chaturvedi Nishi , Dunlop Malcolm , Schulze Matthias B. , Spector Tim , Tsepilov Yakov A. , Lauc Gordan , Aulchenko Yurii S.
Published: July 2024

More than a half of plasma proteins are N-glycosylated. Most of them are synthesized, glycosylated, and secreted to the bloodstream by liver and lymphoid tissues. While associations with N-glycosylation are implicated in the rising number of liver, cardiometabolic, and immune diseases, little is known about the genetic regulation of this process. Here, we performed the largest genome-wide association study of N-glycosylation of the blood plasma proteome in 10,000 individuals. We doubled the number of genetic loci known to be associated with blood N-glycosylation by identifying 16 novel loci and prioritizing 13 novel genes contributing to N-glycosylation. Among these were theGCKR,TRIB1,HP, SERPINA1andCFHgenes. These genes are predominantly expressed in the liver and show a previously unknown genetic link between plasma protein N-glycosylation, metabolic and liver diseases, and inflammatory response. By integrating glycomics, proteomics, transcriptomics, and genomics, we provide a resource that facilitates deeper exploration of disease pathogenesis and supports the discovery of glycan-based biomarkers.
What child and adolescent psychiatry in France for the second quarter of the 21stcentury? An AI-assisted qualitative action research study
Authors: Falissard Bruno , Espi Pauline , Rouquette Alexandra
Published: July 2024

French Child and Adolescent Psychiatry (CAP) faces significant issues, primarily due to an overwhelming increase in demand and insufficient capacity. In response, the French Society for Child and Adolescent Psychiatry and Allied Professions (SFPEADA) initiated an action research project in June 2023 aimed at reimagining the future of CAP in France for the second quarter of the 21st century. Employing a holistic qualitative methodology that merges bottom-up and top-down approaches, the project progressed through four phases: interviews with informed individuals, consultations with trade unions or associations, synthesis of findings using thematic analysis and AI technologies, and public dissemination via a symposium at the ministry of health. The project identified 5 main themes: “CAP and Society”, “Knowledge Integration”, ”Healthcare Delivery”, “Caregivers”, ”System Organization”. This initiative underscores the importance of a collaborative, multidisciplinary approach to address the important needs of child and adolescent mental health in France, advocating for significant systemic changes to enhance CAP’s efficacy and accessibility.
HyperCas12a enables highly-multiplexed epigenome editing screens
Authors: Melore Schuyler M. , Hamilton Marisa C. , Reddy Timothy E.
Published: July 2024

Interactions between multiple genes or cis-regulatory elements (CREs) underlie a wide range of biological processes in both health and disease. High-throughput screens using dCas9 fused to epigenome editing domains have allowed researchers to assess the impact of activation or repression of both coding and non-coding genomic regions on a phenotype of interest, but assessment of genetic interactions between those elements has been limited to pairs. Here, we combine a hyper-efficient version ofLachnospiraceae bacteriumdCas12a (dHyperLbCas12a) with RNA Polymerase II expression of long CRISPR RNA (crRNA) arrays to enable efficient highly-multiplexed epigenome editing. We demonstrate that this system is compatible with several activation and repression domains, including the P300 histone acetyltransferase domain and SIN3A interacting domain (SID). We also show that the dCas12a platform can perform simultaneous activation and repression using a single crRNA array via co-expression of multiple dCas12a orthologues. Lastly, demonstrate that the dCas12a system is highly effective for high-throughput screens. We use dHyperLbCas12a-KRAB and a ∼19,000-member barcoded library of crRNA arrays containing six crRNAs each to dissect the independent and combinatorial contributions of CREs to the dose-dependent control of gene expression at a glucocorticoid-responsive locus. The tools and methods introduced here create new possibilities for highly multiplexed control of gene expression in a wide variety of biological systems.
Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity
Authors: Fang Yue , Meng Lingjie , Xia Jun , Gotoh Yasushiro , Hayashi Tetsuya , Nagasaki Keizo , Endo Hisashi , Okazaki Yusuke , Ogata Hiroyuki
Published: July 2024

Giant viruses are crucial for marine ecosystem dynamics because they regulate microeukaryotic community structure, accelerate carbon and nutrient cycles, and drive the evolution of their hosts through co-evolutionary processes. Previously reported long-term observations revealed that these viruses display fluctuations in abundance. However, the underlying genetic mechanisms driving such dynamics in these viruses remain largely unknown. In this study, we investigated population and intra-population dynamics of giant viruses using time-series metagenomes from eutrophic coastal seawater samples collected over 20 months. A newly developed near-automatic computational pipeline generated 1,065 high-quality metagenome-assembled genomes covering six major giant virus lineages. These genomic data revealed year-round recovery of the viral community at the study site and distinct dynamics of different viral populations classified as persistent (n = 9), seasonal (n = 389), sporadic (n = 318), or others. Notably, year-round recovery patterns were observed at the intra-population genetic diversity level for viruses classified as persistent or seasonal. Our results further indicated that the viral genome dynamics were associated with intra-population diversity; specifically, giant viruses with broader niche breadth tended to exhibit greater levels of microdiversity. We argue that greater microdiversity in viruses likely enhances adaptability and thus survival under the virus–host arms race during prolonged interactions with their hosts.
BRAT1 - a new therapeutic target for glioblastoma
Authors: Haydo Alicia , Schmidt Jennifer , Crider Alisha , Kögler Tim , Ertl Johanna , Hehlgans Stephanie , Hoffmann Marina E. , Rathore Rajeshwari , Güllülü Ömer , Wang Yecheng , Zhang Xiangke , Herold-Mende Christel , Pampaloni Francesco , Tegeder Irmgard , Dikic Ivan , Dai Mingji , Rödel Franz , Kögel Donat , Linder Benedikt
Published: July 2024

Glioblastoma (GBM), the most malignant primary brain tumor in adults, has poor prognosis irrespective of therapeutic advances due to its radio-resistance and infiltrative growth into brain tissue. The present study assessed functions and putative druggability of protein breast cancer type 1 susceptibility protein (BRCA1)-associated Ataxia telangiectasia mutated (ATM)-activator 1 (BRAT1) as a crucial factor driving key aspects of GBM, including enhanced DNA damage response and tumor migration. By a stable depletion of BRAT1 in GBM and glioma stem-like (GSC) cell lines, we observed a delay in DNA double-strand break repair and increased sensitivity to radiation treatment, corroborated byin vitroandin vivostudies demonstrating impaired tumor growth and invasion. Proteomic analyses further emphasize the role of BRAT1’s cell migration and invasion capacity, with a notable proportion of downregulated proteins associated with these processes. In line with the genetic manipulation, we found that treatment with the BRAT1 inhibitor Curcusone D (CurD) significantly reduced GSC migration and invasion in anex vivoslice culture model, particularly when combined with irradiation, resulting a synergistic inhibition of tumor growth and infiltration. Our results reveal that BRAT1 contributes to GBM growth and invasion and suggest that therapeutic inhibition of BRAT1 with CurD or similar compounds might constitute a novel approach for anti-GBM directed treatments.
Asbestos Mineral Fibre Exposure Significantly Affects Volatile Organic Compound Profiles of Mesothelial Cell Lines In Vitro
Authors: Bonsall Sam , Issitt Theo , Peake Nick , Herigstad Mari , Webber Jason , Haywood-Small Sarah
Published: July 2024

Malignant mesothelioma (MM) is a rare cancer caused by exposure to asbestos, this condition continues to represent a significant diagnostic and therapeutic challenge. Due to the long disease latency, non-invasive diagnostic modalities such as breath analysis may enhance MM early detection by identifying the disease specific pattern of volatile organic compounds (VOCs) in exhaled breath. In this study, solid phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS) was used to extract VOCs from the headspace of two mesothelioma cell lines: MSTO-211H (biphasic mesothelioma) and NCI-H28 (epithelioid mesothelioma) in addition to MET-5a (non-malignant mesothelial cell line), following exposure to asbestos mineral fibers (actinolite, amosite, crocidolite and chrysotile) and a non-asbestos fiber control (wollastonite). Multivariate statistical analysis was applied to identify VOC-based biomarkers associated with asbestos exposure within the cell lines. Data confirms that exposure to mineral fibers (including the non-asbestos fiber control) induces significant alterations in the levels of as many as 24 VOCs in each cell line. This is the first study to investigate the impact of asbestos mineral fiber exposure on the VOC profile of MM cell lines. This may be relevant to studies involving mesothelioma patients, as these VOCs could also serve as indicators of asbestos exposure in individuals who have been exposed to asbestos.
High Throughput Variant Libraries and Machine Learning Yield Design Rules for Retron Gene Editors
Authors: Crawford Kate D. , Khan Asim G. , Lopez Santiago C. , Goodarzi Hani , Shipman Seth
Published: July 2024

The bacterial retron reverse transcriptase system has served as an intracellular factory for single-stranded DNA in many biotechnological applications. In these technologies, a natural retron non-coding RNA (ncRNA) is modified to encode a template for the production of custom DNA sequences by reverse transcription. The efficiency of reverse transcription is a major limiting step for retron technologies, but we lack systematic knowledge of how to improve or maintain reverse transcription efficiency while changing the retron sequence for custom DNA production. Here, we test thousands of different modifications to the retron-Eco1 ncRNA and measure DNA production in pooled variant library experiments, identifying regions of the ncRNA that are tolerant and intolerant to modification. We apply this new information to a specific application: the use of the retron to produce a precise genome editing donor in combination with a CRISPR-Cas9 RNA-guided nuclease (an editron). We use high-throughput libraries inS. cerevisiaeto additionally define design rules for editrons. We extend our new knowledge of retron DNA production and editron design rules to human genome editing to achieve the highest efficiency retron-Eco1 editrons to date.
Metagenomic insights into the development of microbial communities of straw and leaf composts
Authors: Kimeklis Anastasiia K. , Gladkov Grigory V. , Orlova Olga V. , Lisina Tatiana O. , Afonin Alexey M. , Aksenova Tatiana S. , Kichko Arina A. , Lapidus Alla L. , Abakumov Evgeny V. , Andronov Evgeny E.
Published: July 2024

The objects of this study are microbial communities formed on two types of contrasting lignocellulosic biomass. To study them, a long-term experiment was set up and conducted on the decomposition of oat straw and leaf litter using soil as a microbial inoculum. Combined analyses of enzymatic activity and NGS data for 16S rRNA gene amplicon and full metagenome sequencing was applied to study taxonomic, CAZy (Carbohydrate-Active enzymes), and PULs (Polysaccharide Utilization Loci) composition of microbial communities at different stages of decomposition between substrates. using a combination of 16S rRNA gene amplicon and long-read nanopore sequencing. In straw degradation, the microbial community demonstrated higher amylase, protease, catalase, and cellulase activities, while peroxidase, invertase, and polyphenol oxidase were more active in leaf litter. Consistent with this, the metagenome analysis showed that the microbiome of straw compost was enriched in genes for metabolic pathways of simpler compounds. At the same time, there were more genes for aromatic compound degradation pathways in leaf litter compost. We identified 9 MAGs (Metagenome-assembled genomes) as the most promising prokaryotic decomposers due to their abnormally high quantity of PULs for their genome sizes, which were confirmed by 16S rRNA gene amplicon sequencing to constitute the bulk of the community at all stages of degradation. MAGs classified as Bacteroidota (Chitinophaga,Ohtaekwangia), and Actinomycetota (Streptomyces) were found in both substrates, while those from Bacillota (Pristimantibacillus) were specific for leaf litter. The most frequent PULs were specialized on xylans and pectins, but not cellulose, suggesting that PUL databases may be lacking PULs for complex substrates.

Importance

Our study explores the microbial communities from natural ecosystems, like soil and lignocellulosic waste, capable of decomposing lignocellulosic substrates. We used a comprehensive approach with chemical analyses of the substrates, amplicon and full-metagenome sequencing data. We have shown that such communities may be a source of identifying the highly effective decomposing species with novel PULs.
CLEC18A interacts with sulfated GAGs and controls clear cell renal cell carcinoma progression
Authors: Jonsson Gustav , Hofmann Maura , Mereiter Stefan , Hartley-Tassell Lauren , Sakic Irma , Oliveira Tiago , Hoffmann David , Novatchkova Maria , Schleiffer Alexander , Penninger Josef M.
Published: July 2024

C-type lectins are a large family of proteins with essential functions in both health and disease. In cancer, some C-type lectins have been found to both promote and inhibit tumor growth, but many of the C-type lectins still remain uncharacterised in a tumor context. Therefore, there is growing interst in further elucidating the mechanisms with which C-type lectins control tumor growth. Here, we report a key role of the CLEC18 family of C-type lectins in the progression of clear cell renal cell carcinoma (ccRCC). The CLEC18 family is conserved across the entire Chordata phylum with recent gene duplication events in humans. We found that CLEC18A is exclusively expressed in the proximal tubule of the kidney and the medial habenula of the brain. We further identified sulfated glycosaminoglycans (GAGs) of proteoglycans as the main CLEC18A ligand, making them unique among C-type lectins. In ccRCC patients, high expression of theCLEC18family lectins in the tumor are associated with improved survival. In mouse models of ccRCC, deletion of the mouse orthologClec18aresulted in enhanced tumor growth. Our results establishes CLEC18A as a novel and critical regulators of ccRCC tumor growth and highlights the potential benefit of modulatingCLEC18expression in the renal tumor microenvironment.
Combining computational modeling and experimental library screening to affinity-mature VEEV-neutralizing antibody F5
Authors: Sumner Christopher A. , Schwedler Jennifer L. , McCoy Katherine M. , Holland Jack , Duva Valery , Gelperin Daniel , Busygina Valeria , Stefan Maxwell A. , Martinez Daniella V. , Juarros Miranda A. , Phillips Ashlee M. , Weilhammer Dina R. , Grigoryan Gevorg , Kent Michael S. , Harmon Brooke N.
Published: July 2024

Engineered monoclonal antibodies (mAbs) have proven to be highly effective therapeutics in recent viral outbreaks due to their specificity and ability to provide immediate protection, regardless of immune status. However, despite technical advancements in the field, an ability to rapidly adapt or increase antibody affinity and by extension, therapeutic efficacy, has yet to be fully realized. We endeavored to stand-up such a pipeline using molecular modeling combined with experimental library screening to increase the affinity of a given antibody, F5, to recombinant E1E2 antigen from Venezuelan Equine Encephalitis Virus (VEEV) subtype IAB (TC-83). F5 is a monoclonal antibody with potent neutralizing activity against VEEV that was isolated from human bone marrow donors. F5 is known to bind to spikes on the surface of VEEV made up of a trimer of heterodimers of the glycoproteins E1 and E2. In this work we modeled the interaction of F5 with the E1E2 trimer of VEEV (TC-83) and generated predictions for mutations to improve binding using a Rosetta-based approach and dTERMen, an informatics approach. Modeling the structure of the complex was complicated by the fact that a high-resolution structure of F5 is not available and the H3 loop of F5 exceeds the length for which current modeling approaches can determine a unique structure. To overcome these challenges nine F5 structures with varying H3 loop conformations were generated using RosettaAntibody, PIGS (Prediction of ImmunoGlobulin Structure), and SWISS-Model and these base antibody structures were evaluated in docking trials to recombinant VEEV E1E2 based on relative binding affinity for several subtypes. The structure that gave the best agreement with the experimental trend in relative binding affinity was used for mutation analysis. A subset of the predicted mutations from both methods were incorporated into a phage display library of scFvs (single-chain variable fragments) and screened for binding affinity to the recombinant E1E2 antigen. Results from this screen were used to identify favorable mutations which were then incorporated into twelve human-IgG1 variants. All twelve variants showed increased binding relative to the parental F5 human-IgG1. The best case showed > 60x increased binding to recombinant E1E2 relative to the parental antibody, notably showing a drastic improvement of the Kd or “off rate” compared to the parental F5 IgG. These results demonstrate the ability of our methods to rapidly increase affinity and could be leveraged for increasing Ab binding breadth to additional viral variants.
Ablation of three major phospho-sites in RyR2 preserves the global adrenergic response but creates an arrhythmogenic substrate
Authors: Zheng Jingjing , Dooge Holly C. , Valdivia Héctor H. , Alvarado Francisco J.
Published: July 2024

Background

Ryanodine receptor 2 (RyR2) is one of the first substrates undergoing phosphorylation upon catecholaminergic stimulation. Yet, the role of RyR2 phosphorylation in the adrenergic response remains debated. To date, three residues in RyR2 are known to undergo phosphorylation upon adrenergic stimulation. We generated a model of RyR2 phospho-ablation of all three canonical phospho-sites (RyR2-S2031A/S2808A/S2814A, triple phospho-mutant, TPM) to elucidate the role of phosphorylation at these residues in the adrenergic response.

Methods

Cardiac structure and function, cellular Ca2+dynamics and electrophysiology, and RyR2 channel activity both under basal conditions and under isoproterenol (Iso) stimulation were systematically evaluated. We used echocardiography and electrocardiography in anesthetized mice, single-cell Ca2+imaging and whole-cell patch clamp in isolated adult cardiomyocytes, and biochemical assays.

Results

Iso stimulation produced normal chronotropic and inotropic responses in TPM mice as well as an increase in the global Ca2+transients in isolated cardiomyocytes. Functional studies revealed fewer Ca2+sparks in permeabilized TPM myocytes, and reduced RyR2-mediated Ca2+leak in intact myocytes under Iso stimulation, suggesting that the canonical sites may regulate RyR2-mediated Ca2+leak. TPM mice also displayed increased propensity for arrhythmia. TPM myocytes were prone to develop early afterdepolarizations (EADs), which were abolished by chelating intracellular Ca2+with EGTA, indicating that EADs require SR Ca2+release. EADs were also blocked by a low concentration of tetrodotoxin, further suggesting reactivation of the sodium current (INa) as the underlying cause.

Conclusion

Phosphorylation of the three canonical residues on RyR2 may not be essential for the global adrenergic responses. However, these sites play a vital role in maintaining electrical stability during catecholamine stimulation by fine-tuning RyR2-mediated Ca2+leak. These findings underscore the importance of RyR2 phosphorylation and a finite diastolic Ca2+leak in maintaining electrical stability during catecholamine stimulation.
Proportional Mortality and Years of Potential Life Lost Due to Liver Diseases among Agricultural Workers, Brazil, 2017 to 2022
Authors: Silva Jailma dos Santos , Arruda Soraia , Nunes Thayane Silva , Dias Wiler de Paula , Awoniyi Adedayo Michael , Meyer Armando , Cremonese Cleber
Published: July 2024

The objective of the study was to describe the profile and calculate the Years of Potential Life Lost (YPLL) due to liver diseases in Brazilian agricultural workers, between 2017 and 2022. For this, we analyzed microdata available in the Mortality Information System (Sistema de Informação de Mortalidade - SIM), considering the outcome as the underlying cause of death with codes K70-K77 (ICD-10). Workers’ profile was characterized according to socio-demographic variables and the Brazilian regions, with a comparison group formed by all other Brazilian workers aged 18 to 69 who died in the same period and from the same underlying cause. Calculations of proportional mortality, YPLL rates, and YPLL rate ratios were applied. In the studied period, 15,362 deaths due to liver diseases were recorded among Brazilian agricultural workers, with an average age at death of 51.3 years (±10.7), concentrated in K70 - Alcoholic liver disease (53.8%). Higher proportional mortality was observed in men (86.2%), Brown race (61.1%), up to 49 years old (40.9%), with ≤7 years of education level (52.4%), and residents in Northeast (56.9%). The total sum of YPLL was 382,869 years among agricultural workers, with YPLL rate of 4,527 years per 100,000 workers and YPLL rate ratio 1.45 times higher than the national average. The concentration of deaths due to K70 raises concern for potential chronic exposure to alcoholic beverages. These results highlight the early causes of deaths resulting from liver diseases among agricultural workers, especially those in the Northeast region of Brazil and of Brown race.
What’s in a name? Protocol for a bibliometric and content analysis of rehabilitation, reablement, reactivation, and restorative health care services
Authors: MacEachern Evan , Wu Miranda C. , Cronin Shawna , Carroll Áine , Inzitari Marco , Perman Gaston , Prvu-Bettger Janet , Nelson Michelle L. A.
Published: July 2024

Background:Various terms are used interchangeably to describe health care services that focus on supporting functional recovery after experiencing a health event. Previous literature has identified these terms as the 4R’s: rehabilitation, reablement, reactivation, and restorative health care services. However, there lacks a clear understanding and delineation between these concepts, making it difficult to measure the efficacy of each program type. This study protocol proposes a bibliometric and content analysis to map the current scientific literature within each 4R term.Methods:Using a predefined search strategy, we will identify and retrieve publications from databases Scopus and PubMed between the years 1924-2024 for each 4R concept. Two independent researchers will screen articles for eligibility. Bibliometric analyses will be conducted using RStudio software and Bibliometrix and Biblioshiny extensions. Bibliometric analyses will each include a performance analysis, citation analysis, co-citation analysis, bibliographic coupling, and co-word analysis to identify key research connections and emerging trends temporally and geographically. Bibliometric indicators of interest will include total publications, yearly output, author names, and countries, among others. In addition, we will also perform a qualitative content analysis to provide a more in-depth examination of the characteristics of each program type.Implications:Our line of inquiry intends to clarify the similarities and differences among the 4R terms to conceptualize each definition. Findings from this study have several implications for research, practice, and policy within the 4Rs, and can overall help to delineate these concepts and facilitate decision-making and resource allocation for these health care services. This study will reveal citation patterns, research connections, and foundation themes that can inform the suitability of practice transfer and resource allocation within and between rehabilitation fields. A methodological understanding of the 4R service types can inform decision-making on the patient, healthcare professional, and system level for each service.
Infantile Colic in Karachi: Exploring Maternal Awareness, Attitude and Management Approaches
Authors: Ali Syed Rohan , Raqib Moosa Abdur , Mehtab Kiran , Nafees Munir , Tafheem Malik Hamdan
Published: July 2024

Infantile colic, characterized by severe abdominal pain and excessive crying, significantly impacts both infants and their parents. This study examined maternal awareness, knowledge, and attitudes towards colic, with a focus on socio-demographic factors. Conducted over eight months with a sample of 400 infants in Karachi, the research employed structured questionnaires and clinical evaluations. Statistical analysis revealed significant variations in colic occurrence based on age (p < 0.001), maternal age (p = 0.005), and educational background (p = 0.001). Gender differences in digestive issues (p = 0.02) and responses to crying based on gestational age were also notable. Additionally, educational status significantly affected perceptions of colic severity (p = 0.000) and its impact on parental mental health (p = 0.03). These findings highlight the necessity for tailored healthcare strategies that consider familial contexts and educational interventions to enhance understanding and management of infantile colic. Future research should explore the influence of gut microbiota and probiotics, aiming to develop empathetic and evidence-based approaches to improve outcomes for affected families.

Objective

This study aimed to provide updated insights into the epidemiology of infantile colic in Karachi, contributing to targeted healthcare interventions and policies aimed at alleviating colic-related distress among infants and their families in urban settings