bluuebunny/crossref_metadata_2025 huggingface dataset:
Survey of collaboration supporting students who are deaf and hard of hearing
Authors: Gustafson Samantha J , Newsome Elsa , Pilling Nicole , Segura Emilee
Published: February 2024

Collaboration between teachers of students who are deaf and hard of hearing (TSDHH) and educational audiologists is essential when developing successful, comprehensive service delivery plans for students who are deaf and hard of hearing. Despite the importance, little is known about how these two professions work together. This study sought to describe the current state of collaboration between educational audiologists and TSDHH and to explore the barriers and facilitators to this collaboration. Anonymous survey responses from 752 educational audiologists and TSDHH showed that collaboration is considered valuable and is occurring frequently, via a variety of formats and despite significant barriers. More research is needed to understand how efforts to minimize barriers to collaboration might improve the quality of collaboration and ultimately impact the success of student support.
Exploring FGFR3 Mutations in the Male Germline: Implications for Clonal Germline Expansions and Paternal Age-Related Dysplasias
Authors: Moura Sofia , Hartl Ingrid , Brumovska Veronika , Calabrese Peter P , Yasari Atena , Striedner Yasmin , Bishara Marina , Mair Theresa , Ebner Thomas , Schütz Gerhard J , Sevcsik Eva , Tiemann-Boege Irene
Published: February 2024

Delayed fatherhood results in a higher risk of inheriting a new germline mutation that might result in a congenital disorder in the offspring. In particular, some FGFR3 mutations increase in frequency with age, but there are still a large number of uncharacterized FGFR3 mutations that could be expanding in the male germline with potentially early- or late-onset effects in the offspring. Here, we used digital polymerase chain reaction to assess the frequency and spatial distribution of 10 different FGFR3 missense substitutions in the sexually mature male germline. Our functional assessment of the receptor signaling of the variants with biophysical methods showed that 9 of these variants resulted in a higher activation of the receptor´s downstream signaling, resulting in 2 different expansion behaviors. Variants that form larger subclonal expansions in a dissected postmortem testis also showed a positive correlation of the substitution frequency with the sperm donor's age, and a high and ligand-independent FGFR3 activation. In contrast, variants that measured high FGFR3 signaling and elevated substitution frequencies independent of the donor's age did not result in measurable subclonal expansions in the testis. This suggests that promiscuous signal activation might also result in an accumulation of mutations before the sexual maturation of the male gonad with clones staying relatively constant in size throughout time. Collectively, these results provide novel insights into our understanding of the mutagenesis of driver mutations and their resulting mosaicism in the male germline with important consequences for the transmission and recurrence of associated disorders.
Turnovers of Sex-Determining Mutation in the Golden Pompano and Related Species Provide Insights into Microevolution of Undifferentiated Sex Chromosome
Authors: Guo Liang , Malara Danilo , Battaglia Pietro , Waiho Khor , Davis D Allen , Deng Yu , Shen Zhongyuan , Rao Ke
Published: February 2024

The suppression of recombination is considered a hallmark of sex chromosome evolution. However, previous research has identified undifferentiated sex chromosomes and sex determination by single SNP in the greater amberjack (Seriola dumerili). We observed the same phenomena in the golden pompano (Trachinotus ovatus) of the same family Carangidae and discovered a different sex-determining SNP within the same gene Hsd17b1. We propose an evolutionary model elucidating the turnover of sex-determining mutations by highlighting the contrasting dynamics between purifying selection, responsible for maintaining W-linked Hsd17b1, and neutral evolution, which drives Z-linked Hsd17b1. Additionally, sporadic loss-of-function mutations in W-linked Hsd17b1 contribute to the conversion of W chromosomes into Z chromosomes. This model was directly supported by simulations, closely related species, and indirectly by zebrafish mutants. These findings shed new light on the early stages of sex chromosome evolution.
Postural Control Characteristics in Alzheimer’s Disease, Dementia With Lewy Bodies, and Vascular Dementia
Authors: Fujita Kosuke , Sugimoto Taiki , Noma Hisashi , Kuroda Yujiro , Matsumoto Nanae , Uchida Kazuaki , Kishino Yoshinobu , Sakurai Takashi
Published: February 2024

Background

Dementia often results in postural control impairment, which could signify central nervous system dysfunction. However, no studies have compared postural control characteristics among various types of dementia. This study aimed to compare static postural control in patients with Alzheimer’s disease (AD), dementia with Lewy bodies (DLB), and vascular dementia (VaD).

Methods

Cross-sectional relationship between the clinical diagnoses (AD, DLB, VaD, or normal cognition [NC]) of outpatients at a memory clinic and their upright postural control characteristics were examined. In the postural control test, participants were instructed to maintain a static upright standing on a stabilometer for 60 seconds under the eyes-open and eyes-closed conditions. Forty postural control parameters, including distance, position, and velocity in the anterior–posterior and medio–lateral directions, derived from the trajectory of the center of mass sway, were calculated. The characteristics of each type of dementia were compared to those of NC, and the differences among the 3 types of dementia were evaluated using linear regression models.

Results

The study included 1 789 participants (1 206 with AD, 111 with DLB, 49 with VaD, and 423 with NC). Patients with AD exhibited distinct postural control characteristics, particularly in some distance and velocity parameters, only in the eyes-closed condition. Those with DLB exhibited features in the mean position in the anterior–posterior direction. In patients with VaD, significant differences were observed in most parameters, except the power spectrum.

Conclusions

Patients with AD, DLB, and VaD display disease-specific postural control characteristics when compared to cognitively normal individuals.
Unsupervised clustering of catalogue-driven features for characterizing temporal evolution of labquake stress
Authors: Karimpouli Sadegh , Kwiatek Grzegorz , Martínez-Garzón Patricia , Dresen Georg , Bohnhoff Marco
Published: February 2024

Earthquake forecasting poses significant challenges, especially due to the elusive nature of stress states in fault systems. To tackle this problem, we use features derived from seismic catalogues obtained from acoustic emission (AE) signals recorded during triaxial stick-slip experiments on natural fractures in three Westerly granite samples. We extracted 47 physically explainable features from AE data that described spatio-temporal evolution of stress and damage in the vicinity of the fault surface. These features are then subjected to unsupervised clustering using the K-means method, revealing three distinct stages with a proper agreement with the temporal evolution of stress. The recovered stages correspond to the mechanical behaviour of the rock, characterized as initial stable (elastic) deformation, followed by a transitional stage leading to an unstable deformation prior to failure. Notably, AE rate, clustering-localization features, fractal dimension, b-value, interevent time distribution, and correlation integral are identified as significant features for the unsupervised clustering. The systematically evolving stages can provide valuable insights for characterizing preparatory processes preceding earthquake events associated with geothermal activities and waste-water injections. In order to address the upscaling issue, we propose to use the most important features and, in case of normalization challenge, removing non-universal features, such as AE rate. Our findings hold promise for advancing earthquake prediction methodologies based on laboratory experiments and catalogue-driven features.
Comorbidity Between Inflammatory Bowel Disease and Asthma and Allergic Diseases: A Genetically Informed Study
Authors: Gong Tong , Brew Bronwyn K , Lundholm Cecilia , Smew Awad I , Harder Arvid , Kuja-Halkola Ralf , Ludvigsson Jonas F , Lu Yi , Almqvist Catarina
Published: February 2024

Background

Little is known about shared origins between inflammatory bowel disease (IBD) and allergic diseases (asthma, allergic rhinitis, and eczema). We aimed to expand current knowledge on the etiological sources of comorbidities between these disorders using a range of genetically informed methods.

Methods

Within-individual and familial co-aggregation analysis was applied to 2 873 445 individuals born in Sweden from 1987 to 2014 and their first- and second-degree relatives. Quantitative genetic modeling was applied to 38 723 twin pairs to decompose the genetic and environmental sources for comorbidity. Polygenic risk score analysis between IBD and allergic diseases was conducted in 48 186 genotyped twins, and linkage disequilibrium score regression was applied using publicly available data to explore the genetic overlap.

Results

IBD was associated with asthma (adjusted odds ratio [aOR], 1.35; 95% confidence interval [CI], 1.30 to 1.40), allergic rhinitis (aOR, 1.27; 95% CI, 1.20 to 1.34), and eczema (aOR, 1.47; 95% CI, 1.38 to 1.56), with similar estimates for ulcerative colitis or Crohn’s disease. The ORs for familial co-aggregation decreased with decreasing genetic relatedness. Quantitative genetic modeling revealed little evidence of common genetic factors between IBD and allergic diseases (eg, IBD and allergic rhinitis; genetic correlation ra = 0.06; 95% CI, −0.03 to 0.15) but did reveal some evidence of unique environmental factors between IBD and eczema (re = 0.16; 95% CI, 0.00 to 0.32). Molecular genetic analyses were similarly null for IBD and allergic diseases, except for a slight association between Crohn’s disease polygenic risk score and eczema (OR, 1.09; 95% CI, 1.06 to 1.12).

Conclusions

We found little evidence to support a shared origin between IBD and any allergic disease but weak evidence for shared genetic and unique environmental components for IBD and eczema.
Relationship Between Hepatitis C Infection and Treatment Status and Coronavirus Disease 2019–Related Hospitalizations in Georgia
Authors: Aslanikashvili Ana , Rylander Charlotta , Manjavidze Tinatin , Gamkrelidze Amiran , Baliashvili Davit , Anda Erik Eik
Published: February 2024

Background

The aim of this study was to evaluate the impact of hepatitis C virus (HCV) infection and treatment status on coronavirus disease 2019 (COVID-19)–related hospitalizations in Georgia.

Methods

We analyzed 2020–2021 Georgian health registry data for COVID-19–positive individuals and categorized the data by HCV infection and treatment status. Logistic regression was used to assess the strengths of the associations.

Results

Treated individuals with HCV had lower odds of COVID-19–related hospitalization compared to anti-HCV-negative individuals, while untreated HCV-viremic and anti-HCV-positive nonviremic individuals had higher odds.

Conclusions

HCV treatment prior to COVID-19 infection was associated with lower odds of COVID-19–related hospitalization, highlighting the benefits of HCV management in the context of the pandemic.
Gut microbiota contribute to variations in honey bee foraging intensity
Authors: Vernier Cassondra L , Nguyen Lan Anh , Gernat Tim , Ahmed Amy Cash , Chen Zhenqing , Robinson Gene E
Published: February 2024

Gut microbiomes are increasingly recognized for mediating diverse biological aspects of their hosts, including complex behavioral phenotypes. Although many studies have reported that experimental disruptions to the gut microbial community result in atypical host behavior, studies that address how gut microbes contribute to adaptive behavioral trait variation are rare. Eusocial insects represent a powerful model to test this, because of their simple gut microbiota and complex division of labor characterized by colony-level variation in behavioral phenotypes. Although previous studies report correlational differences in gut microbial community associated with division of labor, here, we provide evidence that gut microbes play a causal role in defining differences in foraging behavior between European honey bees (Apis mellifera). We found that gut microbial community structure differed between hive-based nurse bees and bees that leave the hive to forage for floral resources. These differences were associated with variation in the abundance of individual microbes, including Bifidobacterium asteroides, Bombilactobacillus mellis, and Lactobacillus melliventris. Manipulations of colony demography and individual foraging experience suggested that differences in gut microbial community composition were associated with task experience. Moreover, single-microbe inoculations with B. asteroides, B. mellis, and L. melliventris caused effects on foraging intensity. These results demonstrate that gut microbes contribute to division of labor in a social insect, and support a role of gut microbes in modulating host behavioral trait variation.
Repurposing cinacalcet suppresses multidrug-resistant Staphylococcus aureus by disruption of cell membrane and inhibits biofilm by targeting IcaR
Authors: Fang Zu-Ye , Zhang Zi-Yuan , Zheng Yun-Dan , Lei Dan , Zhuang Jianpeng , Li Nan , He Qing-Yu , Sun Xuesong
Published: February 2024

Background

MDR Staphylococcus aureus infections, along with the severity of biofilm-associated infections, continue to threaten human health to a great extent. It necessitates the urgent development of novel antimicrobial and antibiofilm agents.

Objectives

To reveal the mechanism and target of cinacalcet as an antibacterial and antimicrobial agent for S. aureus.

Methods

Screening of non-antibiotic drugs for antibacterial and antibiofilm properties was conducted using a small-molecule drug library. In vivo efficacy was assessed through animal models, and the antibacterial mechanism was studied using quantitative proteomics, biochemical assays, LiP-SMap, BLI detection and gene knockout techniques.

Results

Cinacalcet, an FDA-approved drug, demonstrated antibacterial and antibiofilm activity against S. aureus, with less observed development of bacterial resistance. Importantly, cinacalcet significantly improved survival in a pneumonia model and bacterial clearance in a biofilm infection model. Moreover, the antibacterial mechanism of cinacalcet mainly involves the destruction of membrane-targeted structures, alteration of energy metabolism, and production of reactive oxygen species (ROS). Cinacalcet was found to target IcaR, inhibiting biofilm formation through the negative regulation of IcaADBC.

Conclusions

The findings suggest that cinacalcet has potential for repurposing as a therapeutic agent for MDR S. aureus infections and associated biofilms, warranting further investigation.
Temocillin for febrile urinary tract infections caused by ESBL-producing Enterobacteriaceae in children: a monocentric exposed/non-exposed study
Authors: Bayart Jules , Drouet Juliette , Peycelon Matthieu , Mariani Patricia , Le Roux Enora , Husain Maya , Agar Julien , Bonacorsi Stéphane , Caseris Marion
Published: February 2024

Objectives

To compare the efficacy of temocillin with standard of care (SOC) for treatment of ESBL-producing Enterobacteriaceae (ESBL-E) febrile urinary tract infection (ESBL-E FUTI) in children.

Methods

A monocentric retrospective study of children hospitalized with confirmed ESBL-E FUTI from January 2015 to May 2022 was conducted, comparing clinical cure and a 3 month relapse between two groups of patients: ‘exposed’ patients (EP) and ‘non-exposed’ patients (NEP) to temocillin. EP received temocillin for at least 3 days. They were matched (1:1 ratio) on age group, sex and presence of uropathy with NEP who received SOC antibiotic therapy.

Results

Thirty-six temocillin-treated children (EP) were matched with 36 SOC children (NEP); 72.2% were under 2 years old (n = 52) and 75.0% had a congenital uropathy (n = 54). EPs had more FUTI history (97.2%, n = 35) than NEPs (61.1%, n = 22) (P < 0.01). Clinical cure rate was 98.6% overall, with no difference between the two groups, as for the FUTI relapse rate, which was 37.1% for EPs versus 27.8% for NEPs (P = 0.45). In bivariate analyses, factors associated with relapses were congenital uropathy (91.3% versus 66.7%, P = 0.04) and subtypes of uropathy, with refluxing uropathy and posterior urethral valves being the more prevalent. Median duration of hospitalization was longer in the EPs (8.0 versus 5.0 days) (P = 0.01).

Conclusions

The high clinical cure rate and comparable outcomes suggest that temocillin may be an effective therapeutic alternative to standard treatment for ESBL-E FUTI in children.
BioLORD-2023: semantic textual representations fusing large language models and clinical knowledge graph insights
Authors: Remy François , Demuynck Kris , Demeester Thomas
Published: February 2024

Objective

In this study, we investigate the potential of large language models (LLMs) to complement biomedical knowledge graphs in the training of semantic models for the biomedical and clinical domains.

Materials and Methods

Drawing on the wealth of the Unified Medical Language System knowledge graph and harnessing cutting-edge LLMs, we propose a new state-of-the-art approach for obtaining high-fidelity representations of biomedical concepts and sentences, consisting of 3 steps: an improved contrastive learning phase, a novel self-distillation phase, and a weight averaging phase.

Results

Through rigorous evaluations of diverse downstream tasks, we demonstrate consistent and substantial improvements over the previous state of the art for semantic textual similarity (STS), biomedical concept representation (BCR), and clinically named entity linking, across 15+ datasets. Besides our new state-of-the-art biomedical model for English, we also distill and release a multilingual model compatible with 50+ languages and finetuned on 7 European languages.

Discussion

Many clinical pipelines can benefit from our latest models. Our new multilingual model enables a range of languages to benefit from our advancements in biomedical semantic representation learning, opening a new avenue for bioinformatics researchers around the world. As a result, we hope to see BioLORD-2023 becoming a precious tool for future biomedical applications.

Conclusion

In this article, we introduced BioLORD-2023, a state-of-the-art model for STS and BCR designed for the clinical domain.
Broad-spectrum defenders: γδ T cells take on a multitude of immune challenges
Authors: Freen-van Heeren Julian J
Published: February 2024

A recent article in Proceedings of the National Academy of Sciences investigated γδ T cell antigen specificity in mice and humans, in which the authors show that γδ T cell antigen specificity is not constrained to one epitope. Rather, γδ T cells recognize a broad range of diverse antigens containing similar chemical structures or properties. In this News and Views, the importance of γδ T cell antigen polyspecificity during immune responses is highlighted.
Comparative transcriptome profiling across 9 tissues in 2 pika species provides new insights and resources to interpret plateau adaptation
Authors: Zhang Ruobing , Mu Danping , Wu Xinlai , Feijó Anderson , Wen Zhixin , Cheng Jilong , Xia Lin , Yang Qisen , Shan Wenjuan , Ge Deyan
Published: February 2024

As an endemic species of the Qinghai–Tibet Plateau, the Plateau Pika (Ochotona curzoniae) exhibits adaptation to the extremely high-altitude environment and possesses a number of distinct physiological characteristics. In order to explore potential mechanisms underlying the adaptation of plateau pikas, we investigate transcriptomic differences across tissues (heart, liver, spleen, lung, kidney, muscle, cerebellum, left brain, and right brain) of the Plateau Pika, in a comparative framework. We analyze possible mechanisms of adaptive evolution by including a transcriptome analysis across the 9 tissues from 3 male and 4 female O. curzoniae and contrasting results with the 8 male and 4 female Gansu Pika (O. cansus) that inhabits the lower middle altitudes. Differential expression and protein–protein interaction network analyses were used to identify the differentially expressed genes and their primary functions. By analyzing interspecific differences, we identified significant adaptive transcriptional changes in the heart, lung, and spleen of the Plateau Pika. Specifically, upregulated genes in these tissues not only show a substantial association with apoptosis and DNA damage repair, but also demonstrate apparent enrichment in biological pathways related to energy metabolism and immune regulation. The majority of downregulated genes exhibit decreased activity in metabolic pathways particularly in muscle, spleen, kidney, and brain tissues. We further reveal the pivotal gene interaction networks of the 9 tissues. Our study provides valuable insight into adaptive mechanisms underlying evolution of Plateau Pika at extreme altitudes.
Dietary interventions in cancer: a systematic review of all randomized controlled trials
Authors: Ilerhunmwuwa Nosakhare Paul , Abdul Khader Abul Hasan Shadali , Smith Calvin , Cliff Edward R Scheffer , Booth Christopher M , Hottel Evevanne , Aziz Muhammad , Lee-Smith Wade , Goodman Aaron , Chakraborty Rajshekhar , Mohyuddin Ghulam Rehman
Published: February 2024

Background

Prior systematic reviews addressing the impact of diet on cancer outcomes have focused on specific dietary interventions. In this systematic review, we assessed all randomized controlled trials (RCTs) investigating dietary interventions for cancer patients, examining the range of interventions, endpoints, patient populations, and results.

Methods

This systematic review identified all RCTs conducted before January 2023 testing dietary interventions in patients with cancer. Assessed outcomes included quality of life, functional outcomes, clinical cancer measurements (eg, progression-free survival, response rates), overall survival, and translational endpoints (eg, inflammatory markers).

Results

In total, 252 RCTs were identified involving 31 067 patients. The median sample size was 71 (interquartile range 41 to 118), and 80 (32%) studies had a sample size greater than 100. Most trials (n = 184, 73%) were conducted in the adjuvant setting. Weight or body composition and translational endpoints were the most common primary endpoints (n = 64, 25%; n = 52, 21%, respectively). Direct cancer measurements and overall survival were primary endpoints in 20 (8%) and 7 (3%) studies, respectively. Eight trials with a primary endpoint of cancer measurement (40%) met their endpoint. Large trials in colon (n = 1429), breast (n = 3088), and prostate cancer (n = 478) each showed no effect of dietary interventions on endpoints measuring cancer.

Conclusion

Most RCTs of dietary interventions in cancer are small and measure nonclinical endpoints. Although only a small number of large RCTs have been conducted to date, these trials have not shown an improvement in cancer outcomes. Currently, there is limited evidence to support dietary interventions as a therapeutic tool in cancer care.
Gas content and evolution of a sample of YSO associations at d ≲ 3.5 kpc from the Sun
Authors: Zhou Ji-Xuan , Li Guang-Xing , Chen Bing-Qiu
Published: February 2024

Young Stellar Objects (YSO) are newly formed stars from molecular clouds. They stay close to where they were born and serve as good tracers to study gas and star formation. During cloud evolution, young massive stars can disrupt the surrounding gas through stellar feedback, changing the gas distribution. We study the distribution of the gas around a sample of YSO associations located at $d \lesssim 3.5 \,\,\rm kpc$ from the Sun by comparing the location and morphology between 12CO (J  = 1–0) emission, Planck 870 $\mu$m maps and YSO associations. Based on the spatial distribution of the gas compared to that of the YSOs, we classify the YSO associations into six types: direct, close, bubble, complex, diffuse, and clean associations. The complex associations are large structures consisting of both gas-rich and gas-poor segments. We study the velocity dispersion-size relation towards different association types. From the ratio between different types, we estimate a feedback time of ≈ 1.7 Myr in the solar neighbourhood. The sample sets a solid foundation to explore the relationship between interstellar medium evolution, star formation, and Galaxy structure.
Interacting galaxies in the IllustrisTNG simulations – VI: Reconstructed orbits, close encounters, and mergers
Authors: Patton David R , Faria Lawrence , Hani Maan H , Torrey Paul , Ellison Sara L , Thakur Shivani D , Westlake Raven I
Published: February 2024

Cosmological simulations have been used to study interacting galaxies as a function of galaxy pair separation, enabling comparisons with observational studies of galaxy pairs. The study of interacting galaxies as a function of time (i.e. merger stage) has mostly been limited to high-resolution merger simulations, due to the poor time sampling available in cosmological simulations. Building on an earlier study of galaxy pairs in the IllustrisTNG cosmological simulations, we reconstruct the orbits of galaxy pairs involving massive galaxies (M* > 1010 M⊙) at redshifts of 0 ≤ z < 1, using a novel kinematic interpolation scheme to model the orbits in between the IllustrisTNG snapshots (which are separated by 162 Myr, on average). We assess the accuracy of these interpolations using a pre-existing suite of merger simulations, and find that kinematic interpolations provide a remarkable improvement in accuracy compared with interpolations that use only radial separations or 3D positions. We find that nearly 90 per cent of the closest pairs (r < 25 kpc) have had a pericentre encounter within the past Gyr. Many of these close pairs are found on rapidly shrinking orbits, and roughly 85 per cent of these pairs will merge within 1 Gyr. However, approximately 3 per cent of these close pairs appear to be flyby systems that will never merge. These reconstructed orbits will be used in future studies to investigate how and when galaxy properties change during close encounters and mergers between galaxies in IllustrisTNG.
Influence of maternal folate depletion on Art3 DNA methylation in the murine adult brain; potential consequences for brain and neurocognitive health
Authors: Kok Dieuwertje E , Saunders Rachael , Nelson Andrew , Smith Darren , Ford Dianne , Mathers John C , McKay Jill A
Published: February 2024

The developmental origins of health and disease hypothesis suggest early-life environment impacts health outcomes throughout the life course. In particular, epigenetic marks, including DNA methylation, are thought to be key mechanisms through which environmental exposures programme later-life health. Adequate maternal folate status before and during pregnancy is essential in the protection against neural tube defects, but data are emerging that suggest early-life folate exposures may also influence neurocognitive outcomes in childhood and, potentially, thereafter. Since folate is key to the supply of methyl donors for DNA methylation, we hypothesize that DNA methylation may be a mediating mechanism through which maternal folate influences neurocognitive outcomes. Using bisulphite sequencing, we measured DNA methylation of five genes (Art3, Rsp16, Tspo, Wnt16, and Pcdhb6) in the brain tissue of adult offspring of dams who were depleted of folate (n = 5, 0.4 mg folic acid/kg diet) during pregnancy (~19–21 days) and lactation (mean 22 days) compared with controls (n = 6, 2 mg folic acid/kg diet). Genes were selected as methylation of their promoters had previously been found to be altered by maternal folate intake in mice and humans across the life course, and because they have potential associations with neurocognitive outcomes. Maternal folate depletion was significantly associated with Art3 gene hypomethylation in subcortical brain tissue of adult mice at 28 weeks of age (mean decrease 6.2%, P = .03). For the other genes, no statistically significant differences were found between folate depleted and control groups. Given its association with neurocognitive outcomes, we suggest Art3 warrants further study in the context of lifecourse brain health. We have uncovered a potential biomarker that, once validated in accessible biospecimens and human context, may be useful to track the impact of early-life folate exposure on later-life neurocognitive health, and potentially be used to develop and monitor the effects of interventions.
BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies
Authors: Zhou Wanding , Johnson Benjamin K , Morrison Jacob , Beddows Ian , Eapen James , Katsman Efrat , Semwal Ayush , Habib Walid Abi , Heo Lyong , Laird Peter W , Berman Benjamin P , Triche Timothy J , Shen Hui
Published: February 2024

Data from both bulk and single-cell whole-genome DNA methylation experiments are under-utilized in many ways. This is attributable to inefficient mapping of methylation sequencing reads, routinely discarded genetic information, and neglected read-level epigenetic and genetic linkage information. We introduce the BISulfite-seq Command line User Interface Toolkit (BISCUIT) and its companion R/Bioconductor package, biscuiteer, for simultaneous extraction of genetic and epigenetic information from bulk and single-cell DNA methylation sequencing. BISCUIT’s performance, flexibility and standards-compliant output allow large, complex experimental designs to be characterized on clinical timescales. BISCUIT is particularly suited for processing data from single-cell DNA methylation assays, with its excellent scalability, efficiency, and ability to greatly enhance mappability, a key challenge for single-cell studies. We also introduce the epiBED format for single-molecule analysis of coupled epigenetic and genetic information, facilitating the study of cellular and tissue heterogeneity from DNA methylation sequencing.
COSA-1 mediated pro-crossover complex formation promotes meiotic crossing over in C. elegans
Authors: Yang Yuejun , Wang Nan , Liu Guoteng , Nan Wencong , Wang Bin , Gartner Anton , Zhang Hongtao , Hong Ye
Published: February 2024

Accurate chromosome segregation during meiosis requires the establishment of at least one crossover (CO) between each pair of homologous chromosomes. CO formation depends on a group of conserved pro-CO proteins, which colocalize at CO-designated sites during late meiotic prophase I. However, it remains unclear whether these pro-CO proteins form a functional complex and how they promote meiotic CO formation in vivo. Here, we show that COSA-1, a key component required for CO formation, interacts with other pro-CO factors, MSH-5 and ZHP-3, via its N-terminal disordered region. Point mutations that impair these interactions do not affect CO designation, but they strongly hinder the accumulation of COSA-1 at CO-designated sites and result in defective CO formation. These defects can be partially bypassed by artificially tethering an interaction-compromised COSA-1 derivate to ZHP-3. Furthermore, we revealed that the accumulation of COSA-1 into distinct foci is required to assemble functional ‘recombination nodules’. These prevent early CO-designated recombination intermediates from being dismantled by the RTEL-1 helicase and protect late recombination intermediates, such as Holliday junctions, until they are resolved by CO-specific resolvases. Altogether, our findings provide insight into COSA-1 mediated pro-CO complex assembly and its contribution to CO formation.
Tracking pairwise genomic loci by the ParB–ParS and Noc-NBS systems in living cells
Authors: He Xiaohui , Tan Yuxi , Feng Ying , Sun Yadong , Ma Hanhui
Published: February 2024

The dynamics of genomic loci pairs and their interactions are essential for transcriptional regulation and genome organization. However, a robust method for tracking pairwise genomic loci in living cells is lacking. Here we developed a multicolor DNA labeling system, mParSpot (multicolor ParSpot), to track pairs of genomic loci and their interactions in living cells. The mParSpot system is derived from the ParB/ParS in the parABS system and Noc/NBS in its paralogous nucleoid occlusion system. The insertion of 16 base-pair palindromic ParSs or NBSs into the genomic locus allows the cognate binding protein ParB or Noc to spread kilobases of DNA around ParSs or NBSs for loci-specific visualization. We tracked two loci with a genomic distance of 53 kilobases and measured their spatial distance over time. Using the mParSpot system, we labeled the promoter and terminator of the MSI2 gene span 423 kb and measured their spatial distance. We also tracked the promoter and terminator dynamics of the MUC4 gene in living cells. In sum, the mParSpot is a robust and sensitive DNA labeling system for tracking genomic interactions in space and time under physiological or pathological contexts.
Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline
Authors: Rihon Jérôme , Mattelaer Charles-Alexandre , Montalvão Rinaldo Wander , Froeyen Mathy , Pinheiro Vitor Bernardes , Lescrinier Eveline
Published: February 2024

The field of synthetic nucleic acids with novel backbone structures [xenobiotic nucleic acids (XNAs)] has flourished due to the increased importance of XNA antisense oligonucleotides and aptamers in medicine, as well as the development of XNA processing enzymes and new XNA genetic materials. Molecular modeling on XNA structures can accelerate rational design in the field of XNAs as it contributes in understanding and predicting how changes in the sugar–phosphate backbone impact on the complementation properties of the nucleic acids. To support the development of novel XNA polymers, we present a first-in-class open-source program (Ducque) to build duplexes of nucleic acid analogs with customizable chemistry. A detailed procedure is described to extend the Ducque library with new user-defined XNA fragments using quantum mechanics (QM) and to generate QM-based force field parameters for molecular dynamics simulations within standard packages such as AMBER. The tool was used within a molecular modeling workflow to accurately reproduce a selection of experimental structures for nucleic acid duplexes with ribose-based as well as non-ribose-based nucleosides. Additionally, it was challenged to build duplexes of morpholino nucleic acids bound to complementary RNA sequences.
UPF1 ATPase autoinhibition and activation modulate RNA binding kinetics and NMD efficiency
Authors: Chapman Joseph H , Youle Alice M , Grimme Acadia L , Neuman Keir C , Hogg J Robert
Published: February 2024

The RNA helicase UPF1 interacts with mRNAs, mRNA decay machinery, and the terminating ribosome to promote nonsense-mediated mRNA decay (NMD). Structural and biochemical data have revealed that UPF1 exists in an enzymatically autoinhibited ‘closed’ state. Upon binding the NMD protein UPF2, UPF1 undergoes an extensive conformational change into a more enzymatically active ‘open’ state, which exhibits enhanced ATPase and helicase activity. However, mechanically deficient UPF1 mutants (i.e. poorly processive, slow, and mechanochemically uncoupled) can support efficient NMD, bringing into question the roles of UPF1 enzymatic autoinhibition and activation in NMD. Here, we identify two additional important features of the activated open state: slower RNA binding kinetics and enhanced ATP-stimulated RNA dissociation kinetics. Computational modeling based on empirical measurements of UPF1, UPF2 and RNA interaction kinetics predicts that the majority of UPF1–RNA binding and dissociation events in cells occur independently of UPF2 binding. We find that UPF1 mutants with either reduced or accelerated dissociation from RNA have NMD defects, whereas UPF1 mutants that are more dependent on UPF2 for catalytic activity remain active on well-established NMD targets. These findings support a model in which the kinetics of UPF1-mRNA interactions are important determinants of cellular NMD efficiency.
Ribosomal quality control factors inhibit repeat-associated non-AUG translation from GC-rich repeats
Authors: Tseng Yi-Ju , Krans Amy , Malik Indranil , Deng Xiexiong , Yildirim Evrim , Ovunc Sinem , Tank Elizabeth M H , Jansen-West Karen , Kaufhold Ross , Gomez Nicolas B , Sher Roger , Petrucelli Leonard , Barmada Sami J , Todd Peter K
Published: February 2024

A GGGGCC (G4C2) hexanucleotide repeat expansion in C9ORF72 causes amyotrophic lateral sclerosis and frontotemporal dementia (C9ALS/FTD), while a CGG trinucleotide repeat expansion in FMR1 leads to the neurodegenerative disorder Fragile X-associated tremor/ataxia syndrome (FXTAS). These GC-rich repeats form RNA secondary structures that support repeat-associated non-AUG (RAN) translation of toxic proteins that contribute to disease pathogenesis. Here we assessed whether these same repeats might trigger stalling and interfere with translational elongation. We find that depletion of ribosome-associated quality control (RQC) factors NEMF, LTN1 and ANKZF1 markedly boost RAN translation product accumulation from both G4C2 and CGG repeats while overexpression of these factors reduces RAN production in both reporter assays and C9ALS/FTD patient iPSC-derived neurons. We also detected partially made products from both G4C2 and CGG repeats whose abundance increased with RQC factor depletion. Repeat RNA sequence, rather than amino acid content, is central to the impact of RQC factor depletion on RAN translation—suggesting a role for RNA secondary structure in these processes. Together, these findings suggest that ribosomal stalling and RQC pathway activation during RAN translation inhibits the generation of toxic RAN products. We propose augmenting RQC activity as a therapeutic strategy in GC-rich repeat expansion disorders.
Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition
Authors: Xin Ben-Ge , Huang Ling-Yun , Yuan Ling-Gang , Liu Na-Nv , Li Hai-Hong , Ai Xia , Lei Dong-Sheng , Hou Xi-Miao , Rety Stephane , Xi Xu-Guang
Published: February 2024

RNA helicases function as versatile enzymes primarily responsible for remodeling RNA secondary structures and organizing ribonucleoprotein complexes. In our study, we conducted a systematic analysis of the helicase-related activities of Escherichia coli HrpA and presented the structures of both its apo form and its complex bound with both conventional and non-canonical DNAs. Our findings reveal that HrpA exhibits NTP hydrolysis activity and binds to ssDNA and ssRNA in distinct sequence-dependent manners. While the helicase core plays an essential role in unwinding RNA/RNA and RNA/DNA duplexes, the N-terminal extension in HrpA, consisting of three helices referred to as the APHB domain, is crucial for ssDNA binding and RNA/DNA duplex unwinding. Importantly, the APHB domain is implicated in binding to non-canonical DNA structures such as G-quadruplex and i-motif, and this report presents the first solved i-motif-helicase complex. This research not only provides comprehensive insights into the multifaceted roles of HrpA as an RNA helicase but also establishes a foundation for further investigations into the recognition and functional implications of i-motif DNA structures in various biological processes.
DNA-PKcs suppresses illegitimate chromosome rearrangements
Authors: Wang Jinglong , Sadeghi Cheyenne A , Frock Richard L
Published: February 2024

Two DNA repair pathways, non-homologous end joining (NHEJ) and alternative end joining (A-EJ), are involved in V(D)J recombination and chromosome translocation. Previous studies reported distinct repair mechanisms for chromosome translocation, with NHEJ involved in humans and A-EJ in mice predominantly. NHEJ depends on DNA-PKcs, a critical partner in synapsis formation and downstream component activation. While DNA-PKcs inhibition promotes chromosome translocations harboring microhomologies in mice, its synonymous effect in humans is not known. We find partial DNA-PKcs inhibition in human cells leads to increased translocations and the continued involvement of a dampened NHEJ. In contrast, complete DNA-PKcs inhibition substantially increased microhomology-mediated end joining (MMEJ), thus bridging the two different translocation mechanisms between human and mice. Similar to a previous study on Ku70 deletion, DNA-PKcs deletion in G1/G0-phase mouse progenitor B cell lines, significantly impairs V(D)J recombination and generated higher rates of translocations as a consequence of dysregulated coding and signal end joining. Genetic DNA-PKcs inhibition suppresses NHEJ entirely, with repair phenotypically resembling Ku70-deficient A-EJ. In contrast, we find DNA-PKcs necessary in generating the near-exclusive MMEJ associated with Lig4 deficiency. Our study underscores DNA-PKcs in suppressing illegitimate chromosome rearrangement while also contributing to MMEJ in both species.
An engineered baculoviral protein and DNA co-delivery system for CRISPR-based mammalian genome editing
Authors: Capin Julien , Harrison Alexandra , Raele Renata A , Yadav Sathish K N , Baiwir Dominique , Mazzucchelli Gabriel , Quinton Loic , Satchwell Timothy J , Toye Ashley M , Schaffitzel Christiane , Berger Imre , Aulicino Francesco
Published: February 2024

CRISPR-based DNA editing technologies enable rapid and accessible genome engineering of eukaryotic cells. However, the delivery of genetically encoded CRISPR components remains challenging and sustained Cas9 expression correlates with higher off-target activities, which can be reduced via Cas9-protein delivery. Here we demonstrate that baculovirus, alongside its DNA cargo, can be used to package and deliver proteins to human cells. Using protein-loaded baculovirus (pBV), we demonstrate delivery of Cas9 or base editors proteins, leading to efficient genome and base editing in human cells. By implementing a reversible, chemically inducible heterodimerization system, we show that protein cargoes can selectively and more efficiently be loaded into pBVs (spBVs). Using spBVs we achieved high levels of multiplexed genome editing in a panel of human cell lines. Importantly, spBVs maintain high editing efficiencies in absence of detectable off-targets events. Finally, by exploiting Cas9 protein and template DNA co-delivery, we demonstrate up to 5% site-specific targeted integration of a 1.8 kb heterologous DNA payload using a single spBV in a panel of human cell lines. In summary, we demonstrate that spBVs represent a versatile, efficient and potentially safer alternative for CRISPR applications requiring co-delivery of DNA and protein cargoes.
LC3B drives transcription-associated homologous recombination via direct interaction with R-loops
Authors: Yoon Junghyun , Hwang Yiseul , Yun Hansol , Chung Jee Min , Kim Soyeon , Kim Gyeongmin , Lee Yeji , Lee Byoung Dae , Kang Ho Chul
Published: February 2024

Exploring the connection between ubiquitin-like modifiers (ULMs) and the DNA damage response (DDR), we employed several advanced DNA damage and repair assay techniques and identified a crucial role for LC3B. Notably, its RNA recognition motif (RRM) plays a pivotal role in the context of transcription-associated homologous recombination (HR) repair (TA-HRR), a particular subset of HRR pathways. Surprisingly, independent of autophagy flux, LC3B interacts directly with R-loops at DNA lesions within transcriptionally active sites via its RRM, promoting TA-HRR. Using native RNA immunoprecipitation (nRIP) coupled with high-throughput sequencing (nRIP-seq), we discovered that LC3B also directly interacts with the 3′UTR AU-rich elements (AREs) of BRCA1 via its RRM, influencing its stability. This suggests that LC3B regulates TA-HRR both proximal to and distal from DNA lesions. Data from our LC3B depletion experiments showed that LC3B knockdown disrupts end-resection for TA-HRR, redirecting it towards the non-homologous end joining (NHEJ) pathway and leading to chromosomal instability, as evidenced by alterations in sister chromatid exchange (SCE) and interchromosomal fusion (ICF). Thus, our findings unveil autophagy-independent functions of LC3B in DNA damage and repair pathways, highlighting its importance. This could reshape our understanding of TA-HRR and the interaction between autophagy and DDR.
A tool to predict the risk of lower extremity amputation in patients starting dialysis
Authors: Akerboom Bram , Janse Roemer J , Caldinelli Aurora , Lindholm Bengt , Rotmans Joris I , Evans Marie , van Diepen Merel
Published: February 2024

Background

Non-traumatic lower extremity amputation (LEA) is a severe complication during dialysis. To inform decision-making for physicians, we developed a multivariable prediction model for LEA after starting dialysis.

Methods

Data from the Swedish Renal Registry (SNR) between 2010 and 2020 were geographically split into a development and validation cohort. Data from Netherlands Cooperative Study on the Adequacy of Dialysis (NECOSAD) between 1997 and 2009 were used for validation targeted at Dutch patients. Inclusion criteria were no previous LEA and kidney transplant and age ≥40 years at baseline. A Fine–Gray model was developed with LEA within 3 years after starting dialysis as the outcome of interest. Death and kidney transplant were treated as competing events. One coefficient, ordered by expected relevance, per 20 events was estimated. Performance was assessed with calibration and discrimination.

Results

SNR was split into an urban development cohort with 4771 individuals experiencing 201 (4.8%) events and a rural validation cohort with 4.876 individuals experiencing 155 (3.2%) events. NECOSAD contained 1658 individuals experiencing 61 (3.7%) events. Ten predictors were included: female sex, age, diabetes mellitus, peripheral artery disease, cardiovascular disease, congestive heart failure, obesity, albumin, haemoglobin and diabetic retinopathy. In SNR, calibration intercept and slope were –0.003 and 0.912, respectively. The C-index was estimated as 0.813 (0.783–0.843). In NECOSAD, calibration intercept and slope were 0.001 and 1.142 respectively. The C-index was estimated as 0.760 (0.697–0.824). Calibration plots showed good calibration.

Conclusion

A newly developed model to predict LEA after starting dialysis showed good discriminatory performance and calibration. By identifying high-risk individuals this model could help select patients for preventive measures.