bluuebunny/crossref_metadata_2025 huggingface dataset:
Somatic evolution of cancer genes in sex chromosomes
Authors: Akachukwu Amarachi C. , Ratcliff Jasmine S. , Marco Antonio
Published: September 2024

Genes on sex chromosomes have higher evolutionary rates than those on autosomes. However, this does not necessarily apply to somatic evolution in cancer. Many dominant mutations have been described in the so-called proto-oncogenes (OGs), while recessive mutations are typically described in tumor-suppressor genes (TSGs). Evidence indicates that mutations in X-chromosome TSGs are more likely to contribute to cancer than those in autosomal TSGs. Here, we formalize this in several dynamic models and predict, as expected, that mutations spread faster in TSGs located on the X chromosome than on autosomes (faster-X effect). Conversely, mutations in OGs spread faster on autosomes than on the X chromosome, but under high selective pressure, this difference is negligible. Published genomic screenings of cancer samples show evidence of the faster-X effect in TSGs. This pattern is observed in both sexes, suggesting that the maintenance of X-chromosome inactivation during cancer progression plays an important role in the evolution of TSGs. Strikingly, the relative mutation incidence in X-linked TSGs among females across individual studies is bimodal, with one group of studies showing a faster-X effect and another group showing similar incidences for X-linked and autosomal TSGs. This differentiation between cancer samples is not associated with the specific type of cancer or the tissue of origin. This may indicate that X-chromosome inactivation plays a differential role in the involvement of X-linked TSGs across individual cancers.
Harnessing Synaptic Vesicle Release and Recycling Mechanism for Molecule Delivery to Neurons
Authors: Yee Karen Kar Lye , Kumamoto Junichi , Inomata Daijiro , Suzuki Naoki , Harada Ryuhei , Yumoto Norihiro
Published: September 2024

Neurodegenerative clinical trials often fail due to insufficient drug doses in reaching targeted cells and the unintended delivery to non-targeted cells. This study demonstrates an alternative neuron-selective drug delivery system, which utilizes the synaptic vesicle release and recycling mechanism (SVRM) by antibody shuttles targeting synaptic vesicle transmembrane proteins for molecule delivery. Using Synaptotagmin-2 (SYT2), we exemplify that intravenously administered anti-SYT2 antibodies localize to neuromuscular junctions, undergo uptake, and retrograde transport toChAT-positive motor neurons (MNs) in the spinal cord and brainstem. The delivery of anti-microtubule agent andMalat1gapmer antisense oligonucleotide to MNs with anti-SYT2 antibodies induces axon degeneration and reduction of Malat1 RNA expression, respectively. This approach circumvents the blood-spinal cord barrier, enabling selective delivery of therapeutic molecules to neurons while minimizing effects in non-targeted cells. Thus harnessing SVRM presents a promising strategy for enhancing drug concentrations in neurons and improving treatment efficacy for neurodegenerative diseases.
Pediatric Kidney Injury in Communities Impacted by Chronic Kidney Disease of Unknown Etiology (CKDu): A Comprehensive Systematic Review of Epidemiologic Studies
Authors: Strasma Anna , Gerber Anisha , Agi Maluli Isabela , Blackwood Elizabeth R. , Gunasekara Sameera , De Silva P. Mangala C S , Kamath Nivedita , Gonzalez-Quiroz Marvin , Sanders Alison P. , Wyatt Christina , Jayasundara Nishad
Published: September 2024

Background

Chronic kidney disease of unknown etiology (CKDu) is a tubulointerstitial disease that disproportionately affects young, primarily male, agricultural workers in Mesoamerica and South Asia who lack traditional risk factors for kidney disease. Extensive research in adult populations suggests the etiology is complex and indicates that early childhood exposures could have an integral role.

Objectives

To systematically identify, summarize, and compare research in children living in CKDu endemic areas or with relevant CKDu-related exposures.

Methods

A systematic literature search was conducted in six databases for studies that report kidney health outcomes of pediatric populations living in proximity to CKDu-affected areas with no limitations on geography or study design. Studies were independently screened for inclusion and underwent quality assessment using the Appraisal Tool for Cross-Sectional Studies (AXIS) or the JBI Critical Appraisal Tool for Cohort Studies based on the study design by at least two authors. Data are compared narratively and graphically.

Results

We included twenty peer-reviewed publications and two meeting abstracts from eight different countries. The most common study design involved cross-sectional analysis of biological specimens from children in an established CKDu endemic area. Marked decreases in estimated glomerular filtration rate were generally not identified and prevalence of albuminuria differed widely between countries. Novel urinary biomarkers frequently demonstrated subclinical kidney damage, although the specific biomarker(s) varied between studies. Epidemiologic factors associated with evidence of subclinical kidney damage in children included proximity to agriculture or agrochemicals. Despite heterogenous study outcomes, all studies concluded that there were signs of kidney injury in children living in CKDu endemic areas or with a CKDu-relevant environmental exposure.

Conclusion

This systematic review suggests that the pathophysiologic process leading to CKDu may begin prior to adulthood. Future longitudinal research aimed at elucidating the multifaceted factors and exposures impacting entire communities, including children, is imperative for disease prevention strategies.
Low-intensity focused ultrasound stimulation in stroke: An intensity escalation phase I safety and feasibility study
Authors: Huang Ziping , Charalambous Charalambos C. , Chen Mengyue , Kim Taewon , Sokhadze Estate , Song Allen , Jung Sin-Ho , Shekhar Shashank , Feld Jody , Jiang Xiaoning , Feng Wuwei
Published: September 2024

BACKGROUND

Low-intensity focused ultrasound stimulation (LIFUS) has recently emerged as a promising neuromodulation tool for certain neuropsychiatric diseases. However, its safety and feasibility in stroke patients remains unknown. Intensity is a critical safety parameter for LIFUS. We aimed to determine the maximum safe and tolerable intensity of LIFUS in stroke patients, and to explore its effect on upper-extremity motor learning and corticospinal excitability.

METHODS

Subjects with first-ever stroke participated in this Phase I study. We adopted the classic 3+3 dose-escalation paradigm to sham/0, 1, 2, 4, 6, and 8 W/cm2spatial-peak pulse-average intensity (ISPPA, estimated in-vivo transcranial value; LOW: sham/0, 1 and 2 W/cm2, HIGH: 4, 6 and 8 W/cm2). Stopping rules (dose limiting toxicities) were pre-defined: ≥2nd-degree scalp burn, clinical seizures, ≥20% topical apparent diffusion coefficient change, or participant discontinuation due to any reason. A 12-minute LIFUS was applied over the ipsilesional motor cortex while participants were concurrently practicing three blocks of motor sequence learning (MSL) task using the affected hand. We collected the occurrences of pre-defined adverse events, post-minus-pre improvements in MSL response time, and post-minus-pre differences in corticospinal excitability quantified by motor evoked potentials.

RESULTS

ISPPAwas escalated to 8 W/cm2with eighteen stroke participants without meeting stopping rules. Compared to the LOW, the HIGH performed significantly better on the MSL (24.7±13.3% vs. 13.2±10.9%,p=0.01). Similarly, the HIGH also showed signs of increased corticospinal excitability (32.0±34.3% vs. 12.9±48.0%) but did not reach significance,p=0.53.

CONCLUSIONS

Our Phase I safety study suggests that a single session of 12-minute LIFUS up to 8 W/cm2ISPPAis safe and feasible in stroke patients. Higher LIFUS intensities can induce greater MSL retention. The next logical step is to conduct a Phase II study to further test the efficacy of LIFUS and monitor its safety profiles in stroke patients.

REGISTRATION

URL:https://www.clinicaltrials.gov; Unique identifier:NCT05016531
Prevalence of Common Respiratory Viruses in Children: Insights from Post-Pandemic Surveillance
Authors: Adu-Gyamfi Constance , Asamoah Jesse Addo , Frimpong James Opoku , Larbi Richard , Ansah Richard Owusu , Aryeetey Sherihane Naa Ayeley , Gorman Richmond , Acheampong Henry Kyeremateng , Nyarko-Afriyie Emmanuella , Hayford Manuella , Tetteh Henrietta Dede , Boampong Kwadwo , Barnor Veronica , Brenya Peter K. , Ayensu Frederick , Ayisi-Boateng NK. , El-Duah Philip , Drosten Christian , Phillips Richard Odame , Sylverken Augustina Angelina , Owusu Michael
Published: September 2024

Introduction

The COVID-19 pandemic has significantly affected healthcare systems worldwide, impacting the occurrence and management of respiratory illnesses. This has also influenced respiratory infections’ role in childhood mortality. Surveillance of common respiratory viruses in Ghana is limited, making it crucial to assess the prevalence of respiratory viral infections, particularly in children, in the post-pandemic era. This study provides data on the prevalence of respiratory viruses and the associated risk factors in children aged 5 or younger in an urban paediatric hospital setting.

Methods

The study was a cross-sectional study with a convenience sampling method, conducted in four health facilities: Asokwa Children’s Hospital, HopeXchange Medical Centre, University Health Services-KNUST, and Kumasi South Hospital in Kumasi, Ghana, between August 2022 and June 2023. Recruitment was not done in parallel in each hospital. Oropharyngeal swabs were collected from children ≤ 5 years old and screened by RT-qPCR for common respiratory viruses.

Results

Out of the 303 patients enrolled in the study, 165 (54.4%) were male, and 122 (40.3%) were aged from 13 to 36 months. The median age of the patients was 19 months. The most common symptoms reported were cough (87.0%), runny nose (87.0%), and fever (72.0%). Respiratory viruses were detected in 100 (33.0%) of the samples, with 36 (12.0%) testing positive for Human metapneumovirus (HMPV), 27 (8.9%) for RSV, and 20 (6.6%) for Human Adenovirus (HAdV). In 8.0% of the cases, multiple viruses were detected, with HAdV being the most common (75.0%). Children under 6 months (AOR: 4.81, 95% CI: 1.20-24.60) had a higher risk of RSV detection compared to children aged 37 to 60 months. Furthermore, it was found that caregivers with tertiary education had a higher risk of HMPV detection (AOR: 6.91, 95% CI: 1.71-47.3).

Conclusion

The study’s findings emphasize RSV infection in very young children and the potentially significant role of HMPV in causing respiratory infections among children in Ghana. Active surveillance of common respiratory viruses in healthcare facilities could enhance the management of viral respiratory infection cases in the paediatric population in Ghana.
A Systematic Review of the Etiology and Neurobiology of Intermittent Explosive Disorder
Authors: Paliakkara John , Ellenberg Stacy , Ursino Andrew , Smith Abigail A , Evans James , Strayhorn Joseph , Faraone Stephen V. , Zhang-James Yanli
Published: September 2024

Intermittent Explosive Disorder (IED) is characterized by repeated inability to control aggressive impulses. Although the etiology and neurobiology of impulsive anger and impulse control disorders have been reviewed, no systematic review on these aspects has been published for IED specifically. We conducted a systematic search in seven electronic databases for publications about IED, screened by two authors, and retained twenty-four studies for the review. Our findings highlight a multifactorial etiology and neurobiology of IED, emphasizing the role of the amygdala and orbitofrontal cortex in emotional regulation and impulse control, and supporting interventions that target serotonergic signaling. Research also shows that childhood trauma and adverse family environment may significantly contribute to the development of IED. Yet, genetic studies focusing on IED were largely lacking, despite many examining the genetics underlying aggression as a general trait or other related disorders. Future research using consistently defined IED as a phenotype is required to better understand the etiology and underlying mechanisms and assist in informing the development of more effective interventions for IED.
Development and Validation of Nomograms for predicting Coronary Artery Calcification and Severe Coronary Artery Calcification: a retrospective cross-sectional study
Authors: Xue Peng , Lin Ling , Li Peishan , Deng Zhengting , Chen Xiaohu , Zhuang Yanshuang
Published: September 2024

Introduction

There is a significant lack of effective pharmaceutical interventions for treating coronary artery calcification (CAC). Severe CAC (sCAC) poses a formidable challenge to interventional surgery and exhibits robust associations with adverse cardiovascular outcomes. Therefore, it is imperative to develop tools capable of early-stage detection and risk assessment for both CAC and sCAC. This study aims to develop and validate nomograms for the accurate prediction of CAC and sCAC.

Methods

This retrospective cross-sectional study was conducted in Taizhou, Jiangsu Province, China. CAC assessment was performed using non-gated thoracic CT scans. Demographic data and clinical information were collected from patients who were then randomly divided into a training set (70%) or a validation set (30%). Least absolute shrinkage and selection operator (LASSO) regression as well as multiple logistic regression analyses were utilized to identify predictive factors for both CAC and sCAC development. Nomograms were developed to predict the occurrence of CAC or sCAC events. The models’ performance was evaluated through discrimination analysis, calibration analysis, as well as assessment of their clinical utility.

Results

This study included 666 patients with an average age of 75 years, of whom 56% were male. 391 patients had CAC, with sCAC in 134 cases. Through LASSO and multiple logistic regression analysis, age increase, hypertension, carotid artery calcification, CHD, and CHADS2score were identified for the CAC risk predictive nomogram with an area under the receiver operating characteristic (ROC) curve (AUC) of 0.845(95%CI 0.809-0.881) in the training set and 0.810(95%CI 0.751-0.870) in the validation set. Serum calcium level, carotid artery calcification, and CHD were identified for the sCAC risk predictive nomogram with an AUC of 0.863(95%CI 0.825-0.901) in the training set and 0.817(95%CI 0.744-0.890) in the validation set. Calibration plots indicated that two models exhibited good calibration ability. According to the decision curve analysis (DCA) results, both models have demonstrated a positive net benefit within a wide range of risks.

Conclusions

The present study has successfully developed and validated two nomograms to accurately predict CAC and sCAC, both of which have demonstrated robust predictive capabilities.
Global proteomics indicates subcellular-specific anti-ferroptotic responses to ionizing radiation
Authors: Christopher Josie A , Breckels Lisa M , Crook Oliver M , Vazquez-Chantada Mercedes , Barratt Derek , Lilley Kathryn Susan
Published: September 2024

Cells have many protective mechanisms against background levels of ionizing radiation (IR) orchestrated by molecular changes in expression, post-translation modifications and subcellular localization. Radiotherapeutic treatment in oncology attempts to overwhelm such mechanisms, but radio-resistance is an ongoing challenge. Here, global subcellular proteomics combined with Bayesian modelling identified 544 differentially localized proteins in A549 cells upon 6 Gy x-ray exposure, revealing subcellular-specific changes of proteins involved in ferroptosis, an iron-dependent cell death, suggestive of potential radio-resistance mechanisms. These observations were independent of expression changes, emphasizing the utility of global subcellular proteomics and the promising prospect of ferroptosis-inducing therapies for combatting radioresistance.
Sensitive dissection of a genomic regulatory landscape using bulk and targeted single-cell activation
Authors: Vucicevic Dubravka , Hsu Che-Wei , Lopez Zepeda Lorena Sofia , Burkert Martin , Hirsekorn Antje , Bilic Ilija , Kastelic Nicolai , Landthaler Markus , Lacadie Scott A. , Ohler Uwe
Published: September 2024

Transcriptional enhancers are non-coding DNA elements that regulate gene transcription in a temporal and tissue-specific manner. Despite advances in computational and experimental methods, identifying enhancers and their target genes remains challenging. To identify and functionally perturb enhancers at their endogenous sites, we performed a pooled tiling CRISPR activation (CRISPRa) screen surrounding PHOX2B, a regulator of neuronal differentiation and neuroblastoma, revealing many CRISPRa-responsive-elements (CaREs) that alter cellular growth. To determine CaRE target genes, we developed and applied TESLA-seq (TargEted-SingLe-cell-Activation), which combines CRISPRa screening with targeted single-cell RNA-sequencing and enabled the parallel readout of the effect of hundreds of enhancers on all genes in the locus. While most TESLA-revealed CaRE-gene relationships involved neuroblastoma regulatory elements already active in the system, we found many CaREs and target connections normally active only in other tissue types or with no previous evidence. This highlights the power of TESLA-seq to reveal gene regulatory networks, including edges active outside of a given experimental system.
Neutrophil NADPH oxidase breaks the inflammatory IL-1β/IL-17A circuit to enhance pathogen clearance during respiratory virus infections
Authors: Sofoluwe Aderonke , Petropoulos Angelos , Goomanee Abhilesh Salil , Ali-Khan Zehra Fatima , Warnatsch Annika
Published: September 2024

Respiratory virus infections are invariably accompanied by an increase in oxidative stress, characterised by elevated production of Reactive Oxygen Species (ROS) in the lung, which plays a pivotal role in both pathogenesis and host defence. Using a mouse model, neutrophil NADPH Oxidase 2 (Nox2) emerges as a key player, primarily responsible for generation of ROS during the early phases of Influenza A Virus (IAV) infection. Neutrophil Nox2-derived ROS display a multifaceted role, not only unleashing oxidative stress but in turn curbing neutrophil-derived IL-1β signalling. Absence of neutrophil Nox2 triggered heightened production of IL-1β, promoting the proliferation of IL-17-producing gamma delta (γδ) T cells. This early self-amplified augmentation of the IL-β/IL-17 axis counteracted the antiviral interferon response against IAV infection in mice. We extended our findings to humans. Similar patterns of ROS production and cytokine regulation were observed in human neutrophils when exposed to virus analogue poly(I:C) and SARS-CoV-2. Our discovery highlights that ROS, often associated with harm, play a dual role by regulating cytokine signalling and thus influencing the immune response against respiratory viruses.

Highlights

Neutrophil NADPH oxidase 2 is the predominant source of ROS production early after influenza A virus infection.

Neutrophil Nox2-derived ROS uniquely suppress IL-1β, influencing γδ17T cell proliferation.

In absence of neutrophil Nox2, increased neutrophil-derived IL-1β drives proliferation of γδ17T cells.

Early amplification of the IL-β/IL-17 axis counteracts the antiviral interferon response in IAV-infected mice.

Virus infection induces a self-perpetuating loop between human blood-derived IL-1β-producing neutrophils and IL-17-secreting γδ T cells.
Strong Selection, but low repeatability: Temperature-specific effects on genomic predictions of adaptation
Authors: Rego Alexandre , Baur Julian , Girard-Tercieux Camille , de la Paz Celorio-Mancera Maria , Stelkens Rike , Berger David
Published: September 2024

Evolution should be more predictable when natural selection is strong and favors the same outcome. Climate warming is increasing temperatures beyond the optima of many ectotherms, which, due to the inherent non-linear relationship between temperature and the rate of cellular processes, is predicted to impose stronger selection compared to corresponding shifts toward cold temperatures. This suggests that adaptation to climate warming should be relatively predictable. Here, we tested this hypothesis from the level of single-nucleotide polymorphisms to life-history traits, by conducting an evolve-and-resequence experiment on three genetic backgrounds of the seed beetle, Callosobruchus maculatus. Indeed, phenotypic evolution was faster and more repeatable at hot, relative to cold, temperature. However, at the genomic level, adaptation to heat was less repeatable than to cold, especially when comparing responses between backgrounds. As a result, genomic predictions of phenotypic (mal)adaptation in populations exposed to hot temperature were highly accurate within, but inaccurate between, genetic backgrounds. These results seem best explained by an increased importance of epistasis during adaptation to heat and imply that the same biophysical mechanisms that increase the repeatability of phenotypic evolution by exerting strong selection at hot temperature, reduce repeatability at the genome level. Thus, predictions of adaptation in key phenotypes from genomic data may become increasingly difficult as climates warm.
CLIMATE BRAIN - Questionnaires, Tasks and the Neuroimaging Dataset
Authors: Zaremba Dominika , Kossowski Bartosz , Wypych Marek , Jednoróg Katarzyna , Michałowski Jarosław M. , Klöckner Christian A. , Wierzba Małgorzata , Marchewka Artur
Published: September 2024

Climate change presents a fundamental threat to human populations and ecosystems across the globe. Neuroscience researchers have recently started developing ways to advance research on this topic. However, validated questionnaires, experimental stimuli, and fMRI tasks are still needed. Here we describe the CLIMATE BRAIN dataset, a multimodal collection of questionnaire, behavioural, and neuroimaging data related to climate change, acquired from 160 healthy individuals. In particular, it includes data from (1) various questionnaire measures, including the Inventory of Climate Emotions (ICE); (2) a neuroimaging task for measuring emotional reactions to standardized Emotional Climate Change Stories (ECCS); and (3) a neuroimaging task based on Carbon Emission Task (CET) to measure climate action-taking. For technical validation, we provide image quality metrics and show the evidence for the effectiveness of tasks consistent with prior studies. To our knowledge, the proposed dataset is currently the only publicly available resource specifically designed to investigate human brain responses to climate change.
Comprehensive intra-host infection kinetics reveals high arbo-flavivirus transmission potential by neglected vector species,Aedes scutellaris
Authors: Samung Yudthana , Pengon Jutharat , Pethrak Chatpong , Pakparnich Phonchanan , Thaiudomsup Saranya , Suksirisawat Kittitat , Phayakkaphol Anon , Eiamsam-ang Songpol , Phanitchat Thipruethai , Sartsanga Channarong , Jantra Tararat , Sriwichai Patchara , Jupatanakul Natapong
Published: September 2024

Background

Dengue virus (DENV) and Zika virus (ZIKV) are primarily transmitted byAedesmosquitoes. As most studies on vector competence have focused onAedes aegyptiandAedes albopictuswhile neglecting otherAedesspecies, it is possible that the transmission risks might be underestimated. it is necessary to examine additional species that could potentially serve as competent vectors. This is particularly important considering the potential expansion of their geographical range due to climate change or species-specific vector reduction interventions.

Methodology/Principal Findings

In this study, we examined the infection kinetics and transmission potential ofAedes scutellarisfrom Thailand, comparing toAe. aegyptiandAe. albopictus. Our findings demonstrated thatAe. scutellarisandAe. albopictushad lower rates of midgut infection compared toAe. aegyptidue to smaller blood meal sizes during feeding. However, once the infection has establishedAe. scutellarisexhibited efficient replication of ZIKV and DENV1-4 in the midguts, secondary organs, and salivary glands. Notably,Ae. scutellarishad a low salivary gland escape barrier, with comparable transmissibility asAe. aegyptiwhen inoculated with the same viral load.

Conclusion

This study highlights the potential ofAe. scutellarisas a vector for DENV and ZIKV and emphasizes the importance of considering neglected mosquito species in arbovirus transmission and surveillance efforts.

Author Summary

Dengue and Zika are viral infections caused by arthropod-borne flaviviruses, and spread primarily through the bite of infectedAedesmosquitoes. Most research on DENV and ZIKV transmission has primarily focused onAedes aegyptiandAedes albopictuswhile otherAedesspecies are overlooked, thus the epidemiology of the transmission might be underestimated. With climate change together with species-specific mosquito population reduction interventions these neglectedAedesspecies could become increasingly important in sustaining virus transmission. In this study, we examinedAedes scutellaris, a mosquito species that co-habitats withAe. aegyptiandAe. albopictus, to assess its ability to transmit DENV and ZIKV using a combination of blood feeding and intrathoracic injection methods. Our findings show that althoughAe. scutellarishad lower initial infection rates due to smaller blood meals, DENV and ZIKV were able to replicate and transmit at levels comparable toAe. aegyptiwhen exposed to similar virus loads. This highlights the need to study a broader range of species to improve virus control and outbreak prevention strategies.
Both competition and frequency-dependence determine community dynamics in a dune heath ecosystem
Authors: Damgaard Christian , Kaae Mathias Emil , Bak Jesper Leth
Published: September 2024

To investigate community dynamics in a dune heath ecosystem, plant growth was measured in a five-block manipulated experiment with four nitrogen levels using the pin-point method. It was demonstrated that both Lotka-Volterra type interspecific competition and frequency-dependency play significant roles in determining plant growth. For modelling simplicity, plant taxa were divided into heather, wavy hair-grass, and all other vascular species. Significant interspecific competition was observed among all species, except wavy hair-grass on the growth of all other vascular species, and nitrogen addition was found to increase the competitive effect of heather on the growth of all other vascular species. Both heather and wavy hair-grass showed positive feedback dynamics on growth when they were relatively dominant at the plot scale and the effect increased with added nitrogen. Such positive feedback dynamics may lead to the formation of patches, which are a characteristic feature of heath ecosystems. Oppositely, there was a beneficial effect of being relatively rare on the growth of all other vascular species in plots with added nitrogen. The study highlights the importance of the combined effects of interspecific competition and frequency-dependency in regulating plant communities and, consequently, undermines both theoretical and empirical conclusions of modern coexistence theory.
The epitranscriptomic m6A RNA modification modulates synaptic function in ageing and in a mouse model of synucleinopathy
Authors: Chopra Avika , Xylaki Mary , Yin Fanzheng , Castro-Hernández Ricardo , Merghani Madiha , Grande Valentina , Mollenhauer Brit , Fischer André , Outeiro Tgiago F.
Published: September 2024

N6-methyladenosine (m6A) is the most abundant and conserved transcriptional modification in eukaryotic RNA, regulating RNA fate. While the functions of m6A in the development of the mammalian brain have been extensively studied, its roles in synaptic plasticity, cognitive decline, motor function, or other brain circuits remain underexplored. To date, the role of this modification in Parkinson’s disease (PD) and other synucleinopathies has been largely unknown. Here, we investigated the m6A epitranscriptome in a mouse model of synucleinopathy. We performed m6A RNA immunoprecipitation sequencing (meRIP-seq) to obtain the m6A epitranscriptome of the midbrain in young (3 mo) and aged (15 mo) A30P-aSyn transgenic mice (aSyn Tg) and C57BL6 control wild type (Wt) mice. We observed hypermethylation of synaptic genes in 3 mo aSyn Tg mice compared to age-matched Wt mice. This methylation was reduced during ageing, with synaptic genes becoming increasingly hypomethylated. Using immunofluorescence imaging alongside biochemical analysis, we further investigated the expression of m6A regulatory enzymes — writer, N6-Adenosine-Methyltransferase Complex Catalytic Subunit (METTL3); reader, YTH N6-methyladenosine RNA-binding protein (YTHDF1); and eraser, fat mass and obesity-associated protein (FTO) — in the cortex, striatum, hippocampus, and cerebellum of Wt and aSyn Tg mice, as well as in primary cortical neuronal cultures. We observed that the levels of METTL3, YTHDF1 and FTO were similar between Wt and aSyn Tg mice. Interestingly, the writer protein METTL3 was found in both the nucleus and in the post-synaptic compartment in neuronal cultures. Our findings suggest that alterations in the regulation of m6A RNA methylation may be associated with neurodegeneration and ageing and that this level of epitranscriptomic regulation plays a significant role at the synapse.
Symmetry of loop extrusion by dimeric SMC complexes is DNA-tension-dependent
Authors: Pradhan Biswajit , Pinto Adrian , Kanno Takaharu , Tetiker Damla , Baaske Martin D. , Cutt Erin , Chatzicharlampous Constantinos , Schüler Herwig , Deep Amar , Corbett Kevin D. , Aragon Luis , Virnau Peter , Björkegren Camilla , Kim Eugene
Published: September 2024

Structural maintenance of chromosome (SMC) complexes organize and regulate genomes via DNA loop extrusion. During this process, the complexes increase the loop size by reeling in DNA from one or both sides of the loop. The factors governing this symmetry remain unclear. Here, we combine single-molecule analysis and molecular dynamic simulations to investigate the symmetry of loop extrusion of various SMC complexes. We find that whereas monomeric condensin and cohesin are one-sided extruders, the symmetry of dimeric SMCs, such as Smc5/6 and Wadjet, is DNA tension dependent. At low DNA tension (< 0.1pN), Smc5/6 and Wadjet extrude DNA from both sides of the loop. At higher tension, however, they transition to a behavior akin to one-sided extruders, yet still capable of extruding from one or the other side thereby switching the direction of extrusion. Our simulations further reveal that thermal fluctuations significantly influence loop extrusion symmetry, causing variations in DNA reeling rates between the two motors in the dimeric complexes and their direction switching at stalling tensions. Our findings challenge the previous view of loop extrusion symmetry as a fixed characteristic, revealing its dynamic nature and regulation by both intrinsic protein properties and extrinsic factors.
“Mitotic” kinesin-5 is a dynamic brake for axonal growth
Authors: Lu Wen , Lee Brad S. , Ying Deng Helen Xue , Lakonishok Margot , Martin-Blanco Enrique , Gelfand Vladimir I.
Published: September 2024

During neuronal development, neurons undergo significant microtubule reorganization to shape axons and dendrites, establishing the framework for efficient wiring of the nervous system. Previous studies from our laboratory demonstrated the key role of kinesin-1 in driving microtubule-microtubule sliding, which provides the mechanical forces necessary for early axon outgrowth and regeneration inDrosophila melanogaster. In this study, we reveal the critical role of kinesin-5, a mitotic motor, in modulating the development of postmitotic neurons.

Kinesin-5, a conserved homotetrameric motor, typically functions in mitosis by sliding antiparallel microtubules apart in the spindle. Here, we demonstrate that theDrosophilakinesin-5 homolog, Klp61F, is expressed in larval brain neurons, with high levels in ventral nerve cord (VNC) neurons. Knockdown ofKlp61Fusing a pan-neuronal driver leads to severe locomotion defects and complete lethality in adult flies, mainly due to the absence of kinesin-5 in VNC motor neurons during early larval development.Klp61Fdepletion results in significant axon growth defects, both in cultured andin vivoneurons. By imaging individual microtubules, we observe a significant increase in microtubule motility, and excessive penetration of microtubules into the axon growth cone inKlp61F-depleted neurons. Adult lethality and axon growth defects are fully rescued by a chimeric human-Drosophilakinesin-5 motor, which accumulates at the axon tips, suggesting a conserved role of kinesin-5 in neuronal development.

Altogether, our findings show that at the growth cone, kinesin-5 acts as a brake on kinesin-1-driven microtubule sliding, preventing premature microtubule entry into the growth cone. This regulatory role of kinesin-5 is essential for precise axon pathfinding during nervous system development.
ADPKD variants in the PKD2 pore helix cause structural collapse of the gate and distinct forms of channel dysfunction
Authors: Palomero Orhi Estarte , DeCaen Paul G.
Published: September 2024

PKD2 is a member of the polycystin subfamily of transient receptor potential (TRP) ion channel subunits which traffic and function in primary cilia organelle membranes. Millions of individuals carry pathogenic genetic variants in PKD2 that cause a life-threatening condition called autosomal dominant polycystic kidney disease (ADPKD). Although ADPKD is a common monogenetic disorder, there is no drug cure or available therapeutics which address the underlying channel dysregulation. Furthermore, the structural and mechanistic impact of most disease-causing variants are uncharacterized. Using direct cilia electrophysiology, cryogenic electron microscopy (cryo-EM), and super resolution imaging, we have discovered mechanistic differences in channel dysregulation caused by three germline missense variants located in PKD2’s pore helix 1. Variant C632R reduces protein thermal stability, resulting in impaired channel assembly and abolishes primary cilia trafficking. In contrast, variants F629S and R638C retain native cilia trafficking, but exhibit gating defects. Resolved cryo-EM structures (2.7-3.2Å) of the variants indicate loss of critical pore helix interactions and precipitate allosteric collapse of the channels inner gate. Results demonstrate how ADPKD-causing these mutations have divergent and ranging impacts on PKD2 function, despite their shared structural proximity. These unexpected findings underscore the need for mechanistic characterization of polycystin variants, which may guide rational drug development of ADPKD therapeutics.

Regarding polycystin nomenclature

The revised and current IUPHAR/BPS nomenclature creates ambiguity regarding the genetic identity of the polycystin family members of transient receptor potential ion channels (TRPP), especially when cross-referencing manuscripts that describe subunits using the former system1. Traditionally, the products of polycystin genes (e.g., PKD2) are referred to as polycystin proteins (e.g., polycystin-2). For simplicity and to prevent confusion, we will refer to the polycystin gene name rather than differentiating gene and protein with separate names— a nomenclature we have recently outlined (Annual Reviews in Physiology, Esarte Palomero et al. 2023)2
Context-Seq: CRISPR-Cas9 Targeted Nanopore Sequencing for Transmission Dynamics of Antimicrobial Resistance
Authors: Fuhrmeister Erica R. , Kim Sooyeol , Mairal Shruteek A. , McCormack Caroline , Chieng Benard , Swarthout Jenna M. , Paulos Abigail Harvey , Njenga Sammy M. , Pickering Amy J.
Published: September 2024

Antimicrobial resistance (AMR) aligns with a One Health framework in that resistant bacteria and antibiotic resistance genes (ARGs) can be transmitted between humans, animals, and the environment. However, there is a critical need to more precisely understand how and to what extent AMR is exchanged between animals and humans. Metagenomic sequencing has low detection for rare targets such as ARGs, while whole genome sequencing of isolates is burdensome and misses exchange between uncultured bacterial species. We developed a novel, targeted sequencing assay using CRISPR-Cas9 to selectively sequence ARGs and their genomic context with long-read sequencing. Using this method, termed Context-Seq, we investigated overlapping AMR elements containing the ARGsblaCTX-MandblaTEMbetween adults, children, poultry, and dogs in animal-owning households in Nairobi, Kenya. We identified 22 genetically distinct clusters (> 80%ID over ≥ 3000 bp) containingblaTEMand one cluster containingblaCTX-Mthat were shared within and between households. Half of the clusters were shared between humans and animals, while the other half were shared only between animals (poultry-poultry, dog-dog, and dog-poultry). We identified potentially pathogenic hosts of ARGs includingEscherichia coli, Klebsiella pneumonia, andHaemophilus influenzaeacross sample types. Context-Seq complements conventional methods to obtain an additional view of bacterial and mammalian hosts in the proliferation of AMR.
Analysis of polyclonal and monoclonal antibody to the influenza virus nucleoprotein in different oligomeric states
Authors: Myers Mallory L. , Conlon Michael T. , Gallagher John R. , Woolfork De’Marcus D. , Khorrami Noah D. , Park William B. , Stradtman-Carvalho Regan K. , Harris Audray K.
Published: September 2024

Influenza virus nucleoprotein (NP) is one of the most conserved influenza proteins. Both NP antigen and anti-NP antibodies are used as reagents in influenza diagnostic kits, with applications in both clinical practice, and influenza zoonotic surveillance programs. Despite this, studies on the biochemical basis of NP diagnostic serology and NP epitopes are not as developed as for hemagglutinin (HA), the fast-evolving antigen which has been the critical component of current influenza vaccines. Here, we characterized the NP serology of mice, ferret, and human sera and the immunogenic effects of NP antigen presented as different structural complexes. Furthermore, we show that a classical anti-NP mouse mAb HB65 could detect NP in some commercial influenza vaccines. MAb HB65 bound a linear epitope with nanomolar affinity. Our analysis suggests that linear NP epitopes paired with their corresponding characterized detection antibodies could aid in designing and improving diagnostic technologies for influenza virus.
Completing the BASEL phage collection to unlock hidden diversity for systematic exploration of phage-host interactions
Authors: Humolli Dorentina , Piel Damien , Maffei Enea , Heyer Yannik , Agustoni Elia , Shaidullina Aisylu , Willi Luc , Imwinkelried Patrick , Estermann Fabienne , Cuénod Aline , Buser Dominik P. , Alampi Carola , Chami Mohamed , Egli Adrian , Hiller Sebastian , Dunne Matthew , Harms Alexander
Published: September 2024

Research on bacteriophages, the viruses infecting bacteria, has fueled the development of modern molecular biology and inspired their therapeutic application to combat bacterial multidrug resistance. However, most work has so far focused on a few model phages which impedes direct applications of these findings in clinics and suggests that a vast potential of powerful molecular biology has remained untapped. We have therefore recently composed the BASEL collection of Escherichia coli phages (BActeriophage SElection for your Laboratory) which made a relevant diversity of phages infecting the E. coli K-12 laboratory strain accessible to the community. These phages are widely used, but their assorted diversity had remained limited by the E. coli K-12 host. We have therefore now genetically overcome the two major limitations of E. coli K-12, its lack of O-antigen glycans and the presence of resident bacterial immunity. Restoring O-antigen expression resulted in the isolation of diverse additional viral groups like Kagunavirus, Nonanavirus, Gordonclarkvirinae, and Gamaleyavirus, while eliminating all known antiviral defenses of E. coli K-12 additionally enabled us to isolate phages of Wifcevirus genus. Even though some of these viral groups appear to be common in nature, no phages from any of them had previously been isolated using E. coli laboratory strains and they had thus remained largely understudied. Overall, 37 new phage isolates have been added to complete the BASEL collection. These phages were deeply characterized genomically and phenotypically with regard to host receptors, sensitivity to antiviral defense systems, and host range. These results highlighted dominant roles of the O-antigen barrier for viral host recognition and of restriction-modification systems in bacterial immunity. We anticipate that the completed BASEL collection will propel research on phage-host interactions and their molecular mechanisms, deepening our understanding of viral ecology and fostering innovations in biotechnology and antimicrobial therapy.
MtvS Regulates theFrancisellaType V-A CRISPR-Cas System
Authors: Brodmann Maj , Marraffini Luciano A.
Published: September 2024

CRISPR-Cas systems endow bacteria and archaea with adaptive immune systems against mobile genetic elements, playing a fundamental role in shaping microbial communities. Many organisms harbor more than one CRISPR-Cas system, however whether and how these are differentially regulated is not known, in many instances due to the impossibility of studying CRISPR immunity in native hosts. Here we studied the regulation of endogenous type II-B and type V-A CRISPR-Cas systems in opportunistic human pathogenFrancisella novicidaU112. Fluorescence microscopy and transcriptomics experiments revealed that while the type II-B system is constitutively expressed, the type V-A CRISPR-Cas system is differentially expressed at stationary phase and high cell density. Using mass spectrometry and genetics we identified MtvS as a factor required for the differential expression of the type V-A CRISPR-Cas locus. Surprisingly, MtvS-dependent expression of the type V-A CRISPR-Cas system at high cell density is linked quorum sensing like behavior, even thoughF. novicidaU112 lacks canonical quorum sensing genes. Our findings provide an example of how bacteria harboring multiple CRISPR systems regulate their expression.
The Arabidopsis histone H3K4me3-binding ALFIN-like proteins mediate histone H2A ubiquitination and coordinate diverse chromatin modifications
Authors: Su Xiao-Min , Yuan Dan-Yang , Li Lin , Yang Minqi , Chen She , Zhou Yue , He Xin-Jian
Published: September 2024

The histone H3K4 trimethylation (H3K4me3) is widely distributed at numerous actively transcribed protein-coding genes throughout the genome. However, the interplay between H3K4me3 and other chromatin modifications remains poorly understood in plants. In this study, we find that theArabidopsis thalianaH3K4me3-binding ALFIN-LIKE (AL) proteins are associated with H3K4me3-enriched genes at the whole-genome level. The AL proteins contain a C-terminal PHD finger, which has a conserved role in recognizing H3K4me3, and a PHD-associated AL (PAL) domain, which is responsible for binding to diverse chromatin-related proteins. We demonstrate that the AL proteins not only act as subunits of the Polycomb repressive complex 1 (PRC1) to mediate H2A ubiquitination at H3K4me3-enriched genes but also interact with a variety of other chromatin-related proteins. Furthermore, we elucidate the mechanisms by which AL proteins interact with other chromatin-associated proteins to integrate H3K4me3, H2A ubiquitination, H2A.Z deposition, H3K27 demethylation, and chromatin accessibility across the genome. These findings underscore the critical role of AL proteins in linking H3K4me3 with a variety of other chromatin modifications in plants.
Neural representation of vocalization self-monitoring in the bat auditory midbrain
Authors: Ye Huan , Cui Zhongdan , Liu Zhenxu , Qin Xuejiao , Huang Xincao , Bai Yuting , Luo Jinhong
Published: September 2024

During acoustic interaction, mammals, including humans, not only monitor sounds from external sources but also their own vocalizations, the latter of which is known as vocalization feedback monitoring. Yet, it is unclear whether subcortical auditory regions process vocalization feedback. Here, we established an experimental paradigm that allows recording chronically the single-unit activity of the auditory midbrain (inferior colliculus) in freely vocalizing bats. We report that most collicular neurons represented self-produced biosonar vocalizations distinctively from pure tones and vocalization playbacks. Some neurons showed robust excitatory responses to vocalization feedback yet lacked any excitatory response to pure tones covering the entire frequency range of the vocalizations. Surprisingly, some collicular neurons even reversed the response polarity, from vocalization-induced suppression to vocalization-playback-induced excitation. Moreover, approximately a third of the neurons responded faster to self-produced vocalizations than to both vocalization playbacks and pure tones. These findings show that the midbrain inferior colliculus is involved in vocalization feedback processing, an ability suggested to arise locally in the auditory cortex.
Epigenetic regulation of global proteostasis dynamics by RBBP5 ensures mammalian organismal health
Authors: Kubra Syeda , Sun Michelle , Dion William , Catak Ahmet , Luong Hannah , Wang Haokun , Pan Yinghong , Liu Jia-Jun , Ponna Aishwarya , Sipula Ian , Jurczak Michael J. , Liu Silvia , Zhu Bokai
Published: September 2024

Proteostasis is vital for cellular health, with disruptions leading to pathologies including aging, neurodegeneration and metabolic disorders. Traditionally, proteotoxic stress responses were studied as acute reactions to various noxious factors; however, recent evidence reveals that many proteostasis stress-response genes exhibit ∼12-hour ultradian rhythms under physiological conditions in mammals. These rhythms, driven by an XBP1s-dependent 12h oscillator, are crucial for managing proteostasis. By exploring the chromatin landscape of the murine 12h hepatic oscillator, we identified RBBP5, a key subunit of the COMPASS complex writing H3K4me3, as an essential epigenetic regulator of proteostasis. RBBP5 is indispensable for regulating both the hepatic 12h oscillator and transcriptional response to acute proteotoxic stress, acting as a co-activator for proteostasis transcription factor XBP1s. RBBP5 ablation leads to increased sensitivity to proteotoxic stress, chronic inflammation, and hepatic steatosis in mice, along with impaired autophagy and reduced cell survivalin vitro. In humans, lowerRBBP5expression is associated with reduced adaptive stress-response gene expression and hepatic steatosis. Our findings establish RBBP5 as a central regulator of proteostasis, essential for maintaining mammalian organismal health.