bluuebunny/crossref_metadata_2025 huggingface dataset:
Association of complex traits with common genetic variation across genomic regions containing pathogenic copy number variations
Authors: Snihirova Yelyzaveta , Breddels Esmee M. , Frei Oleksandr , Sønderby Ida E. , Andreassen Ole A , van Amelsvoort Therese , Linden David E.J. , van der Meer Dennis
Published: September 2024

Background

Copy Number Variations (CNVs) are structural variation in the genome, which may impact complex human traits and diseases. The investigation of rare CNVs is impeded by low sample size. To understand the mechanisms through which CNVs influence human health, common variation in the genomic region of the CNV from large samples could be used as a proxy.

Methods

Utilising genome-wide association study (GWAS) summary statistics of 20 traits, we assessed the cumulative effect of common genetic variants in eight genomic regions containing pathogenic CNVs, using MAGMA gene-based analysis. We used GSA-MiXeR to estimate the fold enrichment of these CNV regions for the specific phenotypes.

Results

The distal and proximal regions of the 16p11.2 CNV exhibited the highest number of significant associations and were enriched for the highest number of traits: 12 of 27 significant MAGMA associations (44%) were enriched. These CNV regions also had the highest number of phenotype-associated genes related to ion transport, signalling, transcriptional regulation, development, and protein metabolism. We compared the significance of all the genomic regions and the genes in these regions and found two opposing patterns: 1) cumulative value of separate genes, resulting in the higher significance of the whole region than of the particular genes; 2) higher significance of the specific genes that drive the association of the whole region.

Conclusions

Charting the features of genomic regions encompassing CNVs might aid in clarifying CNVs’ role in human disease, especially pinpointing candidate genes within these regions that are associated with complex traits.
Overview and evaluation of a nationwide hospital-based surveillance system for Influenza and COVID-19 in Switzerland (CH-SUR): 2018-2023
Authors: Sobel Jonathan Aryeh , Zanella Marie-Céline , Grant Rebecca , Valera Camille Beatrice , Suveges Mária , Urbini Laura , Mostaguir Khaled , Botero Sara , Roder Ursina , Bosetti Davide , Sommerstein Rami , Heininger Ulrich , Zimmermann Petra , Schreiber Peter W , Flury Domenica , Niederer-Loher Anita , Jent Philipp , Cusini Alexia , Pittet Didier , Harbarth Stephan , Iten Anne , Keiser Olivia ,   the CH-SUR Collaborative Network
Published: September 2024

Background

In 2018, a hospital-based surveillance system for influenza (CH-SUR) was established in six tertiary care hospitals in Switzerland. From March 2020 onwards, this surveillance system was expanded to include more institutions, as well as COVID-19.

Aim

To evaluate quantitatively and qualitatively the surveillance system CH-SUR.

Methods

All patients admitted to one of the participating centres for more than 24 hours and who had a laboratory-confirmed influenza virus or SARS-CoV-2 infection were included in CH-SUR. For all cases, we evaluated the quality of the CH-SUR data, including timeliness and completeness of reporting. A qualitative survey among CH-SUR stakeholders assessed perceived importance, understanding, reliability and adaptability of CH-SUR.

Results

Up to 20 centres participated in CH-SUR. Between December 2018 and October 2023, 7,375 cases of influenza were reported and between March 2020 and October 2023, 49,235 cases of COVID-19 were reported to CH-SUR. During the COVID-19 pandemic, time to data entry and completeness improved over time; the median delay of data entry in CH-SUR was 5 days (IQR=2-23) for COVID-19 and 4 days (IQR=2-15) for influenza during the period 2018-2023. The completeness of variables was high (99.4%), with the exception of COVID-19 or annual influenza vaccination status (respectively 15% and 72% of “Unknown” responses). Stakeholders perceived the system as important, relevant, understandable and adaptable.

Conclusion

CH-SUR has provided critical epidemiological and clinical information on hospitalised influenza and COVID-19 cases across Switzerland during the pandemic. Our evaluation highlighted the importance and relevance of this system among CH-SUR stakeholders, as well as its importance for preparedness and response to future infectious disease outbreaks.
Childhood conduct problems, potential snares in adolescence and problematic substance use in Brazil
Authors: Stocker Fauve , Heron Jon , Hickman Matthew , Wehrmeister Fernando C. , Gonçalves Helen , Menezes Ana Maria B. , Murray Joseph , Hammerton Gemma
Published: September 2024

Objective

Examine whether the relationship between childhood conduct problems and substance use in adulthood is explained through potential snares (police arrest, gang membership, school non-completion) in a Brazilian population-based birth cohort.

Method

Data were analyzed from 4,599 young people from the 1993 Pelotas Birth Cohort in Brazil. The exposure was conduct problems at age 11 years. Outcomes included hazardous alcohol consumption and illicit drug use (age 22 years). Mediators included police arrest (by age 18 years), gang membership (ages 18 and 22 years), and school non-completion (by age 22 years). We performed counterfactual mediation using the parametric g-computation formula to estimate the indirect effect via all three mediators simultaneously.

Results

After adjusting for confounders (including comorbidity), conduct problems were weakly associated with police arrest [OR (95% CI)=1.45 (0.97, 2.16)] and school non-completion [OR (95% CI)=1.46 (1.22, 1.74)], but not with gang membership. Police arrest and gang membership were associated with illicit drug use [OR (95% CI)=3.84 (2.46, 5.99); OR (95% CI)=7.78 (4.30, 14.10), respectively] and with hazardous alcohol use [OR (95% CI)=1.60 (1.08, 2.38); OR (95% CI)=1.88 (1.07, 3.30)]. However, there was no association between school non-completion and either outcome after confounder adjustment. There was little evidence for an indirect effect of conduct problems on hazardous alcohol use and illicit drug use via all three mediators after confounder adjustment.

Conclusion

The indirect effects of childhood conduct problems on substance use in early adulthood via police arrest, gang membership, and school non-completion were very small, after accounting for confounders and comorbidity.
Causal relationship between school-entry age and adolescent health: quasi-experimental evidence from 1.6 million participants in Vietnam
Authors: Busireddy Ishaan , Liao Janny , Nguyen Hoa T. , Dat Vu , Minh Tam Tran Ngo , Thuc Duc Le , De Neve Jan-Walter
Published: September 2024

Background

School-entry age has been suggested to affect human capital development. Little is known, however, about the impacts of school-entry age on adolescent health in low- and middle-income countries where most children and adolescents worldwide reside.

Methods

Data on children’s outcomes were extracted from the longitudinal Young Lives Study in Vietnam, conducted between 2001 and 2016 (N=1,532), and the Vietnam Population and Housing Censuses of 1989, 1999, and 2009 (N=1,595,365). In Vietnam, children need to turn six years old by December 31stto enter Grade 1 in September that school year. As a result of the school-entry age policy, children born on or before December 31ststart school one year earlier compared to children who are born just after December 31st. Using exposure to the policy as an exogenous instrument for school-entry age, we used two-stage least squares regressions to determine the causal effect of school-entry age on education and health outcomes by age 23 years. We considered pre-primary education, school attendance, time spent in school, childbearing, marriage or cohabitation, as well as anthropometric measurements.

Results

Children born after the school-entry age cut-off were more likely to have participated in pre-primary education and were more likely to be in school when compared to children born before the cut-off. A one-year increase in age at the beginning of Grade 1 because of the policy was associated with an increase in the probability of pre-primary education of 13 percentage points (95% CI: 7.8-18.5), daily time spent in school of 0.9 hours (95% CI: 0.5-1.4) and a reduced probability of having an own child of 25.3 percentage points (95% CI: 4.4-46.2). We observed a qualitatively smaller and statistically non-significant relationship between school-entry age and measured body mass index. These results were generally consistent when using alternative specifications of our model, sample, survey rounds, and data sources.

Discussion

Children who are older when entering primary school stayed in school longer and postponed family formation compared to children who entered school earlier because of the school-entry age policy in Vietnam. Relative age for grade should be considered when designing sexual and reproductive health interventions and programs targeted to adolescents.
Social impact of the JACO wheelchair-mounted robotic arm on users and their caregivers
Authors: Gbètoho Atigossou Orthelo Léonel , Faieta Julie , Corcuff Maëlle , Campeau-Lecours Alexandre , Flamand Véronique H. , Routhier François , Bouffard Jason
Published: September 2024

The efficacious implementation of robotic assistive technologies must be built on a thorough understanding of stakeholders’ experiences and perceptions. This study provides an in-depth insight into the experiences and perceptions of users of the JACO wheelchair-mounted robotic arm and those of their caregivers. A sample of JACO users (n = 21; Female : 6; Male : 15) and caregivers (n = 11; Female: 2; Male: 9) participated in individual interviews used to gain qualitative insight into the impact of JACO on their day-to-day lives. Interview transcripts were analyzed using a hybrid deductive-inductive coding process. Thematic analysis was conducted in accordance with theConsortium on Assistive Technology Outcomes Research(CATOR) taxonomy. This article exclusively reports data on the social impact of the JACO wheelchair-mounted robotic arm. In addition, participants completed three questionnaires to gather more objective data for quantitative assessment, these included theCaregiver Assistive Technology Outcome Measure(CATOM), a sociodemographic questionnaire, and a home-based questionnaire to assess the social impact of using JACO. Findings pointed to highly varied experiences among participants, including instances of positive, negative, and absence of effects from the use of JACO. Participants’ feedback fell within two broad categories,Human Assistance,andCost and Use of Resources. This study provides nuanced and varied insight into the spectrum of the social impact of using JACO as perceived by users and their caregivers, highlighting the importance of considering each user as an individual with unique experiences and needs. Continued research is needed to assess the generalizability of these findings.
Latent class growth mixture modelling of HbA1C trajectories identifies individuals at high risk of developing complications of type 2 diabetes mellitus in the UK Biobank
Authors: Handley Dale , Gillett Alexandra C , Bala Renu , Tyrrell Jess , Lewis Cathryn M
Published: September 2024

Aims

Glycated Hemoglobin A1c(HbA1c) is widely used for the diagnosis and management of type 2 diabetes mellitus (T2D), with regular testing in primary care recommended every three to six months. We aimed to identify distinct, long-term HbA1c trajectories following a T2D diagnosis and investigate how these glycaemic control trajectories were associated with health-related traits and T2D complications.

Methods

A cohort of 12,435 unrelated individuals of European ancestry with T2D was extracted from the UK Biobank data linked to primary care records. Latent class growth mixture modelling was applied to identify classes with similar HbA1c trajectories over the 10-years following T2D diagnosis. We tested for associations of HbA1c class membership with sociodemographic factors, biomarkers, polygenic scores, and T2D-related outcomes, using logistic regression and Cox proportional hazards models.

Results

Six HbA1c trajectory classes were identified. The largest class (76.8%) maintained low and stable HbA1c levels over time. The other five classes demonstrated higher and more variable trajectories and included: two with parabolic shapes (starting low and distinguished by the height of their peaks), two with high initial HbA1c levels that declined over time (one rapidly, one slowly), and one class with a rapid increase in HbA1c five years after diagnosis. Younger age at T2D diagnosis, higher fasting glucose levels, higher random glucose levels, and higher body mass index polygenic score were associated with membership of these five classes. These classes were also more likely to be prescribed glucose-lowering medication at diagnosis and had fewer primary care visits in the month and year prior to diagnosis. Relative to the low and stable class, these five showed increased risks of T2D complications, including stroke (HR=1.55 [1.31-1.84]), kidney disease (HR=1.39 [1.27-1.53]), all-cause mortality (HR=1.36 [1.23-1.51]), and progression to combination therapy (HR=3.22 [3.04-3.41]) or insulin (HR=3.21 [2.89-3.55]).

Conclusion

Individuals with T2D who show higher and more variable HbA1c trajectories are at increased risk of developing T2D-related complications. Early identification of patients at risk, based on factors such as age at diagnosis and previous healthcare utilisation could improve patient outcomes.
Automating ACMG Variant Classifications Using BIAS-2015: An Algorithm Overview and Benchmark Against the FDA-Approved eRepo Dataset
Authors: Eisenhart Chris , Mewton Joel , Brickey Rachel , Bayat Vafa
Published: September 2024

In 2015, the American College of Medical Genetics and Genomics (ACMG) in collaboration with the Association of Molecular Pathologists (AMP) published guidelines for the interpretation and classification of germline genomic variants. The ACMG terminology guidelines outlined criteria for assigning one of five categories: benign, likely benign, uncertain significance, likely pathogenic and pathogenic. While the paper laid out 28 different classifiers and the justification for them, it did not provide specific algorithms for implementing these classifiers in an automated manner. Here we present the Bitscopic Interpreting ACMG Standards 2015 (BIAS-2015) software as a complete, open-source algorithm which categorizes variants according to the ACMG classification system. BIAS-2015 evaluates 18 of the 28 ACMG criteria to classify variants in an automated and consistent way while recording the rationale for each classifier to enable in-depth review. We used the genomic data from the ClinGen Evidence Repository (eRepo v1.0.29), one of two FDA-recognized human genetic variant databases, to evaluate the performance of the BIAS-2015 algorithm. All code for BIAS-2015 has been made available on GitHub.
Achievement of diabetes treatment goals in Mexico from 2016–2022: A retrospective analysis of nationally representative surveys
Authors: Ramírez-García Daniel , Méndez-Labra Padme Nailea , Fermín-Martínez Carlos A. , Perezalonso-Espinosa Jerónimo , Díaz-Sánchez Juan Pablo , Paz-Cabrera César Daniel , Vargas-Vázquez Arsenio , Antonio-Villa Neftali Eduardo , Danaei Goodarz , Seiglie Jacqueline A. , Bello-Chavolla Omar Yaxmehen
Published: September 2024

BACKGROUND

Cardiovascular (CVD) risk factor reduction is a cornerstone of diabetes management. Here, we aimed to estimate the prevalence and determinants of individual and combined CVD risk factor control goals amongst individuals living with diagnosed diabetes in Mexico.

METHODS

We analyzed Mexican National Health and Nutrition Surveys from 2016-2022 including individuals aged ≥20 years with diagnosed diabetes. We estimated the prevalence of glycemic, blood pressure, cholesterol, and smoking control, as well as combined control achievement according to current guidelines, as well as the prevalence of antihypertensive, statin and diabetes medication use. We also explored determinants of control achievement amongst individuals with diabetes using weighted logistic regression.

RESULTS

We analyzed data from 2,331 adults with diagnosed diabetes. Glycemic control increased over time reaching 41% (95%CI 30%–52%) by 2022. Blood pressure control remained similar over time reaching 45% (95%CI 35%–55%) in 2022, LDL-C control remained low regardless of the definition (<70 vs. <100 mg/dL), whilst smoking control was high and increased over time to 92% (95%CI 88%–96%) in 2022. Combined risk factor control achievement was low, primarily due to suboptimal LDL-C control, despite a high proportion of medication use. Control achievement was more likely in Northern Mexico, in younger individuals, those with college education or living in states with lower social lag.

CONCLUSIONS

Our results suggest a need to improve comprehensive glycemic and CVD risk factor management for individuals living with diabetes in Mexico to improve diabetes care and reduce risk of adverse outcomes.
The transcriptomic landscape of spinal V1 interneurons reveals a role for En1 in specific elements of motor output
Authors: Trevisan Alexandra J. , Han Katie , Chapman Phillip , Kulkarni Anand S. , Hinton Jennifer M. , Ramirez Cody , Klein Ines , Gatto Graziana , Gabitto Mariano I. , Menon Vilas , Bikoff Jay B.
Published: September 2024

Neural circuits in the spinal cord are composed of diverse sets of interneurons that play crucial roles in shaping motor output. Despite progress in revealing the cellular architecture of the spinal cord, the extent of cell type heterogeneity within interneuron populations remains unclear. Here, we present a single-nucleus transcriptomic atlas of spinal V1 interneurons across postnatal development. We find that the core molecular taxonomy distinguishing neonatal V1 interneurons perdures into adulthood, suggesting conservation of function across development. Moreover, we identify a key role for En1, a transcription factor that marks the V1 population, in specifying one unique subset of V1Pou6f2interneurons. Loss of En1 selectively disrupts the frequency of rhythmic locomotor output but does not disrupt flexion/extension limb movement. Beyond serving as a molecular resource for this neuronal population, our study highlights how deep neuronal profiling provides an entry point for functional studies of specialized cell types in motor output.
The mechanism and consequences of amyloid-β modulating thiamine pyrophosphokinase-1 expression in microglia
Authors: Cheng Xiaoqin , Zhao Ruoqi , Qiu Hongyan , Song Peiwen , Kou Lanwen , Sang Shaoming , Xia Yingfeng , Cai Wenwen , Jin Boru , Huang Qiang , Yuan Peng , Zhong Chunjiu
Published: September 2024

Ample studies attribute cognitive decline in Alzheimer’s disease to amyloid-β deposition1–6. However, brain amyloid-β accumulation that saturates years before the manifestation of clinical symptoms is dissociated with cognitive decline of the disease7. It is unknown how these two processes are mechanistically linked. In this and our accompanied study, we report that thiamine pyrophosphokinase-1 (TPK) deficiency plays essential roles in both processes via distinct mechanisms. Here we describe that diminished microglia Tpk controls the propagation of amyloid-β plaques. In APP/PS1 transgenic mice, microglia showed elevatedTpkexpression at 2-month-old, but reduction in a plaque-centric manner at 8-month-old. Interestingly, lipopolysaccharide, but not amyloid-β, induceedTpkreduction in cultured microglia.Tpkreduction led to microglia dysfunction, showing volatile motility but reduced phagocytosis and weak response to focal tissue injury, with accumulation of intracellular lipid droplets and abnormal mitochrondria. In Alzheimer’s disease mice, microglia-specific knockout ofTpkcaused diminished plaque coverage, exacerbated plaque burden and synaptic loss. However, increased plaques were not accompanied by the development of neurofibrillary tangles or brain atrophy, in contrast to the phenotype described in our accompanied paper with neuronalTpkdeletion. In conclusion, plaque-induced inflammation reducesTpkin microglia, selectively exacerbating the spread of amyloid pathology.
Antagonist actions of CMK-1/CaMKI and TAX-6/Calcineurin along theC. elegansthermal avoidance circuit orchestrate adaptation of nociceptive response to repeated stimuli
Authors: Rudgalvyte Martina , Hu Zehan , Kressler Dieter , Dengjel Joern , Glauser Dominique A.
Published: September 2024

Response decrease following repeated exposure to innocuous or noxious stimuli is a conserved adaptation phenomenon often referred to as habituation. Impaired nociceptive habituation is associated with several pain conditions in human, but the underpinning molecular mechanisms are only partially understood. In the nematodeCaenorhabditis elegans, thermo-nociceptive adaptation to repeated stimuli was previously shown to be regulated by the Ca2+/Calmodulin-dependent protein kinase 1 (named CMK-1), but its downstream effectors were unknown. Here, usingin vitrokinase assays coupled with mass-spectrometry-based phosphoproteomics, we empirically identified hundreds of CMK-1 phospho-substrates. Among them, we found that CMK-1 can phosphorylate the calcineurin A (CnA) protein TAX-6in vitroin a highly conserved regulatory domain, which led us to hypothesize that TAX-6/CnA might be a downstream mediator of CMK-1 signaling in the control of thermo-nociceptive adaptation. Combined genetic and pharmacological manipulations revealed a network of antagonistic actions between CMK-1 and calcineurin pathways in the regulation of the responsiveness of naïve worms and the response adaptation to repeated noxious heat stimuli. However, the results of cell-specific rescue and gain-of-function experiments suggested that CMK-1 acts in AFD and ASER thermosensory neurons and that TAX-6/CnA acts in FLP thermosensory neuron and a set of downstream interneurons to regulate noxious heat avoidance behaviors. Because CMK-1 and TAX-6/CnA act in non-overlapping cell types, the phosphorylation event identifiedin vitromight not be relevant for this phenotype and the complex interaction between the two pathways might rather originate from their action in separate parts of the nervous system. As a whole, our study has identified (i) CMK-1 substrate candidates, which will fuel further research on the intracellular actuation of CMK-1-dependent signaling on various processes, and (ii) a complex set of antagonistic interactions between CMK-1 and calcineurin signaling operating at distributed loci within a sensory-behavior circuit, acting to adjust baseline thermo-nociception and regulate thermo-nociceptive adaptation.
Genomic Analyses Suggest No Risk of Vancomycin Resistance Transfer by Strain VE202-06
Authors: Watson Andrea R. , Chen Wei-An , van Schaik Willem , Norman Jason M.
Published: September 2024

In 2016, the US Food and Drug Administration published guidance for the early development of live biotherapeutic products (LBPs)1. Of particular importance is the characterization of LBP strains and the potential transfer of antimicrobial resistance (AMR) genes to relevant microbial organisms in the recipient’s microbiota. Van der Lelie et al2, make unsupported claims that the LBP strain VE202-06 encodes a transferable vancomycin resistance element. Here we provide our analysis of the potential transfer of AMR by strain VE202-06. These data indicate that strain VE202-06 has no risk of transferring AMR to relevant microbial organisms.
The pericardium forms as a distinct structure during heart formation
Authors: Moran Hannah R. , Nyarko Obed O. , O’Rourke Rebecca , Ching Ryenne-Christine K. , Riemslagh Frederike W. , Peña Brisa , Burger Alexa , Sucharov Carmen C. , Mosimann Christian
Published: September 2024

The heart integrates diverse cell lineages into a functional unit, including the pericardium, a mesothelial sac that supports heart movement, homeostasis, and immune responses. However, despite its critical roles, the developmental origins of the pericardium remain uncertain due to disparate models. Here, using live imaging, lineage tracking, and single-cell transcriptomics in zebrafish, we find the pericardium forms within the lateral plate mesoderm from dedicated anterior mesothelial progenitors and distinct from the classic heart field. Imaging of transgenic reporters in zebrafish documents lateral plate mesoderm cells that emerge lateral of the classic heart field and among a continuous mesothelial progenitor field. Single-cell transcriptomics and trajectories ofhand2-expressing lateral plate mesoderm reveal distinct populations of mesothelial and cardiac precursors, including pericardial precursors that are distinct from the cardiomyocyte lineage. The mesothelial gene expression signature is conserved in mammals and carries over to postnatal development. Light sheet-based live-imaging and machine learning-supported cell tracking documents that during heart tube formation, pericardial precursors that reside at the anterior edge of the heart field migrate anteriorly and medially before fusing, enclosing the embryonic heart to form a single pericardial cavity. Pericardium formation proceeds even upon genetic disruption of heart tube formation, uncoupling the two structures. Canonical Wnt/β-catenin signaling modulates pericardial cell number, resulting in a stretched pericardial epithelium with reduced cell number upon canonical Wnt inhibition. We connect the pathological expression of secreted Wnt antagonists of the SFRP family found in pediatric dilated cardiomyopathy to increased pericardial stiffness: sFRP1 in the presence of increased catecholamines causes cardiomyocyte stiffness in neonatal rats as measured by atomic force microscopy. Altogether, our data integrate pericardium formation as an independent process into heart morphogenesis and connect disrupted pericardial tissue properties such as pericardial stiffness to pediatric cardiomyopathies.
Proteomic andN-glycomic comparison of synthetic and bovine whey proteins and their effect on human gut microbiomes
Authors: Bolino Matthew , Duman Hatice , Avcı İzzet , Kayili Hacı Mehmet , Petereit Juli , Zundel Chandler , Salih Bekir , Karav Sercan , Frese Steven A.
Published: September 2024

Advances in food production systems and customer acceptance have led to the commercial launch of dietary proteins produced via modern biotechnological approaches as alternatives to traditional agricultural sources. At the same time, a deeper understanding of how dietary components interact with the gut microbiome has highlighted the importance of understanding the nuances underpinning diet-microbiome interactions. Novel food proteins with distinct post-translational modifications resulting from their respective production systems have not been characterized, nor how they may differ from their traditionally produced counterparts. To address this, we have characterized the protein composition andN-glycome of a yeast-synthesized whey protein ingredient isolated from commercially available ice cream and compared this novel ingredient to whey protein powder isolate derived from bovine milk. We found that despite strong similarities in protein composition, theN-glycome significantly differs between these protein sources, reflecting the biosynthetic machinery of the production systems. Further, the composition profile and diversity of proteins found in the synthetic whey protein were lower relative to bovine whey protein, despite both being predominantly composed of β-lactoglobulin. Finally, to understand whether these differences inN-glycome profiles affected the human gut microbiome, we tested these proteins in anin vitrofecal fermentation model. We found that the two whey protein sources generated significant differences among three distinct microbial compositions, which we hypothesize is a product of differences inN-glycan composition and degradation by these representative microbial communities. This work highlights the need to understand how differences in novel biotechnological systems affect the bioactivity of these proteins, and how these differences impact the human gut microbiome.
Development of a cell-permeable Biotin-HaloTag ligand to explore functional differences between protein variants across cellular generations
Authors: Yadav Anoop Kumar , Jadhav Abhijeet S. , Szczepanik Pawel , Fagherazzi Paolo , Kabelka Ivo , Vácha Robert , Svenda Jakub , Polasek-Sedlackova Hana
Published: September 2024

HaloTag technology represents a versatile tool for studying proteins. Fluorescent HaloTag ligands employed in sequential labeling led to the discovery of distinct protein variants for histones, cohesins, and MCM complexes. Nonetheless, an efficient biochemical approach to separate the distinct protein variants to study their biological functions is missing. Principally being a gap in technology, the HaloTag toolbox lacks affinity ligands displaying good cell permeability and efficient affinity capture. Here, we describe the design, synthesis, and validation of a new cell-permeable Biotin-HaloTag ligand, which allows rapid labeling of Halo-tagged proteins in live cells and their efficient separation using streptavidin pull-down. Our work outlines how to use the herein-developed affinity ligand in sequential labeling to biochemically separate distinct protein variants and study their biological properties. The approach holds immense potential for addressing fundamental questions concerning essential cellular processes, including genome duplication and chromatin maintenance.
Microcystin shapes theMicrocystisphycosphere through community filtering and by influencing cross-feeding interactions
Authors: Große Rebecca , Heuser Markus , Teikari Jonna E. , Ramakrishnan Dinesh K. , Abdelfattah Ahmed , Dittmann Elke
Published: September 2024

The cyanobacteriumMicrocystiscauses harmful algal blooms (cyanoHABs) that pose a major threat to human health and ecosystem services, particularly due to the prevalence of the potent hepatotoxin microcystin. With their pronounced EPS layer,Microcystiscolonies also serve as a hub for heterotrophic phycosphere bacteria. Here, we tested the hypothesis that the genotypic plasticity in its ability to produce microcystin influences the composition and assembly of theMicrocystisphycosphere microbiome. In an analysis of individual colonies of a naturalMicrocystisbloom, we observed a significantly reduced richness of the community in the presence of microcystin biosynthesis genes. A subsequent synthetic community experiment with 21 heterotrophic strains in co-cultivation with either the wild-type strainM. aeruginosaPCC 7806 or the microcystin-free mutant ΔmcyBrevealed not only a tug-of-war between phototrophic and heterotrophic bacteria, but also a reciprocal dominance of two isolates of the genusSphingomonasandFlavobacterium. In contrast, anAgrobacteriumisolate thrived equally well in both consortia. In substrate utilization tests,Sphingomonasshowed the strongest dependence onMicrocystisexudates with a clear preference for the wild-type strain. Genome sequencing revealed a high potential for complementary cross-feeding, particularly for theAgrobacteriumandSphingomonasisolates but no potential for microcystin degradation. We postulate that strain-specific functional traits, such as the ability to perform photorespiration and to produce vitamin B12, play a crucial role in the cross-feeding interactions, and that microcystin is one of the determining factors in theMicrocystisphycosphere due to its interference with inorganic carbon metabolism.
The binary protein interactome mapping of theGiardia lambliaproteasome lid reveals extra proteasomal functions of GlRpn11
Authors: Das Ankita , Ray Atrayee , Chaudhuri Nibedita Ray , Mukherjee Soumyajit , Dastidar Shubhra Ghosh , Ghosh Alok , Ganguly Sandipan , Jana Kuladip , Sarkar Srimonti
Published: September 2024

Giardia lambliadoes not encode Rpn12 and Sem1, two proteins crucial for assembling the proteasome lid. To understand how the interactions between the giardial proteasome lid subunits may have changed to compensate for their absence, we used the yeast two-hybrid assay to generate a binary protein interaction map of theGiardialid subunits. Most interactions within theGiardiaproteasome lid are stronger than those within theSaccharomyces cerevisiaelid. These may compensate for the absence of Rpn12 and Sem1. A notable exception was the weaker interaction between GlRpn11 and GlRpn8, compared to the strong interaction between Rpn11-Rpn8 of yeast. The Rpn11-Rpn8 dimer provides a platform for lid assembly and their interaction involves the insertion of a methionine residue of Rpn11 into a hydrophobic pocket of Rpn8. Molecular modeling indicates that GlRpn8’s pocket is wider, reconciling the experimental observation of its weak interaction with GlRpn11. This weaker interaction may have evolved to support extra proteasomal functions of GlRpn11, which localizes to multiple subcellular regions where other proteasome subunits have not been detected. One such location is the mitosome. Functional complementation in yeast shows that GlRpn11 can influence mitochondrial function and distribution. This, together with its mitosomal localization, indicates that GlRpn11 functions at the mitosome. Thus, this parasite’s proteasome lid has a simpler subunit architecture and structural attributes that may support dual functionalities for GlRpn11. Such parasite-specific proteasome features could provide new avenues for controlling the transmission ofGiardia.

1

Graphical Abstract

Highlights

Giardiagenome does not encode two proteasomal lid subunits: Rpn12 and Sem1

Unique interactions within the lid may compensate for the absence of these two

GlRpn8:GlRpn11 weakly interacts to support GlRpn11’s extra-proteasomal distribution

GlRpn11 localizes at mitosomes, OZ of VD, and to the VFP

The 182-218 fragment of GlRpn11 may regulate mitosomal function
An efficient pipeline for creating metagenomic-assembled genomes from ancient oral microbiomes
Authors: Standeven Francesca J. , Dahlquist-Axe Gwyn , Speller Camilla F. , Meehan Conor J. , Tedder Andrew
Published: September 2024

Metagenomic-assembled genomes (MAGs) are difficult to recover from ancient DNA (aDNA) due to substantial fragmentation, degradation, and multi-source contamination. These complexities associated with aDNA raise concerns about whether bioinformatic tools intended for interpreting modern DNA are suitable for reconstructing ancient MAGs. Using simulated modern and ancient data, we investigated: 1) how using binning tools designed for modern DNA affects our ability to effectively construct MAGs from ancient genomes; 2) the performance of three different binning tools for aDNA samples; and 3) whether a ‘one size fits all’ approach is suitable for ancient metagenomics. We established that binning tools for modern DNA performed efficiently on simulated modern and ancient DNA. When applied to ‘real’ archaeological DNA spanning 5000 years, we retrieve high-confidence MAGs in most cases.
Stable and dynamic gene expression patterns over diurnal and developmental timescales inArabidopsis thaliana
Authors: Redmond Ethan J , Ronald James , Davis Seth J , Ezer Daphne
Published: September 2024

Developmental processes are known to be circadian regulated in plants. For instance, the circadian clock regulates genes involved in the photoperiodic flowering pathway and the initiation of leaf senescence. Furthermore, signals which entrain the circadian clock, such as energy availability, are known to vary in strength over plant development. However, diurnal oscillations of the Arabidopsis transcriptome have typically been measured in seedlings.

We collected RNA-seq data from Arabidopsis leaves over developmental and diurnal timescales, concurrently: every 4 hours per day, on 3 separate days after a synchronised vegetative-to-reproductive transition. Gene expression varied more over the developmental timescale than on the diurnal timescale, including genes related to a key energy sensor: the Sucrose non-fermenting-1-related protein kinase (SnRK1) complex.

Moreover, regulatory targets of core clock genes displayed changes in rhythmicity and amplitude of expression over development. Cell-type-specific expression showed diurnal patterns that varied in amplitude, but not phase, over development. Some previously identified qRT-PCR housekeeping genes display undesirable levels of variation over both timescales. We identify which common qRT-PCR housekeeping genes are most stable across developmental and diurnal timescales.

In summary, we establish the patterns of circadian transcriptional regulation over plant development, demonstrating how diurnal patterns of expression change over developmental timescales.
Integrated Transcriptome and Metabolome Analyses Reveal the Mechanism Regulating Bulbil Initiation and Development inCystopteris chinensis
Authors: Yu An , Chen Xiaohong , Xi Wenkai , Zhao Xia , Wang Yazhu , Gong Zhihong , Zhou Xiaofeng
Published: September 2024

Cystopteris chinensisis an endangered fern endemic to China, which only has a small wild population due to its poor reproductive ability. However, we recently found that it can produce bulbils on its pinnule to generate new plants but the molecular mechanism underlying this unique phenomenon remained unknown. In this study, we have identified four distinct stages in the initiation and development of bulbils based on morphological and anatomical observation. We performed transcriptome and metabolome analyses on the collected samples at each stage. Through KEGG enrichment analysis, it was found that the phytohormone signal transduction, starch and sucrose metabolism, phenylpropanoid biosynthesis, and flavonoid biosynthesis pathways play a significant role in regulating bulbil initiation and development. Specifically, the involvement of three phytohormones and sugar substances was identified in the process of bulbil initiation. Our study provides the first detailed observation of the bulbils inC. chinensisand explains their initiation and development at the molecular level. However, more in-depth studies are needed to discover the functions of key genes controlling the formation of bulbils to conserve the endangeredC. chinensispopulation.
Eco-toxicity of different agricultural tank-mix adjuvants
Authors: Roessink Ivo , Boerwinkel Marie-Claire , Sijs Rick , Hoffman Hanne , Specker Jan Christof , Bonn Daniel
Published: September 2024

Adjuvants are often used to improve the efficiency of plant protection products. However, there is concern that these compounds themselves might result in ecotoxicological effects. To investigate this concern, we compare the toxicity of different agricultural tank-mix adjuvants for two standard test organisms, i.e. the water fleaDaphnia magnaand the honey beeApis mellifera. Daphnia trials comprised tests at 1, 5 and 20 times the normal prescribed label dosage. It is found that at 48h, the novel polymer-based adjuvant Squall is significantly less harmful toD. magnacompared to traditional surfactant or oil-based adjuvants. ForA. mellifera, we tested topical exposure to label-rate, five and twenty times label-rate. After 96h exposure to polymer- and oil based adjuvants no statistically significant harmful effects were observed. The trisiloxane-based adjuvants, however, did significantly increase bee mortality at higher dose rates, indicating a higher toxicity of these specific compounds.
Viral-mediated Oct4 overexpression and inhibition of Notch signaling synergistically induce neurogenic competence in mammalian Müller glia
Authors: Le Nguyet , Awad Sherine , Palazzo Isabella , Hoang Thanh , Blackshaw Seth
Published: September 2024

Retinal Müller glia in cold-blooded vertebrates can reprogram into neurogenic progenitors to replace neurons lost to injury, but mammals lack this ability. While recent studies have shown that transgenic overexpression of neurogenic bHLH factors and glial-specific disruption of NFI family transcription factors and Notch signaling induce neurogenic competence in mammalian Müller glia, induction of neurogenesis in wildtype glia has thus far proven elusive. Here we report that viral-mediated overexpression of the pluripotency factorOct4(Pou5f1) induces transdifferentiation of wildtype mouse Müller glia into bipolar neurons, and synergistically stimulates glial-derived neurogenesis in parallel with Notch loss of function. Single cell multiomic analysis shows thatOct4overexpression leads to widespread changes in gene expression and chromatin accessibility, inducing activity of both the neurogenic transcription factor Rfx4 and the Yamanaka factors Sox2 and Klf4. This study demonstrates that viral-mediated overexpression of Oct4 induces neurogenic competence in wildtype retinal Muller glia, identifying mechanisms that could be used in cell-based therapies for treating retinal dystrophies.
RFX3 is essential for the development and maturation of human pancreatic islets derived from pluripotent stem cells
Authors: Memon Bushra , Aldous Noura , Elsayed Ahmed K. , Ijaz Sadaf , Hayat Sikander , Abdelalim Essam M.
Published: September 2024

RFX3 in human pancreatic islet development has not been explored. This study aims to investigate the function of RFX3 in human pancreatic islet development using human islet organoids derived from iPSCs, hypothesizing that RFX3 regulates human islet cell differentiation. We generatedRFX3knockout (RFX3KO) iPSC lines using CRISPR/Cas9 and differentiated them into pancreatic islet organoids. Various techniques were employed to assess gene expression, cell markers, apoptosis, proliferation, and glucose-stimulated insulin secretion. Single-cell RNA sequencing (scRNA-seq) datasets from hESC-derived pancreatic islets were re-analyzed to investigateRFX3expression in specific cell populations at various developmental stages. Furthermore, bulk RNA sequencing was conducted to further assess transcriptomic changes. RFX3 was found to be highly expressed in pancreatic endocrine cell populations within pancreatic progenitors (PPs), endocrine progenitors (EPs), and mature islet stages derived from iPSCs. scRNA-seq further confirmed RFX3 expression across different endocrine cell clusters during differentiation.RFX3loss disrupted pancreatic endocrine gene regulation, reduced hormone-secreting islet cells, and impaired beta-cell function and insulin secretion. Despite a significant reduction in pancreatic islet hormones, the pan-endocrine marker CHGA remained unchanged at both EP and islet stages, likely due to an increase in enterochromaffin cells (ECs). This was supported by our findings of high EC marker expression inRFX3KO EPs and islets. In addition,RFX3loss led to smaller islet organoids, elevated TXNIP levels, and increased apoptosis in EPs and islets. These findings underscore the crucial role of RFX3 in regulating human islet cell differentiation and its role in suppressing enterochromaffin cell specification. These insights into RFX3 function have implications for understanding islet biology and potential diabetes susceptibility.
Dynamic phosphorylation of Hcm1 promotes fitness in chronic stress
Authors: Conti Michelle M. , Bail Jillian P. , Li Rui , Zhu Lihua Julie , Benanti Jennifer A.
Published: September 2024

Cell survival depends upon the ability to adapt to changing environments. Environmental stressors trigger an acute stress response program that rewires cell physiology, downregulates proliferation genes and pauses the cell cycle until the cell adapts. Here, we show that dynamic phosphorylation of the yeast cell cycle-regulatory transcription factor Hcm1 is required to maintain fitness in chronic stress. Hcm1 is activated by cyclin dependent kinase (CDK) and inactivated by the phosphatase calcineurin (CN) in response to stressors that signal through increases in cytosolic Ca2+. Expression of a constitutively active, phosphomimetic Hcm1 mutant reduces fitness in stress, suggesting Hcm1 inactivation is required. However, a comprehensive analysis of Hcm1 phosphomutants revealed that Hcm1 activity is also important to survive stress, demonstrating that Hcm1 activity must be toggled on and off to promote gene expression and fitness. These results suggest that dynamic control of cell cycle regulators is critical for survival in stressful environments.
Cortico-hippocampal interactions underlie schema-supported memory encoding in older adults
Authors: Huang Shenyang , Bogdan Paul C. , Howard Cortney M. , Gillette Kirsten , Deng Lifu , Welch Erin , McAllister Margaret L. , Giovanello Kelly S. , Davis Simon W. , Cabeza Roberto
Published: September 2024

Although episodic memory is typically impaired in older adults (OAs) compared to young adults (YAs), this deficit is attenuated when OAs can leverage their rich semantic knowledge, such as their knowledge of schemas. Memory is better for items consistent with pre-existing schemas and this effect is larger in OAs. Neuroimaging studies have associated schema use with the ventromedial prefrontal cortex (vmPFC) and hippocampus (HPC), but most of this research has been limited to YAs. This fMRI study investigated the neural mechanisms underlying how schemas boost episodic memory in OAs. Participants encoded scene-object pairs with varying congruency, and memory for the objects was tested the following day. Congruency with schemas enhanced object memory for YAs and, more substantially, for OAs. FMRI analyses examined how cortical modulation of HPC predicted subsequent memory. Congruency-related vmPFC modulation of left HPC enhanced subsequent memory in both age groups, while congruency-related modulation from angular gyrus (AG) boosted subsequent memory only in OAs. Individual differences in cortico-hippocampal modulations indicated that OAs preferentially used their semantic knowledge to facilitate encoding via an AG-HPC interaction, suggesting a compensatory mechanism. Collectively, our findings illustrate age-related differences in how schemas influence episodic memory encoding via distinct routes of cortico-hippocampal interactions.
Ventrolateral prefrontal cortex in macaques guides decisions in different learning contexts
Authors: Fujimoto Atsushi , Elorette Catherine , Fujimoto Satoka H. , Fleysher Lazar , Russ Brian E. , Rudebeck Peter H.
Published: September 2024

Flexibly adjusting our behavioral strategies based on the environmental context is critical to maximize rewards. Ventrolateral prefrontal cortex (vlPFC) has been implicated in both learning and decision-making for probabilistic rewards, although how context influences these processes remains unclear. We collected functional neuroimaging data while rhesus macaques performed a probabilistic learning task in two contexts: one with novel and another with familiar visual stimuli. We found that activity in vlPFC encoded rewards irrespective of the context but encoded behavioral strategies that depend on reward outcome (win-stay/lose-shift) preferentially in novel contexts. Functional connectivity between vlPFC and anterior cingulate cortex varied with behavioral strategy in novel learning blocks. By contrast, connectivity between vlPFC and mediodorsal thalamus was highest when subjects repeated a prior choice. Furthermore, pharmacological D2-receptor blockade altered behavioral strategies during learning and resting-state vlPFC activity. Taken together, our results suggest that multiple vlPFC-linked circuits contribute to adaptive decision-making in different contexts.