bluuebunny/crossref_metadata_2025 huggingface dataset:
Neuronal APOE4-induced Early Hippocampal Network Hyperexcitability in Alzheimer’s Disease Pathogenesis
Authors: Tabuena Dennis R. , Jang Sung-Soo , Grone Brian , Yip Oscar , Aery Jones Emily A. , Blumenfeld Jessica , Liang Zherui , Koutsodendris Nicole , Rao Antara , Ding Leonardo , Zhang Alex R. , Hao Yanxia , Xu Qin , Yoon Seo Yeon , Leon Samuel De , Huang Yadong , Zilberter Misha
Published: August 2023

The full impact of apolipoprotein E4 (APOE4), the strongest genetic risk factor for Alzheimer’s disease (AD), on neuronal and network function remains unclear. We found hippocampal region-specific network hyperexcitability in young APOE4 knock-in (E4-KI) mice which predicted cognitive deficits at old age. Network hyperexcitability in young E4-KI mice was mediated by hippocampal region-specific subpopulations of smaller and hyperexcitable neurons that were eliminated by selective removal of neuronal APOE4. Aged E4-KI mice exhibited hyperexcitable granule cells, a progressive inhibitory deficit, and E/I imbalance in the dentate gyrus, exacerbating hippocampal hyperexcitability. Single-nucleus RNA-sequencing revealed neuronal cell type-specific and age-dependent transcriptomic changes, including Nell2 overexpression in E4-KI mice. Reducing Nell2 expression in specific neuronal types of E4-KI mice with CRISPRi rescued their abnormal excitability phenotypes, implicating Nell2 overexpression as a cause of APOE4-induced hyperexcitability. These findings highlight the early transcriptomic and electrophysiological alterations underlying APOE4-induced hippocampal network dysfunction and its contribution to AD pathogenesis with aging.
The adaptive immune response toTrichurisin wild versus laboratory mice: An established model system in context
Authors: Mair Iris , Fenn Jonathan , Wolfenden Andrew , Lowe Ann E. , Bennett Alex , Muir Andrew , Thompson Jacob , Dieumerci Olive , Logunova Larisa , Shultz Susanne , Bradley Janette E. , Else Kathryn J.
Published: August 2023

Laboratory model organisms have provided a window into how the immune system functions. An increasing body of evidence, however, suggests that the immune responses of naive laboratory animals may differ substantially to those of their wild counterparts. Past exposure, environmental challenges and physiological condition may all impact on immune responsiveness. Chronic infections of soil-transmitted helminths impose significant health burdens on humans, livestock and wildlife, with limited treatment success. In laboratory mice, Th1 versus Th2 immune polarisation is the major determinant of helminth infection outcome. Here we compared antigen-specific immune responses to the soil-transmitted whipwormTrichuris murisbetween controlled laboratory and wild free-ranging populations of house mice (Mus musculus domesticus). Wild mice harbouring chronic, low-level infections produced lower levels of cytokines in response to Trichuris antigen than laboratory-housed C57BL/6 mice. Wild mouse effector/memory CD4+ T cell phenotype reflected the antigen-specific cytokine response across the Th1/Th2 spectrum. Increasing worm burden was associated with body condition loss. However, local Trichuris-specific Th1/Th2 balance was positively associated with worm burden only in older wild mice. Thus, although the fundamental relationships between the CD4+ T helper cell response and resistance to T. muris infection are similar in both laboratory and wildM.m.domesticus,there are quantitative differences and age-specific effects that are analogous to human immune responses. These context-dependent immune responses demonstrate the fundamental importance of understanding the differences between model and natural systems for translating mechanistic models to ‘real world’ immune function.
ClipperQTL: ultrafast and powerful eGene identification method
Authors: Zhou Heather J. , Ge Xinzhou , Li Jingyi Jessica
Published: August 2023

A central task in expression quantitative trait locus (eQTL) analysis is to identify cis-eGenes (henceforth “eGenes”), i.e., genes whose expression levels are regulated by at least one local genetic variant. Among the existing eGene identification methods, FastQTL is considered the gold standard but is computationally expensive as it requires thousands of permutations for each gene. Alternative methods such as eigenMT and TreeQTL have lower power than FastQTL. In this work, we propose ClipperQTL, which reduces the number of permutations needed from thousands to 20 for data sets with large sample sizes (>450) by using the contrastive strategy developed in Clipper; for data sets with smaller sample sizes, it uses the same permutation-based approach as FastQTL. We show that ClipperQTL performs as well as FastQTL and runs about 500 times faster if the contrastive strategy is used and 50 times faster if the conventional permutation-based approach is used. The R package ClipperQTL is available athttps://github.com/heatherjzhou/ClipperQTL.
Does sex influence element accumulation in honey bees: workers vs drones
Authors: Zarić Nenad M. , Brodschneider Robert , Goessler Walter
Published: August 2023

Honey bees are social insects that have divided their work. Bees have two sexes, male and female. Female honey bees are queens and worker bees, while males are called drones. Worker bees have different tasks in the hive including gathering of food, its processing, caring for brood, protecting the hive, produce wax, nourish workers, drones and queen. Drones are male bees whose only role is to mate with a virgin queen. Many studies have dealt with physiology, behavior, morphology of workers and drones. This is the first study that compared differences in element accumulation and composition between workers and drones honey bees. It was observed that worker honey bees have higher concentration, from 116 % to 517 %, of most elements analyzed. Drones had higher concentration of essential elements to bees, Na, Mg, P, S, K, Zn, Cu and especially Se which was 2.2-fold higher. These differences can be attributed to environmental exposure; reproductive role of drones, high Se in sperm; but mostly to the food workers and drones eat. Worker bees feed on unprocessed food, mostly pollen, which is rich in minerals. Drones are fed by worker bees pre-processed food. Here we show that worker honey bees have a filtering mechanism that enables them to accumulate non-essential elements and not pass them on through the processed food to drones or larva.
RichPathR: a gene set enrichment analysis and visualization tool
Authors: Regmi Binod , Brooks Stephen R. , Uhlman Andrew J. , Sun Hong-Wei
Published: August 2023

Gene set enrichment analysis (GSEA) is an important step for disease and drug discovery. Genomic, transcriptomics, proteomics and epigenetic analysis of tissue or cells generates gene lists that need to be further investigated in the known biological context. The advent of high-throughput technologies generates the vast number of gene lists that are up or down regulated together. One way of getting meaningful insights of the relationship of these genes is utilizing existing knowledge bases linking them with biological functions or phenotypes. Multiple public databases with annotated gene sets are available for GSEA, andenrichRis the most popular web application still requiring custom tools for large-scale mining.richPathRpackage is a collection of R functions that helps researchers carry out exploratory analysis and visualization of gene set enrichment usingEnrichR.

Availability

The package, test data and additional figures can be downloaded fromhttps://github.com/niams-bdmds/richPathR.git.

Contact

sunh1@nih.gov
Dysregulated actin dynamics and cofilin correlate with TDP-43 pathology in sporadic amyotrophic lateral sclerosis
Authors: Jagaraj Cyril Jones , Mehta Prachi , Parakh Sonam , Shadfar Sina , Jamali Shafi , Suchowerska Alexandra K , Sultana Jessica , Fath Thomas , Atkin Julie D
Published: August 2023

Amyotrophic lateral sclerosis (ALS) is a fatal, rapidly progressive neurodegenerative disorder affecting motor neurons, that overlaps significantly with frontotemporal dementia (FTD). Most cases are sporadic (90%) with undefined aetiology, but pathological forms of TAR-binding protein 43 (TDP-43), involving its misfolding, aggregation and mislocalisation from the nucleus to the cytoplasm, are present in motor neurons in almost all cases (97%) and ∼45% FTD cases. Actin is the most abundant protein in eukaryotic cells, with structural roles in the cytoskeleton and diverse signalling functions. This includes neuronal-specific roles in dendritic spines, synapses, axonal growth cones, and plasticity. Actin is in constant dynamic equilibrium between two forms: free monomeric, globular actin (G-actin) and polymeric, filamentous actin (F-actin). Actin dynamics is regulated by several key actin-binding proteins, including tropomyosin 4.2 (Tpm4.2) and cofilin, which depolymerises actin filaments. Cofilin is activated by phosphorylation at Ser3 via LIM domain kinase1/2 (LIMK1/2), which is also regulated by phosphorylation via Rac1/cdc42. Here we demonstrate that actin dynamics is closely associated with pathological TDP-43 in ALS. More F-actin relative to G-actin was detected in lumbar spinal cords from both sporadic ALS patients and a mouse model displaying TDP-43 pathology (rNLS), and in neuronal cells expressing cytoplasmic TDP-43. Hence actin dynamics is dysregulated in sporadic ALS, resulting in more actin polymerization. We also detected increased levels of Tpm 4.2, Rac1/cdc42, and increased phosphorylation of both LIMK1/2 and cofilin, in sporadic ALS patients. TDP-43 also physically interacted with actinin vitroand in cell lysates, providing additional insights into actin dysregulation in ALS. rNLS mice display motor neuron loss and key ALS/MND behavioural phenotypes, and increased cofilin phosphorylation was also detected in these animals at symptom onset, implying that actin dynamics actively contributes to neurodegeneration. Moreover, pharmacological induction of actin polymerization produced features typical of pathological TDP-43 (cytoplasmic mis-localisation and formation of inclusions and stress granules) implying that actin dysregulation contributes to TDP-43 pathology in ALS. Importantly, we also detected more cofilin phosphorylation in spinal motor neurons from sporadic patients compared to healthy controls, revealing that our observations are clinically relevant and present in the relevant cell type. This study therefore identifies dysregulated actin dynamics as a novel disease mechanism associated with TDP-43 pathology and hence most ALS cases. It also implies that regulating cofilin or LIMK1/2 phosphorylation may be a novel therapeutic strategy in ALS, FTD and other diseases involving TDP-43 pathology.
Madariaga and Venezuelan equine encephalitis virus seroprevalence in rodent enzootic hosts in Eastern and Western Panama
Authors: Carrera Jean-Paul , Galué Josefrancisco , de Souza William M. , Torres-Cosme Rolando , Lezcano-Coba Carlos , Cumbrera Alberto , Vasilakis Nikos , Tesh Robert B. , Guzman Hilda , Weaver Scott C. , Vittor Amy Y. , Samudio Rafael , Pascale Juan Miguel , Valderrama Anayansi , Carrera Lorenzo Cáceres , Donnelly Christl A. , Faria Nuno R.
Published: August 2023

While rodents are primary reservoirs of Venezuelan equine encephalitis virus (VEEV), their role in Madariaga virus (MADV) transmission remains uncertain, particularly given their overlapping geographic distribution. This study explores the interplay of alphavirus prevalence, rodent diversity, and land use within Darien and Western Panama provinces. A total of three locations were selected for rodent sampling in Darien province: Los Pavitos, El Real de Santa Maria and Santa Librada. Two sites were selected in Western Panama province: El Cacao and Cirí Grande. We used plaque reduction neutralization tests to assess MADV and VEEV seroprevalences in 599 rodents of 16 species across five study sites. MADV seroprevalence was observed at higher rates in Los Pavitos (Darien province), 9.0%, 95% CI: 3.6-17.6, while VEEV seroprevalence was elevated in El Cacao (Western Panama province), 27.3%, 95% CI: 16.1-40.9, and El Real de Santa María (Darien province), 20.4%, 95% CI: 12.6-29.7. Species likeOryzomys coesi, 23.1%, 95% CI: 5.0-53.8, andTransandinomys bolivaris, 20.0%, 95% CI: 0.5-71.6 displayed higher MADV seroprevalences than other species, whereasTransandinomys bolivaris, 80.0%, 95% CI: 28.3-99.4, andProechimys semispinosus, 27.3%, 95% CI: 17.0-39.6, exhibited higher VEEV seroprevalences. Our findings provide support to the notion that rodents are vertebrate reservoirs of MADV and reveal spatial variations in alphavirus seropositivity among rodent species, with different provinces exhibiting distinct rates for MADV and VEEV. Moreover, specific rodent species are linked to unique seroprevalence patterns for these viruses, suggesting that rodent diversity and environmental conditions might play a significant role in shaping alphavirus distribution.
Estimating seroprevalence of SARS-CoV-2 infection after a highly contagious Omicron outbreak: A cross sectional study in a university setting
Authors: Hou Ching-Wen , Williams Stacy , Trivino-Soto Guillermo , Boyle Veronica , Rainford David , Vicino Selina , Magee Mitch , Chung Yunro , LaBaer Joshua , Murugan Vel
Published: August 2023

Objective

This study aimed to investigate the seroprevalence of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) antibodies among individuals aged 18 years and older

Design

Prospective cohort study.

Settings

Population-based study was conducted within the Arizona State University (ASU) community.

Participants

The study recruited 1,397 adult participants that volunteered over a period of three days (March 1-March 3 of 2022).

Primary outcome measures

Seroprevalence was conducted in the community to assess the presence of SARS-CoV-2-specific antibodies resulting from previous exposure to SARS-CoV-2 and/or vaccination.

Results

The seroprevalence of anti-receptor binding domain (RBD) antibodies was found to be 96.3% using a semi-quantitative chemiluminescent immunoassay and 98% using an electrochemiluminescent immunoassay. For anti-nucleocapsid (NC) antibodies, the seroprevalence was 39.1% by an ELISA assay and 41.4% by an electrochemiluminescent immunoassay. Individuals that experienced breakthrough infections exhibited the highest levels of anti-RBD antibodies. Additionally, saliva samples showed promise as a potential diagnostic biofluid for measuring antibody levels, as they exhibited a strong correlation with the data obtained from serum samples.

Conclusion

Accurate estimation of population-based serosurveillance for SARS-CoV- 2 will monitor the trend of infection in the community and delineate the geographical spread of the infection. Cumulative incidence of SARS-CoV-2 infection during and after outbreaks is crucial for informing the development of effective risk mitigation protocols within the community. Protocols may include measures such as encouraging booster shots, extending mask mandates, or transitioning to online classes. Serosurveys repeated at regular intervals can also guide containment measures in communities and prompt response to future outbreaks.

Strengths and limitations of this study

We simultaneously investigated active infection and seroprevalence for the university population.

Our study was strengthened by having the participants’ self-report data independently validated with diagnostic tests.

Saliva samples could be a potential diagnostic biofluid for measuring antibody levels.

Our study was performed within the university setting therefore it only reflects the COVID-19 situation within that community.

The number of breakthrough infections and the longitudinal samples were small, thus requiring confirmation.
Constructing the brief Diagnostic Criteria for Temporomandibular Disorders (bDC/TMD)
Authors: Durham Justin , Ohrbach Richard , Baad-Hansen Lene , Davies Stephen , De Laat Antoon , Goncalves Daniela Godoi , Gordan Valeria V , Goulet Jean-Paul , Häggman-Henrikson Birgitta , Horton Michael ,   INfORM, Koutris Michail , Law Alan , List Thomas , Lobbezoo Frank , Michelotti Ambra , Nixdorf Donald R. , Oyarzo Juan Fernando , Peck Chris , Penlington Chris , Raphael Karen G. , Santiago Vivian , Sharma Sonia , Svensson Peter , Visscher Corine M. , Yoshiki Imamura , Alstergren Per
Published: August 2023

Background

Despite advances in Temporomandibular disorders’ (TMDs) diagnosis, the diagnostic process continues to be problematic in non-specialist settings.

Objective

To complete a Delphi process to shorten the Diagnostic Criteria for TMD (DC/TMD) to a brief DC/TMD (bDC/TMD) for the diagnoses with the most utility in general dentistry settings.

Methods

A international Delphi panel was created with 23 clinicians representing major specialities, general dentistry, and related fields. The process comprised a full day workshop, four virtual meetings, six rounds of electronic discussion, and finally an open consultation at a virtual international symposium.

Results

Within the physical axis (Axis 1) the self-report Symptom Questionnaire of the DC/TMD did not require shortening from 14 items for the bDC/TMD. The compulsory use of the TMD pain screener was removed reducing the total number of Axis 1 items by 18%. The DC/TMD Axis 1 10-section examination protocol (25 movements, up to 12 sets of bilateral palpations) was reduced to 4 sections in the bDC/TMD protocol involving 3 movements and 3 sets of palpations. Axis I then resulted in two groups of diagnoses: painful TMD (inclusive of secondary headache), and common joint-related TMD with functional implications. The Psychosocial Axis (Axis 2) was shortened to an ultra-brief 11 item assessment.

Conclusion

The bDC/TMD represents a substantially reduced and likely expedited method to establish (grouping) diagnoses in TMDs. This may provide greater utility for settings requiring less granular diagnoses for the implementation of initial treatment, for example non-specialist general dental practice.
Profile of speech and cognitive impairments in a patient with moyamoya disease: a longitudinal case study
Authors: Pashkov A. , Filimonova E. , Martirosyan A. , Ovsyannikov K. , Gunenko G. , Moysak G. , Rzaev J.
Published: August 2023

Moyamoya is a rare chronic brain vascular disease with a set of potential life-threatening consequences due to a high probability of stroke occurrence. Patients suffering from this disease are often presented with diverse and severe sensory, motor and cognitive deficits, which often lead to general inability to work and, in the most severe cases, to complete loss of self-serving skills and gross disturbance of vital homeostatic functions. Here we present a case of a patient with moyamoya disease, who has been dynamically observed over more than 4 years after the first manifestation of her symptoms. We have been tracking the appearance of patient’s new symptoms and resolution of existing ones after neurosurgical treatment (revascularization surgery) with in-depth neurological examination, neuropsychological assessment and fMRI/DTI sessions. This study represents one of the first attempts to rigorously estimate the patterns of deficits at different levels, connecting neural circuits affected by the disease to behavior. Our findings lend further support to the idea that revascularization surgery can improve cognitive performance and highlights the importance of long-term follow-up in understanding the effects of surgery on brain function.
Extended genome-wide association study employing the African Genome Resources Panel identifies novel susceptibility loci for Alzheimer’s Disease in individuals of African ancestry
Authors: Ray Nicholas R. , Kunkle Brian W. , Hamilton-Nelson Kara , Kurup Jiji T. , Rajabli Farid , Cosacak Mehmet I. , Kizil Caghan , Jean-Francois Melissa , Cuccaro Michael , Reyes-Dumeyer Dolly , Cantwell Laura , Kuzma Amanda , Vance Jeffery M. , Gao Sujuan , Hendrie Hugh C. , Baiyewu Olusegun , Ogunniyi Adesola , Akinyemi Rufus O. ,   Alzheimer’s Disease Genetics Consortium, Lee Wan-Ping , Martin Eden R. , Wang Li-San , Beecham Gary W. , Bush William S. , Farrer Lindsay A. , Haines Jonathan L. , Byrd Goldie S. , Schellenberg Gerard D. , Mayeux Richard , Pericak-Vance Margaret A. , Reitz Christiane
Published: August 2023

INTRODUCTION

Despite a two-fold increased risk, individuals of African ancestry have been significantly underrepresented in Alzheimer’s Disease (AD) genomics efforts.

METHODS

GWAS of 2,903 AD cases and 6,265 cognitive controls of African ancestry. Within-dataset results were meta-analyzed, followed by gene-based and pathway analyses, and analysis of RNAseq and whole-genome sequencing data.

RESULTS

A novel AD risk locus was identified inMPDZon chromosome 9p23 (rs141610415, MAF=.002,P=3.68×10−9). Two additional novel common and nine novel rare loci approached genome-wide significance atP<9×10−7. Comparison of association and LD patterns between datasets with higher and lower degrees of African ancestry showed differential association patterns at chr12q23.2 (ASCL1), suggesting that the association is modulated by regional origin of local African ancestry.

DISCUSSION

Increased sample sizes and sample sets from Africa covering as much African genetic diversity as possible will be critical to identify additional disease-associated loci and improve deconvolution of local genetic ancestry effects.
A predictive model of ebolavirus spillover incorporating change in forests and human populations across spatial and temporal scales
Authors: Telford Carson T. , Amman Brian R. , Towner Jonathan S. , Bowden Sarah , Montgomery Joel M. , Lessler Justin , Shoemaker Trevor
Published: August 2023

Past research has found associations between ebolavirus spillover and forest loss and fragmentation, although most predictions of the spatial distribution of ebolaviruses have not utilized these data. Spatial and temporal scales of covariate data measurement have also not previously been accounted for in predictive models of ebolavirus spillover, making it difficult to account for variables that influence ebolavirus transmission dynamics, such as movement and interaction of human and animal populations, trade, and animal behavioral responses to human presence and a changing environment. Using annual data on forest cover, forest loss and fragmentation, human population distribution, and meteorological variables, we developed models of ebolavirus spillover events from 2001-2021 to estimate the annual relative odds of ebolavirus spillover in equatorial Africa in 2021 and 2022. Analyses were done separately for all ebolavirus species (All-species analysis) and Zaire ebolavirus alone (Zaire-only analysis). Locations with the highest estimated relative odds of spillover occurred in patches throughout Democratic Republic of the Congo (DRC), Republic of the Congo, Gabon, Cameroon, and coastal west Africa in a spatial trend that resembled that of maps of forest fragmentation and forest loss. Reduced analyses that ignored forest loss and fragmentation data produced estimates that were distinct from the full analyses, highlighting locations where forest loss and fragmentation drove model predictions, which included coastal west Africa, southern Cameroon, and parts of DRC. Estimated spillover odds and increase in spillover odds at 2022 spillover sites ranked among the highest in equatorial Africa, suggesting the potential of predictive analyses to prioritize locations for surveillance and research efforts.

Significance

Using annually updated data on forest change, human population distribution, and meteorological conditions, we developed models to estimate the relative odds of ebolavirus spillover in 2021 and 2022 in equatorial Africa, identifying locations with elevated odds of spillover and temporal shifts in spillover odds between the two years. Locations were identified whose estimates of spillover odds were driven by forest change. During 2022, two ebolavirus spillover events were identified in locations with elevated spillover odds estimates. Annually updated estimates of ebolavirus spillover can guide public health surveillance programs to high-risk locations at specific times, and guide potential ebolavirus reservoir sampling efforts to locations that recently experienced increases in spillover odds.
Krasloss of heterozygosity promotes MAPK dependent pancreatic ductal adenocarcinoma and induces therapeutic sensitivity
Authors: Fey Sigrid K. , Najumudeen Arafath K. , Ford Catriona , Gilroy Kathryn , Upstill-Goddard Rosie , Chang David K. , Clark William , Nixon Colin , Barry Simon T. , Morton Jennifer P. , Campbell Andrew D. , Sansom Owen J.
Published: August 2023

Pancreatic cancer is characterised by the prevalence of oncogenic mutations inKRAS. Previous studies have reported that alteredKrasgene dosage drives progression and metastatic incidence in pancreatic cancer. While the role of oncogenicKRASmutation is well characterised, the relevance of the partnering wild-typeKRASallele in pancreatic cancer is less well understood and controversial. Usingin vivomouse modelling of pancreatic cancer, we demonstrate that wild-typeKrasrestrains the oncogenic impact of mutantKras, and drastically impacts bothKras-mediated tumourigenesis and therapeutic response. Mechanistically, deletion of wild-typeKrasincreases oncogenicKrassignalling through the downstream MAPK effector pathway, driving pancreatic intraepithelial neoplasia (PanIN) initiation. In addition, in the KPC mouse model, a more aggressive model of pancreatic cancer, loss of wild-type KRAS leads to accelerated initiation but delayed tumour progression. These tumours had altered stroma, downregulatedMyclevels and an enrichment for immunogenic gene signatures. Importantly, loss of wild-typeKrassensitisesKrasmutant tumours to MEK1/2 inhibition though tumours eventually become resistant and then rapidly progress. This study demonstrates the repressive role of wild-typeKrasduring pancreatic tumourigenesis and highlights the critical impact of the presence of wild-type KRAS on tumourigenesis and therapeutic response in pancreatic cancer.
A deep genetic analysis of banana Fusarium wilt pathogens of Cuba in a Latin American and Caribbean diversity landscape
Authors: de la Parte Einar Martínez , Pérez-Vicente Luis , Torres David E. , van Westerhoven Anouk , Meijer Harold J. G. , Seidl Michael F. , Kema Gert H. J.
Published: August 2023

Fusarium wilt of bananas (FWB) is a devastating plant disease that causes significant economic losses in banana production worldwide and is one of the major concerns for Cuban banana cultivation. The disease is caused by members of the soil-borneFusarium oxysporumspecies complex. However, the genetic diversity amongFusariumspecies infecting bananas in Cuba is currently unknown.

We conducted a comprehensive survey of symptomatic banana plants across all production zones of the country and assembled a collection of 170Fusariumisolates. Using genotyping- by-sequencing and whole-genome comparisons, we investigated the genetic diversity across this suite of isolates and compared it with the genetic diversity of a globalFusariumpanel.

Typical FWB symptoms were observed in varieties of the Bluggoe cooking banana and Pisang Awak subgroups in 14 provinces. Phylogenetic analysis revealed thatF. purpurascens, F. phialophorum,andF. tardichlamydosporumcause FWB in Cuba, with the latter dominating the population. Furthermore, we identified between five and seven genetic clusters, withF. tardichlamydosporumisolates divided into at least two distinct subgroups, indicating a high genetic diversity ofFusariumspp. causing FWB in the Americas.

Our study provides unprecedented insights into the population genetic structure and diversity of the FWB pathogen in Cuba and the Latin American and Caribbean regions.
Lysosomal MLKL is balanced by ESCRT to control cell death
Authors: Jamard Catherine , Gil Clara , Castets Marie , Ichim Gabriel , Weber Kathrin
Published: August 2023

Mixed lineage kinase-like (MLKL) is activated by RHIM-domain containing kinase (RIPK)3 to permeabilize the plasma-membrane and execute necroptosis, a form of regulated necrosis. We found that MLKL is activated in an atypical, RIPK3- and necroptosis-independent manner downstream of Toll-like receptor 3, resulting in its translocation to lysosomes and lysosomal membrane permeabilization. Damaged lysosomes then undergo exocytosis, leading to the integration of lysosomal MLKL into the plasma-membrane to trigger cell death. The ESCRT-machinery can repair damaged lysosomes and counteract cell death by packing lysosomal MLKL into intraluminal vesicles, which are subsequently released as extracellular vesicles. In this way, ESCRT-machinery balances life and death decisions by preventing lysosomal MLKL to reach its killing destination, which is the plasma-membrane.
Insights into Digit Evolution from a Fate Map Study of the Forearm
Authors: Oh JDH , Saunders DDZ , McTeir L , Jackson M , Glover JD , Schoenebeck JJ , Lettice LA , Davey MG
Published: August 2023

The cellular and genetic networks which contribute to the development of the zeugopod, (radius and ulna of the forearm, tibia and fibula of the leg) are not well understood, although these bones are susceptible to loss in congenital human syndromes and to the action of teratogens such as thalidomide. Using a new fate mapping approach in transgenic chickens, we show that there is a small contribution ofSHHexpressing cells to the posterior ulna, posterior carpals and digit 3. We establish that while the majority of the ulna develops in response to paracrine SHH signaling in both the chicken and mouse, there are differences in the contribution ofSHHexpressing cells to other tissues of the zeugopod between these two species as well as between the chicken ulna and fibula. This is evidence that although zeugopod bones are clearly homologous according to the fossil record, the zeugopod bones of the wing and leg are formed by subtly different signalling and patterning events during embryonic development, which can be used to understand the shaping of the bird wing skeleton during the evolution of powered flight.
Molecular Mechanism of PP2A/B55α Phosphatase Inhibition by IER5
Authors: Cao Ruili , Jones Daniel TD , Pan Li , Yang Annie , Wang Shumei , Padi Sathish K. R. , Shaun Rawson , Aster Jon C , Blacklow Stephen C
Published: August 2023

PP2A serine/threonine phosphatases are heterotrimeric complexes that execute many essential physiologic functions. These activities are modulated by additional regulatory proteins, such as ARPP19, FAM122A, and IER5. Here, we report the cryoelectron microscopy structure of a complex of PP2A/B55α with the N-terminal structured region of IER5 (IER5-N50), which occludes a surface on B55α used for substrate recruitment, and show that IER5-N50 inhibits PP2A/B55α catalyzed dephosphorylation of pTau in biochemical assays. Mutations of full-length IER5 that disrupt its PP2A/B55α interface interfere with co-immunoprecipitation of PP2A/B55α. These mutations and deletions that remove the nuclear localization sequence of IER5 suppress cellular events such asKRT1expression that depend on association of IER5 with PP2A/B55α. Querying the Alphafold2 predicted structure database identified SERTA domain proteins as high-confidence PP2A/B55α-binding structural homologs of IER5-N50. These studies define the molecular basis of PP2A/B55α inhibition by IER5-family proteins and suggest a roadmap for selective pharmacologic modulation of PP2A/B55α complexes.
A mutant fitness compendium in Bifidobacteria reveals molecular determinants of colonization and host-microbe interactions
Authors: Shiver Anthony L. , Sun Jiawei , Culver Rebecca , Violette Arvie , Wynter Charles , Nieckarz Marta , Mattiello Samara Paula , Sekhon Prabhjot Kaur , Friess Lisa , Carlson Hans K. , Wong Daniel , Higginbottom Steven , Weglarz Meredith , Wang Weigao , Knapp Benjamin D. , Guiberson Emma , Sanchez Juan , Huang Po-Hsun , Garcia Paulo A. , Buie Cullen R. , Good Benjamin , DeFelice Brian , Cava Felipe , Scaria Joy , Sonnenburg Justin , Van Sinderen Douwe , Deutschbauer Adam M. , Huang Kerwyn Casey
Published: August 2023

Bifidobacteria commonly represent a dominant constituent of human gut microbiomes during infancy, influencing nutrition, immune development, and resistance to infection. Despite interest as a probiotic therapy, predicting the nutritional requirements and health-promoting effects of Bifidobacteria is challenging due to major knowledge gaps. To overcome these deficiencies, we used large-scale genetics to create a compendium of mutant fitness inBifidobacterium breve(Bb). We generated a high density, randomly barcoded transposon insertion pool inBb, and used this pool to determineBbfitness requirements during colonization of germ-free mice and chickens with multiple diets and in response to hundreds ofin vitroperturbations. To enable mechanistic investigation, we constructed an ordered collection of insertion strains covering 1462 genes. We leveraged these tools to improve models of metabolic pathways, reveal unexpected host- and diet-specific requirements for colonization, and connect the production of immunomodulatory molecules to growth benefits. These resources will greatly reduce the barrier to future investigations of this important beneficial microbe.
Including organism and environmental heterogeneity in kinematic continuum models of collective behaviour with applications to locust foraging and group structure
Authors: Georgiou F. , Buhl J. , Green J.E.F. , Lamichhane B , Thamwattana N.
Published: August 2023

Collective behaviour occurs at all levels of the natural world, from cells joining together to form complex structures, to locusts interacting to form large and destructive plagues. These complex behaviours arise from simple individual and environmental interactions, and thus lend themselves well to mathematical modelling. One simplifying assumption, that of relative homogeneity of organisms, is often applied to keep the mathematics tractable. However, heterogeneity arising due to the internal state of individuals has an impact on these interactions and thus plays a role in group structure and dynamics.

In this paper, we introduce a continuum model that accounts for this heterogeneity in the form of a state space that models an organisms internal state and converts this to movement characteristics. Using a variety analytic techniques, we investigate the effect of internal state on aggregation density and aggregation formation behaviour, finding that density and formation is most affected by the ratio of attractive to dispersive interactions.

We then apply the model to a concrete example of locust foraging to investigate the effect of food, hunger, and gregarisation on locust group formation and structure. Through numerical simulations we find that the most gregarious and satiated locusts tend to be located towards the centre of locust groups. Conversely, hunger drives locusts towards the edges of the group. Finally, we find that locust group dispersal may be driven in part by hunger.

Author Summary

Collective behaviour occurs at all levels of the natural world, from cells joining together to form complex structures, to locusts interacting to form large and destructive plagues. We can modelling these complex behaviours using mathematical models however we often need to rely on simplifying assumptions to keep the mathematics easy enough to analyse. One simplifying assumption that is often employed is assuming that all the modelled organisms are the same (or in one of only a few possible states). However, this is often not the case in nature where the differences between individuals arising due to internal characteristics, such as hunger or age, often affects their behaviour and thus can change group dynamics.

In this paper we introduce a mathematical model that is able to capture these differences and apply the newly developed model to locust foraging. We find that hunger tends to drive individuals to the edges of aggregations as well as lowers the maximum possible density. These two results combine to give a possible mechanism for the dispersal of locust groups.
Phylogeny and disease links of a widespread and ancient gut phage lineage
Authors: de Jonge Patrick A. , van den Born Bert-Jan H. , Zwinderman Aeilko H. , Nieuwdorp Max , Dutilh Bas E. , Herrema Hilde
Published: August 2023

Viruses are a core component of the human microbiome, impacting health and disease through interactions with gut bacteria1and the immune system2. Most viruses in the human microbiome are bacteriophages, which exclusively infect bacteria. Individual gut bacteriophages can affect bacterial bile acid deconjugation3, and can alter their infection strategy based on dietary content4. Up to recently, most studies of the gut virome have focused on low taxonomic scales (e.g., viral operational taxonomic units), hampering population-level analyses. We previously identified the expansive and widespread CandidatusHeliusviridaebacteriophage family in a cohort with inhabitants of Amsterdam, the Netherlands. Here, we study their biodiversity and evolution in a wide variety of human populations. With a detailed phylogeny based on sequences from six viral genome databases, we now propose the Candidatus orderHeliusviralesto accommodate these viruses. We identifyCa. Heliusviralesviruses in 80% of 5,441 individuals across 39 studies, and also in nine out of thirteen analyzed metagenomes from ancient humans that lived in Europe and North America between 1,000 and 5,000 years ago. We show that a largeCa. Heliusviraleslineage has diversified starting at the appearance ofHomo sapienssome 200,000-300,000 years ago. Ancient peoples and modern hunter-gatherers further have distinctCa. Heliusviralespopulations that are characterized by lower richness than modern urbanized people. Within urbanized people, those suffering from type 1 and type 2 diabetes, as well as inflammatory bowel disease, have higherCa. Heliusviralesrichness than healthy controls. We thus conclude that these ancient core members of the human gut virome have thrived with increasingly westernized lifestyles of the human population.
A short sequence in the tail of SARS-CoV-2 envelope protein controls accessibility of its PDZ Binding Motif to the cytoplasm
Authors: Neitthoffer Benoit , Alvarez Flavio , Larrous Florence , Saguy Célia Caillet , Manneville Sandrine Etienne , Boëda Batiste
Published: August 2023

The carboxy terminal tail of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope protein (E) contains a PDZ-binding motif (PBM) which is crucial for coronavirus pathogenicity. During SARS-CoV-2 infection, the viral E protein is expressed within the Golgi apparatus membrane of host cells with its PBM facing the cytoplasm. In this work we study the molecular mechanisms controlling the presentation of the PBM to host PDZ (PSD-95/Dlg/ZO-1) domain-containing proteins. We show that at the level of the Golgi apparatus, the PDZ-binding motif of the E protein is not detected by E C-terminal specific antibodies neither by PDZ domain-containing protein binding partner. Four alanine substitutions upstream of the PBM in the central region of the E protein tail is sufficient to generate immunodetection by anti-E antibodies and trigger robust recruitment of the PDZ domain-containing protein into the Golgi organelle. Overall, this work suggests that the presentation of the PBM to the cytoplasm is under conformational regulation mediated by the central region of the E protein tail and that PBM presentation probably does not occur at the surface of Golgi cisternae but likely at post-Golgi stages of the viral cycle.
Single-cell evidence for plasmid addiction mediated by toxin-antitoxin systems
Authors: Fraikin Nathan , Van Melderen Laurence
Published: August 2023

Toxin-antitoxin (TA) systems are small selfish genetic modules that increase vertical stability of their replicons. They have long been thought to stabilize plasmids by killing cells that fail to inherit a plasmid copy through a phenomenon called post-segregational killing (PSK) or addiction. While this model has been widely accepted, no direct observation of PSK was reported in the literature. Here, we devised a system that enables visualization of plasmid loss and PSK at the single-cell level using meganuclease-driven plasmid curing. Using theccdsystem, we show that cells deprived of accd-encoding plasmid show hallmarks of DNA damage,i.e. filamentation and induction of the SOS response. Activation ofccd-triggered cell death in most plasmid-free segregants, although some intoxicated cells were able to resume growth, showing that PSK-induced damage can be repaired in a SOS-dependent manner. Damage induced byccdactivates resident lambdoid prophages, which potentiate the killing effect ofccd. The loss of a model plasmid containing TA systems encoding toxins presenting various molecular mechanisms induced different morphological changes, growth arrest and loss of viability. Our experimental setup enables further studies of TA-induced phenotypes and suggests that PSK is a general mechanism for plasmid stabilization by TA systems.
Mapping protein–exopolysaccharide binding interaction inStaphylococcus epidermidisbiofilms by live cell proximity labeling
Authors: Vo Luan H. , Hong Steven , Stepler Kaitlyn E. , Liyanaarachchi Sureshee M. , Yang Jack , Nemes Peter , Poulin Myles B.
Published: August 2023

Bacterial biofilms consist of cells encased in an extracellular polymeric substance (EPS) composed of exopolysaccharides, extracellular DNA, and proteins that are critical for cell–cell adhesion and protect the cells from environmental stress, antibiotic treatments, and the host immune response. Degrading EPS components or blocking their production have emerged as promising strategies for prevention or dispersal of bacterial biofilms, but we still have little information about the specific biomolecular interactions that occur between cells and EPS components and how those interactions contribute to biofilm production.Staphylococcus epidermidisis a leading cause of nosocomial infections as a result of producing biofilms that use the exopolysaccharide poly- (1→6)-β-N-acetylglucosamine (PNAG) as a major structural component. In this study, we have developed a live cell proximity labeling approach combined with quantitative mass spectrometry-based proteomics to map the PNAG interactome of liveS. epidermidisbiofilms. Through these measurements we discovered elastin-binding protein (EbpS) as a major PNAG-interacting protein. Using live cell binding measurements, we found that the lysin motif (LysM) domain of EbpS specifically binds to PNAG present inS. epidermidisbiofilms. Our work provides a novel method for the rapid identification of exopolysaccharide-binding proteins in live biofilms that will help to extend our understanding of the biomolecular interactions that are required for bacterial biofilm formation.
HIV-1 binds dynein directly to hijack microtubule transport machinery
Authors: Badieyan Somayesadat , Lichon Drew , Andreas Michael P. , Gillies John P. , Peng Wang , Shi Jiong , DeSantis Morgan E. , Aiken Christopher R. , Böcking Till , Giessen Tobias W. , Campbell Edward M. , Cianfrocco Michael A.
Published: August 2023

Viruses exploit host cytoskeletal elements and motor proteins for trafficking through the dense cytoplasm. Yet the molecular mechanism that describes how viruses connect to the motor machinery is unknown. Here, we demonstrate the first example of viral microtubule trafficking from purified components: HIV-1 hijacking microtubule transport machinery. We discover that HIV-1 directly binds to the retrograde microtubule-associated motor, dynein, and not via a cargo adaptor, as previously suggested. Moreover, we show that HIV-1 motility is supported by multiple, diverse dynein cargo adaptors as HIV-1 binds to dynein light and intermediate chains on dynein’s tail. Further, we demonstrate that multiple dynein motors tethered to rigid cargoes, like HIV-1 capsids, display reduced motility, distinct from the behavior of multiple motors on membranous cargoes. Our results introduce a new model of viral trafficking wherein a pathogen opportunistically ‘hijacks’ the microtubule transport machinery for motility, enabling multiple transport pathways through the host cytoplasm.
Toxoplasma gondiiactin filaments are tuned for rapid disassembly and turnover
Authors: Hvorecny Kelli L. , Sladewski Thomas E. , De La Cruz Enrique M. , Kollman Justin M. , Heaslip Aoife T.
Published: August 2023

The cytoskeletal protein actin plays a critical role in the pathogenicity ofToxoplasma gondii, mediating invasion and egress, cargo transport, and organelle inheritance. Advances in live cell imaging have revealed extensive filamentous actin networks in the Apicomplexan parasite, but there is conflicting data regarding the biochemical and biophysical properties ofToxoplasmaactin. Here, we imaged thein vitroassembly of individualToxoplasmaactin filaments in real time, showing that native, unstabilized filaments grow tens of microns in length. Unlike skeletal muscle actin,Toxoplasmafilaments intrinsically undergo rapid treadmilling due to a high critical concentration, fast monomer dissociation, and rapid nucleotide exchange. Cryo-EM structures of stabilized and unstabilized filaments show an architecture like skeletal actin, with differences in assembly contacts in the D-loop that explain the dynamic nature of the filament, likely a conserved feature of Apicomplexan actin. This work demonstrates that evolutionary changes at assembly interfaces can tune dynamic properties of actin filaments without disrupting their conserved structure.
Oxidative regulation of TDP-43 self-association by a β-to-α conformational switch
Authors: Gu Jinge , Zhou Xiaoming , Sutherland Lillian , Kato Masato , Jaczynska Klaudia , Rizo Josep , McKnight Steven L.
Published: August 2023

An evolutionarily conserved region of the TDP-43 low complexity domain twenty residues in length can adopt either an α-helical or β-strand conformation. When in the latter conformation, TDP-43 self-associates via the formation of a labile, cross-β structure. Self-association can be monitored via the formation of phase separated protein droplets. Exposure of droplets to hydrogen peroxide leads to oxidation of conserved methionine residues distributed throughout the low complexity domain. Oxidation disassembles the cross-β structure, thus eliminating both self-association and phase separation. Here we demonstrate that this process reciprocally enables formation of α-helical structure in precisely the same region formerly functioning to facilitate β-strand mediated self-association. We further observe that the α-helical conformation allows interaction with a lipid-like detergent, and that exposure to lipids enhances the β-to-α conformational switch. We hypothesize that regulation of this oxidative switch will prove to be important to the control of localized translation within vertebrate cells. The experimental observations reported herein were heavily reliant on studies of 1,6-hexanediol, a chemical agent that selectively dissolves labile structures formed via the self-association of protein domains of low sequence complexity. This aliphatic alcohol is shown to exert its dissociative activity primarily via hydrogen bonding interactions with carbonyl oxygen atoms of the polypeptide backbone. Such observations underscore the central importance of backbone-mediated protein:protein interactions that facilitate the self-association and phase separation of low complexity domains.

Significance Statement

The TDP-43 protein is a constituent of RNA granules involved in regulated translation. TDP-43 contains a C-terminal domain of 150 amino acids of low sequence complexity conspicuously decorated with ten methionine residues. An evolutionarily conserved region (ECR) of 20 residues within this domain can adopt either of two forms of labile secondary structure. Under normal conditions wherein methionine residues are reduced, the ECR forms a labile cross-β structure that enables RNA granule condensation. Upon methionine oxidation, the ECR undergoes a conformational switch to become an α-helix incompatible with self-association and granule integrity. Oxidation of the TDP-43 low complexity domain is hypothesized to occur proximal to mitochondria, thus facilitating dissolution of RNA granules and activation of localized translation.