bluuebunny/crossref_metadata_2025 huggingface dataset:
Altered hippocampal activation in seizure-proneCACNA2D2knockout mice
Authors: Danis Alyssa , Gallagher Ashlynn A. , Anderson Ashley N. , Isakharov Arielle , Beeson Kathleen A. , Schnell Eric
Published: November 2023

The voltage-gated calcium channel subunit α2δ-2 controls calcium-dependent signaling in neurons, and loss of this subunit causes epilepsy in both mice and humans. To determine whether mice without α2δ-2 demonstrate hippocampal activation or histopathological changes associated with seizure activity, we measured expression of the activity-dependent genec-fosand various histopathological correlates of temporal lobe epilepsy in hippocampal tissue from wildtype (WT) and α2δ-2 knockout (CACNA2D2KO) mice using immunohistochemical staining and confocal microscopy. Both genotypes demonstrated similarly sparsec-fosexpression within the hippocampal dentate granule cell layer (GCL) at baseline, consistent with no difference in basal activity of granule cells between genotypes. Surprisingly, when mice were assayed 1 hour after handling-associated convulsions, KO mice had fewer c-fos-positive cells in the dentate gyrus, indicating that activity in the dentate gyrus actually decreased. However, the dentate was significantly more active in KO mice compared to WT after administration of a subthreshold pentylenetetrazole dose, consistent with increased susceptibility to proconvulsant stimuli. Other histopathological markers of temporal lobe epilepsy in these mice, including markers of neurogenesis, glial activation, and mossy fiber sprouting, were similar in WT and KO mice, apart from a small but significant increase in hilar mossy cell density, opposite to what is typically found in mice with temporal lobe epilepsy. This suggests that the differences in seizure-associated hippocampal function in the absence of α2δ-2 protein are likely due to altered functional properties of the network without associated structural changes in the hippocampus at the typical age of seizure onset.

Significance Statement

Calcium channel α2δ subunits play important roles in controlling neuronal circuit structure and function, and mutation of the α2δ-2 isoform of this protein is associated with spontaneous seizures. In this study, we find that seizures in α2δ-2 mutant mice involve altered hippocampal activation without substantial histopathological changes in hippocampal structure. This suggests that the differences in seizure-associated hippocampal function are likely due to altered functional properties of the network as well as to the contribution of additional brain regions to seizures in mice lacking this protein.
Phylogeographic analysis ofBegomoviruscoat and replication-associated proteins
Authors: Crespo-Bellido Alvin , Hoyer J. Steen , Burgos-Amengual Yeissette , Duffy Siobain
Published: November 2023

Begomoviruses are globally distributed plant pathogens that significantly limit crop production. These viruses are traditionally described according to phylogeographic distribution and categorized into two groups: begomoviruses from the Africa, Asia, Europe, and Oceania (AAEO) region and begomoviruses from the Americas. Monopartite begomoviruses are more common in the AAEO region while bipartite viruses predominate in the Americas, where the begomoviruses lack the V2/AV2 gene involved in inter-cellular movement and RNA silencing suppression found in AAEO begomoviruses. While these features are generally accepted as lineage-defining, the number of known species has doubled due to sequence-based discovery since 2010. To reevaluate the geographic groupings after the rapid expansion of the genus, we conducted phylogenetic analyses for begomovirus species representatives of the two longest and most conserved begomovirus proteins: the coat and replication-associated proteins. Both proteins still largely support the broad AAEO and Americas begomovirus groupings, except for sweetpotato-infecting begomoviruses that form an independent, well-supported clade for their coat protein regardless of the region they were isolated from. Our analyses do not support more fine-scaled phylogeographic groupings. Monopartite and bipartite genome organizations are broadly interchanged throughout the phylogenies and the absence of the V2/AV2 gene is highly reflective of the split between Americas and AAEO begomoviruses. We observe significant evidence of recombination within the Americas and within the AAEO region, but rarely between the regions. We speculate that increased globalization of agricultural trade, the invasion of polyphagous whitefly vector biotypes and recombination will blur begomovirus phylogeographic delineations in the future.
Robust detection of SARS-CoV-2 exposure in the population using T-cell repertoire profiling
Authors: Vlasova Elizaveta K. , Nekrasova Alexandra I. , Komkov Alexander Y , Izraelson Mark , Snigir Ekaterina A. , Mitrofanov Sergey I. , Yudin Vladimir S. , Makarov Valentin V. , Keskinov Anton A. , Korneeva Darya , Pivnyuk Anastasia , Shelyakin Pavel V , Mamedov Ilgar Z , Rebrikov Denis V , Chudakov Dmitry M , Yudin Sergey M. , Skvortsova Veronika I. , Britanova Olga V , Shugay Mikhail A.
Published: November 2023

The COVID-19 pandemic offers a powerful opportunity to develop methods for monitoring the spread of infectious diseases based on their signatures in population immunity. Adaptive immune receptor repertoire sequencing (AIRR-seq) has become the method of choice for identifying T cell receptor (TCR) biomarkers encoding pathogen specificity and immunological memory. AIRR-seq can detect imprints of past and ongoing infections and facilitate the study of individual responses to SARS-CoV-2, as shown in many recent studies. Here, we have applied a machine learning approach to two large AIRR-seq datasets with more than 1,200 high-quality repertoires from healthy and COVID-19-convalescent donors to infer TCR repertoire features that were induced by SARS-CoV-2 exposure. The new batch effect correction method allowed us to use data from different batches together, as well as combine the analysis for data obtained using different protocols. Proper standardization of AIRR-seq batches, access to human leukocyte antigen (HLA) typing, and the use of both α- and β-chain sequences of TCRs resulted in a high-quality biomarker database and a robust and highly accurate classifier for COVID-19 exposure. This classifier is applicable to individual TCR repertoires obtained using different protocols, paving the way to AIRR-seq-based immune status assessment in large cohorts of donors.
Bacterial community complexity in the phyllosphere penalises specialists over generalists
Authors: Schlechter Rudolf O. , Remus-Emsermann Mitja N. P.
Published: November 2023

The leaf surface, i.e. the phylloplane, is an oligotrophic and heterogeneous environment due to its topography and uneven distribution of resources. Despite being a limiting environment, leaves host bacteria that are abundant and establish spatially-structured communities. However, factors that drive spatial distribution patterns are not well understood. Since leaf-associated bacteria can have beneficial effects to their host, understanding the rules of the community assembly can lead to novel strategies for crop protection. To investigate changes in population density and spatial distribution of bacteria in synthetic communities, we examined the behaviour of two prevalent bacterial groups in theArabidopsis thalianaleaf microbiota:Methylobacteriumspp. (specialists) andSphingomonasspp. (generalists). We designed synthetic communities composed of two (S2) or three strains (S3) in a full factorial design and tested whether density and spatial structure of communities in S3 can be explained by pairwise comparisons in S2. Our results showed that specialists are more susceptible to changes in population densities and spatial distribution patterns than generalists, with lower densities and aggregation patterns when a specialist is in S3 than in S2. Additionally, pairwise comparisons were not sufficient to explain the observed patterns in S3, suggesting that higher-order interactions play a role in the resulting structure of complex communities at the micrometre scale.
Comparison oftet(X4)-containing contigs from metagenomic sequencing data with plasmid sequences of isolates from a cohort of healthy subjects
Authors: Ding Yichen , Er Shuan , Tan Abel , Gounot Jean-Sebastien , Saw Woei-Yuh , Lin Tan Linda Wei , Teo Yik Ying , Nagarajan Niranjan , Seedorf Henning
Published: November 2023

The recently discovered tigecycline-inactivating enzyme Tet(X4) can confer high-level tigecycline resistance on its hosts, which makes it a public health concern. This study focused on detection, analysis, and characterization of Tet(X4)-positive Enterobacteriaceae from the gut microbiota of a healthy cohort of individuals in Singapore using cultivation-dependent and cultivation-independent approaches. Twelve Tet(X4)-positive Enterobacteriaceae strains that were previously obtained from the cohort were fully genome-sequenced and comparatively analysed. A metagenomic sequencing (MS) dataset of the same samples was mined for contigs that harboured thetet(X4) resistance gene. The sequences oftet(X4)-containing contigs and plasmids sequences were compared. The presence of the resistance genesfloRandcatD(also annotated asestT) was detected in the same cassette in 10 and 12 out of the 12tet(X4)-carrying plasmids, respectively. MS detectedtet(X4)-containing contigs in two out of 109 subjects, while cultivation-dependent analysis previously reported a prevalence of 10.1%. Contig sequences are relatively short (∼14-33 kb) but show high similarity to the respective plasmid sequences of the isolates. The frequent co-occurrence offlorRandcatDwithtet(X4) corroborates the hypothesis that the transmission oftet(X4) may have originated from the veterinary sector. Our findings show that MS can complement efforts in the surveillance of antibiotic resistance genes for clinical samples, while it has a lower sensitivity than a cultivation-based method when the target organism have a low abundance. Further optimisation is required if MS is to be utilised in antibiotic resistance surveillance.
Signal Transduction in an Enzymatic Photoreceptor Revealed by Cryo-Electron Microscopy
Authors: Malla Tek Narsingh , Hernandez Carolina , Menendez David , Bizhga Dorina , Mendez Joshua H. , Muniyappan Srinivasan , Schwander Peter , Stojković Emina A. , Schmidt Marius
Published: November 2023

Phytochromes are essential photoreceptor proteins in plants with homologs in bacteria and fungi that regulate a variety of important environmental responses. They display a reversible photocycle between two distinct states, the red-light absorbing Pr and the far-red light absorbing Pfr, each with its own structure. The reversible Pr to Pfr photoconversion requires covalently bound bilin chromophore and regulates the activity of a C-terminal enzymatic domain, which is usually a histidine kinase (HK). In plants, phytochromes translocate to nucleus where the C-terminal effector domain interacts with protein interaction factors (PIFs) to induce gene expression. In bacteria, the HK phosphorylates a response-regulator (RR) protein triggering downstream gene expression through a two-component signaling pathway. Although plant and bacterial phytochromes share similar structural composition, they have contrasting activity in the presence of light with most BphPs being active in the dark. The molecular mechanism that explains bacterial and plant phytochrome signaling has not been well understood due to limited structures of full-length phytochromes with enzymatic domain resolved at or near atomic resolution in both Pr and Pfr states. Here, we report the first Cryo-EM structures of a wild-type bacterial phytochrome with a HK enzymatic domain, determined in both Pr and Pfr states, between 3.75 and 4.13 Å resolution, respectively. Furthermore, we capture a distinct Pr/Pfr heterodimer of the same protein as potential signal transduction intermediate at 3.75 Å resolution. Our three Cryo-EM structures of the distinct signaling states of BphPs are further reinforced by Cryo-EM structures of the truncated PCM of the same protein determined for the Pr/Pfr heterodimer as well as Pfr state. These structures provide insight into the different light-signaling mechanisms that could explain how bacteria and plants see the light.
Genetic modification ofCandida maltosa, a nonpathogenic CTG species, revealsEFG1function
Authors: Chávez-Tinoco Marco , García-Ortega Luis F. , Mancera Eugenio
Published: November 2023

Candida maltosais closely related to important pathogenicCandidaspecies, but it has been rarely isolated from humans. Therefore, through comparative studies, it could be a powerful model to understand the pathogenicity underpinnings ofCandidaspecies. To facilitate studyingC. maltosaat a molecular level, we built a cohesive genomic sequence composed of 45 scaffolds, a substantial improvement from the thousands of contigs of the available draft. Comparison withC. albicansandC. tropicalisrevealed a reduction in the total number of genes inC. maltosa. However, gene loss seems not to be associated to its avirulence given that most pathogenicity genes were also present inC. maltosa. To genetically editC. maltosawe generated triple auxotrophic strains so that gene deletions can be performed as has been routinely done in pathogenic species. As a proof of concept, we generated gene knockouts of Efg1, a transcription regulator involved in filamentation and biofilm formation in pathogenic species. Although inC. maltosaEfg1 also played a role in these processes, it seems to rather be a repressor of filamentation. The genome assembly and auxotrophic mutants developed are a key step to start usingC. maltosafor comparative studies at a molecular level.
The HIV-1 capsid serves as a nanoscale reaction vessel for reverse transcription
Authors: Jennings Jordan , Bracey Harrison , Nguyen Danny T. , Dasgupta Rishav , Rivera Alondra Vázquez , Sluis-Cremer Nicolas , Shi Jiong , Aiken Christopher
Published: November 2023

The viral capsid performs critical functions during HIV-1 infection and is a validated target for antiviral therapy. Previous studies have established that the proper structure and stability of the capsid are required for efficient HIV-1 reverse transcription in target cells. Moreover, it has recently been demonstrated that permeabilized virions and purified HIV-1 cores undergo efficient reverse transcription in vitro when the capsid is stabilized by addition of the host cell metabolite inositol hexakisphosphate (IP6). However, the molecular mechanism by which the capsid promotes reverse transcription is undefined. Here we show that wild type HIV-1 particles can undergo efficient reverse transcriptionin vitroin the absence of a membrane-permeabilizing agent. This activity, originally termed “natural endogenous reverse transcription” (NERT), depends on expression of the viral envelope glycoprotein during virus assembly and its incorporation into virions. Truncation of the gp41 cytoplasmic tail markedly reduced NERT activity, indicating that gp41 permits the entry of nucleotides into virions. Protease treatment of virions markedly reduced NERT suggesting the presence of a proteinaceous membrane channel. By contrast to reverse transcription in permeabilized virions, NERT required neither the addition of IP6 nor a mature capsid, indicating that an intact viral membrane can substitute for the function of the viral capsid during reverse transcriptionin vitro. Collectively, these results demonstrate that the viral capsid functions as a nanoscale container for reverse transcription during HIV-1 infection.
Empowering Healthcare Professionals in West Africa □ A Feasibility Study and Qualitative Assessment of a Dietary Screening Tool to Identify Adults at High Risk of Hypertension
Authors: Batubo Nimisoere P. , Nwanze Nnenna M. , Alikor Chizindu A. , Auma Carolyn I. , Moore J. Bernadette , Zulyniak Michael A.
Published: November 2023

Background

Dietary risks significantly contribute to hypertension in Nigeria. Food frequency questionnaires (FFQs) can provide valuable dietary assessment but require rigorous validation and careful design to facilitate usability. This study assessed the feasibility and potential effectiveness of implementing a clinical screening tool for identifying adults at high risk of hypertension in West Africa.

Materials and methods

58 consenting adult patients with hypertension and their caregivers and 35 healthcare professionals from a single-centre Nigerian hospital were recruited to complete a 27-item FFQ at two-time points and three 24-hour recalls for comparison in a mixed method study employing both quantitative questionnaires and qualitative techniques to elicit free form text. Data analyses were conducted using R software version 4.3.1 and NVivo version 14. The trial was registered withClinicalTrials.gov:NCT05973760.

Results

The mean age of patients was 42.6 ± 11.9 years, with an average SBP of 140.3 ± 29.8 mmHg and a BMI of 29.5 ± 7.1 Kg/m2. The adherence rate was 87.9%, and the mean completion time was 7:37 minutes. 96.6% of patients found the FFQ easy to complete, comprehensive, and valuable. A minority reported difficulty (3.4%), discomfort (10.3%), and proposed additional foods (6.9%). Healthcare professionals considered the screening tool very important (82.9%) and expressed a willingness to adopt the tool, with some suggestions for clarification. Patients and healthcare professionals found the screening tool favourable for nutritional counselling in hypertension care.

Conclusion

The tailored screening tool (FFQ) demonstrated promising feasibility for integration into clinical care as assessed by patients and healthcare professionals. Successful implementation may benefit from proactive time management and addressing training needs. This user-centred approach provided key insights to refine FFQ and set the foundation for ongoing validity testing and evaluation in clinical practice.
ABCA4-Related Retinopathies in Lebanon: a novel mutation and significant heterogeneity
Authors: Ibrahim Mariam , Jaffal Lama , Assi Alexandre , Helou Charles , El Shamieh Said
Published: November 2023

Mutations inATP-binding cassette transporter type A4(ABCA4) have been linked to several forms of inherited retinal diseases (IRDs) besides the classically defined Stargardt disease (STGD), known asABCA4retinopathies.ABCA4is a sizeable locus harboring 50 exons; thus, its analysis has revealed a rich area of genetic information comprising at least 1,200 disease-causing mutations of varied severity and types. Due to the clinical and genetic heterogeneity, diagnosingABCA4retinopathies is challenging. To date, noABCA4-retinopathy has been detected in Lebanon. Using next-generation sequencing, we sought to pinpoint the mutation spectrum in seven families with different forms of IRDs: STGD, rod-cone and cone-rod dystrophies (RCD and CRD, respectively). EightABCA4mutations were found, including one novel; c.4330G>C; p.(Trp1408Cys). Three families were diagnosed with CRD, two with STGD, and two others with RCD. In conclusion, our study revealed a novel ABCA4 mutation and showed significant genotypic and phenotypic heterogeneity in Lebanon.
Post-Vaccination Syndrome: A Descriptive Analysis of Reported Symptoms and Patient Experiences After Covid-19 Immunization
Authors: Krumholz Harlan M. , Wu Yilun , Sawano Mitsuaki , Shah Rishi , Zhou Tianna , Arun Adith S. , Khosla Pavan , Kaleem Shayaan , Vashist Anushree , Bhattacharjee Bornali , Ding Qinglan , Lu Yuan , Caraballo César , Warner Frederick , Huang Chenxi , Herrin Jeph , Putrino David , Hertz Danice , Dressen Brianne , Iwasaki Akiko
Published: November 2023

Introduction

A chronic post-vaccination syndrome (PVS) after covid-19 vaccination has been reported but has yet to be well characterized.

Methods

We included 241 individuals aged 18 and older who self-reported PVS after covid-19 vaccination and who joined the online Yale Listen to Immune, Symptom and Treatment Experiences Now (LISTEN) Study from May 2022 to July 2023. We summarized their demographics, health status, symptoms, treatments tried, and overall experience.

Results

The median age of participants was 46 years (interquartile range [IQR]: 38 to 56), with 192 (80%) identifying as female, 209 (87%) as non-Hispanic White, and 211 (88%) from the United States. Among these participants with PVS, 127 (55%) had received the BNT162b2 [Pfizer-BioNTech] vaccine, and 86 (37%) received the mRNA-1273 [Moderna] vaccine. The median time from the day of index vaccination to symptom onset was three days (IQR: 1 day to 8 days). The time from vaccination to symptom survey completion was 595 days (IQR: 417 to 661 days). The median Euro-QoL visual analogue scale score was 50 (IQR: 39 to 70). The five most common symptoms were exercise intolerance (71%), excessive fatigue (69%), numbness (63%), brain fog (63%), and neuropathy (63%). In the week before survey completion, participants reported feeling unease (93%), fearfulness (82%), and overwhelmed by worries (81%), as well as feelings of helplessness (80%), anxiety (76%), depression (76%), hopelessness (72%), and worthlessness (49%) at least once. Participants reported a median of 20 (IQR: 13 to 30) interventions to treat their condition.

Conclusions

In this study, individuals who reported PVS after covid-19 vaccination had low health status, high symptom burden, and high psychosocial stress despite trying many treatments. There is a need for continued investigation to understand and treat this condition.
Collateral effects of the COVID-19 pandemic on endocrine treatments for breast and prostate cancer in the UK: implications for bone health
Authors: Barclay Nicola L , Català Marti , Jödicke Annika M. , Prieto-Alhambra Daniel , Newby Danielle , Delmestri Antonella , Man Wai Yi , Serrano Àlvar Roselló , Moncusí Marta Pineda ,   The OPTIMA Consortium
Published: November 2023

Background

The COVID-19 pandemic affected cancer screening, diagnosis and treatment pathways. This study examined the impact of the pandemic on incidence and trends of endocrine treatments in patients with breast or prostate cancer; and endocrine treatment-related side-effects.

Methods

Population-based cohort study using UK primary care Clinical Practice Research Datalink (CPRD) GOLD database. There were 13,701 newly diagnosed breast cancer patients and 12,221 prostate cancer patients with ≥1-year data availability since diagnosis between January 2017-June 2022. Incidence rates (IR) and incidence rate ratios (IRR) were calculated across multiple time periods before and after lockdown to examine the impact of changing social restrictions on endocrine treatments and treatment-related outcomes, including osteopenia, osteoporosis and bisphosphonate prescriptions.

Results

In patients with breast cancer, aromatase inhibitor prescriptions increased during lockdown compared to pre-pandemic (IRR: 1.22 [95% Confidence Interval: 1.11-1.34]), followed by a decrease post-first lockdown (IRR: 0.79 [95%CI: 0.69-0.89]). In patients with prostate cancer, first-generation antiandrogen prescriptions increased compared to pre-pandemic (IRR: 1.23 [95% CI: 1.08-1.4]). For breast cancer patients on aromatase inhibitors, diagnoses of osteopenia, osteoporosis and bisphosphonate prescriptions were reduced across all lockdown periods compared to pre-pandemic (IRR range: 0.31-0.62).

Conclusion

During the first two years of the pandemic, newly diagnosed breast and prostate cancer patients were prescribed more endocrine treatments compared to pre-pandemic, due to restrictions on hospital procedures replacing surgeries with bridging therapies. But breast cancer patients had fewer diagnoses of osteopenia and osteoporosis, and bisphosphonate prescriptions. These patients should be followed up in the coming years for signs of bone thinning. Evidence of poorer management of treatment-related side-effects will allow us to determine whether there is a need to better allocate resources to patients at high risk for bone-related complications.
Faltering mortality improvements at young-middle ages in high-income English-speaking countries
Authors: Timonin Sergey , Leon David A. , Banks Emily , Adair Tim , Canudas-Romo Vladimir
Published: November 2023

Background

Before the COVID-19 pandemic, stagnating life expectancy trends were reported in some high-income countries (HICs). Despite previous evidence from country-specific studies, there is a lack of comparative research that provides a broader perspective and challenges existing assumptions. This study aims to examine longevity trends and patterns in six English-speaking countries (Australia, Canada, Ireland, New Zealand, UK, USA) by combining period and cohort perspectives and to compare them with other HICs.

Methods

Using data from the Human Mortality and WHO Mortality Databases, we estimated partial life expectancy, lifespan inequality and cohort survival differences for 1970-2021, as well as the contribution of causes of death to the gap in life expectancy between English-speaking countries and the average for other HICs in 2017-19.

Results

In the pre-pandemic period, the increase in life expectancy slowed in all English-speaking countries, except Ireland, mainly due to stagnating or rising mortality at young-middle ages. Relative to other HICs, those born in Anglophone countries since the 1970s experienced relative survival disadvantage, largely attributable to injuries (mainly suicides) and substance-related mortality (mainly poisonings). In contrast, older cohorts enjoyed advantages for females in Australia and Canada and for males in all English-speaking countries except the USA.

Conclusions

Although future gains in life expectancy in wealthy societies will increasingly depend on reducing mortality at older ages, adverse health trends at younger ages are a cause for concern. This emerging and avoidable threat to health equity in English-speaking countries should be the focus of further research and policy action.

Key messages

The study highlights striking similarities between English-speaking high-income countries in terms of adverse health outcomes at young-middle ages compared to a group of other high-income countries (HICs).

Each of the Anglophone populations has experienced a marked mortality disadvantage for cohorts born since the early 1970s relative to the average of other HICs, which contrasts with the generally better performance of the older cohorts in some English-speaking countries, particularly for men.

In the most recent pre-pandemic period, i.e. 2017-19, the negative contribution of higher mortality at ages below 50 years to the gap in life expectancy at birth between English-speaking countries (excluding Ireland) and other HICs ranged from 0.15 years for Australian women to 2.06 years for US men.
Sensory kinase KdpD is a tandem serine histidine kinase controlling K+pump KdpFABC on the translational and post-transcriptional level
Authors: Silberberg Jakob M , Ketter Sophie , Böhm Paul JN , Jordan Kristin , Wittenberg Marcel , Grass Julia , Hänelt Inga
Published: November 2023

Two-component systems (TCSs), consisting of a histidine kinase (HK) and a response regulator, serve signal transduction in bacteria, often regulating transcription in response to environmental stimuli. Here, we identify a tandem serine histidine kinase function for KdpD, previously described as a HK of the TCS KdpDE, which controls production of the K+pump KdpFABC. We show that KdpD additionally mediates an inhibitory serine phosphorylation of KdpFABC at high K+levels, using not its C-terminal HK domain but an N-terminal atypical serine kinase (ASK) domain. Sequence analysis of KdpDs from different species highlights that some KdpDs comprise solely ASK and Usp domains. We show that, whileEscherichia coliKdpD’s ASK responds directly to K+levels, a shorter version fromDeinococcus geothermalisis controlled by second messenger cyclic di-AMP. Our findings add to the growing functional diversity of sensor kinases while simultaneously expanding the framework for regulatory mechanisms in bacterial K+homeostasis.
Interneuron migration defects during corticogenesis contribute toDyrk1ahaploinsufficiency syndrome pathogenesis via actomyosin dynamics deregulations
Authors: Hinckelmann Maria Victoria , Dubos Aline , Artot Victorine , Rudolf Gabrielle , Nguyen Thu Lan , Tilly Peggy , Nalesso Valérie , del Mar Muniz Moreno Maria , Birling Marie-Christine , Godin Juliette D. , Brault Véronique , Herault Yann
Published: November 2023

Interneuron development is a crucial step of brain corticogenesis. When affected it often leads to brain dysfunctions, such as epilepsy, intellectual disabilities and autism spectrum disorder. Such defects are observed in theDYRK1A-haploinsufficiency syndrome, caused by mutations ofDYRK1A, and commonly associated to cortical excitatory/inhibitory imbalance. However, how this imbalance is established in this syndrome remains elusive. Here, using mouse models and live imaging, we show thatDyrk1aspecifically regulates the development of the cortical GABAergic system. Unlike projection excitatory neurons, we demonstrate that interneuron tangential migration relies on Dyrk1a dosage and kinase activity through a mechanism involving actomyosin cytoskeleton remodeling. Interestingly, we further demonstrate that mice with heterozygous inactivation ofDyrk1ain interneurons show behavioral defects and epileptic activity, recapitulating phenotypes observed in human patients. Altogether, these data highlight the critical role ofDyrk1ain the development of the GABAergic system and the pathophysiology ofDYRK1A-haploinsufficiency syndrome.
Dynamic extracellular proximal interaction profiling reveals Low-Density Lipoprotein Receptor as a new Epidermal Growth Factor signaling pathway component
Authors: Al Mismar Rasha , Samavarchi-Tehrani Payman , Seale Brendon , Kasmaeifar Vesal , Martin Claire E. , Gingras Anne-Claude
Published: November 2023

Plasma membrane proteins are critical mediators of cell-cell and cell-environment interactions, pivotal in intracellular signal transmission vital for cellular functionality. Proximity-dependent biotinylation approaches such as BioID combined with mass spectrometry have begun illuminating the landscape of proximal protein interactions within intracellular compartments. However, their deployment in studies of the extracellular environment remains scarce. Here, we present extracellular TurboID (ecTurboID), a method designed to profile cell surface interactions in living cells on short timescales. We first report on the careful optimization of experimental and data analysis strategies that enable the capture of extracellular protein interaction information. Leveraging the ecTurboID technique, we unveiled the proximal interactome of multiple plasma membrane proteins, notably the epidermal growth factor receptor (EGFR). This led to identifying the low-density lipoprotein receptor (LDLR) as a newfound extracellular protein associating with EGFR, contingent upon the presence of the EGF ligand. We showed that 15 minutes of EGF stimulation induced LDLR localization to the plasma membrane to associate with proteins involved in EGFR regulation. This modified proximity labelling methodology allows us to dynamically study the associations between plasma membrane proteins in the extracellular environment.

One Sentence Summary

We developed extracellular TurboID (ecTurboID) as a new proximity dependent biotinylation approach that can capture dynamic interactions at the cell surface, identifying Low-Density Lipoprotein Receptor as a new ligand-dependent extracellular partner of Epidermal Growth Factor Receptor.
Fibroblast Nrf2 inhibits profibrotic transcription with Ddx54 and mitigates pathological fibrosis in the mouse heart and kidney
Authors: Nishiji Toshiyuki , Hoshino Atsushi , IKemura Nariko , Alcantara Mellissa C , Higuchi Yusuke , Uchio Yuki , Kirita Yuhei , Taminishi Shunta , Ozaki Yuki , Motooka Daisuke , Kobayashi Ryosuke , Horii Takuro , Hatada Izuho , Matoba Satoaki
Published: November 2023

Background

Tissue fibrosis is a common feature of many organ dysfunctions, such as heart failure and chronic kidney disease. However, no fundamental treatment has been developed. This study aims to identify novel molecular mechanisms for antifibrotic intervention, focusing on fibroblast activation.

Methods

We performed a forward genetic screen using a genome-wide CRISPR library in the context of transforming growth factor β (TGF-β)-mediated connective tissue growth factor (CTGF) expression, and used unbiased techniques such as Cleavage Under Targets and Tagmentation (CUT&Tag) and proximity-dependent biotin labeling by TurboID to reveal the detailed molecular mechanisms.

Results

CRISPR library screening identified a number of players in both the canonical Smad pathway and the non-canonical pathway. In addition to the known factors, the Keap1-Nrf2 pathway was identified as a predominant regulator of TGF-β-mediated CTGF expression.Keap1deletion and consequent Nrf2 activation broadly suppressed profibrotic gene expression, independently of conventional antioxidant effects. CUT&Tag revealed that Nrf2 bound to the proximity of fibrosis-related genes includingCtgfandFn1.Subsequent individual analysis revealed Smad3 and RNA polymerase II binding to the Nrf2 peak site, which was attenuated byKeap1deletion. TurboID experiments further discovered that Nrf2 interacts with Ddx54, which acts as a corepressor. Consistently,Keap1deletion-mediated repression of profibrotic gene expression was reversed by additionalDdx54deletion. The impact of the Keap1-Nrf2 pathway on pathological fibrosis was examined using tamoxifen-inducible fibroblast-specificKeap1knockout mice. Pressure overload for 4 weeks robustly induced cardiac hypertrophy, fibrosis and contractile dysfunction. However, deletion ofKeap1in thePostnlineage attenuated these cardiac pathologies. The anti-fibrotic effects of Keap1 deletion were also confirmed in renal fibrosis in the unilateral ureteral obstruction (UUO) model.

Conclusions

Fibroblast Nrf2 transcriptionally represses fibrosis-related genes in cooperation with the corepressor Ddx54. Fibroblast-specific deletion ofKeap1attenuated pathological fibrosis in pressure overload heart failure and renal fibrosis.
An elevated rate of whole-genome duplications associated with carcinogen exposure in Black cancer patients
Authors: Brown Leanne M. , Hagenson Ryan A. , Koklič Tilen , Urbančič Iztok , Strancar Janez , Sheltzer Jason M.
Published: November 2023

In the United States, Black individuals have higher rates of cancer mortality than any other racial or ethnic group. The sources of these significant racial disparities are not fully understood, and may include social, environmental, and genetic factors that influence cancer onset, diagnosis, and treatment. Here, we examined genomic data from several large-scale cancer patient cohorts to search for racial associations in chromosome copy number alterations. We found that tumors from self-reported Black patients were significantly more likely to exhibit whole-genome duplications (WGDs), a genomic event that enhances metastasis and aggressive disease, compared to tumors from self-reported white patients. Among patients with WGD-positive cancers, there was no significant difference in survival between self-reported Black and white patients, suggesting that the increased incidence of WGD events could contribute to the disparities in patient outcome. We further demonstrate that combustion byproducts are capable of driving genome-duplication events in cell culture, and cancers from self-reported Black patients exhibit mutational patterns consistent with increased exposure to these carcinogens. In total, these findings identify a class of genomic alterations that are associated with environmental exposures and that may influence racial disparities in cancer patient outcome. Additionally, as cancers that have undergone WGD events exhibit unique genetic vulnerabilities, therapies that selectively target WGD-positive cancers may be particularly effective at treating aggressive malignancies in Black patients.
Ocrelizumab B cell depletion has no effect on HERV RNA expression in PBMC in MS patients
Authors: Tarlinton Rachael , Tanasescu Radu , Shannon-Lowe Claire , Gran Bruno
Published: November 2023

Background

Epstein Barr Virus (EBV) infection of B cells is now understood to be one of the triggering events for the development of Multiple Sclerosis (MS), a progressive immune-mediated disease of the central nervous system. EBV infection is also linked to expression of Human endogenous retroviruses (HERVs) of the HERV-W group, a further risk factor for the development of MS (Ocrelizumab is a high-potency disease-modifying treatment (DMT) for MS, which depletes B cells by targeting CD20.

Objectives

We studied the effects of ocrelizumab on gene expression in peripheral blood mononuclear cells (PBMC) from paired samples from 20 patients taken prior to and 6 months after beginning Ocrelizumab therapy. We hypothesised that EBV and HERV-W loads would be lower in post-treatment samples.

Methods

Samples were collected in Paxgene tubes, subject to RNA extraction and Illumina paired end short read mRNA sequencing with mapping of sequence reads to the human genome using Salmon and Differential Gene expression compared with DeSeq2. Mapping was also performed separately to the HERV-D database of HERV sequences and the EBV reference sequence.

Results

Patient samples were more strongly clustered by individual rather than disease type (relapsing/remitting or primary progressive), treatment (pre and post), age, or sex. Fourteen genes, all clearly linked to B cell function were significantly down regulated in the post treatment samples. Interestingly only one pre-treatment sample had detectable EBV RNA and there were no significant differences in HERV expression (of any group) between pre- and post-treatment samples.

Conclusions

While EBV and HERV expression are clearly linked to triggering MS pathogenesis, it does not appear that high level expression of these viruses is a part of the ongoing disease process or that changes in virus load are associated with Ocrelizumab treatment.
Investigation of the mechanical work during ultrasonic fatigue loading using pulsed time-resolved X-ray diffraction
Authors: Jacquemain Vincent , Cheuleu Christophe , Ranc Nicolas , Castelnau Olivier , Michel Vincent , Vinci Doriana , Favier Véronique , Mocuta Cristian , Thiaudiere Dominique
Published: November 2023

In the energy production and transportation industries, numerous metallic structures may be subjected to at least several billions of cycles, i.e. loaded in the very high cycle fatigue domain (VHCF). Therefore, to design structures in the VHCF domain, a reliable methodology is necessary. One useful quantity to characterize plastic activity at the microscopic scale and fatigue damage evolution is the mechanical work supplied to a material. However, the estimation of this mechanical work in a metal during ultrasonic fatigue tests remains challenging. This paper aims to present an innovative methodology to quantify this. An experimental procedure was developed to estimate the mechanical work from stress and total strain evolution measurements during one loading cycle with a time accuracy of about 50 ns. This was achieved by conducting time-resolved X-ray diffraction coupled to strain gauge measurements at a synchrotron facility working in pulsed mode (single-bunch mode).
tomoCAM: fast model-based iterative reconstruction via GPU acceleration and non-uniform fast Fourier transforms
Authors: Kumar Dinesh , Parkinson Dilworth Y. , Donatelli Jeffrey J.
Published: November 2023

X-ray-based computed tomography is a well established technique for determining the three-dimensional structure of an object from its two-dimensional projections. In the past few decades, there have been significant advancements in the brightness and detector technology of tomography instruments at synchrotron sources. These advancements have led to the emergence of new observations and discoveries, with improved capabilities such as faster frame rates, larger fields of view, higher resolution and higher dimensionality. These advancements have enabled the material science community to expand the scope of tomographic measurements towards increasingly in situ and in operando measurements. In these new experiments, samples can be rapidly evolving, have complex geometries and restrictions on the field of view, limiting the number of projections that can be collected. In such cases, standard filtered back-projection often results in poor quality reconstructions. Iterative reconstruction algorithms, such as model-based iterative reconstructions (MBIR), have demonstrated considerable success in producing high-quality reconstructions under such restrictions, but typically require high-performance computing resources with hundreds of compute nodes to solve the problem in a reasonable time. Here, tomoCAM, is introduced, a new GPU-accelerated implementation of model-based iterative reconstruction that leverages non-uniform fast Fourier transforms to efficiently compute Radon and back-projection operators and asynchronous memory transfers to maximize the throughput to the GPU memory. The resulting code is significantly faster than traditional MBIR codes and delivers the reconstructive improvement offered by MBIR with affordable computing time and resources. tomoCAM has a Python front-end, allowing access from Jupyter-based frameworks, providing straightforward integration into existing workflows at synchrotron facilities.
Agricultural value chain participation and farmers' access to credit in northern Ghana
Authors: Osei Timothy Anakwa , Donkoh Samuel A. , Ansah Isaac Gershon Kodwo , Awuni Joseph A. , Cobbinah Mensah Tawiah
Published: November 2023

Purpose

Promoted for its inclusivity, agricultural value chain (AVC) financing leverages social capital and mechanisms such as off-take agreements and forward contracts to reduce borrowing and lending costs and risks for both farmers and lending institutions. AVC financing has been defined as the flow of financial products and services to and among the various actors within the AVC to address constraints of production and distribution and fulfill the needs of those involved in the chain by reducing risk and improving efficiency. This paper investigates how farmers' involvement in AVC affects their access to credit.

Design/methodology/approach

The authors collected primary data from 400 crop farmers in northern Ghana through a semi-structured questionnaire and analyzed the data, using the multinomial endogenous switching regression model.

Findings

Joint participation in AVC increased the amount of formal and informal credit received by 64 and 78%, respectively, compared to nonparticipation. Similarly, participation in AVC horizontal linkage and AVC vertical linkage increased the amount of formal and informal credit received by 40 and 47% and 46 and 74%, respectively, compared to nonparticipation. Irrigation farming, extension visits, knowledge of AVC in the community, access to a storage facility and trust in contract farming significantly influenced farmers' participation in AVC.

Originality/value

The authors’ work offers valuable insights into how different dimensions of value chain participation can impact smallholder farmers' access to credit. This work also underscores the importance of considering both formal and informal credit sources when analyzing the outcomes of value chain participation. The findings could enable formal financial providers to identify, liaise and/or resource informal financial players such as value chain actors to supply both formal and informal credit to farmers in AVCs.
Factors that affect the application of integrated report in listed companies in Vietnam
Authors: Kim Vu Anh Thi , Bui Ngoc Thi , Tran Du Thi
Published: November 2023

Purpose

This study aims to apply the theory of planned behavior, the theory of stakeholders, the theory of technology acceptance to evaluate the factors that affect the application of integrated reporting in Vietnamese listed companies.

Design/methodology/approach

Quantitative research method was used through survey questionnaire. Research data is collected from 144 directors, accountants, administrators of companies listed on Vietnam stock market in the period 2020–2022. Multivariable regression analysis is performed with three independent variables: usefulness, ease of use and environmental influence. Dependent variable is intended to apply integrated report.

Findings

Research results show that all independent variables have a positive impact on the dependent variable. In particular, the environment influence variable has the largest impact (0.443), followed by the level of impact of Usefulness” variable and “Ease of use” variable are 0.243 and 0.241, respectively. The regression model manages to explain 52.8% of the impact of the factors on the application of integrated reports. An analysis of the differences between groups of enterprises by staff size and capital size is carried out, the results hereof show that large enterprises tend to apply more integrated reporting. From the research results, the authors propose recommendations to promote the application of integrated reporting in Vietnamese enterprises to gradually improve the quality of information disclosure, attract investment and accelerate international economic integration.

Originality/value

The study evaluates the current situation of integrated reporting of Vietnamese companies to understand the factors affecting the use of integrated reporting, from which to propose recommendations to promote the application of integrated reporting in Vietnamese enterprises to gradually improve the quality of information disclosure, attract investment and accelerate international economic integration.
Factors influencing consumers' continued use of food delivery apps in the post-pandemic era: insights from Saudi Arabia
Authors: Abed Salma S.
Published: November 2023

Purpose

This research empirically studies consumers' continued intention to use mobile food delivery applications (apps) during the post-pandemic era in Saudi Arabia.

Design/methodology/approach

Using the unified theory of adoption and use of technology 2 (UTAUT2) as a theoretical model, this study collected data from a survey of 304 Saudi Arabian consumers. Structural equation modelling (SEM) was used to examine the proposed model and its hypotheses.

Findings

Social influence and performance expectancy (PE) had the strongest effects on the intention to continue using mobile food delivery apps in the post-pandemic era. In addition, effort expectancy (EE) significantly influenced PE regarding the adoption of food delivery apps. Meanwhile, EE was not an important predictor of the continued intention to use mobile food delivery apps in Saudi Arabia.

Originality/value

This study enriches the literature on consumers' continued intention to use food delivery apps in the post-pandemic era, a subject that has rarely been studied. In addition, this study expands the theoretical potential of the UTAUT2 model by examining the role of trust in continued intention and the effect of PE on EE in the adoption of food delivery apps during the post-pandemic era in Saudi Arabia.