bluuebunny/crossref_metadata_2025 huggingface dataset:
Dendrite architecture determines mitochondrial distribution patterns in vivo
Authors: Donovan Eavan J. , Agrawal Anamika , Liberman Nicole , Kalai Jordan I. , Chua Nicholas J. , Koslover Elena F. , Barnhart Erin L.
Published: July 2022

Mitochondria are critical for neuronal function and must be reliably distributed through complex neuronal architectures. By quantifying in vivo mitochondrial transport and localization patterns in the dendrites of Drosophila visual system neurons, we show that mitochondria make up a dynamic system at steady-state, with significant transport of individual mitochondria within a stable global pattern. Mitochondrial motility patterns are unaffected by visual input, suggesting that neuronal activity does not directly regulate mitochondrial localization in vivo. Instead, we present a mathematical model in which four simple scaling rules enable the robust self-organization of the mitochondrial population. Experimental measurements of dendrite morphology validate key model predictions: to maintain equitable distribution of mitochondria across asymmetrically branched subtrees, dendritic branch points obey a parent-daughter power law that preserves cross-sectional area, and thicker trunks support proportionally bushier subtrees. Altogether, we propose that “housekeeping” requirements, including the need to maintain steady-state mitochondrial distributions, impose constraints on neuronal architecture.
Multi-scale Assessment of Brain Blood Volume and Perfusion in the APP/PS1 Mouse Model of Amyloidosis
Authors: Munting Leon P , Derieppe Marc PP , Voortman Lenard M , Khmelinskii Artem , Suidgeest Ernst , Hirschler Lydiane , Barbier Emmanuel L , de Senneville Baudouin Denis , van der Weerd Louise
Published: July 2022

Vascular dysfunction is increasingly recognized to play a role in the development of Alzheimer’s disease (AD). The relation between vascular dysfunction and the neuropathological amyloid β accumulation characteristic for AD is however unclear. The limited resolution of in vivo imaging techniques, the intricate 3D structure of the microvasculature and the different co-occurring types of amyloid β accumulation in patients hamper studying this relation in patients. Here, we therefore employed the APP/PS1 mouse model, which develops parenchymal amyloid β plaques, to study the effect of parenchymal amyloid β plaques on the structure and function of the vasculature. Blood vessels and amyloid β plaques were fluorescently labeled in vivo with lectin-DyLight594 and methoxy XO4, respectively, in APP/PS1 mice at old age. The brain tissue was cleared post-mortem with the CUBIC clearing protocol, which allowed structural imaging at microscopic resolution of the vessels and plaques in a large 3D volume. Segmentation of the vasculature enabled mapping of the microvascular Cerebral Blood Volume (mCBV), which ranged from 2 % to 5 % in the white matter and the thalamus, respectively. No mCBV differences were observed between APP/PS1 mice and wild type (WT) control mice. The effect of the amyloid β plaques on vascular function was studied in vivo by measuring Cerebral Blood Flow (CBF) and Arterial Transit Time (ATT) with Arterial Spin Labeling (ASL) MRI. Similar to the mCBV findings, no differences were observed in CBF or ATT between APP/PS1 and control mice, indicating that brain vascular morphology and function in this mouse model are preserved in the presence of amyloid β plaques.
Droplet-based microfluidics as a media optimization tool for cyanobacteria
Authors: Cao Jialan , Russo David A. , Xie Ting , Groß G. Alexander , Zedler Julie A. Z.
Published: July 2022

The urgent need to increase sustainability in biotechnology has led to an increased interest in photosynthetic production platforms. Cyanobacteria are particularly attractive for their fast photoautotrophic growth and genetic accessibility. However, the lack of systematic strain optimization is holding back progress towards industrialization. To overcome this bottleneck, here we introduce a droplet-based microfluidics platform capable of one- (1D) and two-dimension (2D) screening of key parameters in cyanobacterial cultivation. We successfully grew three different unicellular, biotechnologically relevant cyanobacteria: Synechocystis sp. PCC 6803, Synechococcus elongatus UTEX 2973 and Synechococcus sp. UTEX 3154. Highly-resolved 1D screening of nitrate, phosphate, carbonate, and salt content show that nitrate and/or phosphate can be limiting in standard cultivation media. Finally, we show that 2D screening results from our microfluidic setup translate well to a laboratory scale high-density cultivation setup. This study demonstrates that droplet-based microfluidics by micro segmented-flow are a powerful tool for nanoscale high-throughput optimization of cyanobacterial cultivation.
A mutant bacterial O-GlcNAcase visualizes a progressive decline of protein O-GlcNAcylation in early Drosophila embryos critical for neurodevelopment
Authors: Zhang Yaowen , Wang Dandan , Yu Haibin , Lei Xiaoyun , Meng Yang , Zhang Na , Chen Fang , Lv Lu , Pan Qian , Qin Hongtao , Zhang Zhuohua , van Aalten Daan M.F. , Yuan Kai
Published: July 2022

Protein O-GlcNAcylation, a monosaccharide posttranslational modification maintained by two evolutionarily conserved enzymes, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), is a major nutrient sensor integrating key metabolic pathways. While mutations in OGT have recently been associated with neurodevelopmental disorders, the dynamics and function of protein O-GlcNAcylation during early embryogenesis remain elusive. Here we develop a new fluorescent probe to visualize O-GlcNAcylation levels in live Drosophila early embryos. Our study shows that protein O-GlcNAcylation declines as the embryos develop to the mid-blastula transition when the facultative heterochromatin makes its first appearance. Lowering O-GlcNAcylation levels by exogenous OGA activity promotes the polycomb group O-GlcNAc protein Polyhomeotic (Ph) to form nuclear foci and K27 trimethylation of histone H3. This enhanced facultative heterochromatin formation fine-tunes the expression of several neurodevelopmental genes including short of gastrulation (sog). We provide evidence that perturbation of O-GlcNAcylation during early embryogenesis affects learning ability in adulthood, highlighting the importance of O-GlcNAcylation homeostasis for the development of the nervous system.
Trans-ancestry meta-analysis improves performance of genetic scores for multiple adiposity-related traits in East Asian populations
Authors: Fairhurst-Hunter Zammy , Lin Kuang , Millwood Iona Y , Pozarickij Alfred , Chen Tzu-Ting , Torres Jason M. , Lun Jian-an , Kartsonaki Christiana , Gan Wei , Mahajan Anubha , Du Huaidong , Sohoni Rajani , Guo Yu , Sansome Sam , Yang Ling , Yu Canqing , Chen Yiping , Lv Jun , Hemani Gibran , Koido Masaru , Kamatani Yoichiro , Spracklen Cassandra N. , Gordon-Larsen Penny , Koprulu Mine , Meng Xiangrui , Kuchenbaecker Karoline , Fatumo Segun , Bhatta Laxmi , Brumpton Ben , Alegre-Díaz Jesús , Kuri-Morales Pablo , Tapia-Conyer Roberto , Graham Sarah E. , Willer Cristen J. , Neville Matt J. , Karpe Fredrik , Graff Mariaelisa , North Kari E , Loos Ruth J.F. , Haiman Christopher A. , Peters Ulrike , Buskye Steve , Gignoux Christopher R. , Wojcik Genevieve , Ling Yen-Fen , Li Liming , McCarthy Mark I , Chen Zhengming , Holmes Michael V , Walters Robin G
Published: July 2022

Genome-wide association studies (GWAS) in predominately European-ancestry (EUR) populations have identified numerous genetic variants associated with adiposity-related traits. An emerging challenge is the limited transferability of genetic scores constructed based on GWAS results from one ancestry for trait prediction in other ancestries. We performed trans-ancestry meta-analysis (TAMA) for eight adiposity-related traits using genetic data from 96,124 East Asian (EAS) and 443,359 EUR individuals. We identified >1400 genomic regions significantly associated with one or more traits. Despite EAS comprising only ∼20% of the study population, genetic scores constructed from the trans-ancestry (TA) results accounted for between 30% and 79% more variation in the adiposity traits in EAS compared with scores derived from the EUR GWAS alone. Furthermore, TA scores also modestly improved variance explained in African/African American, Hispanic and South Asian populations. Our findings highlight the utility of TAMA for increasing variance explained by genetic scores across populations of different ancestries.
Real-Time PCR-based diagnosis of human visceral leishmaniasis using urine samples
Authors: Rahim Samiur , Amin Md. Robed , Sharif Mohiuddin , Rahman Mohammad Tariqur , Karim Muhammad Manjurul
Published: July 2022

Background

Diagnosis of visceral leishmaniasis (VL) through the detection of its causative agents namely Leishmania donovani and L. infantum is traditionally based on Giemsa-stained smears of bone marrow, spleen aspirates, liver or lymph node. Collection of these samples involve invasive procedures and carries the risk of fatal hemorrhage especially during splenic aspiration. Earlier, we reported a Polymerase Chain Reaction (PCR)-based diagnosis of L. donovani in peripheral blood using a novel set of PCR primers with absolute specificity (Khatun et al. 2017). Using the same set of primers and PCR conditions, here we describe diagnosis of L. donovani from urine, for a non-invasive, rapid and safe diagnosis.

Methods

Diagnosis of L. donovani was carried out using urine samples collected from clinically diagnosed VL patients (n=23) of Bangladesh in Real Time PCR. Test results were validated by comparing blood samples from the same set of patients. Sensitivity and specificity of this diagnosis was analyzed using retrospective bone marrow samples, collected earlier from confirmed VL patients (n=19) (Khatun et al. 2017).

Results

The method showed 100% sensitivity in detecting VL in urine and corresponding blood samples and bone marrow samples, as well as 100% specificity in control groups.

Conclusion

Urine-based diagnosis could be a patient-friendly, non-invasive approach for VL detection with precision and perfection.
Wheat NAM genes regulate the majority of early monocarpic senescence transcriptional changes including nitrogen remobilisation genes
Authors: Andleeb Tayyaba , Borrill Philippa
Published: July 2022

Senescence enables the remobilisation of nitrogen and micronutrients from vegetative tissues of wheat (Triticum aestivum L.) into the grain. Understanding the molecular players in this process will enable the breeding of wheat lines with tailored grain nutrient content. The NAC transcription factor NAM-B1 is associated with earlier senescence and higher levels of grain protein, iron, and zinc content due to increased nutrient remobilisation. To investigate how related NAM genes control nitrogen remobilization at the molecular level, we carried out a comparative transcriptomic study at seven time points (3, 7, 10, 13, 19 and 26 days after anthesis) in wild type and NAM RNA interference (RNAi) lines with reduced NAM gene expression. Approximately 2.5 times more genes were differentially expressed in WT than NAM RNAi during this early senescence time course (6,508 vs 2,605 genes). In both genotypes, differentially expressed genes were enriched for GO terms related to photosynthesis, hormones, amino acid transport and nitrogen metabolism. However, nitrogen metabolism genes including glutamine synthetase (GS1 and GS2), glutamate decarboxylase (GAD), glutamate dehydrogenase (GDH) and asparagine synthetase (ASN1) showed stronger or earlier differential expression in WT than in NAM RNAi plants, consistent with higher nitrogen remobilisation. The use of time course data identified the dynamics of NAM-regulated and NAM-independent gene expression changes during senescence, and provides an entry point to functionally characterise the pathways regulating senescence and nutrient remobilisation in wheat.
Investigating genetic diversity within the most abundant and prevalent non-pathogenic leaf-associated bacteria interacting with Arabidopsis thaliana in natural habitats
Authors: Ramirez-Sanchez Daniela , Gibelin-Viala Chrystel , Mayjonade Baptiste , Duflos Rémi , Belmonte Elodie , Pailler Vincent , Bartoli Claudia , Carrere Sébastien , Vailleau Fabienne , Roux Fabrice , Vailleau Fabienne
Published: July 2022

Plants interact simultaneously with highly diversified microbes defined as the plant microbiota. Microbiota modulates plant health and appears as a promising lever to develop innovative, sustainable and eco-friendly agro-ecosystems. Key patterns of microbiota assemblages in plants have been revealed by an extensive number of studies based on taxonomic profiling by metabarcoding. However, understanding the functionality of microbiota and identifying the genetic and molecular mechanisms underlying the interplay between plants and their microbiota are still in its infancy and relies on reductionist approaches primarily based on the establishment of representative microbial collections. In Arabidopsis thaliana, most of these microbial collections include one strain per OTU isolated from a limited number of habitats, thereby neglecting the ecological potential of genetic diversity within microbial species to affect the plant-microbiota molecular dialog. With this study, we aimed at estimating the extent of genetic variation between strains within the most abundant and prevalent leaf-associated non-pathogenic bacterial species in 163 natural populations of A. thaliana located south-west of France. By combining a culture-based collection approach consisting of the isolation of more than 7,000 bacterial colonies with an informative-driven approach, we isolated 35 pure strains from eight non-pathogenic bacterial species. We detected significant intra-specific genetic variation at the genomic level and for growth rate in synthetic media. In addition, significant host genetic variation was detected in response to most bacterial strains in in vitro conditions, with the presence of both negative and positive responses on plant growth. Our study provides new genetic and genomic resources for a better understanding of the plant-microbe ecological interactions at the microbiota level. We also highlight the need of considering genetic variation in both non-pathogenic bacterial species and A. thaliana to decipher the genetic and molecular mechanisms involved in the ecologically relevant dialog between hosts and leaf microbiota.
Sleep-dependent structural neuroplasticity after a spatial navigation task: A diffusion imaging study
Authors: Villemonteix Thomas , Guerreri Michele , Deantoni Michele , Balteau Evelyne , Schmidt Christina , Stee Whitney , Zhang Hui , Peigneux Philippe
Published: July 2022

Evidence for sleep-dependent changes in micro-structural neuroplasticity remains scarce, despite the fact that it is a mandatory correlate of the reorganization of learning-related functional networks. We investigated the effects of post-training sleep on structural neuroplasticity markers measuring standard diffusion tensor imaging (DTI) mean diffusivity (MD) and the revised biophysical neurite orientation dispersion and density imaging (NODDI) free water fraction (FWF) and neurite density (NDI) parameters that enable disentangling whether MD changes result from modifications in neurites or in other cellular components (e.g., glial cells). Thirty-four healthy young adults were scanned using diffusion weighted imaging [DWI] on Day1 before and after 40-minutes route learning (navigation) in a virtual environment, then were sleep deprived (SD) or slept normally (RS) for the night. After recovery sleep for 2 nights, they were scanned again (Day4) before and after 40-minutes route learning (navigation) in an extended environment. Sleep-related microstructural changes were computed on DTI (MD) and NODDI (NDI and FWF) parameters in the cortical ribbon and subcortical hippocampal and striatal regions of interest (ROIs). Results disclosed navigation learning-related decreased DWI parameters in the cortical ribbon (MD, FWF) and subcortical (MD, FWF, NDI) areas. Post-learning sleep-related changes were found at Day4 in the extended learning session (pre- to post-relearning percentage changes), suggesting a rapid sleep-related remodelling of neurites and glial cells subtending learning and memory processes in basal ganglia and hippocampal structures.
Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico
Authors: Castelán-Sánchez Hugo G. , Delaye Luis , Inward Rhys P. D. , Dellicour Simon , Gutierrez Bernardo , Martinez de la Vina Natalia , Boukadida Celia , Pybus Oliver G , de Anda Jáuregui Guillermo , Guzmán Plinio , Garrido Flores Marisol , Fontanelli Óscar , Rosales Maribel Hernández , Meneses Amilcar , Olmedo-Alvarez Gabriela , Herrera-Estrella Alfredo , Sanchez-Flores Alejandro , Muñoz-Medina José Esteban , Comas-García Andreu , Gómez-Gil Bruno , Zárate Selene , Taboada Blanca , López Susana , Arias Carlos F. , Kraemer Moritz U.G. , Lazcano Antonio , Escalera-Zamudio Marina
Published: July 2022

Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant lineages that circulated during the first year of local transmission. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in Mexico. Lineages B.1.1.222 and B.1.1.519 exhibited similar dynamics, constituting clades that likely originated in Mexico and persisted for >12 months. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. For the largest B.1.617.2 clades, we further explored viral lineage movements across Mexico. Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.
Assembly of von Willebrand Factor Tubules within VivoHelical Parameters Requires A1 Domain Insertion
Authors: Javitt Gabriel , Fass Deborah
Published: July 2022

The von Willebrand factor (VWF) glycoprotein is stored in tubular form in Weibel-Palade bodies (WPBs) prior to secretion from endothelial cells into the bloodstream. The organization of VWF in the tubules promotes formation of covalently linked VWF polymers and enables orderly secretion without polymer tangling. Recent studies have described the high-resolution structure of helical tubular cores formedin vitroby the D1D2 and D′D3 amino-terminal protein segments of VWF. Here we show that formation of tubules with the helical geometry observed for VWF in intracellular WPBs requires also the VWA1 (A1) domain. We reconstituted VWF tubules from segments containing the A1 domain and discovered it to be inserted between helical turns of the tubule, altering helical parameters and explaining the increased robustness of tubule formation when A1 is present. The conclusion from this observation is that the A1 domain has a direct role in VWF assembly, along with its known activity in hemostasis post-secretion.

Key points

A cryo-EM structure shows that the A1 domain is necessary for forming VWF helical tubules matching those in Weibel-Palade bodies.

The A1 domain has a role in intracellular VWF supramolecular assembly in addition to platelet binding following secretion and activation.
Genomic Surveillance Identifies SARS-CoV-2 Transmission Patterns in Local University Populations, Wisconsin, USA, 2020–2022
Authors: Ramaiah Arunachalam , Khubbar Manjeet , Bauer Amy , Akinyemi Katherine , Weiner Joshua , Bhattacharyya Sanjib
Published: July 2022

Novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge as the current coronavirus disease 2019 (COVID-19) pandemic extends into its third year. Understanding SARS-CoV-2 circulation in university populations is vital for effective interventions in a higher education setting that will inform pubic health policy during pandemics. In this study, we performed whole-genome sequencing of 537 of 1,717 SARS-CoV-2 positive nasopharyngeal/nasal swab samples collected for nearly 20 months from the two university populations in Wisconsin, United States. We observed that the viral sequences were distributed into 57 lineages/sub-lineages belonging to 15 clades of which the majority were from 21K (Omicron, 36.13%) and 21J (Delta, 30.91%). Nearly 40% (213) of the sequences were Omicron of which BA.1 and its eight descendent lineages account for 91%, while the remaining belong to BA.2 and its six descendent lineages. The independent analysis of these two universities sequences revealed significant differences in circulating the SARS-CoV-2 variants. The genome-based analysis of closely-related strains along with phylogenetic clusters had identified that potential virus transmission occurred within as well as between universities, and between the university and local community. Although this study improves our understanding of distinct transmission patterns of circulating variants in local universities, expanding the genomic surveillance capacity will aid local jurisdictions in identifying emerging SARS-CoV-2 variants like BA.4 and BA.5, and improve data-driven public health mitigation and policy efforts.
Multimorbidity and risk of incident dementia: role of disease clusters and genetic risk for dementia in a cohort of 206,960 participants
Authors: Calvin Catherine M. , Conroy Megan C. , Moore Sarah F. , Kuźma Elżbieta , Littlejohns Thomas J.
Published: July 2022

Importance

Individual conditions have been identified as risk factors for dementia, however, it is important to consider the role of multimorbidity as conditions often co-occur.

Objective

To investigate whether multimorbidity is associated with incident dementia, and whether associations vary by different clusters of disease, and genetic risk for dementia.

Design

A population-based prospective study.

Setting

The UK Biobank cohort.

Participants

206,960 dementia-free women and men aged ≥60 years old at baseline Exposures: Medical conditions were captured as part of a nurse-led verbal interview conducted at assessment centres. The presence of ≥2 long-term conditions from a preselected list of 42 conditions was used to define multimorbidity. High genetic risk for dementia was based on presence of one or two Apolipoprotein (APOE) ε4 alleles.

Main outcome

Incident dementia was derived from hospital inpatient and death registry records.

Results

89,201 (43%) participants had multimorbidity. Over a mean of 11.8 years (standard deviation=2.2), 6,182 participants developed dementia. The incidence rate per 1,000 person years was 1.87 (95% Confidence Interval [CI] 1.80-1.94) and 3.41 (95% CI 3.30-3.53) for those without and with multimorbidity, respectively. In Cox-proportional-hazards models adjusted for age, sex, ethnicity, education, socioeconomic status and APOE-ε4 carrier status, multimorbidity was associated with a 63% increased risk of incident dementia (Hazard Ratio [HR]=1.63, 95% CI 1.55-1.71). The highest dementia risk was observed for the hypertension/diabetes/coronary heart disease (HR=2.20, 95% CI 1.98-2.46) and pain/osteoporosis/dyspepsia (HR=2.00, 95% CI 1.68-2.37) clusters in females and diabetes/hypertension (HR=2.24, 95% CI 1.97-2.55) and coronary heart disease/hypertension/stroke clusters (HR=1.94, 95% CI 1.71-2.20) in males, compared to no multimorbidity. The relative associations were stronger in those with a lower genetic risk of dementia, but the absolute difference in risk between absence and presence of multimorbidity was greater in those with a higher genetic risk for dementia.

Conclusions and Relevance

Multimorbidity was strongly associated with an increased risk of dementia. The strength of associations varied by clusters of disease and genetic risk for dementia. These findings could help with the identification of individuals at high risk of dementia as well as the development of targeted interventions to reduce or delay dementia incidence.
Increased mutation rate and interlocus gene conversion within human segmental duplications
Authors: Vollger Mitchell R. , DeWitt William S. , Dishuck Philip C. , Harvey William T. , Guitart Xavi , Goldberg Michael E. , Rozanski Allison N. , Lucas Julian , Asri Mobin ,   The Human Pangenome Reference Consortium, Munson Katherine M. , Lewis Alexandra P. , Hoekzema Kendra , Logsdon Glennis A. , Porubsky David , Paten Benedict , Harris Kelley , Hsieh PingHsun , Eichler Evan E.
Published: July 2022

Single-nucleotide variants (SNVs) within segmental duplications (SDs) have not been systematically assessed because of the difficulty in mapping short-read sequence data to virtually identical repetitive sequences. Using 102 phased human haplotypes, we constructed 1:1 unambiguous alignments spanning high-identity SDs and compared the pattern of SNVs between unique and SD regions. We find that human SNVs are elevated 60% in SDs compared to unique regions. We estimate that at least 23% of this increase is due to interlocus gene conversion (IGC) with >7 Mbp of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of ~800 protein-coding genes. The latter includes 171 genes that have “relocated” on average 1.61 Mbp in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are evolutionarily older when compared to unique sequences with most of this signal originating from putative IGC loci. SNVs within SDs, however, also exhibit a distinct mutational spectrum where there is a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts. In addition, we observe a 7.6% reduction in the frequency of CpG associated mutations when compared to unique DNA. We hypothesize that these distinct mutational properties help to maintain an overall higher GC content of SD DNA when compared to unique DNA, and we show that these GC-favoring mutational events are likely driven by GC-biased conversion between paralogous sequences.
Origin and segregation of the human germline
Authors: Castillo-Venzor Aracely , Penfold Christopher A. , Morgan Michael D. , Tang Walfred W. C. , Kobayashi Toshihiro , Wong Frederick C. K. , Bergmann Sophie , Slatery Erin , Boroviak Thorsten E. , Marioni John C. , Surani M. Azim
Published: July 2022

Human germline-soma segregation occurs during weeks 2-3 in gastrulating embryos. While direct studies are hindered, here we investigate the dynamics of human primordial germ cell (PGCs) specification using in vitro models with temporally resolved single-cell transcriptomics and in-depth characterisation to in vivo datasets from human and non-human primates, including a 3D marmoset reference atlas. We elucidate the molecular signature for the transient gain of competence for germ cell fate during peri-implantation epiblast development. Further, we show that both the PGCs and amnion arise from transcriptionally similar TFAP2A positive progenitors at the posterior end of the embryo. Notably, genetic loss of function experiments show that TFAP2A is crucial for initiating the PGC fate without detectably affecting the amnion, and its subsequently replaced by TFAP2C as an essential component of the genetic network for PGC fate. Accordingly, amniotic cells continue to emerge from the progenitors in the posterior epiblast, but importantly, this is also a source of nascent PGCs.
A toolkit to handle T-less alignment for U insertion/deletion RNA editing
Authors: Zhang Fan , Aphasizhev Ruslan , Afasizheva Inna , Zhang Liye
Published: July 2022

In the mitochondrial genome of kinetoplastids, the targeted insertion and deletion of uridine in cryptic mRNA is essential to generate functional protein-coding mRNAs, but such process leads to a highly hetergenous and complex RNA population. Few tools were developped to perform alignment based on a T depleted strategy for such mRNA population, however to our knowledge no downstream analysis tool is available so far to allow easy data processing and interpretation. Here, we fill this gap with the T-less-Alignment-Toolkit, which provides useful functions such as duplication removal with UMI, alignment strandness analysis, statistical summary and visualization.

Availability and Implementation

Scripts and toolkits can be downloaded at https://gitee.com/Zhanglab/tless-alignment-toolkit
A deep learning approach for improved detection of homologous recombination deficiency from shallow genomic profiles
Authors: Andre Gregoire , Coletta Tommaso , Pozzorini Christian , Marques Ana C. , Bieler Jonathan , Kempfer Rieke , Chong Chloe , Saitta Alexandra , Smith Ewan , Macheret Morgane , Janiszewski Adrian , Bonilla Ximena , Bonet Jaume , Santos-Silva Hugo , Postl Magdalena , Wozelka-Oltjan Lisa , Arrigo Nils , Willig Adrian , Grimm Christoph , Müllauer Leonhard , Xu Zhenyu
Published: July 2022

Homologous Recombination Deficiency (HRD) is a predictive biomarker of poly-ADP ribose polymerase 1 inhibitors (PARPi) response. Most HRD detection methods are based on genome wide enumeration of scarring events and require deep genome sequence profiles (> 30x). The cost and workflow-specific biases introduced by these genome profiling methods currently limits clinical adoption of HRD testing.

We introduce the Genomic Integrity Index (GII), a Convolutional Neuronal Network, that leverages features from low pass (1x) Whole Genome Sequencing data to distinguish HRD positive and negative samples. In a cohort of 230 ovarian and breast cancer, we found GII supports accurate stratification of samples yielding results that are highly concordant with state-of-the-art HRD detection methods (0.865<AUC<0.996) which require 50x deeper coverage.

We conclude that the deep learning framework supporting GII allows accurate detection of HRD from shallow genome profiles, reducing biases and data generation costs making it uniquely suited for clinical applications.
Accessibility and Reproducible Research Practices in Cardiovascular Literature
Authors: Heckerman Gabriel , Tzng Eileen , Campos-Melendez Arely , Ekwueme Chisomaga , Mueller Adrienne L.
Published: July 2022

Background

Several fields have described low reproducibility of scientific research and poor accessibility in research reporting practices. Although previous reports have investigated accessible reporting practices that lead to reproducible research in other fields, to date no study has explored the extent of accessible and reproducible research practices in cardiovascular science literature.

Methods

To study accessibility and reproducibility in cardiovascular research reporting, we screened 400 randomly selected articles published in 2019 in three top cardiovascular science publications: Circulation, the European Heart Journal, and the Journal of the American College of Cardiology (JACC). We screened each paper for accessible and reproducible research practices using a set of accessibility criteria including protocol, materials, data, and analysis script availability, as well as accessibility of the publication itself. We also quantified the consistency of open research practices within and across cardiovascular study types and journal formats.

Results

We identified that fewer than 2% of cardiovascular research publications provide sufficient resources (materials, methods, data, and analysis scripts) to fully reproduce their studies. After calculating an accessibility score as a measure of the extent to which an articles makes its resources available, we also showed that the level of accessibility varies across study types (p = 2e-16) and across journals (p = 5.9e-13). We further show that there are significant differences in which study types share which resources. We also describe the relationship between accessibility scores and corresponding author nationality.

Conclusion

Although the degree to which reproducible reporting practices are present in publications varies significantly across journals and study types; current cardiovascular science reports frequently do not provide sufficient materials, protocols, data, or analysis information to reproduce a study. In the future, having higher standards of accessibility mandated by either journals or funding bodies will help increase the reproducibility of cardiovascular research.

Funding

Authors Gabriel Heckerman, Arely Campos-Melendez, and Chisomaga Ekwueme were supported by an NIH R25 grant from the National Heart Lung and Blood Institute (R25HL147666). Eileen Tzng was supported by an AHA Institutional Training Award fellowship (18UFEL33960207).
Distinct positions of genetic and oral histories: Perspectives from India
Authors: Biddanda Arjun , Bandyopadhyay Esha , de la Fuente Castro Constanza , Witonsky David , Urban Aragon Jose A. , Pasupuleti Nagarjuna , Moots Hannah M. , Fonseca Renée , Freilich Suzanne , Stanisavic Jovan , Willis Tabitha , Menon Anoushka , Mustak Mohammed S. , Kodira Chinnappa Dilip , Naren Anjaparavanda P. , Sikdar Mithun , Rai Niraj , Raghavan Maanasa
Published: July 2022

Over the past decade, genomic data has contributed to several insights on global human population histories. These studies have been met both with interest and critically, particularly by populations with oral histories that are records of their past and often reference their origins. While several studies have reported concordance between oral and genetic histories, there is potential for tension that may stem from genetic histories being prioritized or used to confirm community-based knowledge and ethnography, especially if they differ. To investigate the interplay between oral and genetic histories, we focused on the southwestern region of India and analyzed whole-genome sequence data from 158 individuals identifying as Bunt, Kodava, Nair, and Kapla. We supplemented limited anthropological records on these populations with oral history accounts from community members and historical literature, focusing on references to non-local origins such as the ancient Scythians in the case of Bunt, Kodava, and Nair, members of Alexander the Great’s army for the Kodava, and an African-related source for Kapla. We found these populations to be genetically most similar to other Indian populations, with the Kapla more similar to South Indian tribal populations that maximize a genetic ancestry related to Andaman Islanders. We did not find evidence of additional genetic sources in the study populations than those known to have contributed to many other present-day South Asian populations. Our results demonstrate that oral and genetic histories may not always provide consistent accounts of population origins and motivate further community-engaged, multi-disciplinary investigations of non-local origin stories in these communities.
Sequence analysis and structural predictions of lipid transfer bridges in the repeating beta groove (RBG) superfamily reveals past and present domain variations affecting form, function and interactions of VPS13, ATG2, SHIP164, Hobbit and Tweek
Authors: Levine Tim P
Published: July 2022

Lipid transfer between organelles requires proteins that shield the hydrophobic portions of lipids as they cross the cytoplasm. In the last decade a new structural form of lipid transfer protein (LTP) has been found: long hydrophobic grooves made of beta-sheet that bridge between organelles at membrane contact sites. Eukaryotes have five families of bridge-like LTPs: VPS13, ATG2, SHIP164, Hobbit and Tweek. These are unified into a single superfamily through their bridges being composed of just one domain, called the repeating beta groove (RBG) domain, which builds into rod shaped multimers with a hydrophobic-lined groove and hydrophilic exterior. Here, sequences and predicted structures of the RBG superfamily were analyzed in depth. Phylogenetics showed that the last eukaryotic common ancestor contained all five RBG proteins, with duplicate VPS13s. These appear to have arisen in even earlier ancestors from shorter forms with 4 RBG domains. The extreme ends of most RBG proteins have amphipathic helices that might be an adaptation for direct or indirect bilayer interaction, although this has yet to be tested. The one exception to this is the C-terminus of SHIP164, which instead has a coiled-coil. Finally, almost the entire length of the exterior surfaces of the RBG bridges are shown to have conserved residues, indicating sites for partner interactions almost all of which are unknown. These findings can inform future cell biological and biochemical experiments.
Host-specific plasmid evolution explains the variable spread of clinical antibiotic-resistance plasmids
Authors: Benz F. , Hall A. R.
Published: July 2022

Antibiotic resistance encoded on plasmids is a pressing global health problem. Predicting which plasmids spread/decline in the long term remains a huge challenge, even though some key parameters influencing plasmid stability have been identified, such as plasmid growth costs and horizontal transfer rates. Here, we show these parameters evolve in a strain-specific way among clinical plasmids/bacteria, and this occurs rapidly enough to alter the relative likelihoods of different bacterium-plasmid combinations spreading/declining. We used experiments with Escherichia coli and antibiotic-resistance plasmids isolated from patients, paired with a mathematical model, to show long-term plasmid stability (beyond antibiotic exposure) was better explained by evolutionary changes in plasmid-stability traits than by initial variation among bacterium-plasmid combinations. Evolutionary trajectories were specific to particular bacterium-plasmid combinations. Genome sequencing and genetic manipulation helped explain this, revealing epistatic (here, strain-dependent) effects of key genetic changes affecting horizontal plasmid transfer. Several genetic changes involved mobile elements and pathogenicity islands. Rapid strain-specific evolution can thus outweigh ancestral phenotypes as a predictor of plasmid stability. Accounting for strain-specific plasmid evolution in natural populations could improve our ability to anticipate and manage successful bacterium-plasmid combinations.
Conjunctive and complementary CA1 hippocampal cell populations relate sensory events to immobility and locomotion
Authors: Inayat Samsoon , McAllister Brendan B. , Whishaw Ian Q. , Mohajerani Majid H.
Published: July 2022

This study investigated the dynamics of recruitment of cells in the CA1 region of the hippocampus in response to sensory stimuli presented during immobility, movement, and their transitions. Two-photon calcium imaging of somal activity in CA1 neuron populations was done in head fixed mice. Sensory stimuli, either a light flash or an air stream, were delivered to the mice when at rest, when moving spontaneously, and while they were induced to run a fixed distance on the conveyor belt. Overall, 99% of 2083 identified cells (from 5 mice) were active across one or more of 20 sensorimotor events. A larger proportion of cells were active during locomotion. Nevertheless, for any given sensorimotor event, only about 17% of cells were active. When considering pairs of sensorimotor event types, the active cell population consisted of conjunctive (C ∈ A and B) cells, active across both events, and complementary (C ∈ A not B or C ∈ B not A) cells that were active only during individual events. Whereas conjunctive cells characterised stable representations of repeated sensorimotor events, complementary cells characterised recruitment of new cells for encoding novel sensorimotor events. The moment-to-moment recruitment of conjunctive and complementary cells across changing sensorimotor events signifies the involvement of the hippocampus in functional networks integrating sensory information with ongoing movement. This role of the hippocampus is well suited for movement guidance that secondarily might include spatial behavior, episodic learning and memory, context representation, and scene construction.
A New CUT&RUN Low Volume-Urea (LoV-U) protocol uncovers Wnt/β-catenin tissue-specific genomic targets
Authors: Zambanini Gianluca , Nordin Anna , Jonasson Mattias , Pagella Pierfrancesco , Cantù Claudio
Published: July 2022

Upon WNT/β-catenin pathway activation, stabilized β-catenin travels to the nucleus where it associates with the TCF/LEF family of transcription factors, which constitutively bind to genomic Wnt Responsive Elements (WREs), to activate transcription of target genes. Discovering the binding profile of β-catenin is therefore required to unambiguously assign direct targets of WNT signaling. Cleavage Under Target and Release Using Nuclease (CUT&RUN) has recently emerged as a prime technique for mapping the binding profile of chromatin interacting proteins. In our attempts to profile different regulators of the WNT/β-catenin transcriptional complex, CUT&RUN performed reliably when targeting transcription factors such as TCF/LEF, but it failed to produce consistent binding patterns of the non-DNA-binding β-catenin. Here, we present a biochemical modification of the CUT&RUN protocol, which we refer to as LoV-U (Low Volume and Urea), that enables the generation of robust and reproducible β-catenin binding profiles. CUT&RUN-LoV-U uncovers direct WNT/β-catenin target genes in human cells, as well as in ex vivo cells isolated from developing mouse tissue. CUT&RUN-LoV-U can profile all classes of chromatin regulators tested and is well suited for simultaneous processing of several samples. We submit that the application of our protocol will allow the detection of the complex system of tissue-specific WNT/β-catenin target genes, together with other non-DNA-binding transcriptional regulators that act downstream of ontogenetically fundamental signaling cascades.
Active shrinkage protects neurons following axonal transection
Authors: Aydın Mehmet Şerif , Bay Sadık , Yiğit Esra Nur , Özgül Cemil , Oğuz Elif Kaval , Konuk Elçin Yenidünya , Ayşit Neşe , Cengiz Nureddin , Erdoğan Ender , Him Aydın , Koçak Mehmet , Eroglu Emrah , Öztürk Gürkan
Published: July 2022

Trauma, vascular events, or neurodegenerative processes can lead to axonal injury and eventual transection (axotomy). Neurons can survive axotomy, yet the underlying mechanisms are not fully understood. Excessive water entry into injured neurons poses a particular risk due to swelling and subsequent death. Using in vitro and in vivo neurotrauma model systems based on laser transection, we demonstrated that axotomy triggers actomyosin contraction coupled with calpain activity. As a consequence, neurons shrink acutely to force water out through aquaporin channels preventing swelling and bursting. Inhibiting shrinkage increased the probability of neuronal cell death by about three-fold. These studies reveal a previously unrecognized cytoprotective response mechanism to neurotrauma and offer a fresh perspective on pathophysiological processes in the nervous system.

One-Sentence Summary

When the axon of a neuron is cut, its soma shrinks to pump out water to avoid deadly swelling.
Highly fucosylated N-glycans at the synaptic vesicle and neuronal plasma membrane
Authors: Bradberry Mazdak M. , Peters-Clarke Trenton M. , Shishkova Evgenia , Chapman Edwin R. , Coon Joshua J.
Published: July 2022

At neuronal synapses, synaptic vesicles (SVs) require glycoproteins for normal trafficking, and N-linked glycosylation is required for delivery of the major SV glycoproteins synaptophysin and SV2A to SVs. The molecular compositions of SV N-glycans, which may drive important neurobiological processes, are largely unknown. In this study, we combined organelle isolation techniques, fluorescence detection of N-glycans, and high-resolution mass spectrometry to characterize N-glycosylation at synapses and SVs from mouse brain. Detecting over 2,500 unique glycopeptides from over 550 glycoproteins, we found that abundant SV proteins harbor N-glycans with fucose on their complex antennae, and we identify a highly fucosylated N-glycan enriched in SVs as compared to synaptosomes. Antennary fucosylation was also characteristic of plasma membrane proteins and cell adhesion molecules with established roles in synaptic function and development. Our results represent the first defined N-glycoproteome of a neuronal organelle and raise new questions in the glycobiology of synaptic pruning and neuroinflammation.
Rho activation drives luminal collapse and eversion in epithelial acini
Authors: Narayanan Vani , Purkayastha Purboja , Yu Bo , Pendyala Kavya , Chukkapalli Sasanka , Cabe Jolene I , Dickinson Richard B. , Conway Daniel E. , Lele Tanmay P
Published: July 2022

Epithelial cells lining a gland and cells grown in a soft extracellular matrix polarize with apical proteins exposed to the lumen and basal proteins in contact with the extracellular matrix. Alterations to polarity, including an apical-out polarity, occur in human cancers. While some aberrant polarity states may result from altered protein trafficking, recent observations of an extraordinary tissue-level inside-out unfolding suggest an alternate pathway for altered polarity. Because mechanical alterations are common in human cancer including an upregulation of RhoA mediated actomyosin tension in acinar epithelia, we explored whether perturbing mechanical homeostasis could cause apical-out eversion. Acinar eversion was robustly induced by direct activation of RhoA in normal and tumor epithelial acini, or indirect activation of RhoA through blockage of β1 integrins, disruption of the LINC complex, oncogenic Ras activation, or Rac1 inhibition. Furthermore, laser ablation of a portion of the untreated acinus was sufficient to induce eversion. Analyses of acini revealed high curvature and low phosphorylated myosin in the apical cell surfaces relative to the basal surfaces. A vertex-based mathematical model which balances tension at cell-cell interfaces revealed a five-fold greater basal cell surface tension relative to the apical cell surface tension. The model suggests that the difference in surface energy between the apical and basal surfaces is the driving force for acinar eversion. Our findings raise the possibility that a loss of mechanical homeostasis may cause apical-out polarity states in human cancers.
DeepBend: An Interpretable Model of DNA Bendability
Authors: Khan Samin Rahman , Sakib Sadman , Rahman M. Sohel , Samee Md. Abul Hassan
Published: July 2022

The bendability of genomic DNA impacts chromatin packaging and protein-DNA binding. However, beyond a handful of known sequence motifs, such as certain dinucleotides and poly(A)/poly(T) sequences, we do not have a comprehensive understanding of the motifs influencing DNA bendability. Recent high-throughput technologies like Loop-Seq offer an opportunity to address this gap but the lack of accurate and interpretable machine learning models still poses a significant challenge. Here we introduce DeepBend, a convolutional neural network model built as a visible neural network where we designed the convolutions to directly capture the motifs underlying DNA bendability and how their periodic occurrences or relative arrangements modulate bendability. Through extensive benchmarking on Loop-Seq data, we show that DeepBend consistently performs on par with alternative machine learning and deep learning models while giving an extra edge through mechanistic interpretations. Besides confirming the known motifs of DNA bendability, DeepBend also revealed several novel motifs and showed how the spatial patterns of motif occurrences influence bendability. DeepBend’s genome-wide prediction of bendability further showed how bendability is linked to chromatin conformation and revealed the motifs controlling bendability of topologically associated domains and their boundaries.