bluuebunny/crossref_metadata_2025 huggingface dataset:
Multilevel neural gradients reflect transdiagnostic effects of major psychiatric conditions on cortical morphology
Authors: Park Bo-yong , Kebets Valeria , Larivière Sara , Hettwer Meike D. , Paquola Casey , van Rooij Daan , Buitelaar Jan , Franke Barbara , Hoogman Martine , Schmaal Lianne , Veltman Dick J. , van den Heuvel Odile , Stein Dan J. , Andreassen Ole A. , Ching Christopher R. K. , Turner Jessica , van Erp Theo G. M. , Evans Alan C. , Dagher Alain , Thomopoulos Sophia I. , Thompson Paul M. , Valk Sofie L. , Kirschner Matthias , Bernhardt Boris C.
Published: November 2021

Abstract

It is increasingly recognized that multiple psychiatric conditions are underpinned by shared neural pathways, affecting similar brain systems. Here, we assessed i) shared dimensions of alterations in cortical morphology across six major psychiatric conditions (autism spectrum disorder, attention deficit/hyperactivity disorder, major depression, obsessive-compulsive disorder, bipolar disorder, schizophrenia) and ii) carried out a multiscale neural contextualization, by cross-referencing shared anomalies against cortical myeloarchitecture and cytoarchitecture, as well as connectome and neurotransmitter organization. Pooling disease-related effects on MRI-based cortical thickness measures across six ENIGMA working groups, including a total of 28,546 participants (12,876 patients and 15,670 controls), we computed a shared disease dimension on cortical morphology using principal component analysis that described a sensory-fugal pattern with paralimbic regions showing the most consistent abnormalities across conditions. The shared disease dimension was closely related to cortical gradients of microstructure and intrinsic connectivity, as well as neurotransmitter systems, specifically serotonin and dopamine. Our findings embed the shared effects of major psychiatric conditions on brain structure in multiple scales of brain organization and may provide novel insights into neural mechanisms into transdiagnostic vulnerability.
A novel mechanism of Euonymine inhibits in-stent restenosis through enhancing contractile phenotype of VSMCs by targeting AKT1 and p38MAPK
Authors: Zhang Li , Tao Yi Ting , Hu Qin , Yang Ren Hua , Jia Jia , Jin Hao Nan , Yang Yong Zhao , Yang Yan , Yu Ming Yang , Wang Yu Ting , Shi Jia Ning , Yu Dan , Tang Guang Ping , Xu Jie , Xiong Bao , Shen Zhi Qiang , Yu Zhuo , Qin Hong Tao , Chen Peng
Published: November 2021

This study aimed to examine the inhibitory effects of Euonymine on in-stent restenosis (ISR) after percutaneous coronary intervention (PCI) and oxidized low-density lipoprotein (ox-LDL)-induced proliferation, migration, and pro-apoptotic of vascular smooth muscle cells (VSMCs) in vitro, and its potential mechanisms. Euonymine is a monomer component extracted from Tripterygium hypoglaucum (Levl) Hutch. Using in vitro models of rabbit carotid balloon injury and porcine atherosclerotic coronary implantation, we confirmed that Euonymine inhibited ISR after PCI. Furthermore, Euonymine inhibited VSMC phenotypic transformation by targeting AKT1 to regulate the PTEN/AKT1/m TOR signaling pathway, with exertion of anti-proliferative, anti-migratory, and pro-apoptotic effects on ox-LDL-induced cell injury model. Additionally, the study demonstrated that Euonymine induced apoptosis of VSMCs via the p38MAPK-related mitochondria-dependent apoptotic pathway. Collectively, these findings indicated that Euonymine drug-eluting stents inhibited ISR after PCI by targeting AKT1 and p38MAPK to enhance the contractile phenotype of VSMCs to prevent intimal hyperplasia development. This provides insights into a potential therapeutic strategy involving the beneficial effect of Euonymine drug-eluting stent on ISR.
The use of disinfectant in barn cleaning alters microbial composition and increases carriage of Campylobacter jejuni in broiler chickens
Authors: Fan Yi , Forgie Andrew J. , Ju Tingting , Marcolla Camila , Inglis Tom , McMullen Lynn M. , Willing Benjamin P. , Korver Douglas R.
Published: November 2021

To maintain food safety and flock health in broiler chicken production, biosecurity approaches to keep chicken barns free of pathogens are important. Canadian broiler chicken producers must deep clean their barns with chemical disinfectants at least once annually (full disinfection; FD) and may wash with water (water-wash; WW) throughout the year. However, many producers use FD after each flock, assuming a greater efficacy of more stringent cleaning protocols, although little information is known regarding how these two cleaning practices affect pathogen population and gut microbiota. In the current study, a cross-over experiment over four production cycles was conducted in seven commercial chicken barns to compare WW and FD. We evaluated the effects of barn cleaning method on the commercial broiler performance, cecal microbiota composition, pathogen occurrence and abundance, as well as short-chain fatty acid concentrations in the month-old broiler gut. The 30-day body weight and mortality rate were not affected by the barn cleaning methods. The WW resulted in a modest but significant effect on the structure of broiler cecal microbiota (weighted-UniFrac; adonis p = 0.05, and unweighted-UniFrac; adonis p = 0.01), with notable reductions in Campylobacter jejuni occurrence and abundance. In addition, the WW group had increased cecal acetate, butyrate and total short-chain fatty acid concentrations, which were negatively correlated with C. jejuni abundance. Our results support the use of WW over FD to enhance the activity of the gut microbiota and potentially reduce zoonotic transmission of C. jejuni in broiler production without previous disease challenges.
Impact of protein identity on tumor-associated antigen uptake into infiltrating immune cells: A comparison of different fluorescent proteins as model antigens
Authors: Yi Rulan , Chen Emily , Roberts Edward W , Krummel Matthew F , Serwas Nina K
Published: November 2021

Effective immune responses depend on efficient antigen uptake in the periphery, transport of those antigens to, and presentation in draining lymph nodes (LNs). These processes have been studied intensively using stable fluorescent proteins (FPs) as model antigens. To date, ZsGreen is the only FP that can be tracked efficiently towards LNs, hence, it is difficult to compare studies using alternated tracking proteins.

Here, we systematically compared six different FPs. We included ZsGreen, ZsYellow, DsRed, AsRed, mCherry, and mRFP based on sequence homology and/or origin species, and generated FP-expressing tumor cell lines. Stability of fluorescent signal was assessed in vitro over time, across different pH environments, and in vivo through FP antigen uptake and transfer to immune cells isolated from tumors and tumor-draining LNs.

ZsGreen could be detected in high percentages of all analyzed tumor-infiltrating immune cells, with highest amounts in tumor-associated macrophages (TAMs) and type 2 conventional dendritic cells (cDC2s). ZsYellow, AsRed, and DsRed followed a similar pattern, but percentages of FP-containing immune cells in the tumor were lower than for ZsGreen. Strikingly, mRFP and mCherry demonstrated a ‘non-canonical’ antigen uptake pattern where percentages of FP-positive tumor-infiltrating immune cells were highest for cDC1s not TAMs and cDC2s despite comparable stabilities and localization of all FPs. Analysis of antigen-containing cells in the LN was hindered by intracellular degradation of FPs. Only ZsGreen could be efficiently tracked to the LN, though some signal was measurable for ZsYellow and DsRed.

In summary, we find that detection of antigen uptake and distribution is subject to variabilities related to fluorophore nature. Future experiments need to consider that these processes might be impacted by protein expression, stability, or other unknown factors. Thus, our data sheds light on potential under-appreciated mechanisms regulating antigen transfer and highlights potential uses and necessary caveats to interpretation based on FP use.
Vitamin A and vitamin E metabolites comodulate amyloid-β aggregation
Authors: Joshi Priyanka , Chia Sean , Yang Xiaoting , Perni Michele , Habchi Johnny , Vendruscolo Michele
Published: November 2021

Alzheimer’s disease is characterized by the presence in the brain of amyloid plaques formed by the aberrant deposition of the amyloid-β peptide (Aβ). Since many vitamins are dysregulated in this disease, we explored whether these molecules participate in protein homeostasis by modulating Aβ aggregation. By screening 18 fat-soluble and water-soluble vitamins, we found that retinoic acid and α-tocopherol, two metabolites of vitamin A and vitamin E, respectively, affect Aβ aggregation both in vitro and in a C. elegans model of Alzheimer’s disease. We also show that effects of these two vitamin metabolites in combination can cancel each other out, suggesting that the complex composition of the cellular environment could have a protective role against protein aggregation through the simultaneous presence of aggregation promoters and inhibitors. Taken together, these results indicate that vitamins and their metabolites may be added to the list of components of the quality control system that regulate protein aggregation.
Evolution of reduced mate harming tendency of males inDrosophila melanogasterpopulations selected for faster life history
Authors: Verma Tanya , Mohapatra Anuska , Senapati Harish Kumar , Muni Rakesh Kumar , Dasgupta Purbasha , Nandy Bodhisatta
Published: November 2021

Detrimental effect of males on female, often termed mate harm, is a hallmark of sexual conflict. Allowed to evolve unchecked, mate harming traits are predicted to bring down average fitness of a population, unless mitigated by the evolution of resistance in females. In addition, life history may also modulate sexual conflict, but the mechanism is not clearly understood. Here we investigated the evolution of mate harm in a set of experimentally evolved laboratory populations ofDrosophila melanogasterwherein a faster aging has evolved in response to >1000 generations of selection for faster development and early reproduction. We quantified mortality and fecundity of Oregon R females held with evolved (ACO) and ancestral males (CO) to show that the evolved males are significantly less detrimental to their mates. We compared our results from the ACO males with that from a phenocopied version of the ancestral regime (CCO) to show that only part of the observed difference in mate harm can be attributed to the evolved difference in body size. We further show that the reduction in mate harming ability evolved despite an increase in courtship activity, especially early in life. We discuss the causative role of an evolved reproductive schedule and altered breeding ecology.

Significance statement

Sexually antagonistic male effects can significantly bring down female fitness. Along with female counter evolution of resistance traits, life history has been conjectured to impose constrains on the evolution of such harming ability in males. Here, we report the evolution of mate harming ability in males of a set of five replicateDrosophila melanogasterpopulations that evolved smaller size and faster aging as a result of >1000 generations of experimental evolution for faster development and early reproduction. We show that in spite of ample scope of sexual selection, the faster aging males have evolved reduced mate harming ability despite being more active in courting their mates. To the best of our knowledge, this is one of the first clear evidences demonstrating the causal relationship between evolution of life history and reduction in sexual antagonism in a population.
Transcriptional evaluation of the ductus arteriosus at the single-cell level uncovers a requirement for vimentin for complete closure
Authors: Salvador Jocelynda , Hernandez Gloria E. , Ma Feiyang , Abrahamson Cyrus W. , Pellegrini Matteo , Goldman Robert , Ridge Karen M. , Iruela-Arispe M. Luisa
Published: November 2021

OBJECTIVE

Failure to close the ductus arteriosus immediately post-birth, patent ductus arteriosus (PDA), accounts for up to 10% of all congenital heart defects. Despite significant advances in PDA management options, including pharmacological treatment targeting the prostaglandin pathway, a proportion of patients fail to respond and must undergo surgical intervention. Thus, further refinement of the cellular and molecular mechanisms that govern vascular remodeling of this vessel is required.

APPROACH AND RESULTS

As anticipated, single-cell RNA sequencing on the ductus arteriosus in mouse embryos at E18.5, P0.5, and P5, revealed broad transcriptional alterations in the endothelial, smooth muscle, and fibroblast cell compartments. Making use of these data sets, vimentin emerged as an interesting candidate for further investigation. Subsequent studies demonstrated that, in fact, mice with genetic deletion of vimentin fail to complete vascular remodeling of the ductus arteriosus, as per presence of a functional lumen.

CONCLUSIONS

Through single-cell RNA-sequencing and by tracking closure of the ductus arteriosus postnatally in mice, we uncovered the unexpected contribution of vimentin in driving complete closure of the ductus arteriosus potentially through regulation of the Notch signaling pathway.

HIGHLIGHTS

Single-cell RNA-sequencing on the ductus arteriosus at E18.5, P0.5, and P5 reveals how the ductus arteriosus undergoes drastic transcriptional changes at the single-cell level.

Endothelial cells increase levels of Vimentin, Notch1 and Jag1 transcripts soon after birth (P0.5), concurrent with ductus arteriosus closure.

Loss of vimentin, the major intermediate filament protein of endothelial cells, prevents proper permanent closure of the ductus arteriosus.
OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
Authors: Steenwyk Jacob L. , Goltz Dayna C. , Buida Thomas J. , Li Yuanning , Shen Xing-Xing , Rokas Antonis
Published: November 2021

Molecular evolution studies, such as phylogenomic studies and genome-wide surveys of selection, often rely on gene families of single-copy orthologs (SC-OGs). Large gene families with multiple homologs in one or more species—a phenomenon observed among several important families of genes such as transporters and transcription factors—are often ignored because identifying and retrieving SC-OGs nested within them is challenging. To address this issue and increase the number of markers used in molecular evolution studies, we developed OrthoSNAP, a software that uses a phylogenetic framework to simultaneously split gene families into SC-OGs and prune species-specific inparalogs. We term SC-OGs identified by OrthoSNAP as SNAP-OGs because they are identified using a splitting and pruning procedure analogous to snapping branches on a tree. From 415,129 orthologous groups of genes inferred across seven eukaryotic phylogenomic datasets, we identified 9,821 SC-OGs; using OrthoSNAP on the remaining 405,308 orthologous groups of genes, we identified an additional 10,704 SNAP-OGs. Comparison of SNAP-OGs and SC-OGs revealed that their phylogenetic information content was similar, even in complex datasets that contain a whole genome duplication, complex patterns of duplication and loss, transcriptome data where each gene typically has multiple transcripts, and contentious branches in the tree of life. OrthoSNAP is useful for increasing the number of markers used in molecular evolution data matrices, a critical step for robustly inferring and exploring the tree of life.
An Immunogold Single Extracellular Vesicular RNA and Protein (AuSERP) Biochip to Predict Responses to Immunotherapy in Non-Small Cell Lung Cancer Patients
Authors: Nguyen Luong T. H. , Wang Xinyu , Kwak Kwang Joo , Zhang Jingjing , Okimoto Tamio , Amann Joseph , Rima Xilal Y. , Yoon Min Jin , Shukuya Takehito , Walters Nicole , Ma Yifan , Belcher Donald , Li Hong , Palmer Andre F. , Carbone David P. , Lee L. James , Reátegui Eduardo
Published: November 2021

Conventional PD-L1 immunohistochemical tissue biopsies only predict 20~40% of non-small cell lung cancer (NSCLC) patients that will respond positively to anti-PD-1/PD-L1 immunotherapy. Herein, we present an immunogold biochip to quantify single extracellular vesicular RNA and protein (AuSERP) as a non-invasive alternative. With only 3 μL of serum, PD-1/PD-L1 proteins on the surface of extracellular vesicles (EVs) and EV PD-1/PD-L1 messenger RNA (mRNA) cargo were detected at a single-vesicle resolution and exceeded the sensitivities of ELISA and qRT-PCR by 1000 times. By testing a cohort of 27 non-responding and 27 responding NSCLC patients, AuSERP indicated that the single-EV mRNA biomarkers surpass the single-EV protein biomarkers at predicting patient responses to immunotherapy. Dual single-EV PD-1/PD-L1 mRNA detection differentiated responders from non-responders with an accuracy of 72.2% and achieved an NSCLC diagnosis accuracy of 93.2%, suggesting the potential for AuSERP to provide enhanced immunotherapy predictions and cancer diagnoses within the clinical setting.
Directional selection at gene expression level contributes to the speciation of Asian rice cultivars
Authors: Xie Lihong , Yu Kehan , Chen Dongjing
Published: November 2021

Differences in expression levels play important roles in phenotypic variation across species, especially those closely related species with limited genomic differences. Therefore, studying gene evolution at expression level is important for illustrating phenotypic differentiation between species, such as the two Asian rice cultivars, Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica. In this study, we evaluated the gene expression variation at inter-subspecies and intra-subspecies level using transcriptome data from seedlings of three indica and japonica rice and defined four groups of genes under different natural selections. We found a substantial of genes (about 79%) that are under stabilizing selection at the expression level in both subspecies, while about 16% of genes are under directional selection. Genes under directional selection have higher expression level and lower expression variation than those under stabilizing selection, which suggest a potential explanation to subspecies adaptation to different environments and interspecific phenotypic differences. Subsequent functional enrichment analysis of genes under directional selection shows that indica rice have experienced the adaptation to environmental stresses, and also show differences in biosynthesis and metabolism pathways. Our study provide an avenue of investigating indica-japonica differentiation through gene expression variation, which may guide to rice breeding and yield improvement.
A versatile mitochondria isolation- and analysis-pipeline generates 3D nano-topographies and mechano-physical surface maps of single organelles
Authors: Joshi Saurabh , Hater Friederike , Eirich Jürgen , Palovaara Joakim , Ellinghaus Henrik , Heinkow Paulina , Callenius Hannah , Peter Annette , Schweser Ole , Kubitschke Martin , Madduri Murali Krishna , Mathew Amal John , Ciacchi Lucio Colombi , Kirstein Janine , Maedler Kathrin , Masseck Olivia Andrea , Finkemeier Iris , Radmacher Manfred , Groß-Hardt Rita
Published: November 2021

Living eukaryotic cells typically contain large quantities of highly dynamic mitochondria, which sustain the cells’ energy and redox homeostasis. Growing evidence suggests that mitochondria can functionally differ among but also within cells. The extent and biological significance of mitochondrial diversity is still largely unexplored, due to technical limitations that hamper profiling of individual organelles. Previous measurements of the cell’s interior have shown that membrane-bound compartments respond to metabolic manipulation by changes in their surface stiffness, suggesting that mechano-physical properties are a valuable readout of mitochondrial function. We here present the establishment of a robust multi-step analysis pipeline that allows one to profile mechano-physical properties of single mitochondria at the nanoscale using Atomic Force Microscopy (AFM). Firstly, we developed a rapid cell-type specific isolation protocol (mRACE), which selectively functionalizes mitochondria with biotin, facilitating isolation by streptavidin decorated microbeads. We established the technique for human and rat cell cultures, the invertebrate Caenorhabditis elegans, and the model plant Arabidopsis thaliana. Based on this versatile tool, we detected diversity of mitochondrially associated proteins among different tissues, reflecting the trophic condition of the source material. Secondly, a rapid filtration-based mitochondria isolation protocol was established, which was combined with mRACE. Lastly, we established an AFM analysis platform, which generates 3D maps of the nano-topography and mechano-physical properties of individual mitochondria. The comparison of mitochondria with each other revealed an unprecedented diversity in their mechano-physical properties and suggests that shape is not the sole determining parameter for outer membrane stiffness. We expect our results to not only introduce a new dimension for basic mitochondrial research, but in addition to open the door for the exploitation of individual mitochondria for diagnostic characterization.
Optimized immunoglobulin knock-ins using Cas9 reveal peritoneal B cell lineage relationships in vivo
Authors: Erickson Steven A. , Zapata-Bultman Eliot , Degenstein Linda , Bendelac Albert
Published: November 2021

Immunoglobulin (Ig) knock-in mice are valuable tools in basic and translational immunological research. Here we present “Speed-Ig,” a rapid Cas9-based method for generating Ig knock-in mouse lines with high on-target integration rates at both heavy and light chain alleles. With standardized target sites and promoter regions, Speed-Ig mice can be used for comparative studies of B cell biology and vaccine optimization in vivo. We used Speed-Ig to create panels of mice with Ig pairs derived from B-1a, B-1b, and B-2 cells. Surprisingly, B-1b and B-2 Ig pairs drove both B-1b and B-2 phenotypes, suggesting a previously unknown lineage relationship between these subsets. We then confirmed the B-1:B-2 relationship with transcription factor reporter lines and through adoptive cell transfer experiments. In summary, our Ig knock-in approach facilitated the discovery of previously unappreciated aspect of innate-like B cell biology.
Multiple spillovers and onward transmission of SARS-CoV-2 in free-living and captive white-tailed deer
Authors: Kuchipudi Suresh V. , Surendran-Nair Meera , Ruden Rachel M. , Yon Michelle , Nissly Ruth H. , Nelli Rahul K. , Li Lingling , Jayarao Bhushan M. , Vandegrift Kurt J. , Maranas Costas D. , Levine Nicole , Willgert Katriina , Conlan Andrew J. K. , Olsen Randall J. , Davis James J. , Musser James M. , Hudson Peter J. , Kapur Vivek
Published: November 2021

Many animal species are susceptible to SARS-CoV-2 and could potentially act as reservoirs, yet transmission of the virus in non-human free-living animals has not been documented. White-tailed deer (Odocoileus virginianus), the predominant cervid in North America, are susceptible to SARS-CoV-2 infection, and experimentally infected fawns can transmit the virus. To test the hypothesis that SARS-CoV-2 may be circulating in deer, we tested 283 retropharyngeal lymph node (RPLN) samples collected from 151 free-living and 132 captive deer in Iowa from April 2020 through December of 2020 for the presence of SARS-CoV-2 RNA. Ninety-four of the 283 deer (33.2%; 95% CI: 28, 38.9) samples were positive for SARS-CoV-2 RNA as assessed by RT-PCR. Notably, between November 23, 2020 and January 10, 2021, 80 of 97 (82.5%; 95% CI 73.7, 88.8) RPLN samples had detectable SARS-CoV-2 RNA by RT-PCR. Whole genome sequencing of the 94 positive RPLN samples identified 12 SARS-CoV-2 lineages, with B.1.2 (n = 51; 54.5%), and B.1.311 (n = 19; 20%) accounting for ~75% of all samples. The geographic distribution and nesting of clusters of deer and human lineages strongly suggest multiple zooanthroponotic spillover events and deer-to-deer transmission. The discovery of sylvatic and enzootic SARS-CoV-2 transmission in deer has important implications for the ecology and long-term persistence, as well as the potential for spillover to other animals and spillback into humans. These findings highlight an urgent need for a robust and proactive “One Health” approach to obtaining a better understanding of the ecology and evolution of SARS-CoV-2.

One-Sentence Summary

SARS-CoV-2 was detected in one-third of sampled white-tailed deer in Iowa between September 2020 and January of 2021 that likely resulted from multiple human-to-deer spillover and deer-to-deer transmission events.
Microbiome restructuring: dominant coral bacterium Endozoicomonas species display differential adaptive capabilities to environmental changes
Authors: Tandon Kshitij , Chiou Yu-Jing , Yu Sheng-Ping , Hsieh Hernyi Justin , Lu Chih-Ying , Hsu Ming-Tsung , Chiang Pei-Wen , Chen Hsing-Ju , Wada Naohisa , Tang Sen-Lin
Published: November 2021

Bacteria in the coral microbiome play a crucial role in determining coral health and fitness, and the coral host often restructures its microbiome composition in response to external factors. An important but often neglected factor determining this microbiome restructuring is the capacity of microbiome members to adapt to a new environment. To address this issue, we examined how the microbiome structure of Acropora muricata corals changed over 9 months following a reciprocal transplant experiment. Using a combination of metabarcoding, genomics, and comparative genomics approaches, we found that coral colonies separated by a small distance harbored different dominant Endozoicomonas related phylotypes belonging to two different species, including a novel species, Candidatus Endozoicomonas penghunesis 4G, whose chromosome level (complete) genome was also sequenced in this study. Furthermore, the two dominant Endozoicomonas species showed varied adaptation capabilities when coral colonies were transplanted in a new environment. The differential adaptation capabilities of dominant members of the microbiome can a) provide distinct advantages to coral hosts when subjected to changing environmental conditions and b) have positive implications for future reefs.
Transcriptional burst kinetics are linked to short term transcriptional memory
Authors: Senecal Adrien , Singer Robert , Coleman Robert
Published: November 2021

Transcriptional bursting is thought to be a stochastic process that allows the dynamic regulation of most genes. The random telegraph model assumes the existence of two states, ON and OFF. However recent studies indicate the presence of additional ON states, suggesting that bursting kinetics and their regulation can be quite complex. We have developed a system to study transcriptional bursting in the context of p53 biology using the endogenous p21 gene tagged with MS2 in human cells. Remarkably, we find that transcriptional bursts from the p21 gene contain multiple ON and OFF states that can be regulated by elevation of p53 levels. Distinct ON states are characterized by differences in burst duration, classified as Short and Long, with long bursts associated with higher Pol II initiation rates. Importantly, the different ON states display memory effects that allow us to predict the likelihood of properties of future bursting events. Long bursting events result in faster re-activation, longer subsequent bursts and higher transcriptional output in the future compared to short bursts. Bursting memory persists up to 2 hours suggesting a stable inheritable promoter architecture. Bursting memory at the p21 gene is the strongest under basal conditions and is suppressed by UV and inhibition of H3K9me1/2, which also increase transcriptional noise. Stabilization of p53 by Nutlin-3a partially reverses suppression of bursting memory suggesting that higher p53 levels may be a key in enforcing memory under conditions of cellular stress. Overall our data uncover a new found bursting property termed Short-Term Transcriptional Memory (STTM) that has the potential to fine-tune transcriptional output at the p21 gene.
The contribution of common regulatory and protein-coding TYR variants in the genetic architecture of albinism
Authors: Michaud Vincent , Lasseaux Eulalie , Green David J. , Gerrard Dave T. , Plaisant Claudio ,   UK Biobank Eye and Vision Consortium, Fitzgerald Tomas , Birney Ewan , Arveiler Benoît , Black Graeme C. , Sergouniotis Panagiotis I.
Published: November 2021

Genetic diseases have been historically segregated into rare Mendelian and common complex conditions.1,2 Large-scale studies using genome sequencing are eroding this distinction and are gradually unmasking the underlying complexity of human traits.3–8 Aiming to gain insights into the genetic architecture of rare recessive disorders, we studied a cohort of 1,313 individuals with albinism, an archetypal Mendelian condition. We investigated the contribution of protein-coding and regulatory variants both rare and common. We focused on TYR, the gene encoding tyrosinase, and found that a high-frequency promoter variant, TYR c.-301C>T [rs4547091], modulates the penetrance of a prevalent, disease-associated missense change, TYR c.1205G>A [rs1126809]. We also found that homozygosity for a haplotype formed by three common, functionally-relevant variants, TYR c.[-301C;575C>A;1205G>A], is associated with a high probability of receiving an albinism diagnosis (OR>82). This genotype is also associated with reduced visual acuity and increased central retinal thickness in UK Biobank participants. Finally, we report how the combined analysis of rare and common variants increases diagnostic yield and informs genetic counselling in families with albinism.
Emergence and spread of a sub-lineage of SARS-CoV-2 Alpha variant B.1.1.7 in Europe, and with further evolution of spike mutation accumulations shared with the Beta and Gamma variants
Authors: Stadtmüller Marlena , Laubner Alexa , Rost Fabian , Winkler Sylke , Patrasová Eva , Šimůnková Lenka , Reinhardt Susanne , Beil Johanna , Dalpke Alexander H. , Yi Buqing
Published: November 2021

SARS-CoV-2 evolution plays a significant role in shaping the dynamics of the COVD-19 pandemic. To monitor the evolution of SARS-CoV-2 variants,through international collaborations, we performed genomic epidemiology analyses on a weekly basis with SARS-CoV-2 samples collected from a border region between Germany, Poland and the Czech Republic in a global background. For identified virus mutant variants, active viruses were isolated and functional evaluations were performed to test their replication fitness and neutralization sensitivity against vaccine elicited serum neutralizing antibodies. Thereby we identified a new B.1.1.7 sub-lineage carrying additional mutations of nucleoprotein G204P and open-reading-frame-8 K68stop. Of note, this B.1.1.7 sub-lineage is the predominant B.1.1.7 variant in several European countries, such as Czech Republic, Austria and Slovakia. The earliest samples belonging to this sub-lineage were detected in November 2020 in a few countries in the European continent, but not in the UK. We have also detected its further evolution with extra spike mutations D138Y and A701V, which are signature mutations shared with the Beta and Gamma variants, respectively. Antibody neutralization assay of virus variant isolations has revealed that the variant with extra spike mutations is 3.2-fold less sensitive to vaccine-elicited antibodies as compared to other B.1.1.7 variants tested, indicating potential for immune evasion, but it also exhibited reduced replication fitness. The wide spread of this B.1.1.7 sub-lineage was related to the pandemic waves in early 2021 in various European countries. These findings about the emergence, spread, evolution, infection and transmission abilities of this B.1.1.7 sub-lineage add to our understanding about the pandemic development in Europe, and could possibly help to prevent similar scenarios in future.
Patient ABO blood type is a major predictor of a positive DAT following a transfusion reaction
Authors: Schnieders Eric , Leon Judith , Knudson C. Michael
Published: November 2021

Background

A direct antiglobulin test (DAT) checks for antibody or complement on the surface of RBCs and is often done following a transfusion reaction. While passive anti-A and anti-B antibodies are known to cause positive DATs, the extent this occurs following transfusion is unknown.

Study Design and methods

DAT results, ABO type and blood product information was recorded on 1097 transfusion reactions at a large academic hospital over 8 years. The effect of patient blood type, product type and plasma compatibility of blood product transfused on DAT results were determined. Statistical significance was determined using Chi-squared testing.

Results

Plasma compatibility of the product was a strong predictor of a positive DAT with plasma compatible transfusions having a 9.4% positive rate while plasma incompatible transfusions were positive 44% of the time (P<0.0001). Patient ABO blood type was a strong predictor of a positive DAT with Type O patients having 6.6% positive rate and non-O patients having a positive rate of 20.6% (P <0.0001). These results were significant for individual blood types as well. Type A, B or AB patients had higher DAT positive rates even when plasma incompatible transfusions were excluded from the analysis (P<0.0001). Platelets were significantly more likely to be associated with a positive DAT when compared to RBC transfusions.

Conclusions

These results show plasma compatibility and ABO types are strong predictors of positive DAT results following a transfusion reaction. Anti-A and anti-B antibodies are estimated to account for about 50% of positive DATs in this study.
Cell-Free Tumor DNA Dominant Clone Allele Frequency (DCAF) Is Associated With Poor Outcomes In Advanced Biliary Cancers Treated With Platinum-Based Chemotherapy
Authors: Uson Junior Pedro Luiz Serrano , Majeed Umair , Yin Jun , Botrus Gehan , Sonbol Mohamad Bassam , Ahn Daniel H. , Starr Jason S. , Jones Jeremy C , Babiker Hani , Inabinett Samantha R , Wylie Natasha , Boyle Ashton WR , Bekaii-Saab Tanios S. , Gores Gregory J , Smoot Rory , Barrett Michael , Nagalo Bolni , Meurice Nathalie , Elliott Natalie , Petit Joachim , Zhou Yumei , Arora Mansi , Dumbauld Chelsae , Barro Oumar , Baker Alexander , Bogenberger James , Buetow Kenneth , Mansfield Aaron , Mody Kabir , Borad Mitesh J.
Published: November 2021

PURPOSE

This investigation sough to evaluate the prognostic value of pre-treatment ctDNA in metastatic biliary tract cancers (BTC) treated with platinum based first-line chemotherapy treatment.

METHODS

We performed a retrospective analysis of 67 patients who underwent ctDNA testing before platinum-based chemotherapy for first-line treatment for metastatic BTC. For analysis we considered the detected gene with highest variant allele frequency (VAF) as the dominant clone allele frequency (DCAF). Results of ctDNA analysis were correlated with patients’ demographics, progression-free survival (PFS) and overall survival (OS).

RESULTS

The median age of patients was 67 years (27-90). 54 (80.6%) of 67 patients evaluated had intrahepatic cholangiocarcinoma; seven had extrahepatic cholangiocarcinoma and six gallbladder cancers. 46 (68.6%) of the patients were treated with cisplatin plus gemcitabine, 16.4% of patients received gemcitabine and other platinum (carboplatin or oxaliplatin) combinations while 15% of patients were treated on a clinical trial with gemcitabine and cisplatin plus additional agents (CX4945, PEGPH20 or nab-paclitaxel). TP53, KRAS, FGFR2, ARID1A, STK11 and IDH1 were the genes with highest frequency as DCAF. Median DCAF was 3% (0-97%). DCAF >3% was associated with worse OS (median OS: 10.8 vs. 18.8 months, p=0.032). Stratifying DCAF in quartiles, DCAF>10% was significantly related to worse PFS (median PFS: 3 months, p=0.014) and worse OS (median OS: 7.0 months, p=0.001). Each 1% increase in ctDNA was associated with a hazard ratio of 13.1 in OS when adjusting for subtypes, metastatic sites, size of largest tumor, age, sex, and CA19-9.

CONCLUSION

DCAF at diagnosis of advanced BTC can stratify patients who have worse outcomes when treated with upfront platinum-based chemotherapy. Each increase in %ctDNA decrease survival probabilities.
A new gene family diagnostic for intracellular biomineralization of amorphous Ca-carbonates by cyanobacteria
Authors: Karim Benzerara , Elodie Duprat , Tristan Bitard-Feildel , Géraldine Caumes , Corinne Cassier-Chauvat , Franck Chauvat , Manuela Dezi , Issa Diop Seydina , Geoffroy Gaschignard , Sigrid Görgen , Muriel Gugger , Purificación López-García , Fériel Skouri-Panet , David Moreira , Isabelle Callebaut
Published: November 2021

Cyanobacteria have massively contributed to carbonate deposit formation over the geological history. They are traditionally thought to biomineralize CaCO3extracellularly as an indirect byproduct of photosynthesis. However, the recent discovery of freshwater cyanobacteria forming intracellular amorphous calcium carbonates (iACC) challenges this view. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and evolutionary history remain elusive. Here, using comparative genomics, we identify a new gene (ccyA) and protein (calcyanin) family specifically associated with cyanobacterial iACC biomineralization. Calcyanin is composed of a conserved C-terminal domain, which likely adopts an original fold, and a variable N-terminal domain whose structure allows differentiating 4 major types among the 35 known calcyanin homologues. Calcyanin lacks detectable full-length homologs with known function. Yet, genetic and comparative genomic analyses suggest a possible involvement in Ca homeostasis, making this gene family a particularly interesting target for future functional studies. Whatever its function, this new gene family appears as a gene diagnostic of intracellular calcification in cyanobacteria. By searching forccyAin publicly available genomes, we identified 13 additional cyanobacterial strains forming iACC. This significantly extends our knowledge about the phylogenetic and environmental distribution of cyanobacterial iACC biomineralization, especially with the detection of multicellular genera as well as a marine species. Phylogenetic analyses indicate that iACC biomineralization is ancient, with independent losses in various lineages and some HGT cases that resulted in the broad but patchy distribution of calcyanin across modern cyanobacteria. Overall, iACC biomineralization emerges as a new case of genetically controlled biomineralization in bacteria.

Significance statement

Few freshwater species of Cyanobacteria have been known to mineralize amorphous CaCO3 (ACC) intracellularly. Despite the geochemical interest of this biomineralization, its evolutionary history and molecular mechanism remain poorly known. Here, we report the discovery of a new gene family that has no homolog with known function, which proves to be a good diagnostic marker of this process. It allowed to find cyanobacteria in several phyla and environments such as seawater, where ACC biomineralization had not been reported before. Moreover, this gene is ancient and was independently lost in various lineages with some later horizontal transfers, resulting in a broad and patchy phylogenetic distribution in modern cyanobacteria.
Flexible Circuit Mechanisms for Context-Dependent Song Sequencing
Authors: Roemschied Frederic A. , Pacheco Diego A. , Ireland Elise C. , Li Xinping , Aragon Max J. , Pang Rich , Murthy Mala
Published: November 2021

Many sequenced behaviors, including locomotion, reaching, and vocalization, are patterned differently in different contexts, enabling animals to adjust to their current environments. However, how contextual information shapes neural activity to flexibly alter the patterning of actions is not yet understood. Prior work indicates such flexibility could be achieved via parallel motor circuits, with differing sensitivities to sensory context [1, 2, 3]; instead we demonstrate here how a single neural pathway operates in two different regimes dependent on recent sensory history. We leverage the Drosophila song production system [4] to investigate the neural mechanisms that support male song sequence generation in two contexts: near versus far from the female. While previous studies identified several song production neurons[5, 6, 7, 8], how these neurons are organized to mediate song patterning was unknown. We find that male flies sing ‘simple’ trains of only one syllable or mode far from the female but complex song sequences consisting of alternations between modes when near to her. We characterize the male song circuit from the brain to the ventral nerve cord (VNC), and find that the VNC song pre-motor circuit is shaped by two key computations: mutual inhibition and rebound excitability [9] between nodes driving the two modes of song. Weak sensory input to a direct brain-to-VNC excitatory pathway (via pC2 brain and pIP10 descending neurons) drives simple song far from the female. Strong sensory input to the same pathway enables complex song production via simultaneous recruitment of P1a neuron-mediated disinhibition of the VNC song pre-motor circuit. Thus, proximity to the female effectively unlocks motor circuit dynamics in the correct sensory context. We construct a compact circuit model to demonstrate that these few computations are sufficient to replicate natural context-dependent song dynamics. These results have broad implications for neural population-level models of context-dependent behavior [10] and highlight that canonical circuit motifs [11, 12, 13] can be combined in novel ways to enable circuit flexibility required for dynamic communication.
The mitochondrial gene CMPK2 functions as a rheostat for macrophage homeostasis in inflammation
Authors: Arumugam Prabhakar , Chauhan Meghna , Rajeev Thejaswitha , Chakraborty Rahul , Shankaran Deepthi , Ramalingam Sivaprakash , Gandotra Sheetal , Rao Vivek
Published: November 2021

In addition to their role in cellular energy production, mitochondria are increasingly recognized as regulators of the innate immune response of phagocytes. Here, we demonstrate that altering expression levels of the mitochondria associated enzyme, cytidine monophosphate kinase 2 (CMPK2), disrupts mitochondrial physiology and significantly de-regulates the resting immune homeostasis of macrophages. Both CMPK2 silenced as well as constitutively over expressing macrophage lines portray mitochondrial stress with marked depolarization of their membrane potential, enhanced ROS and disturbed architecture culminating in the enhanced expression of the pro-inflammatory genes-IL1β, TNFα and IL8. Interestingly, the long-term modulation of CMPK2 expression resulted in an increased glycolytic flux of macrophages akin to the altered physiological state of activated M1 macrophages. While infection induced inflammation for restricting pathogens is regulated, our observation of a total dysregulation of basal inflammation by bidirectional alteration of CMPK2 expression, only highlights a critical role of this gene in mitochondria mediated control of inflammation.
Computational simulations reveal that Abl activity controls cohesiveness of actin networks in growth cones
Authors: Chandrasekaran Aravind , Clarke Akanni , McQueen Philip , Fang Hsiao Yu , Papoian Garegin A. , Giniger Edward
Published: November 2021

Extensive studies of growing axons have revealed many individual components and protein interactions that guide neuronal morphogenesis. Despite this, however, we lack any clear picture of the emergent mechanism by which this nanometer-scale biochemistry generates the multi-micron scale morphology and cell biology of axon growth and guidance in vivo. To address this, we studied the downstream effects of the Abl signaling pathway using a computer simulation software (MEDYAN) that accounts for mechanochemical dynamics of active polymers. Previous studies implicate two Abl effectors, Arp2/3 and Enabled, in Abl-dependent axon guidance decisions. We now find that Abl alters actin architecture primarily by activating Arp2/3, while Enabled plays a more limited role. Our simulations show that simulations mimicking modest levels of Abl activity bear striking similarity to actin profiles obtained experimentally from live-imaging of actin in wild type axons in vivo. Using a graph-theoretical filament-filament contact analysis, moreover, we find that networks mimicking hyperactivity of Abl (enhanced Arp2/3) are fragmented into smaller domains of actin that interact weakly with each other, consistent with the pattern of actin fragmentation observed upon Abl overexpression in vivo. Two perturbative simulations further confirm that high Arp2/3 actin networks are mechanically disconnected and fail to mount a cohesive response to perturbation. Taken together, these data provide a molecular-level picture of how the large-scale organization of the axonal cytoskeleton arises from the biophysics of actin networks.

Highlight summary

How do single-molecule dynamics produce multi-micron scale changes in actin organization in an extending axon? Comparison of computational simulations to in vivo data suggests that Abl kinase and Arp2/3 expand actomyosin networks by fragmenting into multiple domains, thus toggling the axon between states of local vs global internal connectivity.
A universal, single primer amplification protocol (R-SPA) to perform whole genome sequencing of segmented dsRNA reoviruses
Authors: Chrzastek Klaudia , Sellers Holly S. , Kapczynski Darrell R.
Published: November 2021

Background

The Reoviridae family represents the largest family of double-stranded RNA (dsRNA) viruses, and the members have been isolated from a wide range of mammals, birds, reptiles, fishes, insects, plants. Orthoreoviruses, one of the 15 recognized genera in the Reoviridae family, can infect humans and nearly all mammals, and birds. Genomic characterization of reoviruses has not been adopted on a large-scale due to the complexity of obtaining sequences for all 10 segments.

Results

In this study, we developed a time-efficient, and practical method to enrich reovirus sequencing reads from isolates that allowed for full genome recovery using single-primer amplification method coupled with next generation sequencing. We refer to this protocol as reovirus-Single Primer Amplification (R-SPA). Our results demonstrated that most of the genes were covered with at least 500 reads per base space. Furthermore, R-SPA covered both 5’ and 3’ end of each reovirus genes.

Conclusion

A universal and fast amplification protocol that yields double-stranded cDNA in sufficient abundance and facilitates and expedites the whole genome sequencing of reoviruses was presented in this study.