bluuebunny/crossref_metadata_2025 huggingface dataset:
SweepCluster: A SNP clustering tool for detecting gene-specific sweeps in prokaryotes
Authors: Qiu Junhui , Zhou Qi , Ye Weicai , Chen Qianjun , Bao Yun-Juan
Published: March 2021

Background

The gene-specific sweep is a selection process where an advantageous mutation along with the nearby neutral sites in a gene region increases the frequency in the population. It has been demonstrated to play important roles in ecological differentiation or phenotypic divergence in microbial populations. Therefore, identifying gene-specific sweeps in microorganisms will not only provide insights into the evolutionary mechanisms, but also unravel potential genetic markers associated with biological phenotypes. However, current methods were mainly developed for detecting selective sweeps in eukaryotic data of sparse genotypes and are not readily applicable to prokaryotic data. Furthermore, some challenges have not been sufficiently addressed by the methods, such as the low spatial resolution of sweep regions and lack of consideration of the spatial distribution of mutations.

Results

We proposed a novel gene-centric and spatial-aware approach for identifying gene-specific sweeps in prokaryotes and implemented it in a python tool SweepCluster. Our method searches for gene regions with a high level of spatial clustering of pre-selected polymorphisms in genotype datasets assuming a null distribution model of neutral selection. The pre-selection of polymorphisms is based on their genetic signatures, such as elevated population subdivision, excessive linkage disequilibrium, or significant phenotype association. Performance evaluation using simulation data showed that the accuracy and sensitivity of the clustering algorithm in SweepCluster is above 90%. The application of SweepCluster in two real datasets from the bacteriaStreptococcus pyogenesandStreptococcus suisshowed that the impact of pre-selection was dramatic and significantly reduced the uninformative signals. We validated our method using the genotype data fromVibrio cyclitrophicus, the only available dataset of gene-specific sweeps in bacteria, and obtained a concordance rate of 78%. We noted that the concordance rate could be underestimated due to distinct reference genomes and clustering strategies. The application to the human genotype datasets showed that SweepCluster is also applicable to eukaryotic data and recovered the known sweep regions in a wide dynamic range of pre-selection parameters.

Conclusions

SweepCluster is applicable to a broad category of datasets. It will be valuable for detecting gene-specific sweeps in diverse genotypic data and provide novel insights on adaptive evolution.
Affinity selection in germinal centers: Cautionary tales and new opportunities
Authors: Faro Jose , Castro Mario
Published: March 2021

Our current quantitative knowledge of the kinetics of antibody-mediated immunity is partly based on idealized experiments throughout the last decades. However, new experimental techniques often render contradictory quantitative outcomes that shake previously uncontroversial assumptions. This has been the case in the field of T-cell receptors, where recent techniques for measuring the 2-dimensional rate constants of T-cell receptor-ligand interactions exposed contradictory results to those obtained with techniques measuring 3-dimensional interactions. Recently, we have developed a mathematical framework to rationalize those discrepancies focusing on the proper fine-grained description of the underlying kinetic steps involved in the immune synapse. In this perspective article, we apply this approach to unveil potential blind spots in the case of B-cell receptors (BCR) and to rethink the interactions between B cells and follicular dendritic cells (FDC) during the germinal center (GC) reaction. Also, we elaborate on the concept of “catch bonds” and on the recent observations that B-cell synapses retract and pull antigen generating a “retracting force”, and propose some testable predictions that can lead to future research.
A specialist flea beetle manipulates and tolerates the activated chemical defense in its host plant
Authors: Sporer Theresa , Körnig Johannes , Wielsch Natalie , Gebauer-Jung Steffi , Reichelt Michael , Hupfer Yvonne , Beran Franziska
Published: March 2021

Glucosinolates, the characteristic secondary metabolites of Brassicales, are hydrolyzed upon herbivory by myrosinases to toxic and deterrent defense metabolites. The specialist flea beetle,Phyllotreta armoraciae, sequesters glucosinolates in the body despite myrosinase activity, but it is unknown whether plant myrosinase activity influences sequestration and how beetles prevent the hydrolysis of ingested glucosinolates. In feeding experiments performed with the myrosinase-deficientArabidopsis thaliana tgg1×tgg2(tgg) mutant and the corresponding wild type, we found that plant myrosinases reduced the glucosinolate sequestration rate by up to 50% and hydrolyzed a fraction of ingested glucosinolates in adult beetles. Although these results show thatP. armoraciaecannot fully prevent glucosinolate hydrolysis, we observed no negative influence on beetle performance. To understand howP. armoraciaecan avoid the hydrolysis of some ingested glucosinolates, we analyzed their fate directly after ingestion.P. armoraciaerapidly absorbed glucosinolates across the gut epithelium, a strategy that has been proposed to prevent hydrolysis in the gut lumen of sequestering insects. Moreover, beetle gut content suppressedin vitromyrosinase activity, and almost no myrosinase activity was detectable in the feces, which indicates that ingested myrosinases are inactivated in the beetle gut. In summary, we show thatP. armoraciaeuses several strategies to prevent the hydrolysis of ingested glucosinolates but can also tolerate the formation of glucosinolate hydrolysis products.
An ancient route towards salicylic acid and its implications for the perpetualTrichormus–Azollasymbiosis
Authors: de Vries Sophie , Herrfurth Cornelia , Li Fay-Wei , Feussner Ivo , de Vries Jan
Published: March 2021

Despite its small size, the water fernAzollais a giant among plant symbioses. Within each of its leaflets, a specialized leaf cavity is home to a population of nitrogen-fixing cyanobacteria (cyanobionts). While examples of nitrogen fixing cyanobionts are found across the land plant tree of life,Azollais unique in that its symbiosis is perpetual: the cyanobionts are inherited during sexual and vegetative propagation of the fern. What underpins the communication between the two partners? In angiosperms, the phytohormone salicylic acid (SA) is a well-known regulator of plant–microbe interactions. Using HPLC-MS/MS, we pinpoint the presence of SA in the fern; using comparative genomics and phylogenetics, we mined homologs of SA biosynthesis genes across Chloroplastida (Viridiplantae). While canonical isochorismate synthase (ICS) sequences are largely limited to angiosperms, homologs for the entire Phenylalanine ammonia-lyase (PAL)-dependent pathway likely existed in the last common ancestor of land plants. Indeed,A. filiculoidessecondarily lost its ICS, but has the genetic competence to derive SA from benzoic acid. Global gene expression data from cyanobiont-containing and -freeA. filiculoidesunveil a putative feedback loop: SA appears to induce cyanobacterial proliferation, which in turn down-regulates genes in SA biosynthesis and its responses.
Paper-and-pencil questionnaires analysis: a new automated technique to reduce analysis time and errors
Authors: Chabert Clovis , Collado Aurélie , Cheval Boris , Hue Olivier
Published: March 2021

Background and Objective

Questionnaires are essential tools in many scientific fields, including health and medicine. However, the analysis of paper-and-pencil questionnaires is time consuming, source of errors and expensive, limiting its use in large cohort studies. Computer-based questionnaires might be a valuable alternative but they may introduce bias, especially for sensitive questions, and they require programming skills. The aim of this study is to develop a reliable and adaptable open-source technique (i.e. LightQuest) to automatically analyse various types of scanned paper-and-pencil questionnaires with closed questions, including those with inverted scale.

Methods

To evaluate the usefulness of LightQuest, the time needed for 7 experimenters for manually code 10 sets of 4 frequently used questionnaires and the number of errors (i.e. reliability) were compared with the time and errors their made using LightQuest.

Results

LightQuest was twice as fast as the manual analysis, even though the time to create the reference model was taken into account (933s vs. 1935s, t(2)=8.81, p<0.001). Without model creation, the reduced analysis time was more pronounced, with an average of 2.77s.question-1for the manual technique versus 0.55s.question-1for LightQuest (t(2)=22.5, p<0.001). Moreover, during correction of the 5180 questions performed by the 7 experimenters, LightQuest made a total of 2 errors versus 46 with the manual technique (q(2)=4.53, p<0.05).

Conclusion

LightQuest demonstrated clear superiority both in terms of time and reliability. The script of this first open-source technique, which does not require programming skills, is downloadable in supplemental data and may become an asset for all studies using questionnaires.
Systems analysis of gut microbiome influence on metabolic disease in HIV and high-risk populations
Authors: Armstrong Abigail J.S. , Quinn Kevin , Fouquier Jennifer , Li Sam X. , Schneider Jennifer M. , Nusbacher Nichole M. , Doenges Katrina A. , Fiorillo Suzanne , Marden Tyson J. , Higgins Janine , Reisdorph Nichole , Campbell Thomas B. , Palmer Brent E. , Lozupone Catherine A.
Published: March 2021

Poor metabolic health, characterized by insulin resistance and dyslipidemia, is higher in people living with HIV and has been linked with inflammation, anti-retroviral therapy (ART) drugs, and ART-associated lipodystrophy (LD). Metabolic disease is associated with gut microbiome composition outside the context of HIV but has not been deeply explored in HIV infection nor in high-risk men who have sex with men (HR-MSM), who have a highly altered gut microbiome composition. Furthermore, the contribution of increased bacterial translocation and associated systemic inflammation that has been described in HIV-positive and HR-MSM individuals has not been explored. We used a multi-omic approach to explore relationships between impaired metabolic health, defined using fasting blood markers, gut microbes, immune phenotypes and diet. Our cohort included ART-treated HIV positive MSM with and without LD, untreated HIV positive MSM, and HR-MSM. For HIV positive MSM on ART, we further explored associations with the plasma metabolome. We found that elevated plasma lipopolysaccharide binding protein (LBP) was the most important predictor of impaired metabolic health and network analysis showed that LBP formed a hub joining correlated microbial and immune predictors of metabolic disease. Taken together, our results suggest the role of inflammatory processes linked with bacterial translocation and interaction with the gut microbiome in metabolic disease among HIV positive and negative MSM.

Importance Statement

The gut microbiome in people living with HIV (PLWH) is of interest as chronic infection often results in long term comorbidities. Metabolic disease is prevalent in PLWH even in well-controlled infection and has been linked with the gut microbiome in previous studies, but little attention has been given to PLWH. Furthermore, integrated analyses that consider gut microbiome together with diet, systemic immune activation, metabolites, and demographics have been lacking. In a systems-level analysis of predictors of metabolic disease in PLWH and men who are at high risk of acquiring HIV, we found that increased LBP, an inflammatory marker indicative of compromised intestinal barrier function, was associated with worse metabolic health. We also found impaired metabolic health associated with specific dietary components, gut microbes, and host and microbial metabolites. This work lays the framework for mechanistic studies aimed at targeting the microbiome to prevent or treat metabolic endotoxemia in HIV-infected individuals.
Multi-compartment analysis of the complex gradient-echo signal quantifies myelin breakdown in premanifest Huntington’s disease
Authors: Casella Chiara , Kleban Elena , Rosser Anne E. , Coulthard Elizabeth , Rickards Hugh , Fasano Fabrizio , Metzler-Baddeley Claudia , Jones Derek K.
Published: March 2021

White matter (WM) alterations have been identified as a relevant pathological feature of Huntington’s disease (HD). Increasing evidence suggests that WM changes in this disorder are due to alterations in myelin-associated biological processes. Multi-compartmental analysis of the complex gradient-echo MRI signal evolution in WM has been shown to quantify myelinin vivo, therefore pointing to the potential of this technique for the study of WM myelin changes in health and disease. This study first characterized the reproducibility of metrics derived from the complex multi-echo gradient-recalled echo (mGRE) signal across the corpus callosum in healthy participants, finding highest reproducibility in the posterior callosal segment. Subsequently, the same analysis pipeline was applied in this callosal region in a sample of premanifest HD patients (n = 19) and age, sex and education matched healthy controls (n = 21). In particular, we focused on two myelin-associated derivatives: i. the myelin water signal fraction (fm), a parameter dependent on myelin content; and ii. the difference in frequency between myelin and intra-axonal water pools (Δω), a parameter dependent on the ratio between the inner and the outer axonal radii. fmwas found to be lower in HD patients (β = −0.13, p = 0.03), while Δω did not show a group effect. Performance in tests of working memory, executive function, social cognition and movement was also assessed, and a greater age-related decline in executive function was detected in HD patients (β = −0.06, p = 0.006), replicating previous evidence of executive dysfunction in HD. Finally, the correlation between fm, executive function, and proximity to disease onset was explored in patients, and a positive correlation between executive function and fmwas detected (r = 0.542; p = 0.02). This study emphasises the potential of complex mGRE signal analysis for aiding understanding of HD pathogenesis and progression. Moreover, expanding on evidence from pathology and animal studies, it provides novelin vivoevidence supporting myelin breakdown as an early feature of HD.
Cell-intrinsic functions of the transcription factor Bhlhe40 in activated B cells and T follicular helper cells restrain the germinal center reaction and prevent lymphomagenesis
Authors: Rauschmeier René , Reinhardt Annika , Gustafsson Charlotte , Glaros Vassilis , Artemov Artem V. , Taneja Reshma , Adameyko Igor , Månsson Robert , Busslinger Meinrad , Kreslavsky Taras
Published: March 2021

The generation of high-affinity antibodies against pathogens and vaccines requires the germinal center (GC) reaction – a process that relies on a complex interplay between specialized effector subsets of B and CD4 T lymphocytes – GC B cells and T follicular helper (TFH) cells. Intriguingly, several key positive regulators of the GC reaction are common for both cell types. Here, we report that the transcription factor Bhlhe40 is a crucial cell-intrinsic negative regulator affecting both the B and T cell sides of the GC reaction. In activated CD4 T cells, Bhlhe40 was required to restrain proliferation thus limiting the number of TFHcells. In B cells, Bhlhe40 executed its function in the first days after immunization by selectively restricting the generation of the earliest GC B cells but not of early memory B cells or plasmablasts. Conditional Bhlhe40 inactivation confirmed cell-autonomous functions of Bhlhe40 in both GC B and TFHcells, while the GC phenotype was further enhanced upon loss of Bhlhe40 in both cell types. This negative regulation of the GC reaction by Bhlhe40 was of crucial importance, as Bhlhe40-deficient mice with progressing age succumbed to a B cell lymphoma characterized by accumulation of monoclonal GC B-like cells and polyclonal TFHcells in various tissues.
The GT factor ZmGT-3b mediates growth–defense tradeoff by regulating photosynthesis and defense response1
Authors: Zhang Qianqian , Lizhu E , Dai Weixing , Xu Mingliang , Ye Jianrong
Published: March 2021

Plant growth and development face constant threat from various environmental stresses. Transcription factors (TFs) are crucial for maintaining balance between plant growth and defense. Trihelix TFs display multifaceted functions in plant growth, development, and responses to various biotic and abiotic stresses. Here, we explore the role of a trihelix TF, ZmGT-3b, in regulating the growth–defense tradeoff in maize (Zea mays).ZmGT-3bis primed for instant response toFusarium graminearumchallenge by implementing a rapid and significant reduction of its expression to suppress seedling growth and enhance disease resistance.ZmGT-3bknockdown led to diminished growth, but improved disease resistance and drought tolerance in maize seedlings. InZmGT-3bknockdown seedlings, the chlorophyll content and net photosynthetic rate were strongly reduced, whereas the contents of major cell wall components, such as lignin, were synchronically increased. Correspondingly,ZmGT-3bknockdown specifically downregulated photosynthesis-related genes, especiallyZmHY5(encoding a conserved central regulator of seedling development and light responses), but synchronically upregulated genes associated with secondary metabolite biosynthesis and defense-related functions.ZmGT-3bknockdown induced defense-related transcriptional reprogramming and increased biosynthesis of lignin without immune activation. These data suggest that ZmGT-3b is a regulator of plant growth–defense tradeoff that coordinates metabolism during growth-to-defense transitions by optimizing the temporal and spatial expression of photosynthesis- and defense-related genes.

One-sentence summary

ZmGT-3b regulates photosynthesis activity and synchronically suppresses defense response.
Radiation Threats to Humans in Space and an alternative approach with Probiotics
Authors: Diken Dilara , Brodsky Elia , Kaur Harpreet , Mazumder Mohit
Published: March 2021

Space type radiation is an important factor to consider for scientists on International Space Stations, especially high linear transfer energy (LET) since it has imminent effects on microorganisms. The abundances of bacteria are a good indicator of how radiation influences the gut microbiome. The current study is an attempt towards this; thus, we have employed a public dataset (Bioproject code PRJNA368790) of 80 mice samples treated with a range of doses from 0Gy to 1Gy and feces samples were collected at different time points of post radiation treatment. Metagenomic analysis was performed on this data to understand the effect of radiation doses on the abundance of microbial species or microbial diversity implementing the DADA2 and Phyloseq pipelines. Our analyses have shown that 0.1Gy high LET radiation had the significant effect on the species of bacteria. There is a significant decrease in four types of bacteria, i.e., Bifidobacterium longum, Bifidobacterium castoris, Lactobacillus gasseri and Lactobacillus johnsonii, with p-value of 7.05×10-5, 0.020, 0.057and 0.020, respectively. Additionally, pathway analysis indicates the protein coding products of these bacteria are involved in the GABAergic synaptic pathway. Further, our study has shown the significant difference between post radiation time points, i.e., 10 days vs.30 days and suggested the acclimatization period could be around 10 days for these bacteria.
A role for a micron-scale supramolecular myosin array in adherens junction cytoskeletal assembly
Authors: Yu-Kemp Hui-Chia , Szymanski Rachel A. , Gadda Nicole C. , Lillich Madeline L. , Peifer Mark
Published: March 2021

Epithelial cells assemble specialized actomyosin structures at E-Cadherin-based cell-cell junctions, and the force exerted drives cell shape change during morphogenesis. The mechanisms used to build this supramolecular actomyosin structure remain unclear. We used ZO-knockdown MDCK cells, which assemble a robust, polarized and highly organized actomyosin cytoskeleton at the zonula adherens, and combined genetic and pharmacological approaches with super-resolution microscopy to define molecular machines required. To our surprise, inhibiting individual actin assembly pathways (Arp2/3, formins or Ena/VASP) did not prevent or delay assembly of this polarized actomyosin structure. Instead, as junctions matured, micrometer-scale supramolecular myosin arrays assembled, with aligned stacks of myosin filaments adjacent to the apical membrane, while associated actin filaments remained disorganized. This suggested these myosin arrays might bundle actin at mature junctions. Consistent with this, inhibiting ROCK or myosin ATPase disrupted myosin localization/organization, and prevented actin bundling and polarization. These results suggest a novel mechanism by which myosin self-assembly helps drive actin organization to facilitate cell shape change.

We explored mechanisms epithelial cells use to assemble supramolecular actomyosin structures at E-Cadherin-based cell-cell junctions. Our data suggest individual actin assembly pathways are not essential. Instead, microscopy and pharmacological inhibition suggest micrometer-scale supramolecular myosin arrays help bundle actin at mature junctions.
Injury caused by alcoholic cardiomyopathy in spontaneous ethanol drinking rats
Authors: Camargo Victória Mokarzel de Barros , Fioravante Vanessa Caroline , Pinheiro Patricia Fernanda Felipe , Martinez Francisco Eduardo
Published: March 2021

When speaking of pathologies caused or aggravated by the constant ingestion of ethanol, people with liver and central nervous system diseases soon come to mind, however, the acute intake of large amounts of ethanol and chronic abuse induce toxic effects in the majority of tissues. The heart is highlighted, since alcoholic cardiomyopathy (AC) has prevalence among alcoholics of 23 to 40% and occurs more frequently in men than in women. AC is characterized by dilation and poor contraction of one or both ventricles in the presence of increased ventricular wall thickness, along with a long history of ethanol abuse and no other cause identified. Our aim is to quantify the rate of cardiac tissue replacement, collagen fiber deposition and pro inflammatory cytokines in the left ventricle myocardium of volunteer ethanol drinking rats.
Thermal stimulation of pressure phosphenes
Authors: Kholmanskiy Alexander , Konyukhova Elena , Minakhin Andrey
Published: March 2021

To investigate effect on the intensity of pressure phosphenes (PP) of various methods of heating hands, as well as manual influence on cervical spine. This study included subjective assessments of the PP intensity in 10 healthy men, and chronometry of bioelectrical activity of brain and heart using electroencephalography (EEG) and electrocardiography (ECG). EEG and ECG frequency spectra respond synchronously to pressure, heat and light. The time of excitation of potential oscillations in the visual area of the cortex of both hemispheres is consistent with the delay in the onset of PP flaring. The effect of PP stimulation is enhanced when the hands and body are heated in a humid environment and at temperatures above 42 °C. Stimulation of PP by heating indicates the convergence of impulses from neurons of the lateral geniculate body (LGB) and nuclei of the thalamus, which are responsible for thermoreceptors in the skin of the palms and fingers. The thermal stimulation effect of PP is enhanced at temperatures above 42 °C due to the fact that thermoreceptors work as pain receptors. The mechanism of PP generation is dominated by the processes of redistribution and recombination of charges in the layers of the retina and LGB.
Individualized event structure drives individual differences in whole-brain functional connectivity
Authors: Betzel Richard F. , Cutts Sarah A. , Greenwell Sarah , Faskowitz Joshua , Sporns Olaf
Published: March 2021

Resting-state functional connectivity is typically modeled as the correlation structure of whole-brain regional activity. It is studied widely, both to gain insight into the brain’s intrinsic organization but also to develop markers sensitive to changes in an individual’s cognitive, clinical, and developmental state. Despite this, the origins and drivers of functional connectivity, especially at the level of densely sampled individuals, remain elusive. Here, we leverage novel methodology to decompose functional connectivity into its precise framewise contributions. Using two dense sampling datasets, we investigate the origins of individualized functional connectivity, focusing specifically on the role of brain network “events” – short-lived and peaked patterns of high-amplitude cofluctuations. Here, we develop a statistical test to identify events in empirical recordings. We show that the patterns of cofluctuation expressed during events are repeated across multiple scans of the same individual and represent idiosyncratic variants of template patterns that are expressed at the group level. Lastly, we propose a simple model of functional connectivity based on event cofluctuations, demonstrating that group-averaged cofluctuations are suboptimal for explaining participant-specific connectivity. Our work complements recent studies implicating brief instants of high-amplitude cofluctuations as the primary drivers of static, whole-brain functional connectivity. Our work also extends those studies, demonstrating that cofluctuations during events are individualized, positing a dynamic basis for functional connectivity.
The dynamic effect of regulatory genetic variation on thein vivoER stress transcriptional response
Authors: Russell Nikki D. , Chow Clement Y.
Published: March 2021

Genotype x Environment (GxE) interactions occur when environmental conditions drastically change the effect of a genetic variant. In order to truly understand the effect of genetic variation, we need to incorporate multiple environments into our analyses. Many variants, under steady state conditions, may be silent or even have the opposite effect under stress conditions. This study uses anin vivomouse model to investigate how the effect of genetic variation changes with tissue type and cellular stress. Endoplasmic reticulum (ER) stress occurs when misfolded proteins accumulate in the ER. This triggers the unfolded protein response (UPR), a large transcriptional response which attempts to return the cell to homeostasis. This transcriptional response, despite being a well conserved, basic cellular process, is highly variable across different genetic backgrounds, making it an ideal system to study GxE effects. In this study, we sought to better understand how genetic variation alters expression across tissues, in the presence and absence of ER stress. The use of different mouse strains and their F1s allow us to also identify context specificcis- andtrans-regulatory mechanisms underlying variable transcriptional responses. We found hundreds of genes that respond to ER stress in a tissue- and/or genotype-dependent manner. Genotype-dependent ER stress-responsive genes are enriched for processes such as protein folding, apoptosis, and protein transport, indicating that some of the variability occurs in canonical ER stress factors. The majority of regulatory mechanisms underlying these variable transcriptional responses derive fromcis-regulatory variation and are unique to a given tissue or ER stress state. This study demonstrates the need for incorporating multiple environments in future studies to better elucidate the effect of any particular genetic factor in basic biological pathways, like the ER stress response.

Author Summary

The effect of genetic variation is dependent on environmental context. Here we use genetically diverse mouse strains to understand how genetic variation interacts with stress state to produce variable transcriptional profiles. In this study, we take advantage of the endoplasmic reticulum (ER) stress response which is a large transcriptional response to misfolded proteins. Using this system, we uncovered tissue- and ER stress-specific effects of genetic variation on gene expression. Genes with genotype-dependent variable expression levels in response to ER stress were enriched for canonical ER stress functions, such as protein folding and transport. These variable effects of genetic variation are driven by unique sets of regulatory variation that are only active under context-specific circumstances. The results of this study highlight the importance of including multiple environments and genetic backgrounds when studying the ER stress response and other cellular pathways.
Context-dependent miR-21 regulation of TLR7-mediated autoimmune and foreign antigen driven antibody-forming cell and germinal center responses
Authors: Schell Stephanie L. , Bricker Kristen N. , Fike Adam J. , Chodisetti Sathi Babu , Domeier Phillip P. , Choi Nicholas M. , Fasnacht Melinda J. , Luckenbill Sara A. , Ziegler Steven F. , Rahman Ziaur S.M.
Published: March 2021

MicroRNAs (miRNAs) are involved in healthy B cell responses and the loss of tolerance in systemic lupus erythematosus (SLE), though the role of many miRNAs remains poorly understood. Dampening miR-21 activity was previously shown to reduce splenomegaly and blood urea nitrogen levels in SLE-prone mice, but the detailed cellular responses and mechanism of action remains unexplored. Herein, using the TLR7 agonist imiquimod-induced SLE model, we observed that loss of miR-21 inSle1bmice prevented the formation of plasma cells and autoantibody forming cells (AFC), without a significant effect on the magnitude of the germinal center (GC) response. We further observed reduced dendritic cell and monocyte numbers in the spleens of miR-21 deficientSle1b(Sle1b.miR-21KO) mice that were associated with reduced interferon, proinflammatory cytokines, and effector CD4+T cell responses. RNAseq analysis on B cells fromSle1b.miR-21KO mice revealed reduced activation and response to interferon and cytokine and target array analysis revealed modulation of numerous miR-21 target genes in response to TLR7 activation and type I interferon stimulation. Our findings in the B6.Sle1b.Yaa spontaneous model recapitulated the miR-21 role in TLR7-induced responses with an additional role in autoimmune GC and Tfh responses. Finally, immunization with T-dependent antigen revealed a role for miR-21 in foreign antigen driven GC and Ab, but not AFC responses. Our data suggest a potential multifaceted, context-dependent role for miR-21 in autoimmune and foreign antigen driven AFC and GC responses. Further study is warranted to delineate the cell-intrinsic requirements and mechanisms of miR-21 during infection and SLE development.

Key Points

miR-21 has context dependent effects on AFC and GC responses

miR-21 promotes TLR7-driven autoimmunity with activation of multiple B cell pathways

miR-21 is required for optimal B cell responses to T-dependent foreign antigen
A natural mutator allele shapes mutation spectrum variation in mice
Authors: Sasani Thomas A. , Ashbrook David G. , Beichman Annabel C. , Lu Lu , Palmer Abraham A. , Williams Robert W. , Pritchard Jonathan K. , Harris Kelley
Published: March 2021

Summary Paragraph

Although germline mutation rates and spectra can vary within and between species, genetic modifiers of these traits have long eluded detection. In this study, we searched for loci that influence germline mutagenesis using a uniquely powerful resource: a panel of recombinant inbred mouse lines known as theBXD, descended from the laboratory mouse strains C57BL/6J (B) and DBA/2J (D). Each BXD lineage has been maintained by brother-sister mating in the near absence of natural selection, accumulatingde novomutations for up to 50 years on a known genetic background that is a unique linear mosaic ofBandDhaplotypes. We show that mice inheritingDhaplotypes at a quantitative trait locus (QTL) on chromosome 4 accumulate C>A germline mutations at a 50% higher rate than those inheritingBhaplotypes, primarily due to the activity of a C>A-dominated mutational signature known as SBS18. TheBandDQTL haplotypes encode different alleles of the DNA repair geneMutyh, which underlies the heritable colorectal cancer syndrome in which SBS18 was first identified. TheBandD Mutyhalleles are present in wild populations ofMus musculus domesticus, providing evidence that common genetic variation modulates germline mutagenesis in a model mammalian species.
Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance
Authors: Tsai Kaitlyn , Stojković Vanja , Noda-Garcia Lianet , Young Iris D. , Myasnikov Alexander G. , Kleinman Jordan , Palla Ali , Floor Stephen N. , Frost Adam , Fraser James S. , Tawfik Dan S. , Fujimori Danica Galonić
Published: March 2021

Alteration of antibiotic binding sites through modification of ribosomal RNA (rRNA) is a common form of resistance to ribosome-targeting antibiotics. The rRNA-modifying enzyme Cfr methylates an adenosine nucleotide within the peptidyl transferase center, resulting in the C-8 methylation of A2503 (m8A2503). Acquisition ofcfrresults in resistance to eight classes of ribosome-targeting antibiotics. Despite the prevalence of this resistance mechanism, it is poorly understood whether and how bacteria modulate Cfr methylation to adapt to antibiotic pressure. Moreover, direct evidence for how m8A2503 alters antibiotic binding sites within the ribosome is lacking. In this study, we performed directed evolution of Cfr under antibiotic selection to generate Cfr variants that confer increased resistance by enhancing methylation of A2503 in cells. Increased rRNA methylation is achieved by improved expression and stability of Cfr through transcriptional and post-transcriptional mechanisms, which may be exploited by pathogens under antibiotic stress as suggested by natural isolates. Using a variant which achieves near-stoichiometric methylation of rRNA, we determined a 2.2 Å cryo-EM structure of the Cfr-modified ribosome. Our structure reveals the molecular basis for broad resistance to antibiotics and will inform the design of new antibiotics that overcome resistance mediated by Cfr.
MicroMator: Open and Flexible Software for Reactive Microscopy
Authors: Fox Zachary R , Fletcher Steven , Fraisse Achille , Aditya Chetan , Sosa-Carrillo Sebastián , Gilles Sébastien , Bertaux François , Ruess Jakob , Batt Gregory
Published: March 2021

Microscopy image analysis has recently made enormous progress both in terms of accuracy and speed thanks to machine learning methods. This greatly facilitates the online adaptation of microscopy experimental plans using real-time information of the observed systems and their environments. Here we report MicroMator, an open and flexible software for defining and driving reactive microscopy experiments, and present applications to single-cell control and single-cell recombination.
Theory of Mind and Moral Decision-Making in the Context of Autism Spectrum Disorder
Authors: Ringshaw Jessica Ellen , Hamilton Katie , Malcolm-Smith Susan
Published: March 2021

Social impairment in Autism Spectrum Disorder (ASD) has been linked to Theory of Mind (ToM) deficits. However, little research has investigated the relationship between ToM and moral decision-making in children with ASD. This study compared moral decision-making and ToM between aggregate-matched ASD and neurotypical boys (n=38 per group; aged 6-12). In a third-party resource allocation task manipulating recipient merit, wealth and health, neurotypical children allocated significantly more resources to the morally deserving recipient, suggesting equitable allocation. A comparatively larger portion of the ASD group allocated equally. ToM emerged as a predictor of moral decision-making. We suggest that ToM (cognitive empathy) deficits may underly atypical moral decision-making in ASD by limiting the integration of empathic arousal (affective empathy) with moral information.
Standard care vs. awake prone position in adult non-intubated patients with acute hypoxaemic respiratory failure secondary to COVID-19 infection – A multi-centre feasibility randomized controlled trial
Authors: Jayakumar Devachandran , Ramachandran Pratheema , Rabindrarajan Ebenezer , Tirupakuzhi Vijayaraghavan Bharath Kumar , Ramakrishnan Nagarajan , Venkataraman Ramesh
Published: March 2021

Background

The primary manifestation of Corona Virus Disease −2019 (COVID-19) is acute hypoxic respiratory failure secondary to pneumonia and/or acute respiratory distress syndrome. Prone position has been shown to improve outcomes in ventilated patients with moderate to severe acute respiratory distress syndrome. The feasibility and safety of awake prone positioning and its impact on outcomes if any, in non-intubated patients with mild to moderate acute respiratory distress syndrome secondary to COVID-19 is unknown. Results of the observational studies published thus far in this pandemic have been conflicting. In this context, we conducted a multi-centre, parallel group, randomised controlled feasibility study on awake prone positioning in non-intubated patients with COVID-19 pneumonia requiring supplemental oxygen.

Methods

60 patients diagnosed with acute hypoxic respiratory failure secondary to COVID −19 pneumonia requiring 4 or more litres of oxygen to maintain a saturation of ≥ 92% were recruited in this study. Thirty patients each were randomised to either standard care or awake prone group. Patients randomised to the standard care were allowed to change their position as per comfort and patients randomized to the prone group were encouraged to self-prone for at least 6 hours a day. The primary outcome was the proportion of patients adhering to the protocol in each group. Secondary outcomes include failure of therapy leading to escalation of respiratory support, number of hours prone, maximum hours of continuous prone positioning in a day, length of stay in ICU, ICU mortality, total number of patients needing intubation and adverse events.

Results

In the prone group, 43% (13 out of 30) of patients were able to self-prone for 6 or more hours a day. The median maximum prone duration per session was 2 hours. In the supine group, 47% (14 out of 30) were completely supine and 53% spent some hours in the prone position, but none exceeded 6 hours. There was no significant difference in any of the secondary outcomes between the two groups and there were no adverse events.

Interpretation

Awake proning in non-intubated patients with acute hypoxic respiratory failure is feasible and safe under clinical trial conditions. The results of our feasibility study will potentially help in the design of larger definitive trials to address this key knowledge gap.
Engagement with daily testing instead of self-isolating in contacts of confirmed cases of SARS-CoV-2
Authors: Martin Alex F , Denford Sarah , Love Nicola , Ready Derren , Oliver Isabel , Amlôt Richard , Rubin G. James , Yardley Lucy
Published: March 2021

Background

In December 2020, Public Health England with NHS Test and Trace initiated a pilot study in which close contacts of people with confirmed COVID-19 were given the option to carryout lateral flow device antigen tests at home, as an alternative to self-isolation for 10-14 days. In this study, we evaluated acceptability of and engagement with daily testing, and assessed levels of adherence to the rules relating to behaviour following positive or negative test results.

Methods

We conducted a service evaluation of a pilot study, involving an online cross-sectional survey offered to adult (> 18 years) contacts of confirmed COVID-19 cases who were invited to participate in seven days of daily testing instead of isolation. We used a comparison group of contacts who were not offered testing and performed self-isolation. Herein, we examine survey responses from a subset of those who took part in the pilot study and who responded to the evaluation questionnaire.

Results

Acceptability of daily testing was lower among survey respondents who were not offered the option of having it and among people from ethnic minority groups. Overall, 52% of respondents reported being more likely to share details of people that they had been in contact with following a positive test result, if they knew that their contacts would be offered the option of daily testing. Only 2% reported that they would be less likely to provide details of their contacts. On the days that they were trying to self-isolate, 19% of participants reported that they left the house, with no significant demographic group differences. Following a negative test, 13% of respondents reported that they increased their contacts, but most (58%) reported having fewer risky contacts.

Conclusions

Our data suggest that daily testing is potentially acceptable, and may facilitate sharing contact details of close contacts among those who test positive for COVID-19, and promote adherence to self-isolation. A better understanding is needed of how to make this option more acceptable for all households. The impact of receiving a negative test on behaviour remains a risk that needs to be monitored and mitigated by appropriate messaging. Future research should examine attitudes and behaviour in a context where infection levels are lower, testing is more familiar, much of the population has been vaccinated and restrictions on activity have been reduced.
Independent, Diplotype and Haplotype Association Analyses of the Selected MTHFR SNPs with the Risk of Breast Cancers in a South-Asian Population
Authors: Ajaz Sadia , Zaidi Sani-e-Zehra , Mehboob Ali Saleema , Siddiqa Aisha , Memon Muhammad Ali , Abid Aiysha , Khaliq Shagufta
Published: March 2021

PURPOSE

MTHFR is a pivotal enzyme in the folic acid cycle. In specific populations, two functional SNPs in the encoding gene, i.e. rs1801133 (677C/T) and rs1801131 (1298A/C), have shown associations with different diseases including cancers. In the present study, the role of these SNPs was analyzed in breast cancer cases from Pakistani population.

PARTICIPANTS AND METHODS

The pilot study includes 187 participants with 124 breast cancer patients and 63 matched individuals as controls. PCR-RFLP methods validated by Sanger sequencing were used for the polymorphic investigations. Hardy-Weinberg Equilibrium was tested by chi-squared goodness-of-fit test. Independent and combined associations were evaluated by Cochran-Armitage trend-test. Semi-parameteric haplotype analysis was carried out and odds ratios with 95% confidence interval were tabulated. Linkage disequilibrium between two loci was calculated. p-values <0.05 were significant.

RESULTS

Both MTHFR 677C/T and MTHFR 1298A/C SNPs were in Hardy-Weinberg Disequilibium. Cochran-Armitage trend test showed lack of independent associations of these SNPs with the risk for breast cancers. The diplotype analysis revealed that 677CC+1298AC increased the risk of breast cancers significantly [OR: 2.553 (95% CI: 1.177-5.541)], while 677CT+1298AA had a protective effect [OR: 0.537 (95% CI: 0.404-0.713)]. Haplotype analysis did not show any significant association. Interestingly, despite the proximity, these loci were not linked (r2 = 0.042 and 0.046 in cases and controls, respectively).

CONCLUSION

Here, we report association analysis of two putative candidate SNP markers in the MTHFR gene with breast cancers in a South-Asian population. To the best of our knowledge, two diplotype combinations show unique associations with breast cancer susceptibility in this population, which have not been reported earlier. The study implies translational potentials of these polymorphisms for breast cancer management.
COVID-19 Risk Factors and Mortality among Native Americans
Authors: Leggat-Barr Katherine , Uchikoshi Fumiya , Goldman Noreen
Published: March 2021

BACKGROUND

Academic research on the disproportionate impact of COVID-19 among Native Americans has largely been restricted to particular indigenous groups or reservations.

OBJECTIVE

We estimate COVID-19 mortality for Native Americans relative to other racial/ethnic groups and explore how state-level mortality is associated with known risk factors. METHODS: We use the Standard Mortality Ratio (SMR), adjusted for age, to estimate COVID-19 mortality by racial/ethnic groups for the U.S. and 16 selected states that account for three-quarters of the Native American population. The prevalence of risk factors is derived from the American Community Survey and the Behavioral Risk Factor Surveillance System.

RESULTS

The SMR for Native Americans greatly exceeds those for Black and Latino populations and varies enormously across states. There is a strong positive correlation across states between the share of Native Americans living on a reservation and the SMR. The SMR for Native Americans is highly correlated with the income-poverty ratio, the prevalence of multigenerational families, and health insurance (excluding the Indian Health Service). Risk factors associated with socioeconomic status and co-morbidities are generally more prevalent for Native Americans living on homelands, a proxy for reservation status, than for those living elsewhere.

CONCLUSIONS

Most risk factors for COVID-19 are disproportionately high among Native Americans. Reservation life appears to increase the risk of COVID-19 mortality.

CONTRIBUTION

We assemble and analyze a broader set of COVID-19-related risk factors for Native Americans than previous studies, a critical step toward understanding the exceptionally high COVID-19 death rates in this population.
What makes our lungs look red?
Authors: Huang Song , Lopez Cindia
Published: March 2021

What makes our lungs look red? This seems to be a naÏve and trivial question. Indeed, all the textbooks tell us that what makes our body red is the presence of blood, or more precisely the red blood cells (RBC). Here we provide some experimental evidence as well arguments to prove that this belief is wrong, or only partially true. In fact, we identified an important population of red cells located outside of the blood vessels as highly compacted clusters, in the connection tissues of the lungs of several species of animals including rat and human being. These red cells possessed each a nucleus, expressing several biomarkers of different cell types such as PF4, vWF, SCF-1R, CD200R, TGF-b, etc… Interestingly, being morphologically heterogeneous, they react collectively to certain stimuli. For example, they aggregated on collagen fibers forming clusters of cells resembling that observed in vivo. The red cells may have some features of Hematopoietic Stem Cells, since they were capable of differentiating into other cell types such as alveolar macrophages. In nasal polyps, these cells formed vessel-like structures, confined within a CD31-positive tubes. Upon exposure to toxic chemicals, they formed dense networks, suggesting a possible role in coagulation. Furthermore, the number of these red cells was greatly increased in the lungs of diseased donors, especially in the lungs of CF patients. Instead of being secreted as what happens in normal red cells, vWF proteins were tethered on the cytoplasmic membrane of the red cells isolated from the lungs of CF donors, which may explain at least partially the fibrotic nature of the CF lungs.

Taken together, we conclude that what makes the lungs look red is not the red blood cells, rather a distinct population of red cells, we call them Red Soma Cells (RSC). We believe that the discovery and characterization of this important population of cells will have profound theoretic as well as therapeutic implications.