bluuebunny/crossref_metadata_2025 huggingface dataset:
B cells are addicted to immunoglobulin production in the ER
Authors: Caganova Marieta , Taskiran Hakan , Zong Yue , Zach Andreas , Kabrani Eleni , Schmidt Kristin , Goffing Paul , Jellusova Julia , Rajewsky Klaus
Published: March 2022

Resting B cell dependence on the B cell antigen receptor (BCR) has been attributed solely to its signaling competence. We have recently shown that the presence of the BCR is vital for endoplasmic reticulum (ER) homeostasis and mitochondrial function both in primary B cells and Burkitt lymphoma (BL) cell lines. Unexpectedly, in BL Ramos cells this role has been shown to be independent of BCR signals from the cell membrane. Now, we provide evidence that also in mouse resting B cells ER-resident immunoglobulin (Ig) heavy chains control ER homeostasis, calcium storage and mitochondrial homeostasis through ER-mitochondria contacts. These findings demonstrate that BCR expression shapes cellular fitness already at the stage of assembly in the ER and uncover a new layer of B cell dependence on the production of Ig heavy chains in the ER. Sensing protein expression in the ER, with counterselection of compromised cells, might well operate also in other differentiated cells.
A Spatiotemporal Reconstruction of the C. elegans Pharyngeal Cuticle Reveals a Structure Rich in Phase-Separating Proteins
Authors: Kamal Muntasir , Tokmakjian Levon , Knox Jessica , Mastrangelo Peter , Ji Jingxiu , Cai Hao , Wojciechowski Jakub W. , Hughes Michael P. , Takács Kristóf , Chu Xiaoquan , Pei Jianfeng , Grolmusz Vince , Kotulska Malgorzata , Forman-Kay Julie D. , Roy Peter J.
Published: March 2022

Roughly 4.5 million species of ecdysozoan animals repeatedly shed their old cuticle and construct a new one underneath to accommodate growth. How cuticles are constructed is not well understood. Here, we systematically mine gene expression datasets to uncover the spatiotemporal blueprint for how the chitin-based pharyngeal cuticle of the nematode Caenorhabditis elegans is built. We demonstrate that the blueprint correctly predicts expression patterns and functional relevance to cuticle development. We find that as larvae prepare to molt, catabolic enzymes are upregulated and the genes that encode chitin synthase, chitin cross-linkers, and homologs of amyloid regulators subsequently peak in expression. 48% of the gene products secreted during the molt are predicted to be intrinsically disordered proteins (IDPs), many of which belong to four distinct families that are expressed in overlapping waves. These include the IDPAs, IDPBs, and IDPCs that are introduced for the first time here. We find that all four families have sequence properties known to drive phase separation and show in vitro phase separation for one of these proteins. This systematic analysis reveals the massive contribution that IDPs make to the cuticle and highlights how reversibly phase-separating materials may facilitate cuticle disassembly and reassembly during the molt.
A re-emerging arbovirus in livestock in China: Early genomic surveillance and phylogeographic analysis
Authors: Su Shuo
Published: March 2022

Viruses in livestock represent a great risk to public health due to the close contact of their hosts with humans and the potential long-range transportation though animal trade. Here, we show how to predict outbreaks of potential zoonotic pathogens and use spatially-explicit phylogeographic and phylodynamic approaches to provide estimates of key epidemiological parameters. First, we use metagenomic next generation sequencing (mNGS) to identify a Getah virus (GETV) as the pathogen responsible for a re-emerging swine disease in China. The GETV isolate is able to replicate in a variety of cell lines including human cells and shows high pathogenicity in a mouse model suggesting a potential public health risk. We obtained 16 complete genomes and 78 E2 gene sequences from viral strains collected within China from 2017 to 2021 through large-scale surveillance among livestock, pets and mosquitoes. Moreover, phylogenetic analysis reveals that three major GETV lineages are responsible for the current epidemic in livestock in China. We identify three potential positively selected sites and mutations of interest in E2, which may impact the transmissibility and pathogenicity of the virus. We then reconstruct the evolutionary and dispersal history of the virus and test the impact of several environmental factors on the viral genetic diversity through time and on the dispersal dynamic of viral lineages. Of note, we identify temporal variation in livestock meat consumption as a main predictor of viral genetic diversity through time. Finally, phylogeographic analyses indicate that GETV preferentially circulates within areas associated with relatively higher mean annual temperature and pig population density. Our results highlight the importance of continuous surveillance of GETV among livestock in southern Chinese regions associated with relatively high temperatures, and the need to control mosquitoes in the livestock farms. Our analyses of GETV also provide a baseline for future studies of the molecular epidemiology and early warning of emerging arboviruses in China.
The asymmetric ABA response on both sides of root tip is important for tomato root hydrotropism by mediating proton efflux and cell elongation
Authors: Yuan Wei , Liu Jianping , Dai Hui , Zhang Qian , Xu Weifeng , Zhang Jianhua , Li Ying
Published: March 2022

Hydrotropism is an important adaptation of plant roots to the uneven distribution of water, and the current research on hydrotropism is mainly focused on Arabidopsis thaliana. We examined hydrotropism in tomato (Solanum lycopersicum) primary roots. We used RNA sequencing to detect the gene expression on both sides (dry and wet side) of root tips (5 mm from the root cap junction) by splitting root tips longitudinally into two halves. We found that hydrostimulation induced the asymmetric cell elongation between the dry side (lower water potential) and wet side of root tips (higher water potential). ABA biosynthesis gene ABA4 was induced on the dry side as compared to the wet side of root tips. Chemical inhibitors that block ABA biosynthesis can disrupt hydrotropism, and ABA biosynthesis mutant not showed significantly reduced hydrotropism. Furthermore, asymmetric H+ efflux was found in wild-type but not in root tips of ABA biosynthesis mutant not after hydrostimulation. Our results suggest that the asymmetric ABA response on both sides of root tip mediate asymmetric H+ efflux, and then drive the asymmetric cell elongation, which allows the root to bend towards the wet side to take up more water.

Graphical abstract

Involvement of ABA-mediated asymmetric H+ efflux in root hydrotropism.

Compared to the wet side of root tip (higher water potential), the dry side (lower water potential) induces the expression of ABA biosynthesis gene ABA4, thus enhancing proton efflux to promoting cell elongation on the dry side. Because H+ efflux and cell elongation on the dry side of the root tip are higher than that on the wet side, the asymmetric growth of cells on both sides allows the root to bend towards the wet side for taking up more water.

In Brief

The asymmetric ABA response on both sides of root tip (dry side and wet side) sequently mediates root asymmetric H+ efflux, and then drives the asymmetric cell elongation on both sides of root tip, which allows the root to bend towards the wet side for absorbing more water.

Highlights

Hydrotropic bending requires asymmetric cell elongation on the root two sides.

Asymmetric expression of ABA biosynthesis gene ABA4 is required for root hydrotropism.

The H+ efflux on the dry side of the root is increased.

ABA-associated asymmetric H+ efflux driven root hydrotropic bending.
Rhythm of relationships in a social fish over the course of a full year in the wild
Authors: Aslak Ulf , Monk Christopher T. , Brockmann Dirk , Arlinghaus Robert
Published: March 2022

Animals are expected to adjust their social behaviour to cope with challenges in their environment. Therefore, for fish populations, in temperate regions with seasonal and daily environmental oscillations, characteristic rhythms of social relationships should be pronounced. To date, most research concerning fish social networks and biorhythms has occurred in artificial laboratory environments or over confined temporal scales of days to weeks. By contrast, little is known about the social networks of wild, freely roaming fish, including how seasonal and diurnal rhythms modulate social networks over the course of a full year. The advent of high-resolution acoustic telemetry enables us to quantify detailed social interactions in the wild over time-scales sufficient to examine seasonal rhythms at whole-ecosystems scales. Our objective was to explore the rhythms of social interactions in a social fish population at various time-scales over one full year in the wild by examining high-resolution snapshots of dynamic social network. To that end, we tracked the behaviour of 36 adult common carp,Cyprinus carpio, in a 25 ha lake and constructed temporal social networks among individuals across various time-scales, where social interactions were defined by proximity. We compared the network structure to a temporally shuffled null model to examine the importance of social attraction, and checked for persistent characteristic groups (“friendships”) over time. The clustering within the carp social network tended to be more pronounced during daytime than nighttime throughout the year. Social attraction, particularly during daytime, was a key driver for interactions. Shoaling behavior substantially increased during daytime in the wintertime, whereas in summer carp interacted less frequently, but the interaction duration increased. Characteristic groups were more common in the summer months and during nighttime, where the social memory of carp lasted up to two weeks. We conclude that social relationships of carp change diurnally and seasonally. These patterns were likely driven by predator avoidance, seasonal shifts in lake temperature, visibility, forage availability and the presence of anoxic zones. The techniques we employed can be applied generally to high-resolution biotelemetry data to reveal social structures across other fish species at ecologically realistic scales.
Multi-level cellular and functional annotation of single-cell transcriptomes
Authors: Mikolajewicz Nicholas , Brown Kevin R. , Moffat Jason , Han Hong
Published: March 2022

Single-cell RNA-sequencing (scRNA-seq) offers unprecedented insight into heterogenous biology, allowing for the interrogation of cellular populations and gene expression programs at single-cell resolution. Here, we introduce scPipeline, a single-cell analytic toolbox that offers modular workflows for multi-level cellular annotation and user-friendly analysis reports. Novel methods that are introduced to facilitate scRNA-seq annotation include: (i) co-dependency index (CDI)-based differential expression; (ii) cluster resolution optimization using a marker-specificity criterion; (iii) marker-based cell-type annotation with Miko scoring; and (iv) gene program discovery using scale-free shared nearest neighbor network (SSN) analysis. Our unsupervised and supervised procedures were validated using a diverse collection of scRNA-seq datasets and we provide illustrative examples of cellular and transcriptomic annotation of developmental and immunological scRNA-seq atlases. Overall, scPipeline provides a flexible computational framework for in-depth scRNA-seq analysis.
Motor Cortex Excitability in Chronic Low Back Pain
Authors: Corti E.J , Marinovic W , Nguyen A.T , Gasson N , Loftus A.M
Published: March 2022

Introduction

Chronic pain is associated with dysfunctional cortical excitability. Research has identified altered intracortical motor cortex excitability in Chronic Lower Back Pain (CLBP). However, research identifying the specific intracortical changes underlying CLBP has been met with inconsistent findings. In the present case-control study, we examined intracortical excitability of the primary motor cortex using transcranial magnetic stimulation (TMS) in individuals with CLBP.

Methods

Twenty participants with CLBP (Mage = 54.45 years, SDage = 15.89 years) and 18 age- and gender-matched, pain-free controls (M = 53.83, SD = 16.72) were included in this study. TMS was applied to the hand motor area of the right hemisphere and motor evoked potentials (MEPs) were recorded from the first dorsal interosseous muscle of the contralateral hand. Resting motor threshold (rMT) and MEP amplitude were measured using single-pulse stimulation. Short intracortical inhibition (SICI) and intracortical facilitation (ICF) were assessed using paired-pulse stimulation.

Results

Individuals with CLBP had significantly higher rMT (decreased corticospinal excitability) and reduced ICF compared to controls. No significant differences were found in MEP amplitude and SICI.

Conclusion

These findings add to the growing body of evidence that CLBP is associated with deficits in intracortical modulation involving glutamatergic mechanisms.

Significance

This article reports chronic lower back pain is associated with changes in intracortical excitability, specifically reduced intracortical facilitation. Furthermore, the imbalance between facilitation and inhibition may be related to pain intensity. These findings may help clinicians in the treatment of chronic pain with an increased focus on using neuromodulation techniques, targeting maladaptive intracortical facilitation, as a potential therapeutic tool in chronic pain.
Combined administration of inhaled DNase, baricitinib and tocilizumab as rescue treatment in COVID-19 patients with severe respiratory failure
Authors: Gavriilidis Efstratios , Antoniadou Christina , Chrysanthopoulou Akrivi , Ntinopoulou Maria , Smyrlis Andreas , Fotiadou Iliana , Zioga Nikoleta , Kogias Dionysios , Natsi Anastasia-Maria , Pelekoudas Christos , Satiridou Evangelia , Bakola Stefania-Aspasia , Papagoras Charalampos , Mitroulis Ioannis , Peichamperis Paschalis , Mikroulis Dimitrios , Papadopoulos Vasileios , Skendros Panagiotis , Ritis Konstantinos
Published: March 2022

COVID-19-related severe respiratory failure (SRF) leads to mechanical ventilation increasing the in-hospital mortality substantially. Abundancy of lung fibroblasts (LFs) in injured lung tissue has been associated with the progression of respiratory failure in COVID-19. Aiming to reduce mortality in patients with SRF (PaO2/FiO2<100 mmHg) and considering the multi-mechanistic nature of severe COVID-19 pathogenesis, we applied a combined rescue treatment (COMBI) on top of standard-of-care (SOC: dexamethasone and heparin) comprised inhaled DNase to dissolve thrombogenic neutrophil extracellular traps, plus agents against cytokine-mediated hyperinflammation, such as anti-IL-6 receptor tocilizumab and selective JAK1/2 inhibitor baricitinib. COMBI (n=22) was compared with SOC (n= 26), and with two previously and consecutively used therapeutic approaches, including either IL-1 receptor antagonist anakinra (ANA, n=19), or tocilizumab (TOCI, n=11), on top of SOC. In parallel, evaluation of immunothrombosis was assessed in vitro in human LFs, treated with the applied therapeutic agents upon stimulation with COVID-19 plasma. COMBI was associated with lower in-hospital mortality (p=0.014) and intubation rate (p=0.013), shorter duration of hospitalization (p=0.019), and prolonged overall survival after a median follow-up of 110±4 days (p=0.003). In vitro, COVID-19 plasma markedly induced tissue factor/thrombin pathway in LFs, while this effect was inhibited by the immunomodulatory agents of COMBI providing a mechanistic explanation for the clinical observations. These results suggest the design of randomized trials using combined immunomodulatory therapies in COVID-19-associated SRF targeting multiple interconnected pathways of immunothrombosis.
METHYLATION BIOMARKERS ASSOCIATED WITH DRUG-RESISTANT EPILEPSY
Authors: Sánchez Jiménez Patricia , Elizalde-Horcada Marcos , Sanz-García Ancor , Granero-Cremades Inmaculada , De Toledo María , Pulido Paloma , Navas Marta , Gago-Veiga Ana Beatriz , Alonso-Guirado Lola , Alonso-Cerezo María Concepción , Nava-Cedeño Desirée , Abad-Santos Francisco , Torres-Díaz Cristina Virginia , Ovejero-Benito María Carmen
Published: March 2022

Epilepsy is a disabling neurological disease that affects 2% of the population. Drug-resistant epilepsy (DRE) affects 25-30% of epilepsy patients. Understanding its underlying mechanisms is key to adequately manage this condition. To analyze the main epigenetic marks of DRE an epigenome-wide association study was carried out including samples from different regions of DRE patients’ brain and peripheral blood. An Illumina Infinium MethylationEPIC BeadChip array including cortex, hippocampus, amygdala, and peripheral blood from DRE subjected to neurosurgical resection of the epileptogenic zone was used. Overall, 32, 59, 3210, and 6 differentially methylated probes (DMPs) associated with DRE were found in the hippocampus, amygdala, cortex, and peripheral blood, respectively. These DMPs harbored 19, 28, 1574, and 7 genes, respectively, which play different roles in processes such as neurotrophic or calcium signaling. Three of the top DMPs observed in cortex were validated with methylation specific qPCR. Moreover, 163 DMPs associated with neurosurgery response at 6 months were found in the hippocampus. Genes located on these DMPs were involved in diverse processes such as synaptic signaling and central nervous system development. Besides 3 DMPs in blood samples were associated with response to neurosurgery at 12 months. In conclusion, the present study reports genome-wide DNA methylation changes across different regions of the DRE brain. These changes could be useful for further studies to disentangle the bases of DRE to search for therapeutic alternatives for this disease. Furthermore, they could also help identify patients likely to respond to neurosurgery.
Pan-cancer Analyses reveal functional similarities of three lncRNAs across multiple tumors
Authors: Khazaal Abir , Zandavi Seid Miad , Smolnikov Andrei , Fatima Shadma , Vafaee Fatemeh
Published: March 2022

Long non-coding RNAs (lncRNAs) are emerging as key regulators in many biological processes. The dysregulation of lncRNA expression has been associated with many diseases, including cancer. Mounting evidence suggests that lncRNAs are involved in cancer initiation, progression, and metastasis. Thus, understanding the functional implications of lncRNAs in tumorigenesis can aid in developing novel biomarkers and therapeutic targets. Rich cancer datasets, documenting genomic and transcriptomic alterations together with advancement in bioinformatics tools, have presented an opportunity to perform pan-cancer analyses across different cancer types. This study is aimed at conducting a pan-cancer analysis of lncRNAs by performing differential expression and functional analyses between tumor and normal adjacent samples across eight cancer types. Among dysregulated lncRNAs, seven were shared across all cancer types. We focused on three lncRNAs, found to be consistently dysregulated among tumors. It has been observed that these three lncRNAs of interest are interacting with a wide range of genes across different tissues, yet enriching substantially similar biological processes, found to be implicated in cancer progression and proliferation.
A modality independent proto-organization of human multisensory areas
Authors: Setti Francesca , Handjaras Giacomo , Bottari Davide , Leo Andrea , Diano Matteo , Bruno Valentina , Tinti Carla , Cecchetti Luca , Garbarini Francesca , Pietrini Pietro , Ricciardi Emiliano
Published: March 2022

The processing of multisensory information is based upon the capacity of brain regions, such as the superior temporal cortex, to combine information across modalities. However, it is still unclear whether the representation of coherent auditory and visual events does require any prior audiovisual experience to develop and function. In three fMRI experiments, intersubject correlation analysis measured brain synchronization during the presentation of an audiovisual, audio-only or video-only versions of the same narrative in distinct groups of sensory-deprived (congenitally blind and deaf) and typically-developed individuals. The superior temporal cortex synchronized across auditory and visual conditions, even in sensory-deprived individuals who lack any audiovisual experience. This synchronization was primarily mediated by low-level perceptual features and relied on a similar modality-independent topographical organization of temporal dynamics. The human superior temporal cortex is naturally endowed with a functional scaffolding to yield a common representation across multisensory events.
MODEL PREDICTIVE CONTROL OF CANCER CELLULAR DYNAMICS: A NEW STRATEGY FOR THERAPY DESIGN
Authors: Smart Benjamin , de Cesare Irene , Renson Ludovic , Marucci Lucia
Published: March 2022

Recent advancements in Cybergenetics have led to the development of new computational and experimental platforms that enable to robustly steer cellular dynamics by applying external feedback control. Such technologies have never been applied to regulate intracellular dynamics of cancer cells. Here, we show in silico that adaptive model predictive control (MPC) can effectively be used to steer signalling dynamics in Non-Small Cell Lung Cancer (NSCLC) cells to resemble those of wild-type cells, and to support the design of combination therapies. Our optimisation-based control algorithm enables tailoring the cost function to force the controller to alternate different drugs and/or reduce drug exposure, minimising both drug-induced toxicity and resistance to treatment. Our results pave the way for new cybergenetics experiments in cancer cells for drug combination therapy design.
Genetic engineering of Acidithiobacillus ferridurans with CRISPR-Cas9/dCas9 systems
Authors: Chen Jinjin , Liu Yilan , Mahadevan Radhakrishnan
Published: March 2022

Genus Acidithiobacillus includes a group of Gram-negative Fe/S-oxidizing acidophilic chemolithotrophic bacteria that are extensively studied and used for biomining processes. Synthetic biology approaches are key means to study and improve their biomining performance. However, efficient genetic manipulations in Acidithiobacillus are still major bottlenecks. In this study, we report a simple and efficient pAFi system (CRISPR-dCas9) and a scarless pAF system (CRISPR-Cas9) for genetic manipulations in A. ferridurans JAGS. The pAFi system harboring both dCas9 and sgRNA was constructed based on pBBR1MCS-2 to knockdown HdrA and TusA genes, separately, of which the transcription levels were significantly downregulated by 48% and 93%, separately. The pAF system carrying pCas9-sgRNA-homology arms was constructed based on pJRD215 to delete HdrB3 gene and overexpress Rus gene. Our results demonstrated that the pAF system is a fast and efficient genome editing method with an average rate of 15-20% per transconjugant in one recombination event, compared to 10-3 and then 10-2 in two recombination events by traditional markerless engineering strategy. Moreover, with these two systems, we successfully regulated iron and sulfur metabolisms in A. ferridurans JAGS: the deletion of HdrB3 reduced 48% of sulfate production, and substitution overexpression of Rus promoter showed 8.82-fold of mRNA level and enhanced iron oxidation rate. With these high-efficient genetic tools for A. ferridurans, we will be able to study gene functions and create useful recombinants for biomining applications. Moreover, these systems could be extended to other Acidithiobacillus strains and promote the development of synthetic biology-assisted biomining.

Highlights

Two shuttle vectors were constructed for Acidithiobacillus ferridurans

All-in-one pAFi (CRISPR-dCas9) and pAF (CRISPR-Cas9) systems were built up for gene knockdown and genome editing, separately

The transcription levels of HdrA and TusA were reduced 48% and 93% using pAFi system and thus suppressed sulfur oxidation

HdrB3 deletion and Rus overexpression were achieved using pAF system and showed significant effects on sulfur and iron oxidation respectively

Our pAF system facilitated genome editing in Acidithiobacillus ferridurans with high efficiency (15-20%) in less than 4 weeks
Detecting patterns of accessory genome coevolution in bacterial species using data from thousands of bacterial genomes
Authors: Mehta Rohan S , Petit Robert A , Read Timothy D , Weissman Daniel B
Published: March 2022

Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes that we call a “coevolution score”. The method is based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. This approach avoids the need for an accurate phylogenetic tree and allows very large datasets to be analyzed for signatures of recent coevolution. We apply our method to all of the more than 3 million pairs of genes from the entire annotated Staphylococcus aureus accessory genome of 2,756 annotated genes using a database of over 40,000 whole genomes. We find many pairs of genes that that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of dozens of rapidly coevolving genes, primarily consisting of genes involved in metal resistance, virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCCmec complex. Our results reflect the fact that the evolution of many bacterial pathogens since the middle of the twentieth century has largely been driven by antibiotic resistance gene gain, and in the case of S. aureus the SCCmec complex is the most prominent of these elements driving the evolution of resistance. The frequent coincidence of these gene gain or loss events suggests that S. aureus switch between antibiotic-resistant niches and antibiotic-susceptible ones. While we focus on gene gain and loss, our method can also detect genes which tend to acquire substitutions in tandem or, in datasets that include phenotypic information, genotype-phenotype or phenotype-phenotype coevolution.
Sub-cellular level resolution of common genetic variation in the photoreceptor layer identifies continuum between rare disease and common variation
Authors: Currant Hannah , Fitzgerald Tomas W , Patel Praveen J , Khawaja Anthony P ,   UK Biobank Eye and Vision Consortium, Webster Andrew R , Mahroo Omar A , Birney Ewan
Published: March 2022

Photoreceptor cells (PRCs) are the light-detecting cells of the retina. Such cells can be non-invasively imaged using optical coherence tomography (OCT) which is used in clinical settings to diagnose and monitor ocular diseases. Here we present the largest genome-wide association study of PRC morphology to date utilising quantitative phenotypes extracted from OCT images within the UK Biobank. We discovered 111 loci associated with the thickness of one or more of the PRC layers, many of which had prior associations to ocular phenotypes and pathologies. We further identified 10 genes associated with PRC thickness through gene burden testing using exome data. In both cases there was a significant enrichment for genes involved in rare eye pathologies, in particular retinitis pigmentosa. There was evidence for an interaction effect between common genetic variants, VSX2 involved in eye development and PRPH2 known to be involved in retinal dystrophies. We further identified a number of genetic variants with a differential effect across the macular spatial field. Our results suggest a continuum between normal and rare variation which impacts retinal structure, sometimes leading to disease.
Identifying the genes impacted by cell proliferation in proteomics and transcriptomics studies
Authors: Locard-Paulet Marie , Palasca Oana , Jensen Lars Juhl
Published: March 2022

Today, hypothesis-free high-throughput profiling allows relative quantification of thousands of proteins or transcripts across samples and thereby identification of differentially expressed genes. It is used in many biological contexts to characterize differences between cell lines and tissues, identify drug mode of action or drivers of drug resistance, among others. Genes can also be differentially regulated because of confounding factors that were not accounted for in the experimental plan, such as change in cell proliferation. Here, we identified genes for which expression consistently correlates with cell proliferation rates in proteomics and transcriptomics high-throughput data sets to determine the overall impact of cell growth rate on these data. We combined the analysis of 449 cell lines and 1,040 cell lines in five proteomics and three transcriptomics data sets to generate a refined list of 223 confounding genes that correlate with cell proliferation rates. These include many actors in DNA replication and mitosis, and genes periodically expressed during the cell cycle. It constitutes a valuable resource when analyzing high-throughput datasets showing changes in proliferation across conditions. We show how to use this resource to analyze in vitro drug screens and tumor samples. By disregarding the proliferation confounders, one can instead focus on the experiment-specific regulation events otherwise buried in the statistical analysis.
Dynamic single-cell RNA sequencing reveals BCG vaccination curtails SARS-CoV-2 induced disease severity and lung inflammation
Authors: Singh Alok K. , Wang Rulin , Lombardo Kara A. , Praharaj Monali , Bullen C. Korin , Um Peter , Davis Stephanie , Komm Oliver , Illei Peter B. , Ordonez Alvaro A. , Bahr Melissa , Huang Joy , Gupta Anuj , Psoter Kevin J. , Jain Sanjay K. , Bivalacqua Trinity J. , Yegnasubramanian Srinivasan , Bishai William R.
Published: March 2022

COVID-19 continues to exact a toll on human health despite the availability of several vaccines. Bacillus Calmette Guérin (BCG) has been shown to confer heterologous immune protection against viral infections including COVID-19 and has been proposed as vaccine against SARS-CoV-2 (SCV2). Here we tested intravenous BCG vaccination against COVID-19 using the golden Syrian hamster model together with immune profiling and single cell RNA sequencing (scRNAseq). We observed that BCG reduced both lung SCV2 viral load and bronchopneumonia. This was accompanied by an increase in lung alveolar macrophages, a reversal of SCV2-mediated T cell lymphopenia, and reduced lung granulocytes. Single cell transcriptome profiling showed that BCG uniquely recruits immunoglobulin-producing plasma cells to the lung suggesting accelerated antibody production. BCG vaccination also recruited elevated levels of Th1, Th17, Treg, CTLs, and Tmem cells, and differentially expressed gene (DEG) analysis showed a transcriptional shift away from exhaustion markers and towards antigen presentation and repair. Similarly, BCG enhanced lung recruitment of alveolar macrophages and reduced key interstitial macrophage subsets, with both cell-types also showing reduced IFN-associated gene expression. Our observations indicate that BCG vaccination protects against SCV2 immunopathology by promoting early lung immunoglobulin production and immunotolerizing transcriptional patterns among key myeloid and lymphoid populations.
miR319-targeted TCP4/LANCEOLATE directly regulates OVATE and auxin responses to modulate tomato gynoecium patterning and fruit morphology
Authors: Carvalho Airton , Vicente Mateus H. , Ferigolo Leticia F. , Silva Eder M. , Levy Matan , Peres Lazaro E.P. , Sablowski Robert , Schommer Carla , Ori Naomi , Nogueira Fabio T.S.
Published: March 2022

Diversity in fruit morphology is one of the hallmarks of varietal differences among modern cultivars of fruit-bearing crops. As evolutionarily related organs, fruits and leaves share developmental processes, but there are surprisingly few connections between regulatory pathways for fruit and leaf development. Here, we show the regulation of the leaf development-associated TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) TCP4/LANCEOLATE (TCP4/LA) transcription factor by the microRNA319 (miR319) is crucial for gynoecium patterning and establishment of fruit morphology. Loss of miR319 regulation leads to a premature, ectopic TCP4/LA expression during gynoecium patterning, which results in elongated fruits, resembling ovate mutants. TCP4/LA modulates tomato fruit development and morphology partially by directly repressing OVATE expression as early as 5-8 days post-inflorescence (dpi) flower buds. Furthermore, miR319-targeted CINCINNATA-like TCP4/LANCEOLATE controls auxin responses in developing flower buds by directly binding to the SlYUCCA4 promoter. Modulation of auxin biosynthesis by TCP4/LA is shared with other CINCINNATA-like TCPs during Arabidopsis gynoecium patterning. Our study defines a novel miRNA-based molecular link between OVATE, a fundamental gene associated with tomato domestication, and auxin responses in the control of fruit development and morphology. Given the striking variation in fruit shape among members of the Solanaceae family, fine-tuning regulation of gene expression by miRNA coupled with modulation of hormone dynamics may be a common driver in the evolution of fruit-shape diversity.
Using relative brain size as predictor variable: serious pitfalls and solutions
Authors: Smeele Simeon Q.
Published: March 2022

There is a long-standing interest in the effect of relative brain size on other life history variables in a comparative context. Historically, residuals have been used to calculate these effects, but more recently it has been recognised that regression on residuals is not good practice. Instead, absolute brain size and body size are included in a multiple regression, with the idea that this controls for allometry.

I use a simple simulation to illustrate how a case in which brain size is a response variable differs from a case in which relative brain size is a predictor variable. I use the simulated data to test which modelling approach can estimate the underlying causal effects for each case.

The results show that a multiple regression model with both body size and another variable as predictor variable and brain size as response variable work well. However, if relative brain size is a predictor variable, a multiple regression fails to correctly estimate the effect of body size.

I propose the use of structural equation models to simultaneously estimate relative brain size and its effect on the third variable and discuss other potential methods.
A subpopulation of Talin 1 resides in the nucleus and regulates gene expression
Authors: Da Silva Alejandro J. , Hästbacka Hendrik S. E. , Puustinen Mikael C. , Pessa Jenny C. , Goult Benjamin T. , Jacquemet Guillaume , Henriksson Eva , Sistonen Lea
Published: March 2022

Talin 1 (TLN1) is best known for its role at focal adhesions, where it activates β-integrin receptors and transmits mechanical stimuli to the actin cytoskeleton. Interestingly, the localization of TLN1 is not restricted to the focal adhesions, but its function in other cellular compartments remains poorly understood. By utilizing both biochemical and confocal microscopy analyses, we show that TLN1 localizes to the nucleus and that it strongly interacts with the chromatin. Importantly, depletion of endogenous TLN1 results in extensive changes in the gene expression profile of human breast epithelial cells. To determine the impact of nuclear TLN1 on gene regulation, we expressed a TLN1 fusion protein containing a nuclear localization signal. Our results revealed that nuclear TLN1 regulates a specific subset of the TLN1-dependent genes. Taken together, we show that apart from localizing at the plasma membrane and cytoplasm, TLN1 also resides in the nucleus where it functions in the regulation of gene expression.
High resolution reconstruction of a Jumbo bacteriophage infecting capsulated bacteria using hyperbranched tail fibers
Authors: Ouyang Ruochen , Costa Ana Rita , Cassidy C. Keith , Otwinowska Aleksandra , Williams Vera C. J. , Latka Agnieszka , Stansfeld Phill J. , Drulis-Kawa Zusanna , Briers Yves , Pelt Daan M. , Brouns Stan J. J. , Briegel Ariane
Published: March 2022

TheKlebsiellajumbo myophage ϕKp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combined cryo-electron microscopy methods, protein structure prediction methods, molecular simulations, and machine learning approaches to explore the capsid, tail, and tail fibers of this phage at high resolution. We determined the structure of the capsid and tail at 4.3Å and 4.1Å resolution. We observed that the tail fibers were highly branched and rearranged dramatically upon cell surface attachment. This complex configuration involves fourteen putative tail fibers with depolymerase activity that provide ϕKp24 with the ability to infect a broad panel of capsular polysaccharide (CPS) types ofKlebsiella pneumoniae. Taken together, our study provides structural and functional insight into how ϕKp24 adapts to the highly variable surfaces of capsulated bacterial pathogens, which will be useful for the development of phage therapy approaches against pan-drug resistantK. pneumoniaestrains.
Endogenous IL-10 Contributes to Wound Healing and Regulates Tissue Repair
Authors: Short Walker D. , Rae Meredith , Lu Thomas , Padon Benjamin , Prajapati Tanuj J. , Faruk Fayiz , Olutoye Oluyinka O. , Yu Ling , Bollyky Paul , Keswani Sundeep G. , Balaji Swathi
Published: March 2022

Background

Interleukin-10 (IL-10) is essential in fetal regenerative wound healing and likewise promotes a regenerative phenotype in adult dermal wounds. However, the role of endogenous IL-10 in postnatal dermal wound healing is not well established. We sought to determine the role of IL-10 in murine full thickness, excisional wounds that are splinted to prevent contracture and mimic human patterns of wound closure.

Methods

Full thickness, excisional wounds were made in wildtype (WT) and IL-10-/-mice on a C57BL/6J background (F/M, 8wks old). In a subset of wounds, contraction was prevented by splinting with silicone stents (stenting) and maintaining a moist wound microenvironment using a semi-occlusive dressing. Wounds were examined for re-epithelialization, granulation tissue deposition, and inflammatory cell infiltrate at day 7 and fibrosis and scarring at day 30 post-wounding.

Results

We observed no difference in wound healing rate between WT and IL-10-/-mice in either the stented or unstented group. At day 7, unstented IL-10-/-wounds had a larger granulation tissue area and more inflammatory infiltrate than their WT counterparts. However, we did observe more F4/80+cell infiltrate in stented IL-10-/-wounds at day 7. At day 30, stented wounds had increased scar area and epithelial thickness compared to unstented wounds.

Conclusions

These data suggest that endogenous IL-10 expression does not alter closure of full thickness excisional wounds when wound hydration and excessive contraction are controlled. However, the loss of IL-10 leads to increased inflammatory cell infiltration and scarring. These data suggest that previous reports of increased rates of healing in IL-10-/-mice ought to be revisited considering recent advances in wound healing models. Moreover, these new findings suggest that IL-10 contributes to regulation of inflammation without compromising the healing response.
Characterisation of TbSmee1 indicates that endocytosis is required for access of surface-bound cargo to the trypanosome flagellar pocket
Authors: Schichler Daja , Konle Antonia , Spath Eva-Maria , Riegler Sina , Klein Alexandra , Seleznev Anna , Jung Sisco , Wuppermann Timothy , Wetterich Noah , Borges Alyssa , Meyer-Natus Elisabeth , Havlicek Katharina , Cabrera Sonia Pérez , Niedermüller Korbinian , Sajko Sara , Dohn Maximilian , Malzer Xenia , Riemer Emily , Tumurbaatar Tuguldur , Djinovic-Carugo Kristina , Dong Gang , Janzen Christian J. , Morriswood Brooke
Published: March 2022

All endo- and exocytosis in the African trypanosomeTrypanosoma bruceioccurs at a single subdomain of the plasma membrane. This subdomain, the flagellar pocket, is a small vase-shaped invagination containing the root of the cell’s single flagellum. Several cytoskeleton-associated multiprotein complexes are coiled around the neck of the flagellar pocket on its cytoplasmic face. One of these, the hook complex, was proposed to affect macromolecule entry into the flagellar pocket lumen. In previous work, knockdown of the hook complex component TbMORN1 resulted in larger cargo being unable to enter the flagellar pocket. In this study, the hook complex component TbSmee1 was characterised in bloodstream formTrypanosoma bruceiand was found to be essential for cell viability. TbSmee1 knockdown resulted in flagellar pocket enlargement and impaired access to the flagellar pocket membrane by surface-bound cargo, similar to depletion of TbMORN1. Unexpectedly, inhibition of endocytosis by knockdown of clathrin phenocopied TbSmee1 knockdown, suggesting that endocytic activity itself is a prerequisite for the entry of surface-bound cargo into the flagellar pocket.

Characterisation of the essential trypanosome protein TbSmee1 suggests that endocytosis is required for flagellar pocket access of surface-bound cargo.
Place cells are non-randomly clustered by field location in CA1 hippocampus
Authors: Wirtshafter Hannah S. , Disterhoft John F.
Published: March 2022

A challenge in both modern and historic neuroscience has been achieving an understanding of neuron circuits, and determining the computational and organizational principles that underlie these circuits. Deeper understanding of the organization of brain circuits and cell types, including in the hippocampus, is required for advances in behavioral and cognitive neuroscience, as well as for understanding principles governing brain development and evolution. In this manuscript, we pioneer a new method to analyze the spatial clustering of active neurons in the hippocampus. We use calcium imaging and a rewarded navigation task to record from 100s of place cells in the CA1 of freely moving rats. We then use statistical techniques developed for and in widespread use in geographic mapping studies, global Moran’s I and local Moran’s I to demonstrate that cells that code for similar spatial locations tend to form small spatial clusters. We present evidence that this clustering is not the result of artifacts from calcium imaging, and show that these clusters are primarily formed by cells that have place field around previously rewarded locations. We go on to show that, although cells with similar place fields tend to form clusters, there is no obvious topographic mapping of environmental location onto the hippocampus, such as seen in the visual cortex. Insights into hippocampal organization, as in this study, can elucidate mechanisms underlying motivational behaviors, spatial navigation, and memory formation.
APOE ɛ2 vs APOE ɛ4 dosage shows sex-specific links to hippocampus-default network subregion co-variation
Authors: Savignac Chloé , Villeneuve Sylvia , Badhwar AmanPreet , Saltoun Karin , Shafighi Kimia , Zajner Chris , Sharma Vaibhav , Taliun Sarah A Gagliano , Farhan Sali , Poirier Judes , Bzdok Danilo
Published: March 2022

Alzheimer’s disease and related dementias (ADRD) are marked by intracellular tau aggregates in the medial-temporal lobe (MTL) and extracellular amyloid aggregates in the default network (DN). Here, we sought to clarify ADRD-related co-dependencies between the MTL’s most vulnerable structure, the hippocampus (HC), and the highly associative DN at a subregion resolution. We confronted the effects of APOE ɛ2 and ɛ4, rarely investigated together, with their impact on HC-DN co-variation regimes at the population level. In a two-pronged decomposition of structural brain scans from ∼40,000 UK Biobank participants, we located co-deviating structural patterns in HC and DN subregions as a function of ADRD family risk. Across the disclosed HC-DN signatures, recurrent deviations in the CA1, CA2/3, molecular layer, fornix’s fimbria, and their cortical partners related to ADRD risk. Phenome-wide profiling of HC-DN co- variation expressions from these population signatures revealed male-specific associations with air-pollution, and female-specific associations with cardiovascular traits. We highlighted three main factors associated with brain-APOE associations across the different gene variants: happiness, and satisfaction with friendships, and with family. We further showed that APOE ɛ2/2 interacts preferentially with HC-DN co-variation patterns in estimating social lifestyle in males and physical activity in females. Our findings reinvigorate the often-neglected interplay between APOE ɛ2 dosage and sex, which we have linked to fine-grained structural divergences indicative of ADRD susceptibility.
The Use and Misuse of Composite Environmental Indices
Authors: Fischer Shelley M. , Joy Michael K. , Abrahamse Wokje , Milfont Taciano L. , Petherick Lynda M.
Published: March 2022

Composite indices have been widely used to rank the environmental performance of nations. Such environmental indices can be useful in communicating complex information as a single value and have the potential to generate political and media awareness of environmental issues. However, indices that are poorly constructed can hinder efforts to identify environmental failings. Here, we provide a critical review of the theoretical and methodological foundations of environmental indices to enhance our understanding of the accuracy and applicability of such indices. In the present study we classify existing indices according to ranking goal, measurement components, and weighting methods. Using New Zealand and Niger as case studies, we examine correlations between ranks in ten national level indices to outline how measurement components and the goal of ranking itself may provide a more, or less, optimistic view of the state of a country’s environment. Our results suggest that environmental indices that include human health, socioeconomic, and policy indicators (such as human access to sanitation and clean drinking water) are positively correlated with each other, and that those excluding human health, socioeconomic, and policy indicators are also positively correlated with each other, while these two types of environmental indices are negatively correlated to each other. Our results demonstrate that the inclusion of indicators that do not relate to the actual state of natural environments can confound results. When choosing an existing environmental index – or developing a new one – it is important to assess whether the ranking goal and the included indicators are appropriate. This is important because the inclusion of confounding indicators in environmental indices may misrepresent the actual state of natural environments.