bluuebunny/crossref_metadata_2025 huggingface dataset:
New Role of Red Blood Cells in Absorption of DNA Bearing Tumorigenic Mutations from Lung Cancer Tissue
Authors: Liang Nai-Xin , Wang Tao , Zhang Cong , Jiao Zichen , Song Tianqiang , Liang Hongwei , Chen Qihan
Published: January 2021

Red blood cells (RBC) are commonly assumed to be vehicles for oxygen, carbon dioxide, and cells’ metabolic byproducts. In this study, we investigated whether RBC may contain cancer-cell derived DNA and whether such cargo may be used as a biomarker for detecting cancer. Using anin vitroco-culture system, we showed that RBC could absorb DNA bearing tumorigenic mutations from cancer cell lines. Next, we demonstrated that we could detect common genetic mutations, includingEGFR19 deletion, L858R, andKRASG12 in RBC collected from early-stage non-small cell lung cancer patients. We were able to repeat our finding using both next-generation sequencing and droplet digital PCR. Our study highlights a new biological phenomenon involving RBC and their translational potential as a novel liquid biopsy technology platform that can be used for early cancer screening.
Tool for estimating the probability of having COVID-19 with one or more negative RT-PCR results
Authors: Jara Alejandro , Undurraga Eduardo A. , Araos Rafael
Published: January 2021

Early case detection and isolation of infected individuals are critical to controlling COVID-19. RT-PCR is considered the diagnosis gold standard, but false-negatives occur. Based on previous work, we built a user-friendly online tool to estimate the probability of having COVID-19 with negative RT-PCR results and thus avoid preventable SARS-CoV-2 transmission.
Developmental and behavioral phenotypes in a new mouse model of DDX3X syndrome
Authors: Boitnott Andrea , Ung Dévina C , Garcia-Forn Marta , Niblo Kristi , Mendonca Danielle , Flores Michael , Maxwell Sylvia , Ellegood Jacob , Qiu Lily R , Grice Dorothy E , Lerch Jason P , Rasin Mladen-Roko , Buxbaum Joseph D , Drapeau Elodie , Rubeis Silvia De
Published: January 2021

Background

Mutations in the X-linked geneDDX3Xaccount for ~2% of intellectual disability in females, often co-morbid with behavioral problems, motor deficits, and brain malformations.DDX3Xencodes an RNA helicase with emerging functions in corticogenesis and synaptogenesis.

Methods

We generated aDdx3xhaploinsufficient mouse (Ddx3x+/−) with construct validity forDDX3Xloss-of-function mutations. We used standardized batteries to assess developmental milestones and adult behaviors, as well as magnetic resonance imaging and immunostaining of cortical projection neurons to capture early postnatal changes in brain development.

Results

Ddx3x+/−mice show physical, sensory, and motor delays that evolve into behavioral anomalies in adulthood, including hyperactivity, anxiety-like behaviors, cognitive impairments, and motor deficits. Motor function further declines with age. These behavioral changes are associated with a reduction in brain volume, with some regions (e.g., cortex and amygdala) disproportionally affected. Cortical thinning is accompanied by defective cortical lamination, indicating thatDdx3xregulates the balance of glutamatergic neurons in the developing cortex.

Conclusions

These data shed new light on the developmental mechanisms driving DDX3X syndrome and support face validity of this novel pre-clinical mouse model.
Control of topoisomerase II activity and chemotherapeutic inhibition by TCA cycle metabolites
Authors: Lee Joyce H. , Mosher Eric P. , Lee Young-Sam , Bumpus Namandjé N. , Berger James M.
Published: January 2021

Topoisomerase II (topo II) is essential for disentangling newly replicated chromosomes. DNA unlinking involves the physical passage of one DNA duplex through another and depends on the transient formation of double-strand DNA breaks, a step exploited by frontline chemotherapeutics to kill cancer cells. Although anti-topo II drugs are efficacious, they also elicit cytotoxic side effects in normal cells; insights into how topo II is regulated in different cellular contexts is essential to improve their targeted use. Using chemical fractionation and mass spectrometry, we have discovered that topo II is subject to metabolic control through the TCA cycle. We show that TCA metabolites stimulate topo II activityin vitroand that levels of TCA flux modulate cellular sensitivity to anti-topo II drugsin vivo. Our works reveals an unanticipated connection between the control of DNA topology and cellular metabolism, a finding with important ramifications for the clinical use of anti-topo II therapies.
Investigating densities of Symbiodiniaceae in two species of Antipatharians (black corals) from Madagascar
Authors: Gress Erika , Eeckhaut Igor , Godefroid Mathilde , Dubois Philippe , Richir Jonathan , Terrana Lucas
Published: January 2021

Here, we report the first methodological approach to investigate the presence and estimate the density of Symbiodiniaceae cells in corals of the order Antipatharia subclass Hexacorallia, known as black corals. Antipatharians are understudied ecosystem engineers of shallow (<30 m depth), mesophotic (30-150 m) and deep-sea (>200 m) reefs. They provide habitat to a vast number of marine fauna, enhancing and supporting coral reefs biodiversity globally. Nonetheless, little biological and ecological information exists on antipatharians, including the extent at which global change disturbances are threatening these corals. The assumption that they were exempted from threats related to climate change was challenged by findings of high density of dinoflagellates within three antipatharian colonies. Further methodical studies were necessary to investigate the regularity of these findings. An integrated design combining microscopy and molecular techniques was used to investigate the presence and estimate density of Symbiodiniaceae cells within two antipatharians species -Cupressopathes abiesandStichopathes maldivensis-from shallow and mesophotic reefs of SW Madagascar. Symbiodiniaceae-like cells were found within the two species from both shallow and mesophotic reefs, although the overall cell density was very low (0-4 cell mm-3). These findings suggest that high abundance of Symbiodiniaceae is not characteristic of antipatharians, which has relevant implications considering disruptions associated to climate change affecting other corals. However, the high densities of dinoflagellates found in antipatharian colonies exposed to higher light irradiance in other studies should be further examined.
First detection of herpesvirus and prevalence of mycoplasma infection in free-ranging Hermann’s tortoises (Testudo hermanni), and in potential pet vectors
Authors: Ballouard Jean-Marie , Bonnet Xavier , Jourdan Julie , Martinez-Silvestre Albert , Gagno Stéphane , Fertard Brieuc , Caron Sébastien
Published: January 2021

Abstract

Two types of pathogens cause highly contagious upper respiratory tract diseases (URTD) in Chelonians: testudinid herpesviruses (TeHV) and a mycoplasma (Mycoplasma agassizii). In captivity, these infections are frequent and can provoke outbreaks. Pet trade generates international flow of tortoises, often without sanitary checking; individuals intentionally or accidentally released in the wild may spread pathogens. A better understanding of the transmission of infectious agents from captivity to wild tortoises is needed. Many exotic individuals have been introduced in populations of the endangered western Hermann’s tortoise (Testudo hermanni hermanni), notably spur-thighed tortoises (Testudo graeca). We assessed the presence of TeHV and mycoplasma in native western Hermann’s tortoises and in potential pet vectors in south-eastern France. Using a large sample (N=572 tortoises), this study revealed, by PCR, the worrying presence of herpesvirus in 7 free-ranging individuals (3 sub-populations). Additionally,Mycoplasma agassiziiwas detected, by PCR, in 15 of the 18 populations sampled with a frequency ranging from 3.4% (1 of 29 tortoises) to 25% (3 of 12 tortoises). Exotic spur-thighed tortoises showed high frequency of mycoplasma infection in captivity (18.2%) and in individuals (50%) found in native Hermann’s tortoise sub-populations, suggesting that this species could be a significant vector. The paucity of information of TeHV on European tortoise’ URTD in natural settings, especially in combination with mycoplasma, prompts for further studies. Indeed, sick tortoises remain concealed and may not be easily detected in the field. Our results indicate a good health for most infected tortoise but it should be screened in the field as well as in captivity.
Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama
Authors: Titus Benjamin M. , Gibbs H. Lisle , Simões Nuno , Daly Marymegan
Published: January 2021

Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here we conduct range-wide sampling for Pederson’s cleaner shrimp(Ancylomenes pedersoni), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates x 45 evolutionary models x 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 million years ago. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate a novel pathway of species formation that resulted from one of the most biogeographically significant events in Earth’s history.
Evolutionarily conserved transcriptional landscape of the heart defining the chamber specific physiology
Authors: Gandhi Shrey , Witten Anika , deMajo Federica , Gilbers Martijn , Maessen Jos , Schotten Ulrich , de Windt Leon J. , Stoll Monika
Published: January 2021

Cardiovascular disease (CVD) remains the leading cause of death worldwide. A deeper characterization of the regional transcription patterns within different heart chambers may aid to improve our understanding of the molecular mechanisms involved in the function of the heart as well as our ability to develop novel therapeutic strategies. Here, we determined differentially expressed protein coding, long non-coding (lncRNA) and circular RNA (CircRNA) genes within various heart chambers across seven vertebrate species. We identified chamber specific genes, lncRNAs and pathways that are evolutionarily conserved in vertebrates. Further, we identified lncRNA homologs based on sequence, secondary structure, synteny and expressional conservation. Interestingly, most lncRNAs were found to be syntenically conserved. Various factors affect the co-expression patterns of transcripts including (i) genomic overlap, (ii) strandedness and (iii) transcript biotype. We also provide a catalogue of CircRNAs which are abundantly expressed across vertebrate hearts. Finally, we established a repository called EvoACTG (http://evoactg.uni-muenster.de/), which provides information about the conserved expression patterns for both PC genes and non-coding RNAs (ncRNAs) in the various heart chambers, and may serve as a community resource for investigators interested in the (patho)-physiology of CVD. We believe that this study will inform researchers working in the field of cardiovascular biology to explore the conserved yet intertwined nature of both coding and non-coding cardiac transcriptome across various popular model organisms in CVD research.
BisMapR: a strand-specific, nuclease-based method for genome-wide R-loop detection
Authors: Wulfridge Phillip , Sarma Kavitha
Published: January 2021

R-loops are three stranded nucleic acid structures with essential roles in many nuclear processes. However, their unchecked accumulation as seen in some neurodevelopmental diseases and cancers and is associated with compromised genome stability. Genome-wide profiling of R-loops in normal cells and their comparison in disease states can help identify precise locations of pathogenic R-loops and advance efforts to attenuate deviant R-loops while preserving biologically important ones. Toward this, we have developed an antibody-independent R-loop detection strategy, BisMapR, that combines nuclease-based R-loop isolation with non-denaturing bisulfite chemistry to produce high-resolution, genome-wide R-loop profiles that retain strand information. Furthermore, BisMapR achieves greater resolution and is faster than existing strand-specific R-loop profiling strategies. We applied BisMapR to reveal discrete R-loop behavior at gene promoters and enhancers. We show that gene promoters exhibiting antisense transcription form R-loops in both directions. and uncover a subset of active enhancers that, despite being bidirectionally transcribed, form R-loops exclusively on one strand. Thus, BisMapR reveals a previously unnoticed feature of active enhancers and provides a tool to systematically examine their mechanisms in gene expression.
Phosphorylation of JIP4 at S730 presents anti-viral properties against influenza A virus infection
Authors: Del Sarto Juliana , Gerlt Vanessa , Friedrich Marcel Edgar , Anhlan Darisuren , Wixler Viktor , Teixeira Mauro Martins , Boergeling Yvonne , Ludwig Stephan
Published: January 2021

Influenza A virus (IAV) is the causative agent of flu disease that results in annual epidemics and occasional pandemics. IAV alters several signaling pathways of the cellular host response in order to promote its replication. Therefore, our group investigates different host cell pathways modified in IAV infection as promising targets for long-lasting therapeutic approaches. Here, we show that c-Jun NH2-terminal kinase (JNK)-interacting protein (JIP) 4 is dynamically phosphorylated in IAV infection. Lack of JIP4 resulted in higher virus titers with significant differences in viral protein and mRNA accumulation as early as within the first replication cycle. In accordance, decreased IAV titers and protein accumulation was observed during overexpression of JIP4. Strikingly, the anti-viral function of JIP4 does neither originate from a modulation of JNK or p38 MAPK pathways, nor from altered expression of interferons or interferon-stimulated genes, but rather from a direct reduction of viral polymerase activity. Furthermore, interference of JIP4 with IAV replication is linked to phosphorylation of the serine at position 730, that is sufficient to impede with the viral polymerase and is mediated by the Raf/MEK/ERK pathway. Collectively, we provide evidence that JIP4, a host protein modulated in IAV infection, exhibits anti-viral properties that are dynamically controlled by its phosphorylation at S730.
Multiparametric Profiling of Single Nanoscale Extracellular Vesicles by Combined Atomic Force and Fluorescence Microscopy: Correlation and Heterogeneity in Their Molecular and Biophysical Features
Authors: Cavallaro Sara , Pevere Federico , Stridfeldt Fredrik , Görgens André , Paba Carolina , Sahu Siddharth S. , Mamand Doste R. , Gupta Dhanu , El Andaloussi Samir , Linnros Jan , Dev Apurba
Published: January 2021

Being a key player in intercellular communications, nanoscale extracellular vesicles (EVs) offer unique opportunities for both diagnostics and therapeutics. However, their cellular origin and functional identity remain elusive due to the high heterogeneity in their molecular and physical features. Here, for the first time, multiple EV parameters involving membrane protein composition, size and mechanical properties on single small EVs (sEVs) are simultaneously studied by combined fluorescence and atomic force microscopy. Furthermore, their correlation and heterogeneity in different cellular sources are investigated. The study, performed on sEVs derived from Human Embryonic Kidney 293, Cord Blood Mesenchymal Stromal and Human Acute Monocytic Leukemia cell lines, identifies both common and cell line-specific sEV subpopulations bearing distinct distributions of the common tetraspanins (CD9, CD63 and CD81) and biophysical properties. Although the tetraspanin abundances of individual sEVs are independent of their sizes, the expression levels of CD9 and CD63 are strongly correlated. A sEV population co-expressing all the three tetraspanins in relatively high abundance, however, having on average diameters <100 nm and relatively low Young moduli, is also found in all cell lines. Such a multiparametric approach is expected to provide new insights regarding EV biology and functions, potentially deciphering unsolved questions in this field.
Quantitative imaging of transcription in livingDrosophilaembryos reveals the impact of core promoter motifs on promoter state dynamics
Authors: Pimmett Virginia L , Dejean Matthieu , Fernandez Carola , Trullo Antonio , Bertrand Edouard , Radulescu Ovidiu , Lagha Mounia
Published: January 2021

Genes are expressed in stochastic transcriptional bursts linked to alternating active and inactive promoter states. A major challenge in transcription is understanding how promoter composition dictates bursting, particularly in multicellular organisms. We investigate two keyDrosophiladevelopmental promoter motifs, the TATA box (TATA) and the Initiator (INR). Using live imaging inDrosophilaembryos and new computational methods, we demonstrate that bursting occurs on multiple timescales ranging from seconds to minutes. TATA-containing promoters and INR-containing promoters exhibit distinct dynamics, with one or two separate rate-limiting steps respectively. A TATA box is associated with long active states, high rates of polymerase initiation, and short-lived, infrequent inactive states. In contrast, the INR motif leads to two inactive states, one of which relates to promoter-proximal polymerase pausing. Surprisingly, the model suggests pausing is not obligatory, but occurs stochastically for a subset of polymerases. Overall, our results provide a rationale for promoter switching during zygotic genome activation.
Characterizing the properties of bisulfite sequencing data: maximizing power and sensitivity to identify between-group differences in DNA methylation
Authors: Vellame Dorothea Seiler , Castanho Isabel , Dahir Aisha , Mill Jonathan , Hannon Eilis
Published: January 2021

Background

The combination of sodium bisulfite treatment with highly-parallel sequencing is a common method for quantifying DNA methylation across the genome. The power to detect between-group differences in DNA methylation using bisulfite-sequencing approaches is influenced by both experimental (e.g. read depth, missing data and sample size) and biological (e.g. mean level of DNA methylation and difference between groups) parameters. There is, however, no consensus about the optimal thresholds for filtering bisulfite sequencing data with implications for the reproducibility of findings in epigenetic epidemiology.

Results

We used a large reduced representation bisulfite sequencing (RRBS) dataset to assess the distribution of read depth across DNA methylation sites and the extent of missing data. To investigate how various study variables influence power to identify DNA methylation differences between groups, we developed a framework for simulating bisulfite sequencing data. As expected, sequencing read depth, group size, and the magnitude of DNA methylation difference between groups all impacted upon statistical power. The influence on power was not dependent on one specific parameter, but reflected the combination of study-specific variables. As a resource to the community, we have developed a tool, POWEREDBiSeq, which utilizes our simulation framework to predict study-specific power for the identification of DNAm differences between groups, taking into account user-defined read depth filtering parameters and the minimum sample size per group.

Conclusions

Our data-driven approach highlights the importance of filtering bisulfite-sequencing data by minimum read depth and illustrates how the choice of threshold is influenced by the specific study design and the expected differences between groups being compared. The POWEREDBiSeq tool can help users identify the level of data filtering needed to optimize power and aims to improve the reproducibility of bisulfite sequencing studies.
Detection of Rapidly Accumulating Stress-Induced SUMO in Prostate Cancer Cells by a Fluorescent SUMO Biosensor
Authors: Yin Rui , Song Jiacheng , Esquela-Kerscher Aurora , Kerscher Oliver
Published: January 2021

SUMO conjugates and SUMO chains form when SUMO, a small ubiquitin-like modifier protein, is covalently linked to other cellular proteins or itself. During unperturbed growth, cells maintain balanced levels of SUMO conjugates. In contrast, eukaryotic cells that are exposed to proteotoxic and genotoxic insults mount a cytoprotective SUMO-Stress Response (SSR). One hallmark of the SSR is a rapid and massive increase of SUMO conjugates in response to oxidative, thermal, and osmotic stress. Here, we use a recombinant fluorescent SUMO biosensor, KmUTAG-fl, to investigate differences in the SSR in a normal human prostate epithelial cell line immortalized with SV40 (PNT2) and two human prostate cancer cell lines that differ in aggressiveness and response to androgen (LNCaP and PC3). In cells that grow unperturbed, SUMO is enriched in the nuclei of all three cell lines. However, upon 30 minutes of exposure to ultraviolet radiation (UV) or oxidative stress, we detected significant cytosolic enrichment of SUMO as measured by KmUTAG-fl staining. This rapid enrichment in cytosolic SUMO levels was on average 5-fold higher in the LNCaP and PC3 prostate cancer cell lines compared to normal immortalized PNT2 cells. Additionally, this enhanced enrichment of cytosolic SUMO was reversible as cells recovered from stress exposure. Our study validates the use of the fluorescent KmUTAG-fl SUMO biosensor to detect differences of SUMO levels and localization between normal and cancer cells and provides new evidence that cancer cells may exhibit an enhanced SSR.
Linking plasmid-based beta-lactamases to their bacterial hosts using single-cell fusion PCR
Authors: Diebold Peter J. , New Felicia N. , Hovan Michael , Satlin Michael J. , Brito Ilana L.
Published: January 2021

The horizonal transfer of plasmid-encoded genes allows bacteria to adapt to constantly shifting environmental pressures, bestowing functional advantages to their bacterial hosts such as antibiotic resistance, metal resistance, virulence factors, and polysaccharide utilization. However, common molecular methods such as short- and long-read sequencing of microbiomes cannot associate extrachromosomal plasmids with the genome of the host bacterium. Alternative methods to link plasmids to host bacteria are either laborious, expensive or prone to contamination. Here we present the One-step Isolation and Lysis PCR (OIL-PCR) method, which molecularly links target ARGs with the bacterial 16S rRNA gene via fusion PCR performed within an emulsion. After validating this method, we apply it to identify the bacterial hosts of three clinically relevant beta-lactamases in a neutropenic patient population who are particularly vulnerable multidrug-resistant infections. We detect novel associations of two low-abundance genera,RomboutsiaandAgathobacter, with a multi-drug resistant plasmid harbored byKlebsiella pneumoniae. We put forth a robust, accessible, and high-throughput platform for sensitively surveying the bacterial hosts of mobile genes in complex microbial communities.
Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Plasticity ofClytiaMedusa Cell Types
Authors: Chari Tara , Weissbourd Brandon , Gehring Jase , Ferraioli Anna , Leclère Lucas , Herl Makenna , Gao Fan , Chevalier Sandra , Copley Richard R. , Houliston Evelyn , Anderson David J. , Pachter Lior
Published: January 2021

We present an organism-wide, transcriptomic cell atlas of the hydrozoan medusaClytia hemisphaerica, and determine how its component cell types respond to starvation. Utilizing multiplexed scRNA-seq, in which individual animals were indexed and pooled from control and perturbation conditions into a single sequencing run, we avoid artifacts from batch effects and are able to discern shifts in cell state in response to organismal perturbations. This work serves as a foundation for future studies of development, function, and plasticity in a genetically tractable jellyfish species. Moreover, we introduce a powerful workflow for high-resolution,wholeanimal,multiplexed single-cell genomics (WHAM-seq) that is readily adaptable to other traditional or non-traditional model organisms.
CD8+ T cell epitope variations suggest a potential antigen presentation deficiency for spike protein of SARS-CoV-2
Authors: Qiu Congling , Xiao Chanchan , Wang Zhigang , Chen Xiongfei , Gao Lijuan , Deng Jieping , Su Jun , Su Huanxing , Fang Evandro Fei , Zhang Zhang-Jin , Zhu Guodong , Zhang Jikai , Xie Caojun , Yuan Jun , Luo Oscar Junhong , Wang Pengcheng , Chen Guobing
Published: January 2021

COVID-19 is caused by a newly identified coronavirus, SARS-CoV-2, and has become a pandemic around the world. The illustration of the immune responses against SARS-CoV-2 is urgently needed for understanding the pathogenesis of the disease and its vaccine development. CD8+ T cells are critical for virus clearance and induce long lasting protection in the host. Here we identified specific HLA-A2 restricted T cell epitopes in the spike protein of SARS-CoV-2. Seven epitope peptides (n-Sp1, 2, 6, 7, 11, 13, 14) were confirmed to bind with HLA-A2 and potentially be presented by antigen presenting cells to induce host immune responses. Tetramers containing these peptides could interact with specific CD8+ T cells from convalescent COVID-19 patients, and one dominant epitope (n-Sp1) was defined. In addition, these epitopes could activate and generate epitope-specific T cellsin vitro, and those activated T cells showed cytotoxicity to target cells. Meanwhile, all these epitopes exhibited high frequency of variations. Among them, n-Sp1 epitope variation5L>Fsignificantly decreased the proportion of specific T cell activation; n-Sp1 epitope8L>Vvariant showed significantly reduced binding to HLA-A2 and decreased the proportion of n-Sp1-specific CD8+ T cell, which potentially contributes to the immune escape of SAR-CoV-2.
Nuclear translocation of tagged endogenous ERK/MPK-1 MAP Kinase denotes a subset of activation events inC. elegansdevelopment
Authors: Rasmussen Neal R. , Reiner David J.
Published: January 2021

The extracellular signal-regulated kinase (ERK) MAP kinase is utilized downstream of Ras>Raf>MEK signaling to control activation of a wide array of targets. Activation of ERK is elevated in Ras-driven tumors and RASopathies, and is thus a target for pharmacological inhibition. Regulatory mechanisms of ERK activation has been studied extensivelyin vitroand in cultured cells but little in living animals. We used CRISPR to tag the 3’ end of theC. elegansERK-encoding gene,mpk-1. Endogenous MPK-1 protein is ubiquitously expressed with elevated expression in certain tissues. We detected cytosol-to-nuclear translocation of MPK-1 in maturing oocytes and hence validated nuclear translocation as a reporter of some activation events. During developmental patterning of the six vulval precursor cells, MPK-1 is necessary and sufficient for the central cell, P6.p, to assume 1° fate. We observed MPK-1 to be recruited to the nuclei of all six VPCs in a temporal and concentration gradient centered on P6.p. This observation contrasts with previous results using the ERK-nKTR reporter of substrate activation, raising questions about mechanisms and indicators of MPK-1 activation. This system and reagent promise to provide critical insights into regulation of MPK-1 activation within a complex intercellular signaling network.
The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis
Authors: Zhou Ming , Coruh Ceyda , Xu Guanghui , Bourbousse Clara , Lambolez Alice , Law Julie A.
Published: January 2021

DNA methylation shapes the epigenetic landscape of the genome, plays critical roles in regulating gene expression, and ensures transposon silencing. As evidenced by the numerous defects associated with aberrant DNA methylation landscapes, establishing proper tissue-specific methylation patterns is critical. Yet, how such differences arise remains a largely open question in both plants and animals. Here we demonstrate that CLASSY1-4 (CLSY1-4), four locus-specific regulators of DNA methylation that are differentially expressed during plant development, play major roles in controlling tissue-specific DNA methylation patterns. Depending on the tissue, the genetic requirements for specific CLSYs differ significantly and, on a global scale, certainclsymutants are sufficient to largely shift the epigenetic landscape between tissues. Together, these findings not only reveal substantial epigenetic diversity between tissues, but assign these changes to specific CLSY proteins, revealing how locus-specific targeting combined with tissue-specific expression enables the CLSYs to generate epigenetic diversity during plant development.
Remodeling of oxygen-transporting tracheoles drives intestinal regeneration and tumorigenesis
Authors: Tamamouna Vasilia , Rahman M. Mahidur , Petersson Monika , Charalambous Irini , Kux Kristina , Mainor Hannah , Bolender Verena , Isbilir Buse , Edgar Bruce A. , Pitsouli Chrysoula
Published: January 2021

TheDrosophilatracheal system, as the functional equivalent of mammalian blood vessels, responds to hypoxia and transports oxygen throughout the body. Although the signaling pathways involved in tracheal development and the hypoxic response are well-studied, how adult tracheae interact with their target tissues is largely unknown. Here we show that the tracheae that serve the adult intestine are dynamic and respond to enteric infection, oxidative agents, and the development of gut tumors with increased terminal branching. Increased tracheation is necessary for efficient damage-induced intestinal stem cell (ISC)-mediated midgut regeneration and sufficient to drive ISC proliferation in the absence of damage. Gut damage or tumors induce Hif-1α/Sima, which, in turn, stimulates tracheole branching via the FGF(Brachless/Bnl)/FGFR(Breathless/Btl) signaling cascade. Bnl/Btl signaling is required both in the intestinal epithelium and the tracheal system for efficient damage-induced tracheal remodeling and ISC proliferation. We show that chemical orPseudomonas-generated ROS directly affect the trachea and are necessary for branching and intestinal regeneration. Similarly, tracheole branching and the resulting increase in oxygen supply are essential for tumor growth in the midgut. Thus, we have identified a novel mechanism of visceral tracheal-intestinal tissue communication, whereby oxidative damage and tumors induce neo-tracheogenesis in adultDrosophila.This process is reminiscent of cancer-induced neo-angiogenesis in mammals.
Anaerobic Benzene Biodegradation Linked to Growth of Highly Specific Bacterial Clades
Authors: Toth Courtney R. A. , Luo Fei , Bawa Nancy , Webb Jennifer , Guo Shen , Dworatzek Sandra , Edwards Elizabeth A.
Published: January 2021

Reliance on bioremediation to remove benzene from anoxic environments has proven risky for decades but for unknown reasons. Years of research have revealed a strong link between anaerobic benzene biodegradation and the enrichment of highly specific microbes, namelyThermincolain the family Peptococcaceae and the deltaproteobacterial Candidate Sva0485 clade. Using aquifer material from Canadian Forces Base Borden, we compared five bioremediation approaches in batch microcosms. Under conditions simulating natural attenuation or sulfate biostimulation, benzene was not degraded after 1-2 years of incubation and no enrichment of known benzene-degrading microbes occurred. In contrast, nitrate-amended microcosms reported benzene biodegradation coincident with significant growth ofThermincolaspp., along with a functional gene presumed to catalyze anaerobic benzene carboxylation (abcA). Inoculation with 2.5% of a methanogenic benzene-degrading consortium containing Sva0485 (DeltaproteobacteriaORM2) resulted in benzene biodegradation in the presence of sulfate or under methanogenic conditions. The presence of other hydrocarbon co-contaminants decreased rates of benzene degradation by a factor of 2-4. Tracking the abundance of theabcAgene and 16S rRNA genes specific for benzene-degradingThermincolaand Sva0485 is recommended to monitor benzene bioremediation in anoxic groundwater systems to further uncover growth rate limiting conditions for these two intriguing phylotypes.

SYNOPSIS

Anaerobic benzene biodegradation was accelerated by biostimulation with nitrate or by bioaugmentation under methanogenic or sulfate-reducing conditions.
Metabolic adaption to extracellular pyruvate triggers biofilm formation inClostridioides difficile
Authors: Tremblay Yannick D.N. , Durand Benjamin A.R. , Hamiot Audrey , Martin-Verstraete Isabelle , Oberkampf Marine , Monot Marc , Dupuy Bruno
Published: January 2021

Clostridioides difficileinfections are associated with gut microbiome dysbiosis and are the leading cause of hospital acquired diarrhoea. The infectious process is strongly influenced by the microbiota and successful infection relies on the absence of specific microbiota-produced metabolites. Deoxycholic acid (DOC) and short chain fatty acids are microbiota-produced metabolites that limit the growth ofC. difficileand protect the host against this infection. In a previous study, we showed that DOC causesC. difficileto form strongly adherent biofilms after 48 h. Here, our objectives were to identify and characterize key molecules and events required for biofilm formation in the presence of DOC. We applied time-course transcriptomics and genetics to identify sigma factors, metabolic processes and type IV pili that drive biofilm formation. These analyses revealed that extracellular pyruvate induces biofilm formation in the presence of DOC. In the absence of DOC, pyruvate supplementation was sufficient to induce biofilm formation in a process that was dependent on pyruvate uptake by the membrane protein CstA. In the context of the human gut, microbiota-generated pyruvate is a metabolite that limits pathogen colonization. Taken together our results suggest that pyruvate-induced biofilm formation might act as a key process drivingC. difficilepersistence in the gut.
Dynamics and turnover of memory CD8 T cell responses following yellow fever vaccination
Authors: Zarnitsyna Veronika I. , Akondy Rama S. , Ahmed Hasan , McGuire Don J. , Zarnitsyn Vladimir G. , Moore Mia , Johnson Philip L. F. , Ahmed Rafi , Li Kelvin , Hellerstein Marc , Antia Rustom
Published: January 2021

Understanding how immunological memory lasts a lifetime requires quantifying changes in the number of memory cells as well as how their division and death rates change over time. We address these questions by using a statistically powerful mixed-effects differential equations framework to analyze data from two human studies that follow CD8 T cell responses to the yellow fever vaccine (YFV-17D). Models were first fit to the frequency and division rates of YFV-specific memory CD8 T cells 42 days to 1 year post-vaccination. A different dataset, on the loss of YFV-specific CD8 T cells over three decades, was used to assess out of sample predictions of our models. The commonly used exponential and bi-exponential decline models performed relatively poorly. Models with the cell loss following a power law (exactly or approximately) were most predictive. Notably, using only the first year of data, these models accurately predicted T cell frequencies up to 30 years post-vaccination. Our analyses suggest that division rates of these cells drop and plateau at a low level (0.001 per day, ~double estimates for naive T cells) within one year following vaccination, whereas death rates continue to decline for much longer. Our results show that power laws can be predictive for T cell memory, a finding that may be useful for vaccine evaluation and epidemiological modeling. Moreover, since power laws asymptotically decline more slowly than any exponential decline, our results help explain the longevity of immune memory phenomenologically.

Author summary

Immunological memory, generated in response to infection or vaccination, may provide complete or partial protection from antigenically similar infections for the lifetime. Memory CD8 T cells are important players in protection from secondary viral infections but quantitative understanding of their dynamics in humans is limited. We analyze data from two studies where immunization with the yellow fever virus vaccine (YFV-17D) generates a mild acute infection and long-term memory. We find that: (i) the division rate of YFV-17D-specific CD8 T cells drops and stabilizes at ~ 0.1% per day during the first year following vaccination whereas the death rate declines more gradually, and (ii) the number of these cells declines approximately in accordance with a power law (∝time−0.82) for at least several decades following vaccination.
Probing mechanotransduction in living cells by optical tweezers and FRET-based molecular force microscopy
Authors: Sergides M. , Perego L. , Galgani T. , Arbore C. , Pavone F.S. , Capitanio M
Published: January 2021

Cells sense mechanical signals and forces to probe the external environment and adapt to tissue morphogenesis, external mechanical stresses, and a wide range of diverse mechanical cues. Here, we propose a combination of optical tools to manipulate single cells and measure the propagation of mechanical and biochemical signals inside them. Optical tweezers are used to trap microbeads that are used as handles to manipulate the cell plasma membrane; genetically encoded FRET-based force sensors inserted in F-actin and alpha-actinin are used to measure the propagation of mechanical signals to the cell cytoskeleton; while fluorescence microscopy with single molecule sensitivity can be used with a huge array of biochemical and genetic sensors. We describe the details of the setup implementation, the calibration of the basic components and preliminary characterization of actin and alpha-actinin FRET-based force sensors.
SARS-CoV-2 infection in Ivory Coast: a serosurveillance survey among gold mine workers
Authors: Milleliri Jean Marie , Coulibaly Daouda , Nyobe Blaise , Rey Jean-Loup , Lamontagne Franck , Hocqueloux Laurent , Giaché Susanna , Valery Antoine , Prazuck Thierry
Published: January 2021

Background

Eight months after the detection of the first COVID-19 case in Africa, 1,262,476 cases have been reported in African countries compared to 72 million worldwide. The real burden of SARS-CoV-2 infection in West Africa is not clearly defined. The aim of the study was to evaluate the seroprevalence of SARS-CoV-2 in half of the 3,380 workers of several mining companies operating in two mines in the Ivory Coast and having its headquarters in the economic capital Abidjan.

Methods

From 15th July to 13th October 2020, a voluntary serological test campaign was performed in the 3 sites where the companies operate: two mines, and the headquarters in Abidjan.We performed a COVID-PRESTO rapid test for the detection of IgG and IgM on capillary blood. A multivariate analysis was performed to identify independent sociodemographic characteristics associated with a higher SARS-CoV-2 seroprevalence rate.

Results

A total of 1,687 subjects were tested. 91% were male (n= 1,536) and mean age was 37 years old. The overall crude seroprevalence rate was 25.1% (n=422), but differing significantly between different sites, rising from 13.6% (11.2%-16.1%) in mine A to 34.4% (31.1%-37.7%) in mine B and 34.7% (26.2%-43.2%) in Abidjan. Non-resident workers in mines had a significantly lower prevalence rate than those living full-time in mines. Seroprevalence was 26.5% in natives of the Ivory Coast, while people coming from countries other than Africa were less likely to be SARS-CoV-2 seropositive. Among the 422 positive subjects, 74 reported mild symptoms in the three previous months and one was hospitalized for a severe COVID-19 infection.

Conclusion

The prevalence of SARS-CoV-2 infection among mine workers in Ivory Coast is high. The low morbidity observed has probably led to an underestimation of the burden of this infection in West Africa. The high prevalence reported in subjects living in Abidjan, who have not any close contact with mine workers, may be indicative of the real seroprevalence in the Ivory Coast capital.
Induction of labour during the COVID-19 pandemic: a national survey of impact on practice in the UK
Authors: Harkness M , Yuill C , Cheyne H , Stock SJ , McCourt C
Published: January 2021

Background

Induction of labour (IOL) is one of the most commonly performed interventions in maternity care, with outpatient cervical ripening increasingly offered as an option for women undergoing IOL. The COVID-19 pandemic has changed the context of practice and the option of returning home for cervical ripening may now assume greater significance. This work aimed to examine whether and how the COVID-19 pandemic has changed practice around IOL in the UK.

Method

We used an online questionnaire to survey senior obstetricians and midwives at all 156 UK NHS Trusts and Boards that currently offer maternity services. Responses were analysed to produce descriptive statistics, with free text responses analysed using a conventional content analysis approach.

Findings

Responses were received from 92 of 156 UK Trusts and Boards, a 59% response rate. Many Trusts and Boards reported no change to their IOL practice, however 23% reported change in methods used for cervical ripening; 28% a change in criteria for home cervical ripening; 28% stated that more women were returning home during cervical ripening; and 24% noted changes to women’s response to recommendations for IOL. Much of the change was reported as happening in response to attempts to minimise hospital attendance and restrictions on birth partners accompanying women.

Conclusions

The pandemic has changed practice around induction of labour, although this varied significantly between NHS Trusts and Boards. There is a lack of formal evidence to support decision-making around outpatient cervical ripening: the basis on which changes were implemented and what evidence was used to inform decisions is not clear.
Allosteric Regulation of the EphA2 Receptor Intracellular Region by Serine/Threonine Kinases
Authors: Lechtenberg Bernhard C. , Gehring Marina P. , Light Taylor P. , Matsumoto Mike W. , Hristova Kalina , Pasquale Elena B.
Published: January 2021

Eph receptor tyrosine kinases play a key role in cell-cell communication. However, lack of structural information on the entire multi-domain intracellular region of any Eph receptor has hindered detailed understanding of their signaling mechanisms. Here, we use an integrative structural biology approach combining X-ray crystallography, small-angle X-ray scattering and hydrogen-deuterium exchange mass spectrometry, to gain the first insights into the structure and dynamics of the entire EphA2 intracellular region. EphA2 promotes cancer malignancy through a poorly understood non-canonical form of signaling that depends on serine/threonine phosphorylation of the linker connecting the EphA2 kinase and SAM domains. We uncovered two distinct molecular mechanisms that may function in concert to mediate the effects of linker phosphorylation through an orchestrated allosteric regulatory network. The first involves a shift in the equilibrium between a “closed” configuration of the EphA2 intracellular region and an “open” more extended configuration induced by the accumulation of phosphorylation sites in the linker. This implies that cooperation of multiple serine/threonine kinase signaling networks is necessary to promote robust EphA2 non-canonical signaling. The second involves allosteric rearrangements in the kinase domain and juxtamembrane segment induced by phosphorylation of some linker residues, suggesting a link between EphA2 non-canonical signaling and canonical signaling through tyrosine phosphorylation. Given the key role of EphA2 in cancer malignancy, this new knowledge can inform therapeutic strategies.
Quantification of in-plane flexoelectricity in lipid bilayers
Authors: Thomas Nidhin , Agrawal Ashutosh
Published: January 2021

Lipid bilayers behave as 2D dielectric materials that undergo polarization and deformation in the presence of an electric field. This effect has been previously modeled by continuum theories which assume a polarization field oriented normal to the membrane surface. However, the molecular architecture of the lipids reveals that the heqadgroup dipoles are primarily oriented tangential to the membrane surface. Here, we perform atomistic and coarse-grained molecular dynamics simulations to quantify the in-plane polarization undergone by a flat bilayer and a spherical vesicle in the presence of an applied electric field. We use these predictions to compute an effective in-plane flexoelectric coefficient for four different lipid types. Our findings provide the first molecular proof of the in-plane polarization undergone by lipid bilayers and furnish the material parameter required to quantify membrane-electric field interactions.
Elastic stiffness coefficients of thiourea from thermal diffuse scattering
Authors: Büscher Julia , Mirone Alessandro , Stękiel Michał , Spahr Dominik , Morgenroth Wolfgang , Haussühl Eiken , Milman Victor , Bosak Alexei , Ivashko Oleh , von Zimmermann Martin , Dippel Ann-Christin , Winkler Björn
Published: January 2021

The complete elastic stiffness tensor of thiourea has been determined from thermal diffuse scattering (TDS) using high-energy photons (100 keV). Comparison with earlier data confirms a very good agreement of the tensor coefficients. In contrast with established methods to obtain elastic stiffness coefficients (e.g.Brillouin spectroscopy, inelastic X-ray or neutron scattering, ultrasound spectroscopy), their determination from TDS is faster, does not require large samples or intricate sample preparation, and is applicable to opaque crystals. Using high-energy photons extends the applicability of the TDS-based approach to organic compounds which would suffer from radiation damage at lower photon energies.