bluuebunny/crossref_metadata_2025 huggingface dataset:
Pre-treatment of the clinical sample with Proteinase K allows detection of SARS-CoV-2 in the absence of RNA extraction
Authors: Mallmann Larissa , Schallenberger Karoline , Demolliner Meriane , Antunes Eisen Ana Karolina , Hermann Bruna Saraiva , Heldt Fágner Henrique , Hansen Alana Witt , Spilki Fernando Rosado , Fleck Juliane Deise
Published: May 2020

COVID-19 (Coronavirus Disease 2019) outbreak was declared a pandemic, by World Health Organization, on March 11, 2020. Viral detection using RT-qPCR has been among the most important factors helping to control local spread of SARS-CoV-2 and it is considered the “gold standard” for diagnosis. Nevertheless, the RNA extraction step is both laborious and expensive, thus hampering the diagnosis in many places where there are not laboratory staff of funds enough to contribute for diagnosis efforts. Thus, the need to simplify procedures, reduce costs of the techniques used, and expand the capacity of the number of diagnostics of COVID-19 is imperative. In this study, detection of SARS-CoV-2 in the absence of RNA extraction has been successfully achieved through pre-treatment of the clinical sample with Proteinase K. The results show that only the use of proteinase K, without the need to perform the whole standard protocol for sample extraction and purification, can be an efficient technique for the diagnosis of COVID-19, since 91% of the samples matched the results with the standard procedure, with an average increase of 5.64 CT in the RT-qPCR.
Robust and Gradient Thickness Porous Membranes forIn VitroModeling of Physiological Barriers
Authors: Gholizadeh Shayan , Allahyari Zahra , Carter Robert , Delgadillo Luis F. , Blaquiere Marine , Nouguier-Morin Frederic , Marchi Nicola , Gaborski Thomas R.
Published: May 2020

Porous membranes are fundamental elements for tissue-chip barrier and co-culture models. However, the exaggerated thickness of commonly available membranes impedes an accuratein vitroreproduction of the biological multi-cellular continuum as it occursin vivo. Existing techniques to fabricate membranes such as solvent cast, spin-coating, sputtering and PE-CVD result in uniform thickness films. To understand critical separation distances for various barrier and co-culture models, a gradient thickness membrane is needed. Here, we developed a robust method to generate ultrathin porous parylene C (UPP) membranes not just with precise thicknesses down to 300 nm, but with variable gradients in thicknesses, while at the same time having porosities up to 25%. We also show surface etching and increased roughness lead to improved cell attachment. Next, we examined the mechanical properties of UPP membranes with varying porosity and thickness and fit our data to previously published models, which can help determine practical upper limits of porosity and lower limits of thickness. Lastly, we validate a straightforward approach allowing the successful integration of the UPP membranes into a prototyped 3D-printed scaffold enablingin vitrobarrier modeling and investigation of cell-cell interplay over variable distances using thickness gradients.
abPOA: an SIMD-based C library for fast partial order alignment using adaptive band
Authors: Gao Yan , Liu Yongzhuang , Ma Yanmei , Liu Bo , Wang Yadong , Xing Yi
Published: May 2020

Partial order alignment, which aligns a sequence to a directed acyclic graph, is now frequently used as a key component in long-read error correction and assembly. We present abPOA (adaptivebandedPartialOrderAlignment), a Single Instruction Multiple Data (SIMD) based C library for fast partial order alignment using adaptive banded dynamic programming. It can work as a stand-alone multiple sequence alignment and consensus calling tool or be easily integrated into any long-read error correction and assembly workflow. Compared to a state-of-the-art tool (SPOA), abPOA is up to 15 times faster with a comparable alignment accuracy.

Availability and implementation

abPOA is implemented in C. A stand-alone tool and a C/Python software interface are freely available athttps://github.com/yangao07/abPOA.

Contact

ydwang@hit.edu.cnorXINGYI@email.chop.edu
Demonstration of Patient-Specific Simulations To Assess Left Atrial Appendage Thrombogenesis Risk
Authors: García-Villalba Manuel , Rossini Lorenzo , Gonzalo Alejandro , Vigneault Davis , Martinez-Legazpi Pablo , Flores Oscar , Bermejo Javier , McVeigh Elliot , Kahn Andrew M. , del Álamo Juan C.
Published: May 2020

Atrial fibrillation (AF) alters left atrial (LA) hemodynamics, which can lead to thrombosis in the left atrial appendage (LAA), systemic embolism and stroke. A personalized risk-stratification of AF patients for stroke would permit improved balancing of preventive anticoagulation therapies against bleeding risk. We investigated how LA anatomy and function impact LA and LAA hemodynamics, and explored whether patient-specific analysis by computational fluid dynamics (CFD) can predict the risk of LAA thrombosis. We analyzed 4D-CT acquisitions of LA wall motion with an in-house immersed-boundary CFD solver. We considered six patients with diverse atrial function, three without a LAA thrombus (LAAT/TIA-neg), and three with either a LAA thrombus (removed digitally before running the simulations) or a history of transient ischemic attacks (LAAT/TIA-pos). We found that blood inside the left atrial appendage of LAAT/TIA-pos patients had marked alterations in residence time and kinetic energy when compared with LAAT/TIA-neg patients. In addition, we showed how the LA conduit, reservoir and booster functions distinctly affect LA and LAA hemodynamics. While the flow dynamics of fixed-wall and moving-wall simulations differ significantly, fixed-wall simulations risk-stratified our small cohort for LAA thrombosis only slightly worse than moving-wall simulations.
Spiny mice (Acomys) exhibit attenuated hallmarks of aging and rapid cell turnover after UV exposure in the skin epidermis
Authors: Wong Wesley , Kim Austin , Seifert Ashley W. , Maden Malcolm , Crane Justin D.
Published: May 2020

The study of long-lived and regenerative animal models has revealed diverse protective responses to stressors such as aging and tissue injury. Spiny mice (Acomys) are a unique mammalian model of skin regeneration, but their response to other types of physiological skin damage have not been investigated. In this study, we examine how spiny mice skin responds to acute UVB damage or chronological aging compared to non-regenerative C57Bl/6 mice (M. musculus). We find that, compared toM. musculus, the skin epidermis inA. cahirinusexperiences a similar UVB-induced increase in basal cell proliferation but exhibits increased epidermal turnover. Notably,A. cahirinusuniquely form a suprabasal layer co-expressing Keratin 14 and Keratin 10 after UVB exposure concomitant with reduced epidermal inflammatory signaling and reduced markers of DNA damage. In the context of aging, oldM. musculusanimals exhibit typical hallmarks including epidermal thinning, increased inflammatory signaling and senescence. However, these age-related changes are absent in oldA. cahirinusskin. Overall, we find thatA. cahirinushave evolved novel responses to skin damage that reveals new aspects of its regenerative phenotype.
Filamentous recombinant human Tau activates primary astrocytes via an integrin receptor complex
Authors: Wang Peng , Ye Yihong
Published: May 2020

Microtubule-associated protein Tau can form protein aggregates transmissible within the brain, correlating with the progression of tauopathies in humans. The transmission of aggregates requires neuron-released Tau to interact with surface receptors on target cells. However, the underlying molecular mechanisms in astrocytes and downstream effects are unclear. Here, using a spatially resolved proteomic mapping strategy, we show that integrin αV/β1 receptor binds recombinant human Tau, mediating the entry of Tau fibrils in astrocytes. The binding of distinct Tau species to the astrocytic αV/β1 receptor differentially activate integrin signaling. Furthermore, Tau-mediated activation of integrin signaling results in NFκB activation, causing upregulation of pro-inflammatory cytokines and chemokines, induction of a sub-group of neurotoxic astrocytic markers, and release of neurotoxic factors. Our findings suggest that filamentous recombinant human Tau-mediated activation of integrin signaling induces astrocyte conversion towards a neurotoxic state, providing a mechanistic insight into tauopathies.
ATG5 is instrumental in the transition from autophagy to apoptosis during the degeneration of tick salivary glands
Authors: Wang Yanan , Zhang Houshuang , Luo Li , Zhou Yongzhi , Cao Jie , Xuan Xuenan , Suzuki Hiroshi , Zhou Jinlin
Published: May 2020

Female tick salivary glands undergo rapid degeneration several days post engorgement. This degeneration may be caused by the increased concentration of ecdysone in the hemolymph during the fast feeding period and both autophagy and apoptosis occur. In this work, we first proved ATG and Caspase gene expression peaks during degeneration of the tick salivary glands. We explored the regulatory role ofRhipicephalus haemaphysaloidesautophagy related 5 (RhATG5) in the degeneration of tick salivary glands. During the fast feeding phase, RhATG5 was cleaved and both calcium concentration and the transcription of RhCalpains increased in the salivary glands. Recombinant RhATG5 was cleaved by μ-Calpain only in the presence of calcium; the mutant RhATG5191-199Δwas not cleaved. Treatment with 20-hydroxyecdysone (20E) led to programmed cell death in the salivary glands of unfed ticksin vitro, RhATG8-phosphatidylethanolamine (PE) was upregulated in ticks treated with low concentration of 20E. Conversely, RhATG8-PE decreased and RhCaspase-7 increased in ticks treated with a high concentration of 20E and transformed autophagy to apoptosis. High concentrations of 20E led to the cleavage of RhATG5. Calcium concentration and expression of RhCalpains were also upregulated in the tick salivary glands. RNA interference (RNAi) of RhATG5in vitroinhibited both autophagy and apoptosis of the tick salivary glands. RNAi of RhATG5in vivosignificantly inhibited the normal feeding process. These results demonstrated that high concentrations of 20E led to the cleavage of RhATG5 by increasing the concentration of calcium and stimulated the transition from autophagy to apoptosis.
Tumor neoantigen heterogeneity impacts bystander immune inhibition of pancreatic cancer growth
Authors: Das Manisit , Zhou Xuefei , Liu Yun , Das Anirban , Vincent Benjamin G. , Li Jingjing , Liu Rihe , Huang Leaf
Published: May 2020

The threshold for immunogenic clonal fraction in a heterogeneous solid tumor required to induce effective bystander killing of non-immunogenic subclones is unknown. Pancreatic cancer poses crucial challenges for immune therapeutic interventions due to low mutational burden and consequent lack of neoantigens. Here, we designed a model to incorporate artificial neoantigens into genes of interest in cancer cells and to test the potential of said antigens to actuate bystander killing. By precisely controlling the abundance of a neoantigen in the tumor, we studied the impact of neoantigen frequency on immune response and immune escape. Our results showed that a single, strong, widely expressed neoantigen could lead to a robust antitumor response when at least 80% of cancer cells express the neoantigen. Further, immunological assays revealed induction of T-cell responses against a non-target self-antigen on KRAS oncoprotein, when we inoculated animals with a high frequency of tumor cells expressing a test neoantigen. Using nanoparticle-based gene therapy, we successfully altered the tumor microenvironment by perturbing interleukin-12 and interleukin-10 gene expression. The subsequent remodeling of the microenvironment reduced the threshold of neoantigen frequency at which bioluminescent signal intensity for tumor burden decreased 1.5-logfold, marking a robust tumor growth inhibition, from 83% to as low as 29%. Our results thus suggest that bystander killing is rather inefficient in immunologically cold tumors like pancreatic cancer and requires an extremely high abundance of neoantigens. However, the bystander killing mediated antitumor response can be rescued, when supported by adjuvant immune therapy.
Modelling within-host macrophage dynamics in influenza virus infection
Authors: Li Ke , McCaw James M. , Cao Pengxing
Published: May 2020

Human respiratory disease associated with influenza virus infection is of significant public health concern. Macrophages, as part of the front line of host innate cellular defence, have been shown to play an important role in controlling viral replication. However, fatal outcomes of infection, as evidenced in patients infected with highly pathogenic viral strains, are often associated with prompt activation and excessive accumulation of macrophages. Activated macrophages can produce a large amount of pro-inflammatory cytokines, which leads to severe symptoms and at times death. However, the mechanism for rapid activation and excessive accumulation of macrophages during infection remains unclear. It has been suggested that the phenomena may arise from complex interactions between macrophages and influenza virus. In this work, we develop a novel mathematical model to study the relationship between the level of macrophage activation and the level of viral shedding in influenza virus infection. Our model combines a dynamic model of viral infection, a dynamic model of macrophages and the essential interactions between the virus and macrophages. Our model predicts that the level of macrophage activation can be negatively correlated with the level of viral shedding when viral infectivity is sufficiently high. We further identify that temporary depletion of resting macrophages in response to viral infection is a major driver in our model for the negative relationship between macrophage activation and viral shedding, providing new insight into the mechanisms that regulate macrophage activation. Our model serves as a framework to study the complex dynamics of virus-macrophage interactions and provides a mechanistic explanation for existing experimental observations, contributing to an enhanced understanding of the role of macrophages in influenza viral infection.
Reverse regression increases power for detecting trans-eQTLs
Authors: Banerjee Saikat , Simonetti Franco L. , Detrois Kira E. , Kaphle Anubhav , Mitra Raktim , Nagial Rahul , Söding Johannes
Published: May 2020

Trans-acting expression quantitative trait loci (trans-eQTLs) are genetic variants affecting the expression of distant genes. They account for ≥70% expression heritability and could therefore facilitate uncovering mechansisms underlying the origination of complex diseases. However, unlike cis-eQTLs, identifying trans-eQTLs is challenging because of small effect sizes, tissue-specificity, and the severe multiple-testing burden. Trans-eQTLs affect multiple target genes, but aggregating evidence over individual SNP-gene associations is hampered by strong gene expression correlations resulting in correlated p-values. Our method Tejaas predicts trans-eQTLs by performing L2-regularized ‘reverse’ multiple regression of each SNP on all genes, aggregating evidence from many small trans-effects while being unaffected by the strong expression correlations. Combined with a novel non-linear, unsupervised k-nearest-neighbor method to remove confounders, Tejaas predicted 18851 unique trans-eQTLs across 49 tissues from GTEx. They are enriched in open chromatin, enhancers and other regulatory regions. Many overlap with disease-associated SNPs, pointing to tissue-specific transcriptional regulation mechanisms. Tejaas is available under GPL athttps://github.com/soedinglab/tejaas.
Disrupted Endothelial Cell Heterogeneity and Network Organization Impairs Vascular Function in Prediabetic Obesity
Authors: Wilson Calum , Zhang Xun , Lee Matthew D. , MacDonald Margaret , Heathcote Helen H. , Alorfi Nasser M.N. , Buckley Charlotte , Dolan Sharon , McCarron John G.
Published: May 2020

Rationale

Obesity is a major risk factor for diabetes and cardiovascular diseases such as hypertension, heart failure, and stroke. Impaired endothelial function occurs in the earliest stages of obesity and underlies vascular alterations giving rise to cardiovascular disease. However, the mechanisms that link weight gain to endothelial dysfunction are ill-defined. Increasing evidence suggests that, rather than being a population of uniformly responding cells, neighboring endothelial cells are highly heterogeneous and are organized as a communicating multicellular network that controls vascular function.

Objective

To investigate the hypothesis that disrupted endothelial heterogeneity and network-level organization contributes to impaired vascular reactivity in obesity.

Methods and Results

To study obesity-related vascular function without the complications associated with diabetes, we induced a state of prediabetic obesity in rats. Small artery diameter recordings confirmed nitric-oxide mediated vasodilator responses were dependent on increases in endothelial calcium levels and were impaired in obese animals. Single-photon imaging revealed a linear relationship between blood vessel relaxation and network-level calcium responses. Obesity did not alter the slope of this relationship, but impaired network-level endothelial calcium responses. The network itself was comprised of structural and functional components. The structural component, a hexagonal lattice network of endothelial cells, was unchanged in obesity. The functional network contained sub-populations of clustered agonist-sensing cells from which signals were communicate through the network. In obesity there were fewer but larger clusters of agonist-sensing cells and communication path lengths between clusters was increased. Communication between neighboring cells was unaltered in obesity. Altered network organization resulted in impaired, population-level calcium signaling and deficient endothelial control of vascular tone.

Specialized subpopulations of endothelial cells had increased agonist sensitivity. These agonist-responsive cells were spatially clustered in a non-random manner and drove network level calcium responses. Communication between adjacent cells was unaltered in obesity, but there was a decrease in the size of the agonist-sensitive cell population and an increase in the clustering of agonist-responsive cells

Conclusions

The distribution of cells in the endothelial network is critical in determining overall vascular function. Altered cell heterogeneity and arrangement in obesity decrease endothelial function and provide a novel framework for understanding compromised endothelial function in cardiovascular disease.
Ascending dorsal column sensory neurons respond to spinal cord injury and downregulate genes related to lipid metabolism
Authors: Ewan Eric E. , Avraham Oshri , Carlin Dan , Goncalves Tassia Mangetti , Zhao Guoyan , Cavalli Valeria
Published: May 2020

Regeneration failure after spinal cord injury (SCI) results in part from the lack of a pro-regenerative response in injured neurons, but the response to SCI has not been examined specifically in injured sensory neurons. Using RNA sequencing of dorsal root ganglion, we determined that thoracic SCI elicits a transcriptional response distinct from sciatic nerve injury (SNI). Both SNI and SCI induced upregulation of ATF3 and Jun, yet this response failed to promote growth in sensory neurons after SCI. RNA sequencing of purified sensory neurons one and three days after injury revealed that unlike SNI, the SCI response is not sustained. Both SCI and SNI elicited the expression of ATF3 target genes, with very little overlap between conditions. Pathway analysis of differentially expressed ATF3 target genes revealed that fatty acid biosynthesis and terpenoid backbone synthesis were downregulated after SCI but not SNI. Pharmacologic inhibition of fatty acid synthase, the enzyme generating palmitic acid, decreased axon growth and regeneration in vitro. These results supports the notion that decreased expression of lipid metabolism-related genes after SCI, including fatty acid synthase, may restrict axon regenerative capacity after SCI.
The evolution of sex allocation in metapopulations
Authors: Roux Camille , Mullon Charles , Pannell John R.
Published: May 2020

Selection in inbred populations is expected to favor female-biased sex ratios in dioecious populations as a result of local mate competition, a prediction that finds strong support in situations where females have control of the sex ratio. Local mate competition due to inbreeding should also promote female-biased sex allocation in hermaphrodites, with reduced emphasis on the production and dispersal of sperm or pollen relative to that of eggs, ovules or seeds. While inbreeding can be the direct result of the mating system in local populations, it can also be brought about by population turnover in metapopulations with frequent local extinction and recolonization. This effect of population turnover has previously been considered for species with separate sexes. Here, we use both formal analysis and individual-based simulations to explore the effect of population turnover on sex allocation in partially self-fertilizing hermaphroditic metapopulations. Using simulations, we also assess the extent to which different genetic measures of inbreeding and population differentiation predict the equilibrium sex allocation. We find that population turnover can select for strongly female-biased sex allocation in hermaphroditic metapopulations, particularly if amongdeme dispersal is low, even where local demes are fully outcrossing. In such situations,FSTis a good predictor of the equilibrium sex allocation, and much better than the alternative differentiation measuresGSTand Jost’sD. Our study extends predictions for sex allocation in subdivided populations to hermaphroditic species, and draws attention in general to the power of Wright’s hierarchical inbreeding statistics to predict the sex allocation in metapopulations at equilibrium.
Single cell fitness landscapes induced by genetic and pharmacologic perturbations in cancer
Authors: Salehi Sohrab , Kabeer Farhia , Ceglia Nicholas , Andronescu Mirela , Williams Marc , Campbell Kieran R. , Masud Tehmina , Wang Beixi , Biele Justina , Brimhall Jazmine , Ting Jerome , Zhang Allen W. , O’Flanagan Ciara , Dorri Fatemeh , Rusk Nicole , Lee Hak Woo , de Algara Teresa Ruiz , Lee So Ra , Cheng Brian Yu Chieh , Eirew Peter , Kono Takako , Pham Jennifer , Grewal Diljot , Lai Daniel , Moore Richard , Mungall Andrew J. , Marra Marco A. ,   IMAXT Consortium, McPherson Andrew , Bouchard-Côté Alexandre , Aparicio Samuel , Shah Sohrab P.
Published: May 2020

Tumour fitness landscapes underpin selection in cancer, impacting etiology, evolution and response to treatment. Progress in defining fitness landscapes has been impeded by a lack of timeseries perturbation experiments over realistic intervals at single cell resolution. We studied the nature of clonal dynamics induced by genetic and pharmacologic perturbation with a quantitative fitness model developed to ascribe quantitative selective coefficients to individual cancer clones, enable prediction of clone-specific growth potential, and forecast competitive clonal dynamics over time. We applied the model to serial single cell genome (>60,000 cells) and transcriptome (>58,000 cells) experiments ranging from 10 months to 2.5 years in duration. We found that genetic perturbation ofTP53in epithelial cell lines induces multiple forms of copy number alteration that confer increased fitness to clonal populations with measurable consequences on gene expression. In patient derived xenografts, predicted selective coefficients accurately forecasted clonal competition dynamics, that were validated with timeseries sampling of experimentally engineered mixtures of low and high fitness clones. In cisplatin-treated patient derived xenografts, the fitness landscape was inverted in a time-dependent manner, whereby a drug resistant clone emerged from a phylogenetic lineage of low fitness clones, and high fitness clones were eradicated. Moreover, clonal selection mediated reversible drug response early in the selection process, whereas late dynamics in genomically fixed clones were associated with transcriptional plasticity on a fixed clonal genotype. Together, our findings outline causal mechanisms with implication for interpreting how mutations and multi-faceted drug resistance mechanisms shape the etiology and cellular fitness of human cancers.
Light pollution affects West Nile virus exposure risk across Florida
Authors: Kernbach Meredith E. , Martin Lynn B. , Unnasch Thomas R. , Hall Richard J. , Jiang Rays H.Y. , Francis Clinton D.
Published: May 2020

Emerging infectious diseases (EIDs), including zoonotic arboviruses, present a global health threat. Multiple components of human land use change have been linked to arboviral emergence, but one pervasive factor that has received comparatively little attention is light pollution. Although often considered a component of built environments, artificial light at night (ALAN) outpaces the growth and spatial extent of urbanization, and thus affects areas where human population density and anthropogenic land changes are modest. West Nile virus (WNV) emergence has been described as peri-urban, but recent research suggests that its relative ubiquity in human-altered environments might actually be due to ALAN. Indeed, we found previously that experimental ALAN exposure enhanced avian competence to transmit WNV to mosquitoes. In the present study, we asked whether such organismal effects manifest ecologically by determining whether WNV exposure among sentinel chickens in Florida is related to local ALAN conditions. We found strong support for a nonlinear relationship between ALAN and WNV exposure in chickens with peak WNV risk occurring at low ALAN levels. Importantly, effects of ALAN on WNV exposure were stronger than other aspects of urbanization; only ambient temperature in the month prior to sampling had a comparable effect to ALAN. These results represent the first field evidence that ALAN might affect infectious disease exposure risk. We advocate for further research on how ALAN influences zoonotic risk, as well as efforts to study alternative nighttime lighting methods to reduce such risk.

Significance Statement

Light pollution associated with human development is a globally pervasive and rapidly expanding anthropogenic stressor; but despite documented effects on host immune functions and vector behaviors, how it affects infectious disease risk is unknown. Using data from the Florida Department of Health arbovirus surveillance program, we show that light pollution is a stronger predictor of variation in West Nile virus (WNV) exposure risk than many other previously implicated anthropogenic and natural environmental variables. Light pollution effects are nonlinear, so risk is highest in areas with dim light pollution. Our results highlight a new way that light pollution might affect human and wildlife health.
Joint probabilistic modeling of paired transcriptome and proteome measurements in single cells
Authors: Gayoso Adam , Steier Zoë , Lopez Romain , Regier Jeffrey , Nazor Kristopher L , Streets Aaron , Yosef Nir
Published: May 2020

Abstract

The paired measurement of RNA and surface protein abundance in single cells with CITE-seq is a promising approach to connect transcriptional variation with cell phenotypes and functions. However, each data modality exhibits unique technical biases, making it challenging to conduct a joint analysis and combine these two views into a unified representation of cell state. Here we present Total Variational Inference (totalVI), a framework for the joint probabilistic analysis of paired RNA and protein data from single cells. totalVI probabilistically represents the data as a composite of biological and technical factors such as limited sensitivity of the RNA data, background in the protein data, and batch effects. To evaluate totalVI, we performed CITE-seq on immune cells from murine spleen and lymph nodes with biological replicates and with different antibody panels measuring over 100 surface proteins. With this dataset, we demonstrate that totalVI provides a cohesive solution for common analysis tasks like the integration of datasets with matched or unmatched protein panels, dimensionality reduction, clustering, evaluation of correlations between molecules, and differential expression testing. totalVI enables scalable, end-to-end analysis of paired RNA and protein data from single cells and is available as open-source software.
Computational analysis of ligand dose range thermal proteome profiles
Authors: Kurzawa Nils , Becher Isabelle , Sridharan Sindhuja , Franken Holger , Mateus André , Anders Simon , Bantscheff Marcus , Huber Wolfgang , Savitski Mikhail M.
Published: May 2020

Detecting ligand-protein interactions in living cells is a fundamental challenge in molecular biology and drug research. Proteome-wide profiling of thermal stability as a function of ligand concentration promises to tackle this challenge. We present a statistical analysis method with reliable control of the false discovery rate and apply it to several datasets probing epigenetic drugs. We detect off-target drug engagement in unrelated protein families.
Intra-genome variability in the dinucleotide composition of SARS-CoV-2
Authors: Digard Paul , Lee Hui Min , Sharp Colin , Grey Finn , Gaunt Eleanor
Published: May 2020

CpG dinucleotides are under-represented in the genomes of single stranded RNA viruses, and coronaviruses, including SARS-CoV-2, are no exception to this. Artificial modification of CpG frequency is a valid approach for live attenuated vaccine development, and if this is to be applied to SARS-CoV-2, we must first understand the role CpG motifs play in regulating SARS-CoV-2 replication. Accordingly, the CpG composition of the newly emerged SARS-CoV-2 genome was characterised in the context of other coronaviruses. CpG suppression amongst coronaviruses does not significantly differ according to genera of virus, but does vary according to host species and primary replication site (a proxy for tissue tropism), supporting the hypothesis that viral CpG content may influence cross-species transmission. Although SARS-CoV-2 exhibits overall strong CpG suppression, this varies considerably across the genome, and the Envelope (E) open reading frame (ORF) and ORF10 demonstrate an absence of CpG suppression. While ORF10 is only present in the genomes of a subset of coronaviruses, E is essential for virus replication. Across theCoronaviridae, E genes display remarkably high variation in CpG composition, with those of SARS and SARS-CoV-2 having much higher CpG content than other coronaviruses isolated from humans. Phylogeny indicates that this is an ancestrally-derived trait reflecting their origin in bats, rather than something selected for after zoonotic transfer. Conservation of CpG motifs in these regions suggests that they have a functionality which over-rides the need to suppress CpG; an observation relevant to future strategies towards a rationally attenuated SARS-CoV-2 vaccine.
Refined measurement of SecA-driven protein transport reveals indirect coupling to ATP turnover
Authors: Allen William J. , Watkins Daniel W. , Dillingham Mark S. , Collinson Ian
Published: May 2020

The universally conserved Sec system is the primary method cells utilise to transport proteins across membranes. Until recently, measuring the activity – a prerequisite for understanding how biological systems works – has been limited to discontinuous protein transport assays with poor time resolution, or used as reporters large, non-natural tags that interfere with the process. The development of an assay based on a split super-bright luciferase (NanoLuc) changed this. Here, we exploit this technology to unpick the steps that constitute post-translational transport in bacteria. Under the conditions deployed, transport of the model pre-protein substrate proSpy occurs at 200 amino acids per minute with the data best fit by a series of large, ∼30 amino acid, steps each coupled to many (100s) ATP hydrolysis events. Prior to that, there is no evidence for a distinct, rate-limiting initiation event. Kinetic modelling suggests that SecA-driven transport activity is facilitated by the substrate (polypeptide) concentration gradient – in keeping with classical membrane transporters. Furthermore, the features we describe are consistent with a non-deterministic motor mechanism, such as a Brownian ratchet.
Cotranslational protein folding can promote the formation of correct folding intermediate
Authors: Tao P. , Xiao Y.
Published: May 2020

Cotranslational folding is vital for proteins to form correct structures in vivo. However, it is still unclear how a nascent chain folds at atomic resolution during the translation process. Previously, we have built a model of ribosomal exit tunnel and investigated cotranslational folding of a three-helices protein by using all-atom molecular dynamics simulations. Here we shall study the cotranslational folding of three mainly-β proteins using the same method and find that cotranslational folding can enhance helical population in most cases and reduce nonnative long-range contacts before emerging from the ribosomal exit tunnel. After exiting the tunnel, all proteins fall into local minimal states and structural ensembles in cotranslational folding are more helical than in free folding. Importantly, for GTT WW domain, one local minimal state in cotranslational folding is known as correct folding intermediate, which is not found in free folding. This result suggests that cotranslational folding may directly increase folding efficiency by accelerating sampling more than by avoiding the misfolded state, which is a mainstream viewpoint in present. In addition, our method can serve as a general scheme to study cotranslational folding process of proteins.

Statement of Significance

In cell, the formations of correct three-dimensional structures of proteins, namely protein folding, are essential to human health. Misfolding can lead to serious diseases such as Alzheimer’s disease and mad cow disease. As the first step of in vivo folding, the effect of cotranslational folding on the correct folding of proteins has been the focus of scientific research in this century. Although some experiments have shown that cotranslational folding can improve the efficiency of folding, its microscopic mechanism is not yet clear. In this paper, we study the process of cotranslational folding of three proteins by using all-atom molecular dynamics simulations, and try to reveal some aspects of the mechanism of cotranslational folding from a microscopic perspective.
Transcriptomics, metabolomics and lipidomics of chronically injured alveolar epithelial cells reveals similar features of IPF lung epithelium
Authors: Roque Willy , Cuevas-Mora Karina , Sales Dominic , Li Wei Vivian , Rosas Ivan O. , Romero Freddy
Published: May 2020

The current hypothesis suggests that Idiopathic pulmonary fibrosis (IPF) arises as a result of chronic injury to alveolar epithelial cells and aberrant activation of multiple signaling pathways. Dysfunctional IPF lung epithelium manifests many hallmarks of aging tissues, including cellular senescence, mitochondrial dysfunction, metabolic dysregulation, and loss of proteostasis. Unfortunately, this disease is often fatal within 3-5 years from diagnosis, and there is no effective treatment. One of the major limitations to the development of novel treatments in IPF is that current models of the disease fail to resemble several features seen in elderly IPF patients. In this study, we sought to develop anin vitroepithelial injury model using repeated low levels of bleomycin to mimic the phenotypic and functional characteristics of the IPF lung epithelium. Consistent with the hallmarks of the aging lung epithelium, we found that chronic-injured epithelial cells exhibited features of senescence cells, including an increase in β-galactosidase staining, induction of p53 and p21, mitochondrial dysfunction, excessive ROS production, and proteostasis alteration. Next, combined RNA sequencing, untargeted metabolomics, and lipidomics were performed to investigate the dynamic transcriptional, metabolic, and lipidomic profiling of ourin vitromodel. We identified that a total of 8,484 genes with different expression variations between the exposed group and the control group. According to our GO enrichment analysis, the down-regulated genes are involved in multiple biosynthetic and metabolic processes. In contrast, the up-regulated genes in our treated cells are responsible for epithelial cell migration and regulation of epithelial proliferation. Furthermore, metabolomics and lipidomics data revealed that overrepresented pathways were amino acid, fatty acid, and glycosphingolipid metabolism. This result suggests that by using ourin vitromodel, we were able to mimic the transcriptomic and metabolic alterations of those seen in the lung epithelium of IPF patients. We believe this model will be ideally suited for use in uncovering novel insights into the gene expression and molecular pathways of the IPF lung epithelium and performing screening of pharmaceutical compounds.
Targeted sequence capture array for phylogenetics and population genomics in the Salicaceae
Authors: Sanderson Brian J. , DiFazio Stephen P. , Cronk Quentin C. , Ma Tao , Olson Matthew S.
Published: May 2020

Premise of the study

The family Salicaceae has proved taxonomically challenging, especially in the genusSalix, which is speciose and features frequent hybridization and polyploidy. Past efforts to reconstruct the phylogeny with molecular barcodes have failed to resolve the species relationships of many sections of the genus.

Methods

We used the wealth of sequence data in the family to design sequence capture probes to target regions of 300-1200 base pairs of exonic regions of 972 genes.

Results

We recovered sequence data for nearly all of the targeted genes in three species ofPopulusand three species ofSalix. We present a species tree, discuss concordance among gene trees, as well as some population genomic summary statistics for these loci.

Conclusions

Our sequence capture array has extremely high capture efficiency within the generaPopulusandSalix, resulting in abundant phylogenetic information. Additionally, these loci show promise for population genomic studies.
Deterministic Critical Community Size for the SIR System and Viral Strain Selection
Authors: Dos Santos Marcílio Ferreira , Castilho César
Published: May 2020

Abstract

In this paper the concept of Critical Community Size (CCS) for the deterministic SIR model is introduced and its consequences for the disease dynamics are stressed. The disease can fade out after an outburst. Also the principle of competitive exclusion holds no longer true. This is exemplified for the dynamics of two competing virus strains. The virus with higherR0can be eradicated from the population.
Xela DS2 and Xela VS2: two novel skin epithelial-like cell lines from adult African clawed frog (Xenopus laevis) and their response to an extracellular viral dsRNA analogue
Authors: Bui-Marinos Maxwell P. , Varga Joseph F. A. , Vo Nguyen T.K. , Bols Niels C. , Katzenback Barbara A.
Published: May 2020

The skin epithelial layer acts as an important immunological barrier against pathogens and is capable of recognizing and responding to pathogen associated molecular patterns (PAMPs) in human and mouse models. Although presumed, it is unknown whether amphibian skin epithelial cells exhibit the ability to respond to PAMPs such as viral double-stranded RNA (dsRNA). To address this, two cell lines from the dorsal skin (Xela DS2) and ventral skin (Xela VS2) of the African clawed frog (Xenopus laevis) were established. Xela DS2 and Xela VS2 cells have an epithelial-like morphology, express genes associated with epithelial cells, and lack senescence-associated beta-galactosidase activity. Cells grow optimally in 70% Leibovitz’s L-15 medium supplemented with 15% fetal bovine serum at 26°C. Upon treatment with poly(I:C), a synthetic viral dsRNA analogue and known type I interferon inducer, Xela DS2 and Xela VS2 exhibit marked upregulation of key pro-inflammatory and antiviral transcripts suggesting frog epithelial cells participate in the recognition of extracellular viral dsRNA and production of local inflammatory signals; similar to human and mouse models. Currently, these are the only knownXenopus laevisskin epithelial-like cell lines and will be important for future research in amphibian epithelial cell biology, initial host-pathogen interactions, and rapid screening of the effects of environmental stressors, including contaminants, on frog skin epithelial cells.
Condensation of pericentrin proteins in human cells illuminates phase separation in centrosome assembly
Authors: Jiang Xueer , Ho Dac Bang Tam , Mahe Karan , Mia Jennielee , Sepulveda Guadalupe , Antkowiak Mark , Jiang Linhao , Yamada Soichiro , Jao Li-En
Published: May 2020

Abstract

At the onset of mitosis, centrosomes expand the pericentriolar material (PCM) to maximize their microtubule-organizing activity. This step, termed centrosome maturation, ensures proper spindle organization and faithful chromosome segregation. However, as the centrosome expands, how PCM proteins are recruited and held together without membrane enclosure remains elusive. We found that endogenously expressed pericentrin (PCNT), a conserved PCM scaffold protein, condenses into dynamic granules during late G2/early mitosis before incorporating into mitotic centrosomes. Furthermore, the N-terminal portion of PCNT—enriched with conserved coiled-coils (CCs) and low-complexity regions (LCRs)—phase separates into dynamic condensates that selectively recruit PCM proteins and nucleate microtubules in cells. We propose that CCs and LCRs, two prevalent sequence features in the centrosomal proteome, are preserved under evolutionary pressure in part to mediate liquid-liquid phase separation, a process that bestows upon the centrosome distinct properties critical for its assembly and functions.
Host behavior alteration by its parasite: from brain gene expression to functional test
Authors: Grecias Lucie , Hebert Francois Olivier , Alves Verônica Angelica , Barber Iain , Aubin-Horth Nadia
Published: May 2020

Many parasites with complex life cycles modify their intermediate hosts’ behaviour, presumably to increase transmission to their final host. The threespine stickleback (Gasterosteus aculeatus) is an intermediate host in the cestodeSchistocephalus soliduslife cycle, which ends in an avian host, and shows increased risky behaviours when infected. We studied brain gene expression profiles of sticklebacks infected withS.solidusto determine the proximal causes of these behavioural alterations. We show that infected fish have altered expression levels in genes involved in the inositol pathway. We thus tested the functional implication of this pathway and successfully rescued normal behaviours in infected sticklebacks using lithium exposure. We also show that exposed but uninfected fish have a distinct gene expression profile from both infected fish and control individuals, allowing us to separate gene activity related to parasite exposure from consequences of a successful infection. Finally, we find that Selective Serotonin Reuptake Inhibitor (SSRI)-treated sticklebacks and infected fish do not have similarly altered gene expression, despite their comparable behaviours, suggesting that the serotonin pathway is probably not the main driver of phenotypic changes in infected sticklebacks. Taken together, our results allow us to predict that ifS.solidusdirectly manipulates its host, it could target the inositol pathway.
L-bodies are novel RNA-protein condensates driving RNA transport inXenopusoocytes
Authors: Neil Christopher R. , Jeschonek Samantha P. , Cabral Sarah E. , O’Connell Liam C. , Powrie Erin A. , Wood Timothy A. , Mowry Kimberly L.
Published: May 2020

RNP granules are membrane-less compartments within cells, formed by phase separation, that function as regulatory hubs for diverse biological processes. However, the mechanisms by which RNAs and proteins interact to promote RNP granule structure and functionin vivoremain unclear. InXenopus laevisoocytes, maternal mRNAs are transported as large RNPs to the vegetal hemisphere of the developing oocyte, where local translation is critical for proper embryonic patterning. Here, we demonstrate that vegetal transport RNPs represent a new class of cytoplasmic RNP granule, termed Localization-bodies (L-bodies). We show that L-bodies are multiphase RNP granules, containing a dynamic protein-containing phase surrounding a non-dynamic RNA-containing substructure. Our results support a role for RNA as a critical scaffold component within these RNP granules and suggest thatcis-elements within localized mRNAs may drive subcellular RNA localization through control over phase behavior.
The microbiome mediates subchondral bone loss and metabolomic changes after acute joint trauma
Authors: Hahn Alyssa K. , Wallace Cameron W. , Welhaven Hope D. , Brooks Ellen , McAlpine Mark , Christiansen Blaine A. , Walk Seth T. , June Ronald K.
Published: May 2020

Objective

To compare the early responses to joint injury in conventional and germ-free mice.

Design

Post traumatic osteoarthritis PTOA was induced using a non-invasive anterior cruciate ligament rupture model in 20-week old germ-free (GF) and conventional C57BL/6 mice. Injury was induced in the left knees of n=8 GF and n=10 conventional mice. To examine the effects of injury, n=5 GF and n=9 conventional control mice were used. Mice were euthanized seven days post-injury, followed by synovial fluid recovery for global metabolomic profiling and analysis of epiphyseal trabecular bone by micro-computed tomography (μCT). Global metabolomic profiling assessed metabolic differences in the joint response to injury between GF and conventional mice. Magnitude of trabecular bone volume loss measured using μCT assessed early OA progression in GF and conventional mice.

Results

μCT found that GF mice had significantly less trabecular bone loss compared to conventional mice, indicating that the GF status was protective against early OA changes in bone structure. Global metabolomic profiling showed that conventional mice had greater variability in their metabolic response to injury, and a more distinct joint metabolome compared to their corresponding controls. Furthermore, differences in the response to injury in GF compared to conventional mice were linked to mouse metabolic pathways that regulate inflammation associated with the innate immune system.

Conclusions

These results suggest that the gut microbiota promote the development of PTOA during the acute phase following joint trauma possibly through the regulation of the innate immune system.
Mapping transmembrane binding partners for E-cadherin ectodomains
Authors: Shafraz Omer , Xie Bin , Yamada Soichiro , Sivasankar Sanjeevi
Published: May 2020

We combine proximity labeling and single molecule binding assays, to discover novel transmembrane protein interactions in cells. We first screen for candidate binding partners by tagging the extracellular and cytoplasmic regions of a bait protein with TurboID biotin ligase, and identify proximal proteins that are biotin-tagged on both their extracellular and intracellular regions. We then test direct binding interactions between the proximal proteins and the bait, using single molecule Atomic Force Microscope binding assays. Using this approach, we identify novel binding partners for the extracellular region of E-cadherin, an essential cell-cell adhesion protein. We show that the desmosomal proteins desmoglein-2 and desmocollin-3, the focal adhesion protein integrin-α2β1, and the receptor tyrosine kinase ligand ephrin-B1, all directly interact with E-cadherin ectodomains. Our discovery of previously unknown heterophilic E-cadherin binding interactions, suggest the existence of novel cadherin cross-talk in epithelial cells.