bluuebunny/crossref_metadata_2025 huggingface dataset:
EventEpi–A Natural Language Processing Framework for Event-Based Surveillance
Authors: Abbood Auss , Ullrich Alexander , Busche Rüdiger , Ghozzi Stéphane
Published: September 2019

Abstract

According to the World Health Organization (WHO), around 60% of all outbreaks are detected using informal sources. In many public health institutes, including the WHO and the Robert Koch Institute (RKI), dedicated groups of epidemiologists sift through numerous articles and newsletters to detect relevant events. This media screening is one important part of event-based surveillance (EBS). Reading the articles, discussing their relevance, and putting key information into a database is a time-consuming process. To support EBS, but also to gain insights into what makes an article and the event it describes relevant, we developed a natural-language-processing framework for automated information extraction and relevance scoring. First, we scraped relevant sources for EBS as done at RKI (WHO Disease Outbreak News and ProMED) and automatically extracted the articles’ key data: disease, country, date, and confirmed-case count. For this, we performed named entity recognition in two steps: EpiTator, an open-source epidemiological annotation tool, suggested many different possibilities for each. We trained a naive Bayes classifier to find the single most likely one using RKI’s EBS database as labels. Then, for relevance scoring, we defined two classes to which any article might belong: The article is relevant if it is in the EBS database and irrelevant otherwise. We compared the performance of different classifiers, using document and word embeddings. Two of the tested algorithms stood out: The multilayer perceptron performed best overall, with a precision of 0.19, recall of 0.50, specificity of 0.89, F1 of 0.28, and the highest tested index balanced accuracy of 0.46. The support-vector machine, on the other hand, had the highest recall (0.88) which can be of higher interest for epidemiologists. Finally, we integrated these functionalities into a web application called EventEpi where relevant sources are automatically analyzed and put into a database. The user can also provide any URL or text, that will be analyzed in the same way and added to the database. Each of these steps could be improved, in particular with larger labeled datasets and fine-tuning of the learning algorithms. The overall framework, however, works already well and can be used in production, promising improvements in EBS. The source code is publicly available at https://github.com/aauss/EventEpi.
Network-based clustering for drug sensitivity prediction in cancer cell lines
Authors: Pouryahya Maryam , Oh Jung Hun , Mathews James C. , Belkhatir Zehor , Moosmüller Caroline , Deasy Joseph O. , Tannenbaum Allen R.
Published: September 2019

The study of large-scale pharmacogenomics provides an unprecedented opportunity to develop computational models that can accurately predict large cohorts of cell lines and drugs. In this work, we present a novel method for predicting drug sensitivity in cancer cell lines which considers both cell line genomic features and drug chemical features. Our network-based approach combines the theory of optimal mass transport (OMT) with machine learning techniques. It starts with unsupervised clustering of both cell line and drug data, followed by the prediction of drug sensitivity in the paired cluster of cell lines and drugs. We show that prior clustering of the heterogenous cell lines and structurally diverse drugs significantly improves the accuracy of the prediction. In addition, it facilities the interpretability of the results and identification of molecular biomarkers which are significant for both clustering of the cell lines and predicting the drug response.
Evaluating Representations for Gene Ontology Terms
Authors: Duong Dat , Uppunda Ankith , Gai Lisa , Ju Chelsea , Zhang James , Chen Muhao , Eskin Eleazar , Li Jingyi Jessica , Chang Kai-Wei
Published: September 2019

Protein functions can be described by the Gene Ontology (GO) terms, allowing us to compare the functions of two proteins by measuring the similarity of the terms assigned to them. Recent works have applied neural network models to derive the vector representations for GO terms and compute similarity scores for these terms by comparing their vector embeddings. There are two typical ways to embed GO terms into vectors; a model can either embed the definitions of the terms or the topology of the terms in the ontology. In this paper, we design three tasks to critically evaluate the GO embeddings of two recent neural network models, and further introduce additional models for embedding GO terms, adapted from three popular neural network frameworks: Graph Convolution Network (GCN), Embeddings from Language Models (ELMo), and Bidirectional Encoder Representations from Transformers (BERT), which have not yet been explored in previous works. Task 1 studies edge cases where the GO embeddings may not provide meaningful similarity scores for GO terms. We find that all neural network based methods fail to produce high similarity scores for related terms when these terms have low Information Content values. Task 2 is a canonical task which estimates how well GO embeddings can compare functions of two orthologous genes or two interacting proteins. The best neural network methods for this task are those that embed GO terms using their definitions, and the differences among such methods are small. Task 3 evaluates how GO embeddings affect the performance of GO annotation methods, which predict whether a protein should be labeled by certain GO terms. When the annotation datasets contain many samples for each GO label, GO embeddings do not improve the classification accuracy. Machine learning GO annotation methods often remove rare GO labels from the training datasets so that the model parameters can be efficiently trained. We evaluate whether GO embeddings can improve prediction of rare labels unseen in the training datasets, and find that GO embeddings based on the BERT framework achieve the best results in this setting. We present our embedding methods and three evaluation tasks as the basis for future research on this topic.
The investigation of the role of VHL-HIF signaling in DNA repair and apoptosis in zebrafish
Authors: Kim HR , Santhakumar K , Markham E , Baldera D , Bryant HE , El-Khamisy SF , van Eeden FJ
Published: September 2019

pVHL is a tumor suppressor. The lack of its function leads to various tumors, among which ccRCC (clear cell renal cell carcinoma) has the most serious outcome due to its resistance to chemotherapies and radiotherapies. Although HIF promotes the progression of ccRCC, the precise mechanism by which the loss of VHL leads to tumor initiation remains unclear. We exploited two zebrafish vhl mutants, vhl and vll, and Tg(phd3::GFP)i144 fish to identify crucial functions of Vhl in tumor initiation. Through the mutant analysis, we found that the role of pVHL in DNA repair is conserved in zebrafish Vll. Interestingly, we also discovered that Hif activation strongly suppressed genotoxic stress induced DNA repair defects and apoptosis in vll and brca2 mutants and in the embryos lacking ATM activity. These results suggest the potential of HIF as a clinical modulator that can protect cells from accumulating DNA damage and apoptosis which can lead to cancers and neurodegenerative disorders.
scHiCTools: a computational toolbox for analyzing single-cell Hi-C data
Authors: Li Xinjun , Feng Fan , Leung Wai Yan , Liu Jie
Published: September 2019

Single-cell Hi-C (scHi-C) sequencing technologies allow us to investigate three-dimensional chromatin organization at the single-cell level. However, we still need computational tools to deal with the sparsity of the contact maps from single cells and embed single cells in a lower-dimensional Euclidean space. This embedding helps us understand relationships between the cells in different dimensions such as cell-cycle dynamics and cell differentiation. Here, we present an open-source computational toolbox, scHiCTools, for analyzing single cell Hi-C data. The toolbox takes singlecell Hi-C data files as input, and projects single cells in a lower-dimensional Euclidean space. The toolbox includes three commonly used methods for smoothing scHi-C data (linear convolution, random walk, and network enhancing), three projection methods for embedding single cells (fastHiCRep, Selfish, and InnerProduct), three clustering methods for clustering cells (k-means, spectral clustering, and HiCluster) and a build-in function to visualize the cells embedding in a two-dimensional or three-dimensional plot. We benchmark the embedding performance and run time of these methods on a number of scHi-C datasets, and provide some suggestions for practice use. scHiCTools, based on Python3, can run on different platforms, including Linux, macOS, and Windows. Our software package is available at https://github.com/liu-bioinfo-lab/scHiCTools.
MYC-associated factor MAX is an essential regulator of the clock core network
Authors: Blaževitš Olga , Bolshette Nityanand , Vecchio Donatella , Guijarro Ana , Croci Ottavio , Campaner Stefano , Grimaldi Benedetto
Published: September 2019

The circadian transcriptional network is based on a competition between transcriptional activator and repressor complexes regulating the rhythmic expression of clock-controlled genes. We show here that the MYC-Associated factor X, MAX, plays a repressive role in this network and operates through its MYC-independent binding to E-box-containing regulatory regions within the promoters of circadian BMAL1 targets. This clock function of MAX is essential for maintaining a proper circadian rhythm but separated by the role of MAX as a partner of MYC in controlling cell proliferation. We also identified MAX Network Transcriptional repressor, MNT, as a fundamental partner of MAX-mediated circadian regulation. Collectively, our data indicate that MAX is an integral part of the core molecular clock and keeps the balance between positive and negative elements of the molecular clock machinery. Accordingly, alteration of MAX transcriptional complexes may contribute to circadian dysfunction in pathological contexts.
“Green pointillism”: detecting the within-population variability of budburst in temperate deciduous trees with phenological cameras
Authors: Delpierre Nicolas , Soudani Kamel , Berveiller Daniel , Dufrêne Eric , Hmimina Gabriel , Vincent Gaëlle
Published: September 2019

Phenological cameras have been used over a decade for identifying plant phenological markers (budburst, leaf senescence) and more generally the greenness dynamics of forest canopies. The analysis is usually carried out over the full camera field of view, with no particular analysis of the variability of phenological markers among trees.

Here we show that images produced by phenological cameras can be used to quantify the within-population variability of budburst (WPVbb) in temperate deciduous forests. Using 7 site-years of image analyses, we report a strong correlation (r²=0.97) between the WPVbb determined with a phenological camera and its quantification through ground observation.

We show that WPVbb varies strongly (by a factor of 4) from year to year in a given population, and that those variations are linked with temperature conditions during the budburst period, with colder springs associated to a higher differentiation of budburst (higher WPVbb) among trees.

Deploying our approach at the continental scale, i.e. throughout phenological cameras networks, would improve the understanding of the spatial (across populations) and temporal (across years) variations of WPVbb, which have strong implications on forest functioning, tree fitness and phenological modelling.
H. pyloriinfection inhibits autophagy to aggravate DNA damage by p62-mediated Rad51 ubiquitination
Authors: Xie Chuan , Li Nianshuang , Wang Huan , He Cong , Hu Yi , Peng Chao , Ouyang Yaobin , Wang Dejie , Xie Yong , Chen Jiang , Shu Xu , Zhu Yin , Lu Nonghua
Published: September 2019

Helicobacter pylori(H. pylori) infection is the strongest known risk factor for gastric carcinogenesis. DNA damage response (DDR) and autophagy play key roles in tumorigenic transformation. However, it remains unclear howH. pyloriinfection modulate DNA damage and autophagy. Here we report thatH. pyloriinfection promotes DNA damage via suppression of Rad51 expression through inhibition of autophagy and accumulation of p62 in gastric carcinogenesis. We find thatH. pyloriinfection caused alteration of DDR pathway and autophagy in gastric cells and Mongolian gerbils in a CagA-dependent manner. Moreover, loss of autophagy led to promotion of DNA damage inH. pylori-infected cells. Furthermore, knockdown of autophagic substrate p62 upregulated Rad51 expression, and p62 promoted ubiquitination of Rad51 via the direct interaction of the UBA domain with Rad51. Finally,H. pyloriinfection was associated with elevated levels of p62 in gastric intestinal metaplasia and decreased levels of Rad51 in dysplasia compared to theirH. pylori-counterparts. Our findings provide a novel mechanism into the linkage ofH. pyloriinfection, autophagy, DNA damage and gastric tumorigenesis.
Ultrasensitive Molecular Imaging of Mucosal Inflammation Using Leucocyte-Mimicking Particles Targeted to MAdCAM-1
Authors: Fournier Antoine P. , de Lizarrondo Sara Martinez , Rateau Adrien , Gerard-Brisou Axel , Waldner Maximilian J. , Neurath Markus F. , Vivien Denis , Docagne Fabian , Gauberti Maxime
Published: September 2019

Mucosal tissues line the digestive, respiratory, urinary, mammary and reproductive tracts and play critical roles in health and disease as the primary barrier between the external world and the inner body. Clinical evaluation of mucosal tissues is currently performed using endoscopy, such as ileocolonoscopy for the intestinal mucosa, that causes significant patient discomfort and can lead to organ damage. Here, we developed a new contrast agent for molecular magnetic resonance imaging (MRI) that is targeted to mucosal vascular addressin cell adhesion molecule 1 (MAdCAM-1), an adhesion molecule overexpressed by inflamed mucosal tissues. We investigated the diagnostic performance of molecular MRI of MAdCAM-1 to detect mucosal inflammation in several models of acute and chronic intestinal inflammation in mice. We demonstrated that molecular MRI of MAdCAM-1 reveals disease activity and can evaluate the response to inflammatory treatments along the whole intestinal mucosa in clinically relevant models of inflammatory bowel diseases. We also provide evidence that this new technique can detect low, subclinical levels of mucosal inflammation. Molecular MRI of MAdCAM-1 has thus potential applications in early diagnosis, longitudinal follow-up and therapeutic response monitoring in diseases affecting mucosal tissues, such as inflammatory bowel diseases.

One Sentence Summary

Molecular magnetic resonance imaging allows non-invasive evaluation of mucosal inflammation in clinically relevant experimental models.
Viral host-range evolvability changes in response to fluctuating selection
Authors: Mouchka Morgan E. , Dorsey Dillon M. , Malcangio Genna L. , Medina Sarah J. , Stuart Elizabeth C. , Meyer Justin R.
Published: September 2019

The concept of evolvability (the capacity of populations to evolve) has deep historical roots in evolutionary biology. Interest in the subject has been renewed recently by innovations in microbiology that permit direct tests of the causes of evolvability, and with the acknowledgement that evolvability of pathogens has important implications for human health. Here, we investigate how fluctuating selection on the virus, Bacteriophage λ, affects its evolvability. We imposed dynamic selection by altering the expression of two host outer membrane receptors. This, in turn, selected phage to alternately infect the host via a single, or multiple, receptors. Our selection regime resulted in two orthogonal evolutionary behaviors, namely enhanced or reduced evolvability. Strains with enhanced evolvability readily evolved between receptors, losing and gaining the ability to bind multiple receptors more quickly than the ancestral λ. This suggests the receptor-binding protein retained a genetic memory of past states and that evolutionary history can be used to predict future adaptation. Strains with reduced evolvability were refractory to re-specialization and remained generalists on both receptors. Consistent with this behavior, unevolvable strains had reduced rates of molecular evolution in the receptor-binding protein compared to their evolvable counterparts. We found a single mutation in the receptor-binding protein was sufficient to render these strains resistant to evolution and did so by counteracting a receptor-binding trade-off associated with generalism. In this way, cost-free generalization allowed for reduced evolution and evolvability while maximizing success in both environments. Our results suggest the response to fluctuating selection is contingent and can lead to distinct differences in evolvability. These findings contribute to a growing understanding of the causes and consequences of evolvability and have important implications for infectious disease management.
Allele specific expression and gene regulation explain transgressive thermal tolerance in non-native hybrids of the endangered California tiger salamander (Ambystoma californiense)
Authors: Cooper Robert D. , Shaffer H. Bradley
Published: September 2019

Hybridization between native and non-native species is an ongoing global conservation threat. Hybrids that exhibit traits and tolerances that surpass parental values are of particular concern, given their ability to outcompete the native parent. It is crucial to understand the mechanisms that drive these transgressive hybrid traits to diagnose and develop strategies to manage hybrid populations. Here, we explore several aspects of the hybridization between the endangered California tiger salamander (Ambystoma californiense; CTS) and the introduced barred tiger salamander (Ambystoma mavortium; BTS). We assayed critical thermal maximum (CTMax) to compare the ability of CTS, BTS and hybrids to tolerate acute thermal stress, and found that hybrids exhibit a wide range of CTMax values, with 40% (6/15) able to tolerate temperatures greater than either parent. We quantified the genomic response of each individual to discover and compare thermal abatement strategies. We found that CTS and BTS have strikingly different numbers and tissue-specific patterns of overall gene expression, with hybrids expressing intermediate values. We evaluated transgressive and variable phenotypes by uncovering regulatory mechanisms that give rise to these unique traits. F1 hybrids display abundant and variable degrees of allele specific expression (ASE), likely arising from extensive compensatory evolution in gene regulatory mechanisms of the parental lineages. We found that the proportion of genes with allelic imbalance in individual hybrids correlates with their CTMax, suggesting that BTS-biased expression confers improved thermal tolerance. We discuss the implications of these findings with respect to ongoing management of CTS in the face of future climate change.
Multi-trait random regression models increase genomic prediction accuracy for a temporal physiological trait derived from high-throughput phenotyping
Authors: Baba Toshimi , Momen Mehdi , Campbell Malachy T. , Walia Harkamal , Morota Gota
Published: September 2019

Random regression models (RRM) are used extensively for genomic inference and prediction of time-valued traits in animal breeding, but only recently have been used in plant systems. High-throughput phenotyping (HTP) platforms provide a powerful means to collect high-dimensional phenotypes throughout the growing season for large populations. However, to date, selection of an appropriate statistical genomic framework to integrate multiple temporal traits for genomic prediction in plants remains unexplored. Here, we demonstrate the utility of a multi-trait RRM (MT-RRM) for genomic prediction of daily water usage (WU) in rice (Oryza sativa) through joint modeling with shoot biomass (projected shoot area, PSA). Three hundred and fifty-seven accessions were phenotyped daily for WU and PSA over 20 days using a greenhouse-based HTP platform. MT-RRMs that modeled additive genetic and permanent environmental effects for both traits using quadratic Legendre polynomials were used to assess genomic correlations between traits and genomic prediction for WU. Predictive abilities of the MT-RRMs were assessed using two cross-validation (CV) scenarios. The first scenario was designed to predict genetic values for WU at all time points for a set of accessions with unobserved WU. The second scenario was designed to forecast future genetic values for WU for a panel of known accessions with records for WU at earlier time periods. In each scenario we evaluated two MT-RRMs in which PSA records were absent or available for time points in the testing population. Moderate to strong genomic correlations between WU and PSA were observed across the days of imaging (0.29-0.87). In both CV scenarios, MT-RRMs showed better predictive abilities compared to single-trait RRM, and prediction accuracies were greatly improved when PSA records were available for the testing population. In summary, these frameworks provide an effective approach to predict temporal physiological traits that are difficult or expensive to quantify in large populations.
The transcriptional co-repressor CtBP is a negative regulator of growth that antagonizes the Yorkie and JNK/AP-1 pathways
Authors: Sumabat Taryn M. , Worley Melanie I. , Pellock Brett J. , Bosch Justin A. , Hariharan Iswar K.
Published: September 2019

Multicellular organisms require strict growth control mechanisms to ensure that an organ reaches, but does not grossly exceed, its appropriate size and shape. In an unbiased mosaic screen for genes involved in growth regulation, we identified a loss-of-function allele of the geneCtBPthat conferred a growth advantage to homozygous mutant tissue.CtBPencodes a transcriptional co-repressor found in diverse organisms, yet its role in regulating tissue growth is not known. We found thatCtBPfunctions as a negative regulator of growth by restricting the expression of the growth-promoting microRNAbantam(ban).banis a known target of the Hippo pathway effector Yorkie (Yki). We show that loss ofCtBPfunction leads to the activation of a minimal enhancer ofbanvia both Yki-dependent and AP-1 transcription factor-dependent mechanisms. AP-1 is downstream of the Jun N-terminal Kinase (JNK) pathway and thus JNK could regulate growth during development viaban. Furthermore, we show that distinct isoforms of the AP-1 component Fos differ in their ability to activate this enhancer. Since the orthologous pathways in mammalian cells (YAP/TEAD and AP-1) converge on enhancers implicated in tumor progression, a role for mammalian CtBP proteins at those enhancers merits attention.
Incorporating uncertainty is essential to macroecological inferences: Grass, grit, and the evolution of kangaroos
Authors: Brennan Ian G.
Published: September 2019

Studying organismal ecology and evolution on deep timescales provides us opportunities to identify the processes driving patterns in diversity and forms. Macroecological and macroevolutionary studies of trait evolution however, often fail to account for sources of artifactual variation in the data—be it phylogenetic, temporal, or other. In some instances, this may not affect our evolutionary understanding, and accounting for sources of uncertainty may only subdue confidence in our inferences. In more dramatic cases, narrow views of trait uncertainty may result in conclusions that are misleading. Because macroevolutionary analyses are built atop a number of preconceived hypotheses regarding the relationships between taxa, origination and divergence times, intraspecific variation, and environmental variables, it is important to incorporate and present this uncertainty. Here I use a dataset for Australian kangaroos to demonstrate the importance of incorporating uncertainty when testing patterns of diversification. After accounting for fossil age uncertainty, I provide evidence that a proposed Pliocene origin ofMacropuskangaroos is at odds with combined evidence molecular and morphological dating methods. Depending on the estimated crown age of kangaroos, the evolution of hypsodonty is as likely caused by the continental expansion of C4grasses as it is by increasing windborne dust levels or paleotemperature fluctuations. These results suggest that previous interpretations of the radiation of modern kangaroos are not as bulletproof as we believe, and that multiple factors have likely influenced their remarkable diversification across the Australian continent. More broadly, this demonstrates the importance of incorporating uncertainty in comparative ecological and evolutionary studies, and the value in testing the assumptions inherent in our data and the methods we employ.
Cardiomyocyte cell cycling, maturation, and growth by multinucleation in postnatal swine
Authors: Velayutham Nivedhitha , Alfieri Christina M. , Agnew Emma J. , Riggs Kyle W. , Baker R. Scott , Zafar Farhan , Yutzey Katherine E.
Published: September 2019

Aims

Cardiomyocyte (CM) cell cycle arrest, decline of mononucleated-diploid CMs, sarcomeric maturation, and extracellular matrix remodeling are implicated in loss of cardiac regenerative potential in mice after birth. Recent studies show a 3-day neonatal regenerative capacity in pig hearts similar to mice, but postnatal pig CM growth dynamics are unknown. We examined cardiac maturation in postnatal pigs and mice, to determine the relative timing of developmental events underlying heart growth and regenerative potential in large and small mammals.

Methods and Results

Left ventricular tissue from White Yorkshire-Landrace pigs at postnatal day (P)0 to 6 months (6mo) was analyzed to span birth, weaning, and adolescence in pigs, compared to similar physiological timepoints in mice. Collagen remodeling increases by P7 in postnatal pigs, but sarcomeric and gap junctional maturation only occur at 2mo. Also, there is no postnatal transition to beta-oxidation metabolism in pig hearts. Mononucleated CMs, predominant at birth, persist to 2mo in swine, with over 50% incidence of mononucleated-diploid CMs at P7-P15. Extensive multinucleation with 4-16 nuclei per CM occurs beyond P30. Pigs also exhibit increased CM length relative to multinucleation, preceding increase in CM width at 2mo-6mo. Further, robust CM mitotic nuclear pHH3 activity and cardiac cell cycle gene expression is apparent in pig left ventricles up to 2mo. By contrast, in mice, these maturational events occur concurrently in the first two postnatal weeks alongside loss of cardiac regenerative capacity.

Conclusions

Cardiac maturation occurs over a 6mo postnatal period in pigs, despite a similar early-neonatal heart regenerative window as mice. Postnatal pig CM growth includes increase in CM length alongside multinucleation, with CM cell cycle arrest and loss of mononucleated-diploid CMs occurring at 2mo-6mo. These CM characteristics are important to consider for pig preclinical studies and may offer opportunities to study aspects of heart regeneration unavailable in other models.
Premature arterial stiffening in Hutchinson-Gilford Progeria Syndrome linked to early induction of Lysyl Oxidase (LOX) and corrected by LOX inhibition
Authors: von Kleeck Ryan , Brankovic Sonja A. , Roberts Ian , Hawthorne Elizabeth A. , Bruun Kyle , Castagnino Paola , Assoian Richard K.
Published: September 2019

Arterial stiffening is a hallmark of premature aging in Hutchinson-Gilford Progeria Syndrome (HGPS), but the key molecular regulators initiating arterial stiffening in HGPS remain unknown. To identify these early events, we compared arterial mechanics and ECM remodeling in very young HGPS (LMNAG609G/G609G) mice to those of age-matched and much older wild-type (WT) mice. Biaxial inflation-extension tests of carotid arteries of 2-month mice showed that circumferential stiffness of HGPS arteries was comparable to that of 24-month WT controls whereas axial arterial stiffening, an additional hallmark of normal aging, was mostly spared in HGPS. In an effort to identify underlying mechanisms, we examined expression levels of the major stiffness-regulatory molecules in WT and HGPS arteries. Transmission electron microscopy revealed slightly increased amounts of collagen within the elastin folds of HGPS carotid arteries, but this change was barely detectable by immunostaining carotid cross sections or qPCR of isolated aortas for collagens I, III, or V. Elastin integrity was also similar in the WT and HGPS arteries. In contrast, immunostaining readily revealed an increased expression of Lysyl oxidase (LOX) protein in young HGPS carotid arteries relative to aged-matched WT controls. Further analysis showed that HGPS arteries express increased amounts of LOX mRNA, and this effect extends to each of the arterial LOX family members. Remarkably, treatment of HGPS mice with the pan-LOX inhibitor β-aminopropionitrile (BAPN) restored near-normal circumferential arterial mechanics to HGPS carotid arteries, mechanistically and causally linking LOX upregulation to premature arterial stiffening in HGPS. Finally, we show that this premature increase in arterial LOX expression in HGPS foreshadows the increased expression of LOX that accompanies circumferential arterial stiffening during normal aging.
ipaA triggers vinculin oligomerization to strengthen cell adhesion during Shigella invasion
Authors: Valencia-Gallardo Cesar , Aguilar-Salvador Daniel-Isui , Khakzad Hamed , Bou-Nader Charles , Malosse Christian , Lima Diogo Borges , Bello Chakir , Cocom-Chan Benjamin , Quenech’Du Nicole , Mazhar Bilal , Javelaud Delphine , Fattaccioli Jacques , Mauviel Alain , Fontecave Marc , Asnacios Atef , Chamot-Rooke Julia , Malmström Lars , Van Nhieu Guy Tran
Published: September 2019

The Shigella effector IpaA co-opts the focal adhesion protein vinculin to promote bacterial invasion. Here, we show that IpaA triggers an unreported mode of vinculin activation through the cooperative binding of its three vinculin-binding sites (VBSs) leading to vinculin oligomerization via its D1 and D2 head subdomains and highly stable adhesions resisting actin relaxing drugs. Using cross-linking mass spectrometry, we found that while IpaA VBSs1-2 bound to D1, IpaA VBS3 interacted with D2, a subdomain masked to other known VBSs. Structural modeling indicated that as opposed to canonical activation linked to interaction with D1, these combined VBSs interactions triggered major allosteric changes leading to D1D2 oligomerization. A cysteine-clamp preventing these changes and D1D2 oligomerization impaired growth of vinculin microclusters and cell adhesion. We propose that D1D2-mediated vinculin oligomerization occurs during the maturation of adhesion structures to enable the scaffolding of high-order vinculin complexes, and is triggered by Shigella IpaA to promote bacterial invasion in the absence of mechanotransduction.

The Shigella IpaA effector binds to cryptic vinculin sites leading to oligomerization via its head domain. This vinculin oligomerization mode appears required for the maturation and strengthening of cell adhesion but is co-opted by invasive bacteria independent of actomyosin contractility.
Phylogenetic modeling of regulatory element turnover based on epigenomic data
Authors: Dukler Noah , Huang Yi-Fei , Siepel Adam
Published: September 2019

Evolutionary changes in gene expression are often driven by gains and losses of cis-regulatory elements (CREs). The dynamics of CRE evolution can be examined using multi-species epigenomic data, but so far such analyses have generally been descriptive and model-free. Here, we introduce a probabilistic modeling framework for the evolution of CREs that operates directly on raw chromatin immunoprecipitation and sequencing (ChIP-seq) data and fully considers the phylogenetic relationships among species. Our framework includes a phylogenetic hidden Markov model, called epiPhyloHMM, for identifying the locations of multiply aligned CREs, and a combined phylogenetic and generalized linear model, called phyloGLM, for accounting for the influence of a rich set of genomic features in describing their evolutionary dynamics. We apply these methods to previously published ChIP-seq data for the H3K4me3 and H3K27ac histone modifications in liver tissue from nine mammals. We find that enhancers are gained and lost during mammalian evolution at about twice the rate of promoters, and that turnover rates are negatively correlated with DNA sequence conservation, expression level, and tissue breadth, and positively correlated with distance from the transcription start site, consistent with previous findings. In addition, we find that the predicted dosage sensitivity of target genes positively correlates with DNA sequence constraint in CREs but not with turnover rates, perhaps owing to differences in the effect sizes of the relevant mutations. Altogether, our probabilistic modeling framework enables a variety of powerful new analyses.
Active modulation of Hydrogen bonding by sericin enhances cryopreservation outcomes
Authors: Underwood L. , Solocinski J. , Rosiek E. , Osgood Q. , Chakraborty N.
Published: September 2019

Cryopreservation of cells without any toxicity concerns is a critical step in ensuring successful clinical translation of cell-based technologies. Mitigating the toxicity concerns related to most of the commonly used cryoprotectants including dimethyl sulfoxide (DMSO) is an active area of research in cryobiology. In recent years use of additives including polymeric proteins such has sericin have been explored as an additive to cryoprotectant formulations. In this study the thermophysical effect of addition of sericin was investigated. The effect of presence of sericin on the H-bonding strength was investigated using Raman microspectroscopy and other thermophysical effects were quantified using differential scanning calorimetry (DSC) techniques. Finally, the prospect of using sericin as an additive to cryoprotectant formulation was investigated by monitoring cellular viability and growth following exposure to cryogenic temperatures in hepatocellular carcinoma cells. Results indicate significant improvement in post-thaw viability when sericin is used as an additive to DMSO based formulations. While use of trehalose as an additive has beneficial effects by itself, combined usage of sericin and trehalose as additives did result in an improved overall long-term growth potential of the cells.

Statement of Significance

This study provides for powerful biophysical understanding of how sericin can be used as an additive for cryoprotectant solutions, which allows storage of biologics at low temperatures. It is desirable to replace current components of cryoprotectant formulation (such as DMSO) due to innate toxicity and metabolic derangements to cells. The ability of sericin to improve cryoprotective solutions was mechanistically characterized by Raman microspectroscopy, which allows for molecular level characterization of the nature of H-bonding in aqueous environments in presence of solution components. Thermodynamic analysis of the cryoprotectant solutions containing sericin was undertaken to quantify the relation between solution composition and cryopreservation outcome. This analytical study provides a basis for designing better cryoprotectants with lower thermophysical injury and higher cellular yields.
Neuroprotective effects of exogenous erythropoietin in Wistar rats by downregulating apoptotic factors to attenuate N-methyl-D-aspartate-mediated retinal ganglion cells death
Authors: Cheng Wen-Sheng , Lin I-Hung , Feng Kathy Ming , Chang Zhi-Yang , Huang Yu Chuan , Lu Da-Wen
Published: September 2019

The aim of this study was to investigate whether exogenous erythropoietin (EPO) administration attenuates N-methyl-D-aspartate (NMDA)-mediated excitotoxic retinal damage in Wistar rats. The survival rate of retinal ganglion cells (RGCs) were investigated by flat mount analysis and flow cytometry. A group of male Wistar rats were randomly assigned to five groups: negative control, NMDA80 (i.e., 80 nmoles NDMA intravitreally injected), NMDA80 + 10ng EPO, NMDA80 + 50ng EPO, and NMDA80 + 250ng EPO. The NMDA80 + 50ng EPO treatment group was used to evaluate various administrated points (pre-/co-/post-administration of NMDA80). Meanwhile, the transferase dUTP Nick-End Labeling (TUNEL) assay of RGCs, the inner plexiform layer (IPL) thickness and the apoptotic signal transduction pathways of μ-calpain, Bax, and caspase 9 were assessed simultaneously using an immunohistochemical method (IHC). When EPO was co-administered with NMDA, attenuated cell death occurred through the downregulation of the apoptotic indicators: μ-calpain was activated first (peak at ∼18hrs), followed by Bax and caspase 9 (peak at ∼40hrs). Furthermore, the morphology of RGCs has clearly demonstrated the visual recovery of IPL thickness at 40 hours after injection. Exogenous EPO successfully protected RGCs by downregulating apoptotic factors to attenuate NMDA-mediated excitotoxic retinal damage.
Spire stimulates nucleation by Cappuccino and binds both ends of actin filaments
Authors: Bradley Alexander O. , Vizcarra Christina L. , Bailey Hannah M. , Quinlan Margot E.
Published: September 2019

An actin mesh fills both mouse and fly oocytes. The meshes are built by a conserved mechanism and used to establish polarity. Two actin nucleators, Spire and Cappuccino, collaborate to build actin filaments that connect vesicles and the cortex. Direct interaction between Spire and Cappuccino is required for in vitro synergistic actin assembly; however, we understand little about why the interaction is necessary. To mimic the geometry of Spire and Cappuccino in vivo, we immobilized Spire on beads. We found that increased nucleation is a major part of synergy and that Spire alone binds both barbed- and pointed-ends of actin filaments. We identified Spire’s barbed-end binding domain. Partial rescue of fertility by a loss-of-function mutant indicates that barbed-end binding is not necessary for Spire’s in vivo function, but that it may play a role under normal circumstances. We propose that Spire stimulates nucleation by Cappuccino in a manner similar to the collaboration between APC and mDia1.

Actin nucleators Cappuccino and Spire collaborate to build an actin mesh in oocytes. Data demonstrate that the collaboration leads to synergistic actin nucleation, as opposed to elongation. Further, Spire binds both ends of polar, actin filaments, resolving a long-outstanding question.
Assessment of Robustness to Temperature in a Negative Feedback Loop and a Feedforward Loop
Authors: Patel Abhilash , Murray Richard M. , Sen Shaunak
Published: September 2019

Robustness to temperature variation is an important specification for biomolecular circuit design. While cancellation of parametric temperature dependences has been shown to improve temperature robustness of period in a synthetic oscillator design, the performance of other biomolecular circuit designs in different temperature conditions is relatively unclear. Using a combination of experimental measurements and mathematical models, we assess the temperature robustness of two biomolecular circuit motifs — a negative feedback loop and a feedforward loop. We find that the measured responses in both circuits can change with temperature, both in the amplitude and in the transient response. We find that, in addition to the cancellation of parametric temperature dependencies, certain parameter regimes can also facilitate temperature robustness for the negative feedback loop, although at a performance cost. We discuss these parameter regimes of operation in the context of the measured data for the negative feedback loop. These results should help develop a framework for assessing and designing temperature robustness in biomolecular circuits.
Altered gut microbiota and immunity defines Plasmodium vivax survival in Anopheles stephensi
Authors: Sharma Punita , Rani Jyoti , Chauhan Charu , Kumari Seena , Tevatiya Sanjay , Das De Tanwee , Pandey Kailash C , Dixit Rajnikant
Published: September 2019

Blood feeding-enriched gut-microbiota boosts mosquitoes’ anti-Plasmodium immunity. Here, we ask how Plasmodium vivax alters microbiota, anti-Plasmodial immunity and impact tripartite Plasmodium-mosquito-microbiota interactions in the gut lumen. Using a metagenomics analysis, we predominantly detect Elizabethkingia meningitis and Pseudomonas sps. in naïve mosquitoes. Naïve blood fed gut shows a heightened presence of Elizabethkingia, Pseudomonas and Serratia. A parallel RNAseq analysis of blood-fed midguts identify Elizabethkingia-transcripts, which may have role in iron metabolism. Post, a Plasmodium vivax infected blood-meal, however, we do not detect bacterial until circa 36 hours. Intriguingly, transcriptional expression of a selected array of antimicrobial arsenal cecropins 1-2, defensin-1 and gambicin remains low during the first 36 hours–a time frame when ookinietes/early oocysts invade gut. We conclude during the preinvasive phase, Plasmodium vivax outcompetes midgut-microbiota. Suppression of important immune factors, likely due to altered microbiota, may enhance Plasmodium vivax survival. Additional finding of a novel Wolbachia association warrants further research to design ‘paratransgenesis’ tools for malaria control.

Author Summary

Successful malaria transmission relies on the competitive interactions of Plasmodium and mosquito’s tissue specific immune potential. Within 24hrs of blood meal gut-microbiota grows exponentially and lead to robust enhancement of mosquito immune response, which is detrimental to parasite survival and development. But the mechanism how Plasmodium manages to evade this pre-invasive immune barrier is not well known. We investigated the influence of tripartite gut-microbiome-parasite interaction on human malaria parasite Plasmodium vivax in its natural/native vector Anopheles stephensi. Surprisingly we found that infectious blood meal lead to dramatic suppression in gut-bacteria population, a plausible strategy of P. vivax ookinetes to avoid immune responses. Our study suggests that for its own survival Plasmodium vivax causes early suppression of bacterial population, possibly by scavenging Fe from the blood meal which is indispensable for bacterial growth. Disruption and manipulation of this gut-microbe-interaction may help to design new ‘paratransgenesis’ molecular tool for malaria control.
RstA Regulation ofClostridioides difficileToxin Production and Sporulation in Phenotypically Diverse Strains
Authors: Edwards Adrianne N. , Krall Ellen G. , McBride Shonna M.
Published: September 2019

The anaerobic spore-former,Clostridioides difficile, causes significant diarrheal disease in humans and other mammals. Infection begins with the ingestion of dormant spores which subsequently germinate within the host gastrointestinal tract. Here, the vegetative cells proliferate and secrete two exotoxins, TcdA and TcdB, which cause disease symptoms. Although spore formation and toxin production are critical forC. difficilepathogenesis, the regulatory links between these two physiological processes are not well understood and are strain-dependent. Previously, we identified a conservedC. difficileregulator, RstA, that promotes sporulation initiation through an unknown mechanism and directly and indirectly represses toxin gene transcription in the historical isolate, 630Δerm. To test whether perceived strain-dependent differences in toxin production and sporulation are mediated by RstA, we created anrstAmutant in the epidemic 027 ribotype strain, R20291. RstA affects sporulation and toxin gene expression similarly in R20291, although more robust regulatory effects are observed in this strain than in 630Δerm. Reporter assays measuring transcriptional regulation oftcdR, the sigma factor essential for toxin gene expression, identified sequence-dependent effects influencing repression by RstA and CodY, a global nutritional sensor, in four diverseC. difficilestrains. We provide evidence that RstA contributes totcdRbistability in R20291 by biasing cells to a toxin-OFF state. Finally, sequence-dependent and strain-dependent differences were evident in RstA negative autoregulation ofrstAtranscription. Our data establish RstA as an important regulator ofC. difficilevirulence traits, and implicate RstA as a contributor to the variety of sporulation and toxin phenotypes observed in distinct isolates.

IMPORTANCE

Two critical traits ofClostridioides difficilepathogenesis are the production of toxins, which cause disease symptoms, and the formation of spores, which permit survival outside of the gastrointestinal tract. The multifunctional regulator, RstA, promotes sporulation and prevents toxin production in the historical strain, 630Δerm. Here, we show that RstA functions similarly in an epidemic isolate, R20291, although strain-specific effects on toxin andrstAexpression are evident. Our data demonstrate that sequence-specific differences within the promoter for the toxin regulator, TcdR, contribute to regulation of toxin production by RstA and CodY. These sequence differences account for some of the variability in toxin production among isolates, and may allow strains to differentially control toxin production in response to a variety of signals.
Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks
Authors: Madani Tonekaboni Seyed Ali , Mazrooei Parisa , Kofia Victor , Haibe-Kains Benjamin , Lupien Mathieu
Published: September 2019

Cellular identity relies on cell-type–specific gene expression controlled at the transcriptional level by cis-regulatory elements (CREs). CREs are unevenly distributed across the genome, giving rise to individual CREs and clusters of CREs (COREs). Technical and biological features hinder CORE identification. We addressed these issues by developing an unsupervised machine learning approach termed clustering of genomic regions analysis method (CREAM). CREAM automates CORE detection from chromatin accessibility profiles that are enriched in CREs strongly bound by master transcription regulators, proximal to highly expressed and essential genes, and discriminating cell identity. Although COREs share similarities with super-enhancers, we highlight differences in terms of the genomic distribution and structure of these cis-regulatory units. We further show the enhanced value of COREs over super-enhancers to identify master transcription regulators, highly expressed and essential genes defining cell identity. COREs enrich at topologically associated domain (TAD) boundaries. They are also preferentially bound by the chromatin looping factors CTCF and cohesin, in contrast to super-enhancers, forming clusters of CTCF and cohesin binding regions and defining homotypic clusters of transcription regulator binding regions (HCTs). Finally, we show the clinical utility of CREAM to identify COREs across chromatin accessibility profiles to stratify more than 400 tumor samples according to their cancer type and to delineate cancer type–specific active biological pathways. Collectively, our results support the utility of CREAM to delineate COREs underlying, with greater accuracy than individual CREs or super-enhancers, the cell-type–specific biological underpinning across a wide range of normal and cancer cell types.