bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in skin score in early diffuse cutaneous systemic sclerosis are associated with changes in global disease severity
Authors: Zheng Boyang , Nevskaya Tatiana , Baxter Carl A , Ramey Dena R , Pope Janet E , Baron Murray ,   Canadian Scleroderma Research Group, Pope Janet E , Baron Murray , Hudson Marie , Gyger Geneviève , Larché Maggie J , Khalidi Nader A , Masetto Ariel , Sutton Evelyn , Robinson David , Rodriguez-Reyna Tatiana S , Smith Doug , Thorne Carter , Fortin Paul R , Fritzler Marvin J , Pope Janet E , Baron Murray , Hudson Marie , Gyger Geneviève , Larché Maggie J , Khalidi Nader A , Masetto Ariel , Sutton Evelyn , Robinson David , Rodriguez-Reyna Tatiana S , Smith Doug , Thorne Carter , Fortin Paul R , Fritzler Marvin J
Published: June 2019

Objective

To determine whether skin score changes are associated with changes in overall disease severity, function and quality of life in early dcSSc patients.

Methods

A total of 154 and 128 dcSSc patients from the Canadian Scleroderma Research Group database with 1 and 2 year follow-up and a disease duration ⩽5 years without end-stage organ damage and/or significant comorbidity at the initial visit were included. Skin was assessed using the modified Rodnan skin score (mRSS) and disease severity by the summed Medsger disease severity score (DSS) (without skin domain), physician and patient global assessments, function [HAQ disability index (HAQ-DI)] and quality of life [36-item Short Form Health Survey (SF-36) physical component summary (PCS)]. Analyses were repeated in patients with a disease duration ⩽3 years.

Results

At 2 years, 64 (50%) patients had improved skin (mRSS decrease of ⩾5 points and/or ⩾25%). Skin improvers had improved summed DSS (P = 0.002); better physician global assessments of disease activity, severity and damage (all P ⩽ 0.003); better HAQ-DI (P = 0.001) and SF-36 PCS (P = 0.005). Changes in the mRSS were positively correlated with changes in summed DSS (P = 0.006) and other disease outcomes. In the 26 (20.3%) patients with worsened skin (mRSS increase of ⩾5 points and/or ⩾25%), the summed DSS and physician global assessments were worse (P = 0.01 and P ⩽ 0.009, respectively). In the subgroup with a disease duration ⩽3 years, similar associations were found.

Conclusion

At 1 and 2 years, overall disease improvement parallels skin improvement in early dcSSc. This is important for prognosis and reflects the value of mRSS as an outcome measure in trials with these patients.
Novel Cell Death-Inducing Elicitors from Phytophthora palmivora Promote Infection on Hevea brasiliensis
Authors: Pettongkhao Sittiporn , Churngchow Nunta
Published: June 2019

Elicitors play an important role in plant and pathogen interactions. The discovery of new elicitors and their effects on plant defense responses is significant and challenging. In this study, we investigated novel elicitors from Phytophthora palmivora and their effects on plant defenses. A crude elicitor isolated by ethanol precipitation from culture filtrates of P. palmivora induced cell death in tobacco leaves. When tobacco leaves were infiltrated with this cell death-inducing elicitor, the accumulations of H2O2, salicylic acid (SA), scopoletin (Scp), and abscisic acid (ABA) were detected. Accumulations of SA, Scp, and ABA were also induced in rubber tree leaves. P. palmivora infection significantly increased in rubber tree leaves pretreated with the elicitor and cotreated with the elicitor and zoospores of P. palmivora. This elicitor can be described as compound elicitor because Fourier-transform infrared spectroscopy revealed that it consisted of both polysaccharide and protein. We also found that the cell death effect caused by this compound elicitor was completely neutralized by Proteinase K. The compound elicitor was composed of four fractions which were beta-glucan, high-molecular-weight glycoprotein, broad-molecular-weight glycoprotein and 42-kDa protein. Interestingly, the broad-molecular-weight glycoprotein caused the highest level of cell death in tobacco leaves, while the beta-glucan had no effect. The high-molecular-weight glycoprotein, broad-molecular-weight glycoprotein and 42-kDa protein fractions not only caused cell death in tobacco leaves but also induced high levels of SA accumulation. Furthermore, these three fractions clearly promoted P. palmivora infection of rubber tree leaves.
Arm swapping autograft shows functional equivalency of five arms in sea stars
Authors: Wakita Daiki , Aonuma Hitoshi , Tochinai Shin
Published: June 2019

Extant echinoderms show five-part radial symmetry in typical shape. However, we can find some asymmetry in their details, represented by the madreporite position not at the center, different skeletal arrangement in two of the five rays of sea urchins, and a circular cavity formed by two-end closure. We suspect the existence of any difference in hidden information between the five. In our hypothesis, deep equivalency makes no issue in function even after exchanging the position of rays; otherwise, this autograft causes some trouble in behavior or tissue formation. For this attempt, we firstly developed a method to transplant an arm tip to the counterpart of another arm in the sea starPatiria pectinifera. As a result, seven arms were completely implanted—four into the original positions for a control and three into different positions—with underwater surgery where we sutured with nylon thread and physically prevented nearby tube feet extending. Based on our external and internal observation, each grafted arm (i) gradually recovered movement coordination with the proximal body, (ii) regenerated its lost half as in usual distal regeneration, and (iii) formed no irregular intercalation filling any positional gap at the suture, no matter whether two cut arms were swapped. We here suggest a deep symmetry among the five rays of sea stars not only in morphology but also in physiology, representing an evolutionary strategy that has given equal priority to all the radial directions. Moreover, our methodological notes for grafting a mass of body in sea stars would help echinoderm research involving positional information as well as immunology.
An atlas of transcription factors expressed in theDrosophila melanogasterpupal terminalia
Authors: Vincent Ben J. , Rice Gavin R. , Wong Gabriella M. , Glassford William J. , Downs Kayla I. , Shastay Jessica L. , Charles-Obi Kenechukwu , Natarajan Malini , Gogol Madelaine , Zeitlinger Julia , Rebeiz Mark
Published: June 2019

During development, transcription factors and signaling molecules govern gene regulatory networks to direct the formation of unique morphologies. As changes in gene regulatory networks are often implicated in morphological evolution, mapping transcription factor landscapes is important, especially in tissues that undergo rapid evolutionary change. The terminalia (genital and anal structures) ofDrosophila melanogasterand its close relatives exhibit dramatic changes in morphology between species. While previous studies have found network components important for patterning the larval genital disc, the networks governing adult structures during pupal development have remained uncharted. Here, we performed RNA-seq in wholeDrosophila melanogasterterminalia followed byin situhybridization for 100 highly expressed transcription factors during pupal development. We find that the terminalia is highly patterned during pupal stages and that specific transcription factors mark separate structures and substructures. Our results are housed online in a searchable database (flyterminalia.pitt.edu) where they can serve as a resource for the community. This work lays a foundation for future investigations into the gene regulatory networks governing the development and evolution ofDrosophilaterminalia.

We performed RNA-seq in wholeDrosophila melanogasterterminalia (genitalia and analia) followed byin situhybridization for 100 highly expressed transcription factors during pupal development. We find that the pupal terminalia is highly patterned with specific transcription factors marking separate structures and substructures. Our results are housed online in a searchable database (flyterminalia.pitt.edu) where they can serve as a resource for the community. This work lays a foundation for future investigations into the gene regulatory networks governing the development and evolution ofDrosophilaterminalia.
Reproducible Tract Profiles (RTP): from diffusion MRI acquisition to publication
Authors: Lerma-Usabiaga Garikoitz , Perry Michael L. , Wandell Brian A.
Published: June 2019

Reproducible Tract Profiles (RTP) comprises a set of methods to manage and analyze diffusion weighted imaging (DWI) data for reproducible tractography. The tools take MRI data from the scanner and process them through a series of analysis implemented as Docker containers that are integrated into a modern neuroinformatics platform (Flywheel). The platform guarantees that the entire pipeline can be re-executed, using the same data and computational parameters. In this paper, we describe (1) a cloud based neuroinformatics platform, (2) a tool to programmatically access and control the platform from a client, and (3) the DWI analysis tools that are used to identify the positions of 22 tracts and their diffusion profiles. The combination of these three components defines a system that transforms raw data into reproducible tract profiles for publication.

Graphical abstract

Reproducible Tract Profiles (RTP) comprises a set of methods to manage and analyze diffusion weighted imaging (DWI) data for reproducible tractography. The RTP methods comprise two main parts.

Server side software tools for storing data and metadata and managing containerized computations.

Client side software tools that enable the researcher to read data and metadata and manage server-side computations.

The server-side computational tools are embedded in containers that are linked to a JSON file with a complete specification of the computational parameters. The data and computational infrastructure on the server is fully reproducible.
Movement behavioral plasticity of benthic diatoms driven by optimal foraging
Authors: Hu Wen-Si , Huang Mingji , Zhang H. P. , Zhang Feng , Vyverman Wim , Liu Quan-Xing
Published: June 2019

Adaptive locomotion of living organisms contributes to their competitive abilities and helps maintain their fitness in diverse environments. To date, however, our understanding of searching behavior and its ultimate cause remains poorly understood in ecology and biology. Here, we investigate motion patterns of biofilm-inhabiting marine raphid diatomNavicula arenariavar.rostellatain two-dimensional space. We report that individualNaviculacells display a “circular run-and-reversal” movement behavior at different concentrations of dissolved silicic acid (dSi). We show that gliding motions of cells can be predicted accurately with a universal Langevin model. Our experimental results are consistent with an optimal foraging strategy and a maximized diffusivity of the theoretical outcomes in which both circular-run and reversal behaviors are important ingredients. Our theoretical results suggest that the evolving movement behaviors of diatoms may be driven by optimization of searching behavioral strategy, and predicted behavioral parameters coincide with the experimental observations. These optimized movement behaviors are an evolutionarily stable strategy to cope with environmental complexity.

ONE SENTENCE SUMMARY

Novel experiments and modelling reveal that raphid diatoms can actively exploit resources in complex environments by adjusting their movement behavior.
A computational mechanism for seeing dynamic deformation
Authors: Kawabe Takahiro , Sawayama Masataka
Published: June 2019

Human observers perceptually discriminate the dynamic deformation of materials in the real world. However, the psychophysical and neural mechanisms responsible for the perception of dynamic deformation have not been fully elucidated. By using a deforming bar as the stimulus, we showed that the spatial frequency of deformation was a critical determinant of deformation perception. Simulating the response of direction-selective units (i.e., MT pattern motion cells) to stimuli, we found that the perception of dynamic deformation was well explained by assuming a higher-order mechanism monitoring the spatial pattern of direction responses. Our model with the higher-order mechanism also successfully explained the appearance of a visual illusion wherein a static bar apparently deforms against a tilted drifting grating. In particular, it was the lower spatial frequencies in this pattern that strongly contributed to the deformation perception. Finally, by manipulating the luminance of the static bar, we observed that the mechanism for the illusory deformation was more sensitive to luminance than contrast cues.

Significance Statement

From the psychophysical and computational points of view, the present study tried to answer the question, “how do human observers see deformation?”. In the psychophysical experiment, we used a clip wherein a bar dynamically deformed. We also tested the illusory deformation of a bar, which was caused by tilted drifting grating, because it was unclear whether the illusory deformation could be described by our model. In the computational analysis, in order to explain psychophysical data for deformation perception, it was necessary to assume an additional unit monitoring the spatial pattern of direction responses of MT cells that were sensitive to local image motion.
Investigating unexplained genetic variation and its expression in the arbuscular mycorrhizal fungus Rhizophagus irregularis
Authors: Masclaux Frédéric G. , Wyss Tania , Pagni Marco , Rosikiewicz Pawel , Sanders Ian R.
Published: June 2019

Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants. Recently, studies of the AMF Rhizophagus irregularis recorded within-isolate genetic variation that does not completely match the proposed homokaryon or heterokaryon state (where heterokaryons comprise a population of two distinct nucleus genotypes). We re-analysed published data showing that bi-allelic sites (and their frequencies), detected in proposed homo- and heterokaryote R. irregularis isolates, were similar across independent studies using different techniques. This indicated that observed within-fungus genetic variation was not an artefact of sequencing and that such within-fungus genetic variation possibly exists. We looked to see if bi-allelic transcripts from three R. irregularis isolates matched those observed in the genome as this would give a strong indication of whether bi-allelic sites recorded in the genome were reliable variants. In putative homokaryon isolates, very few bi-allelic transcripts matched those in the genome. In a putative heterokaryon, a large number of bi-allelic transcripts matched those in the genome. Bi-allelic transcripts also occurred in the same frequency in the putative heterokaryon as predicted from allele frequency in the genome. Our results indicate that while within-fungus genome variation in putative homokaryon and heterokaryon AMF was highly similar in 2 independent studies, there was little support that this variation is transcribed in homokaryons. In contrast, within-fungus variation thought to be segregated among two nucleus genotypes in a heterokaryon isolate was indeed transcribed in a way that is proportional to that seen in the genome.
Experimental investigation of temperature-dependent denaturation behavior of type-I Collagen
Authors: Derman İ. Deniz , Şenel Esat C. , Ferhanoğlu Onur , Çilesiz İnci
Published: June 2019

Precise investigation of the temperature and the duration for collagen denaturation is critical for a number of applications, such as adjustment of temperature and duration during a laser-assisted tissue welding or collagen-based tissue repair products (films, implants, cross-linkers) preparation procedures. The result of such studies can serve as a guideline to mitigate potential side effects while maintaining the functionality of the collagen. Though a variety of collagen denaturation temperatures have been reported, there has not been a systematic study to report temperature-dependent denaturation rates. In this study, we perform a set of experiments on type-I collagen fiber bundles, extracted from the rat-tail tendon, and provide an Arrhenius model based on the acquired data. The tendons are introduced to buffer solutions having different temperatures, while monitoring the contrast in the crimp sights with a wide field microscope, where collagen fibers bend with respect to their original orientation. For all tested temperatures of 50°C–70 °C and tissues that were extracted from 5 rats, increasing the temperature reduced the contrast. On the average, we observed a decay of the contrast to half of its initial value at 37, 157, and 266 seconds when the collagen was introduced to 70 °C, 65 °C, and 60 °C buffer solutions, respectively. For the lower temperatures tested we only observed to be only about 20% and 2 % decay in the crimp contrast after > 2 hours at 55 °C and 50 °C, respectively. The observed denaturation behavior is also in line with Arrhenius Law, as expected. We are looking forward to expand this study to other types of collagen as a future work. Overall, with further development the data and model we present here could potentially serve as a guideline to determine limits for welding and manufacturing process of collagen-based tissue repair agents.
Asymmetric Cell Growth and Nucleoid Displacement inEscherichia coli
Authors: Gangan Manasi S. , Athale Chaitanya A.
Published: June 2019

Single celled growth ofEscherichia coliis typically considered as an example symmetric division, based on the sizes of daughter cells and precision of center finding of the septum. Here, we investigate the symmetry of membrane addition in the mid-plane and DNA segregation using a video-microscopy approach. We find the membrane expansion dynamics to be asymmetric based on mid-cell photobleaching landmarks in FM4-64, used to stain the membrane. The apparent growth bias ofE. colidoes not correspond to the age of the pole. We find the membrane growth asymmetry is correlated to nucleoid displacement, consistent with ideas of coupling of cell growth and nucleoid positioning. The mobility of the actin-homolog MreB also correlates with membrane growth asymmetry, based on fluorescence recovery after photobleaching (FRAP) measurements of a YFP-fusion. These correlations suggest the small asymmetry of membrane addition observed could potentially drive nucleoid segregation and MreB mobility asymmetry inE. coli.

IMPORTANCE

Asymmetry in bacterial cell division is seen in it’s most simple form in the binomial event of protein segregation that results in ‘noise’ in equal segregation and depends on the protein copy number. In the case of specific proteins this can also affect growth, and result in differentiation. However, during the asexual division ofEscherichia colisingle cells are thought to grow symmetrically and divide equally. We find a slight but consistent asymmetry in growth based on quantitative morphometry of cell pole displacement in time-series of growingE. colicells. Increased cell wall extension in one half of the cell over the other appears to explain the asymmetry in the displacement of cell poles. Interestingly the growth asymmetry is not correlated to the age of the pole (old and new). This observed asymmetry appears to correlate with the asymmetry of nucleoid segregation, resulting in the nucleoids finding the midpoints of the respective daughter cells, and formation of the septum at the geometric centre of the elongated cell just prior to division. The mobility dynamics of the cytoskeletal protein MreB, which organizes the cell membrane, is are more dynamic where membrane growth is faster. Thus we propose a linkage between this observed growth asymmetry and that of MreB dynamics.
The evolutionary dynamics of Oropouche Virus (OROV) in South America
Authors: Gutierrez Bernardo , Wise Emma , Pullan Steven , Logue Christopher , Bowden Thomas A. , Trueba Gabriel , Nunes Marcio , Faria Nuno R. , Pybus Oliver G.
Published: June 2019

The Amazon basin is host to numerous arthropod-borne viral pathogens that cause febrile disease in humans. Among these,Oropouche orthobunyavirus(OROV) is a relatively understudied member of the Peribunyavirales that causes periodic outbreaks in human populations in Brazil and other South American countries. Although several studies have described the genetic diversity of the virus, the evolutionary processes that shape the viral genome remain poorly understood. Here we present a comprehensive study of the genomic dynamics of OROV that encompasses phylogenetic analysis, evolutionary rate estimates, inference of natural selective pressures, recombination and reassortment, and structural analysis of OROV variants. Our study includes all available published sequences, as well as a set of new OROV genomes sequences obtained from patients in Ecuador, representing the first set of viral genomes from this country. Our results show that differing evolutionary processes on the three segments that encompass the viral genome lead to variable evolutionary rates and TMRCAs that could be explained by cryptic reassortment. We also present the discovery of previously unobserved putative N-linked glycosylation sites, and codons which evolve under positive selection on the viral surface proteins, and discuss the potential role of these features in the evolution of the virus through a combined phylogenetic and structural approach.
Multi-tissue probabilistic fine-mapping of transcriptome-wide association study identifies cis-regulated genes for miserableness
Authors: Liao Calwing , Vuokila Veikko , Laporte Alexandre D , Spiegelman Dan , Dion Patrick A. , Rouleau Guy A.
Published: June 2019

Miserableness is a behavioural trait that is characterized by strong negative feelings in an individual. Although environmental factors tend to invoke miserableness, it is common to feel miserable ‘for no reason’, suggesting an innate, potential genetic component. Currently, little is known about the functional relevance of common variants associated with miserableness. To further characterize the trait, we conducted a transcriptome-wide association study (TWAS) on 373,733 individuals and identified 104 signals across brain tissue panels with 37 unique genes. Subsequent probabilistic fine-mapping prioritized 95 genes into 90%-credible sets. Amongst these prioritized hits, C7orf50 had the highest posterior inclusion probability of 0.869 in the brain cortex. Furthermore, we demonstrate that many GWAS hits for miserableness are driven by expression. To conclude, we successfully identified several genes implicated in miserableness and highlighted the power of TWAS to prioritize genes associated with a trait.

Short summary

The first transcriptome-wide association study of miserableness identifies many
genes including c7orf50 implicated in the trait.
Neural Mechanisms of Economic Choices in Mice
Authors: Kuwabara Masaru , Holy Timothy E. , Padoa-Schioppa Camillo
Published: June 2019

Economic choices entail computing and comparing subjective values. Evidence from primates indicates that this behavior relies on the orbitofrontal cortex. Conversely, previous work in rodents provided conflicting results. Here we present a mouse model of economic choice behavior, and we show that the lateral orbital (LO) area is intimately related to the decision process. In the experiments, mice chose between different juices offered in variable amounts. Choice patterns closely resembled those measured in primates. Optogenetic inactivation of LO dramatically disrupted choices by inducing erratic changes of relative value and by increasing choice variability. Neuronal recordings revealed that different groups of cells encoded the values of individual options, the binary choice outcome and the chosen value. These groups match those previously identified in primates, except that the neuronal representation in mice is spatial (in monkeys it is good-based). Our results lay the foundations for a circuit-level analysis of economic decisions.
A novel systems biology approach to evaluate mouse models of late-onset Alzheimer’s disease
Authors: Preuss Christoph , Pandey Ravi , Piazza Erin , Fine Alexander , Uyar Asli , Perumal Thanneer , Garceau Dylan , Kotredes Kevin P , Williams Harriet , Mangravite Lara M , Lamb Bruce T. , Oblak Adrian L. , Howell Gareth R. , Sasner Michael , Logsdon Benjamin A , Carter Gregory W.
Published: June 2019

Background

Late-onset Alzheimer’s disease (LOAD) is the most common form of dementia worldwide. To date, animal models of Alzheimer’s have focused on rare familial mutations, due to a lack of frank neuropathology from models based on common disease genes. Recent multi-cohort studies of postmortem human brain transcriptomes have identified a set of 30 gene co-expression modules associated with LOAD, providing a molecular catalog of relevant endophenotypes.

Results

This resource enables precise gene-based alignment between new animal models and human molecular signatures of disease. Here, we describe a new resource to efficiently screen mouse models for LOAD relevance. A new NanoString nCounter® Mouse AD panel was designed to correlate key human disease processes and pathways with mRNA from mouse brains. Analysis of three mouse models based on LOAD genetics, carrying APOE4 and TREM2*R47H alleles, demonstrated overlaps with distinct human AD modules that, in turn, are functionally enriched in key disease-associated pathways. Comprehensive comparison with full transcriptome data from same-sample RNA-Seq shows strong correlation between gene expression changes independent of experimental platform.

Conclusions

Taken together, we show that the nCounter Mouse AD panel offers a rapid, cost-effective and highly reproducible approach to assess disease relevance of potential LOAD mouse models.
DNA-loop extruding condensin complexes can traverse one another
Authors: Kim Eugene , Kerssemakers Jacob , Shaltiel Indra A. , Haering Christian H. , Dekker Cees
Published: June 2019

Condensin, a key member of the Structure Maintenance of Chromosome (SMC) protein complexes, has recently been shown to be a motor that extrudes loops of DNA1. It remains unclear, however, how condensin complexes work together to collectively package DNA into the chromosomal architecture. Here, we use time-lapse single-molecule visualization to study mutual interactions between two DNA-loop-extruding yeast condensins. We find that these one-side-pulling motor proteins are able to dynamically change each other’s DNA loop sizes, even when located large distances apart. When coming into close proximity upon forming a loop within a loop, condensin complexes are, surprisingly, able to traverse each other and form a new type of loop structure, which we term Z loop – three double-stranded DNA helices aligned in parallel with one condensin at each edge. These Z-loops can fill gaps left by single loops and can form symmetric dimer motors that reel in DNA from both sides. These new findings indicate that condensin may achieve chromosomal compaction using a variety of looping structures.
Control of Intracellular Molecular Networks Using Algebraic Methods
Authors: Vieira Luis Sordo , Laubenbacher Reinhard C. , Murrugarra David
Published: June 2019

Many problems in biology and medicine have a control component. Often, the goal might be to modify intracellular networks, such as gene regulatory networks or signaling networks, in order for cells to achieve a certain phenotype, such as happens in cancer. If the network is represented by a mathematical model for which mathematical control approaches are available, such as systems of ordinary differential equations, then this problem might be solved systematically. Such approaches are available for some other model types, such as Boolean networks, where structure-based approaches have been developed, as well as stable motif techniques.

However, increasingly many published discrete models are mixed-state or multistate, that is, some or all variables have more than two states, and thus the development of control strategies for multistate networks is needed. This paper presents a control approach broadly applicable to general multistate models based on encoding them as polynomial dynamical systems over a finite algebraic state set, and using computational algebra for finding appropriate intervention strategies. To demonstrate the feasibility and applicability of this method, we apply it to a recently developed multistate intracellular model of E2F-mediated bladder cancerous growth, and to a model linking intracellular iron metabolism and oncogenic pathways. The control strategies identified for these published models are novel in some cases and represent new hypotheses, or are supported by the literature in others as potential drug targets.

Our Macaulay2 scripts to find control strategies are publicly available through GitHub at https://github.com/luissv7/multistatepdscontrol.
HB-EGF Signaling is Required for Glucose-Induced Pancreatic β-Cell Proliferation in Rats
Authors: Maachi Hasna , Fergusson Grace , Ethier Melanie , Brill Gabriel N. , Katz Liora S. , Honig Lee B. , Metukuri Mallikarjuna R. , Scott Donald K. , Ghislain Julien , Poitout Vincent
Published: June 2019

The molecular mechanisms of β-cell compensation to metabolic stress are poorly understood. We previously observed that nutrient-induced β-cell proliferation in rats is dependent on Epidermal Growth Factor Receptor (EGFR) signaling. The aim of this study was to determine the role of the EGFR ligand Heparin-Binding EGF-like Growth Factor (HB-EGF) in the β-cell proliferative response to glucose, a β-cell mitogen and key regulator of β-cell mass in response to increased insulin demand. We show that exposure of isolated rat and human islets to HB-EGF stimulates β-cell proliferation. In rat islets, inhibition of EGFR or HB-EGF blocks the proliferative response not only to HB-EGF but also to glucose. Furthermore, knockdown of HB-EGF in rat islets blocks β-cell proliferation in response to glucose ex vivo and in vivo in transplanted glucose-infused rats. Mechanistically, we demonstrate that HB-EGF mRNA levels are increased in β cells in response to glucose in a Carbohydrate Response Element Binding Protein (ChREBP)-dependent manner. In addition, chromatin-immunoprecipitation studies identified ChREBP binding sites in proximity to the HB-EGF gene. Finally, inhibition of Src family kinases, known to be involved in HB-EGF processing, abrogated glucose-induced β-cell proliferation. Our findings identify a novel glucose/HB-EGF/EGFR axis implicated in β-cell compensation to increased metabolic demand.
Diversity in natural transformation frequencies and regulation acrossVibriospecies
Authors: Simpson Chelsea A. , Podicheti Ram , Rusch Douglas B. , Dalia Ankur B. , van Kessel Julia C.
Published: June 2019

In marineVibriospecies, chitin-induced natural transformation enables bacteria to take up DNA from the external environment and integrate it into their genome via homologous recombination. Expression of the master competence regulator TfoX bypasses the need for chitin induction and drives expression of the genes required for competence in severalVibriospecies. Here, we show that TfoX expression in twoVibrio campbelliistrains, DS40M4 and NBRC 15631, enables high frequencies of natural transformation. Conversely, transformation was not achieved in the model quorum-sensing strainV. campbelliiBB120 (previously classified asVibrio harveyi). Surprisingly, we find that quorum sensing is not required for transformation inV. campbelliiDS40M4. This result is in contrast toVibrio choleraethat requires the quorum-sensing regulator HapR to activate the competence regulator QstR. However, similar toV. cholerae, QstR is necessary for transformation in DS40M4. To investigate the difference in transformation frequencies between BB120 and DS40M4, we used previously studiedV. choleraecompetence genes to inform a comparative genomics analysis coupled with transcriptomics. BB120 encodes homologs of all known competence genes, but most of these genes were not induced by ectopic expression of TfoX, which likely accounts for the non-functional natural transformation in this strain. Comparison of transformation frequencies amongVibriospecies indicates a wide disparity among even closely related strains, withVibrio vulnificushaving the lowest functional transformation frequency. We show that ectopic expression of both TfoX and QstR is sufficient to produce a significant increase in transformation frequency inVibrio vulnificus.

Significance

Naturally transformable or competent bacteria are able to take up DNA from their environment, a key method of horizontal gene transfer for acquisition of new DNA sequences. Our research shows thatVibriospecies that inhabit marine environments exhibit a wide diversity in natural transformation capability ranging from non-transformable to high transformation rates in which 10% of cells measurably incorporate new DNA. We show that the role of regulatory systems controlling the expression of competence genes (e.g., quorum sensing) is conserved among closely related species but differs throughout the genus. Expression of two key transcription factors, TfoX and QstR, are necessary and sufficient to stimulate high levels of transformation inVibrio campbelliiand recover low rates of transformation inVibrio vulnificus.
Identification and characterization of cis-regulatory elements for photoreceptor type-specific transcription in zebrafish
Authors: Fang Wei , Wen Yi , Wei Xiangyun
Published: June 2019

Tissue-specific or cell type-specific transcription of protein-coding genes is controlled by both trans-regulatory elements (TREs) and cis-regulatory elements (CREs). However, it is challenging to identify TREs and CREs, which are unknown for most genes. Here, we describe a protocol for identifying two types of transcription-activating CREs—core promoters and enhancers—of zebrafish photoreceptor type-specific genes. This protocol is composed of three phases: bioinformatic prediction, experimental validation, and characterization of the CREs. To better illustrate the principles and logic of this protocol, we exemplify it with the discovery of the core promoter and enhancer of the mpp5b apical polarity gene (also known as ponli), whose red, green, and blue (RGB) cone-specific transcription requires its enhancer, a member of the rainbow enhancer family. While exemplified with an RGB cone-specific gene, this protocol is general and can be used to identify the core promoters and enhancers of other protein-coding genes.
Vesicular stomatitis virus transcription is inhibited by TRIM69 in the interferon-induced antiviral state
Authors: Kueck Tonya , Bloyet Louis-Marie , Cassella Elena , Zang Trinity , Schmidt Fabian , Brusic Vesna , Tekes Gergely , Pornillos Owen , Whelan Sean P. J. , Bieniasz Paul D.
Published: June 2019

Interferons (IFNs) induce the expression of many interferon stimulated genes (ISGs), many of which are responsible for the cellular ‘antiviral state’ in which the replication of numerous viruses is blocked. How the majority of individual ISGs inhibit the replication of particular viruses is unknown. We conducted a loss-of-function screen to identify genes required for the activity of IFNαagainst vesicular stomatitis virus, Indiana serotype (VSVIND), a prototype negative strand RNA virus. Our screen revealed that TRIM69, a member of tripartite motif family of proteins, is a VSVINDinhibitor. TRIM69 potently inhibited VSVINDreplication through a previously undescribed transcriptional inhibition mechanism. Specifically, TRIM69 physically associates with the VSVINDphosphoprotein (P), requiring a specific peptide target sequence encoded therein. P is a cofactor for the viral polymerase, and is required for viral RNA synthesis as well as the assembly of replication compartments. By targeting P, TRIM69 inhibits pioneer transcription of the incoming virion-associated minus strand RNA, thereby preventing the synthesis of viral mRNAs, and consequently impedes all downstream events in the VSVINDreplication cycle. Unlike some TRIM proteins, TRIM69 does not inhibit viral replication by inducing degradation of target viral proteins. Rather, higher-order TRIM69 multimerization is required for its antiviral activity, suggesting that TRIM69 functions by sequestration or anatomical disruption of the viral machinery required for VSVINDRNA synthesis.

SIGNIFICANCE STATEMENT

Interferons are important antiviral cytokines that work by inducing hundreds of host genes whose products inhibit replication of many viruses. While the antiviral activity of interferon has long been known, the identities and mechanisms of action of most interferon-induced antiviral proteins remain to be discovered. We identified gene products that are important for the antiviral activity of interferon against vesicular stomatitis virus (VSV) a model virus that whose genome consists a single RNA molecule with negative sense polarity. We found that a particular antiviral protein, TRIM69, functions by a previously undescribed molecular mechanism. Specifically, TRIM69 interacts with, and inhibits the function, of a particular phosphoprotein (P) component the viral transcription machinery, preventing the synthesis of viral messenger RNAs.
Human pluripotent stem cell modeling of tuberous sclerosis complex reveals lineage-specific therapeutic vulnerabilities
Authors: Delaney Sean P. , Julian Lisa M. , Pietrobon Adam , Yockell-Lelièvre Julien , Doré Carole , Wang Ting T. , Doyon Valerie C. , Raymond Angela , Patten David A. , Kristof Arnold S. , Harper Mary-Ellen , Sun Hongyu , Stanford William L.
Published: June 2019

mTORC1 hyperactivation resulting from inactivating TSC2 mutations underlie the multi-system tumor disorder tuberous sclerosis complex (TSC) and the rare pulmonary neoplasm lymphangioleiomyomatosis (LAM). Mutation-bearing neural precursor cells (NPCs) lead to the formation of TSC brain tumors during development, while the cell of origin of TSC mesenchymal tumors such as LAM is unknown. We report the first model of multi-system TSC cell types, characterized by NPCs and neural crest cells (NCCs) differentiated in parallel from multiple engineered TSC2−/− human pluripotent stem cell (hPSC) lines. These cells successfully model defining phenotypes of neural and mesenchymal TSC, with transcriptomic signatures reflecting those observed in patient tumors, thus establishing TSC2−/− NCCs as a powerful model of LAM. Employing this rich cellular and transcriptomic resource, we identified lineage-specific catabolic signaling mechanisms that drive divergent cell behavior and therapeutic sensitivities that, in turn, demonstrate the power of employing lineage-specific stem cell models to dissect multi-system diseases.
Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation
Authors: Wasik Brian R. , Voorhees Ian E.H. , Barnard Karen N. , Lawrence Brynn K. , Weichert Wendy S. , Hood Grace , Nogales Aitor , Martínez-Sobrido Luis , Holmes Edward C. , Parrish Colin R.
Published: June 2019

Influenza A viruses have regularly jumped to new hosts to cause epidemics or pandemics, an evolutionary process that involves variation in the viral traits necessary to overcome host barriers and facilitate transmission. Mice are not a natural host for influenza virus, but are frequently used as models in studies of pathogenesis, often after multiple passages to achieve higher viral titers that result in clinical disease such as weight loss or death. Here we examine the processes of influenza A virus infection and evolution in mice by comparing deep sequence variation of a human H1N1 pandemic virus, a seasonal H3N2 virus, and a H3N2 canine influenza virus during experimental passage. We also compared replication and sequence variation in wild-type mice expressing N-glycolylneuraminic acid (Neu5Gc) with that seen in mice expressing only N-acetylneuraminic acid (Neu5Ac). Viruses derived from plasmids were propagated in MDCK cells and then passaged in mice up to four times. Full genome deep sequencing of the plasmids, cultured viruses, and viruses from mice at various passages revealed only small numbers of mutational changes. The H3N2 canine influenza virus showed increases in frequency of sporadic mutations in the PB2, PA, and NA segments. The H1N1 pandemic virus grew well in mice, and while it exhibited the maintenance of some minority mutations, there was no clear adaptive evolution. The H3N2 seasonal virus did not establish in the mice. Finally, there were no clear sequence differences associated with the presence or absence of Neu5Gc.

SIGNIFICANCE

Mice are commonly used as a model to study the growth and virulence of influenza A viruses in mammals, but are not a natural host and have distinct sialic acid receptor profiles compared to humans. Using experimental infections with different subtypes of influenza A virus derived from different hosts we found that evolution of influenza A virus in mice did not necessarily proceed through the linear accumulation of host-adaptive mutations, that there was variation in the patterns of mutations detected in each repetition, and the mutation dynamics depended on the virus examined. In addition, variation in the viral receptor, sialic acid, did not effect influenza evolution in this model. Overall this shows that mice provide a useful animal model for influenza, but that host passage evolution will vary depending on the virus being tested.
Prevalence of antimicrobial resistance genes and integrons in commensal Gram-negative bacteria in a college community
Authors: Rubin Julia , Mussio Kaitlyn , Xu Yuqi , Suh Joy , Riley Lee W.
Published: June 2019

Although the human intestinal microbiome has been shown to harbor antimicrobial drug-resistance genes (ARG), the prevalence of such genes in a healthy population and their impact on extraintestinal infections that occur in that community are not well established. This study sought to identify ARG prevalence and their mobile elements in the intestines of a healthy community population at a California university, and compared these genes to those found in uropathogenic Escherichia coli isolated from patients with community-acquired urinary tract infection (CA-UTI). We isolated Gram-negative bacteria (GNB) from fecal samples of healthy volunteers and screened them by polymerase chain reaction (PCR) for ARG encoding resistance against ampicillin (AMP), trimethoprim-sulfamethoxazole (TMP-SMX), gentamicin (GENT), and colistin (COL). We found antimicrobial resistant GNB from 85 (83%) of 102 non-redundant rectal swab samples. Sixty-seven (66%) of these samples contained ß-lactamase genes (blaTEM, blaSHV, blaCTX-M, blaOXA,blaOXY), dihydrofolate reductase (DHFR) genes (dhfr-A17, dhfr-A7, dhfr-A5, dhfr-A21, dhfr-A1, dhfr-A15, and dhfr-B3), and aminoglycoside resistance genes (aadA5, aadA1, and aadB). Integron sequences were found in 37 fecal samples. These genes were found in 11 different GNB species isolated from the fecal samples. The same ARG were found in E. coli strains isolated from patients with CA-UTI examined at the college outpatient health clinic. The high prevalence of clinically-common ARG and integrons harbored by GNB in the intestine of a healthy population suggest that human intestines may serve as a major reservoir of these mobile ARG that appear in E. coli strains causing extraintestinal infections in the same community.

Importance

Increasing frequency of antimicrobial resistance (AMR) in human pathogenic bacteria has compromised our ability to treat infections. Since mobile antibiotic resistance genes (ARG) are readily exchanged between different species of bacteria through horizontal gene transfer, there is interest in investigating sources of these genes. The normal intestinal flora has been shown to contain a wide variety of ARG, which may have been introduced via food-containing AMR bacteria. We sought to assess the prevalence of ARG carriage in the intestines of a healthy population and determine if these ARG are found in E. coli strains that cause community-acquired urinary tract infection (CA-UTI) in the same community. Our findings indicate that the human intestine may serve as an important reservoir as well as a site in which ARG are transferred into E. coli that cause UTI. Further research is needed to reduce ARG carriage and devise new strategies to prevent AMR infections.
Functional specification of CCK+ interneurons by alternative isoforms of Kv4.3 auxiliary subunits
Authors: Oláh Viktor János , Lukacsovich David , Winterer Jochen , Lőrincz Andrea , Nusser Zoltan , Földy Csaba , Szabadics János
Published: June 2019

CCK-expressing interneurons (CCK+INs) are crucial for controlling hippocampal activity. We found two firing phenotypes of CCK+INs in rat CA3 area; either possessing a previously undetected membrane potential-dependent firing or regular firing phenotype, due to different low-voltage-activated potassium currents. These different excitability properties destine the two types for distinct functions, because the former is essentially silenced during realistic 8-15 Hz oscillations. The general excitability, morphology and gene-profiles of the two types were surprisingly similar. Even the expression of Kv4.3 channels were comparable, despite evidences showing that Kv4.3-mediated currents underlie the distinct firing properties. Instead, the firing phenotypes were correlated with the presence of distinct isoforms of Kv4 auxiliary subunits (KChIP1 vs. KChIP4e and DPP6S). Our results reveal the underlying mechanisms of two previously unknown types of CCK+INs and demonstrate that alternative splicing of few genes, which may be viewed as a minor event in the cells’ whole transcriptome, can underlie distinct cell-type identity.
Polarized Entamoeba: A model for stable bleb driven motility
Authors: Krishnan Deepak , Ghosh Sudip Kumar
Published: June 2019

Protozoan parasites Entamoeba histolytica and Entamoeba invadens formed a polarized phenotype, an elongated shape with a single leading edge and a trailing edge when treated with pentoxifylline. The leading edge of the polarized morphology was a spherical protrusion devoid of F-actin but with occasional F-actin scars, indicating the presence of bleb. The polarized form was stable bleb driven since the blebbing was limited to the leading edge. Pentoxifylline induced chemokinesis in Entamoeba as it switched the motility pattern from slow and random to fast and directionally persistent. Pentoxifylline speeded up the cell aggregation in E. invadens during growth and encystation due to enhanced chemotaxis of the polarized form. The transformation of non-polarized adherent trophozoites to nonadherent stable bleb driven form occurred via lamellipodial and bleb driven adherent intermediate phenotypes. The nonadherent polarized phenotype was highly motile under confinement and moved by rearward plasma membrane flow. In contrast to pentoxifylline, adenosine, the adenosine receptor agonist, stimulated the formation of multiple protrusions leading to random motility. Thus pentoxifylline might prevent lateral protrusions by inhibiting adenosine receptor, producing the monopodial polarized morphology.

Summary statement

Pentoxifylline, the adenosine receptor antagonist induced a stable bleb driven polarized morphology in Entamoeba characterized by fast, directionally persistent and highly chemotactic motility.