bluuebunny/crossref_metadata_2025 huggingface dataset:
Microglia dysfunction caused by the loss of Rhoa disrupts neuronal physiology and leads to neurodegeneration
Authors: Socodato Renato , Portugal Camila C. , Canedo Teresa , Rodrigues Artur , Almeida Tiago O. , Henriques Joana F. , Vaz Sandra H. , Magalhães João , Silva Cátia M. , Baptista Filipa I. , Alves Renata L. , Coelho-Santos Vanessa , Silva Ana Paula , Paes-de-Carvalho Roberto , Magalhães Ana , Brakebusch Cord , Sebastião Ana M. , Summavielle Teresa , Ambrósio António F. , Relvas João B.
Published: November 2017

Nervous tissue homeostasis requires regulation of microglia activity. Using conditional gene targeting in mice, we demonstrate that genetic ablation of the small GTPase Rhoa in adult microglia is sufficient to trigger spontaneous microglia activation producing a neurological phenotype (including synapse and neuron loss, impairment of LTP, formation of ß-amyloid plaques and memory deficits). Mechanistically, loss of Rhoa in microglia triggers Src activation and Src-mediated Tnf production, leading to excitotoxic glutamate secretion. Inhibiting Src in microglia Rhoa-deficient mice attenuates microglia dysregulation and the ensuing neurological phenotype. We also found that the Rhoa/Src signaling pathway was disrupted in microglia of the APP/PS1 mouse model of Alzheimer’s disease and that low doses of Aß oligomers triggered microglia neurotoxic polarization through the disruption of Rhoa-to-Src signaling. Overall, our results indicate that disturbing RhoGTPase signaling in microglia can directly cause neurodegeneration.
FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data
Authors: Herman J.S. , Sagar  , Grün D.
Published: November 2017

Differentiation of multipotent cells is a complex process governed by interactions of thousands of genes subject to substantial expression fluctuations. Resolving cell state heterogeneity arising during this process requires quantification of gene expression within individual cells. However, computational methods linking this heterogeneity to biases towards distinct cell fates are not well established. Here, we perform deep single-cell transcriptome sequencing of ~2,000 bone-marrow derived mouse hematopoietic progenitors enriched for lymphoid lineages. To resolve subtle transcriptome priming indicative of distinct lineage biases, we developed FateID, an iterative supervised learning algorithm for the probabilistic quantification of cell fate bias. FateID delineates domains of fate bias within progenitor populations and permits the derivation of high-resolution differentiation trajectories, revealing a common progenitor population of B cells and plasmacytoid dendritic cells, which we validated by in vitro differentiation assays. We expect that FateID will enhance our understanding of the process of cell fate choice in complex multi-lineage differentiation systems.
Anti-phage islands force their target phage to directly mediate island excision and spread
Authors: McKitterick Amelia C. , Seed Kimberley D.
Published: November 2017

To defend against their adversaries, bacteria and phage engage in cycles of adaptation and counter-adaptation that shape their mutual evolution1–3.Vibrio cholerae, the causative agent of the diarrheal disease cholera, is antagonized by phages in the environment as well as in human hosts4,5. The lytic phage ICP1 has been recovered from cholera patient stool and water samples over at least 12 years in Bangladesh6–8and is consequently considered a persistent predator of epidemicV. choleraein this region. In previous work, we demonstrated that mobile genetic elements calledphage-inducible chromosomal island-likeelements (PLEs) protectV. choleraefrom ICP1 infection7,9. PLEs initiate their anti-phage response by excising from the chromosome, however, the mechanism and molecular specificity underlying this response are not known. Here, we show that PLE 1 encodes a large serine recombinase, Int, that exploits an ICP1-specific protein, PexA, as a recombination directionality factor (RDF) to sense and excise in response to ICP1 infection. We validate the functionality and specificity of this unique recombination system, in which the recombinase and RDF are encoded in separate genomes. Additionally, we show that PexA is also hijacked to trigger excision in PLEs found inV. choleraeisolates recovered decades ago. Our results uncover an aspect of the molecular specificity underlying the longstanding conflict between a single predatory phage andV. choleraePLE and contribute to our understanding of the molecular arms race that drives long-term evolution between combatting phage and their bacterial hosts in nature.
Robustness of early warning signals for catastrophic and non-catastrophic transitions
Authors: Dutta Partha Sharathi , Sharma Yogita , Abbott Karen C.
Published: November 2017

Early warning signals (EWS) are statistical indicators that a rapid regime shift may be forthcoming. Their development has given ecologists hope of predicting rapid regime shifts before they occur. Accurate predictions, however, rely on the signals being appropriate to the system in question. Most of the EWS commonly applied in ecology have been studied in the context of one specific type of regime shift (the type brought on by a saddle-node bifurcation, at which one stable equilibrium point collides with an unstable equilibrium and disappears) under one particular perturbation scheme (temporally uncorrelated noise that perturbs the net population growth rate in a density independent way). Whether and when these EWS can be applied to other ecological situations remains relatively unknown, and certainly underappreciated. We study a range of models with different types of dynamical transitions (including rapid regime shifts) and several perturbation schemes (density-dependent uncorrelated or temporally-correlated noise) and test the ability of EWS to warn of an approaching transition. We also test the sensitivity of our results to the amount of available pre-transition data and various decisions that must be made in the analysis (i.e. the rolling window size and smoothing bandwidth used to compute the EWS). We find that EWS generally work well to signal an impending saddle-node bifurcation, regardless of the autocorrelation or intensity of the noise. However, EWS do not reliably appear as expected for other types of transition. EWS were often very sensitive to the length of the pre-transition time series analyzed, and usually less sensitive to other decisions. We conclude that the EWS perform well for saddle-node bifurcation in a range of noise environments, but different methods should be used to predict other types of regime shifts. As a consequence, knowledge of the mechanism behind a possible regime shift is needed before EWS can be used to predict it.
High fidelity lineage tracing in mouse pre-implantation embryos using primed conversion of photoconvertible proteins
Authors: Welling Maaike , Mohr Manuel Alexander , Ponti Aaron , Sabater Lluc Rullan , Boni Andrea , Liberali Prisca , Pelczar Pawel , Pantazis Periklis
Published: November 2017

Accurate lineage reconstruction of mammalian pre-implantation development is essential for inferring the earliest cell fate decisions of mammalian development. Lineage tracing using global labeling techniques is complicated by increasing cell density and rapid embryo rotation, impeding automatic alignment and rendering accurate cell tracking of obtained four-dimensional imaging data sets highly challenging. Here, we exploit the advantageous properties of primed convertible fluorescent proteins (pr-pcFPs) to simultaneously visualize the global green and the photoconverted red population to minimize tracking uncertainties over prolonged time windows. Confined primed conversion of H2B-pr-mEosFP labeled nuclei combined with light-sheet imaging greatly facilitates segmentation, classification, and tracking of individual nuclei from the 4-cell stage up to the blastocyst. Using green and red labels as fiducial markers, we computationally correct for rotational and translational drift and accomplish high fidelity lineage tracing combined with a reduced data size – addressing majors concerns in the field of volumetric embryo imaging.
Saturating Single-Cell atlas Datasets
Authors: Bhaduri Aparna , Nowakowski Tomasz J. , Pollen Alex A. , Kriegstein Arnold R.
Published: November 2017

High throughput methods for profiling the transcriptomes of single cells have recently emerged as transformative approaches for large-scale population surveys of cellular diversity in heterogeneous primary tissues. Efficient generation of such an atlas will depend on sufficient sampling of the diverse cell types while remaining cost-effective to enable a comprehensive examination of organs, developmental stages, and individuals. To examine the relationship between cell number and transcriptional heterogeneity in the context of unbiased cell type classification, we explicitly explored the population structure of a publically available 1.3 million cell dataset from the E18.5 mouse brain. We propose a computational framework for inferring the saturation point of cluster discovery in a single cell mRNA-seq experiment, centered around cluster preservation in downsampled datasets. In addition, we introduce a “complexity index”, which characterizes the heterogeneity of cells in a given dataset. Using Cajal-Retzius cells as an example of a limited complexity dataset, we explored whether biological distinctions relate to technical clustering. Surprisingly, we found that clustering distinctions carrying biologically interpretable meaning are achieved with far fewer cells (20,000). Together, these findings suggest that most of the biologically interpretable insights from the 1.3 million cells can be recapitulated by analyzing 50,000 randomly selected cells, indicating that instead of profiling few individuals at high “cellular coverage”, the much anticipated cell atlasing studies may instead benefit from profiling more individuals, or many time points at lower cellular coverage.

Recent efforts seek to create a comprehensive cell atlas of the human body1,2 Current technology, however, makes it precipitously expensive to perform analysis of every cell. Therefore, designing effective sampling strategies be critical to generate a working atlas in an efficient, cost-effective, and streamlined manner. The advent of single cell and single nucleus mRNA sequencing (RNAseq) in droplet format3,4 now enables large scale sampling of cells from any tissue, and a recently released publicly available dataset of 1.3 million single cells from the E18.5 mouse brain generated with the 10X Chromium5 provides an opportunity to explore the relationship between population structure and the number of sampled cells necessary to reveal the underlying diversity of cell types. Here, we present a framework for how researchers can evaluate whether a dataset has reached saturation, and we estimate how many cells would be required to generate an atlas of the sample analyzed here. This framework can be applied to any organ or cell type specific atlas for any organism.
Energetic Evolution of Cellular Transportomes
Authors: Darbani Behrooz , Kell Douglas B. , Borodina Irina
Published: November 2017

Transporter proteins mediate the translocation of substances across the membranes of living cells. We performed a genome-wide analysis of the compositional reshaping of cellular transporters (the transportome) across the kingdoms of bacteria, archaea, and eukarya. We show that the transportomes of eukaryotes evolved strongly towards a higher energetic efficiency, as ATP-dependent transporters diminished and secondary transporters and ion channels proliferated. This change has likely been important in the development of tissues performing energetically costly cellular functions. The transportome analysis also indicated seven bacterial species, includingNeorickettsia risticiiandNeorickettsia sennetsu, as likely origins of the mitochondrion in eukaryotes, due to the restricted presence therein of clear homologues of modern mitochondrial solute carriers.
Heritability Informed Power Optimization (HIPO) Leads to Enhanced Detection of Genetic Associations Across Multiple Traits
Authors: Qi Guanghao , Chatterjee Nilanjan
Published: November 2017

Genome-wide association studies have shown that pleiotropy is a common phenomenon that can potentially be exploited for enhanced detection of susceptibility loci. We propose heritability informed power optimization (HIPO) for conducting powerful pleiotropic analysis using summary-level association statistics. We find optimal linear combinations of association coefficients across traits that are expected to maximize non-centrality parameter for the underlying test statistics, taking into account estimates of heritability, sample size variations and overlaps across the traits. Simulation studies show that the proposed method has correct type I error, robust to population stratification and leads to desired genome-wide enrichment of association signals. Application of the proposed method to publicly available data for three groups of genetically related traits, lipids (N=188,577), psychiatric diseases (Ncase=33,332, Ncontrol=27,888) and social science traits (N ranging between 161,460 to 298,420 across individual traits) increased the number of genome-wide significant loci by 12%, 200% and 50%, respectively, compared to those found by analysis of individual traits. Evidence of replication is present for many of these loci in subsequent larger studies for individual traits. HIPO can potentially be extended to high-dimensional phenotypes as a way of dimension reduction to maximize power for subsequent genetic association testing.
One-step generation of monoclonal B cell receptor mice capable of class switch recombination and somatic hypermutation
Authors: Jacobsen Johanne T. , Mesin Luka , Markoulaki Styliani , Cavazzoni Cecília B. , Bousbaine Djenet , Jaenisch Rudolf , Victora Gabriel D.
Published: November 2017

We developed a method for rapid generation of B cell receptor (BCR) monoclonal mice expressing pre-rearrangedIghandIgkchains monoallelically from theIghlocus by CRISPR/Cas9 injection into fertilized oocytes. B cells from these mice undergo somatic hypermutation (SHM), class switch recombination (CSR), and affinity-based selection in germinal centers. This method combines the practicality of BCR transgenes with the ability to study Ig SHM, CSR and affinity maturation.
Fine scale diversification of endolithic microbial communities in the hyper-arid Atacama Desert
Authors: Meslier Victoria , Casero Maria Cristina , Dailey Micah , Wierzchos Jacek , Ascaso Carmen , Artieda Octavio , DiRuggiero Jocelyne
Published: November 2017

The expansion of desertification across our planet is accelerating as the result of human activity and global climate change. In hyper-arid deserts, endolithic microbial communities colonize the rocks’ interior as a survival strategy. Yet, the composition of these communities and the drivers promoting their assembly are still poorly understood. Using a sampling strategy that minimized climate regime and biogeography effects, we analyzed the diversity and community composition of endoliths from four different lithic substrates – calcite, gypsum, ignimbrite and granite – collected in the hyper-arid zone of the Atacama Desert, Chile. By combining microscopy, mineralogy, and high throughput sequencing, we found these communities to be highly specific to their lithic substrate, although they were all dominated by the same four main phyla, Cyanobacteria, Actinobacteria, Chloroflexi and Proteobacteria. This finding indicates a fine scale diversification of the microbial reservoir driven by substrate properties. Our data suggest that the overall rock chemistry is not an essential driver of community structure and we propose that the architecture of the rock, i.e. the space available for colonization and its physical structure, linked to water retention capabilities, is ultimately the driver of community diversity and composition at the dry limit of life.

Originality-Significance Statement

In this study, we demonstrated that endolithic microbial communities are highly specific to their substrates, suggesting a fine scale diversification of the available microbial reservoir. By using an array of rock substrates from the same climatic region, we established, for the first time, that the architecture of the rock is linked to water retention and is ultimately the driver of community diversity and composition at the dry limit for life.
Transcriptional landscape and regulatory roles of small non-coding RNAs in the oxidative stress response of the haloarchaeon Haloferax volcanii
Authors: Gelsinger Diego R. , DiRuggiero Jocelyne
Published: November 2017

Haloarchaea in their natural environment are exposed to hyper-salinity, intense solar radiation, and desiccation, all of which generate high levels of oxidative stress. Previous work has shown that Haloarchaea are an order of magnitude more resistant to oxidative stress than most mesophilic organisms. Despite this resistance, the pathways Haloarchaea use to respond to oxidative stress damage are similar to that of non-resistant organisms suggesting that regulatory processes might be key to their robustness. Recently, small non-coding RNAs (sRNAs) were discovered in Archaea under a variety of environmental conditions. We report here the transcriptional landscape and functional roles of sRNAs in the regulation of the oxidative stress response of the model haloarchaeon Haloferax volcanii. Thousands of sRNAs, both intergenic and antisense, were discovered using strand-specific sRNA-seq, comprising around 30% of the transcriptome during non-challenged and oxidative stress conditions. We identified hundreds of differentially expressed sRNAs in response to hydrogen peroxide induced oxidative stress in H. volcanii. Targets of antisense sRNAs decreased in expression when sRNAs were up-regulated indicating that sRNAs are likely playing a negative regulatory role on mRNA targets at the transcript level. Target enrichment of these antisense sRNAs included mRNAs involved in transposons mobility, chemotaxis signaling, peptidase activity, and transcription factors.

IMPORTANCE

While a substantial body of experimental work has been done to uncover functions of sRNAs in gene regulation in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. This study is the first to establish the regulatory effects of sRNAs on mRNAs during the oxidative stress response in the haloarchaeon Haloferax volcanii. Our work demonstrates that common principles for the response to a major cellular stress exist across the 3 domains of life while uncovering pathways that might be specific to the Archaea. This work also underscores the relevance of sRNAs in adaptation to extreme environmental conditions.
Clinker: visualising fusion genes detected in RNA-seq data
Authors: Schmidt Breon M , Davidson Nadia M , Hawkins Anthony DK , Bartolo Ray , Majewski Ian J , Ekert Paul G , Oshlack Alicia
Published: November 2017

Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes, and many are emerging as important therapeutic targets. While there are many ways to identify fusion genes from RNA-seq data, visualising these transcripts and their supporting reads remains challenging. Clinker is a bioinformatics tool written in Python, R and Bpipe, that leverages the superTranscript method to visualise fusion genes. We demonstrate the use of Clinker to obtain interpretable visualisations of the RNA-seq data that lead to fusion calls. In addition, we use Clinker to explore multiple fusion transcripts with novel breakpoints within the P2RY8-CRLF2 fusion gene in B-cell Acute Lymphoblastic Leukaemia (B-ALL).

Availability and Implementation

Clinker is freely available from Github https://github.com/Oshlack/Clinker under a MIT License.

Contact

alicia.oshlack@mcri.edu.au
Age-dependent neurodegeneration and organelle transport deficiencies in mutant TDP43 patient-derived neurons are independent of TDP43 aggregation
Authors: Kreiter N , Pal A , Lojewski X , Corcia P , Naujock M , Reinhardt P , Sterneckert J , Petri S , Wegner F , Storch A , Hermann A
Published: November 2017

TAR DNA-binding protein 43 (TDP43) is a cause of familiar and sporadic amyotrophic lateral sclerosis (ALS). The diverse postulated mechanisms by which TDP43 mutations cause the disease are not fully understood. Human wildtype and TDP43 S393L and G294V mutant spinal motor neuron cultures were differentiated from patient-derived iPSCs. Mutant hTDP43 and wildtype motor neuron cultures did not differ in neuron differentiation capacity during early maturation stage. During aging we detected a dramatic neurodegeneration including neuron loss and pathological neurofilament abnormalities in TDP43 mutant cultures only. Additionally mitochondria and lysosomes of aging spinal motor neurons revealed robust TDP43 mutation dependent abnormal phenotypes in size, shape, speed and motility which all appeared without TDP43 mislocalization or aggregation formation. Furthermore, D-sorbitol – known to induce stress granules and cytoplasmic mislocalization of TDP43 – rescued axonal trafficking phenotypes without any signs of TDP43 mislocalization or aggregation formation. Our data indicate TDP43 mutation-dependent but cytosolic aggregation-independent mechanisms of motor neuron degeneration in TDP43 ALS.
Online detection of auditory attention with mobile EEG: closing the loop with neurofeedback
Authors: Zink Rob , Proesmans Stijn , Bertrand Alexander , Van Huffel Sabine , De Vos Maarten
Published: November 2017

Auditory attention detection (AAD) is promising for use in auditory-assistive devices to detect to which sound the user is attending. Being able to train subjects in achieving high AAD performance would greatly increase its application potential. In order to do so an acceptable temporal resolution and online implementation are essential prerequisites. Consequently, users of an online AAD can be presented with feedback about their performance. Here we describe two studies that investigate the effects of online AAD with feedback. In the first study, we implemented a fully automated closed-loop system that allows for user-friendly recording environments. Subjects were presented online with visual feedback on their ongoing AAD performance. Following these results we implemented a longitudinal case study in which two subjects were presented with AAD sessions during four weeks. The results prove the feasibility of a fully working online (neuro)feedback system for AAD decoding. The detected changes in AAD for the feedback subject during and after training suggest that changes in AAD may be achieved via training. This is early evidence of such training effects and needs to be confirmed in future studies to evaluate training of AAD in more detail. Finally, the large number of sessions allowed to examine the correlation between the stimuli (i.e. acoustic stories) and AAD performance which was found to be significant. Future studies are suggested to evaluate their acoustic stimuli with care to prevent spurious associations.
How Changes in Common Practice Can Improve the Quality of Biomedical Science
Authors: Steinfath Matthias , Vogl Silvia , Violet Norman , Schwarz Franziska , Mielke Hans , Selhorst Thomas , Greiner Matthias , Schöenfelder Gilbert
Published: November 2017

Assessing the impact of recommendations rectifying the reproducibility crisis (publishing both positive and “negative” results and increasing statistical power) on competing objectives, such as discovering causal relationships, avoiding publishing false positive results, and reducing resource consumption, we developed a new probabilistic model. Our model quantifies the impact of each single suggestion for an individual study and their relation and consequences for the entire research process. We can prove that higher-powered experiments can save resources in the overall research process without generating excess false positives. The better the quality of the pre-study information and its exploitation, the more likely this beneficial effect is to occur. Additionally, we quantify the adverse effects of neglecting good practices in the design and conduct of hypotheses-based research, and the responsibility to publish “negative” findings. Our contribution is a plea for adherence to or reinforcement of the good scientific practice and publication of “negative” findings.
Phenome-wide association studies (PheWAS) across large “real-world data” population cohorts support drug target validation
Authors: Diogo Dorothée , Tian Chao , Franklin Christopher S. , Alanne-Kinnunen Mervi , March Michael , Spencer Chris C. A. , Vangjeli Ciara , Weale Michael E. , Mattsson Hannele , Kilpeläinen Elina , Sleiman Patrick M.A. , Reilly Dermot F. , McElwee Joshua , Maranville Joseph C. , Chatterjee Arnaub K , Bhandari Aman ,   the 23andMe Research Team, Reeve Mary-Pat , Hutz Janna , Bing Nan , John Sally , MacArthur Daniel , Salomaa Veikko , Ripatti Samuli , Hakonarson Hakon , Daly Mark J. , Palotie Aarno , Hinds David , Donnelly Peter , Fox Caroline S. , Day-Williams Aaron , Plenge Robert M. , Runz Heiko
Published: November 2017

Phenome-wide association studies (PheWAS), which assess whether a genetic variant is associated with multiple phenotypes across a phenotypic spectrum, have been proposed as a possible aid to drug development through elucidating mechanisms of action, identifying alternative indications, or predicting adverse drug events (ADEs). Here, we evaluate whether PheWAS can inform target validation during drug development. We selected 25 single nucleotide polymorphisms (SNPs) linked through genome-wide association studies (GWAS) to 19 candidate drug targets for common disease therapeutic indications. We independently interrogated these SNPs through PheWAS in four large “real-world data” cohorts (23andMe, UK Biobank, FINRISK, CHOP) for association with a total of 1,892 binary endpoints. We then conducted meta-analyses for 145 harmonized disease endpoints in up to 697,815 individuals and joined results with summary statistics from 57 published GWAS. Our analyses replicate 70% of known GWAS associations and identify 10 novel associations with study-wide significance after multiple test correction (P<1.8x10-6; out of 72 novel associations with FDR<0.1). By leveraging directionality and point estimate of the effect sizes, we describe new associations that may predict ADEs, e.g., acne, high cholesterol, gout and gallstones for rs738409 (p.I148M) in PNPLA3; or asthma for rs1990760 (p.T946A) in IFIH1. We further propose how quantitative estimates of genetic safety/efficacy profiles can be used to help prioritize candidate targets for a specific indication. Our results demonstrate PheWAS as a powerful addition to the toolkit for drug discovery.

One Sentence Summary

Matching genetics with phenotypes in 800,000 individuals predicts efficacy and on-target safety of future drugs.
ADAM17 is the Principal Ectodomain Sheddase of the EGF-Receptor Ligand Amphiregulin
Authors: Hosur Vishnu , Farley Michelle L. , Burzenski Lisa M. , Shultz Leonard D. , Wiles Michael V.
Published: November 2017

The epidermal growth factor (EGF)-receptor ligand amphiregulin (AREG) is a potent growth factor implicated in proliferative skin diseases and in primary and metastatic epithelial cancers. AREGin vitro, synthesized as a pro-peptide, requires conversion to an active peptide by metalloproteases by a process known as ectodomain shedding. Although, (Adam17) a disintegrin and metalloprotease 17 is implicated in ectodomain shedding of AREG, it remains to be establishedin vivowhether ADAM17 contributes to AREG shedding. In the present study, using a curly bare (Rhbdf2cub) mouse model that shows loss-of-hair, enlarged sebaceous glands, and rapid cutaneous wound-healing phenotypes mediated by enhancedAregmRNA and protein levels, we sought to identify the principal ectodomain sheddase of AREG. To this end, we generatedRhbdf2cubmice lacking ADAM17 specifically in the skin and examined the above phenotypes ofRhbdf2cubmice. We find that ADAM17 deficiency in the skin ofRhbdf2cubmice restores a full hair coat, prevents sebaceous-gland enlargement, and impairs the rapid wound-healing phenotype observed inRhbdf2cubmice. Furthermore,in vitro, stimulated shedding of AREG is abolished inRhbdf2cubmouse embryonic keratinocytes lacking ADAM17. Thus, our data demonstrate that ADAM17 is the major ectodomain sheddase of AREG.
New routes for PTP1B allosteric inhibition by multitemperature crystallography, fragment screening and covalent tethering
Authors: Keedy Daniel A. , Hill Zachary B. , Biel Justin T. , Kang Emily , Rettenmaier T. Justin , Brandao-Neto Jose , Pearce Nicholas M. , von Delft Frank , Wells James A. , Fraser James S.
Published: November 2017

Allostery is an inherent feature of proteins and provides alternative routes to regulating function. Small-molecule allosteric inhibitors are often desirable; however, it remains challenging to identify surface sites in proteins which can bind small molecules and modulate function. We identified new allosteric sites in protein tyrosine phosphatase 1B (PTP1B) by combining multiple-temperature X-ray crystallography experiments and structure determination from hundreds of individual small-molecule fragment soaks. New modeling approaches reveal “hidden” low-occupancy conformational states for protein and ligands. Our results converge on a new allosteric site that is conformationally coupled to the active-site WPD loop, a hotspot for fragment binding, not conserved in the closest homolog, and distinct from other recently reported allosteric sites in PTP1B. Targeting this site with covalently tethered molecules allosterically inhibits enzyme activity. Overall, this work demonstrates how the ensemble nature of macromolecular structure revealed by multitemperature crystallography can be exploited for developing allosteric modulators.
Towards a unified resource for transcriptional regulation inEscherichia coliK-12: Incorporating high throughput-generated binding data within the classic framework of regulation of initiation of transcription in RegulonDB
Authors: Santos-Zavaleta Alberto , Sánchez-Pérez Mishael , Salgado Heladia , Velázquez-Ramírez David A. , Gama-Castro Socorro , Tierrafría Víctor H. , Busby Stephen J.W. , Fang Xin , Palsson Bernhard , Galagan James , Collado-Vides Julio
Published: November 2017

Our understanding of the regulation of gene expression has been strongly benefited by the availability of high throughput technologies that enable questioning the whole genome for the binding of specific transcription factors and expression profiles. In the case of genome models, such asEscherichia coliK-12, this knowledge needs to be integrated with the legacy of accumulated genetics and molecular biology pre-genomic knowledge in order to attain deeper levels in the understanding of their biology. In spite of the several repositories and curated databases, there is no effort, nor electronic site yet, to comprehensively integrate the available knowledge from all these different sources around the regulation of gene expression ofE. coliK-12. In this paper, we describe a first effort to expand RegulonDB, the database containing the rich legacy of decades of classic molecular biology experiments supporting what we know about gene regulation and operon organization inE. coliK-12, to include the genome-wide data set collections from 25 ChIP and 18 gSELEX publications, respectively, in addition to around 60 expression profiles used in their curation. Three essential features for the integration of this information coming from different methodological approaches are; first, a controlled vocabulary within an ontology for precisely defining growth conditions, second, the criteria to separate elements with enough evidence to consider them involved in gene regulation from isolated sites, and third, an expanded computational model supporting this knowledge. Altogether, this constitutes the basis for adequately gathering and enabling the comparisons and integration strongly needed to manage and access such wealth of knowledge. This version of RegulonBD is a first step toward what should become the unifying access point for current and future knowledge on gene regulation inE. coliK-12. Furthermore, this model platform and associated methodologies and criteria, can well be emulated for gathering knowledge on other microbial organisms.
Similarity corpus on microbial transcriptional regulation
Authors: Oscar Lithgow-Serrano , Socorro Gama-Castro , Cecilia Ishida-Gutiérrez , Citlali Mejía-Almonte , Víctor Tierrafría , Sara Martínez-Luna , Alberto Santos-Zavaleta , David Velázquez-Ramírez , Julio Collado-Vides
Published: November 2017

The ability to express the same meaning in different ways is a well known property of natural language. This amazing property is the source of major difficulties in natural language processing. Given the constant increase in published literature, its curation and information extraction would strongly benefit by efficient automatic processes, for which, corpora of sentences evaluated by experts is a valuable resource. Given our interest in applying such approaches to the benefit of curation of the biomedical literature, specifically about gene regulation in microbial organisms, we decided to build a corpus with graded textual similarity evaluated by curators, and designed specifically oriented to our purposes. Based on the predefined statistical power of future analyses, we defined features of the design including sampling, selection criteria, balance, and size among others. A non-fully crossed-design was performed for each pair of sentences by 3 evaluators from 7 different groups, adapting the SEMEVAL scale to our goals in four successive iterative sessions with a clear improvement in the consensuated guidelines and inter-rater-reliability results. Alternatives for the corpus evaluation are widely discussed. To the best of our knowledge this is the first similarity corpus in this domain of knowledge. We have initiated its incorporation in our research towards high throughput curation strategies based in natural language processing.
The CD11a and EPCR marker combination simplifies and improves the purification of mouse hematopoietic stem cells
Authors: Karimzadeh Alborz , Scarfone Vanessa , Chao Connie , Grathwohl Karin , Fathman John W. , Fruman David , Serwold Thomas , Inlay Matthew A.
Published: November 2017

Hematopoietic stem cells (HSCs) are the self-renewing multipotent progenitors to all blood cell types. Identification and isolation of HSCs for study has depended on the expression of combinations of surface markers on HSCs that reliably distinguish it from other cell types. However, the increasing number of markers required to isolate HSCs has made it tedious, expensive, and difficult for newcomers, suggesting the need for a simpler panel of HSC markers. We previously showed that phenotypic HSCs could be separated based on expression of CD11a, and that only the CD11a negative fraction contained true HSCs. Here, we show that CD11a and another HSC marker, EPCR, can be used to effectively identify and purify HSCs. We introduce a new two-color HSC sorting method that can highly enrich for HSCs with efficiencies comparable to the gold standard combination of CD150 and CD48. Our results demonstrate that adding CD11a and EPCR to the HSC biologist’s toolkit improves the purity of and simplifies isolation of HSCs.

Significance Statement

The study of hematopoietic stem cells (HSCs) and their purification for transplantation requires a panel of surface markers that can be used to distinguish HSCs from other cell types. The number of markers necessary to identify HSCs continues to grow, making it increasingly difficult to identify HSCs by flow cytometry. In this study, we identified a combination of two surface markers, CD11a and EPCR, to enrich for HSCs in the mouse bone marrow without the need for additional markers. This simplified panel could aid HSC research by reducing the number of markers necessary to identify and isolate HSCs.
Bringing Diffuse X-ray Scattering Into Focus
Authors: Wall Michael E. , Wolff Alexander M. , Fraser James S.
Published: November 2017

X-ray crystallography is experiencing a renaissance as a method for probing the protein conformational ensemble. The inherent limitations of Bragg analysis, however, which only reveals the mean structure, have given way to a surge in interest in diffuse scattering, which is caused by structure variations. Diffuse scattering is present in all macromolecular crystallography experiments. Recent studies are shedding light on the origins of diffuse scattering in protein crystallography, and provide clues for leveraging diffuse scattering to model protein motions with atomic detail.
Foxp1 regulation of neonatal vocalizations via cortical development
Authors: Usui Noriyoshi , Araujo Daniel J. , Kulkarni Ashwinikumar , Co Marissa , Ellegood Jacob , Harper Matthew , Toriumi Kazuya , Lerch Jason P. , Konopka Genevieve
Published: November 2017

The molecular mechanisms driving brain development at risk in autism spectrum disorders (ASDs) remain mostly unknown. Previous studies have implicated the transcription factor FOXP1 in both brain development and ASD pathophysiology. However, the specific molecular pathways both upstream of and downstream from FOXP1 are not fully understood. To elucidate the contribution of FOXP1-mediated signaling to brain development and, in particular, neocortical development, we generated forebrain-specific Foxp1 conditional knockout mice. We show that deletion of Foxp1 in the developing forebrain leads to impairments in neonatal vocalizations as well as neocortical cytoarchitectonic alterations via neuronal positioning and migration. Using a genomics approach, we identified the transcriptional networks regulated by Foxp1 in the developing neocortex and found that such networks are enriched for downstream targets involved in neurogenesis and neuronal migration. We also uncovered mechanistic insight into Foxp1 function by demonstrating that sumoylation of Foxp1 during embryonic brain development is necessary for mediating proper interactions between Foxp1 and the NuRD complex. Furthermore, we demonstrated that sumoylation of Foxp1 affects neuronal differentiation and migration in the developing neocortex. Together, these data provide critical mechanistic insights into the function of FOXP1 in the developing neocortex and may reveal molecular pathways at risk in ASD.
3DBVSMAPPER: a program for automatically generating bond-valence sum landscapes. Corrigendum
Authors: Sale Matthew , Avdeev Maxim
Published: November 2017

An equation in the article by Sale & Avdeev [J. Appl. Cryst. (2012), 45, 1054–1056] is corrected.
Hydrogen bonds in crystalline D-alanine: diffraction and spectroscopic evidence for differences between enantiomers
Authors: Belo Ezequiel A. , Pereira Jose E. M. , Freire Paulo T. C. , Argyriou Dimitri N. , Eckert Juergen , Bordallo Heloisa N.
Published: November 2017

Enantiomeric amino acids have specific physiological functions in complex biological systems. Systematic studies focusing on the solid-state properties of D-amino acids are, however, still limited. To shed light on this field, structural and spectroscopic studies of D-alanine using neutron powder diffraction, polarized Raman scattering and ab initio calculations of harmonic vibrational frequencies were carried out. Clear changes in the number of vibrational modes are observed as a function of temperature, which can be directly connected to variations of the N—D bond lengths. These results reveal dissimilarities in the structural properties of D-alanine compared with L-alanine.
An analytical model of harmonic content no-load magnetic fields and Back EMF in axial flux PM machines regarding the iron saturation and winding distribution
Authors: Baghayipour Mohammadreza , Darabi Ahmad , Dastfan Ali
Published: November 2017

Purpose

This paper aims to propose an analytical model for the harmonic content no-load magnetic fields and Back electric motive force (EMF) in double-sided TORUS-type non-slotted axial flux permanent magnet (TORUS-NS AFPM) machines with surface-mounted magnets considering the winding distribution and iron saturation effects.

Design/methodology/approach

First, a procedure to calculate the winding distribution with a rectangular cross-section is proposed. The magnetic field distribution and magnetic motive force (MMF) drop due to saturation in iron cores are then exactly extracted in a 2-D analytical model. The consequent influence on air-gap magnetic field and Back EMF are also calculated using a new iterative algorithm. The results are compared with those of the conventional analytical model without saturation, 2-D finite element analysis (FEA) and an experiment on a fabricated prototype machine.

Findings

Unlike the conventional method, the new method yields the no-load magnetic field distributions in air-gap and iron cores and Back EMF very exactly such that the results well match to those of the FEA and experiment.

Originality/value

Unlike the conventional winding factor, the winding distribution is considered here along the both axial and circumferential directions, which improves the accuracy level of results for non-slotted structures with relatively large air-gaps. The magnetic field distribution and MMF drop-in iron parts are also calculated as the basis for exact recalculation of air-gap magnetic field and Back EMF. Because of small computational burden beside superior accuracy, the proposed model can be treated as an accurate and fast substitute for FEA to be used during the design procedure or for predicting the other performance characteristics of TORUS-NS AFPM machines.
Partial discharge signal self-adaptive sparse decomposition noise abatement based on spectral kurtosis and S-transform
Authors: Zhang Anan , He Cong , Sun Maoyi , Li Qian , Li Hong Wei , Yang Lin
Published: November 2017

Purpose

Noise abatement is one of the key techniques for Partial Discharge (PD) on-line measurement and monitoring. However, how to enhance the efficiency of PD signal noise suppression is a challenging work. Hence, this study aims to improve the efficiency of PD signal noise abatement.

Design/methodology/approach

In this approach, the time–frequency characteristics of PD signal had been obtained based on fast kurtogram and S-transform time–frequency spectrum, and these characteristics were used to optimize the parameters for the signal matching over-complete dictionary. Subsequently, a self-adaptive selection of matching atoms was realized when using Matching Pursuit (MP) to analyze PD signals, which leading to seldom noise signal element was represented in sparse decomposition.

Findings

The de-noising of PD signals was achieved efficiently. Simulation and experimental results show that the proposed method has good adaptability and significant noise abatement effect compared with Empirical Mode Decomposition, Wavelet Threshold and global signal sparse decomposition of MP.

Originality/value

A self-adaptive noise abatement method was proposed to improve the efficiency of PD signal noise suppression based on the signal sparse representation and its MP algorithm, which is significant to on-line PD measurement.
A high-efficiency micromixing effect by pulsed AC electrothermal flow
Authors: Hadjiaghaie Vafaie Reza
Published: November 2017

Purpose

The on-chip high-throughput mixing process is one of the main challenges in the preparation process in clinical diagnostics. Because of high laminar flow in micro-channel, the fluid should be disturbed by external force. This paper aims to study pulsed AC electrothermal flow and the multiphysic interaction between the fluid behavior, external electric field, temperature field and convection-diffusion field to generate perturbation effect inside the channel.

Design/methodology/approach

A set of numerical simulations were carried out by multiphysic interactions between the fluid behavior, external electric field, temperature field and convection-diffusion field to generate the pulsed AC electrothermal flow inside the channel. Behavior of electrode–electrolyte system is discussed using the electrical lumped circuit model.

Findings

Highly efficient temperature gradients are generated by applying pulsed electric potential over the electrodes; as a result, efficient secondary flows form inside the channel. The proposed method increases the interfacial contact area between the fluids and enhances the molecular diffusion transport phenomena. Maximum temperature rise of 4.1 K is observed in the gap between the electrodes for 0.08 S/m fluid medium, where the electric field is much stronger than elsewhere. Velocity field and concentration analysis reveal high performance perturbation effects for the mixing process. The periodic stretching and folding effects increase the interfacial contact area between the fluids by using pulsed AC electrothermal flow. Based on the results, 83 per cent mixing efficiency is achieved for 0.08 S/m fluid medium with a microchannel length of 400 µm. Both the mixing efficiency and generated temperature rise increase by increasing the fluid ionic strength.

Originality/value

The ability to generate low temperature rise is very important for AC electrothermally driven fluidic chips such as immunoassay chips. In the present research, a novel actuation mechanism has been proposed to generate AC electrothermal manipulation mechanism and enhance the mixing efficiency by using pulsed AC electrothermal flow.
Analysis and design of an interior permanent magnet synchronous machine with double-layer PMs for electric vehicles based on multi-physics fields
Authors: Li Ya , Liu Xiping , Liu Zhangqi
Published: November 2017

Purpose

This paper aims to present an interior permanent magnet synchronous machine (IPMSM) with double-layer PMs used for electric vehicles, of which the integrated simulation of electromagnetic field, stress field and temperature field are analyzed.

Design/methodology/approach

Some electromagnetic characteristics including iron loss, efficiency and flux linkage are obtained by finite element analysis. The mechanical strength of rotor at the maximum speed and the temperature rise at the rated load are calculated by three-dimensional finite element analysis (FEA).

Findings

The results show that the presented IPMSM can work with sufficient mechanical strength, machine temperature rise and high efficiency during field-weakening operation. The experiments were carried out to verify the FEA, and acceptable results can be achieved.

Originality/value

This paper proposed a novel IPMSM with the double-layer permanent magnets, which is designed and checked by the multi-physics fields, and the high efficiency in all operational regions can be achieved for this machine.
Plant propagation algorithm for integration of distributed generation in power systems
Authors: Mahajan Shreya , Vadhera Shelly
Published: November 2017

Purpose

The purpose of this study/paper is to integrate distributed generation optimally in power system using plant propagation algorithm. Distributed generation is a growing concept in the field of electricity generation. It mainly comprises small generation units installed at calculated points of a power system network. The challenge of optimal allocation and sizing of DG is of utmost importance.

Design/methodology/approach

Plant propagation algorithm and particle swarm optimisation techniques have been implemented where a weighting factor-based multi-objective function is minimised. The objective is to cut down real losses and to improve the voltage profile of the system.

Findings

The results obtained using plant propagation algorithm technique for IEEE 33-bus systems are compared to those attained using particle swarm optimisation technique. The paper deals with the optimisation of weighting factor-based objective function, which counterpoises the losses and improves the voltage profile of the system and, therefore, helps to deliver the best outcomes.

Originality/value

This paper fulfils an identified need to study the multi-objective optimisation techniques for integration of distributed generation in the concerned power system network. The paper proposes a novel plant-propagation-algorithm-based technique in appropriate allocation and sizing of distributed generation unit.