bluuebunny/crossref_metadata_2025 huggingface dataset:
Preparation of single-cell suspension from mouse breast cancer focusing on preservation of original cell state information and cell type composition
Authors: Pavel Abaffy , Sandra Lettlova , Jaroslav Truksa , Mikael Kubista , Radek Sindelka
Published: October 2019

Single-cell analysis of gene expression has become a very popular method during the last decade. Unfortunately, appropriate standardization and workflow optimization remain elusive. The first step of the single cell analysis requires that the solid tissue be disassociated into a suspension of individual cells. However, during this step several technical bias can arise which can later result in the misinterpretation of the data. The goal of this study was to identify and quantify the effect of these technical factors on the quality of the single-cell suspension and the subsequent interpretation of the produced expression data. We tested the effects of various enzymes used for dissociation, several centrifugation forces, dissociation temperatures and the addition of Actinomycin D, a gene expression inhibitor. RT-qPCR was used to assess the effect from each parameter alteration, while a single-cell RNA sequencing experiment was used to confirm the optimized factors. Our concluding results provide a complete protocol for the tissue dissociation of mouse mammary tumour from 4T1 cells that preserves the original cell state and is suitable for any single-cell RNA sequencing analysis. Furthermore, our workflow may serve as a guide for the optimization of the dissociation procedure of any other tissue of interest, which would ultimately improve the reproducibility of the reported data.
Interaction of YAP with the Myb-MuvB (MMB) complex defines a transcriptional program to promote the proliferation of cardiomyocytes
Authors: Gründl Marco , Walz Susanne , Hauf Laura , Schwab Melissa , Werner Kerstin Marcela , Spahr Susanne , Ade Carsten P. , Gaubatz Stefan
Published: October 2019

The Hippo signalling pathway and its central effector YAP regulate proliferation of cardiomyocytes and growth of the heart. Using genetic models in mice we show that the increased proliferation of cardiomyocytes due to loss of the Hippo-signaling component SAV1 depends on the Myb-MuvB (MMB) complex. Similarly, proliferation of postnatal cardiomyocytes induced by constitutive active YAP requires MMB. Genome studies revealed that YAP and MMB regulate an overlapping set of cell cycle genes in cardiomyocytes. We find that YAP binds directly to B-MYB, a subunit of MMB, in a manner dependent on the YAP WW domains and a PPXY motif in B-MYB. Disruption of the interaction by overexpression of the YAP binding domain of B-MYB strongly inhibits the proliferation of cardiomyocytes. Our results point to MMB as a critical downstream effector of YAP in the control of cardiomyocyte proliferation.
Native Electrospray-based Metabolomics Enables the Detection of Metal-binding Compounds
Authors: Aron Allegra , Petras Daniel , Schmid Robin , Gauglitz Julia M. , Büttel Isabell , Antelo Luis , Zhi Hui , Saak Christina C. , Malarney Kien P. , Thines Eckhard , Dutton Rachel J. , Raffatellu Manuela , Dorrestein Pieter C.
Published: October 2019

Metals are essential for the molecular machineries of life, and microbes have evolved a variety of small molecules to acquire, compete for, and utilize metals. Systematic methods for the discovery of metal-small molecule complexes from biological samples are limited. Here we describe a two-step native electrospray ionization mass spectrometry method, in which double-barrel post-column metal-infusion and pH adjustment is combined with ion identity molecular networking, a rule-based informatics workflow. This method can be used to identify metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion features with the same chromatographic profiles. As this native metal metabolomics approach can be easily implemented on any liquid chromatography-based mass spectrometry system, this method has the potential to become a key strategy for elucidating and understanding the role of metal-binding molecules in biology.
Ecological divergence and hybridization of Neotropical Leishmania parasites
Authors: Van den Broeck Frederik , Savill Nicholas J. , Imamura Hideo , Sanders Mandy , Maes Ilse , Cooper Sinclair , Mateus David , Jara Marlene , Adaui Vanessa , Arevalo Jorge , Llanos-Cuentas Alejandro , Garcia Lineth , Cupolillo Elisa , Miles Michael , Berriman Matthew , Schnaufer Achim , Cotton James A. , Dujardin Jean-Claude
Published: October 2019

The tropical Andes is an important natural laboratory to understand speciation and diversification in many taxa. Here, we examined the evolutionary history of parasites of the Leishmania braziliensis species complex based on whole genome sequencing of 67 isolates from 47 localities in Peru. We firstly show the origin of near-clonal Andean Leishmania lineages that diverged from admixed Amazonian ancestors, accompanied by a significant reduction in genome diversity and large structural variations implicated in host-parasite interactions. Beside a clear dichotomy between Andean and Amazonian species, patterns of population structure were strongly associated with biogeographical origin. Molecular clock analyses and ecological niche modeling suggested that the history of diversification of the Andean lineages is limited to the Late Pleistocene and intimately associated with habitat contractions driven by climate change. These results support a wider model on trypanosomatid evolution where major parasite lineages emerge through ecological fitting. Second, genome-scale analyses provided evidence of meiotic recombination between Andean and Amazonian Leishmania species, resulting in full-genome hybrids. The mitochondrial genome of these hybrids consisted of homogeneous uniparental maxicircles, but minicircles originated from both parental species, leaving a mosaic ancestry of minicircle-encoded guide RNA genes. We further show that mitochondrial minicircles - but not maxicircles - show a similar evolutionary pattern as the nuclear genome, suggesting that biparental inheritance of minicircles is universal and may be important to alleviate maxicircle-nuclear incompatibilities. By comparing full nuclear and mitochondrial genome ancestries, our data expands our appreciation on the genetic consequences of diversification and hybridization in parasitic protozoa.
MutantZp1results in Zona Pellucida Lacking and Female Infertility in Rats and Humans
Authors: Lv Chao , Huang Hua-Lin , Wang Yan , Peng Tian-Liu , Tan Hang-Jing , Zeng Ming-Hua , Quan Ru-Ping , Deng Hong-Wen , Xiao Hong-Mei
Published: October 2019

Zona pellucida (ZP) plays a vital role in reproductive processes including oogenesis, fertilization and preimplantation development of embryo. The ZP of humans is composed of four glycoproteins (ZP1-ZP4), same as rats ZP. Our previous research reported a first case of human infertility due toZP1mutation, but the mechanism was unclear. Here we developed a genome editingin vivorat model and a co-transfectedin vitrocell model to investigate the pathogenic effect. In rat homozygous for the homologous mutation, ZP were absent in all of collected eggs. Further the growing and fully grown oocytes in the mutant ovaries completely lack a ZP but with detectable intracellular ZP1 protein. After mating with male rats, none of the mutant female rats got pregnant. Moreover, the co-transfected cell experiments and the ovarian experiments showed that the truncated ZP1 sequestered intracellularly ZP3 and ZP4 to impede their release outside, resulting in an intracellular accumulation of ZP1, ZP3 and ZP4, leading to absence of ZP in mutant oocytes. Our results clearly establish the causal role ofZP1mutation on ZP defects and female infertility.

Summary statement

Rat model mirrored completely the phenotypes observed in humans, infertility and abnormal eggs that lack a zona pellucida, through the negative effects ofZP1mutation.
The Role of Gene Encoding Variation ofDRD4in the Relationship between Inattention and Seasonal Daylight
Authors: Vollebregt M.A. , Franke B. , Buitelaar J.K. , Arnold L.E. , Faraone S.V. , Grevet E.H. , Reif A. , Zayats T. , Bralten J. , Bau C.H.D. , Haavik J. , Kuntsi J. , Cupertino R.B. , Loo S.K. , Lundervold A.J. , Ribasés M. , Sánchez-Mora C. , Ramos-Quiroga J.A. , Asherson P. , Swanson J.M. , Arns M.
Published: October 2019

Daylight is the strongest synchronizer of human circadian rhythms. The circadian pathway hypothesis posits that synchrony between daylight and the circadian system relates to (in)attention. The dopamine neurotransmitter system is implicated in regulating the circadian system as well as in (attention)-deficit hyperactivity disorder [ADHD]. We studied the role of functional genetic variation in the gene encoding of dopamine-receptor-D4 (DRD4) in the relationship between inattention and seasonal daylight (changes). Gene-by-environment (GxE) mega-analyses were performed across eight studies including 3757 adult participants (with and without ADHD). We tested 1) theSpring-focus hypothesis, in which attention in 7R-carriers normalizes with increasing daylight levels preceding measurement, 2) theSummer-born ADHD hypothesis, in which 7R-carriers report more inattention when born in spring/summer than in autumn/winter, 3) theWinter-born ADHD hypothesis, opposing the second hypothesis. TheSpring-focus hypothesiswas upheld (1386 ADHD, 760 controls;d=-0.16 between periods); 7R-carriers reported evenlessinattention than 7R-non-carriers after winter solstice (d=0.27 between genotype-groups). Results were diagnosis-independent. Sensitivity analyses at individual study level confirmed the circannual patterns for 7R-carriers. Incorporating geographic changes into the independent measure, we also calculated changes in sunlight levels. This approach likewise showed that inattention correlated negatively with increasing light levels in 7R-carriers (r=-.135). Results emphasize peripheral effects of dopamine and the effects of (seasonal) daylight changes on cognition.
Population mobility and dengue fever transmission in a major city in Southeastern Brazil, 2007-2015
Authors: Johansen Igor C. , Castro Marcia C. , Alves Luciana C. , Carmo Roberto L.
Published: October 2019

Background

Around 14% of world dengue virus (DENV) cases occur in the Americas, the majority of them in Brazil. Although socioeconomic, environmental and behavioral correlates of dengue have been analyzed for different contexts, the role played by population mobility on DENV epidemics, especially at the local level, remains scant. This study assesses whether the daily pattern of population mobility is associated with DENV transmission in Campinas, a Brazilian major city with over 1.2 million inhabitants in São Paulo state.

Methodology/Principal Findings

DENV notifications from 2007 to 2015 were geocoded at street level (n=114,884) and combined with sociodemographic and environmental data from the 2010 Population Census. Population mobility was extracted from the Origin-Destination Survey (ODS), carried out in 2011, and daily precipitation was obtained from satellite imagery. Zero-Inflated Negative Binomial (ZINB) regression models controlled by demographic and environmental factors revealed that high population mobility had a substantial positive effect on higher risk for DENV transmission. High income and residence in apartments were found to be protective against the disease, while unpaved streets, number of strategic points (such as scrapyards and tire repair shops), and precipitation were consistently risk factors for DENV infection.

Conclusions/Significance

The use of fine-scale geographical data can unravel transmission idiosyncrasies not evident from a coarse spatial analysis. Even in a major city like Campinas, the vast majority of population daily mobility occurs at short distances. Based on our results, public policies on DENV transmission control should dedicate special attention to local hubs of population mobility, especially during high transmission weeks and in high dengue incidence areas.

Author Summary

Currently, about half of the world population is at risk of a dengue infection. Numerous studies have addressed the socioeconomic and environmental determinants of the disease. However, little is known about the role played by population mobility on dengue transmission, particularly at the local scale. This study aims at investigating this issue. Our hypothesis was that population movements are a prominent driving force for dengue diffusion locally. We investigated the case of Campinas, a municipality with over 1.2 million inhabitants in Brazil that recorded dengue epidemics in 2007, 2014 and 2015. Our study focused on the years 2007 to 2015, comprising more than 114 thousand cases, geocoded to the household address, and combined with socioeconomic, environmental and daily population mobility data. Our results showed that even controlling for demographic and environmental factors, population mobility was the most important predictor for dengue fever incidence.
Intracellular localization and gene expression analysis provide new insights on LEA proteins’ diversity in anhydrobiotic midge
Authors: Kondratyeva Sabina A. , Nesmelov Alexander A. , Cherkasov Alexander V. , Miyata Yugo , Tokumoto Shoko , Kikawada Takahiro , Gusev Oleg A. , Shagimardanova Elena I.
Published: October 2019

Anhydrobiosis, an adaptive ability to withstand complete desiccation, is in insects limited to a single species: the nonbiting midge Polypedilum vanderplanki (the sleeping chironomid). Evolution of anhydrobiosis in a single representative of a large genus is associated with drastic changes in genome structure, including the emergence of new multimember gene families directly involved in desiccation tolerance. Among them, Late Embryogenesis Abundant (LEA) proteins, which protect other proteins from aggregation caused by desiccation, are believed to originate via horizontal gene transfer from a bacterial donor. To obtain new insights on the biological background of the expanded 27-member LEA protein group in P. vanderplanki, we investigated the expression of corresponding genes in a P. vanderplanki-derived cell line, capable of anhydrobiosis, in a normal state and during induction of desiccation tolerance. We found that all LEA proteins genes identified in P. vanderplanki’s genome except PvLea16 and PvLea17 are also expressed in Pv11 cells. Their expression was elevated in response to anhydrobiosis-inducing trehalose treatment. Expression patterns of PvLea genes were well preserved in Pv11 cells in comparison to P. vanderplanki’s larvae both in the control group and during the anhydrobiosis cycle. We also investigated localization of LEA proteins in Pv11 cells and Sf9 cells and found a different level of conservation in intracellular localization of the protein expressed in mammalian and insect cells.
Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers
Authors: Habimana R. , Okeno T.O. , Ngeno K. , Mboumba S. , Assami P. , Gbotto A. , Keambou C.T. , Nishimwe K. , Mahoro J. , Yao N.
Published: October 2019

Rwanda has about 4.5 million of indigenous chicken (IC) that are very low in productivity. To initiate any genetic improvement programme, IC needs to be accurately characterized. The key purpose of this study was to ascertain the genetic diversity of IC in Rwanda using microsatellite markers. Blood samples of IC sampled from 5 agro-ecological zones were collected from which DNA was extracted, amplified by PCR and genotyped using 28 microsatellite markers. A total of 325 (313 indigenous and 12 exotic) chicken were genotyped and revealed a total number of 305 alleles varying between 2 and 22 with a mean of 10.89 per locus. 186 distinct alleles and 60 private alleles were also observed. The frequency of private alleles was highest in samples from the Eastern region, whereas those from the North West had the lowest. The influx of genes was lower in the Eastern agro-ecological zone than the North West. The mean observed heterozygosity was 0.6155, whereas the average expected heterozygosity was 0.688. The overall inbreeding coefficient among the population was 0.040. Divergence from the Hardy-Weinberg equilibrium was significant in 90% of loci in all the populations. The analysis of molecular variance revealed that about 92% of the total variation originated from variation within populations. Additionally, the study demonstrated that IC in Rwanda could be clustered into four gene groups. In conclusion, there was considerable genetic diversity in IC in Rwanda, which represents a crucial genetic resource that can be conserved or optimized through genetic improvement.
Discrete populations of isotype-switched memory B lymphocytes are maintained in murine spleen and bone marrow
Authors: Riedel René , Addo Richard , Ferreira-Gomes Marta , Heinz Gitta Anne , Heinrich Frederik , Kummer Jannis , Greiff Victor , Schulz Daniel , Klaeden Cora , Cornelis Rebecca , Menzel Ulrike , Kröger Stefan , Stervbo Ulrik , Köhler Ralf , Haftmann Claudia , Kühnel Silvia , Lehmann Katrin , Maschmeyer Patrick , McGrath Mairi , Naundorf Sandra , Hahne Stefanie , Sercan-Alp Özen , Siracusa Francesco , Stefanowski Jonathan , Weber Melanie , Westendorf Kerstin , Zimmermann Jakob , Hauser Anja E. , Reddy Sai T. , Durek Pawel , Chang Hyun-Dong , Mashreghi Mir-Farzin , Radbruch Andreas
Published: October 2019

Here we describe tissue-resident memory B lymphocytes of spleen and bone marrow. Single cell transcriptomes and B cell receptor repertoires identify several exclusive populations of isotype-switched memory B cells (Bsm) in murine spleen and bone marrow, and one interconnected population of 10-20%. A population of marginal zone-like Bsm is located exclusively in the spleen while a novel population of quiescent Bsm is located exclusively in the bone marrow. Cells of two further populations, present in both, spleen and bone marrow, differ in repertoire between the two organs, i.e. are resident as well. Finally, another interconnected population of Bsm of the B1 lineage is present in spleen and bone marrow. In the bone marrow, all Bsm individually dock onto VCAM1+ stromal cells, resting in terms of activation, proliferation and mobility. The discrete B cell memory of bone marrow may be key to rapid secondary humoral responses to systemic antigens.
Amplitude effects allow short jetlags and large seasonal phase shifts in minimal clock models
Authors: Ananthasubramaniam Bharath , Schmal Christoph , Herzel Hanspeter
Published: October 2019

Mathematical models of varying complexity have helped shed light on different aspects of circadian clock function. In this work, we question whether minimal clock models (Goodwin models) are sufficient to reproduce essential phenotypes of the clock: a small phase response curve (PRC), fast jetlag and seasonal phase shifts. Instead of building a single best model, we take an approach where we study the properties of a set of models satisfying certain constraints; here a one-hour pulse PRC with a range of three hours and clock periods between 22h and 26h. Surprisingly, almost all these randomly parameterized models showed a four hour change in phase of entrainment between long and short days and jetlag durations of three to seven days in advance and delay. Moreover, intrinsic clock period influenced jetlag duration and entrainment amplitude and phase. Fast jetlag was realized in this model by means of an interesting amplitude effect: the association between clock amplitude and clock period termed ‘twist’. This twist allows amplitude changes to speed up and slow down clocks enabling faster shifts. These findings were robust to the addition of positive feedback to the model. In summary, the known design principles of rhythm generation – negative feedback, long delay and switch-like inhibition (we review these in detail) – are sufficient to reproduce the essential clock phenotypes. Furthermore, amplitudes play a role in determining clock properties and must be always considered, although they are difficult to measure.
Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)
Authors: Cádiz María I. , López María E. , Díaz-Domínguez Diego , Cáceres Giovanna , Yoshida Grazyella M. , Gomez-Uchida Daniel , Yáñez José M.
Published: October 2019

Nile tilapia (Oreochromis niloticusLinnaeus, 1758) belong to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs in this species began in the late 1980s to enhance some traits of commercial interest. The resulting domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genome-wide SNP data, using two complementary methods based in extended haplotype homozygosity (EHH)._Whole-genome sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia from two countries (Brazil and Costa Rica) was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control pipelines, a total of ~1.3M high-quality SNPs were inferred and used as input for the Integrated Haplotype Score (|iHS|) and standardized log-ratio of integrated EHH between pairs of populations (Rsb) methods. We detected 16, 174 and 96 candidate genes subjected to selection in strain A, B, and C, respectively. These candidate genes represent putative genomic landmarks that could contain functions of biological and commercial interest.
A Synthetic Biology Approach to Sequential Stripe Patterning and Somitogenesis
Authors: Wu Fuqing , He Changhan , Fang Xin , Baez Javier , Ohnmacht Thai , Zhang Qi , Chen Xingwen , Allison Kyle R. , Kuang Yang , Wang Xiao
Published: October 2019

Reaction-diffusion (RD) based clock and wavefront model has long been proposed as the mechanism underlying biological pattern formation of repeated and segmented structures including somitogenesis. However, systematic molecular level understanding of the mechanism remains elusive, largely due to the lack of suitable experimental systems to probe RD quantitatively in vivo. Here we design a synthetic gene circuit that couples gene expression regulation (reaction) with quorum sensing (diffusion) to guide bacterial cells self-organizing into stripe patterns at both microscopic and colony scales. An experimentally verified mathematical model confirms that these periodic spatial structures are emerged from the integration of oscillatory gene expression as the molecular clock and the outward expanding diffusions as the propagating wavefront. Furthermore, our paired model-experiment data illustrate that the RD-based patterning is sensitive to initial conditions and can be modulated by external inducers to generate diverse patterns, including multiple-stripe pattern, target-like pattern and ring patterns with reversed fluorescence. Powered by our synthetic biology setup, we also test different topologies of gene networks and show that network motifs enabling robust oscillations are foundations of sequential stripe pattern formation. These results verified close connections between gene network topology and resulting RD driven pattern formation, offering an engineering approach to help understand biological development.
ECMarker: Interpretable machine learning model identifies gene expression biomarkers predicting clinical outcomes and reveals molecular mechanisms of human disease in early stages
Authors: Jin Ting , Nguyen Nam D. , Talos Flaminia , Wang Daifeng
Published: October 2019

Gene expression and regulation, a key molecular mechanism driving human disease development, remains elusive, especially at early stages. Integrating the increasing amount of population-level genomic data and understanding gene regulatory mechanisms in disease development are still challenging. Machine learning has emerged to solve this, but many machine learning methods were typically limited to building an accurate prediction model as a “black box”, barely providing biological and clinical interpretability from the box. To address these challenges, we developed an interpretable and scalable machine learning model, ECMarker, to predict gene expression biomarkers for disease phenotypes and simultaneously reveal underlying regulatory mechanisms. Particularly, ECMarker is built on the integration of semi- and discriminative- restricted Boltzmann machines, a neural network model for classification allowing lateral connections at the input gene layer. This interpretable model is scalable without needing any prior feature selection and enables directly modeling and prioritizing genes and revealing potential gene networks (from lateral connections) for the phenotypes. With application to the gene expression data of non-small cell lung cancer (NSCLC) patients, we found that ECMarker not only achieved a relatively high accuracy for predicting cancer stages but also identified the biomarker genes and gene networks implying the regulatory mechanisms in the lung cancer development. Additionally, ECMarker demonstrates clinical interpretability as its prioritized biomarker genes can predict survival rates of early lung cancer patients (p-value < 0.005). Finally, we identified a number of drugs currently in clinical use for late stages or other cancers with effects on these early lung cancer biomarkers, suggesting potential novel candidates on early cancer medicine. ECMarker is open source as a general-purpose tool at https://github.com/daifengwanglab/ECMarker.
Silicon Nanowires for Intracellular Optical Interrogation with Sub-Cellular Resolution
Authors: Rotenberg Menahem Y. , Elbaz Benayahu , Nair Vishnu , Schaumann Erik , Yamamoto Naomi , Matino Laura , Santoro Francesca , Tian Bozhi
Published: October 2019

Current techniques for intracellular electrical interrogation are substrate bound and are technically demanding, or lack high spatial resolution. In this work, we use silicon nanowires, which are spontaneously internalized by many cell types, to achieve photo-stimulation with sub-cellular resolution. Myofibroblasts loaded with silicon nanowires remain viable and can undergo cell division. Stimulation of silicon nanowires at separate intracellular locations results in local calcium fluxes. We also show that nanowire-containing myofibroblasts can electrically couple to cardiomyocytes in co-culture and that photo-stimulation of the nanowires increases the spontaneous activation rate in neighboring cardiomyocytes. Finally, we demonstrate that this methodology can be extended to the interrogation of signaling in neuron–glia interactions using nanowire-containing oligodendrocytes.
Transcriptome profiles in brains of mice heterozygous for a DYT1 dystonia-associated mutation in the endogenous Tor1a gene
Authors: Mitchell Sara B. , Chimenti Michael S. , Kawano Hiroyuki , Tom Yuen Tsun Ming , Sjurson Ashley E. , Iwabuchi Sadahiro , Knudtson Kevin L , Bair Thomas B , Kolbe Diana , Harata N. Charles
Published: October 2019

In patients with the brain disorder dystonia, body movement is severely affected – with involuntary muscle contractions and abnormal postures, causing extensive deterioration of the patient’s quality of life. The most common inherited form of this disorder is DYT1 dystonia, which is caused by a mutation in TOR1A gene and autosomal dominant. The molecular mechanisms that underlie the effects of the TOR1A mutation on brain function remain unclear. To understand these, we examined the gene expression profiles (transcriptome) in four brain regions (cerebral cortex, hippocampus, striatum and cerebellum) in a mouse model, the heterozygous ΔE-torsinA knock-in mice which genetically reproduce the mutation in DYT1 dystonia. The samples were obtained at 2 to 3 weeks of age, a period during which synaptic abnormalities have been reported. Pairwise comparisons of brain regions revealed differential gene expression irrespective of genotype. A comparison of heterozygous to wild-type mice failed to reveal genotype-dependent differences in gene expression in any of the four brain regions when examined individually. However, genotype-dependent differences became apparent when the information for all brain regions was combined. These results suggest that any changes in the transcriptome within a brain region were subtle at this developmental stage, but that statistically significant changes occur across all brain regions. Such changes in the transcriptome, although subtle in degree, could underlie the processes that give rise to DYT1 dystonia.
Found in Transcription: Gene fusions arise through defects in RNA processing in the absence of chromosomal rearrangements
Authors: Jiang Yue , Apostolides Michael J. , Husić Mia , Siddaway Robert , Yu Man , Mark Stephanie , Ramani Arun K. , Hawkins Cynthia , Brudno Michael
Published: October 2019

Recent advancements in high throughput sequencing analysis have enabled the characterization of cancer-driving fusions, improving our understanding of cancer development. Most fusion calling methods, however, examine either RNA or DNA information alone and are limited to a rigid definition of what constitutes a fusion. For this study we developed a pipeline that incorporates several fusion calling methods and considers both RNA and DNA to capture a more complete representation of the tumour fusion landscape. Interestingly, most of the fusions we identified were specific to RNA, with no evidence of corresponding genomic restructuring. Further, while the average total number of fusions in tumour and normal brain tissue samples is comparable, their overall fusion profiles vary significantly. Tumours have an over-representation of fusions occurring between coding genes, whereas fusions involving intergenic or non-coding regions comprised the vast majority of those in normals. Tumours were also more abundant in unique, sample-specific fusions compared to normals, though several fusions exhibited strong recurrence in the tumour type examined (diffuse intrinsic pontine glioma; DIPG) and were absent from both normal tissues and other cancers. Intriguingly, tumours also show broad up- or down-regulation of spliceosomal gene expression, which significantly correlates with fusion number (p=0.007). Our results show that RNA-specific fusions are abundant in both tumour and normal tissue and are associated with spliceosomal gene dysregulation. RNA-specific fusions should be considered as a potential mechanism that may contribute to cancer formation initiation and maintenance alongside more traditional structural events.
Antagonism of PP2A is an independent and conserved function of HIV-1 Vif and causes cell cycle arrest
Authors: Marelli Sara , Williamson James C , Protasio Anna V , Naamati Adi , Greenwood Edward JD , Deane Janet E , Lehner Paul J , Matheson Nicholas J
Published: October 2019

The seminal description of cellular restriction factor APOBEC3G and its antagonism by HIV-1 Vif has underpinned two decades of research on the host-virus interaction. As well as APOBEC3G and its homologues, however, we have recently discovered that Vif is also able to degrade the PPP2R5 family of regulatory subunits of key cellular phosphatase PP2A (PPP2R5A-E) (Greenwood et al., 2016; Naamati et al., 2019). We now identify amino acid polymorphisms at positions 31 and 128 of HIV-1 Vif which selectively regulate the degradation of PPP2R5 family proteins. These residues covary across HIV-1 virusesin vivo, favouring depletion of PPP2R5A-E. Through analysis of point mutants and naturally occurring Vif variants, we further show that degradation of PPP2R5 family subunits is both necessary and sufficient for Vif-dependent G2/M cell cycle arrest. Antagonism of PP2A by HIV-1 Vif is therefore independent of APOBEC3 family proteins, and regulates cell cycle progression in HIV-infected cells.
Minutes-timescale 3D isotropic imaging of entire organs at subcellular resolution by content-aware compressed-sensing light-sheet microscopy
Authors: Fang Chunyu , Chu Tingting , Yu Tingting , Huang Yujie , Li Yusha , Wan Peng , Feng Wenyang , Wang Xuechun , Mei Wei , Zhu Dan , Fei Peng
Published: October 2019

Instant 3D imaging of entire organs and organisms at cellular resolution is a recurring challenge in life science. Here we report on a computational light-sheet microscopy able to achieve minute-timescale mapping of entire macro-scale organs at high spatial resolution, thereby overcoming the throughput limit of current 3D microscopy implementations. Through combining a dual-side confocally-scanned Bessel light-sheet illumination which provides thinner-and-wider optical sectioning of deep tissues, with a content-aware compressed sensing (CACS) computation pipeline which further improves the contrast and resolution based on a single acquisition, our method yields 3D images with high, isotropic spatial resolution and rapid acquisition improved by two-orders of magnitude. We demonstrate the imaging of whole brain (∼400 mm3), entire gastrocnemius and tibialis muscles (∼200 mm3) of mouse at subcellular resolution (0.5-μm isovoxel) and ultra-high throughput of 5∼10 minutes per sample. Various system-level cellular analyses, such as mapping cell populations at different brain sub-regions, tracing long-distance projection neurons over the entire brain, and calculating neuromuscular junction occupancy across whole muscle, were also readily enabled by our method.
MinION sequencing of seafood in Singapore reveals creatively labelled flatfishes, confused roe, pig DNA in squid balls, and phantom crustaceans
Authors: Ho Jonathan K. I. , Puniamoorthy Jayanthi , Srivathsan Amrita , Meier Rudolf
Published: October 2019

Food mislabelling is a growing world-wide problem that is increasingly addressed through the authentication of ingredients via techniques like mass spectrometry or DNA-sequencing. However, traditional DNA sequencing methods are slow, expensive, and require well-equipped laboratories. We here test whether these problems can be overcome through the use of Nanopore sequencing. We sequenced 92 single and 13 mixed-species samples bought in supermarkets and restaurants in Singapore which has a large and diverse seafood trade. We successfully obtained DNA barcodes for 94% and 100% of the single- and mixed-species products after correcting the numerous sequencing errors of MinION reads with a correction pipeline optimized for DNA barcodes. We find comparatively low levels of clear-cut mislabelling for single-species samples (7.6 %) while the rates are higher for mixed-species samples (38.5 %). These low rates are somewhat deceptive, however, because of the widespread use of vague common species names that do not allow for a precise assessment of the expected ingredients. With regard to the clearly mislabelled single-species products, higher-value products (e.g., prawn roe, wild-caught Atlantic salmon, halibut) are replaced with lower-value ingredients (e.g., fish roe, Pacific salmon, arrowtooth flounder) while more serious problems are observed for mixed-species samples. Cuttlefish and prawn balls repeatedly contained pig DNA and 100% of all mixed samples labelled as containing crustaceans (‘crab’, ‘prawn’, ‘lobster’) only yielded fish barcodes. We conclude that there is a need for more regular testing of seafood samples and suggest that due to speed and low-cost, MinION would be a good instrument for this purpose. We also emphasize the need for developing clearer labelling guidelines.
Tuning movement for sensing in an uncertain world
Authors: Chen Chen , Murphey Todd D. , MacIver Malcolm A.
Published: October 2019

While animals track or search for targets, sensory organs make small unexplained movements on top of the primary task-related motions. While multiple theories for these movements exist—in that they support infotaxis, gain adaptation, spectral whitening, and high-pass filtering—predicted trajectories show poor fit to measured trajectories. We propose a new theory for these movements called energy-constrained proportional betting, where the probability of moving to a location is proportional to an expectation of how informative it will be balanced against the movement’s predicted energetic cost. Trajectories generated in this way show good agreement with measured target tracking trajectories of electric fish. Similarly good agreement was found across three published datasets on visual and olfactory tracking tasks in insects and mammals. Our theory unifies the metabolic cost of motion with information theory. It predicts sense organ movements in animals and can prescribe sensor motion for robots to enhance performance.
X-ray back-diffraction: can we further increase the energy resolution by tuning the energy slightly below that of exact backscattering?
Authors: Hönnicke Marcelo Goncalves , Cusatis Cesar , Conley Raymond , Kakuno Edson Massayuki , Kasman Elina , Huang XianRong , Bouet Nathalie , Zhou Juan , Cai Yong Q. , Basso Marques Joao , Vicentin Flavio Cesar
Published: October 2019

X-ray beams at energies tuned slightly below that of exact backscattering (extreme conditions, where X-ray back-diffraction is almost extinguished – called residual XBD) are better focused if the experiment is carried out at lower energies in order to avoid multiple-beam diffraction effects. Following previous work by the authors [Hönnicke, Conley, Cusatis, Kakuno, Zhou, Bouet, Marques & Vicentin (2014). J. Appl. Cryst.
47, 1658–1665], herein efforts are directed towards characterizing the residual XBD beam of an ultra-thin Si 220 crystal (UTSiXTAL) at ∼3.2 keV. To achieve the residual XBD condition the UTSiXTAL was cooled from 310 to 273 K. The results indicate that under this extreme condition the energy resolution can be further improved. Issues with the energy resolution measurements due to incoming beam divergence and the ultra-thin crystal flatness are discussed.
Crystal structures of two coordination isomers of copper(II) 4-sulfobenzoic acid hexahydrate and two mixed silver/potassium 4-sulfobenzoic acid salts
Authors: Squattrito Philip J. , Lambright-Mutthamsetty Kelly J. , Giolando Patrick A. , Kirschbaum Kristin
Published: October 2019

A reaction of copper(II) carbonate and potassium 4-sulfobenzoic acid in water acidified with hydrochloric acid yielded two crystalline products. Tetraaquabis(4-carboxybenzenesulfonato)copper(II) dihydrate, [Cu(O3SC6H4CO2H)2(H2O)4]·2H2O, (I), crystallizes in the triclinic space group P\overline{1} with the Cu2+ ions located on centers of inversion. Each copper ion is coordinated to four water molecules in a square plane with two sulfonate O atoms in the apical positions of a Jahn–Teller-distorted octahedron. The carboxylate group is protonated and not involved in coordination to the metal ions. The complexes pack so as to create a layered structure with alternating inorganic and organic domains. The packing is reinforced by several O—H...O hydrogen bonds involving coordinated and non-coordinated water molecules, the carboxylic acid group and the sulfonate group. Hexaaquacopper(II) 4-carboxybenzenesulfonate, [Cu(H2O)6](O3SC6H4CO2H)2, (II), also crystallizes in the triclinic space group P\overline{1} with Jahn–Teller-distorted octahedral copper(II) aqua complexes on the centers of inversion. As in (I), the carboxylate group on the anion is protonated and the structure consists of alternating layers of inorganic cations and organic anions linked by O—H...O hydrogen bonds. A reaction of silver nitrate and potassium 4-sulfobenzoic acid in water also resulted in two distinct products that have been structurally characterized. An anhydrous silver potassium 4-carboxybenzenesulfonate salt, [Ag0.69K0.31](O3SC6H4CO2H), (III), crystallizes in the monoclinic space group C2/c. There are two independent metal sites, one fully occupied by silver ions and the other showing a 62% K+/38% Ag+ (fixed) ratio, refined in two slightly different positions. The coordination environments of the metal ions are composed primarily of sulfonate O atoms, with some participation by the non-protonated carboxylate O atoms in the disordered site. As in the copper compounds, the cations and anions cleanly segregate into alternating layers. A hydrated mixed silver potassium 4-carboxybenzenesulfonate salt dihydrate, [Ag0.20K0.80](O3SC6H4CO2H)·2H2O, (IV), crystallizes in the monoclinic space group P21/c with the Ag+ and K+ ions sharing one unique metal site coordinated by two water molecules and six sulfonate O atoms. The packing in (IV) follows the dominant motif of alternating inorganic and organic layers. The protonated carboxylate groups do not interact with the cations directly, but do participate in hydrogen bonds with the coordinated water molecules. (IV) is isostructural with pure potassium 4-sulfobenzoic acid dihydrate.
The effects of technology acceptance and use behaviour on women’s entrepreneurship motivation factors
Authors: Özsungur Fahri
Published: October 2019

Purpose

The purpose of this paper is to determine the effects of factors affecting the acceptance and use of technology on the factors affecting women’s entrepreneurship motivation.

Design/methodology/approach

This study was conducted with 156 women entrepreneurs in Turkey in February 2019. A mixed method evaluation design has been adopted in the study.

Findings

The findings revealed that effort expectancy was negatively associated with behaviour intention and push factor and positively associated with pull factor. Performance expectancy was positively associated with balance factor, push factor and behaviour intention. Hedonic motivation was positively associated with behaviour intention and emotional factor. Behaviour intention was negatively associated with use behaviour. Facilitating conditions was positively associated with push factor. Habit was positively associated with behaviour intention and negatively associated with pull, push, balance and emotional factors. Necessities and habit were not motivation factors for women entrepreneurs.

Research limitations/implications

The sample was restricted to women entrepreneurs, limiting the generalizability of the findings.

Practical implications

The practical implications of the study show that effort expectancy, performance expectancy, hedonic motivation, facilitating conditions and habit are the key factors for the women’s entrepreneurship motivation. Women’s entrepreneurship commissions to be established in chambers of commerce and industry can improve entrepreneurial motivation.

Originality/value

This is the first study that reveals the effects of technology acceptance and use behaviours on women’s entrepreneurship motivation. Theoretical background, discussion, managerial implications, limitations and recommendations for future studies are discussed.
China, India and the contest for the Indo-Pacific
Authors: Robertson Peter , Yuan Jingdong , Mudiyanselage Harsha Konara
Published: October 2019

Purpose

The purpose of this paper is to describe how China’s rapid growth and increasing resource dependence have changed its relationship with India and their respective defense strategies. In particular, we consider China's Belt and Road Initiative, India's “Act East” policy and the strategic and economic value of the Indian Ocean and South China Sea regions.

Design/methodology/approach

The authors find no econometric evidence of interactions between China and India’s military spending using a Richardson-Baumol arms race model. Likewise, in a cross-county panel data study of military spending, they find that China’s military spending has no independent effect on military spending in other countries. The authors also show that once wage costs and other sources of military inflation are accounted for, the pattern of real defense spending growth is much less intense than is suggested by nominal data. Nevertheless, they show that China has been undertaking intense military modernization with rapidly rising capital-labor ratios in its defense spending.

Findings

The authors find little evidence of a traditional arms race, but also show that China, and to a lesser extent India, have been realigning their military capabilities to these new security risks while maintaining overall military burden on the economy.

Research limitations/implications

Econometric analysis is limited by data availability and is necessarily historical, whereas the security situation is very fluid and may change in the short term.

Practical implications

The paper identifies factors that are likely to influence China and India's attitudes to defense spending in the coming years.

Social implications

The paper finds that there is not an arms race in the traditional sense but may be an arms race in terms of new technologies and military modernization.

Originality/value

This is a very much underexplored topic in economics. The authors take an interdisciplinary approach showing how economics tools can be used to help understand this important issue in international relations.
Using narrative distance to invite transformative learning experiences
Authors: Taeger Stephan
Published: October 2019

Purpose

The purpose of this paper is to introduce narrative distance as a phenomenon that can help create transformative learning experiences (TLEs). Narrative distance is defined as the cognitive or emotional space afforded by indirect communication that invites listeners to make sense of content. In ways similar to a book, movie or play, narrative distance invites participants to draw conclusions for themselves (Craddock, 2002).

Design/methodology/approach

After examining how other fields have discussed concepts related to narrative distance and its affordances, this paper illustrates how this phenomenon can satisfy many of Wilson and Parrish’s (2011) key indicators for TLEs.

Findings

Six principles are offered for incorporating narrative distance into instructional design.

Originality/value

Instructional design has not explored indirect communication that is similar to narrative in any significant way.
Women in the Egyptian parliament: a different agenda?
Authors: Abdelgawad Hala , Hassan Mazen
Published: October 2019

Purpose

Theoretically, the quality of representation is likely to be enhanced when more societal segments are included in formal political structures. An interesting question, however, is whether a similar correlation holds empirically outside established Western democracies. In the 2015 Egyptian parliament, women representation achieved an all-time high of 14.9% of total seats – nearly four times the historical Egyptian average. It is asked whether female legislators riding this unprecedent tide were different from their male colleagues in terms of their socio-economic backgrounds. But more importantly, the authors examine whether this increased representation led to any change in inclusion of more women’s issues in the legislative agenda, and how traditional topics are debated.

Design/methodology/approach

The authors conducted a content analysis of selected parliamentary scripts – generating on an original data set – to trace the topics and interventions raised by female MPs. The authors draw on the extensive literature on women’s representation, giving special attention to the structure versus agency dichotomy in this quest.

Findings

The authors conclude that female MPs were as active in parliamentary debates as to their male colleagues. Moreover, women did stress women issues more than men. The results indicate that the inclusion of traditionally under-represented groups does affect parliamentary agendas.

Originality/value

The authors conducted a content analysis of selected parliamentary scripts – generating on an original data set – to trace the topics and interventions raised by female MPs based on a case study of the 2015 Egyptian parliament.