bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic epidemiology of penicillin-non-susceptible Streptococcus pneumoniae
Authors: Dewé Tamsin C. M. , D’Aeth Joshua C. , Croucher Nicholas J.
Published: October 2019

Penicillin-non-susceptible

Streptococcus pneumoniae

(PNSP) were first detected in the 1960s, and are now common worldwide, predominantly through the international spread of a limited number of strains. Extant PNSP are characterized by mosaic pbp2x, pbp2b and pbp1a genes generated by interspecies recombinations, with the extent of these alterations determining the range and concentrations of β-lactams to which the genotype is non-susceptible. The complexity of the genetics underlying these phenotypes has been the subject of both molecular microbiology and genome-wide association and epistasis analyses. Such studies can aid our understanding of PNSP evolution and help improve the already highly-performing bioinformatic methods capable of identifying PNSP from genomic surveillance data.
RNAseq studies reveal distinct transcriptional response to vitamin A deficiency in small intestine versus colon, uncovering novel vitamin A-regulated genes
Authors: Chai Zhi , Lyu Yafei , Chen Qiuyan , Wei Cheng-Hsin , Snyder Lindsay M. , Weaver Veronika , Sebastian Aswathy , Albert István , Li Qunhua , Cantorna Margherita T. , Ross A. Catharine
Published: October 2019

Vitamin A (VA) deficiency remains prevalent in resource limited countries, affecting over 250 million preschool aged children. Vitamin A deficiency is associated with reduced intestinal barrier function and increased risk of mortality due to mucosal infection. UsingCitrobacter rodentium(C. rodentium) infection in mice as a model for diarrheal diseases in humans, previous reports showed reduced pathogen clearance and survival in vitamin A deficient (VAD) mice compared to their vitamin A sufficient (VAS) counterparts.

Objectives

To characterize and compare the impact of preexisting VA deficiency on gene expression patterns in the small intestine (SI) and the colon, and to discover novel target genes in VA-related biological pathways.

Methods

VAD mice were generated by feeding VAD diet to pregnant C57/BL6 dams and their post-weaning offspring. RNAseq were performed using the total mRNAs extracted from SI and colon. Differentially Expressed Gene (DEG), Gene Ontology (GO) enrichment, and Weighted Gene Co-expression Network Analysis (WGCNA) were performed to characterize expression and co-expression patterns.

Results

DEGs compared between VAS and VAD groups detected 49 SI and 94 colon genes. By GO information, SI DEGs were significantly enriched in categories relevant to retinoid metabolic process, molecule binding, and immune function. Immunity related pathways, including “humoral immune response” and “complement activation” were positively associated with VA in SI. Three co-expression modules showed significant correlation with VA status in SI; these modules contained four known retinoic acid targets. In addition, other SI genes of interest (e.g.Mbl2,Cxcl14, andNr0b2) in these modules were suggested as new candidate genes regulated by VA. Furthermore, our analysis showed that markers of two cell types in SI, mast cells and Tuft cells, were significantly altered by VA status. In colon, “cell division” was the only enriched category and was negatively associated with VA. Thus, comparison of co-expression modules between SI and colon indicated distinct networks under the regulation of dietary VA and suggest that preexisting VAD could have a significant impact on the host response to a variety of disease conditions.
Effect of number and placement of EEG electrodes on measurement of neural tracking of speech
Authors: Montoya-Martínez Jair , Vanthornhout Jonas , Bertrand Alexander , Francart Tom
Published: October 2019

Measurement of neural tracking of natural running speech from the electroencephalogram (EEG) is an increasingly popular method in auditory neuroscience and has applications in audiology. The method involves decoding the envelope of the speech signal from the EEG signal, and calculating the correlation with the envelope of the audio stream that was presented to the subject. Typically EEG systems with 64 or more electrodes are used. However, in practical applications, set-ups with fewer electrodes are required. Here, we determine the optimal number of electrodes, and the best position to place a limited number of electrodes on the scalp. We propose a channel selection strategy based on an utility metric, which allows a quick quantitative assessment of the influence of a channel (or a group of channels) on the reconstruction error. We consider two use cases: a subject-specific case, where the optimal number and position of the electrodes is determined for each subject individually, and a subject-independent case, where the electrodes are placed at the same positions (in the 10-20 system) for all the subjects. We evaluated our approach using 64-channel EEG data from 90 subjects. In the subject-specific case we found that the correlation between actual and reconstructed envelope first increased with decreasing number of electrodes, with an optimum at around 20 electrodes, yielding 29% higher correlations using the optimal number of electrodes compared to all electrodes. This means that our strategy of removing electrodes can be used to improve the correlation metric in high-density EEG recordings. In the subject-independent case, we obtained a stable decoding performance when decreasing from 64 to 22 channels. When the number of channels was further decreased, the correlation decreased. For a maximal decrease in correlation of 10%, 32 well-placed electrodes were sufficient in 91% of the subjects.
An integrated multi-omic single cell atlas to redefine human B cell memory
Authors: Glass David R. , Tsai Albert G. , Oliveria John Paul , Hartmann Felix J. , Kimmey Samuel C. , Calderon Ariel A. , Borges Luciene , Bendall Sean C.
Published: October 2019

To evaluate the impact of heterogeneous B cells in health and disease, comprehensive profiling is needed at a single cell resolution. We developed a highly-multiplexed screen to quantify the co-expression of 351 surface molecules on low numbers of primary cells. We identified dozens of differentially expressed molecules and aligned their variance with B cell isotype usage, metabolism, biosynthesis activity, and signaling response. Here, we propose a new classification scheme to segregate peripheral blood B cells into ten unique subsets, including a CD45RB+ CD27- early memory population and a CD19hiCD11c+ memory population that is a potent responder to immune activation. Furthermore, we quantify the contributions of antibody isotype and cell surface phenotype to various cell processes and find that phenotype largely drives B cell function. Taken together, these findings provide an extensive profile of human B cell diversity that can serve as a resource for further immunological investigations.
Extreme storms cause rapid, context-dependent shifts in nearshore subtropical bacterial communities
Authors: Ares Ángela , Brisbin Margaret Mars , Sato Kirk N. , Martín Juan P. , Iinuma Yoshiteru , Mitarai Satoshi
Published: October 2019

Climate change scenarios predict tropical cyclones will increase in both frequency and intensity, which will escalate the amount of terrestrial run-off and mechanical disruption affecting coastal ecosystems. Bacteria are key contributors to ecosystem functioning, but relatively little is known about how they respond to extreme storm events, particularly in nearshore subtropical regions. In this study, we combine field observations and mesocosm experiments to assess bacterial community dynamics and changes in physicochemical properties during early- and late-season tropical cyclones affecting Okinawa, Japan. Storms caused large and fast influxes of freshwater and terrestrial sediment—locally known as red soil pollution—and caused moderate increases of macronutrients—especially SiO2 and PO43-. We detected shifts in relative abundances of marine bacteria and the introduction of terrestrially-derived bacteria, including putative coral and human pathogens, during storm events. Soil input alone did not substantially affect marine bacterial communities in mesocosms, indicating that other components of run-off or other storm effects likely exert a larger influence on bacterial communities. The storm effects were short-lived and bacterial communities quickly recovered following both storm events. The early- and late-season storms caused different physicochemical and bacterial community changes, demonstrating the context-dependency of extreme storm responses in a subtropical coastal ecosystem.
Riboflavin Directly Mediates the Dealkylation by Microbial Cytochrome P450 Monooxygeneses
Authors: Zhang Chengchang , Lu Meiling , Lin Lin , Huang Zhangjian , Zhang Rongguang , Wu Xuri , Chen Yijun
Published: October 2019

As a vast repertoire of enzymes in nature, microbial cytochrome P450 monooxygenases require an activated form of flavin as a cofactor for the catalytic activity. Riboflavin is the precursor of FAD and FMN that serve as indispensable cofactors for flavoenzymes. In contrast to previous notion, here we describe the identification of an electron transfer process directly mediated by riboflavin for the N-dealkylation by microbial P450 monooxygenases. The electron relay from NADPH to riboflavin and then via activated oxygen to heme was proposed based on the combination of X-ray crystallography, molecular modeling and molecular dynamics simulation, site-directed mutagenesis and biochemical analysis of representative microbial P450 monooxygenases. This study provides new insights into the electron transfer mechanism in microbial P450 enzyme catalysis and likely in plants and mammals.
Germline burden of rare damaging variants negatively affects human healthspan and lifespan
Authors: Shindyapina Anastasia V. , Zenin Aleksandr A. , Tarkhov Andrei E. , Fedichev Peter O. , Gladyshev Vadim N.
Published: October 2019

Genome-wide association studies often explore links between particular genes and phenotypes of interest. Known genetic variants, however, are responsible for only a small fraction of human lifespan variation evident from genetic twin studies. To account for the missing longevity variance, we hypothesized that the cumulative effect of deleterious variants may affect human longevity. Here, we report that the burden of rarest protein-truncating variants (PTVs) negatively impacts both human healthspan and lifespan in two large independent cohorts. Longer-living subjects have both fewer rarest PTVs and less damaging PTVs. In contrast, we show that the burden of frequent PTVs and rare non-PTVs is less deleterious, lacking association with longevity. The combined effect of rare PTVs is similar to that of known variants associated with longer lifespan and accounts for 1 − 2 years of lifespan variability. We further find that somatic accumulation of PTVs accounts for a minute fraction of mortality and morbidity acceleration and hence provides little support for its causal role in aging. Thus, damaging mutations, germline and somatic, can only contribute to aging as a result of higher-order effects including interactions of multiple forms of damage.
Diversification of metazoan Kexin-like proprotein convertases: insights from the leechHelobdella
Authors: Tao Wei-Yu , Cheng Ya-Chih , Song Mi Hye , Weisblat David A. , Kuo Dian-Han
Published: October 2019

Intercellular communication is quintessential for multicellularity and often mediated by secreted peptide ligands. In Metazoa, proprotein convertases are a major class of endoproteases partaking in the proteolytic processing of these ligands, which is in turn required for their signaling activities. In vertebrates, the best-studied convertase substrates are neuropeptides, peptide hormones, and members of the TGFβ/BMP-family. Each ligand is processed by a particular subset of convertases. Therefore, the diversification of convertases may have contributed to the growing complexity of cellular communication in metazoan evolution. However, proprotein convertases have not been systematically explored in Metazoa. Here, we sampled the representative metazoan genomes and established that six Kexin-like proprotein convertases were present in the last common ancestor of protostomes and deuterostomes. Among these, we identified a novel PCSKX orthologous group (OG) that was lost in vertebrates. Spiralian protosomes have, in general, maintained all six OGs. Therefore, we characterized the functional divergence of the Kexin-like OGs in the leechHelobdella, an experimentally tractable spiralian. Gene expression patterns suggested that PCSK1 and PCSK2 are specialized for the processing of neuropeptides and peptide hormones in bilaterians and that the newly identified PCSKX is probably functionally similar to furin and PCSK7. Finally, we showed that, distinct from the BMP morphogen in vertebrate embryos, the convertase-mediated proteolytic cleavage is not required for the short-range BMP signaling in the dorsoventral patterning of leech ectoderm. Together, our data revealed the complexity of the Kexin-like proprotein convertase gene family and their roles in generating diverse patterns of cellular communication in Metazoa.
The Bovine Genome Variation Database (BGVD): Integrated Web-database for Bovine Sequencing Variations and Selective Signatures
Authors: Chen Ningbo , Fu Weiwei , Zhao Jianbang , Shen Jiafei , Chen Qiuming , Zheng Zhuqing , Chen Hong , Sonstegard Tad S. , Lei Chuzhao , Jiang Yu
Published: October 2019

Next-generation sequencing has yielded a vast amount of cattle genomic data for the global characterization of population genetic diversity and the identification of regions of the genome under natural and artificial selection. However, efficient storage, querying and visualization of such large datasets remain challenging. Here, we developed a comprehensive Bovine Genome Variation Database (BGVD, http://animal.nwsuaf.edu.cn/BosVar) that provides six main functionalities: Gene Search, Variation Search, Genomic Signature Search, Genome Browser, Alignment Search Tools and the Genome Coordinate Conversion Tool. The BGVD contains information on genomic variations comprising ∼60.44 M SNPs, ∼6.86 M indels, 76,634 CNV regions and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data and resources from NCBI, the UCSC Genome Browser and AnimalQTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale.
The zebrafish dorsolateral habenula is required for updating learned behaviors
Authors: Palumbo Fabrizio , Serneels Bram , Pelgrims Robbrecht , Yaksi Emre
Published: October 2019

Operant conditioning requires multiple cognitive processes, such as learning, prediction of potential outcomes and decision making. It is less clear how interactions of these processes lead to the behavioral adaptations that allow animals to cope with a changing environment. We showed that juvenile zebrafish can perform conditioned place avoidance learning, with an improving performance across development. Ablation of the dorsolateral habenula (dlHb), a brain region involved in associative learning and prediction of outcomes, led to an unexpected improvement in performance and delayed memory extinction. Interestingly, while the control animals exhibited rapid adaptation to a changing learning rule, dlHb ablated animals failed to adapt. Altogether, our results show that the dlHb plays a central role in switching animals’ strategies while integrating new evidence with prior experience.
Brain aging comprises many modes of structural and functional change with distinct genetic and biophysical associations
Authors: Smith Stephen M. , Elliott Lloyd T. , Alfaro-Almagro Fidel , McCarthy Paul , Nichols Thomas E. , Douaud Gwenaëlle , Miller Karla L.
Published: October 2019

Brain imaging can be used to study how individuals’ brains are aging, compared against population norms. This can inform on aspects of brain health; for example, smoking and blood pressure can be seen to accelerate brain aging. Typically, a single “brain age” is estimated per subject, whereas here we we identified 62 modes of subject variability, from 21,407 subjects’ multimodal brain imaging data in UK Biobank. The modes represent different aspects of brain aging, showing distinct patterns of functional and structural brain change, and distinct patterns of association with genetics, lifestyle, cognition, physical measures and disease. While conventional brain-age modelling found no genetic associations, 34 modes had genetic associations. We suggest that it is important not to treat brain aging as a single homogeneous process, and that modelling of distinct patterns of structural and functional change will reveal more biologically meaningful markers of brain aging in health and disease.
Unique repression domains of Pumilio utilize deadenylation and decapping factors to accelerate destruction of target mRNAs
Authors: Arvola René M. , Chang Chung-Te , Buytendorp Joseph P. , Levdansky Yevgen , Valkov Eugene , Freddolino Peter L. , Goldstrohm Aaron C.
Published: October 2019

Pumilio is an RNA-binding protein that represses a network of mRNAs to control embryogenesis, stem cell fate, fertility, and neurological functions inDrosophila. We sought to identify the mechanism of Pumilio-mediated repression and find that it accelerates degradation of target mRNAs, mediated by three N-terminal Repression Domains (RDs), which are unique to Pumilio orthologs. We show that the repressive activities of the Pumilio RDs depend on specific subunits of the Ccr4-Not (CNOT) deadenylase complex. Depletion of Pop2, Not1, Not2, or Not3 subunits alleviates Pumilio RD-mediated repression of protein expression and mRNA decay, whereas depletion of other CNOT components had little or no effect. Moreover, the catalytic activity of Pop2 deadenylase is important for Pumilio RD activity. Further, we show that the Pumilio RDs directly bind to the CNOT complex. We also report that the decapping enzyme, Dcp2, participates in repression by the N-terminus of Pumilio. These results support a model wherein Pumilio utilizes CNOT deadenylase and decapping complexes to accelerate destruction of target mRNAs. Because the N-terminal RDs are conserved in mammalian Pumilio orthologs, the results of this work broadly enhance our understanding of Pumilio function and roles in diseases including cancer, neurodegeneration, and epilepsy.
Molecularly-Defined Hippocampal Inputs Regulate Population Dynamics in the Prelimbic Cortex to Suppress Context Fear Memory Recall
Authors: Hallock Henry L. , Quillian Henry M. , Maynard Kristen R. , Mai Yishan , Chen Huei-Ying , Hamersky Gregory R. , Shin Joo Heon , Maher Brady J. , Jaffe Andrew E. , Martinowich Keri
Published: October 2019

Associating fearful events with the context in which they occur is critical for survival. Dysregulation of context-fear memory processing is a hallmark symptom of several neuropsychiatric disorders, including generalized anxiety disorder (GAD) and post-traumatic stress disorder (PTSD). Both the hippocampus and prelimbic subregion (PrL) of the medial prefrontal cortex (mPFC) have been linked with context fear memory recall in rodents, but the mechanisms by which hippocampal-prelimbic circuitry regulates this process remains poorly understood. Spatial and genetic targeting of this circuit in mice allowed us to use molecular profiling to show that hippocampal neurons with projections to the PrL (vHC-PrL projectors) are a transcriptomically-distinct sub-population that is enriched for expression of genes associated with both GAD and PTSD. We further show that stimulation of this population of vHC-PrL projectors suppresses context fear memory recall and impairs the ability of PrL neurons to dynamically distinguish between distinct phases of fear learning. Using transgenic and circuit-specific molecular targeting approaches, we demonstrate that unique patterns of activity-dependent gene transcription within vHC-PrL projectors causally regulate excitatory/inhibitory balance in the PrL during context fear memory recall. Together, our data illuminate the molecular mechanisms by which hippocampal-prelimbic circuitry regulates the retrieval of contextually-mediated fear memories.
“Alkyladenine DNA glycosylase associates with transcription elongation to coordinate DNA repair with gene expression”
Authors: Montaldo Nicola P. , Bordin Diana L. , Brambilla Alessandro , Rösinger Marcel , Fordyce Martin Sarah L. , Bjørås Karine Øian , Bradamante Stefano , Aas Per Arne , Furrer Antonia , Olsen Lene C. , Otterlei Marit , Sætrom Pål , Bjørås Magnar , Samson Leona D. , van Loon Barbara
Published: October 2019

Base excision repair (BER) initiated by alkyladenine DNA glycosylase (AAG; aka MPG) is essential for removal of aberrantly methylated DNA bases. Genome instability and accumulation of aberrant bases accompany multiple diseases including cancer and neurological disorders. While BER is well studied on naked DNA, it remains unclear how BER efficiently operates on chromatin. Here we show that AAG binds to chromatin and forms complex with active RNA polymerase (pol) II. This occurs through direct interaction with Elongator and results in transcriptional co-regulation. Importantly, at co-regulated genes aberrantly methylated bases accumulate towards 3’end, in regions enriched for BER enzymes AAG and APE1, Elongator and active RNA pol II. Active transcription and functional Elongator are further crucial to ensure efficient BER, by promoting AAG and APE1 chromatin recruitment. Our findings provide novel insights to maintaining genome stability in actively transcribing chromatin, and reveal roles of aberrantly methylated bases in regulation of gene expression.
On the evolution of neural decisions from uncertain visual input to uncertain actions
Authors: Tomassini Alessandro , Price Darren , Zhang Jiaxiang , Rowe James B
Published: October 2019

Behavior can be conceived as the result of a sequence in which the outcomes of perceptual decisions inform decisions on which action to take. However, the relationship between these processes, and spatiotemporal dynamics of the visual-to-motor transformation remains unclear. Here, we combined accumulation-to-threshold models and electro-magnetoencephalography, to trace neural correlates of sensorimotor decisions in space, time and frequency. We challenge the assumption of sequential decisions, with evidence that visuomotor processing unfolds through a continuous flow of information from sensory to motor regions. Action selection is initiated before regional visual decisions are completed. By linking behavior and physiology through theoretical decision models, we identify simultaneous forward and backward flow of information for visuomotor decisions between sensory and motor regions, in beta and gamma ranges. The model of integrated visuomotor decisions provides a powerful approach to investigate behavioral disorders that impair the ability to use sensory inputs to guide appropriate actions.
A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici
Authors: Badet Thomas , Oggenfuss Ursula , Abraham Leen , McDonald Bruce A. , Croll Daniel
Published: October 2019

Background

The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures.

Results

Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ∼60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable elements content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species.

Conclusions

Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.
From sectors to speckles: The impact of long-range migration on gene surfing
Authors: Paulose Jayson , Hallatschek Oskar
Published: October 2019

Range expansions lead to distinctive patterns of genetic variation in populations, even in the absence of selection. These patterns and their genetic consequences have been well-studied for populations advancing through successive short-ranged migration events. However, most populations harbor some degree of long-range dispersal, experiencing rare yet consequential migration events over arbitrarily long distances. Although dispersal is known to strongly affect spatial genetic structure during range expansions, the resulting patterns and their impact on neutral diversity remain poorly understood. Here, we systematically study the consequences of long-range dispersal on patterns of neutral variation during range expansion in a class of dispersal models which spans the extremes of local (effectively short-ranged) and global (effectively well-mixed) migration. We find that sufficiently long-ranged dispersal leaves behind a mosaic of monoallelic patches, whose number and size are highly sensitive to the distribution of dispersal distances. We develop a coarse-grained model which connects statistical features of these spatial patterns to the evolution of neutral diversity during the range expansion. We show that growth mechanisms that appear qualitatively similar can engender vastly different outcomes for diversity: depending on the tail of the dispersal distance distribution, diversity can either be preserved (i.e. many variants survive) or lost (i.e. one variant dominates) at long times. Our results highlight the impact of spatial and migratory structure on genetic variation during processes as varied as range expansions, species invasions, epidemics, and the spread of beneficial mutations in established populations.
Identification of a core module for bone mineral density through the integration of a co-expression network and GWAS data
Authors: Sabik Olivia L , Calabrese Gina M , Taleghani Eric , Ackert-Bicknell Cheryl L , Farber Charles R
Published: October 2019

Recently, the “omnigenic” model of the genetic architecture of complex traits proposed two general categories of causal genes, core and peripheral. Core genes are hypothesized to play a direct role in regulating disease; thus, their identification has the potential to reveal critical regulators and novel therapeutic targets. Here, we sought to identify genes with “core-like” characteristics for bone mineral density (BMD), one of the most significant predictors of osteoporotic fracture. This was accomplished by analyzing genome-wide association study (GWAS) data through the lens of a cell-type and timepoint-specific gene co-expression network for mineralizing osteoblasts. We identified a single co-expression network module that was enriched for genes implicated by GWAS and partitioned BMD heritability, correlated with in vitro osteoblast mineralization, and enriched for genes, which when mutated in humans or mice, led to a skeletal phenotype. Further characterization of this module identified four novel genes (B4GALNT3, CADM1, DOCK9, and GPR133) located within BMD GWAS loci with colocalizing expression quantitative trait loci (eQTL) and altered BMD in mouse knockouts, suggesting they are causal genetic drivers of BMD in humans. Our network-based approach identified a “core” module for BMD and provides a resource for expanding our understanding of the genetics of bone mass.
Robust Estimation of Bacterial Cell Count from Optical Density
Authors: Beal Jacob , Farny Natalie G. , Haddock-Angelli Traci , Selvarajah Vinoo , Baldwin Geoff S. , Buckley-Taylor Russell , Gershater Markus , Kiga Daisuke , Marken John , Sanchania Vishal , Sison Abigail , Workman Christopher T. ,   the iGEM Interlab Study Contributors
Published: October 2019

Optical density (OD) is a fast, cheap, and high-throughput measurement widely used to estimate the density of cells in liquid culture. These measurements, however, cannot be compared between instruments without a standardized calibration protocol and are challenging to relate to actual cell count. We address these shortcomings with an interlaboratory study comparing three OD calibration protocols, as applied to eight strains of E. coli engineered to constitutively express varying levels of GFP. These three protocols—comparison with colloidal silica (LUDOX), serial dilution of silica microspheres, and a reference colony-forming unit (CFU) assay—are all simple, low-cost, and highly accessible. Based on the results produced by the 244 teams completing this interlaboratory study, we recommend calibrating OD using serial dilution of silica microspheres, which readily produces highly precise calibration (95.5% of teams having residuals less than 1.2-fold), is easily assessed for quality control, and as a side effect also assesses the effective linear range of an instrument. Moreover, estimates of cell count from silica microspheres can be combined with fluorescence calibration against fluorescein to obtain units of Molecules of Equivalent Fluorescein (MEFL), allowing direct comparison and data fusion with equivalently calibrated flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
Significant improvement of reprogramming efficiency by transient overexpression of ZGA inducer Dux but not Dppa2/4
Authors: Yang Lei , Liu Xuefei , Song Lishuang , Di Anqi , Su Guanghua , Bai Chunling , Wei Zhuying , Li Guangpeng
Published: October 2019

Cloned animal have been reported by somatic cell nuclear transfer (SCNT) for many years. However, the SCNT is extremely inefficient, and zygotic genome activation (ZGA) is required for SCNT and chemical mediated reprogramming. To identify candidate factors that facilitate ZGA in reprogramming, we performed siRNA-repressor and mRNA-inducer screening, which revealed Dux, Dppa2, and Dppa4 as key factors enhancing the ZGA in SCNT. Direct injection of ZGA-inducers had no significant effect on the SCNT blastocyst formation, and even destroyed the ZGA. Through a inducible Dux transgenic mouse model, we demonstrate that transient overexpression of Dux not only improved SCNT efficiency, but also increased the efficiency of chemical reprogramming. Transcriptome profiling revealed that Dux treated SCNT embryos were similar to fertilized embryos. Furthermore, transient overexpression of Dux combined with inactivation of DNA methyltransferases (Dnmts) further promote the overall development of SCNT-derived animals. These findings enhance our understanding of ZGA-regulators in somatic reprogramming.
Oscillation-driven memory encoding, maintenance and recall in an entorhinal-hippocampal circuit model
Authors: Kurikawa Tomoki , Mizuseki Kenji , Fukai Tomoki
Published: October 2019

During the execution of working memory tasks, task-relevant information is processed by local circuits across multiple brain regions. How this multi-area computation is conducted by the brain remains largely unknown. To explore such mechanisms in spatial working memory, we constructed a neural network model involving parvalbumin-positive, somatostatin-positive and vasoactive intestinal polypeptide-positive interneurons in the hippocampal CA1 and the superficial and deep layers of medial entorhinal cortex (MEC). Our model is based on a hypothesis that cholinergic modulations differently regulate information flows across CA1 and MEC at memory encoding, maintenance and recall during delayed nonmatching-to-place tasks. In the model, theta oscillation coordinates the proper timing of interactions between these regions. Furthermore, the model predicts that MEC is engaged in decoding as well as encoding spatial memory, which we confirmed by experimental data analysis. Thus, our model accounts for the neurobiological characteristics of the cross-area information routing underlying working memory tasks.
Evolutionary regain of lost gene circuit function
Authors: Gouda Mirna Kheir , Manhart Michael , Balázsi Gábor
Published: October 2019

Evolutionary reversibility - the ability to regain a lost function - is an important problem both in evolutionary and synthetic biology, where repairing natural or synthetic systems broken by evolutionary processes may be valuable. Here, we use a synthetic positive-feedback (PF) gene circuit integrated into haploidSaccharomyces cerevisiaecells to test if the population can restore lost PF function. In previous evolution experiments, mutations in a gene eliminated the fitness costs of PF activation. Since PF activation also provides drug resistance, exposing such compromised or broken mutants to both drug and inducer should create selection pressure to regain drug resistance and possibly PF function. Indeed, evolving seven PF mutant strains in the presence of drug revealed three adaptation scenarios through genomic mutations outside of the PF circuit that elevate PF basal expression, possibly by affecting transcription, translation, degradation and other fundamental cell functions. Nonfunctional mutants gained drug resistance without ever developing high expression, while quasi-functional and dysfunctional PF mutants developed high expression which then diminished, although more slowly for dysfunctional mutants where revertant clones arose. These results highlight how intracellular context, such as the growth rate, can affect regulatory network dynamics and evolutionary dynamics, which has important consequences for understanding the evolution of drug resistance and developing future synthetic biology applications.

Significance Statement

Natural or synthetic genetic modules can lose their function over long-term evolution if the function is costly. How populations can evolve to restore broken functions is poorly understood. To test the reversibility of evolutionary breakdown, we use yeast cell populations with a chromosomally integrated synthetic gene circuit. In previous evolution experiments the gene circuit lost its costly function through various mutations. By exposing such mutant populations to conditions where regaining gene circuit function would be beneficial we find adaptation scenarios with or without repairing lost gene circuit function. These results are important for drug resistance or future synthetic biology applications where loss and regain of function play a significant role.
A Mechanical Model of Early Somite Segmentation
Authors: Adhyapok Priyom , Piatkowska Agnieszka M , Norman Michael J , Clendenon Sherry G , Stern Claudio D , Glazier James A , Belmonte Julio M
Published: October 2019

The clock-and-wavefront model (CW) hypothesizes that the formation of somites in vertebrate embryos results from the interplay of molecular oscillations with a wave traveling along the body axis. This model however does not explain how molecular information is interpreted by cells to modulate their rearrangement into somites. Here we performed Scanning Electron Microscopy (SEM) on the pre-somitic mesoderm (PSM) of chicken embryos at stages 11-12 to describe in detail the cell shape changes occurring along the axis of the PSM. This reveals a wave of epithelialization of the dorsal PSM that precedes somite segmentation. Signs of spatially periodic apical constriction appear in this layer starting at least 3-4 somite lengths caudal to the most recently formed somite. The sizes of these clusters correspond to the typical diameter of chicken somites. We propose that a mechanical instability process leads to the separation of cells into these structures and positions the future inter-somite boundaries. We present a model in which a wave of apical constriction leads to increasing tension and periodic failure of adhesion junctions within the dorsal epithelial layer of the PSM, thus positioning somite boundaries. This model can produce spatially periodic segments whose size depends on the speed of the contraction wave (W) and the rate of increase of apical contractility (Λ). The Λ/W ratio determines whether this mechanism produces spatially and temporally regular or irregular segments, and whether segment sizes increase with the wave speed (scaling) as in the CW model. We discuss the limitations of a purely mechanical model of somite segmentation and the role of biomechanics along with CW during somitogenesis.
From aura to jargon: the social life of authentication
Authors: Södergren Jonatan
Published: October 2019

Purpose

Authenticity has emerged as a prevailing purchase criterion that seems to include both real and stylised versions of the truth. The purpose of this paper is to address the negotiation of authenticity by examining the means by which costume designers draw on cues such as historical correctness and imagination to authenticate re-enactments of historical epochs in cinematic artwork.

Design/methodology/approach

To understand and analyse how different epochs were re-enacted required interviewing costume designers who have brought reimagined epochs into being. The questions were aimed towards acknowledging the socio-cultural circulation of images that practitioners draw from in order to project authenticity. This study was conducted during a seven-week internship at a costume store called Independent Costume in Stockholm as part of a doctoral course in cultural production.

Findings

Authenticity could be found in citations that neither had nor resembled something with an indexical link to the original referent as long as the audience could make a connection to the historical epoch sought to re-enact. As such, it would seem that imagination and historical correctness interplay in impressions of authenticity. Findings suggest that performances of authentication are influenced by socially instituted discursive practices (i.e. jargons) and collective imagination.

Originality/value

This paper contributes to the literature on social and performative aspects of authentication as well as its implications for brands in the arts and culture sector.
How website browsing impacts expectations of store features
Authors: Loupiac Philippine , Goudey Alain
Published: October 2019

Purpose

E-commerce has become a key component of brand retail strategies since the advent of omni-channel distributions. Many researchers have investigated the strategic role of e-commerce, and some recent articles show the importance of exploring the impact of this distribution model on consumer behaviour. However, there is no study focusing on how visits to a website create expectations of the shop. Relying on the expectancy-value theory and the omni-channel literature, the purpose of this paper is to fill this gap by focusing on how the digital channel can create expectations for the physical channel.

Design/methodology/approach

This study is based on 24 semi-directive interviews with consumers, and all interviews included a browsing session on a real website. The methodology consists of both a thematic analysis of the interviews and a lexicographic analysis of the verbatim.

Findings

The findings reveal that direct online experience on a website will create beliefs about the physical stores of the same brand. These beliefs will, in turn, influence consumer attitudes towards the store. The study is the first to highlight such a link between channels and to explain in detail how this relationship arises.

Originality/value

The main contribution of this work includes showing the existence of a strong link between web-based and physical retail. From a managerial perspective, the study suggests that, from an omni-channel perspective, the design of the website impacts expectations towards the physical store in terms of its atmosphere, its location, its merchandising and even its level of crowding.
Exploring the effect of internal and external integration on the performance of professional service outsourcing
Authors: Liu Zuoming , Jayaraman Vaidyanathan
Published: October 2019

Purpose

This paper aims to investigate how the professional service outsourcing (PSO) firm’s external knowledge integration with global clients, internal integration across various functional units and the synergistic effects between them in improving PSO performance.

Design/methodology/approach

Drawing on the theory of organizational learning, a conceptual framework is proposed with hypothesized relationships. The relationships in this conceptual model were tested using a structural equation model (SEM) to analyze a survey dataset including 192 Indian-based professional service providers.

Findings

A service provider’s performance is positively associated with its external integration with global clients and internal integration across various functional units. Synergistic effect is generated from balanced high-level external and internal integration in improving PSO performance.

Research limitations/implications

This study contributes to the much-needed efforts in studying PSO, a new and fast-growing cross-border professional service activity, and provides helpful managerial implications to practicing global clients and offshore PSO service providers on how to successfully manage and govern the outsourcing process to achieve expected benefits.

Originality/value

This study focuses on offshore service provider’s viewpoint to extend traditional supply-chain integration regarding cooperative and mutually beneficial mechanisms to the context of PSO.
Excess body weight and abdominal obesity in relation to selected psychosocial characteristics in primary school children
Authors: Vassiloudis Ioannis , Costarelli Vassiliki
Published: October 2019

Purpose

The purpose of this paper is to investigate excess body weight and abdominal obesity in relation to selected psychosocial characteristics such as self-perception, self-esteem and anxiety, in primary school children.

Design/methodology/approach

A school-based cross-sectional study was conducted with a total of 528 students 10-12 years of age, randomly selected, from the area of Athens, Greece. The Greek versions of the self-perception profile for children (SPPC) and the state-trait anxiety inventory for children (STAI-C) questionnaires have been used to determine the children’s self-perception/self-esteem and the status of anxiety, respectively. Standard anthropometric measurements were also taken. Pearson correlation coefficient was used to test for possible linear correlations between data variables. One-way ANOVA and independentt-test were used to determine statistically significant differences between the means of children’s body mass index (BMI) – abdominal obesity groups. For multiple comparisons, Bonferroni post-tests were run.

Findings

Overweight and obese children and children with abdominal obesity had lower scores in all of the domains of SPPC self-perception, the SPPC global self-esteem and the STAI-C anxiety levels in comparison to normal weight children. BMI and abdominal obesity correlated negatively with each one of the five domains of the SPPC self-perception (p < 0.001) and the SPPC global self-esteem (p < 0.001) and positively with the STAI-C anxiety levels (p < 0.005). One-way ANOVA and independentt-test revealed statistically significant differences between the means of children’s BMI and abdominal obesity groups in all the domains of SPPC self-perception (p < 0.001), the SPPC global self-esteem (p < 0.001) and the STAI-C anxiety levels (p < 0.005). There were no gender differences in the psychometric characteristics assessed in this study.

Originality/value

Primary school children with excess body weight and abdominal obesity have increased anxiety levels and they score lower in key psychosocial characteristics, in comparison to normal weight children.
Buying a family car: relevant factors for teenagers
Authors: de Sa Joao Duarte Saleme , Mainardes Emerson Wagner , Andrade Daniel Modenesi de
Published: October 2019

Purpose

The purpose of this paper is to find out the relevant factors, according to teenagers, that influence the buying decision of the family car.

Design/methodology/approach

Research carried out in three stages: one qualitative research (by using focal groups), and two quantitative research studies (descriptive and cross-sectional).

Findings

The authors identified three factors that are important for teenagers when influencing the purchase of the family car: safety, sportiness and comfort. The identification of these factors shows that the millennial generation tends to emphasize aspects of individual interest, such as status and performance, and family context, such as safety and comfort, rather than social aspects, such as the type of fuel and environmental impact.

Practical implications

The authors recommend the development of automobiles that prioritize the three factors mentioned herein in order to reverse the trend of declining car purchase.

Originality/value

The authors presented the relevant attributes in buying decisions of family cars according to teenagers. The authors also indicated the automobile attributes that are relevant for a more informed, connected, and with an increasing purchase power generation in contrast with previous generations, whose social context was prior to the emergence of social media.