bluuebunny/crossref_metadata_2025 huggingface dataset:
Empirical measures of mutational effects define neutral models of regulatory evolution inSaccharomyces cerevisiae
Authors: Hodgins-Davis Andrea , Duveau Fabien , Walker Elizabeth , Wittkopp Patricia J
Published: February 2019

Understanding how phenotypes evolve requires disentangling the effects of mutation generating new variation from the effects of selection filtering it. Evolutionary models frequently assume that mutation introduces phenotypic variation symmetrically around the population mean, yet few studies have tested this assumption by deeply sampling the distributions of mutational effects for particular traits. Here, we examine distributions of mutational effects for gene expression in the budding yeastSaccharomyces cerevisiaeby measuring the effects of thousands of point mutations introduced randomly throughout the genome. We find that the distributions of mutational effects differ for the 10 genes surveyed and violate the assumption of normality. For example, all ten distributions of mutational effects included more mutations with large effects than expected for normally distributed phenotypes. In addition, some genes also showed asymmetries in their distribution of mutational effects, with new mutations more likely to increase than decrease the gene’s expression or vice versa. Neutral models of regulatory evolution that take these empirically determined distributions into account suggest that neutral processes may explain more expression variation within natural populations than currently appreciated.

Significance statement

New mutations tend to arise randomly throughout the genome, but their phenotypic effects are often not random. This disconnect results from interactions among genes that define the genotype-phenotype map. The structure of this map is poorly known and different for each trait, making it challenging to predict the distribution of mutational effects for specific phenotypes. Empirical measures of the distribution of mutational effects are thus necessary to understand how traits can change in the absence of natural selection. In this work, we define such distributions for expression of ten genes inS. cerevisiaeand show that they predict greater neutral expression divergence than commonly used models of phenotypic evolution.
Modeling ribosome dwell times and relationships with tRNA loading and codon usage in mammals
Authors: Gobet Cédric , Weger Benjamin , Marquis Julien , Martin Eva , Gachon Frederic , Naef Felix
Published: February 2019

Protein translation depends on mRNA-specific initiation, elongation and termination rates. While the regulation of ribosome elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here, we combined ribosome and tRNA profiling to investigate the relations between ribosome elongation rates, (aminoacyl-) tRNA levels and codon usage in mammals. We modeled codon-specific ribosome dwell times and translation fluxes from ribosome profiling, considering pair-interactions between ribosome sites. In mouse liver, the model revealed site and codon specific dwell times, as well as codon pair-interactions clustering by amino acids. While translation fluxes varied significantly across diurnal time and feeding regimen, codon dwell times were highly stable, and conserved in human. Fasting had no effect on codon dwell times in mouse liver. Profiling of total and aminoacyl-tRNAs revealed highly heterogeneous levels that correlated with codon usage and showed specific isoacceptor patterns. tRNAs for several amino acids were lowly loaded, which was conserved in fasted mice. Finally, codons with low levels of charged tRNAs and high codon usage relative to tRNA abundance exhibited long dwell times. Together, these analyses pave the way towards understanding the complex interactions between tRNA loading, codon usage and ribosome dwell times in mammals.
Genetic variation influences pluripotent ground state stability in mouse embryonic stem cells through a hierarchy of molecular phenotypes
Authors: Skelly Daniel A. , Czechanski Anne , Byers Candice , Aydin Selcan , Spruce Catrina , Olivier Chris , Choi Kwangbom , Gatti Daniel M. , Raghupathy Narayanan , Stanton Alexander , Vincent Matthew , Dion Stephanie , Greenstein Ian , Pankratz Matthew , Porter Devin K. , Martin Whitney , Qin Wenning , Harrill Alison H. , Choi Ted , Churchill Gary A. , Munger Steven C. , Baker Christopher L. , Reinholdt Laura G.
Published: February 2019

Mouse embryonic stem cells (mESCs) cultured under controlled conditions occupy a stable ground state where pluripotency-associated transcriptional and epigenetic circuitry are highly active. However, mESCs from some genetic backgrounds exhibit metastability, where ground state pluripotency is lost in the absence of ERK1/2 and GSK3 inhibition. We dissected the genetic basis of metastability by profiling gene expression and chromatin accessibility in 185 genetically heterogeneous mESCs. We mapped thousands of loci affecting chromatin accessibility and/or transcript abundance, including eleven instances where distant QTL co-localized in clusters. For one cluster we identifiedLifrtranscript abundance as the causal intermediate regulating 122 distant genes enriched for roles in maintenance of pluripotency. Joint mediation analysis implicated a single enhancer variant ~10kb upstream ofLifrthat alters chromatin accessibility and precipitates a cascade of molecular events affecting maintenance of pluripotency. We validated this hypothesis using reciprocal allele swaps, revealing mechanistic details underlying variability in ground state metastability in mESCs.
Large, three-generation CEPH families reveal post-zygotic mosaicism and variability in germline mutation accumulation
Authors: Sasani Thomas A. , Pedersen Brent S. , Gao Ziyue , Baird Lisa , Przeworski Molly , Jorde Lynn B. , Quinlan Aaron R.
Published: February 2019

The number of de novo mutations (DNMs) found in an offspring’s genome is known to increase with both paternal and maternal age. But does the rate of mutation accumulation in parental gametes differ across families? To answer this question, we analyzed DNMs in 33 large, three-generation families collected in Utah by the Centre d’Etude du Polymorphisme Humain (CEPH) consortium. We observed significant variability in parental age effects on DNM counts across families, ranging from 0.24 to 3.33 additional DNMs per year. Using up to 14 grandchildren in these families, we find that 3% of DNMs originated following primordial germ cell specification (PGCS) in a parent, and differ from non-mosaic germline DNMs in their mutational spectra. We also identify a median of 3 gonosomal mutations per sample in the F1 generation, which, along with post-PGCS DNMs, occur at equivalent frequencies on the paternal and maternal haplotypes. These results demonstrate that the rate of germline mutation accumulation varies among families with similar ancestry, and confirm that parental mosaicism is a substantial source of de novo mutations in children.

Data and code availability

Code used for statistical analysis and figure generation has been deposited on GitHub as a collection of annotated Jupyter Notebooks:https://github.com/quinlan-lab/ceph-dnm-manuscript. Data files containing germline de novo mutations, as well as the gonosomal and post-primordial germ cell specification (PGCS) mosaic mutations, are included with these Notebooks. To mitigate compatibility/version issues, we have also made all notebooks available in a Binder environment, accessible at the above GitHub repository.
High-Fidelity Nanopore Sequencing of Ultra-Short DNA Sequences
Authors: Wilson Brandon D. , Eisenstein Michael , Soh H. Tom
Published: February 2019

Nanopore sequencing offers a portable and affordable alternative to sequencing-by-synthesis methods but suffers from lower accuracy and cannot sequence ultra-short DNA. This puts applications such as molecular diagnostics based on the analysis of cell-free DNA or single-nucleotide variants (SNV) out of reach. To overcome these limitations, we report a nanopore-based sequencing strategy in which short target sequences are first circularized and then amplified via rolling-circle amplification to produce long stretches of concatemeric repeats. These can be sequenced on the Oxford Nanopore Technology’s (ONT) MinION platform, and the resulting repeat sequences aligned to produce a highly-accurate consensus that reduces the high error-rate present in the individual repeats. Using this approach, we demonstrate for the first time the ability to obtain unbiased and accurate nanopore data for target DNA sequences of < 100 bp. Critically, this approach is sensitive enough to achieve SNV discrimination in mixtures of sequences and even enables quantitative detection of specific variants present at ratios of < 10%. Our method is simple, cost-effective, and only requires well-established processes. It therefore expands the utility of nanopore sequencing for molecular diagnostics and other applications, especially in resource-limited settings.

One Sentence Summary

We introduce a simple method of accurately sequencing ultra-short (<100bp) target DNA on a nanopore sequencing platform.
Evolutionary dynamics of phage resistance in bacterial biofilms
Authors: Simmons Matthew , Bond Matthew C. , Drescher Knut , Bucci Vanni , Nadell Carey D.
Published: February 2019

Interactions among bacteria and their viral predators, the bacteriophages, are likely among the most common ecological phenomena on Earth. The constant threat of phage infection to bacterial hosts, and the imperative of achieving infection on the part of phages, drives an evolutionary contest in which phage-resistant bacteria emerge, often followed by phages with new routes of infection. This process has received abundant theoretical and experimental attention for decades and forms an important basis for molecular genetics and theoretical ecology and evolution. However, at present, we know very little about the nature of phage-bacteria interaction – and the evolution of phage resistance – inside the surface-bound communities that microbes usually occupy in natural environments. These communities, termed biofilms, are encased in a matrix of secreted polymers produced by their microbial residents. Biofilms are spatially constrained such that interactions become limited to neighbors or near-neighbors; diffusion of solutes and particulates is reduced; and there is pronounced heterogeneity in nutrient access and therefore physiological state. These factors can dramatically impact the way phage infections proceed even in simple, single-strain biofilms, but we still know little of their effect on phage resistance evolutionary dynamics. Here we explore this problem using a computational simulation framework customized for implementing phage infection inside multi-strain biofilms. Our simulations predict that it is far easier for phage-susceptible and phage-resistant bacteria to coexist inside biofilms relative to planktonic culture, where phages and hosts are well-mixed. We characterize the negative frequency dependent selection that underlies this coexistence, and we then test and confirm this prediction using an experimental model of biofilm growth measured with confocal microscopy at single-cell and single-phage resolution.
Single-cell activity in human STG during perception of phonemes is organized according to manner of articulation
Authors: Lakretz Yair , Ossmy Ori , Friedmann Naama , Mukamel Roy , Fried Itzhak
Published: February 2019

A long-standing controversy persists in psycholinguistic research regarding the way phonemes are coded in human auditory cortex during speech perception. Whereas the motor theory of speech perception suggests that phonemes are organized in terms of common articulatory gestures that generate them, auditory theories argue that phonetic processing is organized based on common spectro-temporal patterns in phoneme waveforms. Here, we recorded spiking activity in the superior temporal gyrus (STG) from six neurosurgical patients who performed a listening task with phoneme stimuli. Using a Naïve-Bayes model, we show that single-cell responses to phonemes are governed by articulatory features that have acoustic correlates (manner-of-articulation) and organized according to sonority, with two main clusters for sonorants and obstruents. We further find that ‘neural similarity’ (i.e. the similarity of evoked spiking activity between pairs of phonemes), is comparable to the ‘perceptual similarity’ (i.e. how much the pair of phonemes sound similar) based on perceptual confusion assessed behaviorally in healthy subjects. Thus phonemes that were perceptually similar, also had similar neural responses. Our findings establish that phonemes are encoded according to manner-of-articulation, supporting the auditory theories of perception, and that the perceptual representation of phonemes can be reflected by the activity of single neurons in STG.
Polar relaxation by dynein-mediated removal of cortical myosin II
Authors: Chapa-y-Lazo Bernardo , Hamanaka Motonari , Wray Alexander , Balasubramanian Mohan K. , Mishima Masanori
Published: February 2019

Nearly 6 decades ago, Lewis Wolpert proposed the relaxation of the polar cell cortex by the radial arrays of astral microtubules as a mechanism for cleavage furrow induction (White and Borisy, 1983; Wolpert, 1960). While this mechanism has remained controversial (Rappaport, 1996), recent work has provided evidence for polar relaxation by astral microtubules (Chen et al., 2008; Dechant and Glotzer, 2003; Foe and Dassow, 2008; Murthy and Wadsworth, 2008; Werner et al., 2007), although its molecular mechanisms remain elusive. Here, using C. elegans embryos, we show that polar relaxation is achieved through dynein-mediated removal of myosin II from the polar cortexes. Mutants that position centrosomes closer to the polar cortex accelerated furrow induction whereas suppression of dynein activity delayed furrowing. We provide evidence that dynein-mediated removal of myosin II from the polar cortexes triggers cortical flow towards the cell equator, which induces the assembly of the actomyosin contractile ring. These studies for the first time provide a molecular basis for the aster-dependent polar relaxation, which works in parallel with equatorial stimulation to promote robust cytokinesis.
Protein tertiary structure modeling driven by deep learning and contact distance prediction in CASP13
Authors: Hou Jie , Wu Tianqi , Cao Renzhi , Cheng Jianlin
Published: February 2019

Prediction of residue-residue distance relationships (e.g. contacts) has become the key direction to advance protein tertiary structure prediction since 2014 CASP11 experiment, while deep learning has revolutionized the technology for contact and distance distribution prediction since its debut in 2012 CASP10 experiment. During 2018 CASP13 experiment, we enhanced our MULTICOM protein structure prediction system with three major components: contact distance prediction based on deep convolutional neural networks, contact distance-driven template-free (ab initio) modeling, and protein model ranking empowered by deep learning and contact prediction, in addition to an update of other components such as template library, sequence database, and alignment tools. Our experiment demonstrates that contact distance prediction and deep learning methods are the key reasons that MULTICOM was ranked 3rd out of all 98 predictors in both template-free and template-based protein structure modeling in CASP13. Deep convolutional neural network can utilize global information in pairwise residue-residue features such as co-evolution scores to substantially improve inter-residue contact distance prediction, which played a decisive role in correctly folding some free modeling and hard template-based modeling targets from scratch. Deep learning also successfully integrated 1D structural features, 2D contact information, and 3D structural quality scores to improve protein model quality assessment, where the contact prediction was demonstrated to consistently enhance ranking of protein models for the first time. The success of MULTICOM system in the CASP13 experiment clearly shows that protein contact distance prediction and model selection driven by powerful deep learning holds the key of solving protein structure prediction problem. However, there are still major challenges in accurately predicting protein contact distance when there are few homologous sequences to generate co-evolutionary signals, folding proteins from noisy contact distances, and ranking models of hard targets.
Interneuron functional diversity in the mouse accessory olfactory bulb
Authors: Maksimova Marina A. , Cansler Hillary L. , Zuk Kelsey E. , Torres Jennifer M. , Roberts Dylan J. , Meeks Julian P.
Published: February 2019

Abstract/Summary

In the mouse accessory olfactory bulb (AOB), inhibitory interneurons play an essential role in gating behaviors elicited by sensory exposure to social odors. Several morphological classes have been described, but the full complement of interneurons remains incomplete. In order to develop a more comprehensive view of interneuron function in the AOB, we performed targeted patch clamp recordings from partially-overlapping subsets of genetically-labeled and morphologically-defined interneuron types.Gad2(GAD65),Calb2(calretinin), andCort(cortistatin)-cre mouse lines were used to drive selective expression of tdTomato in AOB interneurons.Gad2andCalb2-labeled interneurons were found in the internal, external, and glomerular layers, whereasCort-labeled interneurons were enriched within the lateral olfactory tract (LOT) and external cellular layer (ECL). We found that external granule cells (EGCs) from all genetically-labeled subpopulations possessed intrinsic functional differences that allowed them to be readily distinguished from internal granule cells (IGCs). EGCs showed stronger voltage-gated Na+and non-inactivating voltage-gated K+currents, decreased IHcurrents, and robust excitatory synaptic input. These specific intrinsic properties did not correspond to any genetically-labeled type, suggesting that transcriptional heterogeneity among EGCs and IGCs is not correlated with expression of these particular marker genes. Intrinsic heterogeneity was also seen among AOB juxtaglomerular cells (JGCs), with a major subset ofCalb2-labeled JGCs exhibiting spontaneous and depolarization-evoked plateau potentials. These data identify specific physiological features of AOB interneurons types that will assist in future studies of AOB function.

Significance Statement

The mouse accessory olfactory bulb (AOB) plays a critical role in processing social chemosensory information. Several morphologically-identified types of AOB inhibitory interneurons are thought to refine and restrict information flow from the AOB to its downstream targets in the limbic system. However, little is known about the electrophysiological and transcriptional diversity among AOB interneuron types. We systematically investigated intrinsic electrophysiological diversity across 5 AOB cell populations in three transgenic mouse lines. Analysis of 26 intrinsic physiological features revealed feature combinations associated with identified morphological AOB cell types, but few associated with the transgenic lines we studied. The results provide quantitative information about functional diversity in AOB interneurons and provide an improved foundation for future studies of AOB circuit function.
Quantifying the dynamics of hematopoiesis byin vivoIdU pulse-chase, mass cytometry and mathematical modeling
Authors: Erez Amir , Mukherjee Ratnadeep , Day Alexandre , Mehta Pankaj , Altan-Bonnet Grégoire
Published: February 2019

We present a new method to directly quantify the dynamics of differentiation of multiple cellular subsets in unperturbed mice. We combine a pulse-chase protocol of IdU injections with subsequent analysis by mass cytometry (CyTOF), and mathematical modeling of the IdU dynamics. Measurements by CyTOF allow for a wide range of cells to be analyzed at once, due to the availability of a large staining panel without the complication of fluorescence spill-over. These are also compatible with direct detection of integrated iodine signal, with minimal impact on immunophenotyping based on surface markers. Mathematical modeling beyond a binary classification of surface marker abundance allows for a continuum of cellular states as the cells transition from one state to another. Thus, we present a complete and robust method for directly quantifying differentiation at the systemic level, allowing for system-wide comparisons between different mouse strains and/or experimental conditions.
Ouabain enhances cell-cell adhesion mediated by β1-subunits of the Na+,K+-ATPase in CHO fibroblasts
Authors: Vilchis-Nestor Claudia Andrea , Roldán María Luisa , Padilla-Benavides Teresita , Shoshani Liora
Published: February 2019

Adhesion is an important characteristic of epithelial cells to provide a crucial barrier to pathogens and substances. In polarized epithelial cells, cell-adhesion depends on tight junctions, adherent junctions and the Na+,K+-ATPase. All these are located in the basolateral membrane of the cells. The hormone ouabain, a cardiotonic steroid, binds to the α subunit of the Na+,K+-ATPase, and inhibits the pump activity when used at above μM concentrations. At physiological nM concentrations, ouabain affects the adhesive properties of epithelial cells by inducing the expression of cell adhesion molecules through activation of signaling pathways associated to the α subunit. Our group showed that non-adherent CHO cells transfected with the canine β1subunit become adhesive, and that homotypic interactions between β1subunits of the Na+,K+-ATPase occur between neighboring epithelial cells. Therefore, in this study we investigated whether the adhesion between β1subunits was also affected by ouabain. We used CHO fibroblasts stably expressing the β1subunit of the Na+,K+-ATPase (CHO-β1) and studied the effect of ouabain on cell adhesion. Aggregation assays showed that ouabain increased the adhesion between CHO-β1cells. Immunofluorescence and biotinylation assays showed that ouabain (50 nM) increases the expression of the β1 subunit of the Na+,K+-ATPase at the cell membrane. We also screened the effect of ouabain on activation of signaling pathways in CHO-β1cells, and their effect on cell adhesion. We found that c-Src, is activated by ouabain and is therefore likely to regulate the adhesive properties of CHO-β1cells. Collectively, our findings suggest that the β1subunits adhesion is modulated by the levels of expression and activation of the Na+,K+-ATPase at the plasma membrane, which is regulated by ouabain.
An Interscholastic Network to Generate LexA Enhancer Trap Lines inDrosophila
Authors: Kockel Lutz , Griffin Catherine , Ahmed Yaseen , Fidelak Lauren , Rajan Arjun , Gould Ethan P. , Haigney Miles , Ralston Benjamin , Tercek Rex J. , Galligani Lara , Rao Sagar , Huq Lutfi , Bhargava Hersh K. , Dooner Ailis C. , Lemmerman Emily G. , Malusa Ruby F. , Nguyen Tran H. , Chung Julie S. , Gregory Sara M. , Kuwana Kiyomasa M. , Regenold Jonathan T. , Wei Alexander , Ashton Jake , Dickinson Patrick , Kim Steven , Martel Kate , Cai Connie , Chen Carissa , Price Stephen , Qiao Jeffrey , Shepley David , Zhang Joanna , Chalasani Meghana , Nguyen Khanh , Aalto August , Kim ByungJun , Tazawa-Goodchild Erik , Sherwood Amanda , Rahman Ahmad , Wu Sum Ying Celeste , Lotzkar Joel , Michaels Serena , Aristotle Hillary , Clark Antigone , Gasper Grace , Xiang Evan , Schlör Frieda Luna , Lu Melissa , Haering Kate , Friberg Julia , Kuwana Alyssa , Lee Jonathan , Liu Alan , Norton Emma , Hamad Leena , Lee Clara , Okeremi Dara , diTullio Harry , Dumoulin Kat , Chi Sun Yu Gordon , Derossi Grayson S. , Horowitch Rose E. , Issa Elias C. , Le Dan T. , Morales Bryce C. , Noori Ayush , Shao Justin , Cho Sophia , Hoang Mai N. , Johnson Ian M. , Lee Katherine C. , Lee Maria , Madamidola Elizabeth A. , Schmitt Katrina E. , Byan Gabriel , Park Taeyoung , Chen Jonathan , Monovoukas Alexi , Kang Madison J. , McGowan Tanner , Walewski Joseph J. , Simon Brennan , Zu Sophia J. , Miller Gregory P. , Fitzpatrick Kate B. , Lantz Nicole , Fox Elizabeth , Collette Jeanette , Kurtz Richard , Duncan Chris , Palmer Ryan , Rotondo Cheryl , Janicki Eric , Chisholm Townley , Rankin Anne , Park Sangbin , Kim Seung K.
Published: February 2019

Binary expression systems like the LexA-LexAop system provide a powerful experimental tool kit to study gene and tissue function in developmental biology, neurobiology and physiology. However, the number of well-defined LexA enhancer trap insertions remains limited. In this study, we present the molecular characterization and initial tissue expression analysis of nearly 100 novel StanEx LexA enhancer traps, derived from theStonEx1index line. This includes 76 insertions into novel, distinct gene loci not previously associated with enhancer traps or targeted LexA constructs. Additionally, our studies revealed evidence for selective transposase-dependent replacement of a previously-undetectedKPelement on chromosome III within the StanEx1genetic background during hybrid dysgenesis, suggesting a molecular basis for the over-representation of LexA insertions at theNK7.1locus in our screen. Production and characterization of novel fly lines were performed by students and teachers in experiment-based genetics classes within a geographically diverse network of public and independent high schools. Thus, unique partnerships between secondary schools and university-based programs have produced and characterized novel genetic and molecular resources inDrosophilafor open-source distribution, and provide paradigms for development of science education through experience-based pedagogy.
Extraction-free direct PCR from dried serum spots permits HBV genotyping and RAS identification by Sanger and minION sequencing
Authors: Astbury Stuart , Costa Nunes Soares Marcia Maria Da , Peprah Emmanuel , King Barnabas , Gomes Jardim Ana Carolina , Shimizu Jacqueline Farinha , Jalal Paywast , Saeed Chiman H , Sabeer Furat T , Irving William L , Tarr Alexander W , McClure C Patrick
Published: February 2019

In order to achieve the commitment made by the World Health Organisation to eliminate viral hepatitis by 2030, it is essential that clinicians can obtain basic sequencing data for hepatitis B virus (HBV) infected patients. While accurate diagnosis of HBV is achievable in most clinical settings, genotyping and identification of resistance-associated substitutions (RAS) present a practical challenge in regions with limited healthcare and biotechnology infrastructure. Here we outline two workflows for generating clinically relevant HBV sequence data directly from dried serum spot (DSS) cards without DNA extraction using either Sanger, or the portable MinION sequencing platforms. Data obtained from the two platforms were highly consistent and allowed determination of HBV genotype and RAS. This is the first demonstration of MinION sequencing from DSS, illustrating the broad utility of this sequencing technology. We demonstrated the clinical application of this technology using sera sampled on DSS cards obtained from both Iraq and Brazil. The sample stability provided by DSS cards, combined with the rapid PCR and sequencing protocols will enable regional/national centres to provide information relevant to patient management. By providing viable workflows for both the Sanger and MinION sequencing platforms, which vary greatly in the infrastructure and expertise required, we demonstrate that MinION sequencing is a viable method for HBV genotyping in resource-limited settings. These workflows could also be applied to sequencing of other blood borne DNA viruses and bacterial pathogens.
Cell type specific transcriptional reprogramming of maize leaves duringUstilago maydisinduced tumor formation
Authors: Villajuana-Bonequi Mitzi , Matei Alexandra , Ernst Corinna , Hallab Asis , Usadel Björn , Doehlemann Gunther
Published: February 2019

Ustilago maydisis a biotrophic pathogen and well-established genetic model to understand the molecular basis of biotrophic interactions.U. maydissuppresses plant defense and induces tumors on all aerial parts of its host plant maize. In a previous study we found thatU. maydisinduced leaf tumor formation builds on two major processes: the induction of hypertrophy in the mesophyll and the induction of cell division (hyperplasia) in the bundle sheath. In this study we analyzed the cell-type specific transcriptome of maize leaves 4 days post infection. This analysis allowed identification of key features underlying the hypertrophic and hyperplasic cell identities derived from mesophyll and bundle sheath cells, respectively. We examined the differentially expressed (DE) genes with particular focus on maize cell cycle genes and found that three A-type cyclins, one B-, D- and T-type are upregulated in the hyperplasic tumorous cells, in which theU. maydiseffector protein See1 promotes cell division. Additionally, most of the proteins involved in the formation of the pre-replication complex (pre-RC, that assure that each daughter cell receives identic DNA copies), the transcription factors E2Fand DPa as well as several D-type cyclins are deregulated in the hypertrophic cells.
Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing
Authors: Senabouth Anne , Andersen Stacey , Shi Qianyu , Shi Lei , Liu Ping , Jiang Feng , Zhang Wenwei , Wing Kristof , Daniszewski Maciej , Lukowski Samuel W , Hung Sandy SC , Nguyen Quan , Fink Lynn , Beckhouse Ant , Jiang Hui , Pébay Alice , Hewitt Alex W , Powell Joseph E
Published: February 2019

The libraries generated by high-throughput single cell RNA-sequencing platforms such as the Chromium from 10X Genomics require considerable amounts of sequencing, typically due to the large number of cells. The ability to use this data to address biological questions is directly impacted by the quality of the sequence data. Here we have compared the performance of the Illumina NextSeq 500 and NovaSeq 6000 against the BGI MGISEQ-2000 platform using identical Single Cell 3’ libraries consisting of over 70,000 cells. Our results demonstrate a highly comparable performance between the NovaSeq 6000 and MGISEQ-2000 in sequencing quality, and cell, UMI, and gene detection. However, compared with the NextSeq 500, the MGISEQ-2000 platform performs consistently better, identifying more cells, genes, and UMIs at equalised read depth. We were able to call an additional 1,065,659 SNPs from sequence data generated by the BGI platform, enabling an additional 14% of cells to be assigned to the correct donor from a multiplexed library. However, both the NextSeq 500 and MGISEQ-2000 detected similar frequencies of gRNAs from a pooled CRISPR single cell screen. Our study provides a benchmark for high capacity sequencing platforms applied to high-throughput single cell RNA-seq libraries.
In Silico Analysis and Modeling of Novel Pathogenic Single Nucleotide Polymorphisms (SNPs) in HumanCD40LGGene
Authors: Abdelmoneim Abdelrahman H. , Mustafa Mujahed I. , Mahmoud Thwayba A. , Murshed Naseem S. , Hassan Mohamed A.
Published: February 2019

Background:

The X-linked hyper-immunoglobulin M syndrome (XHIGM) is a rare, inherited immune deficiency disorder. It is more common in males. Characterized by elevated serum IgM levels and low to undetectable levels of serum IgG, IgA and IgE. Hyper-IgM syndrome is caused by mutations in theCD40LGgene. Located in human Xq26. CD40LG acts as an immune modulator in activated T cells.

Method:

We used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein.

Result:

8 novel SNPs out of 233 were found to have most deleterious effect on the protein structure and function.While modeling ofnsSNPs was studied by Project HOPE software.

Conclusion:

Better understanding of Hyper-IgM syndrome caused by mutations in CD40LG gene was achieved using in silico analysis. This is the first in silico functional analysis of CD40LG gene and 8 novel mutations were found using different bioinformatics tools, and they could be used as diagnostic markers for hyper-IgM syndrome. These 8 novel SNPs may be important candidates for the cause of different types of human diseases byCD40LGgene.
Bdnf promoter IV-expressing cells in the hippocampus modulate fear expression and hippocampal-prefrontal synchrony in mice
Authors: Hallock Henry L. , Quillian Henry M. , Mai Yishan , Maynard Kristen R. , Hill Julia L. , Martinowich Keri
Published: February 2019

Brain-derived neurotrophic factor (BDNF) signaling regulates synaptic plasticity in the hippocampus (HC) and prefrontal cortex (PFC), and has been extensively linked with fear memory expression in rodents. Notably, disrupting BDNF production from promoter IV-derived transcripts enhances fear expression in mice, and decreases fear-associated HC-PFC synchrony, suggesting that Bdnf transcription from promoter IV plays a key role in HC-PFC function during fear memory retrieval. To understand how promoter IV-derived BDNF affects fear expression and HC-PFC connectivity, we generated a viral construct that selectively targets cells expressing promoter IV-derived Bdnf transcripts (“p4-cells”) for tamoxifen-inducible Cre-mediated recombination (AAV8-p4Bdnf-ERT2CreERT2-PEST). Using this construct, we found that ventral (vHC) p4-cells are recruited during fear expression, and that activation of these cells causes exaggerated fear expression that co-occurs with disrupted vHC-PFC synchrony in mice. Our data highlight how this novel construct can be used to interrogate genetically-defined cell types that selectively contribute to BDNF-dependent behaviors.
SorCS1-mediated Sorting of Neurexin in Dendrites Maintains Presynaptic Function
Authors: Ribeiro Luís F. , Verpoort Ben , Nys Julie , Vennekens Kristel M. , Wierda Keimpe D. , Wit Joris de
Published: February 2019

The pre- and postsynaptic membranes comprising the synaptic junction differ in protein composition. The mechanisms that maintain the polarized distribution of synaptic membrane proteins are poorly understood. The sorting receptor SorCS1 is a critical trafficking regulator of neuronal receptors, including neurexin (Nrxn), a presynaptic adhesion molecule essential for synaptic transmission. We find that SorCS1 controls a balance between axonal and dendritic Nrxn1α surface levels. Newly synthesized Nrxn1α traffics to the somatodendritic surface, followed by endocytosis. SorCS1 interacts with the Rab11 effector protein Rab11FIP5/Rip11 to facilitate the transition of internalized Nrxn1α from early to recycling endosomes and bias Nrxn1α surface polarization toward the axon. In the absence of SorCS1, Nrxn1α accumulates in early endosomes and mis-polarizes to the dendritic surface, impairing presynaptic function. The axonal/dendritic balance of Nrxn1α surface distribution is activity-dependent, indicating that SorCS1-mediated sorting in somatodendritic endosomes dynamically controls Nrxn1α axonal surface polarization required for proper presynaptic function.
Generalized Rayleigh-Plesset Theory for Cell Size Maintenance in Viruses and Bacteria
Authors: Malmi-Kakkada Abdul N. , Thirumalai D.
Published: February 2019

The envelopes covering bacterial cytoplasm possess remarkable elastic properties. They are rigid enough to resist large pressures while being flexible enough to adapt to growth under environmental constraints. Similarly, the virus shells play an important role in their functions. However, the effects of mechanical properties of the outer shell in controlling and maintaining the sizes of bacteria or viruses are unknown. Here, we present a hydrodynamic “bubbles with shell” model, motivated by the study of bubble stability in fluids, to demonstrate that shell rigidity and turgor pressure control the sizes of bacteria and viruses. A dimensionless compliance parameter, expressed in terms of the Young’s modulus of the shell, its thickness and the turgor pressure, determines membrane response to deformation and the size of the organisms. By analyzing the experiment data, we show that bacterial and viral sizes correlate with shell elasticity, which plays a critical role in regulating size.
A test for Hardy-Weinberg equilibrium on the X chromosome for sex-biased admixed populations
Authors: Backenroth Daniel , Carmi Shai
Published: February 2019

Genome-wide scans for deviations from Hardy-Weinberg equilibrium (HWE) are commonly applied to detect genotyping errors. In contrast to the autosomes, genotype frequencies on the X chromosome do not reach HWE within a single generation. Instead, if allele frequencies in males and females initially differ, they oscillate for a few generations towards equilibrium. Several populations world-wide have experienced recent sex-biased admixture, namely, their male and female founders differed in ancestry and thus in allele frequencies. Sex-biased admixture makes testing for HWE difficult on X, because deviations arenaturallyexpected, even under random mating post-admixture and error-free genotyping. In this paper, we develop a likelihood ratio test and aχ2test that detect deviations from HWE on X while allowing for natural deviations due to sex-biased admixture. We demonstrate by simulations that our tests are powerful for detecting deviations due to non-random mating, while at the same time they do not reject the null under historical sex-biased admixture and random mating thereafter. We also demonstrate that when applied to 1000 Genomes project populations (e.g., as a quality control step), our tests reject fewer SNPs (among those showing frequency differences between the sexes) than other tests.
A Molecular Tension Sensor for N-Cadherin Reveals Distinct Forms of Mechanosensitive Adhesion Assembly in Adherens and Synaptic Junctions
Authors: Puranam Ishaan , Urs Aarti , Kirk Brenna , Newell-Litwa Karen A. , Hoffman Brenton
Published: February 2019

N-cadherin mediates physical linkages in a variety of force-generating and load-bearing tissues. To enable visualization and quantification of mechanical loads experienced by N-Cadherin, we developed a genetically-encoded FRET-based tension sensor for this protein. We observe that N-Cadherin supports non-muscle myosin II (NMII) activity-dependent loads within the adherens junctions (AJs) of VSMCs and the synaptic junctions (SJs) of neurons. To probe the relationship between mechanical loads and AJ/SJ formation, we evaluated the relationships between N-cadherin tension and the size of these adhesion structures. In VSMCs, no relationship between N-cadherin tension and AJ size was observed, consistent with previously observed homeostatic regulation of mechanical loading. In neurons, a strong correlation between SJ size and N-cadherin load was observed, demonstrating an absence of homeostatic regulation. Treatment with glycine, a known initiator of synapse maturation, lead to increased SJ size and N-cadherin load, suggesting a role for mechanosensitive signaling in this process. Correspondingly, we observe that NMII activity is required for the Src-mediated phosphorylation of NMDAR subunit GluN2B at Tyr 1252, which is a key event in synaptic potentiation. Together these data demonstrate N-cadherin tension is subject to cell type specific regulation and that mechanosensitive signaling occurs within SJs.
Manatee genomics supports a special conservation area in the Guianas coastline under the influence of the Amazon River plume
Authors: Vilaça Sibelle T. , Lima Camilla S. , Mazzoni Camila J. , Santos Fabricio R. , Thoisy Benoit de
Published: February 2019

The West Indian manatee (Trichechus manatus) occurs along the Atlantic coastline and adjacent freshwater systems of South, Central and North America, from Alagoas (Brazil) to Florida (USA) and Greater Antilles. The Amazonian manatee (Trichechus inunguis) is the only Sirenian adapted exclusively to freshwater and endemic to the Amazon River basin. Previous studies have reported hybrids between T. inunguis and T. manatus close to the mouth of the Amazon River, composing a likely extensive hybrid zone along the Guianas coast of South America under the influence of the Amazon River plume. We have used ddRAD SNP data, and sequences of nuclear and mtDNA loci to characterize the genomic composition of manatees along the French Guiana coastline. We found this population to be formed by introgressed or later generation interspecific hybrids, and also describe the first T. inunguis found outside the Amazon River basin. Our results indicate that T. inunguis can survive in the Amazon River plume and have colonized independent water streams of the Guianas coastline where they likely hybridize with T. manatus. This hypothesis offers a plausible explanation for the known extension of the hybrid zone between the two species along the Guianas coastline. It also reinforces the importance of the Amazon plume, which flows westwards to the Guianas coastline and favors the dispersion of the freshwater species. This habitat functions as a large estuary-like system that provides an ecological continuum from Amazon River mouth to the disconnected waterflows of the Guianas, which deserves a status of special conservation area.
F-BAR Cdc15 Promotes Gef1-mediated Cdc42 Activation During Cytokinesis and Cell Polarization inS. pombe
Authors: Hercyk Brian S. , Das Maitreyi E.
Published: February 2019

Cdc42, a Rho-family GTPase, is a master regulator of cell polarity. Recently it has been shown that Cdc42 also facilitates proper cytokinesis in the fission yeast,Schizosaccharomyces pombe. Cdc42 is activated by two partially redundant GEFs Gef1 and Scd1. Although both the GEFs activate Cdc42, their deletion mutants display distinct phenotypes, indicating that they are differentially regulated, by an unknown mechanism. During cytokinesis, Gef1 localizes to the division site and activates Cdc42 to initiate ring constriction and septum ingression. Here we report that the F-BAR domain containing Cdc15 promotes Gef1 localization to its functional sites. We show thatcdc15promotes Gef1 association with the cytokinetic nodes to activate Cdc42 during ring assembly. Moreover,cdc15phospho-mutants phenocopy polarity phenotypes ofgef1mutants. In a hypermorphiccdc15mutant, Gef1 localizes precociously to the division site, and is readily detected at the cortical patches and the cell cortex. Correspondingly, the hypermorphiccdc15mutant shows increased bipolarity during interphase and precocious Cdc42 activation at the division site during cytokinesis. Finally, loss ofgef1in hypermorphiccdc15mutants abrogates the increased bipolarity and precocious Cdc42 activation phenotype. We did not see any change in the localization of the other GEF Scd1 in a Cdc15-dependent manner. Taken together our data indicates that Cdc15 promotes Cdc42 activation specifically via Gef1 localization to the division site to facilitate proper cytokinesis and to the cell cortex to promote bipolarity.
Active Ageing Index in Korea – Comparison with China and EU countries
Authors: Um Jinpil , Zaidi Asghar , Choi Sung‐Jae
Published: February 2019

The evidence‐based policymaking relies on the use and robustness of the available data. Many conceptual and operational difficulties restrict this process, not least in making use of evidence to identify policy priorities. The Active Ageing Index (AAI), developed originally for the 28 European Union countries, offers a strong motivation in this respect. This paper reports on the development of the AAI for Korea, a country where speed and level of population aging is among the highest in the world. Drawing on the comparative analysis of the AAI results for Korea, China, and European countries, we find that Korea's AAI (35.3) is higher than the average of the AAI for all EU countries (33.9) but lower than China (37.3). Fitting Korea into the overall ranking with the EU countries and China (ranked 7), Korea is ranked 11, just behind Germany (10). The AAI results in Korea show that the employment domain performs extremely well compared with the EU countries, but other domains, especially “Social participation” and “Independent, healthy and secure living,” are achieving less favorable outcomes. High employment among the current cohorts of older workers in Korea can be attributed largely to the constraints of low pension income status.
Factors influencing resubstantiation of child neglect in South Korea: A comparison with other maltreatment cases
Authors: Kim Sewon , Yoo Joan P. , Chin Meejung , Jang Hwa Jung , Kim Hyun‐Soo , Lee Sang‐Gyun , Lee Bong Joo
Published: February 2019

While a high prevalence of child neglect cases has been reported by Child Protective Services (CPS) in Western countries, child neglect cases reported to South Korea's Child Protection Agency (CPA) present different trends than those in Western countries. Nevertheless, child neglect is an understudied area within child welfare. Thus, a need exists to investigate the unique characteristics of child neglect cases substantiated by the CPA in Korea. This study investigates the unique characteristics of child neglect cases and examines how factors associated with the resubstantiation of these cases differ from those of other maltreatment cases. Using CPA administrative data, we employed a multilevel discrete‐time hazard analysis to analyze the risk and protective factors associated with the resubstantiation of child neglect cases and compared the results with other maltreatment cases. In both cases, younger children, perpetrators with alcohol problems, families receiving welfare, and months of agency operation were associated with resubstantiation. For child neglect cases, the provision of child and parent services, and CPAs located in metropolitan area were protective factors that reduced the risk of resubstantiation. The finding in this study highlights the need to expand the provision of services to child neglect cases to prevent resubstantiation.
Turnover intention predictors among social workers in China
Authors: Lin Wenyi , Deng Mengyuan
Published: February 2019

The purpose of this study was to examine factors that best predict turnover among social workers in nonprofit organizations in Guangzhou, Guangdong Province of China. A sample of 312 social workers was selected to complete a self‐administered anonymous survey in 2014. A multiple logistical regression model was used to explain the different factors that influence social workers’ intention to leave their current jobs. The findings showed that age, education, perceived working condition, the perceived prospect of the social work profession, and social support predict turnover intention among social workers.
Solid organ transplantation in the HIV‐infected patient: Guidelines from the American Society of Transplantation Infectious Diseases Community of Practice
Authors: Blumberg Emily A. , Rogers Christin C. ,   the American Society of Transplantation Infectious Diseases Community of Practice
Published: February 2019

These updated guidelines from the Infectious Diseases Community of Practice of the American Society of Transplantation review the management of transplantation in HIV‐infected individuals. Transplantation has become the standard of care for patients with HIV and end‐stage kidney or liver disease. Although less data exist for thoracic organ and pancreas transplantation, it is likely that transplantation is also safe and effective for these recipients as well. Despite what is typically a transient decline in CD4+ T lymphocytes, HIV remains well controlled and infection risks are similar to those of HIV‐uninfected transplant recipients. The availability of effective directly active antivirals for the treatment of Hepatitis C is likely to improve outcomes in HIV and HCV co‐infected individuals, a population previously noted to have decreased survival. Drug interactions remain an important consideration, and integrase inhibitor‐based regimens are preferred due to the absence of interactions with calcineurin and mTOR inhibitors. Additionally, despite the use of more potent immunosuppression, rejection rates exceed those found in HIV‐uninfected recipients. Ongoing research evaluating HIV‐positive organ donors may provide support for utilizing these donors for HIV‐positive patients in need of transplantation.