bluuebunny/crossref_metadata_2025_split huggingface dataset:
BrucellaEipB is a periplasmic β-spiral protein required for envelope stress resistance and infection
Authors: Herrou Julien , Willett Jonathan W. , Fiebig Aretha , Czyż Daniel M. , Cheng Jason X. , Ultee Eveline , Briegel Ariane , Bigelow Lance , Babnigg Gyorgy , Kim Youngchang , Crosson Sean 
Published: February 2019

SummaryThe Gram-negative cell envelope is a remarkably diverse structure with core components that include an inner membrane, an outer membrane, and a peptidoglycan layer in the periplasmic space between. We show that a conserved DUF1849-family protein, EipB, is secreted to the periplasmic space ofBrucella, a monophyletic group of intracellular pathogens. In the periplasm, EipB folds into an unusual fourteen-stranded β-spiral structure that contains a conserved disulfide bond. EipB has structural features that resemble the LolA and LolB lipoprotein delivery system, though the overall topology and fold of EipB is distinct from LolA/LolB. Deletion ofeipBresults in defects in both cell envelope integrityin vitroand in maintenance of spleen colonization in a mouse model ofB. abortusinfection. Transposon disruption ofttpA, which encodes a periplasmic tetratricopeptide repeat (TPR) protein, is synthetically lethal witheipBdeletion inB. abortus.ttpAis a known virulence determinant inB. melitensis, and our studies ofttpAdeletion and overexpression strains provide evidence thatttpA, likeeipB, contributes to cell envelope function inBrucella. We conclude thateipBandttpAfunction in theBrucellaperiplasmic space to maintain cell envelope integrity and to facilitate survival in a mammalian host.ImportanceBrucellaspecies cause brucellosis, a global zoonosis. A gene encoding a conserved uncharacterized protein, EipB, is present in all sequencedBrucellaand several other genera in the classAlphaproteobacteria.To our knowledge, this study presents the first functional and structural characterization of a protein from the DUF1849 family, to which EipB belongs. EipB is secreted to the periplasm where it forms a spiral-like anti-parallel β structure. Deletion ofBrucella eipBresults in defects of the cell envelope and in reduced virulence in an animal model of disease.eipBgenetically interacts withttpA, which also encodes a periplasmic protein. We propose that EipB and TtpA function as part of a system required for cell envelope homeostasis in selectAlphaproteobacteria.
Neuronal L-Type Calcium Channel Signaling to the Nucleus Requires a Novel CaMKIIα-Shank3 Interaction
Authors: Perfitt Tyler L. , Wang Xiaohan , Stephenson Jason R. , Nakagawa Terunaga , Colbran Roger J. 
Published: February 2019

ABSTRACTThe molecular mechanisms that couple plasma membrane receptors/channels to specific intracellular responses, such as increased gene expression, are incompletely understood. The postsynaptic scaffolding protein Shank3 associates with Ca2+ permeable receptors or ion channels that can activate many downstream signaling proteins, including calcium/calmodulin-dependent protein kinase II (CaMKII). Here, we show that Shank3/CaMKIIα complexes can be specifically co-immunoprecipitated from mouse forebrain lysates, and that purified activated (Thr286 autophosphorylated) CaMKIIα binds directly to Shank3 between residues 829-1130. Mutation of three basic residues in Shank3 (R949RK951) to alanine disrupts CaMKII binding to Shank3 fragments in vitro, as well as CaMKII association with full-length Shank3 in heterologous cells. Our shRNA/rescue studies revealed that Shank3 binding to both CaMKII and L-type calcium channels (LTCCs) is required for increased phosphorylation of the nuclear CREB transcription factor induced by depolarization of cultured hippocampal neurons. Thus, this novel Shank3-CaMKII interaction is essential for the initiation of a specific long-range signal from plasma membrane LTCCs to the nucleus that is required for activity-dependent changes in neuronal gene expression during learning and memory.
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

AbstractUnderstanding 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 statementNew 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

AbstractProtein 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.
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

AbstractThe 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 availabilityCode 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

AbstractNanopore 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 SummaryWe 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

AbstractInteractions 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

AbstractA 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

AbstractNearly 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

AbstractPrediction 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/SummaryIn 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 StatementThe 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

AbstractWe 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.