bluuebunny/crossref_metadata_2025 huggingface dataset:
A redox-regulated type III metacaspase controls cell death in a marine diatom
Authors: Graff van Creveld Shiri , Ben-Dor Shifra , Mizrachi Avia , Alcolombri Uria , Hopes Amanda , Mock Thomas , Rosenwasser Shilo , Vardi Assaf
Published: October 2018

Programmed cell death (PCD) in marine phytoplankton was suggested as one of the mechanisms that facilitates large scale bloom demise. Yet, the molecular basis for algal PCD machinery is rudimentary. Metacaspases are considered ancestral proteases that regulate cell death, but their activity and role in algae are still elusive. Here we biochemically characterized a recombinant metacaspase 5 from the model diatom Phaeodactylum tricornutum (PtMC5), revealing calcium-dependent protease activity. This activity includes auto-processing and cleavage following arginine. PtMC5 overexpressing cells exhibited higher metacaspase activity and were more sensitive to a diatom-specific infochemical compared to WT cells. Mutagenesis of potential disulfide-forming cysteines decreased PtMC5 activity, suggesting redox regulation. This cysteine pair is widespread in diatom type III metacaspases, but was not found in any other taxa. The characterization of a cell death associated protein in marine phytoplankton will enable deeper understanding of the ecological significance of PCD in bloom dynamics.
Longitudinal Visual Analytics for Unpacking the Cancer Journey
Authors: Yuan Zhou , Finan Sean , Warner Jeremy , Savova Guergana , Hochheiser Harry
Published: October 2018

Retrospective cancer research requires identification of patients matching both categorical and temporal inclusion criteria, often based on factors exclusively available in clinical notes. Although natural language processing approaches for inferring higher-level concepts have shown promise for bringing structure to clinical texts, interpreting results is often challenging, involving the need to move between abstracted representations and constituent text elements. We discuss qualitative inquiry into user tasks and goals, data elements and models resulting in an innovative natural language processing pipeline and a visual analytics tool designed to facilitate interpretation of patient summaries and identification of cohorts for retrospective research.
Contribution of sensory encoding to measured bias
Authors: Jin Miaomiao , Glickfeld Lindsey L.
Published: October 2018

Perceptual decision-making is a complex process that involves sensory integration followed by application of a cognitive threshold. Signal detection theory (SDT) provides a mathematical framework for attributing the underlying neurobiological processes to these distinct phases of perceptual decision-making. In particular, SDT reveals the sensitivity (d’) of the neuronal response distributions and the bias (c) of the decision criterion, which are commonly thought to reflect sensory and cognitive processes, respectively. However, neuronal representations of bias have been observed in sensory areas, suggesting that some changes in bias are due to effects on sensory encoding. To directly test whether sensory encoding can influence bias, we optogenetically manipulated neuronal excitability in primary visual cortex (V1) during a detection task. Increasing excitability in V1 significantly decreased behavioral bias, while decreasing excitability had the opposite effect. To determine whether this change in bias is consistent with the effects on sensory encoding, we made extracellular recordings from V1 neurons in passively viewing mice. Indeed, we found that optogenetic manipulation of excitability shifted the neuronal bias in the same direction as the behavioral bias, despite using a fixed artificial decision criterion to predict hit and false alarm rates from the neuronal firing rates. To test the generality these effects, we also manipulated the quality of V1 encoding by changing stimulus contrast or inter-stimulus interval. These stimulus manipulations also resulted in consistent changes in bias measured both behaviorally and neuronally. Thus, changes in sensory encoding are sufficient to drive changes in bias measured using SDT.
Geometric principles of second messenger dynamics in dendritic spines
Authors: Cugno Andrea , Bartol Thomas M. , Sejnowski Terrence J. , Iyengar Ravi , Rangamani Padmini
Published: October 2018

Dendritic spines are small, bulbous protrusions along dendrites in neurons and play a critical role in synaptic transmission. Dendritic spines come in a variety of shapes that depend on their developmental state. Additionally, roughly 14−19% of mature spines have a specialized endoplasmic reticulum called the spine apparatus. How does the shape of a postsynaptic spine and its internal organization affect the spatio-temporal dynamics of short timescale signaling? Answers to this question are central to our understanding the initiation of synaptic transmission, learning, and memory formation. In this work, we investigated the effect of spine and spine apparatus size and shape on the spatio-temporal dynamics of second messengers using mathematical modeling using reaction-diffusion equations in idealized geometries (ellipsoids, spheres, and mushroom-shaped). Our analyses and simulations showed that in the short timescale, spine size and shape coupled with the spine apparatus geometries govern the spatiotemporal dynamics of second messengers. We show that the curvature of the geometries gives rise to pseudo-harmonic functions, which predict the locations of maximum and minimum concentrations along the spine head. Furthermore, we showed that the lifetime of the concentration gradient can be fine-tuned by localization of fluxes on the spine head and varying the relative curvatures and distances between the spine apparatus and the spine head. Thus, we have identified several key geometric determinants of how the spine head and spine apparatus may regulate the short timescale chemical dynamics of small molecules that control synaptic plasticity.
Identification of essential regulatory elements in the human genome
Authors: Wells Alex , Heckerman David , Torkamani Ali , Yin Li , Ren Bing , Telenti Amalio , Iulio Julia di
Published: October 2018

The identification of essential regulatory elements is central to the understanding of the consequences of genetic variation. Here we use novel genomic data and machine learning techniques to map essential regulatory elements and to guide functional validation. We train an XGBoost model using 38 functional and structural features, including genome essentiality metrics, 3D genome organization and enhancer reporter STARR-seq data to differentiate between pathogenic and control non-coding genetic variants. We validate the accuracy of prediction by using data from tiling-deletion-based and CRISPR interference screens of activity of cis-regulatory elements. In neurodevelopmental disorders, the model (ncER, non-coding Essential Regulation) maps essential genomic segments within deletions and rearranged topologically associated domains linked to human disease. We show that the approach successfully identifies essential regulatory elements in the human genome.
The COMA complex is required for positioning Ipl1 activity proximal to Cse4 nucleosomes in budding yeast
Authors: Halwachs Josef Fischböck , Singh Sylvia , Potocnjak Mia , Hagemann Götz , Solis Victor , Woike Stephan , Steger Medini Ghodgaonkar , Feuillet Jessica Andreani , Herzog Franz
Published: October 2018

Kinetochores are macromolecular protein complexes assembled on centromeric chromatin that ensure accurate chromosome segregation by linking DNA to spindle microtubules and integrating safeguard mechanisms. A kinetochore-associated pool of Ipl1Aurora B kinase, a subunit of the chromosomal passenger complex (CPC), was previously implicated in feedback control mechanisms. To study the kinetochore subunit connectivity built on budding yeast point centromeres and its CPC interactions we performed crosslink-guided in vitro reconstitution. The Ame1/Okp1CENP-U/Q heterodimer, forming the COMA complex with Ctf19/Mcm21CENP-P/O, selectively bound Cse4CENP-A nucleosomes through the Cse4 N-terminus and thereby establishes a direct link to the outer kinetochore MTW1 complex. The Sli15/Ipl1INCENP/Aurora B core-CPC interacted with COMA through the Ctf19 C-terminus, and artificial tethering of Sli15 to Ame1/Okp1 rescued synthetic lethality upon Ctf19/Mcm21 deletion in a Sli15 centromere-targeting deficient mutant. This study reveals characteristics of the inner kinetochore architecture assembled at point centromeres and the relevance of its Sli15/Ipl1 interaction for CPC function.
A direct comparison of genome alignment and transcriptome pseudoalignment
Authors: Yi Lynn , Liu Lauren , Melsted Páll , Pachter Lior
Published: October 2018

Motivation

Genome alignment of reads is the first step of most genome analysis workflows. In the case of RNA-Seq, transcriptome pseudoalignment of reads is a fast alternative to genome alignment, but the different “coordinate systems” of the genome and transcriptome have made it difficult to perform direct comparisons between the approaches.

Results

We have developed tools for converting genome alignments to transcriptome pseudoalignments, and conversely, for projecting transcriptome pseudoalignments to genome alignments. Using these tools, we performed a direct comparison of genome alignment with transcriptome pseudoalignment. We find that both approaches produce similar quantifications. This means that for many applications genome alignment and transcriptome pseudoalignment are interchangeable.

Availability and Implementation

bam2tcc is a C++14 software for converting alignments in SAM/BAM format to transcript compatibility counts (TCCs) and is available at https://github.com/pachterlab/bam2tcc. kallisto genomebam is a user option of kallisto that outputs a sorted BAM file in genome coordinates as part of transcriptome pseudoalignment. The feature has been released with kallisto v0.44.0, and is available at https://pachterlab.github.io/kallisto/.

Supplementary Material

N/A

Contact

Lior Pachter (lpachter@caltech.edu)
High throughput droplet single-cell Genotyping of Transcriptomes (GoT) reveals the cell identity dependency of the impact of somatic mutations
Authors: Nam Anna S. , Kim Kyu-Tae , Chaligne Ronan , Izzo Franco , Ang Chelston , Abu-Zeinah Ghaith , Omans Nathaniel D. , Taylor Justin , Pastore Alessandro , Alonso Alicia , Mariani Marisa , Cubillos-Ruiz Juan R. , Tam Wayne , Hoffman Ronald , Scandura Joseph M. , Rabadan Raul , Abdel-Wahab Omar , Smibert Peter , Landau Dan A.
Published: October 2018

Defining the transcriptomic identity of clonally related malignant cells is challenging in the absence of cell surface markers that distinguish cancer clones from one another or from admixed non-neoplastic cells. While single-cell methods have been devised to capture both the transcriptome and genotype, these methods are not compatible with droplet-based single-cell transcriptomics, limiting their throughput. To overcome this limitation, we present single-cell Genotyping of Transcriptomes (GoT), which integrates cDNA genotyping with high-throughput droplet-based single-cell RNA-seq. We further demonstrate that multiplexed GoT can interrogate multiple genotypes for distinguishing subclonal transcriptomic identity. We apply GoT to 26,039 CD34+ cells across six patients with myeloid neoplasms, in which the complex process of hematopoiesis is corrupted by CALR-mutated stem and progenitor cells. We define high-resolution maps of malignant versus normal hematopoietic progenitors, and show that while mutant cells are comingled with wildtype cells throughout the hematopoietic progenitor landscape, their frequency increases with differentiation. We identify the unfolded protein response as a predominant outcome of CALR mutations, with significant cell identity dependency. Furthermore, we identify that CALR mutations lead to NF-κB pathway upregulation specifically in uncommitted early stem cells. Collectively, GoT provides high-throughput linkage of single-cell genotypes with transcriptomes and reveals that the transcriptional output of somatic mutations is heavily dependent on the native cell identity.
Response of Australian pied oystercatchersHaematopus longirostristo increasing abundance of the beach bivalve preyDonax deltoides
Authors: Totterman Stephen L.
Published: October 2018

This study measured the response of Australian pied oystercatchersHaematopus longirostrison South Ballina Beach, New South Wales, Australia during a recovery in the stock of the primary prey speciesDonax deltoides, a large beach clam and commonly known as the ‘pipi’. It was predicted that oystercatcher counts would increase when pipi abundance increased (numerical response) and that oystercatcher feeding rates would also increase (functional response). Between Oct 2009 and Mar 2015, mean pipi density increased from c. zero to 30 pipis/m2. Mean oystercatcher feeding rates increased to an asymptote of c. 0.26 pipis/min. Breeding season mean counts of adult-plumage oystercatchers increased from 23 to 43, largely driven by non-territorial birds. Prey size selection was absent, both among different prey types and among pipis > 20 mm. This report provides some insights into the feeding ecology of oystercatchers on sandy ocean beaches that should be valuable in planning future studies.
Identifying stationary phases in multivariate time-series for highlighting behavioural modes and home range settlements
Authors: Patin Rémi , Étienne Marie-Pierre , Lebarbier Émilie , Chamaillé-Jammes Simon , Benhamou Simon
Published: October 2018

Recent advances in bio-logging open promising perspectives in the study animal movements at numerous scales. It is now possible to record time-series of animal locations and ancillary data (e.g. activity level derived from on-board accelerometers) over extended areas and long durations with a high spatial and temporal resolution. Such time-series are often piecewise stationary, as the animal may alternate between different stationary phases (i.e. characterised by a specific mean and variance of some key parameter for limited periods). Identifying when these phases start and end is a critical first step to understand the dynamics of the underlying movement processes.

We introduce a new segmentation-clustering method we called segclust2d. It can segment bi-(or more generally multi-) variate time-series and possibly cluster the various segments obtained, corresponding to phases assumed to be stationary. It is easy to use, as it only requires specifying the minimum length of a segment (to prevent over-segmentation) based on biological considerations.

Although this method can be applied to time-series of any nature, we focus here on two-dimensional piecewise time-series whose phases correspond at small scale to the expressions of different behavioural modes such as transit, feeding and resting, as characterised by two joint metrics such as speed and turning angles or, at larger scale, to temporary home ranges, characterised by stationary distributions of bivariate coordinates.

Using computer simulations, we show that segcust2d can rival and even outperform previous, more complex methods, which were specifically developed to highlight changes in movement modes or home range shifts (based on Hidden Markov or Ornstein-Uhlenbeck modelling, respectively), which, contrary to our method, require truly informative initial guesses to be efficient. Furthermore we demonstrate it on actual examples involving a zebra’s small scale movements and an elephant’s large scale movements, to illustrate the identification of various movement modes and of home range shifts, respectively.
MicroRNAs buffer genetic variation at specific temperatures during embryonic development
Authors: Amourda Christopher , Chong Jeronica , Saunders Timothy E.
Published: October 2018

Successful embryogenesis requires the coordination of developmental events. Perturbations, such as environmental changes, must be buffered to ensure robust development. However, how such buffering occurs is currently unknown in most developmental systems. Here, we demonstrate that seven miRNAs are differentially expressed duringDrosophilaembryogenesis at varying temperatures within natural physiological ranges. Lack of miR-3-309, -31a, -310c, -980 or -984c causes developmental delays specifically at a given temperature. Detailed analysis on miR-310c and -984c shows that their targets are typically mis-expressed in mutant backgrounds, with phenotypes more pronounced at temperatures where miRNAs show highest expression in wild-type embryos. Our results show that phenotypes may arise at specific temperatures while remaining silent at others, even within typical temperature ranges. Our work uncovers that miRNAs mask genetic variation at specific temperatures to increase embryonic robustness, highlighting another layer of complexity in miRNA expression.
Digital therapeutics for distributed response to global pandemics
Authors: Hacohen Adar , Cohen Reuven , Efroni Sol , Barzel Baruch , Bachelet Ido
Published: October 2018

Despite advances in the development of drugs and vaccines, the spread of infectious diseases remains an imminent threat to our global health, in extreme cases potentially having detrimental consequences. At present our response to this threat is based on physically distributing therapeutic material, which utilizes the same transportation networks that support the spread of the infectious agent itself. Such competition is at risk of failure in the face of a rapidly spreading pathogen, especially given the inevitable delay from the initial outbreak to the development and execution of our response. Moreover, based on our existing transportation networks, we show that such physical distribution is intrinsically inefficient, leading to an uneven concentration of the therapeutic within a small fraction of destinations, while leaving the majority of the population deprived. This suggests that outrunning a virulent epidemic can only be achieved if we develop a mitigation strategy that bypasses the existing distribution networks of biological and chemical material. Here we propose such a response, utilizing digitizable therapeutics, which can be distributed as digital sequence files and synthesized on location, exposing an extremely efficient mitigation scheme that systematically outperforms physical distribution. Our proposed strategy, based for example on nucleic acid therapeutics, is plausibly the only viable mitigation plan, based on current technology, that can face a violently spreading pathogen. Complementing the current paradigm, which ranks drugs based on efficacy, our analysis demonstrates the importance of balancing efficacy with distributability, finding that in some cases the latter plays the dominant role in the overall mitigation efficiency.
Haplotype assignment of longitudinal viral deep-sequencing data using co-variation of variant frequencies
Authors: Pang Juanita , Venturini Cristina , Tamuri Asif U. , Roy Sunando , Breuer Judith , Goldstein Richard A.
Published: October 2018

Longitudinal deep sequencing of viruses can provide detailed information about intra-host evolutionary dynamics including how viruses interact with and transmit between hosts. Many analyses require haplotype reconstruction, identifying which variants are co-located on the same genomic element. Most current methods to perform this reconstruction are based on a high density of variants and cannot perform this reconstruction for slowly evolving viruses. We present a new approach, HaROLD (HAplotype Reconstruction Of Longitudinal Deep sequencing data), which performs this reconstruction based on identifying co-varying variant frequencies using a probabilistic framework. We test this method with synthetic data sets of mixed cytomegalovirus and norovirus genomes, demonstrating high accuracy when longitudinal samples are available.
DNA replication initiation in Bacillus subtilis; Structural and functional characterisation of the essential DnaA-DnaD interaction
Authors: Martin Eleyna , Williams Huw E. L. , Pitoulias Matthaios , Stevens Daniel , Winterhalter Charles , Craggs Timothy D. , Murray Heath , Searle Mark S. , Soultanas Panos
Published: October 2018

The homotetrameric DnaD protein is essential in low G+C content gram positive bacteria and is involved in replication initiation at oriC and re-start of collapsed replication forks. It interacts with the ubiquitously conserved bacterial master replication initiation protein DnaA at the oriC but structural and functional details of this interaction are lacking, thus contributing to our incomplete understanding of the molecular details that underpin replication initiation in bacteria. DnaD comprises N-terminal (DDBH1) and C-terminal (DDBH2) domains, with contradicting bacterial two-hybrid and yeast two-hybrid studies suggesting that either the former or the latter interact with DnaA, respectively. Using Nuclear Magnetic Resonance (NMR) we show that both DDBH1 and DDBH2 interact with the N-terminal domain I of DnaA and studied the DDBH2 interaction in structural detail by NMR. We revealed two families of conformations for the DDBH2-DnaA domain I complex and showed that the DnaA-interaction patch of DnaD is distinct from the DNA-interaction patch, suggesting that DnaD can bind simultaneously DNA and DnaA. Using sensitive single-molecule FRET techniques we revealed that DnaD remodels DnaA-DNA filaments consistent with stretching and/or untwisting. Furthermore, the DNA binding activity of DnaD is redundant for this filament remodelling. This in turn suggests that DnaA and DnaD are working collaboratively in the oriC to locally melt the DNA duplex during replication initiation.
A computational framework for systematic exploration of biosynthetic diversity from large-scale genomic data
Authors: Navarro-Muñoz Jorge C. , Selem-Mojica Nelly , Mullowney Michael W. , Kautsar Satria , Tryon James H. , Parkinson Elizabeth I. , De Los Santos Emmanuel L.C. , Yeong Marley , Cruz-Morales Pablo , Abubucker Sahar , Roeters Arne , Lokhorst Wouter , Fernandez-Guerra Antonio , Dias Cappelini Luciana Teresa , Thomson Regan J. , Metcalf William W. , Kelleher Neil L. , Barona-Gomez Francisco , Medema Marnix H.
Published: October 2018

Genome mining has become a key technology to explore and exploit natural product diversity through the identification and analysis of biosynthetic gene clusters (BGCs). Initially, this was performed on a single-genome basis; currently, the process is being scaled up to large-scale mining of pan-genomes of entire genera, complete strain collections and metagenomic datasets from which thousands of bacterial genomes can be extracted at once. However, no bioinformatic framework is currently available for the effective analysis of datasets of this size and complexity. Here, we provide a streamlined computational workflow, tightly integrated with antiSMASH and MIBiG, that consists of two new software tools, BiG-SCAPE and CORASON. BiG-SCAPE facilitates rapid calculation and interactive visual exploration of BGC sequence similarity networks, grouping gene clusters at multiple hierarchical levels, and includes a ‘glocal’ alignment mode that accurately groups both complete and fragmented BGCs. CORASON employs a phylogenomic approach to elucidate the detailed evolutionary relationships between gene clusters by computing high-resolution multi-locus phylogenies of all BGCs within and across gene cluster families (GCFs), and allows researchers to comprehensively identify all genomic contexts in which particular biosynthetic gene cassettes are found. We validate BiG-SCAPE by correlating its GCF output to metabolomic data across 403 actinobacterial strains. Furthermore, we demonstrate the discovery potential of the platform by using CORASON to comprehensively map the phylogenetic diversity of the large detoxin/rimosamide gene cluster clan, prioritizing three new detoxin families for subsequent characterization of six new analogs using isotopic labeling and analysis of tandem mass spectrometric data.
methyl-ATAC-seq measures DNA methylation at accessible chromatin
Authors: Spektor R , Tippens ND , Mimoso CA , Soloway PD
Published: October 2018

Chromatin features are characterized by genome-wide assays for nucleosome location, protein binding sites, 3-dimensional interactions, and modifications to histones and DNA. For example, Assay for Transposase Accessible Chromatin sequencing (ATAC-seq) identifies nucleosome-depleted (open) chromatin, which harbors potentially active gene regulatory sequences; and bisulfite sequencing (BS-seq) quantifies DNA methylation. When two distinct chromatin features like these are assayed separately in populations of cells, it is impossible to determine, with certainty, where the features are coincident in the genome by simply overlaying datasets. Here we describe methyl-ATAC-seq (mATAC-seq), which implements modifications to ATAC-seq, including subjecting the output to BS-seq. Merging these assays into a single protocol identifies the locations of open chromatin, and reveals, unambiguously, the DNA methylation state of the underlying DNA. Such combinatorial methods eliminate the need to perform assays independently and infer where features are coincident.
Dopaminergic medication reduces striatal sensitivity to negative outcomes in Parkinson’s disease
Authors: McCoy Brónagh , Jahfari Sara , Engels Gwenda , Knapen Tomas , Theeuwes Jan
Published: October 2018

Reduced levels of dopamine in Parkinson’s disease (PD) contribute to changes in learning, resulting from the loss of midbrain dopamine neurons that transmit a teaching signal to the striatum. Dopamine medication used by PD patients has previously been linked to either behavioral changes during learning itself or adjustments in approach and avoidance behavior after learning. To date, however, very little is known about the specific relationship between dopaminergic medication-driven differences during learning and subsequent changes in approach/avoidance tendencies in individual patients. We assessed 24 PD patients on and off dopaminergic medication and 24 healthy controls (HC) performing a probabilistic reinforcement learning task, while undergoing functional magnetic resonance imaging. During learning, medication in PD reduced an overemphasis on negative outcomes. When patients were on medication, learning rates were lower for negative (but not positive) outcomes and concurrent striatal BOLD responses showed reduced prediction error sensitivity. Medication-induced shifts in negative learning rates were predictive of changes in approach/avoidance choice patterns after learning, and these changes were accompanied by striatal BOLD response alterations. These findings highlight dopamine-driven learning differences in PD and provide new insight into how changes in learning impact the transfer of learned value to approach/avoidance responses in novel contexts.
The G protein-biased PZM21 and TRV130 act as partial agonists of μ-opioid receptors signaling to ion channel targets
Authors: Yudin Yevgen , Rohacs Tibor
Published: October 2018

Opioids exert many of their acute effects through modulating ion channels via Gβγ subunits. Some of their side effects are attributed to β-arrestin recruitment, and several biased agonists that do not activate this pathway have been developed recently. Here we tested the effects of TRV130, PZM21 and herkinorin, three G-protein biased agonists of μ-opioid receptors (μOR), on ion channel targets. Compared to the full μOR agonist DAMGO, all three biased agonists induced smaller activation of G protein-coupled inwardly rectifying potassium channels (GIRK2), and smaller inhibition of Transient Receptor Potential Melastatin (TRPM3) channels. Furthermore, co-application of TRV130 or PZM21, but not herkinorin reduced the effects of DAMGO on both ion channels. CaV2.2 was also inhibited less by PZM21 and TRV130 than by DAMGO. TRV130, PZM21 and herkinorin were also less effective than DAMGO in inducing dissociation of the Gαi /Gβγ complex. We conclude that TRV130, PZM21 are partial agonists of μOR.
Synergistic interactions between confinement and macromolecular crowding spatially order transcription and translation in cell-free expression
Authors: Elizabeth Norred S. , Dabbs Rosemary M. , Chauhan Gaurav , Caveney Patrick M. , Collier C. Patrick , Abel Steven M. , Simpson Michael L.
Published: October 2018

Synergistic interactions between macromolecular crowding and confinement spatially organize transcription and translation in cells. Yet, reproducing such spatial ordering in cell-free expression platforms has proven to be elusive. Here we report crowding- and confinement-driven spatial self-organization of cell-free expression that mimics expression behavior within and around the nucleoid of prokaryotes. These experiments use Ficoll-70 to approximate cellular macromolecular crowding conditions within cell-size lipid vesicles. Intriguingly, there was an abrupt change in transcriptional dynamics when crowding reached physiologically relevant levels. Imaging experiments revealed that this change in transcriptional dynamics was coincident with localization of plasmid DNA and mRNA at the vesicle wall. Computer simulations demonstrated that crowding leads to an entropically induced attraction between plasmid DNA and the wall, causing localization of DNA near the wall at sufficiently high crowding levels. The experiments demonstrate cell-like spatial organization of translation, where translational activity is controlled by chromosomally-templated positioning of mRNA. This cell-free system provides a flexible experimental platform to probe the underlying mechanisms of self-organization of membrane-less structures in cells and the spatial control of gene expression.
GAL4 drivers specific for Type Ib and Type Is motor neurons inDrosophila
Authors: Perez-Moreno Juan J. , O’Kane Cahir J.
Published: October 2018

TheDrosophilalarval neuromuscular system is extensively used by researchers to study neuronal cell biology, andDrosophilaglutamatergic motor neurons (MNs) have become a major model system. There are two main Types of glutamatergic MNs, Ib and Is, with different structural and physiological properties at synaptic level at the neuromuscular junction. To generate genetic tools to identify and manipulate MNs of each Type, we screened forGAL4driver lines for this purpose. Here we describeGAL4drivers specific for examples of neurons within each Type, Ib or Is. These drivers showed high expression levels and were expressed in only few MNs, making them amenable tools for specific studies of both axonal and synapse biology in identified Type I MNs.
TADs pair homologous chromosomes to promote interchromosomal gene regulation
Authors: Viets Kayla , Sauria Michael , Chernoff Chaim , Anderson Caitlin , Tran Sang , Dove Abigail , Goyal Raghav , Voortman Lukas , Gordus Andrew , Taylor James , Johnston Robert J.
Published: October 2018

Homologous chromosomes colocalize to regulate gene expression in processes including genomic imprinting and X-inactivation, but the mechanisms driving these interactions are poorly understood. InDrosophila, homologous chromosomes pair throughout development, promoting an interchromosomal gene regulatory mechanism called transvection. Despite over a century of study, the molecular features that facilitate chromosome-wide pairing are unknown. The “button” model of pairing proposes that specific regions along chromosomes pair with a higher affinity than their surrounding regions, but only a handful of DNA elements that drive homologous pairing between chromosomes have been described. Here, we identify button loci interspersed across the fly genome that have the ability to pair with their homologous sequences. Buttons are characterized by topologically associated domains (TADs), which drive pairing with their endogenous loci from multiple locations in the genome. Fragments of TADs do not pair, suggesting a model in which combinations of elements interspersed along the full length of a TAD are required for pairing. Though DNA-binding insulator proteins are not associated with pairing, buttons are enriched for insulator cofactors, suggesting that these proteins may mediate higher order interactions between homologous TADs. Using a TAD spanning thespinelessdgene as a paradigm, we find that pairing is necessary but not sufficient for transvection.spinelesspairing and transvection are cell-type-specific, suggesting that local buttoning and unbuttoning regulates transvection efficiency between cell types. Together, our data support a model in which specialized TADs button homologous chromosomes together to facilitate cell-type-specific interchromosomal gene regulation.
Quantitative Analysis of Interactive Behavior of Mitochondria and Lysosomes Using Structured Illumination Microscopy
Authors: Chen Qixin , Shao Xintian , Hao Mingang , Tian Zhiqi , Wang Chenran , Liu Fei , Zang Kai , Wang Fengshan , Ling Peixue , Guan Jun-Lin , Diao Jiajie
Published: October 2018

Super-resolution optical microscopy has extended the spatial resolution of cell biology from the cellular level to the nanoscale, enabling the observation of the interactive behavior of single mitochondria and lysosomes. Quantitative parametrization of interaction between mitochondria and lysosomes under super-resolution optical microscopy, however, is currently unavailable, which has severely limited our understanding of the molecular machinery underlying mitochondrial functionality. Here, we introduce an M-value to quantitatively investigate mitochondria and lysosome contact (MLC) and mitophagy under structured illumination microscopy. We found that the M-value for an MLC is typically less than 0.4, whereas in mitophagy it ranges from 0.5 to 1.0. This system permits further investigation of the detailed molecular mechanism governing the interactive behavior of mitochondria and lysosomes.
Using long-read sequencing to detect imprinted DNA methylation
Authors: Gigante Scott , Gouil Quentin , Lucattini Alexis , Keniry Andrew , Beck Tamara , Tinning Matthew , Gordon Lavinia , Woodruff Chris , Speed Terence P. , Blewitt Marnie E. , Ritchie Matthew E.
Published: October 2018

Systematic variation in the methylation of cytosines at CpG sites plays a critical role in early development of humans and other mammals. Of particular interest are regions of differential methylation between parental alleles, as these often dictate monoallelic gene expression, resulting in parent of origin specific control of the embryonic transcriptome and subsequent development, in a phenomenon known as genomic imprinting. Using long-read nanopore sequencing we show that, with an average genomic coverage of approximately ten, it is possible to determine both the level of methylation of CpG sites and the haplotype from which each read arises. The long-read property is exploited to characterise, using novel methods, both methylation and haplotype for reads that have reduced basecalling precision compared to Sanger sequencing. We validate the analysis both through comparison of nanopore-derived methylation patterns with those from Reduced Representation Bisulfite Sequencing data and through comparison with previously reported data.

Our analysis successfully identifies known imprinting control regions as well as some novel differentially methylated regions which, due to their proximity to hitherto unknown monoallelically expressed genes, may represent new imprinting control regions.
Nuclear actin interactome analysis links actin to KAT14 histone acetyl transferase and mRNA splicing
Authors: Viita Tiina , Kyheröinen Salla , Prajapati Bina , Virtanen Jori , Varjosalo Markku , Vartiainen Maria K.
Published: October 2018

In addition to its essential functions within the cytoskeleton, actin also localizes to the cell nucleus, where it is linked to many important nuclear processes from gene expression to maintenance of genomic integrity. However, the molecular mechanisms by which actin operates in the nucleus remain poorly understood. Here we have used two complementary mass spectrometry (MS) techniques, AP-MS and BioID-MS, to identify binding partners for nuclear actin. Common high-confidence interactions highlight the role of actin in chromatin remodeling complexes and identify the hATAC histone modifier as a novel actin-containing nuclear complex. Further analysis demonstrates that actin binds directly to the hATAC subunit KAT14, and modulates its histone acetyl transferase activity in vitro and in cells. BioID-MS, which can detect also transient interactions, links actin to several steps of transcription as well as to RNA processing. Alterations in nuclear actin levels disturb alternative exon skipping of the SMN2 minigene, suggesting also a functional role for actin in RNA splicing. This interactome analysis thus identifies both novel direct binding partners and functional roles for nuclear actin, as well as forms a platform for further mechanistic studies on how actin operates during essential nuclear processes.
A two-step mechanism for the inactivation of microtubule organizing center function at the centrosome
Authors: Magescas Jérémy , Zonka Jennifer C. , Feldman Jessica L.
Published: October 2018

During mitosis, the centrosome acts as a microtubule organizing center (MTOC), orchestrating microtubules into the mitotic spindle through its pericentriolar material (PCM). This activity is biphasic, cycling through assembly and disassembly during the cell cycle. Although hyperactive centrosomal MTOC activity is a hallmark of some cancers, little is known about how the centrosome is inactivated as an MTOC. Analysis of endogenous PCM proteins inC. elegansrevealed that the PCM is composed of distinct protein territories that are removed from the centrosome at different rates and using different behaviors. Inhibition of PP2A phosphatases stabilized the PCM and perturbation of cortical pulling forces altered the timing and behavior by which proteins were removed from the centrosome. These data indicate that PCM disassembly is a two-step process, beginning with a phosphatase-dependent dissolution of PCM proteins followed by the ejection of ruptured PCM by cortical forces, ultimately inactivating MTOC function at the centrosome.
Single-Cell Transcriptomics Unveils Gene Regulatory Network Plasticity
Authors: Iacono Giovanni , Massoni-Badosa Ramon , Heyn Holger
Published: October 2018

Single-cell RNA sequencing (scRNA-seq) plays a pivotal role in our understanding of cellular heterogeneity. Current analytical workflows are driven by categorizing principles that consider cells as individual entities and classify them into complex taxonomies. We have devised a conceptually different computational framework based on a holistic view, where single-cell datasets are used to infer global, large-scale regulatory networks. We developed correlation metrics that are specifically tailored to single-cell data, and then generated, validated and interpreted single-cell-derived regulatory networks from organs and perturbed systems, such as diabetes and Alzheimer’s disease. Using advanced tools from graph theory, we computed an unbiased quantification of a gene’s biological relevance, and accurately pinpointed key players in organ function and drivers of diseases. Our approach detected multiple latent regulatory changes that are invisible to single-cell workflows based on clustering or differential expression analysis. In summary, we have established the feasibility and value of regulatory network analysis using scRNA-seq datasets, which significantly broadens the biological insights that can be obtained with this leading technology.
Stepwise evolution and convergent recombination underlie the global dissemination of carbapenemase-producingEscherichia coli
Authors: Patiño-Navarrete Rafael , Rosinski-Chupin Isabelle , Cabanel Nicolas , Gauthier Lauraine , Takissian Julie , Madec Jean-Yves , Hamze Monzer , Bonnin Remy A. , Naas Thierry , Glaser Philippe
Published: October 2018

Carbapenem-resistantEnterobacteriaceaeare considered by WHO as “critical” priority pathogens for which novel antibiotics are urgently needed. The dissemination of carbapenemase-producingEscherichia coli(CP-Ec) in the community is a major public health concern. However, the global molecular epidemiology of CP-Ecisolates, as well as the genetic bases for the emergence and global dissemination of specific lineages, remain largely unknown. Here, by combining a thorough genomic and evolutionary analysis ofEcST410 isolates with a broad analysis of 12,584E. coli and Shigellagenomes, we showed that the fixation of carbapenemase genes depends largely on a combination of mutations inftsIencoding the penicillin binding protein 3 and in the porin genesompCandompF. MutatedftsIgenes and a specificompCallele inducing reduced susceptibility to diverse β-lactams spread across the species by recombination. The selection of CP-Eclineages able to disseminate is more complex than the mere acquisition of carbapenemase genes.
The winner takes it all: how semelparous insects can become periodical
Authors: Diekmann Odo , Planqué Robert
Published: October 2018

The aim of this short note is to give a simple explanation for the remarkable periodicity of Magicicada species, which appear as adults only every 13 or 17 years, depending on the region. We show that a combination of two types of density dependence may drive, for large classes of initial conditions, all but one year class to extinction. Competition for food leads to negative density dependence in the form of a uniform (i.e., affecting all age classes in the same way) reduction of the survival probability. Satiation of predators leads to positive density dependence within the reproducing age class. The analysis focuses on the full life cycle map derived by iteration of a semelparous Leslie matrix.
Neural G0: a quiescent-like state found in neuroepithelial-derived cells and glioma
Authors: Feldman Heather M. , Toledo Chad M. , Arora Sonali , Hoellerbauer Pia , Corrin Philip , Carter Lucas , Kufeld Megan , Bolouri Hamid , Basom Ryan , Delrow Jeffrey , McFaline-Figueroa José L. , Trapnell Cole , Pollard Steven M. , Patel Anoop , Plaisier Christopher L. , Paddison Patrick J.
Published: October 2018

Single cell RNA-seq has emerged as a powerful tool for resolving cellular states associated with normal and maligned developmental processes. Here, we used scRNA-seq to examine the cell cycle states of expanding human neural stem cells (hNSCs). From this data, we created a cell cycle classifier, which, in addition to traditional cell cycle phases, also identifies a putative quiescent-like state in neuroepithelial-derived cell types during mammalian neurogenesis and in gliomas. This state, Neural G0, is enriched for expression of quiescent NSC genes and other neurodevelopmental markers found in non-dividing neural progenitors. For gliomas, Neural G0 cell populations and gene expression is significantly associated with less aggressive tumors and extended patient survival. Genetic screens to identify modulators of Neural G0 revealed that knockout of genes associated with the Hippo/Yap and p53 pathways diminished Neural G0in vitro, resulting in faster G1 transit, down regulation of quiescence-associated markers, and loss of Neural G0 gene expression. Thus, Neural G0 represents a dynamic quiescent-like state found in neuro-epithelial derived cells and gliomas.
High stretchability, strength and toughness of living cells enabled by hyperelastic vimentin network
Authors: Hu Jiliang , Li Yiwei , Hao Yukun , Zheng Tianqi , Parada German Alberto , Wu Huayin , Lin Shaoting , Wang Shida , Zhao Xuanhe , Goldman Robert D. , Cai Shengqiang , Guo Ming
Published: October 2018

In many normal and abnormal physiological processes, including cellular migration during normal development and invasion in cancer metastasis, cells are required to withstand severe deformations. The structural integrity of eukaryotic cells under small deformations has been known to depend on the cytoskeleton including actin filaments (F-actin), microtubules and intermediate filaments (IFs). However, it remains unclear how cells resist severe deformations since both F-actin and microtubules fluidize or disassemble under moderate strains. Here, we demonstrate that vimentin intermediate filaments (VIFs), a marker of mesenchymal cells, dominate cytoplasmic mechanics at large deformations. Our results show that cytoskeletal VIFs form a stretchable, hyperelastic network. This network works synergistically with other dissipative cytoplasmic components, substantially enhancing the strength, stretchability, resilience and toughness of the living cytoplasm.
Cell-type–specific eQTL of primary melanocytes facilitates identification of melanoma susceptibility genes
Authors: Zhang Tongwu , Choi Jiyeon , Kovacs Michael A. , Shi Jianxin , Xu Mai ,   NISC Comparative Sequencing Program,   Melanoma Meta-Analysis Consortium, Goldstein Alisa M. , Trower Adam J. , Bishop D. Timothy , Iles Mark M. , Duffy David L. , MacGregor Stuart , Amundadottir Laufey T. , Law Matthew H. , Loftus Stacie K. , Pavan William J. , Brown Kevin M.
Published: October 2018

Most expression quantitative trait locus (eQTL) studies to date have been performed in heterogeneous tissues as opposed to specific cell types. To better understand the cell-type–specific regulatory landscape of human melanocytes, which give rise to melanoma but account for <5% of typical human skin biopsies, we performed an eQTL analysis in primary melanocyte cultures from 106 newborn males. We identified 597,335cis-eQTL SNPs prior to linkage disequilibrium (LD) pruning and 4997 eGenes (FDR < 0.05). Melanocyte eQTLs differed considerably from those identified in the 44 GTEx tissue types, including skin. Over a third of melanocyte eGenes, including key genes in melanin synthesis pathways, were unique to melanocytes compared to those of GTEx skin tissues or TCGA melanomas. The melanocyte data set also identifiedtrans-eQTLs, including those connecting a pigmentation-associated functional SNP with four genes, likely throughcis-regulation ofIRF4. Melanocyte eQTLs are enriched incis-regulatory signatures found in melanocytes as well as in melanoma-associated variants identified through genome-wide association studies. Melanocyte eQTLs also colocalized with melanoma GWAS variants in five known loci. Finally, a transcriptome-wide association study using melanocyte eQTLs uncovered four novel susceptibility loci, where imputed expression levels of five genes (ZFP90,HEBP1,MSC,CBWD1, andRP11-383H13.1) were associated with melanoma at genome-wide significantP-values. Our data highlight the utility of lineage-specific eQTL resources for annotating GWAS findings, and present a robust database for genomic research of melanoma risk and melanocyte biology.
Crystal structures and kinetics ofN-acetylneuraminate lyase fromFusobacterium nucleatum
Authors: Kumar Jay Prakash , Rao Harshvardhan , Nayak Vinod , Ramaswamy S.
Published: October 2018

N-Acetyl-D-neuraminic acid lyase (NanA) catalyzes the breakdown of sialic acid (Neu5Ac) toN-acetyl-D-mannosamine (ManNAc) and pyruvate. NanA plays a key role in Neu5Ac catabolism in many pathogenic and bacterial commensals where sialic acid is available as a carbon and nitrogen source. Several pathogens or commensals decorate their surfaces with sialic acids as a strategy to escape host innate immunity. Catabolism of sialic acid is key to a range of host–pathogen interactions. In this study, atomic resolution structures of NanA fromFusobacterium nucleatum(FnNanA) in ligand-free and ligand-bound forms are reported at 2.32 and 1.76 Å resolution, respectively. F. nucleatumis a Gram-negative pathogen that causes gingival and periodontal diseases in human hosts. Like other bacterialN-acetylneuraminate lyases, FnNanA also shares the triosephosphate isomerase (TIM)-barrel fold. As observed in other homologous enzymes, FnNanA forms a tetramer. In order to characterize the structure–function relationship, the steady-state kinetic parameters of the enzyme are also reported.