bluuebunny/crossref_metadata_2025 huggingface dataset:
Disruption of genes associated with Charcot-Marie-Tooth type 2 lead to common behavioural, cellular and molecular defects inCaenorhabditis elegans
Authors: Soh Ming S. , Cheng Xinran , Liu Jie , Neumann Brent
Published: April 2019

Charcot-Marie-Tooth (CMT) disease is an inherited peripheral motor and sensory neuropathy. The disease is divided into demyelinating (CMT1) and axonal (CMT2) neuropathies, and although we have gained molecular information into the details of CMT1 pathology, much less is known about CMT2. Due to its clinical and genetic heterogeneity, coupled with a lack of animal models, common underlying mechanisms remain elusive. In order to understand the biological importance of CMT2-casuative genes, we have studied the behavioural, cellular and molecular consequences of mutating nine different genes associated with CMT2 in the nematodeCaenorhabditis elegans(lin-41/TRIM2, dyn-1/DMN2, unc-116/KIF5A, fzo-1/MFN2, osm-9/TRPV4, cua-1/ATP7A, hsp-25/HSPB1, hint-1/HINT1, nep-2/MME). We show thatC. elegansdefective for these genes display debilitated movement in crawling and swimming assays. Severe morphological defects in cholinergic motors neurons are also evident in two of the mutants (dyn-1andunc-116). Furthermore, we establish novel methods for quantifying muscle morphology and use these to demonstrate striking loss of muscle structure across the mutants that correspond with reductions in muscle function. Finally, using electrophysiological recordings of neuromuscular junction (NMJ) activity, we uncover reductions in spontaneous postsynaptic current frequency inlin-41, dyn-1, unc-116andfzo-1mutants. By comparing the consequences of mutating numerous CMT2-related genes, this study reveals common deficits in muscle structure and function, as well as NMJ signalling when these genes are disrupted.
Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts
Authors: Nair Surag , Kim Daniel S. , Perricone Jacob , Kundaje Anshul
Published: April 2019

Motivation

Genome-wide profiles of chromatin accessibility and gene expression in diverse cellular contexts are critical to decipher the dynamics of transcriptional regulation. Recently, convolutional neural networks (CNNs) have been used to learn predictive cis-regulatory DNA sequence models of context-specific chromatin accessibility landscapes. However, these context-specific regulatory sequence models cannot generalize predictions across cell types.

Results

We introduce multi-modal, residual neural network architectures that integrate cis-regulatory sequence and context-specific expression of trans-regulators to predict genome-wide chromatin accessibility profiles across cellular contexts. We show that the average accessibility of a genomic region across training contexts can be a surprisingly powerful predictor. We leverage this feature and employ novel strategies for training models to enhance genome-wide prediction of shared and context-specific chromatin accessible sites across cell types. We interpret the models to reveal insights into cis and trans regulation of chromatin dynamics across 123 diverse cellular contexts.

Availability

The code is available athttps://github.com/kundajelab/ChromDragoNN

Contact

akundaje@stanford.edu
Nuclear RNA export factor variant initiates piRNA-guided co-transcriptional silencing
Authors: Murano Kensaku , Iwasaki Yuka W. , Ishizu Hirotsugu , Mashiko Akane , Shibuya Aoi , Kondo Shu , Adachi Shungo , Suzuki Saori , Saito Kuniaki , Natsume Tohru , Siomi Mikiko C. , Siomi Haruhiko
Published: April 2019

The PIWI-interacting RNA (piRNA) pathway preserves genomic integrity by repressing transposable elements (TEs) in animal germ cells. Among PIWI-clade proteins inDrosophila, Piwi transcriptionally silences its targets through interactions with cofactors, including Panoramix (Panx) and forms heterochromatin characterized by H3K9me3 and H1. Here, we identified Nxf2, a nuclear RNA export factor (NXF) variant, as a protein that forms complexes with Piwi, Panx, and p15. Panx-Nxf2-p15 complex formation is necessary in the silencing by stabilizing protein levels of Nxf2 and Panx. Notably, ectopic targeting of Nxf2 initiates co-transcriptional repression of the target reporter in a manner independent of H3K9me3 marks or H1. However, continuous silencing requires HP1a and H1. In addition, Nxf2 directly interacts with target TE transcripts in a Piwi-dependent manner. These findings suggest a model in which the Nxf2-Panx-p15 complex enforces the association of Piwi with target transcripts to trigger co-transcriptional repression, prior to heterochromatin formation in the nuclear piRNA pathway.

Highlights

Nxf2 plays an essential role in the Piwi–piRNA pathway

Formation of Piwi-Panx-Nxf2-p15 (PPNP) complexes stabilizes both Panx and Nxf2

The PPNP complex triggers transcriptional silencing before heterochromatin formation

Nxf2 directly binds to target transcripts in a Piwi-dependent manner
U-PASS: unified power analysis and forensics for qualitative traits in genetic association studies
Authors: Gao Zheng , Terhorst Jonathan , Van Hout Cristopher , Stoev Stilian
Published: April 2019

Despite the availability of existing calculators for statistical power analysis in genetic association studies, there has not been a model-invariant and test-independent tool that allows for both planning of prospective studies and systematic review of reported findings. In this work, we develop a web-based application U-PASS (Unified Power analysis of ASsociation Studies), implementing a unified framework for the analysis of common association tests for binary qualitative traits. The application quantifies the shared asymptotic power limits of the common association tests, and visualizes the fundamental statistical trade-off between risk allele frequency (RAF) and odds ratio (OR). The application also addresses the applicability of asymptotics-based power calculations in finite samples, and provides guidelines for single- SNP-based association tests. In addition to designing prospective studies, U-PASS enables researchers to retrospectively assess the statistical validity of previously reported associations.

Availability and implementation

U-PASS is available as a web-based R Shiny application at https://power.stat.lsa.umich.edu. Source code is available at https://github.com/Pill-GZ/U-PASS.

Contact

gaozheng@umich.edu

Supplementary information

Supplementary data are available in the application.
Hyperactive TORC1 sensitizes yeast cells to endoplasmic reticulum stress by compromising cell wall integrity
Authors: Ahmed Khadija , Carter David E. , Lajoie Patrick
Published: April 2019

The disruption of protein folding homeostasis in the endoplasmic reticulum (ER) results in an accumulation of toxic misfolded proteins and activates a network of signaling events collectively known as the unfolded protein response (UPR). While UPR activation upon ER stress is well characterized, how other signaling pathways integrate into the ER proteostasis network is unclear. Here, we sought to investigate how the target of rapamycin complex 1 (TORC1) signaling cascade acts in parallel with the UPR to regulate ER stress sensitivity. UsingS. cerevisiae, we found that TORC1 signaling is attenuated during ER stress and constitutive activation of TORC1 increases sensitivity to ER stressors such as tunicamycin and inositol deprivation. This phenotype is independent of the UPR. Transcriptome analysis revealed that TORC1 hyperactivation results in cell wall remodelling. Conversely, hyperactive TORC1 sensitizes cells to cell wall stressors, including the antifungal caspofungin. Elucidating the crosstalk between the UPR, cell wall integrity, and TORC1 signaling may uncover new paradigms through which the response to protein misfolding is regulated, and thus have crucial implications for the development of novel therapeutics against pathogenic fungal infections.

IMPORTANCE

The prevalence of pathogenic fungal infections, coupled with the emergence of new fungal pathogens, has brought these diseases to the forefront of global health problems. While antifungal treatments have advanced over the last decade, patient outcomes have not substantially improved. These shortcomings are largely attributed to the evolutionary similarity between fungi and humans, which limits the scope of drug development. As such, there is a pressing need to understand the unique cellular mechanisms that govern fungal viability. Given thatSaccharomyces cerevisiaeis evolutionarily related to a number of pathogenic fungi, and in particular to theCandidaspecies, most genes fromS. cerevisiaeare highly conserved in pathogenic fungal strains. Here we show that hyperactivation of TORC1 signaling sensitizesS. cerevisiaecells to both endoplasmic reticulum stress and cell wall stressors by compromising cell wall integrity. Therefore, targeting TORC1 signaling and endoplasmic reticulum stress pathways may be useful in developing novel targets for antifungal drugs.
Noda-like RNA viruses infectingCaenorhabditisnematodes: sympatry, diversity and reassortment
Authors: Frézal Lise , Jung Hyeim , Tahan Stephen , Wang David , Félix Marie-Anne
Published: April 2019

Three RNA viruses related to nodaviruses were previously described to naturally infect the nematodeCaenorhabditis elegansand its relativeC. briggsae. Here we report on a collection of over 50 viral variants from wild-caughtCaenorhabditis. We describe the discovery of a new related virus, the Mělník virus, infectingC. briggsae, which similarly infects intestinal cells. In France, a frequent pattern of co-infection ofC. briggsaeby the Santeuil virus and Le Blanc virus was observed at the level of an individual nematode and even a single cell. We do not find evidence of reassortment between the RNA1 and RNA2 molecules of Santeuil and Le Blanc viruses. However, by studying patterns of evolution of each virus, reassortments of RNA1 and RNA2 among variants of each virus were identified. We develop assays to test the relative potency and competitive ability of the viral variants and detect an interaction between host genotype and Santeuil virus genotype, such that the result of the competition depends on the host strain.

Importance

The roundwormCaenorhabditis elegans is a laboratory model organism in biology. We study natural populations of this small animal and its relativeC. briggsaeand the viruses that infect them. We previously discovered three RNA viruses related to nodaviruses and here describe a fourth one, called the Melnik virus. These viruses have a genome composed of two RNA molecules. We find that two viruses may infect the same animal and the same cell. The two RNA molecules may be exchanged between variants of a given viral species. We study the diversity of each viral species and devise an assay of their competitive ability. Using this assay, we show that the outcome of the competition also depends on the host.
Parsers, Data Structures and Algorithms for Macromolecular Analysis Toolkit (MAT): Design and Implementation
Authors: Kalyan Gazal , Junghare Vivek , S S John , Chattopadhyay Anupam , Mitra Pralay , Hazra Saugata
Published: April 2019

The structural information of biological macromolecules are stored in .pdb, .mm-cif and lately mmtf files and thus it requires accurate and efficient biological tools for various utilities. Here, we describe Macromolecular Analysis Toolkit (MAT) that parses .pdb, .mmcif and .mmtf files; and builds data structures from the input. This original program is written in C++ programming language to ensure efficiency and consistency to organize structural information in an integral way. The novelty of the program lies in the addition of new structure-based biological algorithms and applications. This package also stands out from other similar libraries by being 1) faster and 2) accurate. We also provide detailed comparison of available parsers on the whole PDB database. The parser of MAT is designed in such a way that it allows quick extraction and organized loading of the core data structure. The same data structure is extended to accommodate information from the .mmcif and .mmtf file parsers. Tokenization of the data allows the extraction of information from disordered text, making it compatible for accurate identification of the entities present in the .pdb file. Additionally, we add a new approach of performance optimization by creating a few derived data structures, namely kD-Tree, Octree and graphs, for certain applications that need spatial coordinate calculations. MAT provides advanced data structure which is time efficient and is designed to avail reusability and consistency in a systematic framework. MAT parser can be accessed online through bitbucket at https://bitbucket.org/gazalk/pdb_parser/.
Redox potential defines functional states of adult hippocampal stem cells
Authors: Adusumilli Vijay S , Walker Tara L , Overall Rupert W , Klatt Gesa M , Zeidan Salma A , Fischer Tim J , Zocher Sara , Sykes Alex M , Reinhardt Susanne , Dahl Andreas , Kirova Dilyana G , Mansfeld Jörg , Rünker Annette E , Kempermann Gerd
Published: April 2019

Intracellular redox states regulate the balance between stem cell maintenance and activation. Increased levels of reactive oxygen species (ROS) are linked to proliferation and lineage specification. In contrast to this general principle, we show that in the hippocampus of adult mice it is the quiescent neural stem cells (NSCs) that maintain the highest ROS levels (hiROS). Classifying NSCs based on intracellular ROS content identified subpopulations with distinct molecular profiles, corresponding to functional states. Shifts in ROS content primed cells for a subsequent transition of cellular state, with lower cellular ROS content marking activity and differentiation. Physical activity, a known physiological activator of adult hippocampal neurogenesis, recruited the quiescent hiROS NSCs into proliferation via a transient Nox2-dependent ROS surge. In the absence of Nox2, baseline neurogenesis was unaffected, but the activity-induced increase in proliferation disappeared. These results describe a novel mechanism linking the modulation of cellular ROS by behavioral cues to the maintenance and activation of adult NSCs.

Highlights

Quiescent adult hippocampal stem cells are characterized by high intracellular ROS

Changes in intracellular ROS content precede changes in cellular state

Acute physical activity recruits quiescent cells into active proliferation

This recruitment is marked by a Nox2-dependent ROS spike in hiROS stem cells and represents an independent mode of cell cycle entry

Graphical Abstract
The Central Role of the Tail in Switching Off Myosin II in Cells
Authors: Yang Shixin , Lee Kyoung Hwan , Woodhead John L. , Sato Osamu , Ikebe Mitsuo , Craig Roger
Published: April 2019

Myosin II is a motor protein playing an essential role in cell motility. The molecule can exist as a polymer that pulls on actin to generate motion, or as an inactive monomer with a compact structure, in which its tail is folded and its two heads interact with each other. This conformation functions in cells as an energy-conserving storage and transport molecule. The mechanism of inhibition is not fully understood. We have carried out a 3D reconstruction of the switched-off form revealing for the first time multiple interactions between the tail and the two heads that trap ATP hydrolysis products, block actin binding, obstruct head phosphorylation, and prevent filament formation. Blocking these essential features of myosin function can explain the high degree of inhibition of the folded form of myosin, serving its energy-conserving, storage function in cells. The structure also suggests a mechanism for unfolding when activated by phosphorylation.
Sound comparison of seven TMS coils at matched stimulation strength
Authors: Koponen Lari M. , Goetz Stefan M. , Tucci Debara L. , Peterchev Angel V.
Published: April 2019

Background

Accurate data on the sound emitted by transcranial magnetic stimulation (TMS) coils is lacking.

Methods

We recorded the sound waveforms of seven coils with high bandwidth. We estimated the neural stimulation strength by measuring the induced electric field and applying a strength–duration model to account for different waveforms.

Results

Across coils, at maximum stimulator output and 25 cm distance, the sound pressure level (SPL) was 98–125 dB(Z) per pulse and 75–97 dB(A) for a 15 Hz pulse train. At 5 cm distance, these values were estimated to increase to 112–139 dB(Z) and 89–111 dB(A), respectively.

Conclusions

The coils’ sound was below, but near, relevant exposure limits for operators and may exceed some limits for the subject. Exposure standards may inadequately capture some risks to hearing. For persons near operating TMS coils we recommend hearing protection, and we consider it essential for the TMS subject.

Highlights

Coil click varies by over 20 dB(Z) between TMS coils at matched stimulation strength.

Close to TMS coil, sound pressure level may reach nearly 140 dB(Z).

For rTMS, the continuous sound level can exceed 110 dB(A).

Hearing protection is recommended during TMS, especially for the subject.
Atrx deletion in neurons leads to sexually-dimorphic dysregulation of miR-137 and spatial learning and memory deficits
Authors: Tamming Renee J. , Dumeaux Vanessa , Langlois Luana , Ellegood Jacob , Qiu Lily R. , Jiang Yan , Lerch Jason P. , Bérubé Nathalie G.
Published: April 2019

Mutations in the ATRX chromatin remodeler are associated with syndromic and non-syndromic intellectual disability. Emerging evidence points to key roles for ATRX in preserving neuroprogenitor cell genomic stability, whereas ATRX function in differentiated neurons and memory processes are still unresolved. Here, we show that Atrx deletion in mouse forebrain glutamatergic neurons causes distinct hippocampal structural defects identified by magnetic resonance imaging. Ultrastructural analysis revealed fewer presynaptic vesicles and an enlarged postsynaptic area at CA1 apical dendrite-axon junctions. These synaptic defects are associated with impaired long-term contextual memory in male, but not female mice. Mechanistically, we identify ATRX-dependent and sex-specific alterations in synaptic gene expression linked to Mir137 levels, a known regulator of presynaptic processes and spatial memory. We conclude that ablation of Atrx in excitatory forebrain neurons leads to sexually dimorphic outcomes on miR-137 and on spatial memory, identifying a promising therapeutic target for neurological disorders caused by ATRX dysfunction.

Summary statement

Ablation of the ATRX chromatin remodeler specifically in forebrain excitatory neurons of mice causes male-specific deficits in long-term spatial memory associated with miR-137 overexpression, transcriptional changes and structural alterations corresponding to pre- and post-synaptic abnormalities.
Origin of elevational replacements in a clade of nearly flightless birds – most diversity in tropical mountains accumulates via secondary contact following allopatric speciation
Authors: Cadena Carlos Daniel , Céspedes Laura N.
Published: April 2019

Tropical mountains are biodiversity hotspots. In particular, mountains in the Neotropics exhibit remarkable beta diversity reflecting species turnover along elevational gradients. Elevational replacements of species have been known since early surveys of the tropics, but data on how such replacements arise are scarce, limiting our understanding of mechanisms underlying patterns of diversity. We employed a phylogenetic framework to evaluate hypotheses accounting for the origin of elevational replacements in the genusScytalopus(Rhinocryptidae), a speciose clade of passerine birds with limited dispersal abilities occurring broadly in the Neotropical montane region. We found that species ofScytalopushave relatively narrow elevational ranges, closely related species resemble each other in elevational distributions, and most species replacing each other along elevational gradients are distantly related to each other. Although we cannot reject the hypothesis that a few elevational replacements may reflect parapatric speciation along mountain slopes, we conclude that speciation inScytalopusoccurs predominantly in allopatry within elevational zones, with most elevational replacements resulting from secondary contact of formerly allopatric lineages. Our study suggests that accumulation of species diversity in montane environments reflects colonization processes as opposed toin situdivergence even in dispersal-limited animals.
Impaired KCC2 phosphorylation leads to neuronal network dysfunction and neurodevelopmental pathogenesis
Authors: Pisella Lucie I. , Gaiarsa Jean-Luc , Diabira Diabé , Zhang Jinwei , Khalilov Ilgam , Duan JingJing , Kahle Kristopher T. , Medina Igor
Published: April 2019

KCC2 is a vital neuronal K+/Cl-co-transporter that is implicated in the etiology of numerous neurological diseases. It is subject to developmental dephosphorylation at threonine 906 and 1007, the functional importance of which remains unclear. We engineered mice with heterozygous phospho-mimetic mutations T906E and T1007E (KCC2E/+) to prevent the normal developmental dephosphorylation of these sites. Immature (P15) but not juvenile (P30)KCC2E/+mice exhibited altered GABAergic inhibition, an increased glutamate/GABA synaptic ratio, and higher seizure susceptibility.KCC2E/+mice also had abnormal ultra-sonic vocalizations at P10-P12 and impaired social behavior at P60. Post-natal bumetanide treatment restored network activity at P15 but not social behavior at P60. Our data show that post-translational KCC2 regulation controls the GABAergic developmental sequencein vivo. The post-translational deregulation of KCC2 could be a risk factor for the emergence of neurological pathology and the presence of depolarizing GABA is not essential for manifestation of behavioral changes.
Metabolic and metagenomic profiling of hydrocarbon-degrading microorganisms obtained from the deep biosphere of the Gulf of México
Authors: Moreno-Ulloa Aldo , Diaz Victoria Sicairos , Tejeda-Mora Javier A. , Macias Contreras Marla I. , Díaz Castillo Fernando , Guerrero Abraham , Sanchez Ricardo Gonzales , Duhalt Rafael Vazquez , Licea-Navarro Alexei
Published: April 2019

Marine microbes are capable of degrading hydrocarbons; however, those inhabiting the deep biosphere (>1000 m) remain largely unexplored. Microbial metabolism could lead to the generation of diverse chemistries (some with therapeutic activities), but the impact of using hydrocarbons as the sole source of microbial energy in the synthesis of metabolites, remains obscure. Here, we investigated the metagenomic and metabolomic profile of two deep-marine sediments (>1 200 m deep, designated as A7 and B18) collected from the Gulf of México (GM) when grown for 28 days with a simple mixture of 4 hydrocarbons and complex hydrocarbon mixture (petroleum API 40) as their sole source of energy. State of the art techniques and analysis (e.g., Global Natural Products Social Molecular Networking, network annotation propagation [NAP], and MS2LDA) were used to describe the chemistries associated to the microbial utilization of hydrocarbons. The metagenomic sequencing analysis suggests a predominant abundance of Proteobacteria in environmental and API 40-enriched samples, while the abundance of Pseudomonas increased after microbial growth with API 40. The metabolomic analysis suggests the presence of diverse chemistries predominantly associated with lipid and lipid-like and phenyl propanoids and polyketides superclass (Classyfire annotation). Hydrocarbon derivatives were detected as carboxylic acids (e.g., azelaic and sebacic acid) or alcohols, while non-hydrocarbon related chemistries were also detected including tetracycline-related metabolites and sphinganines. Our study provides valuable chemical and microbiological information of microbes inhabiting one of the most understudied ecosystems in the earth, the deep marine biosphere.
Molecular Transport across Lipid Membranes Controls Cell-Free Expression Level and Dynamics
Authors: Caveney Patrick M. , Dabbs Rosemary M. , McClintic William T. , Collier C. Patrick , Simpson Michael L.
Published: April 2019

Essential steps toward synthetic cell-like systems require controlled transport of molecular species across the boundary between encapsulated expression and the external environment. When molecular species (e.g. small ions, amino acids) required for expression (i.e. expression resources) may cross this boundary, this transport process plays an important role in gene expression dynamics and expression variability. Here we show how the location (encapsulated or external) of the expression resources controls the level and the dynamics of cell-free protein expression confined in permeable lipid vesicles. Regardless of the concentration of encapsulated resources, external resources were essential for protein production. Compared to resource poor external environments, plentiful external resources increased expression by ~7-fold, and rescued expression when internal resources were lacking. Intriguingly, the location of resources and the membrane transport properties dictated expression dynamics in a manner well predicted by a simple transport-expression model. These results suggest membrane engineering as a means for spatio-temporal control of gene expression in cell-free synthetic biology applications and demonstrate a flexible experimental platform to understand the interplay between membrane transport and expression in cellular systems.
Proton-control of transitions in an amino-acid transporter
Authors: Wu Z. , Alibay I. , Newstead S. , Biggin P. C.
Published: April 2019

Amino acid transport into the cell is often coupled to the proton electrochemical gradient, as found in the solute carrier (SLC) 36 family of proton coupled amino acid transporters (PATs). Although no structure of a human PAT exists, the crystal structure of a related homolog, GkApcT, from bacteria has recently been solved in an inward occluded state and allows an opportunity to examine how protons are coupled to amino acid transport. Our working hypothesis is that release of the amino acid substrate is facilitated by deprotonation of a key glutamate residue (E115), located at the bottom of the binding pocket and which forms part of the intracellular gate, allowing the protein to transition from an inward-occluded to an inward-open conformation. During unbiased molecular dynamics, we observed a transition from the inward-occluded state captured in the crystal structure, to a much more open state, which we consider likely to be representative of the inward-open substrate release state. To explore this and the role of protons in these transitions, we have used umbrella sampling to demonstrate that the transition from inward-occluded to inward-open is more energetically favourable when E115 is deprotonated. That E115 is likely to be protonated in the inward-occluded state and deprotonated in the inward-open state is further confirmed via the use of absolute binding free energies. Finally, we also show, via the use of absolute binding free energy calculations, that the affinity of the protein for alanine is very similar regardless of either the state or the protonation of E115, presumably reflecting key interactions deep within the binding cavity. Together, our results give a detailed picture of the role of protons in driving one of the major transitions in this transporter.

Significance Statement

For transporter proteins that utilize the proton gradient to drive the uptake of solutes, the precise mechanistic details of proton-coupling remain poorly understood. Structures can only infer the position of protons. All-atom molecular dynamics simulations however, are the ideal complementary tool. Here, we report extensive MD simulations on GkApcT, a proton-coupled transporter. We observe a spontaneous transition from the crystallographically derived inward-occluded state, to an inward-open state, which we then characterise with umbrella sampling and absolute binding free energy calculations. The results suggest that a conserved glutamate is protonated in the inward-occluded state and subsequent deprotonation of this glutamate allows the transporter to move into the inward-open state, thus facilitating substrate release into the cell.
Mutational Analysis of an Intrinsically Disordered Region in the E. coli Phosphatase CheZ, a Regulator of Chemotaxis
Authors: Ward Amber , Kamegne Marilyne , Dillard Paulette , Moore John T.
Published: April 2019

As a model for Intrinsically Disordered Region (IDR) structure-function, we investigated the IDR present in the E. coli chemotaxis regulatory phosphatase CheZ. The CheZ IDR (amino acids 169-200) is attractive for study because CheZ is part of an exceptionally well characterized and easily tractable system and has an available high-resolution crystal structure. The CheZ IDR contains striking evolutionarily conserved regions that are functionally critical as shown by the fact that changes in single specific amino acids in the conserved IDR regions are able to abolish normal chemotaxis. We have focused on identifying suppressor mutations in the coding region of CheZ G188E, a variant with a >80% reduction in chemotactic swarm activity. Our screen identified 6 suppressor mutations that restored swarm activity to wild-type levels. Interestingly, the suppressor mutations were found not in the CheZ coding region, but in CheY, the phosphoprotein substrate of the CheZ phosphatase. The 6 suppressor mutations were restricted to two amino acid codons. Three suppressor mutations were found at position CheY A42 and three at position CheY M60. A model for how the changes in CheY restore CheZ activity is presented. These studies in dissection of the CheZ IDR will be useful in extending our understanding of IDR structure-function. The accumulating knowledge of IDR principles will be a significant component of a broadening understanding of protein biophysics with direct implications in basic protein structure and protein engineering research.
Global analyses of the dynamics of mammalian microRNA metabolism
Authors: Kingston Elena R. , Bartel David P.
Published: April 2019

Rates of production and degradation together specify microRNA (miRNA) abundance and dynamics. Here, we used approach-to-equilibrium metabolic labeling to assess these rates for 176 miRNAs in contact-inhibited mouse embryonic fibroblasts (MEFs), 182 miRNAs in dividing MEFs, and 136 miRNAs in mouse embryonic stem cells (mESCs). MicroRNA duplexes, each comprising a mature miRNA and its passenger strand, are produced at rates as fast as 114 ± 49 copies/cell per min, which exceeds rates reported for any mRNAs. These duplexes are rapidly loaded into Argonaute, with <10 min typically required for duplex loading and silencing-complex maturation. Within Argonaute, guide strands have stabilities that vary by 100-fold. Half-lives also vary globally between cell lines, with median values ranging from 6.3 to 34 h in mESCs and contact-inhibited MEFs, respectively. Moreover, relative half-lives for individual miRNAs vary between cell types, implying the influence of cell-specific factors in dictating turnover rate. The apparent influence of miRNA regions most important for targeting, together with the effect of one target on miR-7a-5p accumulation, suggest that targets fulfill this role. Analysis of the tailing and trimming of miRNA 3′ termini showed that the flux was typically greatest through the isoform tailed with a single uridine, although changes in this flux did not correspond to changes in stability, which suggested that the processes of tailing and trimming might be independent from that of decay. Together these results establish a framework for describing the dynamics and regulation of miRNAs throughout their lifecycle.
UNI-EM: An Environment for Deep Neural Network-Based Automated Segmentation of Neuronal Electron Microscopic Images
Authors: Urakubo Hidetoshi , Bullmann Torsten , Kubota Yoshiyuki , Oba Shigeyuki , Ishii Shin
Published: April 2019

Recently, there has been a rapid expansion in the field of micro-connectomics, which targets the three-dimensional (3D) reconstruction of neuronal networks from a stack of two-dimensional (2D) electron microscopic (EM) images. The spatial scale of the 3D reconstruction grows rapidly owing to deep neural networks (DNNs) that enable automated image segmentation. Several research teams have developed their own software pipelines for DNN-based segmentation. However, the complexity of such pipelines makes their use difficult even for computer experts and impossible for non-experts. In this study, we developed a new software program, called UNI-EM, that enables 2D- and 3D-DNN-based segmentation for non-computer experts. UNI-EM is a software collection for DNN-based EM image segmentation, including ground truth generation, training, inference, postprocessing, proofreading, and visualization. UNI-EM comes with a set of 2D DNNs, i.e., U-Net, ResNet, HighwayNet, and DenseNet. We further wrapped flood-filling networks (FFNs) as a representative 3D DNN-based neuron segmentation algorithm. The 2D- and 3D-DNNs are known to show state-of-the-art level segmentation performance. We then provided two-example workflows: mitochondria segmentation using a 2D DNN as well as neuron segmentation using FFNs. Following these example workflows, users can benefit from DNN-based segmentation without any knowledge of Python programming or DNN frameworks.
Untangling featural and conceptual object representations
Authors: Grootswagers Tijl , Robinson Amanda K. , Shatek Sophia M. , Carlson Thomas A.
Published: April 2019

How are visual inputs transformed into conceptual representations by the human visual system? The contents of human perception, such as objects presented on a visual display, can reliably be decoded from voxel activation patterns in fMRI, and in evoked sensor activations in MEG and EEG. A prevailing question is the extent to which brain activation associated with object categories is due to statistical regularities of visual features within object categories. Here, we assessed the contribution of mid-level features to conceptual category decoding using EEG and a novel fast periodic decoding paradigm. Our study used a stimulus set consisting of intact objects from the animate (e.g., fish) and inanimate categories (e.g., chair) and scrambled versions of the same objects that were unrecognizable and preserved their visual features (Long, Yu, & Konkle, 2018). By presenting the images at different periodic rates, we biased processing to different levels of the visual hierarchy. We found that scrambled objects and their intact counterparts elicited similar patterns of activation, which could be used to decode the conceptual category (animate or inanimate), even for the unrecognizable scrambled objects. Animacy decoding for the scrambled objects, however, was only possible at the slowest periodic presentation rate. Animacy decoding for intact objects was faster, more robust, and could be achieved at faster presentation rates. Our results confirm that the mid-level visual features preserved in the scrambled objects contribute to animacy decoding, but also demonstrate that the dynamics vary markedly for intact versus scrambled objects. Our findings suggest a complex interplay between visual feature coding and categorical representations that is mediated by the visual system’s capacity to use image features to resolve a recognisable object.
Diverse phenotypic responses and phosphate content in foxtail millet genotypes under greenhouse and field conditions
Authors: Ceasar S. Antony , Ramakrishnan M. , Vinod K. K. , Roch G. Victor , Upadhyaya Hari D. , Baker Alison , Ignacimuthu S.
Published: April 2019

Phosphorous (P) is an important macronutrient for the growth of all agricultural crops. This study reports phenotype analysis for P responses in field (two different seasons, monsoon and summer) and greenhouse, using 54 genotypes of foxtail millet (Setaria italica) under P-fertilized (P+) and unfertilized (P-) conditions. Variation was seen for plant height, leaf number and length, tillering ability and seed yield traits. Genotypes ISe 1234 and ISe 1541 were P+ responders, and the genotypes ISe 1181, ISe 1655, ISe 783 and ISe 1892 tend more towards low P tolerance for total seed yield. Genotypes that performed well under P-conditions were almost as productive as genotypes that performed well under P+ conditions suggesting some genotypes are well adapted to nutrient-poor soils. In the greenhouse, significant variation was seen for root hair density and root hair number and for fresh and dry weights of shoot and root under P-stress. However, there was not much difference in the shoot and root total P and inorganic phosphate (Pi) levels of five selected high and low responding genotypes. In the root and leaf tissues, total P and Pi contents of five high responding genotypes were higher than the five low responding genotypes.

Highlight

Enormous phenotypic and phosphate content variation of foxtail millet under low-phosphate supply in greenhouse and natural field conditions identifies genotypic plasticity for future breeding for improved P use efficiency.
Membrane dynamics of Notch-bound γ-secretase produces two distinct Notch conformations
Authors: Tang N. , Dehury B. , Kepp K. P.
Published: April 2019

Cleavage of Notch by the major intramembrane aspartyl protease complex γ-secretase is a central event in cell regulation and is also important to Alzheimer’s disease, with more than 200 mutations in the catalytic subunit of γ-secretase (PS1) causing severe early-onset forms of the disease. Recently, cryogenic electron microscopy (cryo-EM) has revealed the electron density of the protein-Notch complex in frozen solution, indicating major changes upon substrate binding and a possible helix unwinding to expose peptide bonds. In order understand the all-atom dynamics that cause this process, and to test the Notch binding in a membrane protein rather than solution, we developed an all-atom model of mature wild-type γ-secretase bound to Notch in a complete membrane-water system and studied the system using three independent 500-nanosecond molecular dynamics simulations. Our ensembles are in essential agreement with known cryo-EM data. As in previous simulations we find unusual β-strand transitions in exposed parts of PS1. We also observe the atomic helix motions that cause loss of helicity in bound Notch by direct comparison to corresponding 500 ns simulations of free Notch, in particular five residues to the N-terminal site of the primary cleavage site. Most importantly, we identify three conformation states, with two of them differing in the Notch-bound catalytic site. These dynamics produce a ping-pong relationship of positioning the S3 cleavage sites of Notch relative to the aspartates. These conformation states are not visible in the cryo-EM data; probably the density is an average snapshot of the two states. Our identified conformation states rationalize how Notch cleavage can be imprecise and yield multiple products. Our identified conformation states may aid efforts to develop conformation-selective drugs that target C99 and Notch cleavage differently.

Statement of Significance

The atomic dynamics underlying cleavage of Notch by γ-secretase in the membrane is of major biological importance. Electron microscopy has revealed the protein-Notch complex in frozen solution, showing major changes upon substrate binding and helix unwinding to expose peptide bonds, but does not explain why substrate cleavage is imprecise and produces several products. Our model of wild-type γ-secretase bound to Notch in a complete membrane-water system equilibrated by 3 × 500 nanoseconds of molecular dynamics strongly complements the electron microscopy data: We identify the specific loop and helix motions that cause the β-strand transitions in PS1 and the loss of helicity in specific residues of bound Notch. We identify different conformations of Notch, which importantly affect the S3 cleavage site; the open state may cause the imprecise cleavage with earlier release of products. Our identified states can aid development of conformation-selective drugs that target C99 and Notch cleavage differently.
Time-resolved X-ray reflection phases of the nearly forbidden Si(222) reflection under laser excitation
Authors: Tsai Yi-Wei , Chang Ying-Yi , Lee Jey-Jau , Liu Wen-Chung , Wu Yu-Hsin , Liu Wei-Rein , Liu Hsing-Yu , Lee Kun-Yuan , Weng Shih-Chang , Sheu Hwo-Shuenn , Chiu Mau-Sen , Lee Yin-Yu , Hsu Chia-Hung , Chang Shih-Lin
Published: April 2019

The covalent electron density, which makes Si(222) measurable, is subject to laser excitation. The three-wave Si(222)/(13 {\overline 1}) diffraction at 7.82 keV is used for phase measurements. It is found that laser excitation causes a relative phase change of around 4° in Si(222) in the first 100 ps of excitation and this is gradually recovered over several nanoseconds. This phase change is due to laser excitation of covalent electrons around the silicon atoms in the unit cell and makes the electron density deviate further from the centrosymmetric distribution.
Abnormally long audit report lags and future stock price crash risk: evidence from China
Authors: Habib Ahsan , Huang Hedy Jiaying
Published: April 2019

Purpose

Although a substantial body of literature investigates the determinants of audit report lag (ARL), scant empirical evidence exists on the consequences of ARL. The purpose of this paper is to examine the association between abnormally long ARL and future stock price crash risk.

Design/methodology/approach

This quantitative study employed a large scale (14,445 firm-year observations) of annual financials, audit and ownership information for the Chinese listed companies during 2002–2013 which were retrieved from the China Stock Market and Accounting Research database.

Findings

This study finds evidence that abnormally long ARL increases the risk of a future stock price crash. Furthermore, the study finds that this adverse consequence is more pronounced for firms with a poor internal control environment.

Practical implications

Recently literature started to explore the consequences of abnormal ARL such as going concern audit opinion and restatements in the subsequent periods. This paper reveals that abnormal ARL has consequences for investor wealth losses as well. This is relevant in China, where the ongoing economic growth has attracted, and will continue to attract, a growing body of domestic and international investors. Understanding what factors could expose investors to wealth losses is of paramount importance for allocating their scarce capital.

Originality/value

This study extends the scant literature on the consequences of ARL, and provides useful insights for the Chinese regulatory authorities when considering the appropriateness of the current filing deadline for listed firms.
Comparison of advanced economies’ performance in bubbles mitigation
Authors: Gallego Neira Emilio , Martínez de Ibarreta Carlos
Published: April 2019

Purpose

This paper aims to analyze the effectiveness of macroprudential and fiscal policies taken from a sample of ten advanced economies in relation to the mitigation of real-estate and credit bubbles by comparing their performance.

Design/methodology/approach

This comparison is elaborated with a seemingly unrelated regression methodology, which allows the assessment of individual countries’ performance and improves the estimation of the dependent variables versus an individual regression.

Findings

The analysis concludes that countercyclical measures have been more effective to control the growth of household debt. Furthermore, this study validates that macroprudential measures focused on the residential sector meet their objective of controlling the growth of house prices, whereas those macroprudential measures with more generic targets are effective to control the growth of household debt.

Originality/value

As opposed to previous panel-regression studies, which have analyzed the performance of macroprudential and fiscal measures in generic terms, this paper compares the performance of these tools in ten advanced economies. Based on the analysis performed, several recommendations are derived for policymakers.
The internationalization process of Chinese research institutions since the reform and opening-up
Authors: Chen Wu , Li Yanping
Published: April 2019

Purpose

The purpose of this paper is to systematically review the evolution, characteristics, motivations, entry patterns, organizational structure and effectiveness of the internationalization of Chinese research institutions in the past 40 years of reform and opening-up.

Design/methodology/approach

This paper describes the evolution and practice of Chinese research institutions “going out” by constructing a theoretical framework diagram and uses official statistics and existing research to explain the authors’ points.

Findings

The research results show that the internationalization of research institutions has undergone four phases: sprout period, starting period, adjustment period and accelerating period. It shows a rapid growth of investment scale, diversification of investment entities, rich and varied forms, and transition to major countries along the “One Belt and One Road.” Expanding the international market, tracking and acquiring technological frontiers, nurturing domestic R&D talents, and evading the risks of political, economic, cultural and scientific differences between home and host countries are the main motivations for Chinese research institutions to “go global.” Multinational corporations have entered the host country with modes such as M&A, greenfield investment and joint R&D alliances in their own strengths and also presented a variety of organizational structures such as integrated R&D networks.

Originality/value

This paper systematically summarizes the internationalized experience model of research institutions with Chinese characteristics since the reform and opening-up. From the perspective of internationalization model transformation, policy integration and cooperation among emerging economies, it presents the opportunities and challenges faced by the research institutions in the process of internationalization and provides a theoretical basis for improving the internationalization ability of research institutions.
End-to-end learning via a convolutional neural network for cancer cell line classification
Authors: Akogo Darlington A. , Palmer Xavier-Lewis
Published: April 2019

Purpose

Computer vision for automated analysis of cells and tissues usually include extracting features from images before analyzing such features via various machine learning and machine vision algorithms. The purpose of this work is to explore and demonstrate the ability of a Convolutional Neural Network (CNN) to classify cells pictured via brightfield microscopy without the need of any feature extraction, using a minimum of images, improving work-flows that involve cancer cell identification.

Design/methodology/approach

The methodology involved a quantitative measure of the performance of a Convolutional Neural Network in distinguishing between two cancer lines. In their approach, they trained, validated and tested their 6-layer CNN on 1,241 images of MDA-MB-468 and MCF7 breast cancer cell line in an end-to-end fashion, allowing the system to distinguish between the two different cancer cell types.

Findings

They obtained a 99% accuracy, providing a foundation for more comprehensive systems.

Originality/value

Value can be found in that systems based on this design can be used to assist cell identification in a variety of contexts, whereas a practical implication can be found that these systems can be deployed to assist biomedical workflows quickly and at low cost. In conclusion, this system demonstrates the potentials of end-to-end learning systems for faster and more accurate automated cell analysis.