bluuebunny/crossref_metadata_2025 huggingface dataset:
Contrast Energy and Contour Interaction
Authors: Bedell Harold E. , Siderov John , Pluháček František
Published: December 2019

SIGNIFICANCE

Contour interaction describes an impairment of visual acuity produced by nearby flanking features, which exerts a significant impact in many clinical tests of visual acuity. Our results indicate that the magnitude of interaction depends either on the flanker contrast energy (i.e., the product of flanker contrast and width) or the flanker contrast alone, depending on the contrast energy of the flankers.

PURPOSE

The discrimination of acuity targets is impaired by the presence of nearby flanking contours, a phenomenon known as contour interaction.

METHODS

In this study, we measured percent correct identification for threshold size, high-contrast Sloan letters at the fovea and at 5° in the inferior visual field for different combinations of flanking-bar width, and Weber contrast corresponding to specific fixed values of contrast energy (width × contrast, in %-min arc).

RESULTS

For flanking bars with low-contrast energy, contour interaction exhibited no systematic dependence on the flanking-bar width. However, when the flanking bars had higher contrast energy, narrower high-contrast bars produced significantly greater contour interaction than wider bars of lower contrast.

CONCLUSIONS

The results are consistent with the interpretation that contour interaction depends primarily on the contrast energy of flanking contours when their contrast energy is low. As the contrast energy of the flanking contours increases, the magnitude of contour interaction depends on the flanker contrast. For high-contrast flanking contours, the magnitude of contour interaction saturates when the width of the flanking contours is approximately 20% of letter size.
Psychrobacillus vulpis sp. nov., a new species isolated from faeces of a red fox in Spain
Authors: Rodríguez Miguel , Reina José Carlos , Béjar Victoria , Llamas Inmaculada
Published: December 2019

A facultative anaerobic, chemoheterotrophic, endospore-forming, Gram-stain-positive rod, designated as strain Z8T, was isolated from red fox (Vulpes vulpes) faeces sampled at Tablas de Daimiel National Park, Ciudad Real, Spain. Strain Z8T grew at 0–37 °C (optimum, 28 °C), in the presence of 0–5.5 % (w/v) NaCl (2.5 %, w/v) and at pH 6–10 (pH 7). The strain was motile and positive for catalase, oxidase, H2S and siderophore production, acid and alkaline phosphatases, and N-acetylglucosamine, adipic acid and malate assimilation. It hydrolysed starch, DNA, l-tyrosine, Tween 20, Tween 80 and lecithovitellin. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Z8T is a member of the genus

Psychrobacillus

, showing high sequence similarity to

Psychrobacillus lasiicapitis

NEAU-3TGS17T (99.2 %) and

Psychrobacillus soli

NHI-2TT (99.1 %), and around 98 % to other known species of the genus

Psychrobacillus

. Digital DNA–DNA hybridization and average nucleotide identity values were lower than 24 and 79 %, respectively, with the most related species. In silico G+C content was 35.9 mol%. The major cellular fatty acids of strain Z8T were iso-C14 : 0, iso-C15 : 0 and anteiso-C15 : 0. The novel strain contained diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as predominant polar lipids, and the main respiratory isoprenoid quinone was MK-8. Based on the 16S rRNA phylogenetic analysis, together with MLSA (recA, rpoB and gyrB), phylogenomic, chemotaxonomic and phenotypic results, we demonstrate that strain Z8T represents a novel species of the genus Psychrobacillus, for which the name Psychrobacillus vulpis sp. nov., is proposed. The type strain is Z8T (=CECT 9721T=LMG 31001T).
Luteimonas yindakuii sp. nov. isolated from the leaves of Dandelion (Taraxacum officinale) on the Qinghai-Tibetan Plateau
Authors: Zhang Sihui , Wang Xiaoxia , Yang Jing , Lu Shan , Lai Xin-He , Jin Dong , Pu Ji , Li Junqin , Huang Yuyuan , Zhang Gui , Zhu Wentao , Huang Ying , Tian Zhi , Zhou Juan , Dong Kui , Lei Wenjing , Ren Zhihong , Wang Suping , Xu Jianguo
Published: December 2019

Two strains (S-1072T and 1626) of Gram-stain-negative, oxidase- and catalase-positive, aerobic, rod-shaped, motile bacteria with a single polar flagellum, were isolated from the leaves of Dandelion (Taraxacum officinale) on the Qinghai–Tibet Plateau of China. The cells grew optimally at 28 °C, pH 7.0 and with 0.5 % (w/v) NaCl on brain–heart infusion agar. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains S-1072T and 1626 belong to the genus

Luteimonas

, sharing the highest similarity with

Luteimonas arsenica

CCTCC AB 2014326T (97.0 %),

Luteimonas terricola

CGMCC 1.8985T (96.9 %) and

Luteimonas aestuarii

KCTC 22048T (96.6 %). The phylogenomic tree indicated that strains S-1072T and 1626 were most closely related to

Luteimonas abyssi

CGMCC 1.12611T. The biochemical characteristics revealed that strains S-1072T and 1626 could neither produce trypsin nor produce acid from d-glucose, N-acetylglucosamine and maltose, distinguishing them from four closest relatives. The DNA G+C contents of strains S-1072T and 1626 were 69.2 and 69.3 mol% respectively. The digital DNA–DNA hybridization values of our isolates with their four closely related species were below the 70 % threshold. The predominant menaquinone was Q-8 (98.7 %) and the major polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids (>10 %) were iso-C15 : 0, iso-C16 : 0 and summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1
ω9c). Based on the data obtained, strains S-1072T and 1626 should be classified as a novel species of the genus

Luteimonas

, for which the name Luteimonas yindakuii sp. nov. is proposed. The type strain is S-1072T (=CGMCC 1.13927T=JCM 33487T).
Wickerhamomyces psychrolipolyticus f.a., sp. nov., a novel yeast species producing two kinds of lipases with activity at different temperatures
Authors: Shimizu Yumi , Konno Yusuke , Tomita Yosuke
Published: December 2019

Two yeast strains isolated from soil collected in Hokkaido, Japan, were found to secrete two extracellular lipases that exhibited activities at both 25 and 4 °C. Both strains could utilize olive oil, rapeseed oil, lard and fish oil as sole carbon sources. The similarity of the D1/D2 domain of the large subunit ribosomal RNA (LSU rRNA) sequence of these yeast strains to that of other yeasts in the GenBank database was very low (<96 %). The phylogenetic trees based on the LSU rRNA sequences and translation elongation factor-1-α (tef1-α) sequences indicated that both strains represented a member of the Wickerhamomyces /Candida clade. Sexual reproduction was not observed. The name Wickerhamomyces psychrolipolyticus f.a., sp. nov is proposed for this newly described yeast species producing cold-active lipases. This novel species is distinguishable from the type strains of other related species, Wickerhamomyces alni, Candida ulmi and Candida quercuum due to their abilities to grow at 4 to 30 °C, to produce lipase that is active also at 4 °C and to assimilate soluble starch.
Towards establishing internal validity for correlated gene expression measures in imaging genomics of functional networks: why distance corrections and external face validity alone fall short. Reply to “Distance is not everything in imaging genomics of functional networks: reply to a commentary on Correlated gene expression supports synchronous activity in brain networks”
Authors: Pantazatos Spiro P. , Schmidt Mike
Published: December 2019

The primary claim of the Richiardi et. al. 2015 Science article1is that a measure of correlated gene expression, significant strength fraction (SSF), is related to resting state fMRI (rsfMRI) networks. However, there is still debate about this claim and whether spatial proximity, in the form of contiguous clusters, accounts entirely, or only partially, for SSF2,3. Here, thirteen distributed networks were simulated by combining 34 contiguous clusters randomly placed throughout cortex, with resulting edge distance distributions similar to rsfMRI networks. Cluster size was modulated (6-15mm radius) to test its influence on SSF false positive rate (SSF-FPR) among the simulated ‘noise’ networks. The contribution of rsfMRI networks on SSF-FPR was examined by comparing simulations using: 1) all cortical samples 2) all samples with non-rsfMRI cluster centers and 3) only non-rsfMRI samples. Results show that SSF-FPR is influenced only by cluster size (r>0.9, p<0.001), not by rsfMRI samples. Simulations using 14mm radius clusters most resembled rsfMRI networks. When thresholding at p<10-4, the SSF-FPR was 0.47. Genes that maximize SF have highglobalspatial autocorrelation. In conclusion, SSF is unrelated to rsfMRI networks. The main conclusion of Richiardi et. al. 2015 is based on a finding that is ∼50% likely to be a false positive, not less than 0.01% as originally reported in the article1. We discuss why distance corrections alone and external face validity are insufficient to establish a trustworthy relationship between correlated gene expression measures and rsfMRI networks, and propose more rigorous approaches to preclude common pitfalls in related studies.
An evolution-based high-fidelity method of epistasis measurement: theory and application to influenza
Authors: Pedruzzi Gabriele , Rouzine Igor M.
Published: December 2019

Linkage effects in a multi-locus population strongly influence its evolution. The models based on the traveling wave approach enable us to predict the speed of evolution and the statistics of phylogeny. However, predicting the evolution of specific sites and pairs of sites in the multi-locus context remains a mathematical challenge. In particular, the effects of epistasis, the interaction of gene regions contributing to phenotype, is difficult both to predict theoretically and detect experimentally in sequence data. A large number of false interactions arise from stochastic linkage effects and indirect interactions, which mask true interactions. Here we develop a method to filter out false-positive interactions. We start by demonstrating that the averaging of the two-way haplotype frequencies over a multiple independent populations is necessary but not sufficient, because it still leaves high numbers of false interactions. To compensate for this residual stochastic noise, we develop a triple-way haplotype method isolating true interactions. The fidelity of the method is confirmed using simulated genetic sequences evolved with a known epistatic network. The method is then applied to a large database sequences of neurominidase protein of influenza A H1N1 obtained from various geographic locations to infer the epistatic network responsible for the difference between the pre-pandemic virus and the pandemic strain of 2009. These results present a simple and reliable technique to measure site-site interactions from sequence data.

Author’s summary

Interaction of genomic sites creating “fitness landscape” is very important for predicting the escape of viruses from drugs and immune response and for passing through fitness valleys. Many efforts have been invested into measuring these interactions from DNA sequence sets. Unfortunately, reproducibility of the results remains low, due partly to a very small fraction of interaction pairs, and partly to stochastic noise intrinsic for evolution masking true interactions. Here we propose a method based on analysis of genetic sequences at three genomic sites to clean stochastic linkage and apply it to influenza virus sequence data.
A Holistic Analysis of the Intestinal Stem Cell Niche Network
Authors: Hansen Darrick M. , Giles Paloma Ivon Meneses , He Xi C. , Chen Shiyuan , Paulson Ariel , Dekaney Christopher M. , Wang Jennifer , Hu Deqing , Venkatraman Aparna , Kim Woosook , Kaddis John , Olack Barbara J. , Dunn James C.Y. , Kuo Calvin , Henning Susan , Hanash Alan M. , Houchen Courtney W. , Lynch John , Martin Martin G. , Niland Joyce C. , Stelzner Matthias , Wong Melissa , Wang Timothy C. , Yu Jian , Yan Kelley , Li Linheng
Published: December 2019

Although many studies into the intestinal stem cell (ISC) niche have been carried out, they have focused on the role of a single cell type or molecular signal. However, no holistic comparisons of the predominant cell types and signals present within the intestinal mucosa have been conducted to date. We utilize bulk RNA sequencing to profile 20 different mucosal cell types covering four major cell categories: epithelial, stromal, endothelial and immune. We further examined the stromal signaling environment using scRNAseq to provide a more comprehensive view of the signaling microenvironment within the intestinal mucosa. We identified the primary signals for the major ISC regulatory pathways and their respective cellular sources. Our analysis suggests that a ‘niche network’ exists, with no single cell type being responsible for ISC self-renewal, proliferation, or differentiation; rather, each cell type within the network carries out specific functions in a highly cooperative and coordinated manner.
AnthOligo: Automating the design of oligonucleotides for capture/enrichment technologies
Authors: Jayaraman Pushkala , Mosbruger Timothy , Hu Taishan , Tairis Nikolaos G , Wu Chao , Clark Peter M , D’Arcy Monica , Ferriola Deborah , Mackiewicz Katarzyna , Gai Xiaowu , Monos Dimitrios , Sarmady Mahdi
Published: December 2019

A number of methods have been devised to address the need for targeted genomic resequencing. One of these methods, Region-specific extraction (RSE) of DNA is characterized by the capture of long DNA fragments (15-20 kb) by magnetic beads, after enzymatic extension of oligonucleotides hybridized to selected genomic regions. Facilitating the selection of the most optimal capture oligos targeting a region of interest, satisfying the properties of temperature (Tm) and entropy (ΔG), while minimizing the formation of primer dimers in a pooled experiment is therefore necessary. Manual design and selection of oligos becomes an extremely arduous task complicated by factors such as length of the target region and number of targeted regions. Here we describe, AnthOligo, a web-based application developed to optimally automate the process of generation of oligo sequences to be used for the targeting and capturing the continuum of large and complex genomic regions. Apart from generating oligos for RSE, this program may have wider applications in the design of customizable internal oligos to be used as baits for gene panel analysis or even probes for large-scale comparative genomic hybridization (CGH) array processes.

Implementation and Availability

The application written in Java8 and run on Tomcat9 is a lightweight Java Spring MVC framework that provides the user with a simple interface to upload an input file in BED format and customize parameters for each task. A Redis-likeMapReduceframework is implemented to run sub-tasks in parallel to optimize time and system resources alongside a ‘task-queuing’ system that runs submitted jobs as a server-side background daemon. The task of probe design in AnthOligo commences when a user uploads an input file and concludes with the generation of a result-set containing an optimal set of region-specific oligos.

AnthOligo is currently available as a public web application with URL:http://antholigo.chop.edu.
Impact of temperature onLegionella pneumophila, its protozoan host cells, and the microbial diversity of the biofilm community of a pilot cooling tower
Authors: Paniagua Adriana Torres , Paranjape Kiran , Hu Mengqi , Bédard Émilie , Faucher Sébastien
Published: December 2019

Legionella pneumophila (Lp)is a waterborne bacterium known for causing Legionnaires’ Disease, a severe pneumonia. Cooling towers are a major source of outbreaks, since they provide ideal conditions forLpgrowth and produce aerosols. In such systems,Lptypically grow inside protozoan hosts. Several abiotic factors such as water temperature, pipe material and disinfection regime affect the colonization of cooling towers byLp.The local physical and biological factors promoting the growth ofLpin water systems and its spatial distribution are not well understood. Therefore, we built a lab-scale cooling tower to study the dynamics ofLpcolonization in relationship to the resident microbiota and spatial distribution. The pilot was filled with water from an operating cooling tower harboring low levels ofLp. It was seeded withVermamoeba vermiformis, a natural host ofLp, and then inoculated withLp.After 92 days of operation, the pilot was disassembled, the water was collected, and biofilm was extracted from the pipes. The microbiome was studied using16S rRNAand18S rRNAgenes amplicon sequencing. The communities of the water and of the biofilm were highly dissimilar. The relative abundance ofLegionellain water samples reached up to 11% whereas abundance in the biofilm was extremely low (≤0.5 %). In contrast, the host cells were mainly present in the biofilm. This suggest thatLpgrows in host cells associated with biofilm and is then released back into the water following host cell lysis. In addition, water temperature shaped the bacterial and eukaryotic community of the biofilm, indicating that different parts of the systems may have different effects onLegionellagrowth.
Automatic Detection of Synaptic Partners in a Whole-BrainDrosophilaEM Dataset
Authors: Buhmann Julia , Sheridan Arlo , Gerhard Stephan , Krause Renate , Nguyen Tri , Heinrich Larissa , Schlegel Philipp , Lee Wei-Chung Allen , Wilson Rachel , Saalfeld Stephan , Jefferis Gregory , Bock Davi , Turaga Srinivas , Cook Matthew , Funke Jan
Published: December 2019

The study of neural circuits requires the reconstruction of neurons and the identification of synaptic connections between them. To scale the reconstruction to the size of whole-brain datasets, semi-automatic methods are needed to solve those tasks. Here, we present an automatic method for synaptic partner identification in insect brains, which uses convolutional neural networks to identify post-synaptic sites and their pre-synaptic partners. The networks can be trained from human generated point annotations alone and require only simple post-processing to obtain final predictions. We used our method to extract 244 million putative synaptic partners in the fifty-teravoxel full adult fly brain (FAFB) electron microscopy (EM) dataset and evaluated its accuracy on 146,643 synapses from 702 neurons with a total cable length of 312 mm in four different brain regions. The predicted synaptic connections can be used together with a neuron segmentation to infer a connectivity graph with high accuracy: between 92% and 96% of edges linking connected neurons are correctly classified as weakly connected (less than five synapses) and strongly connected (at least five synapses). Our synaptic partner predictions for the FAFB dataset are publicly available, together with a query library allowing automatic retrieval of up- and downstream neurons.
Humans use a local code for tactile perception
Authors: Bhattacharjee Arindam , Braun Christoph , Schwarz Cornelius
Published: December 2019

Humans are classically thought to use either spectral decomposition or averaging to identify vibrotactile signals. These are general purpose ‘global’ codes that require integration of the signal over long stretches of time. Natural vibrotactile signals, however, likely contain short signature events that can be detected and used for inference of textures, instantaneously, with minimal integration, suggesting a hitherto ignored ‘local code’. Here, by employing pulsatile stimuli and a change detection psychophysical task, we studied whether humans make use of local cues. We compared three local cues based on instantaneous skin position and its derivatives, as well as six global cues, calculated as summed powers (with exponents 1,2, and 3) of velocity and acceleration. Deliberate manipulation of pulse width and amplitude (local+global) as well as pulse frequency (global) allowed us to disentangle local from global codes. The results singled out maximum velocity, an instantaneous code, as a likely and dominant coding variable that humans rely on to perform the task. Comparing stimuli containing versus lacking local cues, demonstrated that performances exclusively using global cues are rather poor compared to situations where local ones are available as well. Our results are in line with the notion that humans not only do use local cues but that local cues may even play a dominant role in perception. Our results parallel previous results in rodents, pointing to the possibility that quite similar coding strategies evolved in whisker and finger tactile systems.

Significance statement

The brain is believed to select coding symbols in sensory signals that would most efficiently convey functionally relevant information about the world. For instance, the visual system is widely believed to use spatially local features, like edge orientation, to delineate a visual scene. For the tactile system only global, general purpose coding schemes have been discussed so far. Based on the insight that moving contacts, characteristic for active touch, feature short-lived stick-slip events, frictional movements that transfer fair amounts of texture information, one should expect the brain to use a temporally local code, extracting and instantaneously analyzing short snippets of skin movement. Here, we provide the first analytical psychophysical evidence in humans that this indeed is the case.
YbeY is required for ribosome small subunit assembly and tRNA processing in human mitochondria
Authors: D’Souza Aaron R. , Van Haute Lindsey , Powell Christopher A. , Rebelo-Guiomar Pedro , Rorbach Joanna , Minczuk Michal
Published: December 2019

Mitochondria contain their own translation apparatus which enables them to produce the polypeptides encoded in their genome. The mitochondrially-encoded RNA components of the mitochondrial ribosome require various post-transcriptional processing steps. Additional protein factors are required to facilitate the biogenesis of the functional mitoribosome. We have characterised a mitochondrially-localized protein, YbeY, which interacts with the assembling mitoribosome through the small subunit. Loss of YbeY leads to a severe reduction in mitochondrial translation and a loss of cell viability, caused by less accurate mitochondrial mt-tRNASer(AGY)processing from the primary transcript and an accumulation of immature mitochondrial small subunit. Our results suggest that YbeY performs a dual function in mitochondria coupling tRNA processing to mitoribosome biogenesis.

Issue Section

Nucleic Acid Enzymes

Abstract Figure
Developmental programming: Transcriptional regulation of visceral and subcutaneous adipose by prenatal bisphenol-A in female sheep
Authors: Dou John F. , Puttabyatappa Muraly , Padmanabhan Vasantha , Bakulski Kelly M.
Published: December 2019

Background

Bisphenol-A (BPA) exposure is widespread and early life exposure is associated with metabolic syndrome. While visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) are implicated in the development of metabolic syndrome, the adipose depot-specific effects of prenatal BPA treatment are poorly understood.

Objective

To determine the impact of prenatal BPA exposure on the transcriptome of VAT and SAT adipose depots.

Methods

RNA sequencing was performed on SAT and VAT from 21-month old control and prenatal BPA-treated female sheep. Differences in transcriptional profiling of SAT and VAT in controls and the effect of prenatal BPA treatment on individual genes and gene pathways were determined.

Results

There were 179 differentially expressed genes (padjusted<0.05, log2-fold change >2.5) between SAT and VAT. Development and immune response pathways were upregulated in SAT, while metabolic pathways were upregulated in VAT. In SAT, BPA-treatment resulted in differential expression of 108 genes (78% upregulated with BPA) and altered pathways (immune response downregulated, RNA processing upregulated). In contrast in VAT, BPA-treatment differentially expressed 4 genes and upregulated chromatin and RNA processing pathways.

Conclusion

Prenatal BPA-treatment induces adult depot-specific alterations in RNA expression in inflammation, RNA processing, and chromatin, reflecting the diverse roles of SAT and VAT in regulating lipid storage and insulin sensitivity. These adipose tissue transcriptional dysregulations may contribute to the metabolic disorders observed in prenatal BPA-treated female sheep.
The mitotic crosslinking protein PRC1 acts as a mechanical dashpot to resist microtubule sliding
Authors: Gaska Ignas , Armstrong Mason , Alfieri April , Forth Scott
Published: December 2019

Cell division in eukaryotes requires the regulated assembly of the spindle apparatus. The proper organization of microtubules within the spindle is driven by motor proteins that exert forces to push and slide filaments, while non-motor proteins can crosslink filaments into higher order motifs such as overlapping bundles. It has not been clear how active and passive forces are integrated to produce regulated mechanical outputs within spindles. Here we employ a combined optical tweezers and TIRF microscopy instrument to directly measure the resistive forces produced by the mitotic crosslinking protein PRC1. We observe that PRC1 generates frictional forces that resist microtubule sliding. These forces scale with microtubule sliding velocity and the number of PRC1 crosslinks, but do not depend on overlap length or PRC1 density within overlaps. Our results suggest that PRC1 ensembles act like a mechanical dashpot, producing significant resistance against fast motions, but minimal resistance against slow motions, allowing for the integration of diverse motor activities into a single mechanical outcome.
Novel intramolecular base-pairing of the U8 snoRNA underlies a Mendelian form of cerebral small vessel disease
Authors: Badrock Andrew P. , Uggenti Carolina , Wacheul Ludivine , Crilly Siobhan , Jenkinson Emma M. , Rice Gillian I. , Kasher Paul R. , Lafontaine Denis L.J. , Crow Yanick J. , O’Keefe Raymond T.
Published: December 2019

How mutations in the non-coding U8 snoRNA cause the neurological disorder leukoencephalopathy with calcification and cysts (LCC) is poorly understood. We report the first vertebrate mutant U8 animal model for interrogating LCC-associated pathology. Mutant U8 zebrafish exhibit defective central nervous system development and ribosomal RNA (rRNA) biogenesis, with tp53 activation which monitors ribosome biogenesis. Importantly, LCC patient fibroblasts demonstrate rRNA processing defects. Human precursor-U8 (pre-U8) containing a 3’ extension rescued mutant U8 zebrafish, indicating conserved biological function. Analysis of LCC-associated U8 alleles in zebrafish revealed that one null and one hypomorphic, but still functional, allele combine to cause LCC. Mutations involving any one of seven nucleotides within the human pre-U8 3’ extension, or 5’ region of U8, alter processing of pre-U8, and identify a novel base-pairing interaction between the 5’ end and 3’ extension of human pre-U8. Variants in these seven nucleotides, one of which is present on a single allele in almost all patients, act as hypomorphic mutations. Given that biallelic null U8 alleles are likely incompatible with human development, identification of hypomorphic mutations mediating viable embryogenesis furthers understanding of LCC molecular pathology and cerebral vascular homeostasis.
Single cell lineage dynamics of the endosymbiotic cell type in a soft coralXeniaspecies
Authors: Hu Minjie , Zheng Xiaobin , Fan Chen-Ming , Zheng Yixian
Published: December 2019

Many hard and soft corals harbor algae for photosynthesis. The algae live inside coral cells in a specialized membrane compartment called symbiosome, which shares the photosynthetically fixed carbon with coral host cells, while host cells provide inorganic carbon for photosynthesis1. This endosymbiotic relationship is critical for corals, but increased environmental stresses are causing corals to expel their endosymbiotic algae, i.e. coral bleaching, leading to coral death and degradation of marine ecosystem2. To date, the molecular pathways that orchestrate algal recognition, uptake, and maintenance in coral cells remain poorly understood. We report chromosome-level genome assembly of a fast-growing soft coral,Xeniaspecies (sp.)3, and its use as a model to decipher the coral-algae endosymbiosis. Single cell RNA-sequencing (scRNA-seq) identified 13 cell types, including gastrodermis and cnidocytes, inXenia sp. Importantly, we identified the endosymbiotic cell type that expresses a unique set of genes implicated in the recognition, phagocytosis/endocytosis, maintenance of algae, and host coral cell immune modulation. By applying scRNA-seq to investigate algal uptake in our newXenia sp.. regeneration model, we uncovered a dynamic lineage progression from endosymbiotic progenitor state to mature endosymbiotic and post-endosymbiotic cell states. The evolutionarily conserved genes associated with the endosymbiotic process reported herein open the door to decipher common principles by which different corals uptake and expel their endosymbionts. Our study demonstrates the potential of single cell analyses to examine the similarities and differences of the endosymbiotic lifestyle among different coral species.
TDP-43 dysfunction restricts dendritic complexity by inhibiting CREB activation and altering gene expression
Authors: Herzog Josiah J. , Deshpande Mugdha , Xu Weijin , Rahman Reazur , Suib Hannah , Rosbash Michael , Rodal Avital A. , Paradis Suzanne
Published: December 2019

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two related neurodegenerative diseases that present with similar TDP-43 pathology in patient tissue. TDP-43 is an RNA-binding protein and forms aggregates in neurons of ALS and FTD patients as well as in a subset of patients diagnosed with other neurodegenerative diseases. Despite our understanding that TDP-43 is essential for many aspects of RNA metabolism, it remains obscure how TDP-43 dysfunction contributes to neurodegeneration. Interestingly, several neurological disorders display altered dendritic morphology and complexity, which are thought to precede neurodegeneration. In this study, we used TRIBE (targets of RNA-binding proteins identified by editing) as a new approach to identify signaling pathways that regulate dendritic branching downstream of TDP-43. We found that TDP-43 targets are enriched for pathways that signal to the CREB transcription factor. We further found that TDP-43 dysfunction inhibits CREB activation and CREB transcriptional output, and restoring CREB signaling rescued defects in dendritic branching. Our data therefore provide a novel mechanism by which TDP-43 dysfunction interferes with dendritic branching, and define new pathways for therapeutic intervention in neurodegenerative diseases.
STING controls Herpes Simplex Virusin vivoindependent of type I interferon induction
Authors: Yamashiro Lívia H. , Wilson Stephen C. , Morrison Huntly M. , Karalis Vasiliki , Chung Jing-Yi J. , Chen Katherine J. , Bateup Helen S. , Szpara Moriah L. , Lee Angus Y. , Cox Jeffery S. , Vance Russell E.
Published: December 2019

The Stimulator of Interferon Genes (STING) pathway initiates potent immune responses upon recognition of DNA derived from bacteria, viruses and tumors. To signal, the C-terminal tail (CTT) of STING recruits TBK1, a kinase that phosphorylates serine 365 (S365) in the CTT. Phospho-S365 acts as a docking site for IRF3, a transcription factor that is phosphorylated and activated by TBK1, leading to transcriptional induction of type I interferons (IFNs). IFNs are essential for antiviral immunity and are widely viewed as the primary output of STING signaling in mammals. However, other more evolutionarily ancestral responses, such as induction of NF-κB or autophagy, also occur downstream of STING. The relative importance of the various outputs of STING signaling duringin vivoinfections is unclear. Here we report that mice harboring a serine 365-to-alanine (S365A) point mutation in STING exhibit normal susceptibility toMycobacterium tuberculosisinfection but, unexpectedly, are resistant to Herpes Simplex Virus (HSV)-1, despite lacking STING-induced type I IFN responses. Likewise, we findIrf3-/-mice exhibit resistance to HSV-1. By contrast, resistance to HSV-1 is abolished in mice lacking the STING CTT or TBK1, suggesting that STING protects against HSV-1 upon TBK1 recruitment by the STING CTT, independent of IRF3 or type I IFNs. Interestingly, we find that STING-induced autophagy is a TBK1-dependent IRF3-independent process that is conserved in the STING S365A mice, and autophagy has previously been shown to be required for resistance to HSV-1. We thus propose that autophagy and perhaps other ancestral interferon-independent functions of STING are required for STING-dependent antiviral responsesin vivo.
Lateralized alpha activity and slow potentials shifts over visual cortex track the time course of both endogenous and exogenous orienting of attention
Authors: Keefe Jonathan M. , Störmer Viola S.
Published: December 2019

Spatial attention can be oriented endogenously, based on current task goals, or exogenously, triggered by salient events in the environment. Based upon literature demonstrating differences in the time course and neural substrates of each type of orienting, these two attention systems are often treated as fundamentally distinct. However, recent studies suggest that rhythmic neural activity in the alpha band (8-13Hz) and slow waves in the event-related potential (ERP) may emerge over parietal-occipital cortex following both endogenous and exogenous attention cues. To assess whether these neural changes index common processes of spatial attention, we conducted two within-subject experiments varying the two main dimensions over which endogenous and exogenous attention tasks typically differ: cue informativity (spatially predictive vs. non-predictive) and cue format (centrally vs. peripherally presented). This task design allowed us to tease apart neural changes related to top-down goals and those driven by the reflexive orienting of spatial attention, as well as examine their interactions in a novel hybrid cross-modal attention task. Our data demonstrate that both central and peripheral cues elicit lateralized ERPs over parietal-occipital cortex, though at different points in time, consistent with these ERPs reflecting the orienting of spatial attention. Lateralized alpha activity was also present across all tasks, emerging rapidly for peripheral cues and sustaining only for spatially informative cues. Overall, these data indicate that distinct slow-wave ERPs index the spatial orienting of endogenous and exogenous attention, while lateralized alpha activity represents a common signature of visual enhancement in anticipation of potential targets across both types of attention.
Fast and accurate defocus for improved tunability of cryo-EM experiments
Authors: Danev Radostin , Iijima Hirofumi , Matsuzaki Mizuki , Motoki Sohei
Published: December 2019

Current data collection strategies in electron cryo-microscopy (cryo-EM) record multiframe movies with static optical settings. This limits the number of adjustable parameters that can be used to optimize the experiment. Here, we propose a method for fast and accurate defocus (FADE) modulation during movie acquisition. It uses the objective lens aperture as an electrostatic pole that locally modifies the electron beam potential. The beam potential variation is converted to defocus modulation by the typically undesired chromatic aberration of the objective lens. The simplicity, electrostatic principle and low electrical impedance of the device will allow fast switching speeds that will enable per-frame defocus values in cryo-EM movies. Researchers will be able to define custom defocus “recipes” and tailor the experiment for optimal information extraction from their sample. The FADE method could help to convert the microscope into a more dynamic and flexible optical platform that delivers better performance in cryo-EM single particle analysis and electron cryo-tomography.
Extended synaptotagmin regulates plasma membrane-endoplasmic reticulum contact site structure and lipid transfer functionin vivo
Authors: Nath Vaisaly R , Mishra Shirish , Basak Bishal , Trivedi Deepti , Raghu Padinjat
Published: December 2019

Inter-organelle communication between closely apposed membranes is proposed at Membrane Contact Sites (MCS). However the regulation of MCS structure and their functional relevancein vivoremain debated. The extended synaptotagmins (Esyt) are evolutionarily conserved proteins proposed to function at MCS. However, loss of all three Esyts in yeast or mammals shows minimal phenotypes questioning the functional importance of Esyt. We report that inDrosophilaphotoreceptors, MCS number is regulated by PLCβ activity. Photoreceptors of a null allele ofDrosophilaextended synaptotagmin(dEsyt)show loss of ER-PM MCS. Loss of dEsyt results in mislocalization of RDGB, an MCS localized lipid transfer protein, required for photoreceptor structure and function, ultimately leading to retinal degeneration.dEsytdepletion enhanced the retinal degeneration, reduced light responses and slower rates of plasma membrane PIP2resynthesis seen inrdgBmutants. Thus, dEsyt function and PLCβ signaling regulate ER-PM MCS structure and lipid transfer inDrosophilaphotoreceptors.
Water uptake analysis in Japanese mustard spinach: A numerical approach
Authors: Shimada Aoi , Seki Takuya , Ichikawa Musubu
Published: December 2019

We constructed an experimental system consisting of a syringe pump and water level feedback control to reveal the dynamics of water uptake in Japanese mustard spinach. We also analyzed differences in time-lapse images to quantify turgor movement in these plants. By performing harmonic analysis using the discrete Fourier transform on these dynamics, the frequency domain was obtained. These methods enabled the detailed visualization of plant dynamics.

Highlight

In this study, the water uptake dynamics of Japanese mustard spinaches were measured in detail and image difference analysis was performed to investigate the plants’ turgor movements. Frequency domain analysis of the plant dynamics was carried out using a discrete Fourier transform.
MinYS: Mine Your Symbiont by targeted genome assembly in symbiotic communities
Authors: Guyomar Cervin , Delage Wesley , Legeai Fabrice , Mougel Christophe , Simon Jean-Christophe , Lemaitre Claire
Published: December 2019

Most metazoans are associated with symbionts. Characterizing the effect of a particular symbiont often requires to get access to its genome, which is usually done by sequencing the whole community. We present MinYS, a targeted assembly approach to assemble one particular genome of interest from such metagenomic data. First, taking advantage of a reference genome, a subset of the reads is assembled into a set of backbone contigs. Then, this draft assembly is completed using the whole metagenomic readset in ade novomanner. The resulting assembly is output as a genome graph, allowing to distinguish different strains with potential structural variants coexisting in the sample. MinYS was applied to 50 pea aphid re-sequencing samples, with low and high diversity, in order to recover the genome sequence of its obligatory bacterial symbiont,Buchnera aphidicola. It was able to return high quality assemblies (one contig assembly in 90% of the samples), even when using increasingly distant reference genomes, and to retrieve large structural variations in the samples. Due to its targeted essence, it outperformed standard metagenomic assemblers in terms of both time and assembly quality.
Human defensive freezing is associated with acute threat coping, long term hair cortisol levels and trait anxiety
Authors: Hashemi Mahur M. , Zhang Wei , Kaldewaij Reinoud , Koch Saskia B.J. , Jonker Rosa , Figner Bernd , Klumpers Floris , Roelofs Karin
Published: December 2019

The detection and anticipation of threat facilitates innate defensive behaviours including freezing reactions. Freezing in humans is characterized by reductions in body sway and heart rate and limited evidence suggests that individual differences in freezing reactions are associated with hypothalamic-pituitary-adrenal (HPA) axis activity and anxiety. However, previous measurements of human freezing reactions were largely based on passive threat contexts where natural variations in adaptive threat coping could not be assessed. In a well powered sample (N=419), we studied individual differences in anticipatory freezing reactions, by measuring body sway and heart rate, during an active shooting task where shooting decisions had to be taken under threat of shock. We linked freezing measures to subsequent actions and predictors of anxiety-related psychopathology, including accumulated long-term (3 months) hair cortisol concentrations (HCC) and trait anxiety. The anticipation of threat of shock elicited significant body sway- and heart rate reductions consistent with freezing. Whereas both freezing-related reductions in body sway and heart rate were associated with faster correct shooting decisions, body sway reductions were additionally related to more impulsive shooting (false alarms). Individual differences in threat-related reductions in body sway but not heart rate were further associated to lower HCC and higher trait anxiety. The observed links between freezing and subsequent defensive actions as well as predictors of stress-related psychopathology suggest the potential value of defensive freezing reactions as somatic marker for stress-vulnerability and resilience.
22q11.2 duplication: a review of neuropsychiatric correlates and a newly observed case of prototypic sociopathy
Authors: Vyas Sonam , Constantino John N. , Baldridge Dustin
Published: December 2019

Callous-unemotional (CU) traits are highly disabling behavioral characteristics, common predictors of delinquency and criminality, and pathognomonic for antisocial personality disorder. They are highly heritable, but their specific molecular genetic causes are unknown. Here, we briefly review the literature on neuropsychiatric correlates of 22q11.2 duplication and describe a newly identified case of a 737-kb microduplication within the low copy repeat (LCR) B-D region, involving a 13-yr-old early adoptee with mild developmental delay and severe, chronic antisocial behavior of early childhood onset. When psychiatric symptoms have been reported in relation to duplications in this specific region, 19% of the reports feature aggression—but never previously CU traits—as a component of the phenotype. We discuss the potential implications of gain of function in this chromosomal region for heritable origins of sociopathy and their possible relation to genetic influences on aggression.
Examining healthy beverages in the hospitality industry: evidence from Australia and New Zealand
Authors: Hallak Rob , Lee Craig , Onur Ilke
Published: December 2019

Purpose

The purpose of this paper is to report on a study that examines the sale and provision of healthy beverages across four sectors of the hospitality industry: restaurants, cafes, pubs and quick-service/takeaways. Specifically, the research investigates perceptions of demand for healthy products, challenges to distribution and strategies for increasing supply. In addition, business managers’ attitudes and behaviours with regard to offering healthy beverages, including probiotic beverages (i.e. kombucha, kefir, etc.), are explored, as these are among the fastest growing drinks category.

Design/methodology/approach

Data were collected in 2018 through 400 telephone interviews with hospitality business managers from Australia (n=250) and New Zealand (n=150). Data were analysed through SPSS and Stata using descriptive statistics and Probit regression, with a binary outcome variable of “sell/ do not sell” probiotics to consumers.

Findings

Results suggest that the business’ decision to sell healthy beverages is influenced by perceptions of consumer demand, profit margins, shelf life of the products and if locally produced.

Originality/value

The findings from this exploratory study present new insights on how hospitality firms respond to consumer demand for healthy options, and the factors influencing their decision to incorporate healthier beverages in their menus.
Measurement of the real urbanization level in China and its international comparison
Authors: Cai Jiming , Guonan Du , Yuan Liu
Published: December 2019

Purpose

The purpose of this paper is to estimate the real urbanization level in China so as to provide a measurement that can be compared with the international level.

Design/methodology/approach

Taking into consideration 300m residents living in the administrative towns (300m residents here are referred to the population in administrative towns, including those in all counties), the gap between the urbanization rate of China and that of the world average becomes much wider.

Findings

China, however, implements the administrative system of government at the central, provincial, municipal, county and township levels. By city, it means the jurisdiction at and above the level of county, which includes the municipality directly under the central government, prefecture-level municipal and county. By town, it means the jurisdiction below the level of county (including the Chengguan Town, or capital town, where the county government is located) and exclusive of rural townships.

Originality/value

China has witnessed rapid development for 40 years since the reform and opening up in 1978. Nowadays, China has already stepped into the period of post-industrialization, with its urbanization rate (UR) of permanent population reaching 58.58 percent. However, on the basis of registered population, the UR is 43.37 percent, which is not only far below the average level of 81.3 percent in high-income countries, but also lower than the average of 65.8 percent in upper middle-income countries which are comparable to China in terms of per capita income. (The classification of state income level is based on the data of national income per capita and division standards in 2016 from the World Bank, in which annual revenue per capita in high-income countries reaches over US$12,736 and that in upper middle-income countries between US$4,126 and US$12,735.)