bluuebunny/crossref_metadata_2025 huggingface dataset:
Common default mode network dysfunction across psychopathologies: A neuroimaging meta-analysis of the n-back working memory paradigm
Authors: Farruggia Michael C. , Laird Angela R. , Mattfeld Aaron T.
Published: February 2020

The National Institute of Mental Health's (NIMH) Research Domain Criteria (RDoC) classifies disorders based on shared aspects of behavioral and neurobiological dysfunction. One common behavioral deficit observed in various psychopathologies, namely ADHD, addiction, bipolar disorder, depression, and schizophrenia, is a deficit in working memory performance. However, it is not known to what extent, if any, these disorders share common neurobiological abnormalities that contribute to decrements in performance. The goal of the present study was to examine convergence and divergence of working memory networks across psychopathologies. We used the Activation Likelihood Estimate (ALE) meta-analytic technique to collapse prior data obtained from published studies using the n-back working memory paradigm in individuals with a DSM-criteria diagnosis of the aforementioned disorders. These studies examined areas in the brain that showed increases in activity as a function of working memory-related load compared to a baseline condition, both within subjects and between healthy individuals and those with psychiatric disorder. A meta-analysis of 281 foci covering 81 experiments and 2,629 participants found significant convergence of hyperactivity in medial prefrontal cortex (mPFC) for DSM-diagnosed individuals compared to healthy controls. Foci from ADHD, addiction, bipolar disorder, schizophrenia, and major depression studies contributed to the formation of this cluster. These results provide evidence that default-mode intrusion may constitute a shared seed of dysregulation across multiple psychopathologies, ultimately resulting in poorer working memory performance.
Directed assembly and concentrating of micro/nanoparticles, cells, and vesicles via low-power near-infrared laser generated plasmonic microbubbles
Authors: Ohannesian Nareg , Li Jingting , Misbah Ibrahim , Zhao Fusheng , Shih Wei-Chuan
Published: February 2020

Directed assembly and concentrating of micro- and nanoparticles via laser generated plasmonic microbubbles in a liquid environment is an emerging technology. For effective heating, visible light has been primarily employed in existing demonstrations. In this paper, we demonstrate a new plasmonic platform based on nanoporous gold disk (NPGD) array. Thanks to the highly tunable localized surface plasmon resonance of the NPGD array, microbubble of controlled size can be generated by near-infrared (NIR) light. Using NIR light provides several key advantages over visible light in less interference with standard microscopy and fluorescence imaging, preventing fluorescence photobleaching, less susceptible to absorption and scattering in turbid biological media, and much reduced photochemistry, phototoxicity and whatsoever. The large surface-to-volume ratio of NPGD further facilitates the heat transfer from these gold nanoheaters to the surroundings, achieving unprecedented low-power operation. While the microbubble is formed, the surrounding liquid circulates and direct microparticles randomly dispersed in the liquid to the bottom NPGD surface, yielding unique assemblies of microstructures. Such capability can also be employed in concentrating suspended colloidal nanoparticles at desirable sites and with preferred configuration, both enhancing the sensor performance. In addition to various micro- and nanoparticles, the plasmonic microbubbles are also shown to collect biological cells and nanovesicles. By using a spatial light modulator (SLM) to project the laser in arbitrary patterns, parallel assembly can be achieved to fabricate an array of clusters. These assemblies have been characterized using optical microscopy, scanning electron microscope, hyperspectral localized surface plasmon resonance imaging and hyperspectral Raman imaging.
Genome-wide investigation of gene-cancer associations for the prediction of novel therapeutic targets in oncology
Authors: Bazaga Adrián , Leggate Dan , Weisser Hendrik
Published: February 2020

A major cause of failed drug discovery programs is suboptimal target selection, resulting in the development of drug candidates that are potent inhibitors, but ineffective at treating the disease. In the genomics era, the availability of large biomedical datasets with genome-wide readouts has the potential to transform target selection and validation. In this study we investigate how computational intelligence methods can be applied to predict novel therapeutic targets in oncology. We compared different machine learning classifiers applied to the task of drug target classification for nine different human cancer types. For each cancer type, a set of “known” target genes was obtained and equally-sized sets of “non-targets” were sampled multiple times from the human protein-coding genes. Models were trained on mutation, gene expression (TCGA), and gene essentiality (DepMap) data. In addition, we generated a numerical embedding of the interaction network of protein-coding genes using deep network representation learning and included the results in the modeling. We assessed feature importance using a random forests classifier and performed feature selection based on measuring permutation importance against a null distribution. Our best models achieved good generalization performance based on the AUROC metric. With the best model for each cancer type, we ran predictions on more than 15,000 protein-coding genes to identify potential novel targets. Our results indicate that this approach may be useful to inform early stages of the drug discovery pipeline.
Preliminary Evidence of the role of estrogen and tamoxifen-induced regulation of complement proteins in rat hippocampus
Authors: Kumar Pavan , Dhar Pushpa
Published: February 2020

Effects of Estrogen (E2) is widespread in the human body; still, an unresolved paradox. Neurodegeneration and neuroinflammation are inherently associated with age progression, debilitating by hormone deprivation, especially in female. Senescent cells accumulate with age and promote tissue deterioration in the body system. Neurodegenerative diseases drive a healthy life towards to morbidity and feebleness; despite the different etiology, uncontrolled inflammation is one of the significant causals factors. We here used post-menopausal model (ovariectomized female rat), E2 replenishment therapy reduces the expression of inflammatory mediators, such as complement proteins (C3, C1q, and C3aR) in these animals.

E2 therapy could limit the ovariectomy-induced increase of inflammatory events in brain regions such as the hippocampus. Also, the duration of hormone deprivation could be a determinant for the intensity of the anti-inflammatory actions of estrogen. On the whole, considerable evidence, including that from the present study supports the view that complement biosynthesis, which plays a significant role in phagocytosis of cellular debris and synaptic pruning of postnatal neural circuits goes uncontrolled and could be the inducing factor for enhanced neurodegeneration following hormone deprivation.
TOR coordinates nucleotide availability with ribosome biogenesis in plants
Authors: Busche Michael , Scarpin M. Regina , Hnasko Robert , Brunkard Jacob O.
Published: February 2020

TARGET OF RAPAMYCIN (TOR) is a conserved eukaryotic Ser/Thr protein kinase that coordinates growth and metabolism with nutrient availability. We conducted a medium-throughput functional genetic screen to discover essential genes that promote TOR activity in plants, and identified a critical regulatory enzyme, cytosolic phosphoribosyl pyrophosphate (PRPP) synthetase (PRS4). PRS4 synthesizes cytosolic PRPP, a key upstream metabolite in nucleotide synthesis and salvage pathways. We found thatprs4knockouts are embryo-lethal inA. thaliana, and that silencingPRS4expression inN. benthamianacauses pleiotropic developmental phenotypes, including dwarfism, aberrant leaf shape, and delayed flowering. Transcriptomic analysis revealed that ribosome biogenesis is among the most strongly repressed processes inprs4knockdowns. Building on these results, we discovered that TOR activity is inhibited by chemical or genetic disruption of nucleotide biosynthesis, but that this effect can be reversed by supplying plants with physiological levels of nucleotides. Finally, we show that TOR transcriptionally promotes nucleotide biosynthesis to support the demands of ribosomal RNA synthesis. We propose that TOR coordinates ribosome biogenesis with nucleotide availability in plants to maintain metabolic homeostasis and support growth.
Genetic Analyses of Blood Cell Structure for Biological and Pharmacological Inference
Authors: Akbari Parsa , Vuckovic Dragana , Jiang Tao , Kundu Kousik , Kreuzhuber Roman , Bao Erik L. , Mayer Louisa , Collins Janine H. , Downes Kate , Georges Michel , Grassi Luigi , Guerrero Jose A. , Kaptoge Stephen , Knight Julian C. , Meacham Stuart , Sambrook Jennifer , Seyres Denis , Stegle Oliver , Verboon Jeffrey M. , Walter Klaudia , Watkins Nicholas A. , Danesh John , Roberts David J. , Di Angelantonio Emanuele , Sankaran Vijay G. , Frontini Mattia , Burgess Stephen , Kuijpers Taco , Peters James E. , Butterworth Adam S. , Ouwehand Willem H. , Soranzo Nicole , Astle William J.
Published: February 2020

Thousands of genetic associations with phenotypes of blood cells are known, but few are with phenotypes relevant to cell function. We performed GWAS of 63 flow-cytometry phenotypes, including measures of cell granularity, nucleic acid content, and reactivity, in 39,656 participants in the INTERVAL study, identifying 2,172 variant-trait associations. These include associations mediated by functional cellular structures such as secretory granules, implicated in vascular, thrombotic, inflammatory and neoplastic diseases. By integrating our results with epigenetic data and with signals from molecular abundance/disease GWAS, we infer the hematopoietic origins of population phenotypic variation and identify the transcription factor FOG2 as a regulator of plateletα-granularity. We show how flow cytometry genetics can suggest cell types mediating complex disease risk and suggest efficacious drug targets, presenting Daclizumab/Vedolizumab in autoimmune disease as positive controls. Finally, we add to existing evidence supporting IL7/IL7-R as drug targets for multiple sclerosis.
A High-Throughput Gravimetric Phenotyping Platform for Real-Time Physiological Screening of Plant–Environment Dynamic Responses
Authors: Dalal Ahan , Shenhar Itamar , Bourstein Ronny , Mayo Amir , Grunwald Yael , Averbuch Nir , Attia Ziv , Wallach Rony , Moshelion Menachem
Published: February 2020

Food security for the growing global population is a major concern. The data provided by genomic tools far exceeds the supply of phenotypic data, creating a knowledge gap. To meet the challenge of improving crops to feed the growing global population, this gap must be bridged.

Physiological traits are considered key functional traits in the context of responsiveness or sensitivity to environmental conditions. Many recently introduced high-throughput phenotyping techniques are based on remote sensing or imaging and are capable of directly measuring morphological traits, but measure physiological parameters only indirectly.

This paper describes a method for direct physiological phenotyping that has several advantages for the functional phenotyping of plant–environment interactions. It aims to help users overcome the many challenges encountered in the use of load-cell gravimetric systems and pot experiments. The suggested techniques will enable users to distinguish between soil weight, plant weight and soil water content, providing a method for continuous and simultaneous measurement of dynamic soil, plant and atmosphere conditions, alongside key physiological traits. This method allows researchers to closely mimic field stress scenarios while taking into consideration the environment’s effect on the plant’s physiology. This method also minimizes pot effects, which are one of the major problems in pre-field phenotyping. It includes a feedback fertigation system that enables a truly randomized experimental design with a field-like plant density. This system detects the soil-water content limiting threshold (θ) and allows for the translation of data into knowledge through the use of a real-time analytic tool and an online statistical resource. This method for the rapid and direct measurement of the physiological responses of multiple plants to a dynamic environment has great potential for use in screening for beneficial traits associated with responses to abiotic stress, in the context of pre-field breeding and crop improvement.

This high-throughput, whole-plant water relations gravimetric phenotyping method enables direct and simultaneous real-time measurements and analysis of multiple yield-related physiological traits involved in dynamic plant–environment interactions.
Machine learning reveals heterogeneous responses to FAK, Rac, Rho, and Cdc42 inhibition on vascular smooth muscle cell spheroid formation and morphology
Authors: Vaidyanathan Kalyanaraman , Wang Chuangqi , Krajnik Amanda , Yu Yudong , Choi Moses , Lin Bolun , Heo Su-Jin , Kolega John , Lee Kwonmoo , Bae Yongho
Published: February 2020

Atherosclerosis and vascular injury are characterized by neointima formation caused by the aberrant accumulation and proliferation of vascular smooth muscle cells (VSMCs) within the vessel wall. Understanding how to control VSMCs would advance the effort to treat vascular disease. However, the response to treatments aimed at VSMCs is often different among patients with the same disease condition, suggesting patient-specific heterogeneity in VSMCs. Here, we present an experimental and computational method called HETEROID (Heterogeneous Spheroid), which examines the heterogeneity of the responses to drug treatments at the single-spheroid level by combining a VSMC spheroid model and machine learning (ML) analysis. First, we established a VSMC spheroid model that mimics neointima formation induced by atherosclerosis and vascular injury. We found that FAK-Rac/Rho, but not Cdc42, pathways regulate the VSMC spheroid formation through N-cadherin. Then, to identify the morphological subpopulations of drug-perturbed spheroids, we used an ML framework that combines deep learning-based spheroid segmentation and morphological clustering analysis. Our ML approach reveals that FAK, Rac, Rho, and Cdc42 inhibitors differentially affect the spheroid morphology, suggesting there exist multiple distinct pathways governing VSMC spheroid formation. Overall, our HETEROID pipeline enables detailed quantitative characterization of morphological changes in neointima formation, that occurs in vivo, by single-spheroid analysis of various drug treatments.
Beliefs and attitudes towards child epilepsy: A structural equation model
Authors: Silva Luanna G. , Beltrão Izabel C. S. L. , Bandeira Paulo F. R. , Delmondes Gyllyandeson A. , Alencar Cicero D. , Damasceno Simone S. , Kerntopf Marta R.
Published: February 2020

Infantile epilepsy is a chronic neurological disease permeated by negative beliefs and attitudes that strengthen social stigma and discrimination, as well as profoundly limit the routine of the affected child. Therefore, the objective of this study was to analyze the possible influencing factors of the beliefs and attitudes towards childhood epilepsy among users of the Family Health Strategy. 300 subjects participated. Variable associations were significant (p<0.05) between religions with positive beliefs and attitudes in the neurological dimension (β: 1.040; p: 0.044); an increase in educational level had a significant relationship with negative beliefs and attitudes in the environmental/psychophysical dimension (β: −0.723; p: 0.040); having a child was significant for negative beliefs and attitudes in the environmental/psychophysical dimension (β: 1.120; p: 0.043) and for positive beliefs in the metaphysical dimension (β: −0,244; p: 0.028). This research contributed to the identification of factors influencing beliefs and attitudes towards childhood epilepsy existing in the studied Brazilian cultural context with the aim of contributing to a better implementation of actions directed to education in epilepsy.
Mate sharing in male stump-tailed macaques as a possible case of coalition-like behavior to modify the group-wise fitness distribution
Authors: Toyoda Aru , Maruhashi Tamaki , Malaivijitnond Suchinda , Koda Hiroki , Ihara Yasuo
Published: February 2020

In multi-male multi-female groups of animals, male reproductive success is often skewed toward top-ranking males. Coalition formation by middle- to low-rankers can be seen as a collaborative effort to modify the distribution of reproductive success within the group, so that they gain more than they would do otherwise. It has been pointed out, on the other hand, that a coalition of top-ranking males could hardly be profitable in the sense that they would gain little additional benefit from making collaborative effort. Here we report our novel observation of facultative sharing of mating opportunities among males in a wild population of stump-tailed macaques (Macaca arctoides) as a possible case of coalition-like behavior in which dominant males jointly guard females from mating with subordinate males and actively share mating opportunities within the allies. First, we report our novel observation of facultative sharing of mating opportunities in male stump-tailed macaques, where two or more males remain in close proximity to and copulate with a female in turn without contesting or sneaking. Second, considering the kind of coalition formation in which dominant males collaboratively exclude subordinates from mating competition and thereby strengthen the reproductive skew that already exists, we specify, by means of mathematical modeling, the condition for this kind of coalition formation to be selectively favored. Finally, we derive predictions about the occurrence of the coalition-like behavior depending on ecological and demographic factors, and test them empirically using data from the five groups of stump-tailed macaques in our study population.
An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism
Authors: Thompson Mitchell G. , Blake-Hedges Jacquelyn M. , Pereira Jose Henrique , Hangasky John A. , Belcher Michael S. , Moore William M. , Barajas Jesus F. , Cruz-Morales Pablo , Washington Lorenzo J. , Haushalter Robert W. , Eiben Christopher B. , Liu Yuzhong , Skyrud Will , Benites Veronica T. , Barnum Tyler P. , Baidoo Edward E. K. , Scheller Henrik V. , Marletta Michael A. , Shih Patrick M. , Adams Paul D. , Keasling Jay D.
Published: February 2020

Due to low abundance in many staple food crops, the essential amino acid lysine must be produced industrially to meet global food supply needs. Despite intensive study, manipulation, and agricultural importance, the steps of plant lysine catabolism beyond the 2-oxoadipate (2OA) intermediate remain undescribed. Recently we described a missing step in the D-lysine catabolic pathway of the bacteriumPseudomonas putidain which 2OA is converted to D-2-hydroxyglutarate (D2HG) via hydroxyglutarate synthase (HglS), an enzyme belonging to the previously uncharacterized DUF1338 protein family. Here we solve the structure of HglS to 1.1Å resolution in the substrate-free form and in complex with 2OA. Structural similarity to hydroxymandelate synthase suggested a successive decarboxylation and intramolecular hydroxylation mechanism forming 2HG in a Fe(II)- and O2-dependent manner, which is validated experimentally. 2OA specificity was mediated by a single arginine (R74), highly conserved across nearly all DUF1338 family proteins, including in 76% of plant enzymes. InArabidopsis thaliana, a DUF1338 homolog is coexpressed with known lysine catabolism enzymes, and mutants show significant germination rate defects consistent with disrupted lysine catabolism. Structural and biochemical analysis of theOryza sativahomolog FLO7 revealed identical activity to HglS despite low sequence identity. Our results suggest that nearly all DUF1338 containing enzymes likely catalyze the same biochemical reaction, exerting the same physiological function across bacteria and eukaryotes.

Significance

To meet human demands, millions of tons of lysine are produced by bacterial fermentation annually due to its low abundance in staple crops. Here, we show the last missing step of lysine catabolism in nearly all plant endosperms is likely catalyzed by an iron-dependant DUF1338-containing enzyme homologous to the bacterial hydroxyglutarate synthase. Structural and bioninformatic analyses of DUF1338-containing enzymes showed high conservation of critical catalytic and specificity-conferring residues across multiple domains of life despite low sequence identity. These results suggest that the DUF1338 family evolved a specific physiological function within lysine catabolism across multiple domains of life.
Defective influenza A virus RNA products mediate MAVS-dependent upregulation of human leukocyte antigen class I proteins
Authors: Rahim Mir Munir A. , Parsons Brendon D. , Price Emma L. , Slaine Patrick D. , Chilvers Becca L. , Seaton Gregory S. , Wight Andrew , Dey Sayanti , Grandy Shannen L. , Anderson Lauryn E. , Zamorano Cuervo Natalia , Grandvaux Nathalie , Gaglia Marta M. , Kelvin Alyson A. , Khaperskyy Denys A. , McCormick Craig , Makrigiannis Andrew P.
Published: February 2020

Influenza A virus (IAV) increases presentation of class I human leukocyte antigen (HLA) proteins that limit antiviral responses mediated by natural killer (NK) cells, but molecular mechanisms have not yet been fully elucidated. We observed that infection with A/Fort Monmouth/1/1947 (H1N1) IAV significantly increased presentation of HLA-B, -C and -E on lung epithelial cells. Virus entry was not sufficient to induce HLA upregulation, because UV-inactivated virus had no effect. We found that HLA upregulation was elicited by aberrant internally-deleted viral RNAs (vRNAs) known as mini viral RNAs (mvRNAs) and defective interfering RNAs (DI RNAs), which bind to retinoic acid-inducible gene-I (RIG-I) and initiate mitochondrial antiviral signaling (MAVS) protein-dependent antiviral interferon (IFN) responses. Indeed, MAVS was required for HLA upregulation in response to IAV infection or ectopic mvRNA/DI RNA expression. The effect was partially due to paracrine signalling, as we observed that IAV infection or mvRNA/DI RNA-expression stimulated production of IFN-β and IFN-λ1, and conditioned media from these cells elicited a modest increase in HLA surface levels in naïve epithelial cells. HLA upregulation in response to aberrant viral RNAs could be prevented by chemical blockade of IFN receptor signal transduction. While HLA upregulation would seem to be advantageous to the virus, it is kept in check by the viral non-structural 1 (NS1) protein; we determined that NS1 limits cell-intrinsic and paracrine mechanisms of HLA upregulation. Taken together, our findings indicate that aberrant IAV RNAs stimulate HLA presentation, which may aid viral evasion of innate immunity.

IMPORTANCE

Human leukocyte antigens (HLA) are cell surface proteins that regulate innate and adaptive immune responses to viral infection by engaging with receptors on immune cells. Many viruses have evolved ways to evade host immune responses by modulating HLA expression and/or processing. Here, we provide evidence that aberrant RNA products of influenza virus genome replication can trigger RIG-I/MAVS-dependent remodeling of the cell surface, increasing surface presentation of HLA proteins known to inhibit the activation of an immune cell known as a natural killer (NK) cell. While this HLA upregulation would seem to be advantageous to the virus, it is kept in check by the viral non-structural 1 (NS1) protein, which limits RIG-I activation and interferon production by the infected cell.
Loss ofslc39a14causes simultaneous manganese deficiency and hypersensitivity in zebrafish
Authors: Tuschl Karin , White Richard J , Valdivia Leonardo E , Niklaus Stephanie , Bianco Isaac H , Sealy Ian M , Neuhauss Stephan CF , Houart Corinne , Wilson Stephen W , Busch-Nentwich Elisabeth M
Published: February 2020

Mutations in SLC39A14, a manganese uptake transporter, lead to a neurodegenerative disorder characterised by accumulation of manganese in the brain and rapidly progressive dystonia-parkinsonism (Hypermanganesemia with Dystonia 2, HMNDYT2). Similar to the human phenotype, zebrafishslc39a14U801-/-mutants show prominent brain manganese accumulation and abnormal locomotor behaviour. In order to identify novel potential targets of manganese neurotoxicity, we performed transcriptome analysis of individual homozygous mutant and siblingslc39a14U801zebrafish at five days post fertilisation unexposed and exposed to MnCl2. Anatomical gene enrichment analysis confirmed that differentially expressed genes map to the central nervous system and eye. Biological interpretation of differentially expressed genes suggests that calcium dyshomeostasis, activation of the unfolded protein response, oxidative stress, mitochondrial dysfunction, lysosomal disruption, apoptosis and autophagy, and interference with proteostasis are key events in manganese neurotoxicity. Differential expression of visual phototransduction genes also predicted visual dysfunction in mutant larvae which was confirmed by the absence of visual background adaptation and a diminished optokinetic reflex. Surprisingly, we found a group of differentially expressed genes in mutant larvae that normalised upon MnCl2treatment suggesting that, in addition to neurotoxicity, manganese deficiency is present either subcellularly or in specific cells or tissues. This may have important implications for treatment as manganese chelation may aggravate neurological symptoms. Our analyses show thatslc39a14U801-/-mutant zebrafish present a powerful model to study the cellular and molecular mechanisms underlying disrupted manganese homeostasis.

Significance statement

Manganese neurotoxicity leading to progressive dystonia-parkinsonism is a characteristic feature of Hypermanganesemia with dystonia 2 (HMNDYT2) caused by mutations in SLC39A14, a manganese uptake transporter. Transcriptional profiling inslc39a14U801loss-of-function zebrafish suggests that, in addition to manganese neurotoxicity, subcellular or cell type specific manganese deficiency contributes to the disease phenotype. Both manganese overload and deficiency appear to be associated with Ca2+dyshomeostasis. We further demonstrate that activation of the unfolded protein response, oxidative stress, mitochondrial dysfunction, apoptosis and autophagy, and disrupted proteostasis are likely downstream events in manganese neurotoxicity. Our study shows that the zebrafishslc39a14U801loss-of-function mutant is a powerful model to elucidate the mechanistic basis of diseases affected by manganese dyshomeostasis.
Quantifying protein-protein interactions by molecular counting with mass photometry
Authors: Soltermann Fabian , Foley Eric D.B. , Pagnoni Veronica , Galpin Martin R. , Benesch Justin L.P. , Kukura Philipp , Struwe Weston B.
Published: February 2020

Interactions between biomolecules control the processes of life in health, and their malfunction in disease, making their characterization and quantification essential. Immobilization- and label-free analytical techniques are particular desirable because of their simplicity and minimal invasiveness, but struggle to quantify tight interactions. Here, we show that we can accurately count, distinguish by molecular mass, and thereby reveal the relative abundances of different un-labelled biomolecules and their complexes in mixtures at the single-molecule level by mass photometry. These measurements enable us to quantify binding affinities over four orders of magnitude at equilibrium for both simple and complex stoichiometries within minutes, as well as to determine the associated kinetics. Our results introduce mass photometry as a rapid, simple and label-free method for studying sub-μM binding affinities, with potential to be extended towards a universal approach for characterising complex biomolecular interactions.
Single cell transcriptome profiling of the Atlantic cod immune system
Authors: Guslund Naomi , Solbakken Monica Hongrø , Jakobsen Kjetill S. , Qiao Shuo-Wang
Published: February 2020

The Atlantic cod’s unusual immune system, entirely lacking the Major Histocompatibility class II pathway, has prompted intriguing questions about what mechanisms are used to combat bacterial infections and how immunological memory is generated. Here, we examine the diversity of 8,180 spleen cells and peripheral blood leukocytes by single cell RNA sequencing. Unbiased transcriptional clustering revealed eleven distinct immune cell signatures. Resolution at the single cell level enabled characterisation of the major cell subsets including the cytotoxic T cells, B cells, erythrocytes, thrombocytes, neutrophils and macrophages. Further, we describe for the first time rare cell subsets which may represent dendritic cells, natural killer-like cells and a population of cytotoxic cells expressing GATA-3. We propose putative gene markers for each cluster and describe the relative proportions of each cell type in the spleen and peripheral blood leukocytes. By single cell analysis, this study provides the most detailed molecular and cellular characterization of the immune system of the Atlantic cod so far.
What the Zebrafish’s Eye Tells the Zebrafish’s Brain: Retinal Ganglion Cells for Prey Capture and Colour Vision
Authors: Zhou M , Bear J , Roberts PA , Janiak FK , Semmelhack J , Yoshimatsu T , Baden T
Published: February 2020

In vertebrate vision, the tetrachromatic larval zebrafish permits non-invasive monitoring and manipulating of neural activity across the nervous systemin vivoduring ongoing behaviour. However, despite a perhaps unparalleled understanding of links between zebrafish brain circuits and visual behaviours, comparatively little is known about what their eyes send to the brain in the first place via retinal ganglion cells (RGCs). Major gaps in knowledge include any information on spectral coding, and information on potentially critical variations in RGC properties across the retinal surface to acknowledge asymmetries in the statistics of natural visual space and behavioural demands. Here, we usein vivotwo photon (2P) imaging during hyperspectral visual stimulation as well as photolabeling of RGCs to provide the first eye-wide functional and anatomical census of RGCs in larval zebrafish.

We find that RGCs’ functional and structural properties differ across the eye and include a notable population of UV-responsive On-sustained RGCs that are only found in the acute zone, likely to support visual prey capture of UV-bright zooplankton. Next, approximately half of RGCs display diverse forms of colour opponency - long in excess of what would be required to satisfy traditional models of colour vision. However, most information on spectral contrast was intermixed with temporal information. To consolidate this series of unexpected findings, we propose that zebrafish may use a novel “dual-achromatic” strategy segregated by a spectrally intermediate background subtraction system. Specifically, our data is consistent with a model where traditional achromatic image-forming vision is mainly driven by long-wavelength sensitive circuits, while in parallel UV-sensitive circuits serve a second achromatic system of foreground-vision that serves prey capture and, potentially, predator evasion.
Oviposition in flight: theSabethes albiprivusincredible egg-throwing behavior
Authors: Vieira Genilton , Bersot Maria Ignez Lima , Pereira Glauber Rocha , de Abreu Filipe Vieira Santos , Nascimento-Pereira Agostinho Cardoso , Santos Neves Maycon Sebastião Alberto , Rosa-Freitas Maria Goreti , de Albuquerque Motta Monique , Lourenço-de-Oliveira Ricardo
Published: February 2020

Mosquitoes display highly variable oviposition strategies and behavior. By using a high-speed camera, we detailly documented for the first time the egg-throwing strategy of the sylvatic yellow fever vectorSabethes albiprivusTheobald in laboratory. An oviposition trap made with sapucaia nut for field collection of tree-hole mosquitoes and obtainingSa. albiprivuseggs either in the field or in the laboratory colony is described.
A Self-Attention Model for Inferring Cooperativity between Regulatory Features
Authors: Ullah Fahad , Ben-Hur Asa
Published: February 2020

Deep learning has demonstrated its predictive power in modeling complex biological phenomena such as gene expression. The value of these models hinges not only on their accuracy, but also on the ability to extract biologically relevant information from the trained models. While there has been much recent work on developing feature attribution methods that discover the most important features for a given sequence, inferring cooperativity between regulatory elements, which is the hallmark of phenomena such as gene expression, remains an open problem. We present SATORI, a Self-ATtentiOn based model to detect Regulatory element Interactions. Our approach combines convolutional layers with a self-attention mechanism that helps us capture a global view of the landscape of interactions between regulatory elements in a sequence. A comprehensive evaluation demonstrates the ability of SATORI to identify numerous statistically significant TF-TF interactions, many of which have been previously reported. Our method is able to detect higher numbers of experimentally verified TF-TF interactions than existing methods, and has the advantage of not requiring a computationally expensive post-processing step. Finally, SATORI can be used for detection of any type of feature interaction in models that use a similar attention mechanism, and is not limited to the detection of TF-TF interactions.
Functional signatures of evolutionarily young CTCF binding sites
Authors: Azazi Dhoyazan , Mudge Jonathan M. , Odom Duncan T. , Flicek Paul
Published: February 2020

The introduction of novel CTCF binding sites in gene regulatory regions in the rodent lineage is partly the effect of transposable element expansion. The exact mechanism and functional impact of evolutionarily novel CTCF binding sites are not yet fully understood. We investigated the impact of novel species-specific CTCF binding sites in twoMusgenus subspecies,Mus musculus domesticusandMus musculus castaneus,that diverged 0.5 million years ago. The activity of the B2-B4 family of transposable elements independently in both lineages leads to the proliferation of novel CTCF binding sites. A subset of evolutionarily young sites may harbour transcriptional functionality, as evidenced by the stability of their binding across multiple tissues inM. musculus domesticus(BL6), while overall the distance of species-specific CTCF binding to the nearest transcription start sites and/or topologically-associated domains (TADs) is largely similar tomusculus-common CTCF sites. Remarkably, we discovered a recurrent regulatory architecture consisting of a CTCF binding site and an interferon gene that appears to have been tandemly duplicated to create a 15-gene cluster on chromosome 4, thus forming a novel BL6 specific immune locus, in which CTCF may play a regulatory role. Our results demonstrate that thousands of CTCF binding sites show multiple functional signatures rapidly after incorporation into the genome.
Species boundaries and molecular markers for the classification of 16SrI phytoplasmas inferred by genome analysis
Authors: Cho Shu-Ting , Kung Hung-Jui , Huang Weijie , Hogenhout Saskia A. , Kuo Chih-Horng
Published: February 2020

Phytoplasmas are plant-pathogenic bacteria that impact agriculture worldwide. The commonly adopted classification system for phytoplasmas is based on the restriction fragment length polymorphism (RFLP) analysis of their 16S rRNA genes. With the increased availability of phytoplasma genome sequences, the classification system can now be refined. This work examined 11 strains in the 16SrI group within the genus ‘CandidatusPhytoplasma’ and investigated the possible species boundaries. We confirmed that the RFLP classification method is problematic due to intragenomic variation of the 16S rRNA genes and uneven weighing of different nucleotide positions. Importantly, our results based on the molecular phylogeny, differentiations in chromosomal segments and gene content, and divergence in homologous sequences, all supported that these strains may be classified into multiple operational taxonomic units (OTUs) equivalent to species. Strains assigned to the same OTU share >97% genome-wide average nucleotide identity (ANI) and >78% of their protein-coding genes. In comparison, strains assigned to different OTUs share <94% ANI and <75% of their genes. Reduction in homologous recombination between OTUs is one possible explanation for the discontinuity in genome similarities, and these findings supported the proposal that 95% ANI could serve as a cutoff for distinguishing species in bacteria. Additionally, critical examination of these results and the raw sequencing reads led to the identification of one genome that was presumably mis-assembled by combining two sequencing libraries built from phytoplasmas belonging to different OTUs. This finding provided a cautionary tale for working on uncultivated bacteria. Based on the new understanding of phytoplasma divergence and the current genome availability, we developed five molecular markers that could be used for multilocus sequence analysis (MLSA). By selecting markers that are short yet highly informative, and are distributed evenly across the chromosome, these markers provided a cost-effective system that is robust against recombination. Finally, examination of the effector gene distribution further confirmed the rapid gains and losses of these genes, as well as the involvement of potential mobile units (PMUs) in their molecular evolution. Future improvements on the taxon sampling of phytoplasma genomes will allow further expansions of similar analysis, and thus contribute to phytoplasma taxonomy and diagnostics.
Gjd2b-mediated gap junctions promote glutamatergic synapse formation and dendritic elaboration in Purkinje neurons
Authors: Sitaraman Sahana , Yadav Gnaneshwar , Jabeen Shaista , Agarwal Vandana , Thirumalai Vatsala
Published: February 2020

Gap junctions between neurons serve as electrical synapses, in addition to conducting metabolites and signaling molecules. These functions of gap junctions have led to the idea that during development, gap junctions could prefigure chemical synapses. We present evidence for this idea at a central, glutamatergic synapse and provide some mechanistic insights. Here, we show that reduction or loss of Gjd2b-containing gap junctions led to a decrease in glutamatergic synapse density in cerebellar Purkinje neurons (PNs) in larval zebrafish. Gjd2b-/-larvae exhibited faster mEPSCs and a consistent decrease in dendritic arbor size. These PNs also showed decreased branch elongations but normal rate of branch retractions. Further, the dendritic growth deficits in gjd2b-/-mutants were rescued by expressing full length Gjd2b in single PNs. This suggests that Gjd2b may form heterotypic channels with other connexins in gjd2b-/-larvae, though it is not clear if PNs in wild type animals make homotypic or heterotypic gap junction channels. Dendritic growth deficits were not rescued by expressing a deletion mutant of Gjd2b unable to form functional channels. Finally, the expression levels of five isoforms ofcamkiiwere increased in gjd2b-/-larvae and inhibition of CaMKII restored dendritic arbor lengths of mutant larvae to wild type levels. These results suggest a link between signaling via Gjd2b-containing gap junctions, CaMKII function and dendritic growth. In sum, our results demonstrate that Gjd2b-mediated gap junctions are key regulators of glutamatergic synapse formation and dendritic elaboration in PNs.
Crocus Sativusand Its Active Compound, Crocin Inhibits the Endothelial Activation and Monocyte-Endothelial Cells Interaction in Stimulated Human Coronary Artery Endothelial Cells
Authors: Mohd Kasim Noor Alicezah , Abu Bakar Nurul Ain , Ahmad Radzi , Abd Rahim Iman Nabilah , Abdul Rahman Thuhairah Hasrah , Anisah Froemming Gabriele Ruth , Nawawi Hapizah Mohd
Published: February 2020

Crocus sativus L.or saffron has been shown to have anti-atherogenic effects. However, its effects on key events in atherogenesis such as endothelial activation and monocyte-endothelial cell binding in lipolysaccharides (LPS)-stimulatedin vitromodel have not been extensively studied.

Objectives

To investigate the effects of saffron and its bioactive derivative crocin on the gene and protein expressions of biomarkers of endothelial activation in LPS stimulated human coronary artery endothelial cells (HCAECs).

Methodology

HCAECs were incubated with different concentrations of aqueous ethanolic extracts of saffron and crocin together with LPS. Protein and gene expressions of endothelial activation biomarkers were measured using ELISA and qRT-PCR, respectively. Adhesion of monocytes to HCAECs was detected by Rose Bengal staining. Methyl-thiazol-tetrazolium assay was carried out to assess cytotoxicity effects of saffron and crocin.

Results

Saffron and crocin up to 25.0 and 1.6 μg/ml respectively exhibited >85% cell viability. Saffron treatment reduced sICAM-1, sVCAM-1 and E-selectin proteins (concentrations: 3.13, 6.25, 12.5 and 25.0 μg/ml; 3.13, 12.5 and 25.0 μg/ml; 12.5 and 25.0, respectively) and gene expressions (concentration: 12.5 and 25.0μg/ml; 3.13, 6.25 and 25.0 μg/ml; 6.25, 12.5 25.0; respectively). Similarly, treatment with crocin reduced protein expressions of sICAM-1, sVCAM-1 and E-selectin (concentration: 0.2, 0.4, 0.8 and 1.6 μg/ml; 0.4, 0.8 and 1.6 μg/ml; 0.8 and 1.6 μg/ml; respectively] and gene expression (concentration: 0.8 and 1.6 μg/ml; 0.4, 0.8 and 1.6 μg/ml; and 1.6 μg/ml, respectively). Monocyte-endothelial cell interactions were reduced following saffron treatment at concentrations 6.3, 12.5 and 25.00 μg/ml. Similarly, crocin also suppressed cellular interactions at concentrations 0.04, 0.08, 1.60 μg/ml.

Conclusion

Saffron and crocin exhibits potent inhibitory action for endothelial activation and monocyte-endothelial cells interaction suggesting its potential anti-atherogenic properties.
Sero-prevalence of brucellosis, Q-fever and Rift Valley Fever in humans and livestock in Somali region, Ethiopia
Authors: Ibrahim Mohammed , Schelling Esther , Zinsstag Jakob , Hattendorf Jan , Andargie Emawayish , Tschopp Rea
Published: February 2020

Information on zoonotic diseases in humans and livestock are limited in pastoral/agro-pastoral communities in Ethiopia. A multi-stage cross sectional cluster design study was implemented with the aim to establish the seroprevalence of zoonotic diseases including brucellosis, Q-fever and Rift Valley Fever (RVF) in humans and livestock in Adadle woreda of the Somali region, Ethiopia. Blood samples were collected from humans and livestock and tested by relevant serological tests. For brucellosis, Rose Bengal test (RBT) and indirect ELISA was used for screening and confirmatory diagnosis respectively. Indirect and competitive ELISA were also used for Q-fever and RVF respectively. The individual seropositivity of Q-fever in livestock was 9.6% (95% CI 5.9-15.1) in cattle, 55.7% (95% CI 46.0-65.0) in camels, 48.8% (95% CI 42.5-55.0) in goats, and 28.9% (95% CI 25.0-33.2) in sheep. In humans, seropositivity of Q-fever was 27.0% (95% CI 20.4-34.0), with prevalence in males of 28.9% vs 24.2% in females (OR= 1.3; 95% CI 0.6-2.5). Camel seropositivity of Q-fever was significantly associated with age (OR= 8.1; 95% CI 2.8-23.7). The individual apparent seroprevalence of RVF was 13.2% (95% CI 8.7-18.8) in humans, 17.9 % (95% CI 11.0-27.8) in cattle, 42.6% (95% CI 34.8-50.7) in camels, 6.3% (95% CI 3.3-11.6) in goats and 7.4% (95% CI 4.7-11.5) in sheep. Camels had the highest seropositivity of both Q-fever (55.7%; 95% CI 46.0-65.0) and RVF (42.6%; 95% CI 34.8-50.7). Only a weak correlation was observed between human and livestock seropositivity for both Q-fever and RVF. Only cattle and camels were seropositive for brucellosis by iELISA. The individual seroprevalence of brucellosis was 2.8(0.9-6.4) in humans, 1.5% (95% CI 0.2-5.2) in cattle and 0.6% (95% CI 0.0-3.2) in camels. This study showed the importance of zoonoses in Somali regional state and is the first published study to describe RVF exposure in humans and livestock in the country. Collaboration between public and animal health sectors for further investigation on these zoonoses using the One Health concept is indispensable.
Two dominant brain states reflect optimal and suboptimal attention
Authors: Yamashita Ayumu , Rothlein David , Kucyi Aaron , Valera Eve M. , Esterman Michael
Published: February 2020

Attention is not constant but fluctuates from moment to moment. Previous studies dichotomized these fluctuations into optimal and suboptimal states based on behavioral performance and investigated the difference in brain activity between these states. Although these studies implicitly assume there are two states, this assumption is not guaranteed. Here, we reversed the logic of these previous studies and identified unique states of brain activity during a sustained attention task. We demonstrate a systematic relationship between dynamic brain activity patterns (brain states) and behavioral underpinnings of sustained attention by explaining behavior from two dominantly observed brain states. In four independent datasets, a brain state characterized by default mode network activity was behaviorally optimal and a brain state characterized by dorsal attention network activity was suboptimal. Thus, our study provides compelling evidence for behaviorally optimal and suboptimal attentional states from the sole viewpoint of brain activity. We further demonstrated how these brain states were impacted by motivation, mind wandering, and attention-deficit hyperactivity disorder. Within-subject level modulators (motivation and mind wandering) impacted the optimality of behavior in the suboptimal brain state. In contrast, between-subject level differences (ADHD vs healthy controls) impacted the optimal brain state character, namely its frequency.
The cellular basis of protease activated receptor type 2 (PAR2) evoked mechanical and affective pain
Authors: Hassler Shayne N , Kume Moeno , Mwirigi Juliet M. , Ahmad Ayesha , Shiers Stephanie , Wangzhou Andi , Ray Pradipta R , Belugin Serge N , Naik Dhananjay K. , Burton Michael D. , Vagner Josef , Boitano Scott , Akopian Armen N , Dussor Gregory , Price Theodore J
Published: February 2020

Protease-activated receptor type-2 (PAR2) has long been implicated in inflammatory and visceral pain, but the cellular basis of PAR2-evoked pain has not been delineated. While many studies have attributed PAR2-evoked pain to sensory neuron expression, RNA-sequencing experiments are ambiguous on detection ofF2rl1mRNA. Moreover, many pharmacological tools for PAR2 have been shown to be non-specific as they also act on the Mas-related (Mrg) family of g-protein coupled receptors (GPCRs) that are highly enriched in sensory neurons. We sought to bring clarity to the cellular basis of PAR2 pain. We developed a PAR2 conditional mutant mouse by loxp targeting of exon 2 of theF2rl1gene and specifically deleted PAR2 in all sensory neurons using thePirtCremouse line. Our behavioral findings show that PAR2 agonist-evoked mechanical hyperalgesia and facial grimacing, but not thermal hyperalgesia, is completely dependent on PAR2 expression in sensory neurons that project to the hindpaw in male and female mice.F2rl1mRNA is expressed in a discrete population (~4%) of sensory neurons that also express theNppbandIL31ragenes. This cell population has previously been implicated in itch, but our work shows that PAR2 activation in these cells causes clear pain-related behaviors from the skin. Our findings clarify the mechanism through which proteases, like tryptase and elastase, cause pain via PAR2 activation in a small subset of nociceptors.