bluuebunny/crossref_metadata_2025 huggingface dataset:
Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data
Authors: Chen Xiao , Sanchis-Juan Alba , French Courtney E , Connell Andrew J , Delon Isabelle , Kingsbury Zoya , Chawla Aditi , Halpern Aaron L , Taft Ryan J ,   NIHR BioResource, Bentley David R , Butchbach Matthew ER , Raymond F Lucy , Eberle Michael A
Published: October 2019

Purpose

Spinal muscular atrophy (SMA), caused by loss of the SMN1 gene, is a leading cause of early childhood death. Due to the near identical sequences of SMN1 and SMN2, analysis of this region is challenging. Population-wide SMA screening to quantify the SMN1 copy number (CN) is recommended by the American College of Medical Genetics.

Methods

We developed a method that accurately identifies the CN of SMN1 and SMN2 using genome sequencing (GS) data by analyzing read depth and eight informative reference genome differences between SMN1/2.

Results

We characterized SMN1/2 in 12,747 genomes, identified 1568 samples with SMN1 gains or losses and 6615 samples with SMN2 gains or losses and calculated a pan-ethnic carrier frequency of 2%, consistent with previous studies. Additionally, 99.8% of our SMN1 and 99.7% of SMN2 CN calls agreed with orthogonal methods, with a recall of 100% for SMA and 97.8% for carriers, and a precision of 100% for both SMA and carriers.

Conclusion

This SMN copy number caller can be used to identify both carrier and affected status of SMA, enabling SMA testing to be offered as a comprehensive test in neonatal care and an accurate carrier screening tool in GS sequencing projects.
An Emergent Neural Coactivity Code for Dynamic Memory
Authors: El-Gaby Mohamady , Reeve Hayley M , Lopes-dos-Santos Vítor , Campo-Urriza Natalia , Perestenko Pavel V , Lukács István , Paulsen Ole , Dupret David
Published: October 2019

Coincidental spike discharge amongst distributed groups of neurons is thought to provide an efficient mechanism for encoding percepts, actions and cognitive processes1–3. Short timescale coactivity can indeed bind neurons with similar tuning, giving rise to robust representations congruent with those of the participating neurons4–6. Alternatively, coactivity may also play a role in information processing through encoding variables not represented by individual neurons. While this type of emergent coactivity-based coding has been described for physically well-defined variables, including percepts and actions7–10, its role in encoding abstract cognitive variables remains unknown. Coactivity-based representation could provide a flexible code in dynamic environments, where animals must regularly learn short-lived behavioural contingencies. Here, we tested this possibility by training mice to discriminate two new behavioural contingencies every day, while monitoring and manipulating neural ensembles in the hippocampal CA1. We found that, while the spiking of neurons within their place fields is organised into congruent coactivity patterns representing discrete locations during unsupervised exploration of the learning enclosure, additional neurons synchronised their activity into spatially-untuned patterns that discriminated opposing learning contingencies. This contingency discrimination was an emergent property of millisecond timescale coactivity rather than the tuning of individual neurons, and predicted trial-by-trial memory performance. Moreover, optogenetic suppression of plastic inputs from the upstream left CA3 region during learning selectively impaired the computation of contingency-discriminating, but not space-representing CA1 coactivity patterns. This manipulation, but not silencing the more stable right CA3 inputs, impaired memory of the contingency discrimination. Thus, the computation of an emergent, coactivity-based discrimination code necessitates plastic synapses and supports dynamic, two-contingency memory.
Single-cell analysis of human retina identifies evolutionarily conserved and species-specific mechanisms controlling development
Authors: Lu Yufeng , Shiau Fion , Yi Wenyang , Lu Suying , Wu Qian , Pearson Joel D. , Kallman Alyssa , Zhong Suijuan , Hoang Thanh , Zuo Zhentao , Zhao Fangqi , Zhang Mei , Tsai Nicole , Zhuo Yan , He Sheng , Zhang Jun , Stein-O’Brien Genevieve L. , Sherman Thomas D. , Duan Xin , Fertig Elana J. , Goff Loyal A. , Zack Donald J. , Handa James T. , Xue Tian , Bremner Rod , Blackshaw Seth , Wang Xiaoqun , Clark Brian S.
Published: October 2019

The development of single-cell RNA-Sequencing (scRNA-Seq) has allowed high resolution analysis of cell type diversity and transcriptional networks controlling cell fate specification. To identify the transcriptional networks governing human retinal development, we performed scRNA-Seq over retinal organoid andin vivoretinal development, across 20 timepoints. Using both pseudotemporal and cross-species analyses, we examined the conservation of gene expression across retinal progenitor maturation and specification of all seven major retinal cell types. Furthermore, we examined gene expression differences between developing macula and periphery and between two distinct populations of horizontal cells. We also identify both shared and species-specific patterns of gene expression during human and mouse retinal development. Finally, we identify an unexpected role forATOH7expression in regulation of photoreceptor specification during late retinogenesis. These results provide a roadmap to future studies of human retinal development, and may help guide the design of cell-based therapies for treating retinal dystrophies.
Impaired Efflux of the Siderophore Enterobactin Induces Envelope Stress inEscherichia coli
Authors: Guest Randi L. , Court Emily A. , Waldon Jayne L. , Schock Kiersten A. , Raivio Tracy L.
Published: October 2019

The Cpx response is one of several envelope stress responses that monitor and maintain the integrity of the gram-negative bacterial envelope. While several conditions that are known or predicted to generate misfolded inner membrane proteins activate the Cpx response, the molecular nature of the Cpx inducing cue is not yet known. Studies have demonstrated that mutation of multidrug efflux pumps activates the Cpx response in many gram-negative bacteria. InVibrio cholerae, pathway activation is due to accumulation of the catechol siderophore vibriobactin. However, the mechanism by which the Cpx response is activated by mutation of efflux pumps inEscherichia coliremains unknown. Here we show that inhibition of efflux by deletion oftolC, the outer membrane channel of several multidrug efflux pumps, activates the Cpx response inE. colias a result of impaired efflux of the siderophore enterobactin. Enterobactin accumulation in thetolCmutant reduces activity of the NADH oxidation arm of the aerobic respiratory chain. However, NADH dehydrogenase I, NADH dehydrogenase II, and cytochromebo3do not contribute to Cpx pathway activation in theE. coli tolCmutant. We show that the Cpx response down-regulates transcription of the enterobactin biosynthesis operon. These results suggest that the Cpx response promotes adaptation to envelope stress in enteric bacteria that are exposed to iron-limited environments, which are rich in envelope-damaging compounds and conditions.
G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation
Authors: Sargent Luke , Liu Yating , Leung Wilson , Mortimer Nathan T. , Lopatto David , Goecks Jeremy , Elgin Sarah C. R.
Published: October 2019

Scientists are sequencing new genomes at an increasing rate with the goal of associating genome contents with phenotypic traits. After a new genome is sequenced and assembled, structural gene annotation is often the first step in analysis. Despite advances in computational gene prediction algorithms, most eukaryotic genomes still benefit from manual gene annotation. Undergraduates can become skilled annotators, and in the process learn both about genes/genomes and about how to utilize large datasets. Data visualizations provided by a genome browser are essential for manual gene annotation, enabling annotators to quickly evaluate multiple lines of evidence (e.g., sequence similarity, RNA-Seq, gene predictions, repeats). However, creating genome browsers requires extensive computational skills; lack of the expertise required remains a major barrier for many biomedical researchers and educators.

To address these challenges, the Genomics Education Partnership (GEP;https://gep.wustl.edu/) has partnered with the Galaxy Project (https://galaxyproject.org) to develop G-OnRamp (http://g-onramp.org), a web-based platform for creating UCSC Assembly Hubs and JBrowse genome browsers. G-OnRamp can also convert a JBrowse instance into an Apollo instance for collaborative genome annotations in research and educational settings. G-OnRamp enables researchers to easily visualize their experimental results, educators to create Course-based Undergraduate Research Experiences (CUREs) centered on genome annotation, and students to participate in genomics research.

Development of G-OnRamp was guided by extensive user feedback from in-person workshops. Sixty-five researchers and educators from over 40 institutions participated in these workshops, which produced over 20 genome browsers now available for research and education. For example, genome browsers for four parasitoid wasp species were used in a CURE engaging 142 students taught by 13 faculty members — producing a total of 192 gene models. G-OnRamp can be deployed on a personal computer or on cloud computing platforms, and the genome browsers produced can be transferred to the CyVerse Data Store for long-term access.
No genetic evidence for involvement of alcohol dehydrogenase genes in risk for Parkinson’s disease
Authors: Kim Jonggeol Jeffrey , Bandres-Ciga Sara , Blauwendraat Cornelis ,   International Parkinson’s Disease Genomics Consortium, Gan-Or Ziv
Published: October 2019

Multiple genes have been implicated in Parkinson’s disease (PD), including causal gene variants and risk variants typically identified using genome-wide association studies (GWAS). Variants in the alcohol dehydrogenase genes ADH1C and ADH1B are among the genes that have been associated with PD, suggesting that this family of genes may be important in PD. As part of the International Parkinson’s Disease Genomics Consortium’s (IPDGC) efforts to scrutinize previously reported risk factors for PD, we explored genetic variation in the alcohol dehydrogenase genes ADH1A, ADH1B, ADH1C, ADH4, ADH5, ADH6, and ADH7 using imputed GWAS data from 15,097 cases and 17,337 healthy controls. Rare-variant association tests and single-variant score tests did not show any statistically significant association of alcohol dehydrogenase genetic variation with the risk for PD.
Natural image reconstruction from brain waves: a novel visual BCI system with native feedback
Authors: Rashkov Grigory , Bobe Anatoly , Fastovets Dmitry , Komarova Maria
Published: October 2019

Here we hypothesize that observing the visual stimuli of different categories trigger distinct brain states that can be decoded from noninvasive EEG recordings. We introduce an effective closed-loop BCI system that reconstructs the observed or imagined stimuli images from the co-occurring brain wave parameters. The reconstructed images are presented to the subject as a visual feedback. The developed system is applicable to training BCI-naïve subjects because of the user-friendly and intuitive way the visual patterns are employed to modify the brain states.
Comprehensive palmitoyl-proteomic analysis identifies distinct protein signatures for large and small cancer-derived extracellular vesicles
Authors: Mariscal Javier , Vagner Tatyana , Kim Minhyung , Zhou Bo , Chin Andrew , Zandian Mandana , Freeman Michael R. , You Sungyong , Zijlstra Andries , Yang Wei , Vizio Dolores Di
Published: October 2019

Extracellular vesicles (EVs) are membrane-enclosed particles that play an important role in cancer progression and have emerged as a promising source of circulating biomarkers. ProteinS-acylation, also known as palmitoylation, has been proposed as a post-translational mechanism that modulates the dynamics of EV biogenesis and protein cargo sorting. However, technical challenges have limited large-scale profiling of the whole palmitoyl-proteins of EVs. We successfully employed a novel approach that combines low-background acyl-biotinyl exchange (LB-ABE) with label-free proteomics to analyze the palmitoyl proteome of large EVs (L-EVs) and small EVs (S-EVs) from prostate cancer cells. Here we report the first palmitoyl-protein signature of EVs, and demonstrate that L- and S-EVs harbor proteins associated with distinct biological processes and subcellular origin. We identified STEAP1, STEAP2, and ABBC4 as prostate cancer-specific palmitoyl proteins enriched in both EV populations in comparison with the originating cell lines. Importantly, the presence of the above proteins in EVs was significantly reduced upon inhibition of palmitoylation in the producing cells. These results suggest that palmitoylation may be involved in the differential sorting of proteins to distinct EV populations and allow for better detection of disease biomarkers.
A pair of esterases from a commensal gut bacterium remove acetylations from all positions on complex β-mannans
Authors: Michalak Leszek , La Rosa Sabina Leanti , Leivers Shaun Allan , Lindstad Lars Jordhøy , Kjendseth Åsmund Røhr , Aachmann Finn Lillelund , Westereng Bjørge
Published: October 2019

β-Mannans and xylans are important components of the plant cell wall and they are acetylated to be protected from degradation by glycoside hydrolases. β-Mannans are widely present in human and animal diets as fiber from leguminous plants and as thickeners and stabilizers in processed foods. There are many fully characterized acetylxylan esterases (AcXEs), however, the enzymes deacetylating mannans are less understood. Here we present two carbohydrate esterases, RiCE2 and RiCEX, from the Firmicute Roseburia intestinalis, which together deacetylate complex galactoglucomannan (GGM). The 3D-structure of RiCEX with a mannopentaose in the active site shows that the CBM35 domain of RiCEX forms a confined complex, where the axially oriented C2-hydroxyl of a mannose residue points towards the Ser41 of the catalytic triad. Cavities on the RiCEX surface may accept galactosylations at the C6 positions of mannose adjacent to the mannose residue being deacetylated (subsite −1 and +1). In depth characterization of the two enzymes using time-resolved NMR, HPLC and mass spectrometry demonstrates that they work in a complementary manner. RiCEX exclusively removes the axially oriented 2-O-acetylations on any mannose residue in an oligosaccharide, including double acetylated mannoses, while the RiCE2 is active on 3-O-, 4-O- and 6-O-acetylations. Activity of RiCE2 is dependent on RiCEX removing 2-O-acetylations from double acetylated mannose. Furthermore, transacetylation of oligosaccharides with the 2-O specific RiCEX provided new insight to how temperature and pH affects acetyl migration on mannooligosaccharides.

Significance statement

Acetylations are an important feature of hemicellulose, altering the physical properties of the plant cell wall, and limiting enzyme accessibility. Removal of acetyl groups from beta-mannan is a key step towards efficient utilization of mannans as a carbon source for gut microbiota and in biorefineries. We present detailed insight into mannan deacetylation by two highly substrate-specific acetyl-mannan esterases (AcMEs) from a prevalent gut commensal Firmicute, which cooperatively deacetylate complex galactoglucomannan. The 3D structure of RiCEX with mannopentaose in the active site has a unique two-domain architecture including a CBM35 and an SGNH superfamily hydrolytic domain. Discovery of mannan specific esterases improves the understanding of an important step in dietary fiber utilization by gut commensal Firmicutes.
Toxoplasmainduces stripping of perisomatic inhibitory synapses
Authors: Carrillo Gabriela L. , Ballard Valerie A. , Glausen Taylor , Boone Zack , Teamer Joseph , Hinkson Cyrus L. , Wohlfert Elizabeth A. , Blader Ira J. , Fox Michael A.
Published: October 2019

Infection and inflammation within the brain induces changes in neuronal connectivity and function. The intracellular protozoan parasite,Toxoplasma gondii, is one pathogen that infects the brain and can cause encephalitis and seizures. Persistent infection by this parasite is also associated with behavioral alterations and an increased risk for developing psychiatric illness, including schizophrenia. Current evidence from studies in humans and mouse models suggest that both seizures and schizophrenia result from a loss or dysfunction of inhibitory synapses. In line with this, we recently reported that persistentToxoplasma gondiiinfection alters the distribution of glutamic acid decarboxylase 67 (GAD67), an enzyme that catalyzes GABA synthesis in inhibitory synapses. These changes could reflect a redistribution of presynaptic machinery in inhibitory neurons or a loss of inhibitory nerve terminals. To directly assess the latter possibility, we employed serial block face scanning electron microscopy (SBFSEM) and quantified inhibitory perisomatic synapses in neocortex and hippocampus following parasitic infection. Not only did persistent infection lead to a significant loss of perisomatic synapses, it induced the ensheathment of neuronal somata by phagocytic cells. Immunohistochemical, genetic, and ultrastructural analyses revealed that these phagocytic cells included reactive microglia. Finally, ultrastructural analysis identified phagocytic cells enveloping perisomatic nerve terminals, suggesting they may participate in synaptic stripping. Thus, these results suggest that microglia contribute to perisomatic inhibitory synapse loss following parasitic infection and offer a novel mechanism as to how persistentToxoplasma gondiiinfection may contribute to both seizures and psychiatric illness.

MAIN POINTS

Toxoplasma-infection leads the loss of perisomatic inhibitory synapses

Phagocytic microglia ensheath neuronal somata followingToxoplasma-infection

Microglia contact and envelop perisomatic nerve terminals, suggesting thatToxoplasmainduces synaptic stripping
A Long Lost Key Opens an Ancient Lock:DrosophilaMyb Causes a Synthetic Multivulval Phenotype in Nematodes
Authors: Vorster Paul J. , Goetsch Paul , Wijeratne Tilini U. , Guiley Keelan Z. , Andrejka Laura , Tripathi Sarvind , Larson Braden J. , Rubin Seth M. , Strome Susan , Lipsick Joseph S.
Published: October 2019

The five-protein MuvB core complex (LIN9/Mip130, LIN37/Mip40, LIN52, LIN54/Mip120, and LIN53/p55CAF1/RBBP4) has been highly conserved during the evolution of animals. This nuclear complex interacts with proteins encoded by theRBtumor suppressor gene family and its associated E2F-DP transcription factors to form DREAM complexes that repress the expression of genes that regulate cell cycle progression and cell fate. The MuvB core complex also interacts with proteins encoded by theMyboncogene family to form the Myb-MuvB complexes that activate many of the same target genes. We show that animal-typeMybgenes and proteins are present in Bilateria, Cnidaria, and Placozoa, the latter including some of the simplest known animal species. However, bilaterian nematode worms appear to have lost their animal-typeMybgenes hundreds of millions of years ago. Nevertheless, the amino acids in the LIN9 and LIN52 proteins that directly interact with the MuvB-binding domains of human B-Myb andDrosophilaMyb are conserved inC. elegans. Here we show that, despite greater than 500 million years since their last common ancestor, theDrosophila melanogasterMyb protein can bind to the nematode LIN9 and LIN52 family proteinsin vitroand can cause a synthetic multivulval (synMuv) phenotypein vivo. This phenotype is similar to that caused by loss-of-function mutations inC. eleganssynMuvB class genes including those that encode homologs of the MuvB core, RB, E2F, and DP. Furthermore, amino acid substitutions in the MuvB-binding domain ofDrosophilaMyb that disrupt its functionsin vitroandin vivoalso disrupt its activity inC. elegans. We speculate that nematodes and other animals may contain another protein that can bind to LIN9 and LIN52 in order to activate transcription of genes repressed by DREAM complexes.
The PRR14 heterochromatin tether encodes modular domains that mediate and regulate nuclear lamina targeting
Authors: Dunlevy Kelly L. , Medvedeva Valentina , Wilson Jade E. , Hoque Mohammed , Pellegrin Trinity , Maynard Adam , Kremp Madison M. , Wasserman Jason S. , Poleshko Andrey , Katz Richard A.
Published: October 2019

A large fraction of epigenetically silent heterochromatin is anchored to the nuclear periphery via “tethering proteins” that function to bridge heterochromatin and the nuclear membrane or nuclear lamina. We identified previously a human tethering protein, PRR14, that binds heterochromatin through an N-terminal domain, but the mechanism and regulation of nuclear lamina association remained to be investigated. Here we identify a centrally located, evolutionarily conserved PRR14 nuclear lamina binding domain (LBD) that is both necessary and sufficient for positioning of PRR14 at the nuclear lamina. We also show that PRR14 associates dynamically with the nuclear lamina, and provide evidence that such dynamics are regulated through phosphorylation of the LBD. We also show that the evolutionary conserved PRR14 C-terminal Tantalus domain encodes a PP2A phosphatase recognition site that regulates PRR14 nuclear lamina association. The overall findings demonstrate a heterochromatin anchoring mechanism whereby the PRR14 tether simultaneously binds heterochromatin and the nuclear lamina through two modular domains. Furthermore, the identification of a modular LBD may provide an engineering strategy for delivery of cargo to the nuclear lamina.
A method for rapid selection of randomly induced mutations in a gene of interest using CRISPR/Cas9 mediated activation of gene expression
Authors: Ng William A. , Ma Andrew , Chen Molly , Reed Bruce H.
Published: October 2019

We have developed a CRISPR/Cas9 based method for isolating randomly induced recessive lethal mutations in a gene of interest (GOI) by selection within the F1 progeny of a single genetic cross. Our method takes advantage of the ability to overexpress a GOI using CRISPR/Cas9 mediated activation of gene expression. In essence, the screening strategy is based upon the idea that if overexpression of a wild type allele can generate a phenotype, then overexpression of a newly induced loss-of-function allele will lack this phenotype. As a proof-of-principle, we used this method to select EMS induced mutations of the Drosophila genehindsight(hnt). From approximately 45,000 F1 progeny we recovered 8 new EMS induced loss-of-functionhntalleles that we characterized as an allelic series of hypomorphic mutations. This new method can, in theory, be used to recover randomly induced point mutants in a GOI and can be applied to any circumstance where CRISPR/Cas9 mediated activation of gene expression is associated with lethality or a visible phenotype.
Proximate Predictors of Variation in Egg Rejection Behavior by Hosts of Avian Brood Parasites
Authors: Abolins-Abols Mikus , Hauber Mark E.
Published: October 2019

The rejection of parasitic eggs by hosts of avian brood parasites is one of the most common and effective defenses against parasitism. Despite its adaptive significance, egg rejection often shows substantial intraspecific variation: some individuals are more likely to remove or abandon parasitic eggs than others. Understanding variation in egg rejection requires that we study factors linked to both the ability to perceive parasitic eggs, as well as factors that may influence the rejection of a foreign egg once it has been recognized. Here we asked what cognitive, physiological, and life-history factors explained variation in the rejection of model eggs by American Robin Turdus migratorius females. We found that the probability of egg rejection was related to the clutch size at the time of parasitism: in support of Weber’s law, females with fewer eggs were more likely to reject the model eggs. In turn, females with greater mass and higher corticosterone levels were less likely to reject eggs, and egg rejection probability was negatively related to incubation progress. Our data thus suggest that proximate predictors of an individual’s egg rejection behavior include components of the nest’s perceptual environment, life-history factors, as well as the physiological state of the animal. However, much of the variation in the responses of robins to the model eggs remained unexplained. Future experiments should aim to understand the causal roles of these and other factors in generating within- and among-individual variation in the rejection of parasitic eggs.
Pathway Commons: 2019 Update
Authors: Rodchenkov Igor , Babur Ozgun , Luna Augustin , Aksoy Bulent Arman , Wong Jeffrey V. , Fong Dylan , Franz Max , Siper Metin Can , Cheung Manfred , Wrana Michael , Mistry Harsh , Mosier Logan , Dlin Jonah , Wen Qizhi , O’Callaghan Caitlin , Li Wanxin , Elder Geoffrey , Smith Peter T. , Dallago Christian , Cerami Ethan , Gross Benjamin , Dogrusoz Ugur , Demir Emek , Bader Gary D. , Sander Chris
Published: October 2019

Pathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g., metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (1) tools to search this comprehensive resource, (2) a download site offering integrated bulk sets of pathway data (e.g., tables of interactions and gene sets), (3) reusable software libraries for working with pathway information in several programming languages (Java, R, Python, and Javascript), and (4) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4,794 detailed human biochemical processes (i.e., pathways) and ∼2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.
Long-term alterations in brain and behavior after postnatal Zika virus infections in infant macaques
Authors: Raper Jessica , Kovacs-Balint Zsofia , Mavigner Maud , Gumber Sanjeev , Burke Mark W. , Habib Jakob , Mattingly Cameron , Fair Damien , Earl Eric , Feczko Eric , Styner Martin , Jean Sherrie M. , Cohen Joyce K. , Suthar Mehul S. , Sanchez Mar M. , Alvarado Maria C. , Chahroudi Ann
Published: October 2019

Considering the impact that Zika virus (ZIKV) infection has on the fetal nervous system and given that the postnatal period is also a time of rapid brain growth, it is important to understand the potential neurobehavioral consequences of ZIKV infection during infancy. Postnatal ZIKV infection in a rhesus macaque (RM) model resulted in long-term behavioral, motor, and cognitive changes, including increased emotional reactivity, decreased social contact, loss of balance, and deficits in visual recognition memory at one year of age. Structural and functional MRI showed that ZIKV-infected infant RMs had persistent enlargement of lateral ventricles, smaller volumes and altered functional connectivity between brain areas important for socioemotional behavior, cognitive, and motor function (e.g. amygdala, hippocampus, cerebellum). Neuropathological changes corresponded with neuroimaging results and were consistent with the behavioral and memory deficits. Overall, this study demonstrates that postnatal ZIKV infection of infants in this model has long lasting neurodevelopmental consequences.
A flexible network of Vimentin intermediate filaments promotes the migration of amoeboid cancer cells through confined environments
Authors: Tudor Sara M. , Lavenus Sandrine B. , Logue Jeremy S.
Published: October 2019

The spread of tumor cells to distant sites is promoted by their ability to switch between mesenchymal and amoeboid (bleb-based) migration. Because of this, inhibitors of metastasis must account for each motility mode. To this end, here we determine the precise role of the Vimentin intermediate filament system in regulating the migration of amoeboid human cancer cells. Vimentin is a classic marker of epithelial to mesenchymal transition and is therefore, an ideal target for a metastasis inhibitor. However, the role of Vimentin in amoeboid migration has not been determined. Since amoeboid, leader bleb-based migration occurs in confined spaces and Vimentin is known to be a major determinant of cell mechanical properties, we hypothesized that a flexible Vimentin network is required for fast amoeboid migration. This was tested using our PDMS slab-based approach for the confinement of cells, RNAi, over-expression, pharmacological treatments, and measurements of cell stiffness. In contrast to Vimentin RNAi, inducing the bundling of Vimentin was found to inhibit fast amoeboid migration and proliferation. Importantly, these effects were independent of changes in actomyosin contractility. Collectively, our data supports a model whereby the perturbation of cell mechanical properties by Vimentin bundling inhibits the invasive properties of cancer cells.
Visualization and Analysis of Whole Depot Adipose Tissue Neural Innervation
Authors: Willows Jake W. , Blaszkiewicz Magdalena , Lamore Amy , Borer Samuel , Dubois Amanda L. , Garner Emma , Breeding William P. , Tilbury Karissa B. , Khalil Andre , Townsend Kristy L.
Published: October 2019

Little is known about the diversity and function of adipose tissue nerves due, in part, to the inability to effectively visualize the various nerve subtypes residing within these tissues. The tools currently available for researchers to image and quantify adipose tissue innervation are limited and dependent on optical clearing techniques and light sheet microscopy. Here we present a method of tissue processing that uses mechanical force to compress tissue to decrease tissue thickness in the z-axis by expanding it in the x and y-axes whilst leaving cells intact. This has been combined with autofluorescence quenching techniques to permit intact whole tissues to be mounted on slides and imaged on any microscope, with a complementary means to perform whole tissue neurite density quantification. We have included examples of how this technique can be used to further our current knowledge of adipose-nerve communication by characterizing the nerves, nerve-subtypes, and neurovascular interactions within subcutaneous white adipose tissue in mice.
Breeding at higher latitude as measured by stable isotope is associated with higher photoperiod threshold and delayed reproductive development in a songbird
Authors: Singh D. , Reed S.R. , Kimmitt A.A. , Alford K. A. , Ketterson E.D.
Published: October 2019

Many organisms time reproduction to photoperiod, a constant from year to year. Predicting how anthropogenic change will influence future timing demands greater knowledge of the current role of photoperiod. We held two closely related bird populations in a common environment. One population is resident; the other winters in sympatry with the resident population but migrates north prior to reproducing. We increased photoperiod gradually and measured preparation for migration and reproduction, using feather stable isotopes to estimate breeding latitude. We predicted population differences in the minimum stimulatory day length to elicit a response (CPP, critical photoperiod) and co-variation between CPP and distance migrated. We found clear population differences in CPP and greater CPP in longer distance migrants. We conclude that current geographic variation in reproductive timing has a genetic or early developmental basis and recommend that future research focus on how anthropogenic changes will interact with CPP to adjust timing of reproduction and migration.
Optogenetic modulation of TDP-43 oligomerization fast-forwards ALS-related pathologies in the spinal motor neurons
Authors: Asakawa Kazuhide , Handa Hiroshi , Kawakami Koichi
Published: October 2019

Cytoplasmic aggregation of TDP-43 characterizes degenerating neurons in most cases of amyotrophic lateral sclerosis (ALS), yet the mechanisms and cellular outcomes of TDP-43 pathology remain largely elusive. Here, we develop an optogenetic TDP-43 variant (opTDP-43), whose multimerization status can be modulated in vivo through external light illumination. Using the translucent zebrafish neuromuscular system, we demonstrate that short-term light stimulation reversibly induces cytoplasmic opTDP-43 mislocalization, but not aggregation, in the spinal motor neuron, leading to an axon outgrowth defect associated with myofiber denervation. In contrast, opTDP-43 forms pathological aggregates in the cytoplasm after longer-term illumination and seeds non-optogenetic TDP-43 aggregation. Furthermore, we find that an ALS-linked mutation in the intrinsically disordered region (IDR) exacerbates the light-dependent opTDP-43 toxicity on locomotor behavior. Together, our results propose that IDR-mediated TDP-43 oligomerization triggers both acute and long-term pathologies of motor neurons, which may be relevant to the pathogenesis and progression of ALS.
Thermodynamic destabilization informs pathogenicity assessment of a variant of uncertain significance in cardiac myosin binding protein C
Authors: Pricolo Maria Rosaria , Herrero-Galán Elías , Mazzaccara Cristina , Losi Maria Angela , Alegre-Cebollada Jorge , Frisso Giulia
Published: October 2019

In the era of Next Generation Sequencing (NGS), genetic testing for inherited disorders identifies an ever-increasing number of variants whose pathogenicity remains unclear. These variants of uncertain significance (VUS) limit the reach of genetic testing in clinical practice. The VUS for Hypertrophic Cardiomyopathy (HCM), the most common familial heart disease, constitute over 60% of entries for missense variants shown in ClinVar database. We have studied a novel VUS (c.1809T>G-p.I603M) in the most frequently mutated gene in HCM, MYBPC3, which codes for cardiac myosin-binding protein C (cMyBPC). Our determinations of pathogenicity integrate bioinformatics evaluation and functional studies of RNA splicing and protein thermodynamic stability. In silico prediction and mRNA analysis indicated no alteration of RNA splicing induced by the variant. At the protein level, the p.I603M mutation maps to the C4 domain of cMyBPC. Although the mutation does not perturb much the overall structure of the C4 domain, the stability of C4 I603M is severely compromised as detected by circular dichroism and differential scanning calorimetry experiments. Taking into account the highly destabilizing effect of the mutation in the structure of C4, we propose reclassification of variant p.I603M as likely pathogenic. Looking into the future, the workflow described here can be used to refine the assignment of pathogenicity of variants of uncertain significance in MYBPC3.
Availability of Zinc Impacts Interactions BetweenStreptococcus sanguinisandPseudomonas aeruginosain Co-culture
Authors: Li Kewei , Gifford Alex , Hampton Thomas , O’Toole George A.
Published: October 2019

Airway infections associated with cystic fibrosis (CF) are polymicrobial. We reported previously that clinical isolates ofP. aeruginosapromote the growth of a variety of streptococcal species. To explore the mechanistic basis of this interaction, we performed a genetic screen to identify mutants ofStreptococcus sanginuisSK36 whose growth was no longer enhanced byP. aeruginosaPAO1. Mutations in zinc uptake systems ofS. sanginuisSK36 reduced growth of these strains by 1-3 log compared to wild-typeS. sanginuisSK36 when grown in coculture withP. aeruginosaPA01, while exogenous zinc (0.1-10 μm) rescued the coculture defect of zinc uptake mutants ofS. sanginuisSK36. Zinc uptake mutants ofS. sanginuisSK36 had no obvious growth defect in monoculture. Consistent with a competition for zinc driving coculture dynamics,S. sanginuisSK36 grown in coculture withP. aeruginosashowed increased expression of zinc uptake genes compared toS. sanginuisgrown alone. Strains ofP. aeruginosaPAO1 defective in zinc transport also supported more robust growth byS. sanginuiscompared to coculture with wild-typeP. aeruginosaPAO1. An analysis of 118 CF sputum samples revealed that total zinc levels varied from ~5-145 μM. At relatively low zinc levels,PseudomonasandStreptococcuswere found in approximately equal abundance; at higher zinc levels, we observed an increasing relative abundance ofPseudomonasand decline ofStreptococcus, perhaps as a result of increasing zinc toxicity. Together, our data indicate that the relative abundance of these microbes in the CF airway may be impacted by zinc levels.

IMPORTANCE

Polymicrobial infections in CF likely impact patient health, but the mechanism(s) underlying such interactions are poorly understood. Here we show that interactions betweenPseudomonasandStreptococcusare modulated by zinc availability using anin vitromodel system, and clinical data are consistent with this model. Together with previous studies, our work supports a role for metal homeostasis as a key factor driving microbial interactions.
Label-free characterization of Amyloid-β-plaques and associated lipids in brain tissues using stimulated Raman scattering microscopy
Authors: Schweikhard Volker , Baral Andrea , Krishnamachari Vishnu , Hay William C. , Fuhrmann Martin
Published: October 2019

The brains of patients with neurodegenerative diseases such as Alzheimer’s Disease (AD) often exhibit pathological alterations that involve abnormal aggregations of proteins and lipids. Here, we demonstrate that high-resolution, label-free, chemically-specific imaging using Stimulated Raman Scattering Microscopy (SRS) provides novel insights into the biophysical properties and biochemical composition of such pathological structures. In brain slices of a mouse model of AD, SRS reveals large numbers of Amyloid-β plaques that commonly form a characteristic, three-dimensional core-shell structure, with a fibrillar proteinaceous core surrounded by a halo-like shell of lipid-rich deposits. SRS spectroscopic imaging allows for a clean, label-free visualization of the misfolded (β-sheet) Amyloid-β content in the plaque core. Surrounding lipid-rich deposits are found to contain comparatively high concentrations of membrane lipids (sphingomyelin, phosphatidylcholine), but lower levels of cholesterol than healthy white matter structures. Overall, the SRS spectra of plaque-associated lipids closely resemble those of nearby neurites, with the notable difference of a higher degree of lipid unsaturation compared to healthy brain structures. We hypothesize that plaque-associated lipid deposits may result from neuritic dystrophy associated with AD, and that the observed increased levels of unsaturation could help identify the kinds of pathological alterations taking place. Taken together, our results highlight the potential of Stimulated Raman Scattering microscopy to contribute to a deeper understanding of neurodegenerative diseases.
CDK8 and CDK19 kinases have non-redundant oncogenic functions in hepatocellular carcinoma
Authors: Bacevic Katarina , Prieto Susana , Caruso Stefano , Camasses Alain , Dubra Geronimo , Ursic-Bedoya José , Lozano Anthony , Butterworth Jacqueline , Zucman-Rossi Jessica , Hibner Urszula , Fisher Daniel , Gregoire Damien
Published: October 2019

Hepatocellular carcinoma (HCC) is a common cancer with high mortality. The limited therapeutic options for advanced disease include treatment with Sorafenib, a multi-kinase inhibitor whose targets include the Mediator kinase CDK8. Since CDK8 has reported oncogenic activity in Wnt-dependent colorectal cancer, we investigated whether it is also involved in HCC. We find that CDK8 and its paralogue CDK19 are significantly overexpressed in HCC patients, where high levels correlate with poor prognosis. Liver-specific genetic deletion of CDK8 in mice is well supported and protects against chemical carcinogenesis. Deletion of either CDK8 or CDK19 in hepatic precursors had little effect on gene expression in exponential cell growth but prevented oncogene-induced transformation. This phenotype was reversed by concomitant deletion of TP53. These data support important and non-redundant roles for mediator kinases in liver carcinogenesis, where they genetically interact with the TP53 tumor suppressor.
Fractal Dimension of Cortical Functional Connectivity Networks Predicts Severity in Disorders of Consciousness
Authors: Varley TF. , Craig M. , Adapa R. , Finoia P. , Williams G. , Alanson J. , Pickard J. , Menon DK. , Stamatakis EA.
Published: October 2019

Recent evidence suggests that the quantity and quality of conscious experience may be a function of the complexity of activity in the brain, and that consciousness emerges in a critical zone on the axes of order/randomness and integration/differentiation. We propose fractal shapes as a measure of proximity to this critical point, as fractal dimension encodes information about complexity beyond simple entropy or randomness, and fractal structures are known to emerge in systems nearing a critical point. To validate this, we tested the several measures of fractal dimension on the brain activity from healthy volunteers and patients with disorders of consciousness of varying severity. We used a Compact Box Burning algorithm to compute the fractal dimension of cortical functional connectivity networks as well as computing the fractal dimension of the associated adjacency matrices using a 2D box-counting algorithm. To test whether brain activity is fractal in time as well as space, we used the Higuchi temporal fractal dimension on BOLD time-series. We found significant decreases in the fractal dimension between healthy volunteers (n=15), patients in a minimally conscious state (n=10), and patients in a vegetative state (n=8), regardless of the mechanism of injury. We also found significant decreases in adjacency matrix fractal dimension and Higuchi temporal fractal dimension, which correlated with decreasing level of consciousness. These results suggest that cortical functional connectivity networks display fractal character and that this is predictive of level of consciousness in a clinically relevant population, with more fractal (i.e. more complex) networks being associated with higher levels of consciousness. This supports the hypothesis that level of consciousness and system complexity are positively associated, and is consistent with previous EEG, MEG, and fMRI studies.
HOX13-dependent chromatin accessibility modulates the target repertoires of the HOX factors
Authors: Desanlis Ines , Kherdjemil Yacine , Mayran Alexandre , Bouklouch Yasser , Gentile Claudia , Sheth Rushikesh , Zeller Rolf , Drouin Jacques , Kmita Marie
Published: October 2019

Hox genes encode essential transcription factors that control patterning during embryonic development. Distinct combinations of nested Hox expression domains establish cell and tissue identities1–3. Consequently, spatial or temporal de-regulation of Hox genes can cause severe alterations of the body plan3. While HOX factors have very similar DNA binding motifs, their binding specificity is, in part, mediated by co-factors4–6. Yet, the interplay between HOX binding specificities and the cellular context remains largely elusive. To gain insight into this question, we took advantage of developing limbs for which the differential expression of Hox genes is well-characterized7. We show that the transcription factors HOXA13 and HOXD13 (hereafter referred as HOX13) allow another HOX factor, HOXA11, to bind loci initially assumed to be HOX13-specific. Importantly, HOXA11 is unable to bind these loci in distal limbs lacking HOX13 function indicating that HOX13 modulates HOXA11 target repertoire. In addition, we find that the HOX13 factors implement the distal limb developmental program by triggering chromatin opening, a defining property of pioneer factors8,9. Finally, single cell analysis of chromatin accessibility reveals that HOX13 factors pioneer chromatin opening in a lineage specific manner. Together, our data uncover a new mechanism underlying HOX binding specificity, whereby tissue-specific variations in the target repertoire of HOX factors rely, at least in part, on HOX13-dependent chromatin accessibility.
Varietal differences in physiological and biochemical responses to salinity stress in six finger millet plants
Authors: Mukami Asunta , Ng’etich Alex , Syombua Easter , Oduor Richard , Mbinda Wilton
Published: October 2019

Finger millet is one of the most important cereals that are often grown in semiarid and arid regions of East-Africa. Salinity is known to be a major impediment for the crop growth and production. This study was aimed to understand the mechanisms of physiological and biochemical responses to salinity stress of Kenyan finger millet varieties (GBK043137, GBK043128, GBK043124, GBK043122, GBK043094, GBK043050) grown across different agroecological zones under NaCl-induced salinity stress. Seeds were germinated on the sterile soil and treated using various concentrations of NaCl (100, 200 and 300 mM) for two weeks. Again, the early-seedling stage of germinated plants was irrigated with the same salt concentrations for 60 days. Results indicated depression in germination percentage, shoot and root growth rate, leaf relative water content, chlorophyll content contents, leaf K+ concentration, and leaf K+/Na+ ratios increased salt levels. Contrary, proline and malonaldehyde (MDA) contents reduced sugar content and leaf total proteins. At the same time, the leaf Na+ and Cl− amounts of all plants increased substantially with rising stress levels. Clustering analysis revealed that GBK043094 and GBK043137 were placed together and identified as salt-tolerant varieties based on their performance under salt stress. Overall, our findings indicated a significant varietal variability for most of the parameters analysed. These superior varieties identified could be potentially used as promising genetic resources in future breeding programmes development directed towards salt-tolerant finger millet hybrids. Further analysis at genomic level need to be undertaken to better understand the genetic factors that promote salinity tolerance in finger millet.