bluuebunny/crossref_metadata_2025 huggingface dataset:
Respiratory Syncytial Virus in Infants and Children with Prader-Willi syndrome
Authors: Miller JL , Thornton E
Published: June 2020

BACKGROUND

Prader-Willi syndrome (PWS) is a complex disorder affecting approximately 1/15,000-1/30,000 people. Infants with PWS are at risk for serious complications with Respiratory Syncytial Virus (RSV) due to low muscle tone and a weakened pulmonary system.

OBJECTIVES

Understanding RSV incidence, hospitalization rates, lingering effects, and morbidity in children with PWS may help with planning health care, insurance and vaccine recommendations in children with PWS.

METHODS

Links to volunteer surveys were provided via direct email and social media to families throughout the United States with children having PWS. The contact distribution lists were provided by PWSA(USA) and the Foundation for Prader-Willi Research.

RESULTS

A total of 220 surveys were completed by the parents/caregivers of children with PWS. Of those respondents, 60 (27.27%) had contracted the RSV virus during early childhood. Of those with RSV, 44 children required hospitalization, with 16 reporting multiple hospitalizations, some for several weeks. Of those with the virus, 22 required PICU admission, 10 required intubation, 20 needed CPAP, and 46 children needed supplemental oxygen during the infection. Of those who had contracted RSV, 42% were over age 1 year at the time of infection, and 17 children developed chronic lung issues after the RSV infection. The case lethality was 1.37%.

Only 38% had received the RSV Synagis shot, and 19% received more than one season of the vaccination. Prematurity prevalence was only 28%, but 99% reported that their child had significant hypotonia.

Approximately 30% of parents sited lack of insurance authorization or failure of the physician to recommend the treatment.

CONCLUSIONS

The risk of contracting RSV for young children with PWS is high. The implications of contracting RSV include death or lung damage, along with high medical expenditures, which could be ameliorated with routine administration of the Synagis vaccine.
Differential Gene Expression Analysis and Cytological Evidence Reveal a Sexual Stage of an Amoeba with Multiparental Cellular and Nuclear Fusion
Authors: Tekle Yonas I. , Wang Fang , Heidari Alireza , Stewart Alanna Johnson
Published: June 2020

Sex is a hallmark of eukaryotes but its evolution in microbial eukaryotes is poorly elucidated. Recent genomic studies revealed microbial eukaryotes possess genetic toolkit necessary for sexual reproduction. However, the mechanism of sexual development in a majority of microbial eukaryotes including amoebozoans is poorly characterized. The major hurdle in studying sex in microbial eukaryotes is lack of observational evidence, primarily due to its cryptic nature. In this study, we used a tractable fusing amoeba,Cochliopodium,to investigate sexual development using stage specific Differential Gene Expression (DGE) and cytological analyses. Both DGE and cytological results showed that most of the meiosis and sex-related genes are upregulated inCochliopodiumundergoing fusion in laboratory culture. Relative gene ontology (GO) category representations in unfused (single) and fused cells revealed functional skew of the fused transcriptome toward DNA metabolism, nucleus and ligases that are suggestive of a commitment to sexual development. While single cells GO categories were dominated by metabolic pathways and other processes indicative of vegetative phase. Our study provides strong evidence that the fused cells represent a sexual stage inCochliopodium.Our findings have further implications in understanding the evolution and mechanism of inheritance involving multiparents in other eukaryotes with similar reproductive strategy.
Allosteric inhibition of adenylyl cyclase type 5 by G-protein: a molecular dynamics study
Authors: Frezza Elisa , Amans Tina-Méryl , Martin Juliette
Published: June 2020

Adenylyl cyclases (ACs) have a crucial role in many signal transduction pathways, in particular in the intricate control of cyclic AMP (cAMP) generation from adenosine triphosphate (ATP). Using homology models developed from existing structural data and docking experiments, we have carried out all-atom, microsecond-scale molecular dynamics simulations on the AC5 isoform of adenylyl cyclase bound to the inhibitory G-protein subunit Gαi in the presence and in the absence of ATP. The results show that Gαi have significant effects on the structure and flexibility of adenylyl cyclase, as observed earlier for the binding of ATP and Gsα. New data on Gαi bound to the C1 domain of AC5 help to explain how Gαi inhibits enzyme activity and to get insight on its regulation. Simulations also suggest a crucial role of ATP in the regulation of stimulation and inhibition of AC5.

Author summary

The neurons that compose the human brain are able to respond to multiple inputs from other neurons. The chemical “integration” of these inputs then decides whether a given neuron passes on a signal or not. External chemical messages act on neurons via proteins in their membranes that trigger cascades of reactions within the cell. One key molecule in these signaling cascades is cyclic adenosine monophosphate (cAMP) that is chemically synthesized from adenosine triphosphate (ATP) by the enzyme adenylyl cyclase (AC). We are investigating the mechanisms that control how much cAMP is produced as a function of the signals received by the neuron. In particular, we have studied the inhibition effect of a key protein, termed Gαi, on AC, and we compare it with the stimulator effect of another key protein termed Gsα. Using microsecond molecular simulations, we have been able to show how binding Gαi to AC changes its structure and its dynamics so that its enzymatic activity is quenched and that ATP seems to have a crucial role in the regulation of stimulation and inhibition of AC5.
Dynein collective behavior in mitotic nuclear positioning ofSaccharomyces cerevisiae
Authors: Jain Kunalika , Khetan Neha , Palani Saravanan , Athale Chaitanya A.
Published: June 2020

1

Positioning the nucleus at the bud-neck prior duringSaccharomyces cerevisiaemitosis during anaphase involves pulling forces of cytoplasmic dynein localized in the daughter cell. While genetic analysis has revealed a complex network positioning the nucleus, quantification of the forces acting on the nucleus and dyneins numbers driving the process has remained difficult. In order to better understand the role of motor-microtubule mechanics during nuclear positioning and the role of dynein, we have used a computational model of nuclear mobility inS. cerevisiaeand reconciled it to the mobility of labelled spindle pole bodies (SPBs) measured by quantifying fluorescence microscopy time-series. We model the apparent random-walk mobility of SPBs by combining diffusion of the nucleus and active pushing of MTs at the cell membrane. By minimizing the deviation between tracks of fluorescently tagged SPBs and simulations, we estimate the effective cytoplasmic viscosity to be 0.5 Pa s. The directed transport of nuclei during the budding process is similarly quantified by tracking the daughter SPB (SPB-D) in experiment. Using force-balance, we find 2 to 8 motors are required to pull the nucleus to the bud-neck. Simulations of the cytoplasmic MT (cMT) ‘search and capture’ by dynein suggest single motor binding is followed by a rapid saturation of number of bound motors. The short time and length of MT interactions with the cortex and minimal collective dynein force required, predict a functional role for dynein clustering in nuclear positioning.
Effects of gonadectomy and androgen on neuronal plasticity in motivation and reward related brain regions in the male rat
Authors: Huijgens Patty T. , Snoeren Eelke M.S. , Meisel Robert L. , Mermelstein Paul G.
Published: June 2020

Gonadal hormones affect neuronal morphology to ultimately regulate behavior. Here, we investigated the effect of both castration and androgen replacement on spine plasticity in the nucleus accumbens shell and core (NAcSh and NAcC), caudate putamen (CPu), medial amygdala (MeA), and medial preoptic nucleus (MPN). Intact and castrated (GDX) male rats were treated with dihydrotestosterone (DHT, 1.5mg) or vehicle (oil) in 3 experimental groups: intact-oil, GDX-oil and GDX-DHT. Spine density and morphology, measured 24 hours after injection, were determined through 3D reconstruction of DiI-labeled dendritic segments. GDX decreased spine density in the MPN, which was rescued by DHT treatment. MeA spine density increased in GDX-DHT animals compared to intact-oil animals. In the NAcSh, DHT decreased spine density, and also rapidly increased the number of pCREB+ cell bodies. These findings indicate that androgen signaling plays a role in the regulation of spine plasticity within neurocircuits involved in motivated behaviors.
PlexinA4-Semaphorin3A mediated crosstalk between main cortical interneuron classes is required for superficial interneurons lamination
Authors: Limoni Greta , Niquille Mathieu , Murthy Sahana , Jabaudon Denis , Dayer Alexandre
Published: June 2020

In the mammalian cerebral cortex, the developmental events governing the allocation of different classes of inhibitory interneurons (INs) into distinct cortical layers are poorly understood. Here we report that the guidance receptor PlexinA4 (PLXNA4) is upregulated in serotonin receptor 3a-expressing (HTR3A+) cortical INs (hINs) as they invade the cortical plate and that it regulates their laminar allocation to superficial cortical layers. We find that the PLXNA4 ligand Semaphorin3A (SEMA3A) acts as a chemorepulsive factor on hINs migrating into the nascent cortex and demonstrate that SEMA3A specifically controls their laminar positioning through PLXNA4. We identify that deep layer INs constitute a major source of SEMA3A in the developing cortex and demonstrate that cell-type specific genetic deletion of SEMA3A in these INs specifically affects the laminar allocation of hINs. These data demonstrate that in the neocortex, deep layer INs control the laminar allocation of hINs into superficial layers.
Evolutionary Based Adaptive Dosing Algorithms: Beware the Cost of Cumulative Risk
Authors: Mistry Hitesh B.
Published: June 2020

Application of theories from ecology to cancer is growing. One such idea involves using drug sensitive cells to control drug resistant cells by cycling treatment on and off based on a marker of tumour burden. Many literature studies have highlighted the benefit of this approach when using time till reaching a certain level of burden as an end-point. These studies though have not considered that patients need to survive up until a certain time-point with a higher level of tumour burden compared to standard dosing to gain this benefit. Within this study once this cumulative cost is accounted for it can be seen that adaptive dosing, counter-intuitively, is likely to lead to poorer prognosis than continuous dosing. This study highlights that evolutionary based adaptive dosing algorithms may not be the “parachute” its protagonists believe it to be.
Modeling a co-culture ofClostridium autoethanogenumandClostridium kluyverito increase syngas conversion to medium-chain fatty-acids
Authors: Benito-Vaquerizo Sara , Diender Martijn , Olm Ivette Parera , dos Santos Vitor Martins , Schaap Peter J. , Sousa Diana Z. , Suarez-Diez Maria
Published: June 2020

Microbial fermentation of synthesis gas (syngas) is becoming more attractive for sustainable production of commodity chemicals. To date, syngas fermentation focuses mainly on the use ofClostridiumspecies for the production of small organic molecules such as ethanol and acetate. The cocultivation of syngas-fermenting microorganisms with chain-elongating bacteria can expand the range of possible products, allowing, for instance, the production of medium-chain fatty acids (MCFA) and alcohols from syngas. To explore these possibilities, we report herein a genome-scale, constraint-based metabolic model to describe growth of a co-culture ofClostridium autoethanogenumandClostridium kluyverion syngas for the production of valuable compounds. Community flux balance analysis was used to gain insight into the metabolism of the two strains and their interactions, and to reveal potential strategies enabling production of butyrate and hexanoate. The model suggests that addition of succinate is one strategy to optimize the production of medium-chain fatty-acids from syngas with this co-culture. According to the predictions, addition of succinate increases the pool of crotonyl-CoA and the ethanol/acetate uptake ratio inC. kluyveri, resulting in the flux of up to 60% of electrons into hexanoate. Other potential way to optimize butyrate and hexanoate is to increase ethanol production byC. autoethanogenum. Deletion of either formate transport, acetaldehyde dehydrogenase or formate dehydrogenase (ferredoxin) from the metabolic model ofC. autoethanogenumleads to a (potential) increase in ethanol production up to 150%, which is clearly very attractive.
A predictive model of gene expression reveals the role of regulatory motifs in the mating response of yeast
Authors: Pomeroy Amy E. , Pena Matthew I. , Houser John R. , Dixit Gauri , Dohlman Henrik G. , Elston Timothy C. , Errede Beverly
Published: June 2020

Cells use signaling pathways to receive and process information about their environment. These systems are nonlinear, relying on feedback and feedforward regulation to respond appropriately to changing environmental conditions. Mathematical models developed to describe signaling pathways often fail to show predictive power, because the models are not trained on data that probe the diverse time scales on which feedforward and feedback regulation operate. We addressed this limitation using microfluidics to expose cells to a broad range of dynamic environmental conditions. In particular, we focus on the well-characterized mating response pathway ofS. cerevisiae(yeast). This pathway is activated by mating pheromone and initiates the transcriptional changes required for mating. Although much is known about the molecular components of the mating response pathway, less is known about how these components function as a dynamical system. Our experimental data revealed that pheromone-induced transcription persists following removal of pheromone and that long-term adaptation of the transcriptional response occurs when pheromone exposure is sustained. We developed a model of the regulatory network that captured both persistence and long-term adaptation of the mating response. We fit this model to experimental data using an evolutionary algorithm and used the parameterized model to predict scenarios for which it was not trained, including different temporal stimulus profiles and genetic perturbations to pathway components. Our model allowed us to establish the role of four regulatory motifs in coordinating pathway response to persistent and dynamic stimulation.
Trypanocidal activity of the anthocyanidin delphinidin, a non-competitive inhibitor of arginine kinase
Authors: Valera-Vera Edward , Reigada Chantal , Sayé Melisa , Digirolamo Fabio A. , Galceran Facundo , Miranda Mariana R. , Pereira Claudio A.
Published: June 2020

The enzyme arginine kinase fromTrypanosoma cruzi(TcAK) catalyzes the interconversion of arginine and phosphoarginine to maintain the ATP/ADP cell balance, and is involved in the parasites energetic homeostasis and stress responses. Using virtual screening approaches, some plant-derived polyphenolic pigments such as anthocyanidins, were predicted to inhibit TcAK activity. In this work, it was demonstrated that the anthocyanidin delphinidin showed a non-competitive inhibition mechanism of TcAKin vitro(Ki arginine = 1.32 μM and Ki ATP = 500 μM). Molecular docking simulations predicted that delphinidin occupies a hydrophobic pocket close to the ATP/ADP binding site. Delphinidin also exerted trypanocidal activity overT. cruzitrypomastigotes with a calculated IC50of 19.51 μM. Anthocyanidins are low-toxicity natural products which can be exploited for the development of trypanocidal drugs with less secondary effects than those currently used for the treatment of Chagas disease.
Cogno-Vest: A Torso-Worn, Force Display to Experimentally Induce Specific Hallucinations and Related Bodily Sensations
Authors: Fadaei J. Atena , Jeanmonod Kenny , Kannape Olivier A. , Potheegadoo Jevita , Bleuler Hannes , Hara Masayuki , Blanke Olaf
Published: June 2020

Recent advances in virtual reality and robotic technologies have allowed researchers to explore the mechanisms underlying bodily aspects of self-consciousness which are largely attributed to the multisensory and sensorimotor processing of bodily signals (bodily self-consciousness, BSC). One key contribution to BSC, that is currently poorly addressed due to the lack of a wearable solution, concerns realistic collision sensations on the torso. Here, we introduce and validate a novel torso-worn force display, the Cogno-vest, to provide mechanical touch on the user’s back in a sensorimotor perception experiment. In a first empirical study, we characterized human finger poking (N=28). In order to match these poking characteristics and meet the wearability criteria, we used bi-directional, push-pull solenoids as a force actuator in the Cogno-vest. Subsequently, and based on an iterative, multidisciplinary design procedure, a bodyconforming, unisex, torso-worn force display was prototyped. Finally, we conducted a behavioral study that investigated BSC in 25 healthy participants by introducing conflicting sensorimotor signals between their hand and torso (back). Using the final reiteration of the Cogno-vest we successfully replicated previous findings on illusory states of BSC, characterized by presence hallucinations (PH) and passivity symptoms, and achieved higher illusion ratings compared to static conditions used in prior studies.
Drosophila Hedgehog can act as a morphogen in the absence of regulated Ci processing
Authors: Little Jamie C. , Garcia-Garcia Elisa , Sul Amanda , Kalderon Daniel
Published: June 2020

Extracellular Hedgehog (Hh) proteins induce transcriptional changes in target cells by inhibiting the proteolytic processing of full-length Drosophila Ci or mammalian Gli proteins to nuclear transcriptional repressors and by activating the full-length proteins, which are otherwise held inactive by cytoplasmic binding partners and subject to accelerated degradation following activation. We used Ci variants expressed at physiological levels to investigate the contributions of these mechanisms to dose-dependent Hh signaling at the anteroposterior (AP) border of Drosophila wing imaginal discs. Ci variants that cannot be processed supported a normal pattern of graded target gene activation and the development of adults with normal wing morphology when supplemented by constitutive Ci repressor, showing that Hh can signal normally in the absence of regulated processing. The full-length Ci-155 protein profile of these variants revealed a linear gradient of Hh-stimulated degradation, allowing derivation of a spatial profile of inhibition of processing of normal C-155 by Hh. The processing-resistant Ci variants were also significantly activated in the absence of Hh by elimination of Cos2, acting through association with the CORD domain of Ci, or PKA, revealing separate inhibitory roles of these two components in addition to their well-established roles in promoting Ci-155 processing.
Transcriptomic and proteomic regulation through abundant, dynamic, and independent arginine methylation by Type I and Type II PRMTs
Authors: Lehman Stephanie M. , Chen Hongshan , Burgos Emmanuel S. , Maron Maxim , Gayatri Sitaram , Nieves Edward , Bai Dina L. , Sidoli Simone , Gupta Varun , Marunde Matthew R. , Bone James R. , Sun Zu-Wen , Bedford Mark T. , Shabanowitz Jeffrey , Hunt Donald F. , Shechter David
Published: June 2020

Arginine methylation is essential for both cellular viability and development and is also dysregulated in cancer. PRMTs catalyze the post translational monomethylation (Rme1/MMA, catalyzed by Type I-III), asymmetric (Rme2a/ADMA, Type I enzymes)-, or symmetric (Rme2s/SDMA, Type II enzymes) dimethylation of arginine. Despite many studies, a thorough integration of PRMT enzyme substrate determination and proteomic and transcriptomic consequences of inhibiting Type I and II PRMTs is lacking. To characterize cellular substrates for Type I (Rme2a) and Type II (Rme2s) PRMTs, human A549 lung adenocarcinoma cells were treated with either Type I (MS023) or Type II (GSK591) inhibitors. Using total proteome hydrolysis, we developed a new mass spectrometry approach to analyze total arginine and lysine content. We showed that Rme1 was a minor population (∼0.1% of total arginine), Rme2a was highly abundant (∼1.1%), and Rme2s was intermediate (∼0.4%). While Rme2s was mostly eliminated by GSK591 treatment, total Rme1 and Rme2a were more resistant to perturbation. To quantitatively characterize substrate preferences of the major enzymes PRMT1, PRMT4(CARM1), and PRMT5, we used oriented peptide array libraries (OPAL) in methyltransferase assays. We demonstrated that while PRMT5 tolerates aspartic acid residues in the substrate, PRMT1 does not. Importantly, PRMT4 methylated previously uncharacterized hydrophobic motifs. To integrate our studies, we performed PTMScan on PRMT-inhibited A549 cells and enriched for methylated arginine containing tryptic peptides. For detection of highly charged peptides, a method to analyze the samples using electron transfer dissociation was developed. Proteomic analysis revealed distinct methylated species enriched in nuclear function, RNA-binding, intrinsically disordered domains, and liquid-liquid phase separation. Parallel studies with proteomics and RNA-Seq revealed distinct, but ontologically overlapping, consequences to PRMT inhibition. Overall, we demonstrate a wider PRMT substrate diversity and methylarginine functional consequence than previously shown.
Elevated somatic mutation burdens in normal human cells due to defective DNA polymerases
Authors: Robinson Philip S. , Coorens Tim H.H. , Palles Claire , Mitchell Emily , Abascal Federico , Olafsson Sigurgeir , Lee Bernard , Lawson Andrew R.J. , Lee-Six Henry , Moore Luiza , Sanders Mathijs A. , Hewinson James , Martin Lynn , Pinna Claudia M.A. , Galvotti Sara , Campbell Peter J. , Martincorena Iñigo , Tomlinson Ian , Stratton Michael R.
Published: June 2020

Mutation accumulation over time in normal somatic cells contributes to cancer development and is proposed as a cause of ageing. DNA polymerases Pol ε and Pol δ replicate DNA with high fidelity during normal cell divisions. However, in some cancers defective proofreading due to acquired mutations in the exonuclease domains of POLE or POLD1 causes markedly elevated somatic mutation burdens with distinctive mutational signatures. POLE and POLD1 exonuclease domain mutations also cause familial cancer predisposition when inherited through the germline. Here, we sequenced normal tissue DNA from individuals with germline POLE or POLD1 exonuclease domain mutations. Increased mutation burdens with characteristic mutational signatures were found to varying extents in all normal adult somatic cell types examined, during early embryogenesis and in sperm. Mutation burdens were further markedly elevated in neoplasms from these individuals. Thus human physiology is able to tolerate ubiquitously elevated mutation burdens. Indeed, with the exception of early onset cancer, individuals with germline POLE and POLD1 exonuclease domain mutations are not reported to show abnormal phenotypic features, including those of premature ageing. The results, therefore, do not support a simple model in which all features of ageing are attributable to widespread cell malfunction directly resulting from somatic mutation burdens accrued during life.
Metagenomic reconstruction of nitrogen and carbon cycling pathways in forest soil: Influence by different hardwood tree species
Authors: Kelly Charlene N. , Schwaner Geoffrey W. , Cumming Jonathan R. , Driscoll Timothy P.
Published: June 2020

The soil microbiome plays an essential role in processing and storage of nitrogen (N) and carbon (C), and is influenced by vegetation above-ground through imparted differences in chemistry, structure, mass of plant litter, root physiology, and dominant mycorrhizal associations. We used shotgun metagenomic sequencing and bioinformatic analysis to quantify the abundance and distribution of gene families involved in soil microbial N and C cycling beneath three deciduous hardwood tree species: ectomycorrhizal (ECM)-associatedQuercus rubra(red oak), ECM-associatedCastanea dentata(American chestnut), and arbuscular mycorrhizal (AM)-associatedPrunus serotina(black cherry). Chestnut exhibited the most distinct soil microbiome of the three species, both functionally and taxonomically, with a general suppression of functional genes in the nitrification, denitrification, and nitrate reduction pathways. These changes were related to low inorganic N availability in chestnut stands as soil was modified by poor, low-N litter quality relative to red oak and black cherry soils.

IMPORTANCE

Previous studies have used field biogeochemical process rates, isotopic tracing, and targeted gene abundance measurements to study the influence of tree species on ecosystem N and C dynamics. However, these approaches do not enable a comprehensive systems-level understanding of the relationship between microbial diversity and metabolism of N and C below-ground. We analyzed microbial metagenomes from soils beneath red oak, American chestnut, and black cherry stands and showed that tree species can mediate the abundance of key microbial genes involved in N and (to a lesser extent) C metabolism pathways in soil. Our results highlight the genetic framework underlying tree species’ control over soil microbial communities, and below-ground C and N metabolism, and may enable land managers to select tree species to maximize C and N storage in soils.
Robust, flexible, and scalable tests for Hardy-Weinberg Equilibrium across diverse ancestries
Authors: Kwong Alan M. , Blackwell Thomas W. , LeFaive Jonathon , de Andrade Mariza , Barnard John , Barnes Kathleen C. , Blangero John , Boerwinkle Eric , Burchard Esteban G. , Cade Brian E. , Chasman Daniel I. , Chen Han , Conomos Matthew P. , Cupples L. Adrienne , Ellinor Patrick T. , Eng Celeste , Gao Yan , Guo Xiuqing , Irvin Marguerite Ryan , Kelly Tanika N. , Kim Wonji , Kooperberg Charles , Lubitz Steven A. , Mak Angel C. Y. , Manichaikul Ani W. , Mathias Rasika A. , Montasser May E. , Montgomery Courtney G. , Musani Solomon , Palmer Nicholette D. , Peloso Gina M. , Qiao Dandi , Reiner Alexander P. , Roden Dan M. , Shoemaker M. Benjamin , Smith Jennifer A. , Smith Nicholas L. , Su Jessica Lasky , Tiwari Hemant K. , Weeks Daniel E. , Weiss Scott T. ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium,   TOPMed Analysis Working Group, Scott Laura J. , Smith Albert V. , Abecasis Gonçalo R. , Boehnke Michael , Kang Hyun Min
Published: June 2020

Traditional Hardy-Weinberg equilibrium (HWE) tests (the χ2test and the exact test) have long been used as a metric for evaluating genotype quality, as technical artifacts leading to incorrect genotype calls often can be identified as deviations from HWE. However, in datasets comprised of individuals from diverse ancestries, HWE can be violated even without genotyping error, complicating the use of HWE testing to assess genotype data quality. In this manuscript, we present the Robust Unified Test for HWE (RUTH) to test for HWE while accounting for population structure and genotype uncertainty, and evaluate the impact of population heterogeneity and genotype uncertainty on the standard HWE tests and alternative methods using simulated and real sequence datasets. Our results demonstrate that ignoring population structure or genotype uncertainty in HWE tests can inflate false positive rates by many orders of magnitude. Our evaluations demonstrate different tradeoffs between false positives and statistical power across the methods, with RUTH consistently amongst the best across all evaluations. RUTH is implemented as a practical and scalable software tool to rapidly perform HWE tests across millions of markers and hundreds of thousands of individuals while supporting standard VCF/BCF formats. RUTH is publicly available athttps://www.github.com/statgen/ruth.
Hypomyelination reduces parvalbumin interneuron density and auditory cortex inhibitory function
Authors: de Carvalho Borges Beatriz , Meng Xiangying , Long Patrick , Kanold Patrick Oliver , Corfas Gabriel
Published: June 2020

For a long time, myelin was thought to be restricted to excitatory neurons, and studies on dysmyelination focused primarily on excitatory cells. Recent evidence showed that axons of inhibitory neurons in the neocortex are also myelinated, but the role of myelin on inhibitory circuits remains unknown. Here we studied the impact of mild hypomyelination on both excitatory and inhibitory connectivity in the primary auditory cortex (A1) with well-characterized mouse models of hypomyelination due to loss of oligodendrocyte ErbB receptor signaling. Using laser-scanning photostimulation, we found that mice with mild hypomyelination have reduced functional inhibitory connections to A1 L2/3 neurons without changes in excitatory connections, resulting in altered excitatory/inhibitory balance. These effects are not associated with altered expression of GABAergic and glutamatergic synaptic components, but with reduced density of parvalbumin-positive (PV+) neurons, which reflects reduced PV expression by interneurons rather than PV+neuronal loss. While immunostaining shows that hypomyelination occurs in both PV+and PV-axons, there is a strong correlation between MBP and PV expression suggesting that myelination influences PV expression. Together, the results demonstrate that mild hypomyelination impacts A1 neuronal networks, reducing inhibitory activity, and shifting networks towards excitation.
Transcriptome and metabolome analysis of crGART, a novel cell model of de novo purine synthesis deficiency: Alterations in CD36 expression and activity
Authors: Mazzarino Randall C , Baresova Veronika , Zikánová Marie , Duval Nathan , Wilkinson Terry G. , Patterson David , Vacano Guido N.
Published: June 2020

In humans, GART [phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) / phosphoribosylglycinamide synthetase (EC 6.3.4.13) / phosphoribosylaminoimidazole synthetase (EC 6.3.3.1)] is a trifunctional protein which catalyzes the second, third, and fifth reactions of the ten step de novo purine synthesis (DNPS) pathway. The second step of DNPS is conversion of phosphoribosylamine (5-PRA) to glycineamide ribonucleotide (GAR). 5-PRA is extremely unstable under physiological conditions and is unlikely to accumulate in the absence of GART activity. Recently, a HeLa cell line null mutant for GART was constructed via CRISPR-Cas9 mutagenesis. This cell line, crGART, is an important cellular model of DNPS inactivation that does not accumulate DNPS pathway intermediates. In the current study, we characterized the crGART versus HeLa transcriptomes in purine-supplemented and purine-depleted growth conditions. We observed multiple transcriptome changes and discuss pathways and ontologies particularly relevant to Alzheimer disease and Down syndrome. We also report initial analysis of the Cluster of Differentiation (CD36) gene, which is highly expressed in crGART versus HeLa.
A novel and highly effective mitochondrial uncoupling drug in T-cell leukemia
Authors: da Silva-Diz Victoria , Cao Bin , Lancho Olga , Chiles Eric , Alasadi Amer , Luo Shirley , Augeri David , Minuzzo Sonia , Indraccolo Stefano , Su Xiaoyang , Jin Shengkan , Herranz Daniel
Published: June 2020

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy. Despite recent advances in treatments with intensified chemotherapy regimens, relapse rates and associated morbidities remain high. In this context, metabolic dependencies have emerged as a druggable opportunity for the treatment of leukemia. Here, we tested the antileukemic effects of MB1-47, a newly developed mitochondrial uncoupling compound. MB1-47 treatment in T-ALL cells robustly inhibited cell proliferation via both cytostatic and cytotoxic effects as a result of compromised mitochondrial energy and macromolecule depletion, which severely impair nucleotide biosynthesis. Mechanistically, acute treatment with MB1-47 in primary leukemias promoted AMPK activation and downregulation of mTOR signaling, stalling anabolic pathways that support leukemic cell survival. Indeed, MB1-47 treatment in mice harboring murine NOTCH1-induced leukemias or human T-ALL PDXs led to a potent antileukemic effect with 2-fold extension in survival without overlapping toxicities. Overall, our findings demonstrate a critical role for mitochondrial oxidative phosphorylation in T-ALL and uncover MB1-47-driven mitochondrial uncoupling as a novel therapeutic strategy for the treatment of this disease.
Engineering a virus-like particle to display peptide insertions using an apparent fitness landscape
Authors: Robinson Stephanie A. , Hartman Emily C. , Ikwuagwu Bon C. , Francis Matthew B. , Tullman-Ercek Danielle
Published: June 2020

Peptide insertions in the primary sequence of proteins expand functionality by introducing new binding sequences, chemical handles, or membrane disrupting motifs. With these properties, proteins can be engineered as scaffolds for vaccines or targeted drug delivery vehicles. Virus-like particles (VLPs) are promising platforms for these applications since they are genetically simple, mimic viral structure for cell uptake, and can deliver multiple copies of a therapeutic agent to a given cell. Peptide insertions in the coat protein of VLPs can increase VLP uptake in cells by increasing cell binding, but it is difficult to predict how an insertion affects monomer folding and higher order assembly. To this end, we have engineered the MS2 VLP using a high-throughput technique, called Systematic Mutagenesis and Assembled Particle Selection (SyMAPS). In this work, we applied SyMAPS to investigate a highly mutable loop in the MS2 coat protein to display 9,261 non-native tripeptide insertions. This library generates a discrete map of three amino acid insertions permitted at this location, validates the FG loop as a valuable position for peptide insertion, and illuminates how properties such as charge, flexibility, and hydrogen bonding can interact to preserve or disrupt capsid assembly. Taken together, the results highlight the potential to engineer VLPs in systematic manner, paving the way to exploring the applications of peptide insertions in biomedically relevant settings.
SARS CoV-2 Serosurvey in Addis Ababa, Ethiopia
Authors: Kempen John H. , Abashawl Aida , Kinfemichael Hilkiah , Difabachew Mesfin Nigussie , Kempen Christopher J. , Debele Melaku Tesfaye , Menkir Abel A. , Assefa Maranatha T. , Asfaw Eyob H. , Habtegabriel Leul B. , Addisie Yohannes Sitotaw , Nilles Eric J. , Longenecker Joseph C.
Published: June 2020

The global COVID-19 pandemic caused by SARS CoV-2 is causing both mortality/morbidity and collateral social and economic damage related to public panic and aggressive public policy measures to contain the disease worldwide.(1) The epidemic appears to have taken hold much more slowly in sub-Saharan Africa than most of the world.(2) Antibody testing to evaluate the population proportion previously infected with SARS CoV-2 has the potential to guide public policy, but has not been reported so far for sub-Saharan Africa.
Platelets can contain SARS-CoV-2 RNA and are hyperactivated in COVID-19
Authors: Zaid Younes , Puhm Florian , Allaeys Isabelle , Naya Abdallah , Oudghiri Mounia , Khalki Loubna , Limami Youness , Zaid Nabil , Sadki Khalid , El Haj Rafiqua Ben , Maher Wissal , Lamiae Belayachi , Belefquih Bouchra , Benouda Amina , Cheikh Amine , Cherrah Yahia , Flamand Louis , Guessous Fadila , Boilard Eric
Published: June 2020

Rationale

In addition to the overwhelming lung inflammation that prevails in COVID-19, hypercoagulation and thrombosis contribute to the lethality of subjects infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Platelets are chiefly implicated in thrombosis. Moreover, they can interact with viruses and are an important source of inflammatory mediators. While a lower platelet count is associated with severity and mortality, little is known about platelet function during COVID-19.

Objective

To evaluate the contribution of platelets to inflammation and thrombosis in COVID-19 patients.

Methods and Results

We document the presence of SARS-CoV-2 RNA in platelets of COVID-19 patients. Exhaustive assessment of cytokines in plasma and in platelets revealed the modulation of platelet-associated cytokine levels in COVID-19, pointing to a direct contribution of platelets to the plasmatic cytokine load. Moreover, we demonstrate that platelets release their alpha- and dense-granule contents and phosphatidylserine-exposing extracellular vesicles. Functionally, platelets were hyperactivated in COVID-19 subjects, with aggregation occurring at suboptimal thrombin concentrations. Furthermore, platelets adhered more efficiently onto collagen-coated surfaces under flow conditions.

Conclusions

These data suggest that platelets could participate in the dissemination of SARS-CoV-2 and in the overwhelming thrombo-inflammation observed in COVID-19. Thus, blockade of platelet activation pathways may improve outcomes in this disease.

KEY POINTS

Platelets are a source of inflammatory cytokines and degranulate in COVID-19 Platelets contain SARS-CoV-2 RNA molecules and are prone to activation in COVID-19

Subject terms

Infectious diseases/Emerging infectious diseases, SARS-CoV-2, COVID-19, Hematology, Platelets
The overlap of genetic susceptibility to schizophrenia and cardiometabolic disease can be used to identify metabolically different groups of individuals
Authors: Strawbridge Rona J. , Johnston Keira J. A. , Bailey Mark E. S. , Baldasarre Damiano , Cullen Breda , Eriksson Per , DeFaire Ulf , Ferguson Amy , Gigante Bruna , Giral Philippe , Graham Nicholas , Hamsten Anders , Humphries Steve E. , Kurl Sudhir , Lyall Donald M. , Lyall Laura M. , Pirro Matteo , Pell Jill P. , Savonen Kai , Sennblad Bengt , Smit Andries J. , Tremoli Elena , Tomainen Tomi-Pekka , Veglia Fabrizio , Ward Joey , Smith Daniel J.
Published: June 2020

Understanding why individuals with severe mental illness (Schizophrenia, Bipolar Disorder and Major Depressive Disorder) have increased risk of cardiometabolic disease (including obesity, type 2 diabetes and cardiovascular disease), and identifying those at highest risk of cardiometabolic disease are important priority areas for researcher. We explored whether genetic variation could identify individuals with different metabolic profiles. Loci previously associated with schizophrenia, bipolar disorder and major depressive disorder were identified from literature and those overlapping loci genotyped on the Illumina CardioMetabo and Immuno chips (representing cardiometabolic processes and diseases) were selected. In the IMPROVE study (high cardiovascular risk) and UK Biobank (general population) multidimensional scaling was applied to genetic variants implicated in both mental and cardiometabolic illness. Visual inspection of the resulting plots used to identify distinct clusters. Differences between clusters were assessed using chi-squared and Kruskall-Wallis tests. In IMPROVE, genetic loci associated with both cardiometabolic disease and schizophrenia (but not bipolar or major depressive disorders) identified three groups of individuals with distinct metabolic profiles. The grouping was replicated in UK Biobank, albeit with less distinction between metabolic profiles. This study provides proof of concept that common biology underlying mental and physical illness can identify subsets of individuals with different cardiometabolic profiles.
Longitudinal immunological analyses reveal inflammatory misfiring in severe COVID-19 patients
Authors: Lucas Carolina , Wong Patrick , Klein Jon , Castro Tiago B.R. , Silva Julio , Sundaram Maria , Ellingson Mallory K. , Mao Tianyang , Oh Ji Eun , Israelow Benjamin , Tokuyama Maria , Lu Peiwen , Venkataraman Arvind , Park Annsea , Mohanty Subhasis , Wang Haowei , Wyllie Anne L. , Vogels Chantal B.F. , Earnest Rebecca , Lapidus Sarah , Ott Isabel M. , Moore Adam J. , Muenker M. Catherine , Fournier John B. , Campbell Melissa , Odio Camila D. , Casanovas-Massana Arnau ,   Yale IMPACT Team, Herbst Roy , Shaw Albert C. , Medzhitov Ruslan , Schulz Wade L. , Grubaugh Nathan D. , Cruz Charles Dela , Farhadian Shelli , Ko Albert I. , Omer Saad B. , Iwasaki Akiko
Published: June 2020

Recent studies have provided insights into the pathogenesis of coronavirus disease 2019 (COVID-19)1-4. Yet, longitudinal immunological correlates of disease outcome remain unclear. Here, we serially analysed immune responses in 113 COVID-19 patients with moderate (non-ICU) and severe (ICU) disease. Immune profiling revealed an overall increase in innate cell lineages with a concomitant reduction in T cell number. We identify an association between early, elevated cytokines and worse disease outcomes. Following an early increase in cytokines, COVID-19 patients with moderate disease displayed a progressive reduction in type-1 (antiviral) and type-3 (antifungal) responses. In contrast, patients with severe disease maintained these elevated responses throughout the course of disease. Moreover, severe disease was accompanied by an increase in multiple type 2 (anti-helminths) effectors including, IL-5, IL-13, IgE and eosinophils. Unsupervised clustering analysis of plasma and peripheral blood leukocyte data identified 4 immune signatures, representing (A) growth factors, (B) type-2/3 cytokines, (C) mixed type-1/2/3 cytokines, and (D) chemokines that correlated with three distinct disease trajectories of patients. The immune profile of patients who recovered with moderate disease was enriched in tissue reparative growth factor signature (A), while the profile for those with worsened disease trajectory had elevated levels of all four signatures. Thus, we identified development of a maladapted immune response profile associated with severe COVID-19 outcome and early immune signatures that correlate with divergent disease trajectories.
Point prevalence of SARS-CoV-2 and infection fatality rate in Orleans and Jefferson Parish, Louisiana, May 9-15, 2020
Authors: Feehan Amy K , Fort Daniel , Garcia-Diaz Julia , Price-Haywood Eboni , Velasco Cruz , Sapp Eric , Pevey Dawn , Seoane Leonardo
Published: June 2020

Using a novel recruitment method to reduce selection bias with paired molecular and antibody testing for SARS-CoV-2 infection, we determined point prevalence in a racially diverse municipality. Infections were highly variable by ZIP and differed by race. Overall census-weighted prevalence was 7.8% and the calculated infection fatality rate was 1.63%.
Detection of Major Depressive Disorder Using Vocal Acoustic Analysis and Machine Learning
Authors: Espinola Caroline Wanderley , Gomes Juliana Carneiro , Pereira Jessiane Mônica Silva , dos Santos Wellington Pinheiro
Published: June 2020

Purpose

Diagnosis and treatment in psychiatry are still highly dependent on reports from patients and on clinician judgement. This fact makes them prone to memory and subjectivity biases. As for other medical fields, where objective biomarkers are available, there has been an increasing interest in the development of such tools in psychiatry. To this end, vocal acoustic parameters have been recently studied as possible objective biomarkers, instead of otherwise invasive and costly methods. Patients suffering from different mental disorders, such as major depressive disorder (MDD), may present with alterations of speech. These can be described as uninteresting, monotonous and spiritless speech, low voice.

Methods

Thirty-three individuals (11 males) over 18 years old were selected, 22 of which being previously diagnosed with MDD, and 11 healthy controls. Their speech was recorded in naturalistic settings, during a routine medical evaluation for psychiatric patients, and in different environments for healthy controls. Voices from third parties were removed. The recordings were submitted to to a vocal feature extraction algorithm, and to different machine learning classification techniques.

Results

The results showed that support vector machines (SVM) models provided the greatest classification performances for different kernels, with PUK kernel providing accuracy of 89.14% for the detection of MDD.

Conclusion

The use of machine learning classifiers with vocal acoustics features has shown to be very promising for the detection of major depressive disorder, but further tests with a larger sample will be necessary to validate our findings.
A model of COVID-19 transmission and control on university campuses
Authors: Lopman Ben , Liu Carol Y. , Guillou Adrien Le , Handel Andreas , Lash Timothy L. , Isakov Alexander P. , Jenness Samuel M.
Published: June 2020

In response to the COVID-19 pandemic, institutions of higher education in almost every nation closed in the first half of 2020. University administrators are now facing decisions about if and how to safely return students, staff and faculty to campus. To provide a framework to evaluate various strategies, we developed a susceptible-exposed-infectious-recovered (SEIR) type deterministic compartmental transmission model of SARS-CoV-2 among students, staff and faculty. Our goals were to support the immediate pandemic planning at our own university, and to provide a flexible modeling framework to inform the planning efforts at similar academic institutions. We parameterized the model for our institution, Emory University, a medium-size private university in Atlanta, Georgia. Control strategies of isolation and quarantine are initiated by screening (regardless of symptoms) or testing (of symptomatic individuals). We explore a range of screening and testing frequencies and perform a probabilistic sensitivity analysis of input parameters. We find that monthly and weekly screening can reduce cumulative incidence by 30% and 81% in students, respectively, while testing with a 2-, 4- and 7-day delay results in an 92%, 85% and 73% reduction in cumulative incidence in students over the semester, respectively. Smaller reductions are observed among staff and faculty. A testing strategy requires far fewer diagnostic assays to be implemented than a screening assay. Our intervention model is conservative in that we assume a fairly high reproductive number. We find that community-introduction of SARS-CoV-2 infection onto campus may be controlled with effective testing, isolation, contract tracing and quarantine, but that cases, hospitalization, and (in some scenarios) deaths may still occur. In addition to estimating health impacts, this model can help to predict the resource requirements in terms of diagnostic capacity and isolation/quarantine facilities associated with different strategies.