bluuebunny/crossref_metadata_2025 huggingface dataset:
Working Memory and Impulsivity and Artificial Neural Networks
Authors: Tiitto Markus Ville , Lodder Robert A.
Published: October 2020

Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder characterized by inattention, hyperactivity, and impulsivity. The treatment of ADHD could potentially be improved with the development of combination therapies targeting multiple systems. Both the number of children diagnosed with ADHD and the use of stimulant medications for its treatment have been rising in recent years, and concern about side-effects and future problems that medication may cause have been increasing. An alternative treatment strategy for ADHD attracting wide interest is the targeting of neuropsychological functioning, such as executive function impairments. Computerized training programs (including video games) have drawn interest as a tool to train improvements in executive function deficits in children with ADHD. Our lab is currently conducting a pilot study to assess the effects of the online game Minecraft as a therapeutic video game (TVG) to train executive function deficits in children with ADHD. The effect of the TVG intervention in combination with stimulants is being investigated to develop a drug-device combination therapy that can address both the dopaminergic dysfunction and executive function deficits present in ADHD. Although the results of this study will be used to guide the clinical development process, additional guidance for the optimization of the executive function training activities will be provided by a computational model of executive functions built with artificial neural networks (ANNs). This model uses ANNs to complete virtual tasks resembling the executive function training activities that the study subjects practice in the Minecraft world, and the schedule of virtual tasks that result in maximum improvements in ANN performance on these tasks will be investigated as a method to inform the selection of training regimens in future clinical studies.
Hidden genetic variation in plasticity provides the potential for rapid adaptation to novel environments
Authors: Walter Greg M. , Clark James , Terranova Delia , Cozzolino Salvatore , Cristaudo Antonia , Hiscock Simon J. , Bridle Jon
Published: October 2020

Rapid environmental change is forcing populations into novel environments where plasticity will no longer maintain fitness. When populations are exposed to novel environments, evolutionary theory predicts that genetic variation in fitness will increase and should be associated with genetic differences in plasticity. If true, then genetic variation in plasticity can increase adaptive potential in novel environments, and population persistence via rapid adaptation is more likely. To test whether genetic variation in fitness increases in novel environments and is associated with plasticity, we transplanted 8,149 clones of 314 genotypes of a Sicilian daisy (Senecio chrysanthemifolius) within and outside its native range, and quantified genetic variation in fitness, and plasticity in leaf traits and gene expression. Although mean fitness declined by 87% in the novel environment, genetic variance in fitness increased threefold and was correlated with plasticity in leaf traits. High fitness genotypes showed greater plasticity in gene expression, but lower plasticity in most leaf traits. Interestingly, genotypes with greater fitness in the novel environment had the lowest fitness at the native site. These results suggest that standing genetic variation in plasticity could help populations to persist and adapt to novel environments, despite remaining hidden in native environments.
Evidence of shared genetic influences underlying schizophrenia and alcohol use disorder, but not alcohol consumption
Authors: Johnson Emma C. , Kapoor Manav , Hatoum Alexander S. , Zhou Hang , Polimanti Renato , Wendt Frank R. , Walters Raymond K. , Lai Dongbing , Kember Rachel L. , Hartz Sarah , Meyers Jacquelyn L. , Peterson Roseann E. , Ripke Stephan , Bigdeli Tim B. , Fanous Ayman H. , Pato Carlos N. , Pato Michele T. , Goate Alison M. , Kranzler Henry R. , O’Donovan Michael C. , Walters James T.R. , Gelernter Joel , Edenberg Howard J. , Agrawal Arpana
Published: October 2020

Background

Alcohol use disorder (AUD) and schizophrenia (SCZ) frequently co-occur, and recent genome-wide association studies (GWAS) have identified significant genetic correlations between them. In parallel, mounting evidence from GWAS suggests that alcoholconsumptionis only weakly genetically correlated with SCZ, but this has not yet been systematically investigated.

Methods

We used the largest published GWAS for AUD (total cases = 77,822) and SCZ (total cases = 46,827) to systematically identify genetic variants that influence both disorders (in either the same or opposite direction of effect) as well as disorder-specific loci, and contrast our findings with GWAS data for drinks per week (DPW; N = 537,349) as a measure of alcohol consumption.

Results

We identified 55 independent genome-wide significant SNPs with the same direction of effect on AUD and SCZ, 9 with robust opposite effects, and 99 with disorder-specific effects. We also found evidence for 12 genes whose pleiotropic associations with AUD and SCZ are consistent with mediation via gene expression in the prefrontal cortex. The genetic covariance between AUD and SCZ was concentrated in genomic regions functional in brain tissues (p = 0.001). The genetic correlation between DPW and SCZ (rg= 0.102, SE = 0.022) was significantly lower than that for AUD and SCZ (rg= 0.392, SE = 0.029; p-value of the difference = 9.3e-18), and the genetic covariance between DPW and SCZ was not enriched for any meaningful tissue-specific categories.

Conclusions

Our findings provide a detailed view of genetic loci that influence risk of both AUD and SCZ, suggest that biological commonalities underlying genetic variants with an effect on both disorders are manifested in brain tissues, and provide further evidence that SCZ shares meaningful genetic overlap with AUD and not merely alcohol consumption.
Predictive modeling of virus inactivation by UV
Authors: Rockey Nicole C. , Henderson James B. , Chin Kaitlyn , Raskin Lutgarde , Wigginton Krista R.
Published: October 2020

Disinfection strategies are commonly applied to inactivate pathogenic viruses in water, food, air, and on surfaces to prevent the spread of infectious diseases. Determining how quickly viruses are inactivated to mitigate health risks is not always feasible due to biosafety restrictions or difficulties with virus culturability. Therefore, methods that would rapidly predict kinetics of virus inactivation by UV254would be valuable, particularly for emerging and difficult-to-culture viruses. We conducted a rapid systematic literature review to collect high-quality inactivation rate constants for a wide range of viruses. Using these data and basic virus information (e.g., genome sequence attributes), we developed and evaluated four different model classes, including linear and non-linear approaches, to find the top performing prediction model. For both the (+) ssRNA and dsDNA virus types, multiple linear regressions were the top performing model classes. In both cases, the cross-validated root mean squared relative prediction errors were similar to those associated with experimental rate constants. We tested the models by predicting and measuring inactivation rate constants for two viruses that were not identified in our systematic review, including a (+) ssRNA mouse coronavirus and a dsDNA marine bacteriophage; the predicted rate constants were within 7% and 71% of the experimental rate constants, respectively. Finally, we applied our models to predict the UV254rate constants of several viruses for which high-quality UV254inactivation data are not available. Our models will be valuable for predicting inactivation kinetics of emerging or difficult-to-culture viruses.
Streptococcus pneumoniae,S. mitis, andS. oralisproduce a phosphatidylglycerol-dependent,ltaS-independent glycerophosphate-linked glycolipid
Authors: Wei Yahan , Joyce Luke R. , Wall Ashley M. , Guan Ziqiang , Palmer Kelli L.
Published: October 2020

Lipoteichoic acid (LTA) is a cell surface polymer of Gram-positive bacteria. LTA participates in host-microbe interactions including modulation of host immune reactions. It was previously reported that the major human pathogenStreptococcus pneumoniaeand the closely related oral commensalsS. mitisandS. oralisproduce Type IV LTAs. Herein, using liquid chromatography/mass spectrometry (LC/MS)-based lipidomic analysis, we found that in addition to Type IV LTA biosynthetic precursors,S. mitis,S. oralis, andS. pneumoniaealso produce glycerophosphate (Gro-P)-linked dihexosyl-diacylglycerol (DAG), which is a biosynthetic precursor of Type I LTA. Mutants incdsAandpgsAproduce dihexosyl-DAG but lack (Gro-P)-dihexosyl-DAG, indicating that the Gro-P moiety is derived from phosphatidylglycerol (PG), whose biosynthesis requires these genes.S. mitis, but neitherS. pneumoniaenorS. oralis, encodes an ortholog of the PG-dependent Type I LTA synthase,ltaS. By heterologous expression analyses, we confirmed thatS. mitis ltaSconfers poly-(Gro-P) synthesis in bothEscherichia coliandStaphylococcus aureus, and thatS. mitis ltaScan rescue the severe growth defect of aS. aureus ltaSmutant. However, despite these observations, we do not detect a poly-(Gro-P) polymer inS. mitisusing an anti-Type I LTA antibody. Moreover, (Gro-P)-linked dihexosyl-DAG is still synthesized by aS. mitis ltaSmutant, demonstrating thatS. mitisLtaS does not catalyze the transfer of Gro-P from PG to dihexosyl-DAG. Finally, aS. mitis ltaSmutant has increased sensitivity to human serum, demonstrating thatltaSconfers a beneficial but currently undefined function inS. mitis. Overall, our results demonstrate thatS. mitis,S. pneumoniae, andS. oralisproduce a (Gro-P)-linked glycolipid via a PG-dependent,ltaS-independent mechanism.

Importance

LTA is an important cell wall component synthesized by Gram-positive bacteria. Disruption of LTA production can confer severe physiological defects and attenuation of virulence. We report here the detection of a biosynthetic precursor of Type I LTA, in addition to the previously characterized Type IV LTA, in the total lipid extracts ofS. pneumoniae,S. oralis, andS. mitis. Our results indicate that a novel mechanism is responsible for producing the Type I LTA intermediate. Our results are significant because they identify a novel feature ofS. pneumoniae,S. oralis, andS. mitisglycolipid biology.
Inter-species variation in number of bristles on forewings of tiny insects does not impact clap-and-fling aerodynamics
Authors: Kasoju Vishwa T. , Ford Mitchell P. , Ngo Truc T. , Santhanakrishnan Arvind
Published: October 2020

Flight-capable miniature insects of body length (BL) < 2 mm typically possess wings with long bristles on the fringes. Though their flight is challenged by needing to overcome significant viscous resistance at chord-based Reynolds number (Rec) on the order of 10, these insects use clap-and-fling mechanism coupled with bristled wings for lift augmentation and drag reduction. However, inter-species variation in the number of bristles (n) and inter-bristle gap (G) to bristle diameter (D) ratio (G/D) and their effects on clap-and-fling aerodynamics remain unknown. Forewing image analyses of 16 species of thrips and 21 species of fairyflies showed thatnand maximum wing span were both positively correlated with BL. We conducted aerodynamic force measurements and flow visualization on simplified physical models of bristled wing pairs that were prescribed to execute clap-and-fling kinematics atRec=10 using a dynamically scaled robotic platform. 23 bristled wing pairs were tested to examine the isolated effects of changing dimensional (G, D, span) and non-dimensional (n, G/D) geometric variables on dimensionless lift and drag. Within biologically observed ranges ofnandG/D, we found that: (a) increasingGprovided more drag reduction than decreasingD; (b) changingnhad minimal impact on lift generation; and (c) varyingG/Dproduced minimal changes in aerodynamic forces. Taken together with the broad variation inn(32-161) across the species considered here, the lack of impact of changingnon lift generation suggests that tiny insects may experience reduced biological pressure to functionally optimizenfor a given wing span.

SUMMARY STATEMENT

Integrating morphological analysis of bristled wings seen in miniature insects with physical model experiments, we find that aerodynamic forces are unaffected across the broad biological variation in number of bristles.
Spatio-temporal Memory for Navigation in a Mushroom Body Model
Authors: Zhu Le , Mangan Michael , Webb Barbara
Published: October 2020

Insects, despite relatively small brains, can perform complex navigation tasks such as memorising a visual route. The exact format of visual memory encoded by neural systems during route learning and following is still unclear. Here we propose that interconnections between Kenyon cells in the Mushroom Body (MB) could encode spatio-temporal memory of visual motion experienced when moving along a route. In our implementation, visual motion is sensed using an event-based camera mounted on a robot, and learned by a biologically constrained spiking neural network model, based on simplified MB architecture and using modified leaky integrate-and-fire neurons. In contrast to previous image-matching models where all memories are stored in parallel, the continuous visual flow is inherently sequential. Our results show that the model can distinguish learned from unlearned route segments, with some tolerance to internal and external noise, including small displacements. The neural response can also explain observed behaviour taken to support sequential memory in ant experiments. However, obtaining comparable robustness to insect navigation might require the addition of biomimetic pre-processing of the input stream, and determination of the appropriate motor strategy to exploit the memory output.
Lipidomic profiling of clinical prostate cancer reveals targetable alterations in membrane lipid composition
Authors: Butler Lisa M. , Mah Chui Yan , Machiels Jelle , Vincent Andrew D. , Irani Swati , Mutuku Shadrack , Spotbeen Xander , Bagadi Muralidhararao , Waltregny David , Moldovan Max , Dehairs Jonas , Vanderhoydonc Frank , Bloch Katarzyna , Das Rajdeep , Stahl Jurgen , Kench James , Gevaert Thomas , Derua Rita , Waelkens Etienne , Nassar Zeyad D. , Selth Luke A. , Trim Paul J. , Snel Marten F. , Lynn David J. , Tilley Wayne D. , Horvath Lisa G. , Centenera Margaret M. , Swinnen Johannes V.
Published: October 2020

Dysregulated lipid metabolism is a prominent feature of prostate cancer that is driven by androgen receptor (AR) signaling. Herein, we used quantitative mass spectrometry to define the “lipidome” in prostate tumors with matched benign tissues (n=21), independent tissues (n=47), and primary prostate explants cultured with a clinical AR antagonist, enzalutamide (n=43). Significant differences in lipid composition were detected and spatially visualized in tumors compared to matched benign samples. Notably, tumors featured higher proportions of monounsaturated lipids overall and elongated fatty acid chains in phosphatidylinositol and phosphatidylserine lipids. Significant associations between lipid profile and malignancy were validated in unmatched samples, and PL composition was characteristically altered in patient tissues that responded to AR inhibition. Importantly, targeting of altered tumor-related lipid features, via inhibition of acetyl CoA carboxylase 1, significantly reduced cellular proliferation in tissue explants (n=13). This first characterization of the prostate cancer lipidome in clinical tissues revealed enhanced fatty acid synthesis, elongation and desaturation as tumor-defining features, with potential for therapeutic targeting.
Experimental and mathematical modelling of magnetically labelled mesenchymal stromal cell delivery
Authors: Yeo E.F. , Markides H. , Schade A.T. , Studd A.J. , Oliver J.M. , Waters S.L. , El Haj A.J.
Published: October 2020

A key challenge for stem cell therapies is the delivery of therapeutic cells to the repair site. Magnetic targeting has been proposed as a platform for defining clinical sites of delivery more effectively. In this paper we use a combinedin vitroexperimental and mathematical modelling approach to explore the magnetic targeting of mesenchymal stromal cells (MSCs) labelled with magnetic nanoparticles using an external magnet. This study aims to (i) demonstrate the potential of magnetic tagging for MSC delivery, (ii) examine the effect of red blood cells (RBCs) on MSC capture efficacy and (iii) highlight how mathematical models can provide both insight into mechanics of therapy and predictions about cell targetingin vivo.

In vitroMSCs are cultured with magnetic nanoparticles and circulated with RBCs over an external magnet. Cell capture efficacy is measured for varying magnetic field strengths and RBC percentages. We use a 2D continuum mathematical model to represent the flow of magnetically tagged MSCs with RBCs. Numerical simulations demonstrate qualitative agreement with experimental results showing better capture with stronger magnetic fields and lower levels of RBCs. We additionally exploit the mathematical model to make hypotheses about the role of extravasation and identify futurein vitroexperiments to quantify this effect.
Abdominal pain assessment in rabbits: using the CANCRS to recognize pain and testing its internal validity over time
Authors: Banchi Penelope , Quaranta Giuseppe , Ricci Alessandro , von Degerfeld Mitzy Mauthe
Published: October 2020

A composite scale for pain assessment in rabbits has been previously designed and tested (CANCRS). The present study describes the refinement of the scale and the evaluation of its ability to detect pain variations over time. Furthermore, a comparison between the CANCRS and the Visual Analogue Scale (VAS) has been performed, to underline the differences between an objective (CANCRS) and a subjective (VAS) assessment of abdominal pain. In the first part of the study, 86 rabbits (n=47 heathy patients and n=39 patients with gastrointestinal stasis syndrome) underwent pain assessments with the VAS and the CANCRS. Thirty-two patients with gastrointestinal stasis syndrome participated to the second part of the study. These patients underwent four pain assessments with the CANCRS. The first assessment took place before meloxicam administration and the others after 30, 60 and 90 minutes. The CANCRS showed differences between healthy and diseased rabbits (P= 0.0001), median scores were 5 (IQR 4 - 6) and 9 (IQR 7 - 11) respectively. The VAS showed differences between healthy and diseased rabbits (P= 0.02), the median scores were 4 (IQR 2 - 5.35) and 5.3 (IQR 2.65 - 6.45) respectively. The cut-off scores for the CANCRS and for the VAS for differentiation between healthy and diseased patients were 7 (Sp 89%, Se 79%) and 4.4 (Sp 59%, Se 69%) respectively. Sensitivity and specificity for each parameter of the CANCRS were calculated, in order to obtain weighting factors. Accordingly, the evaluation of respiratory pattern and vocalizations should be excluded from the CANCRS, since their performances in pain evaluation are poor. Internal validity of the CANCRS was tested assessing pain before and after the analgesic treatment and the results showed significancy at each time point. The CANCRS showed better performances than the VAS and its responsiveness to pain variations has been verified.
Assessment of fasting blood glucose, serum electrolyte, albumin, creatinine, urea and lipid profile among hypertensive patients and non-hypertensive participants at wolaita sodo university teaching and referral hospital, SNNPR, Ethiopia
Authors: Haile Berhanu , Wolde Mistire , Gebregziabiher Tatek
Published: October 2020

Background

Hypertension is a silent killer that requires long term management to avoid complications. It is one of major public health problem in developing counties like Ethiopia. Hypertension increases the risk of morbidity and mortality and has negative consequences on the cognitive and physical fitness of productivity in adults.

Objective

To assess fasting blood glucose, serum electrolyte, albumin, creatinine, urea, and lipid profile among hypertensive patients and non-hypertensive participants at wolaita sodo teaching and referral hospital.

Methods

A comparative cross-sectional study was conducted from December 2019 to February 2020. On the study a total of 156 study participants (78 cases and 78 controls) were involved. Each study participant, after signing informed consent, interviewed about the socio-demographic and anthropometric characteristic features. Then 5ml of the blood sample was collected from each 78 patients with hypertension and each 78 samples from apparently healthy subjects from WSUTRH during the period. Fasting blood glucose, serum electrolyte, albumin, creatinine, urea, and lipid profile level were measured in each group. The Data were analyzed by using Epi data version 3.1 and SPSS version 21.0 software (IBM Corporation, USA) and results were summarized using means and percentages and presented by using figures and tables. P-value < 0.05 was considered to be significant at 95% confidence level. Any abnormal laboratory results of study subjects dispatched and communicated with physicians for better management.

Results

The mean age of hypertensives and control study groups were 50 ± 10.0 and 51 ±11.3 years respectively. The body mass index of hypertensives and control study groups were 53.4% and 34.2% overweighed respectively. The mean ± SD of fasting blood glucose, total cholesterol, LDL-C, TG, RFT were significantly increases while serum sodium, calcium, albumin, and HDL-Cholesterol significantly decreased in hypertensives when compared with non-hypertensives and serum potassium was no statistical significance among case and control groups.

Conclusion

In present study, we observed that the hypertensive group was at risk for developing biochemical alteration in creatinine, urea, fasting blood glucose, lipid profile, electrolytes, and albumin test parameters with an increased period of time.

Recommendation

Regular measurements of biochemical parameters strongly needed for hypertensive patients.
SVIM-asm: Structural variant detection from haploid and diploid genome assemblies
Authors: Heller David , Vingron Martin
Published: October 2020

Motivation

With the availability of new sequencing technologies, the generation of haplotype-resolved genome assemblies up to chromosome scale has become feasible. These assemblies capture the complete genetic information of both parental haplotypes, increase structural variant (SV) calling sensitivity and enable direct genotyping and phasing of SVs. Yet, existing SV callers are designed for haploid genome assemblies only, do not support genotyping or detect only a limited set of SV classes.

Results

We introduce our method SVIM-asm for the detection and genotyping of six common classes of SVs from haploid and diploid genome assemblies. Compared against the only other existing SV caller for diploid assemblies, DipCall, SVIM-asm detects more SV classes and reached higher F1 scores for the detection of insertions and deletions on two recently published assemblies of the HG002 individual.

Availability and Implementation

SVIM-asm has been implemented in Python and can be easily installed via bioconda. Its source code is available at github.com/eldariont/svim-asm.

Contact

vingron@molgen.mpg.de

Supplementary information

Supplementary data are available online.
Parabrachial complex processes dura inputs through a direct trigeminal ganglion-to-parabrachial connection
Authors: Uddin Olivia , Anderson Michael , Smith Jesse , Masri Radi , Keller Asaf
Published: October 2020

Migraines cause significant disability and contribute heavily to healthcare costs. Irritation of the meninges’ outermost layer (the dura mater), and trigeminal ganglion activation contribute to migraine initiation. Maladaptive changes in central pain-processing regions are also important in maintaining pain. The parabrachial complex (PB) is a central region that mediates chronic pain. PB receives diverse sensory information, including a direct input from the trigeminal ganglion. We hypothesized that PB processes inputs from the dura. Usingin vivoelectrophysiology recordings from single units in anesthetized rats we identified 58 neurons in lateral PB that respond reliably and with short latency to electrical dura stimulation. After injecting tracer into PB, anatomical examination reveals retrogradely labeled cell bodies in the trigeminal ganglion. Neuroanatomical tract-tracing revealed a population of neurons in the trigeminal ganglion that innervate the dura and project directly to PB. These findings indicate that PB is strategically placed to process dura inputs, and suggest that it is directly involved in the pathogenesis of migraine headaches.
Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure
Authors: Zoni Valeria , Shinoda Wataru , Vanni Stefano
Published: October 2020

Lipid droplets (LD) are intracellular organelles responsible for lipid storage, and they emerge from the endoplasmic reticulum (ER) upon the accumulation of neutral lipids, mostly triglycerides (TG), between the two leaflets of the ER membrane. LD biogenesis takes place at ER sites that are marked by the protein seipin, which subsequently recruits additional proteins to catalyse LD formation. Deletion of seipin, however, does not abolish LD biogenesis, and its precise role in controlling LD assembly remains unclear. Here we use molecular dynamics simulations to investigate the molecular mechanism through which seipin promotes LD formation. We find that seipin clusters TG molecules inside its unconventional ring-like oligomeric structure, and that both its luminal and transmembrane regions contribute to this process. Diacylglycerol, the precursor of TG, also clusters inside the seipin oligomer, in turn promoting TG accumulation. Our results suggest that seipin remodels the membrane of specific ER sites to prime them for LD biogenesis.

Significance statement

Metabolic disorders related to aberrant fat accumulation, including lipodystrophy and obesity, are a particularly serious health concern. In cells, fat accumulates in intracellular organelles, named lipid droplets (LDs). LDs form in the endoplasmic reticulum, where triglycerides, the most abundant form of fat, is produced. The Bernardinelli-Seip congenital lipodystrophy type 2 protein, seipin, has been identified as a key regulator of LD formation, but its mechanism of action remains debated and its molecular details mostly obscure. Here, we use molecular dynamics simulations to investigate the mechanism of seipin. We find that seipin can cluster and trap both triglycerides and its precursor, diacylglycerol. Our results suggest that seipin organizes the lipid composition of specific ER sites to prime them for LD biogenesis.
Reef environments shape microbial partners in a highly connected coral population
Authors: Kriefall NG , Kanke MR , Aglyamova GV , Davies SW
Published: October 2020

Corals from more thermally variable environments often fare better under thermal stress compared to those from less thermally variable environments, an important finding given that ocean warming threatens corals worldwide. Evidence is mounting that thermal tolerance can be attributed to the coral itself, as well as microbial communities present within the holobiont (coral host and its associated microorganisms). However, few studies have characterized how thermally variable environments structure multiple holobiont membersin situ. Here, using 2b-RAD sequencing of the coral and metabarcoding of algal (ITS2) and bacterial (16S) communities, we show evidence that reef zones (locales differing in proximity to shore, physical characteristics, and environmental variability) structure algal and bacterial communities at different scales within a highly connected coral population (Acropora hyacinthus) in French Polynesia. Fore reef (more stable) algal communities were on average more diverse than the back reef (more variable), suggesting that variability constrains algal diversity. In contrast, microbial communities were structured on smaller scales with site-specific indicator species and enriched functions across reef zones. Our results illuminate how associations with unique microbial communities can depend on spatial scale across highly dispersive coral populations, which may have fitness consequences in thermally divergent regions and rapidly changing oceans.
Fast volumetric mapping of human brain slices
Authors: Pesce Luca , Laurino Annunziatina , Gavryusev Vladislav , Mazzamuto Giacomo , Sancataldo Giuseppe , Scardigli Marina , Roffilli Matteo , Silvestri Ludovico , Costantini Irene , Pavone Francesco Saverio
Published: October 2020

We still lack a detailed map of the anatomical disposition of neurons in the human brain. A complete map would be an important step for deeply understanding the brain function, providing anatomical information useful to decipher the neuronal pattern in healthy and diseased conditions. Here, we present several important advances towards this goal, obtained by combining a new clearing method, advanced Light Sheet Microscopy and automated machinelearning based image analysis. We perform volumetric imaging of large sequentially stained human brain slices, labelled for two different neuronal markers NeuN and GAD67, discriminating the inhibitory population and reconstructing the brain connectivity.
A robust sequencing assay of a thousand amplicons for the high-throughput population monitoring of Alpine ibex immunogenetics
Authors: Kessler Camille , Brambilla Alice , Waldvogel Dominique , Camenisch Glauco , Biebach Iris , Leigh Deborah M , Grossen Christine , Croll Daniel
Published: October 2020

Genetic variation is a major factor determining susceptibility to diseases. Polymorphism at the major histocompatibility complex (MHC) and other immune function loci can underlie health and reproductive success of individuals. Endangered species of low population size could be severely compromised to evolve disease resistance due to reduced adaptive variation. A major impediment to screen adaptive genetic variation in wild species is the difficulty to comprehensively genotype immune-related loci based on low input material. Here, we design and validate a targeted amplicon sequencing assay to parallelize the analysis of a thousand loci of the MHC, other immunity-related genes, and genome-wide markers for the assessment of population structure. We apply the approach to Alpine ibex, one of the most successful examples of restoration of a large mammal in Europe. We used 51 whole genome sequenced individuals to select representative target SNPs. We integrated SNP call data from four related species for amplification robustness and genotyped 158 Alpine ibex individuals for validation. We show that the genome-wide markers perform equally well at resolving population structure as RAD-seq or low-coverage genome sequencing datasets with orders of magnitude more markers. The targeted amplicon sequencing assay is robust to >100-fold variation in input DNA quantity and generates useful genotype information from fecal samples. The amplicon marker set also identified recent species hybridization events with domestic goats. The immune loci show unexpectedly high degrees of differentiation within the species. Our assay strategy can realistically be implemented into population genetic surveys of a large range of species.
Developmental and MAPK-responsive transcription factors drive distinct malignant subtypes and genetic dependencies in pancreatic cancer
Authors: Laise Pasquale , Turunen Mikko , Garcia Alvaro Curiel , Tomassoni Lorenzo , Maurer H. Carlo , Elyada Ela , Schmierer Bernhard , Worley Jeremy , Kesner Jordan , Tan Xiangtian , Fernandez Ester Calvo , Wong Kelly , Wasko Urszula N , Tagore Somnath , Wang Alexander L. E. , Ge Sabrina , Iuga Alina C. , Griffin Aaron , Wong Winston , Manji Gulam A. , Alvarez Mariano J. , Notta Faiyaz , Tuveson David A. , Olive Kenneth P. , Califano Andrea
Published: October 2020

Despite extensive efforts, reproducible assessment of pancreatic ductal adenocarcinoma (PDA) heterogeneity and plasticity at the single cell level remains elusive. Systematic, network-based analysis of regulatory protein activity in single cells identified three PDA Developmental Lineages (PDLs), coexisting in virtually all tumors, whose transcriptional states are mechanistically driven by aberrant activation of Master Regulator (MR) proteins associated with gastrointestinal lineages (GLS state), morphogen and EMT pathways (MOS state), and acinar-to-ductal metaplasia (ALS state), respectively. Each PDL is further subdivided into sub-states characterized by low vs. high MAPK pathway activity. This taxonomy was remarkably conserved across multiple cohorts, cell lines, and PDX models, and harmonized with bulk profile analyses. Cross-state plasticity and MR essentiality was confirmed by barcode-based lineage tracing and CRISPR/Cas9 assays, respectively, while MR ectopic expression induced PDL transdifferentiation. Together these data provide a mechanistic foundation for PDA heterogeneity and a roadmap for targeting PDA cellular subtypes.
Exploring the role of life history traits and introduction effort in understanding invasion success in mammals: A case study of Barbary ground squirrels
Authors: van der Marel Annemarie , Waterman Jane M. , López-Darias Marta
Published: October 2020

Invasive species –species that have successfully overcome the barriers of transport, introduction, establishment, and spread– are a risk to biodiversity and ecosystem function. Introduction effort is one of the main factors underlying invasion success, but life history traits are also important as they influence population growth. In this contribution, we first investigated life history traits of the Barbary ground squirrel, Atlantoxerus getulus, a species with a very low introduction effort. We then studied if their invasion success was due to a very fast life history profile by comparing their life history traits to those of other successful invasive mammals. Next, we examined whether the number of founders and/or a fast life history influences the invasion success of squirrels. Barbary ground squirrels were on the fast end of the “fast-slow continuum”, but their life history was not the only contributing factor to their invasion success, as the life history profile is comparable to other invasive species that do not have such a low introduction effort. We also found that neither life history traits nor the number of founders explained the invasion success of introduced squirrels in general. These results contradict the concept that introduction effort is the main factor explaining invasion success, especially in squirrels. Instead, we argue that invasion success can be influenced by multiple aspects of the new habitat or the biology of the introduced species.
M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity
Authors: Bag Indira , Chen Shue , Rosin Leah F. , Chen Yang , Liu Chen-Yu , Yu Guo-Yun , Lei Elissa P.
Published: October 2020

Genome organization is driven by forces affecting transcriptional state, but the relationship between transcription and genome architecture remains unclear. Here, we identified theDrosophilatranscription factor Motif 1 Binding Protein (M1BP) in physical association with thegypsychromatin insulator core complex, including the universal insulator protein CP190. M1BP is required for enhancer-blocking and barrier activities of thegypsyinsulator as well as its proper nuclear localization. Genome-wide, M1BP specifically colocalizes with CP190 at Motif 1-containing promoters, which are enriched at topologically associating domain (TAD) borders. M1BP facilitates CP190 chromatin binding at many shared sites and vice versa. Both factors promote Motif 1-dependent gene expression and transcription near TAD borders genome-wide. Finally, loss of M1BP reduces chromatin accessibility and increases both inter- and intra-TAD local genome compaction. Our results reveal physical and functional interaction between CP190 and M1BP to activate transcription at TAD borders and mediate chromatin insulator-dependent genome organization.
Transcriptome and Chromatin Landscape of iNKT cells are Shaped by Subset Differentiation and Antigen Exposure
Authors: Murray Mallory Paynich , Engel Isaac , Seumois Gregory , Herrera de la Mata Sara , Rosales Sandy Lucette , Sethi Ashu , Logandha Ramamoorthy Premlal Ashmitaa , Seo Goo-Young , Greenbaum Jason , Vijayanand Pandurangan , Scott-Browne James P. , Kronenberg Mitchell
Published: October 2020

Invariant natural killer T cells (iNKT cells) differentiate into thymic and peripheral NKT1, NKT2 and NKT17 subsets. We determined if the gene programs associated with these thymic subsets were maintained in peripheral sites, the influence of tissue location, and if there were large-scale changes after antigen exposure. RNA-seq and ATAC-seq analyses showed that iNKT cells in any subset were similar, regardless of tissue location. Lung iNKT cell subsets possessed the most distinct location-specific features, shared with other innate lymphocytes in the lung, possibly consistent with increased activation. After antigenic stimulation, iNKT cells underwent chromatin and transcription changes leading to two populations: one similar to follicular helper T cells and the other like NK or effector cells. Phenotypic analysis indicated these changes were observed long-term, suggesting that iNKT cells gene programs are not fixed, but they are capable of chromatin remodeling after antigen to give rise to several new subsets.
Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase inMycobacterium tuberculosis
Authors: Wang Heng , Xu Min , Engelhart Curtis A , Zhang Xi , Yan Baohua , Pan Miaomiao , Xu Yuanyuan , Fan Shilong , Liu Renhe , Xu Lan , Hua Lan , Schnappinger Dirk , Chen Shawn
Published: October 2020

Mycobacteria tuberculosis(Mtb) remains the deadliest pathogenic bacteria worldwide. The search for new antibiotics to treat drug-sensitive as well as drug-resistant tuberculosis has become a priority. The essential enzyme phenylalanyl-tRNA synthetase (PheRS) is an antibacterial drug target because of the large differences between bacterial and human PheRS counterparts. In a high-throughput screening of 2148 bioactive compounds, PF-3845, which is a known inhibitor of human fatty acid amide hydrolase (FAAH), was identified inhibiting Mtb PheRS atKi∼0.73 ± 0.055 µM. The inhibition mechanism was studied with enzyme kinetics, protein structural modelling and crystallography, in comparison to a PheRS inhibitor of the noted phenyl-thiazolylurea-sulfonamide class. The 2.3-Å crystal structure of Mtb PheRS in complex with PF-3845 revealed its novel binding mode, in which a trifluoromethyl-pyridinylphenyl group occupies the Phe pocket while a piperidine-piperazine urea group binds into the ATP pocket through an interaction network enforced by a sulfate ion. It represents the first non-nucleoside bi-substrate competitive inhibitor of bacterial PheRS. PF-3845 inhibits thein vitrogrowth of Mtb H37Rv at ∼24 µM, and the potency of PF-3845 increased against Mtb pheS-FDAS, suggesting on target activity in mycobacterial whole cells. PF-3845 does not inhibit human cytoplasmic or mitochondrial PheRSs in biochemical assay, which can be explained from the crystal structures. Further elaboration of the piperidine-piperazine urea moiety by medicinal chemistry effort will produce potential antibacterial lead with improved selectivity on the cellular level.
Voltage-gated Ca2+influx in murine white fat adipocytes: stimulation by growth hormone but not membrane depolarization
Authors: Akaniro-Ejim Nneoma E , Smith Paul A.
Published: October 2020

In white fat adipocytes voltage-gated Ca2+channels are constitutively active. Since the adipocyte membrane potential (Vm) is controlled by Cl−we investigated if changes in [Cl−]ocan affect the activity of voltage-gated Ca2+channels and intracellular calcium, [Ca2+]i.

Adipocytes were isolated from epididymal fat of CD-1 mice. [Ca2+]iwas imaged with epifluorescent microscopy at 28°C. Constitutive voltage-gated channel activity was confirmed by the ability of verapamil to decrease [Ca2+]i.

Substitution of [Cl−]oto 113, 53 and 18 mM with the membrane impermeant gluconate anion decreased [Ca2+]ifrom 114±8.7 to 106±7.5, 101±7.1 and 97±6 nM respectively. Substitution of [Cl−]owith glutamate mimicked the ability of gluconate to decrease [Ca2+]i.

To explore if anions affected [Ca2+]ivia chelation of external Ca2+, [Ca2+]owas analyzed by potentiometry. Gluconate, glutamate, aspartate and methylsulphonate had Ca2+association constants of 17±1.8, 12±1, 8.2±4.1 and 3.3±0.5 L−1M respectively.

Substitution of 134 mM [Cl−]owith gluconate decreased [Ca2+]ofrom 2.6 mM to 200 μM; the effect of this anion on [Ca2+]iwas mimicked by a decrease of [Ca2+]oto 200 μM in standard [Cl−]osolution. Conversely, titration of [Ca2+]ofrom 200 μM back to 2.6 mM in 134 mM gluconate solutions abolished the effect of this anion on [Ca2+]i. Substitution of [Cl−]owith methylsulphonate to affect Vm did not affect [Ca2+]i. Whereas, growth hormone at 10-20 nM increased [Ca2+]i, an effect blocked by verapamil or absence of [Ca2+]o. In conclusion, growth hormone, but not changes in Vm, can increase voltage-gated Ca2+channel activity and [Ca2+]iin white fat adipocytes.

Key points

[Ca2+]iplays a key role in the metabolic and endocrine functions of white fat adipocytes.

In adipocytes basal [Ca2+]iis maintained by voltage-gated Ca2+channels constitutively active at their resting membrane potential, Vm, which is predominantly controlled by Cl−permeability.

Substitution of [Cl−]oto depolarize Vm with gluconate or glutamate, did not increase but decreased [Ca2+]i. an action due to chelation of extracellular Ca2+. This effect was not seen with methylsulphonate, which did no chelate Ca2+but did not affect [Ca2+]i.

Growth hormone elevated, [Ca2+]ian effect blocked by inhibitors of voltage-gated Ca2+channels

In adipocytes, voltage-gated Ca2+channel activity appear recalcitrant to changes in Vm, but are however gated by growth hormone.
Salvage NAD+Biosynthetic Pathway Enzymes Moonlight as Molecular Chaperones to Protect Against Proteotoxicity
Authors: Pinkerton Meredith , Ruetenik Andrea , Bazylianska Viktoriia , Nyvltova Eva , Barrientos Antoni
Published: October 2020

Human neurodegenerative proteinopathies are disorders associated with abnormal protein depositions in brain neurons. They include polyglutamine (polyQ) conditions such as Huntington’s disease (HD) and α-synucleinopathies such as Parkinson’s disease (PD). Overexpression of NMNAT/Nma1, an enzyme in the NAD+biosynthetic salvage pathway, acts as an efficient suppressor of proteotoxicities in yeast, fly, and mouse models. Screens in yeast models of HD and PD allowed us to identify three additional enzymes of the same pathway that achieve similar protection against proteotoxic stress: Npt1, Pnc1, and Qns1. Here, we report that their ability to maintain proteostasis is independent of their catalytic activity and does not require cellular protein quality control systems such as the proteasome or autophagy. Furthermore, we show that, under proteotoxic stress, the four proteins are recruited as molecular chaperones with holdase and foldase activities. The NAD+salvage proteins act by preventing misfolding and, together with the Hsp90 chaperone, promoting the refolding of extended polyQ domains or α-synuclein. We conclude that the entire salvage NAD+biosynthetic pathway links NAD+metabolism and proteostasis and emerges as a target for therapeutics to combat age-associated neurodegenerative proteotoxicities. Our observations also illustrate the existence of an evolutionarily conserved strategy of repurposing or moonlighting housekeeping enzymes under stress conditions to maintain proteostasis.
The Endothelin Receptor Antagonist Macitentan Ameliorates Endothelin-Mediated Vasoconstriction and Promotes Neuroprotection of Retinal Ganglion Cells in Rats
Authors: Stankowska Dorota L. , Zhang Wei , He Shaoqing , Krishnamoorthy Vignesh R. , Harris Payton , Hall Trent , Chaphalkar Renuka M. , Kodati Bindu , Chavala Sai H. , Krishnamoorthy Raghu R.
Published: October 2020

Purpose

To determine if dietary administration of the dual ETA/ ETBreceptor antagonist, macitentan, could protect retinal ganglion cells (RGCs) following endothelin-1 (ET-1) mediated vasoconstriction in Brown Norway rats.

Methods

Adult male and female Brown Norway rats were either untreated or treated with macitentan (5 mg/kg body weight) once a day for 3 days followed by intravitreal injection of either 4 μl of 500 μM ET-1 (2 nmole/eye) or vehicle in one eye. Imaging of the retinal vasculature using fluorescein angiography was carried out at various time points, including, 5, 10, 15, 25 and 30 minutes. Following the imaging of the vasculature, rats were either treated with macitentan (5 mg/kg/body weight in dietary gels) or untreated (control gels without medication). Following treatments, rats were euthanized, retinal flat mounts were prepared, immunostained for RGC marker Brn3a, imaged and surviving RGCs were counted in a masked manner.

Results

Vasoconstrictive effects following intravitreal ET-1 injection were greatly reduced in rats administered with macitentan in the diet prior to the ET-1 administration. ET-1 intravitreal injection produced a 31% loss of RGCs which was significantly reduced in macitentan-treated rats. Following ET-1 administration, GFAP immunostaining was increased in the ganglion cell layer as well as in the retrolaminar region, suggestive of astrocytic activation by ET-1 administration. RGC numbers in macitentan treated and ET-1 injected rats were similar to that observed in control retinas.

Conclusions

ET-1-mediated neurodegeneration could occur through both vascular and cellular mechanisms. The endothelin receptor antagonist, macitentan, has neuroprotective effects in retinas of Brown Norway rats that occurs through different mechanisms, including, enhancement of RGC survival and reduction ET-1 mediated vasoconstriction.
Repression of lysosomal transcription factors Tfeb and Tfe3 is essential for the migration and function of microglia
Authors: Iyer Harini , Shen Kimberle , Meireles Ana M. , Talbot William S.
Published: October 2020

As the primary phagocytic cells of the central nervous system, microglia exquisitely regulate their lysosomal activity to facilitate brain development and homeostasis. However, mechanisms that coordinate lysosomal activity with microglia development, migration, and function remain unclear. Here we show that embryonic macrophages require the lysosomal GTPase RagA and the GTPase-activating protein Folliculin to colonize the brain in zebrafish. We demonstrate that embryonic macrophages inrragamutants show increased expression of lysosomal genes but display significant downregulation of immune and migration-related genes. Furthermore, we find that RagA and Folliculin repress the key lysosomal transcription factor Tfeb, and its homologs Tfe3a and Tfe3b, in the macrophage lineage. Using RNA-Sequencing, we establish that Tfeb and Tfe3 are required for activation of lysosomal target genes under conditions of stress but not for basal expression of lysosomal pathways. Collectively, our data define a lysosomal regulatory circuit essential for macrophage development and function in vivo.

Teaser

The degradation machinery of the cell must be carefully controlled for the normal formation and function of key immune cells called microglia.