bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of morphine, oxycodone and the biased MOR agonist SR-17018 for tolerance and efficacy in mouse models of pain
Authors: Pantouli Fani , Grim Travis W. , Schmid Cullen L. , Acevedo-Canabal Agnes , Kennedy Nicole M. , Bannister Thomas D. , Bohn Laura M.
Published: October 2020

The mu opioid receptor-selective agonist, SR-17018, preferentially activates GTPγS binding over βarrestin2 recruitment in cellular assays. In mice, SR-17018 stimulates GTPγS binding in brainstem and produces antinociception with potencies similar to morphine. However, it produces much less respiratory suppression and mice do not develop antinociceptive tolerance in the hot plate assay upon repeated dosing. Herein we evaluate the effects of acute and repeated dosing of SR-17018, oxycodone and morphine in additional models of pain-related behaviors. In the mouse warm water tail immersion assay, an assessment of spinal reflex to thermal nociception, repeated administration of SR-17018 produces tolerance as does morphine and oxycodone. SR-17018 retains efficacy in a formalin-induced inflammatory pain model upon repeated dosing, while oxycodone does not. In a chemotherapeutic-induced neuropathy pain model SR-17018 is more potent and efficacious than morphine or oxycodone, moreover, this efficacy is retained upon repeated dosing of SR-17018. These findings demonstrate that, with the exception of the tail flick test, SR-17018 retains efficacy upon chronic treatment across several pain models.
Mechanistic theory predicts the effects of temperature and humidity on inactivation of SARS-CoV-2 and other enveloped viruses
Authors: Morris Dylan H. , Yinda Kwe Claude , Gamble Amandine , Rossine Fernando W. , Huang Qishen , Bushmaker Trenton , Fischer Robert J. , Matson M. Jeremiah , Doremalen Neeltje van , Vikesland Peter J. , Marr Linsey C. , Munster Vincent J. , Lloyd-Smith James O.
Published: October 2020

Environmental conditions affect virus inactivation rate and transmission potential. Understanding those effects is critical for anticipating and mitigating epidemic spread. Ambient temperature and humidity strongly affect the inactivation rate of enveloped viruses, but a mechanistic, quantitative theory of those effects has been elusive. We measure the stability of the enveloped respiratory virus SARS-CoV-2 on an inert surface at nine temperature and humidity conditions and develop a mechanistic model to explain and predict how temperature and humidity alter virus inactivation. We find SARS-CoV-2 survives longest at low temperatures and extreme relative humidities; median estimated virus half-life is over 24 hours at 10 °C and 40 % RH, but approximately 1.5 hours at 27 °C and 65 % RH. Our mechanistic model uses simple chemistry to explain the increase in virus inactivation rate with increased temperature and the U-shaped dependence of inactivation rate on relative humidity. The model accurately predicts quantitative measurements from existing studies of five different human coronaviruses (including SARS-CoV-2), suggesting that shared mechanisms may determine environmental stability for many enveloped viruses. Our results indicate scenarios of particular transmission risk, point to pandemic mitigation strategies, and open new frontiers in the mechanistic study of virus transmission.
Real-time luminescence assay for cytoplasmic cargo delivery of extracellular vesicles
Authors: Somiya Masaharu , Kuroda Shun’ichi
Published: October 2020

Extracellular vesicles (EVs) have been considered to deliver biological cargos between cells and mediate intercellular communication. However, the mechanisms that underlie the biological process of EV uptake and cytoplasmic cargo release in recipient cells are largely unknown. Quantitative and real-time assays for assessment of the cargo delivery efficiency inside recipient cells have not been feasible. In this study, we developed an EV cargo delivery (EVCD) assay using a split luciferase called the NanoBiT system. Recipient cells expressing LgBiT, a large subunit of luciferase, emit luminescence when the EV cargo proteins fused with a small luminescence tag (HiBiT tag) that can complement LgBiT are delivered to the cytoplasm of recipient cells. Using the EVCD assay, the cargo delivery efficiency of EVs could be quantitatively measured in real time. This assay was highly sensitive in detecting a single event of cargo delivery per cell. We found that modification of EVs with a virus-derived fusogenic protein significantly enhanced the cytoplasmic cargo delivery; however, in the absence of a fusogenic protein, the cargo delivery efficiency of EVs was below the threshold of the assay. The EVCD assay could assess the effect of entry inhibitors on EV cargo delivery. Furthermore, using a luminescence microscope, the cytoplasmic cargo delivery of EVs was directly visualized in living cells. This assay could reveal the biological mechanism of the cargo delivery processes of EVs.
A comparison of Remdesivir versus Au22Glutathione18in COVID-19 golden hamsters: a better therapeutic outcome of gold compound
Authors: He Zhesheng , Ye Fei , Zhang Chunyu , Fan Jiadong , Du Zhongying , Zhao Wencong , Yuan Qing , Niu Wenchao , Gao Fuping , He Bo , Cao Peng , Zhao Lina , Gao Xuejiao , Gao Xingfa , Sun Bo , Dong Yuhui , Zhao Jincun , Qi Jianxun , Jiang Huaidong , Gong Yong , Tan Wenjie , Gao Xueyun
Published: October 2020

We firstly disclose single compound yields better therapeutic outcome than Remdesivir in COVID-19 hamster treatments as it is armed with direct inhibition viral replication and intrinsic suppression inflammatory cytokines expression. Crystal data reveals that Au (I), released from Au22Glutathione18(GA), covalently binds thiolate of Cys145 of SARS-CoV-2 Mpro. GA directly decreases SARS-CoV-2 viral replication (EC50: ~0.24 μM) and intrinsically down-regulates NFκB pathway therefore significantly inhibiting expression of inflammatory cytokines in cells. The lung viral load and inflammatory cytokines in GA-treated COVID-19 transgenic mice are found to be significantly lower than that of control mice. When COVID-19 golden hamsters are treated by GA, the lung inflammatory cytokines levels are significantly lower than that of Remdesivir while their lung viral load are decreased to same level. The pathological results show that GA treatment significantly reduce lung inflammatory injuries when compared to that of Remdesivir-treated COVID-19 golden hamsters.

One Sentence Summary

We found that gold cluster molecule directly inhibits SARS-CoV-2 replication and intrinsically suppresses inflammatory cytokines expression in COVID-19 transgenic mouse and golden hamster model, gold cluster providing a better lung injury protection than Remdesivir in COVID-19 golden hamsters via intranasally dropping administration.
Neural correlates of hand-object congruency effects during action planning
Authors: Zhang Zuo , Nelissen Natalie , Zeidman Peter , Filippini Nicola , Diedrichsen Jörn , Bracci Stefania , Friston Karl , Rounis Elisabeth
Published: October 2020

Selecting hand actions to manipulate an object is affected both by perceptual factors and by action goals. Affordances are associated with the automatic potentiation of motor representations to an object, independent of the goal of the actor. In previous studies, we have demonstrated an influence of the congruency between hand and object orientations on response times when reaching to turn an object, such as a cup. In this study, we investigated how the representation of hand postures triggered by planning to turn a cup were influenced by this congruency effect, in an fMRI scanning environment. Healthy participants were asked to reach and turn a real cup that was placed in front of them either in an upright orientation or upside down. They were instructed to use a hand orientation that was either congruent or incongruent with the cup orientation. As expected, the motor responses were faster when the hand and cup orientations were congruent. There was increased activity in a network of brain regions involving object-directed actions during action planning, which included bilateral primary and extrastriate visual, medial and superior temporal areas, as well as superior parietal, primary motor and premotor areas in the left hemisphere. Specific activation of the dorsal premotor cortex (PMd) was associated with hand-object orientation congruency during planning, and prior to any action taking place. Activity in that area and its connectivity with the lateral occipito-temporal cortex (LOTC) increased when planning incongruent actions. The increased activity in premotor areas in trials where the orientation of the hand was incongruent to that of the object suggests a role in eliciting competing representations specified by hand postures in LOTC.
A hyper-attenuated variant of Rift Valley fever virus (RVFV) generated by a mutagenic drug (favipiravir) unveils potential virulence markers
Authors: Borrego Belén , Brun Alejandro
Published: October 2020

SUMMARY/ABSTRACT

In a previous work, we showed that favipiravir, a promising drug with antiviral activity against a number of RNA viruses, led to the extinction of RVFV from infected cell cultures. Nevertheless, certain drug concentrations allowed the recovery of a virus variant showing increased resistance to favipiravir. In this work, we characterized this novel resistant variant both at genomic and phenotypic levelin vitroandin vivo. Interestingly, the resistant virus displayed reduced growth rates in insect cells and was highly attenuated but still immunogenicin vivo. Some amino acid substitutions were identified in the viral RNA-dependent RNA-polymerase (RdRp) gene and in the encoded IFN antagonist NSs gene, in catalytic core motifs and nuclear localization associated positions respectively. These data may help to characterize novel potential virulence markers, offering additional strategies for further safety improvements of RVF live attenuated vaccine candidates.

SIGNIFICANCE STATEMENT

Live attenuated virus vaccines usually provide long lasting immune responses upon administration. These vaccines are not recommended for use in immune compromised hosts, due to the presence of uncontrolled residual virulence. Cell culture virus propagation in the presence of mutagenic drugs often results in weakened virus lacking virulence as well as limited spreading capabilities. Here, we have characterized a mutagen-induced RVFV variant (40F-p8) that is not virulent in a highly sensitive mouse strain lacking antiviral response. The observed lack of virulence correlates with the presence of specific mutations along key residues in the viral genome, unveiling potential virulence determinants. Thus, 40F-p8 constitutes the basis for a novel RVFV vaccine strain with additional safety features.
Genetic-variant hotspots and hotspot clusters in the human genome facilitating adaptation while increasing instability
Authors: Long Xi , Xue Hong
Published: October 2020

Background

Genetic variants, underlining phenotypic diversity, are known to distribute unevenly in the human genome. A comprehensive understanding of the distributions of different genetic variants is important for insights into genetic functions and disorders.

Methods

Herein, a sliding-window scan of regional densities of eight kinds of germline genetic variants, including single-nucleotide-polymorphisms (SNPs) and four size-classes of copy-number-variations (CNVs) in the human genome has been performed.

Results

The study has identified 44,379 hotspots with high genetic-variant densities, and 1,135 hotspot clusters comprising more than one type of hotspots, accounting for 3.1% and 0.2% of the genome respectively. The hotspots and clusters are found to co-localize with different functional genomic features, as exemplified by the associations of hotspots of middle-size CNVs with histone-modification sites, work with balancing and positive selections to meet the need for diversity in immune proteins, and facilitate the development of sensory-perception and neuroactive ligand-receptor interaction pathways in the function-sparse late-replicating genomic sequences. Genetic variants of different lengths co-localize with retrotransposons of different ages on a ‘long-with-young’ and ‘short-with-all’ basis. Hotspots and clusters are highly associated with tumour suppressor genes and oncogenes (p< 10−10), and enriched with somatic tumour CNVs and the trait- and disease-associated SNPs identified by genome-wise association studies, exceeding tenfold enrichment in clusters comprising SNPs and extra-long CNVs.

Conclusions

In conclusion, the genetic-variant hotspots and clusters represent two-edged swords that spearhead both positive and negative genomic changes. Their strong associations with complex traits and diseases also open up a potential ‘Common Disease-Hotspot Variant’ approach to the missing heritability problem.
APP accumulates around dense-core amyloid plaques with presynaptic proteins in Alzheimer’s disease brain
Authors: Jordà-Siquier Tomàs , Petrel Melina , Kouskoff Vladimir , Cordelières Fabrice , Frykman Susanne , Müller Ulrike , Mulle Christophe , Barthet Gaël
Published: October 2020

In Alzheimer’s disease (AD), a central role is given to the extracellular deposition of Aβ peptides, remotely produced by the proteolysis of the amyloid precursor protein (APP). This contrasts with other neurodegenerative diseases which are characterized by the intraneuronal aggregation of full-length proteins such as huntingtin, α-synuclein or TDP-43. Importantly, the distribution of APP around amyloid plaques is poorly characterized. Here, we combined an extensive set of methodological and analytical tools to investigate neuropathological features of APP in the human AD hippocampus and in two mouse models of AD. We report that APP remarkably accumulates in the surrounding of dense-core amyloid plaques together with the secretases necessary to produce Aβ peptides. In addition, the Nter domain, but not the Cter domain of APP is enriched in the core of amyloid plaques uncovering a potential pathological role of the secreted APP-Nter in dense-core plaques. To investigate the subcellular compartment in which APP accumulates, we labelled neuritic and synaptic markers and report an enrichment in presynaptic proteins (Syt1, VAMP2) and phosphorylated-Tau. Ultrastructural analysis of APP accumulations reveals abundant multivesicular bodies containing presynaptic vesicles proteins and autophagosomal built-up of APP. Altogether, our data supports a role of presynaptic APP in AD pathology and highlights APP accumulations as a potential source of Aβ and Nter peptides to fuel amyloid plaques.
Phylogenetic analysis of the salinipostin γ-butyrolactone gene cluster uncovers new potential for bacterial signaling-molecule diversity
Authors: Creamer Kaitlin E. , Kudo Yuta , Moore Bradley S. , Jensen Paul R.
Published: October 2020

Bacteria communicate by small-molecule chemicals that facilitate intra- and inter-species interactions. These extracellular signaling molecules mediate diverse processes including virulence, bioluminescence, biofilm formation, motility, and specialized metabolism. The signaling molecules produced by members of the phylum Actinobacteria are generally comprised of γ-butyrolactones, γ-butenolides, and furans. The best known actinomycete γ-butyrolactone is A-factor, which triggers specialized metabolism and morphological differentiation in the genus Streptomyces. Salinipostins A-K are unique γ-butyrolactone molecules with rare phosphotriester moieties that were recently characterized from the marine actinomycete genus Salinispora. The production of these compounds has been linked to the 9-gene biosynthetic gene cluster spt. Critical to salinipostin assembly is the γ-butyrolactone synthase encoded by spt9. Here, we report the global distribution of spt9 among sequenced bacterial genomes, revealing a surprising diversity of gene homologs across 12 bacterial phyla, the majority of which are not known to produce γ-butyrolactones. Further analyses uncovered a large group of spt-like gene clusters outside of the genus Salinispora, suggesting the production of new salinipostin-like diversity. These gene clusters show evidence of horizontal transfer between many bacterial taxa and location specific homologous recombination exchange among Salinispora strains. The results suggest that γ-butyrolactone production may be more widespread than previously recognized. The identification of new γ-butyrolactone biosynthetic gene clusters is the first step towards understanding the regulatory roles of the encoded small molecules in Actinobacteria.

Importance

Signaling molecules orchestrate a wide variety of bacterial behaviors. Among Actinobacteria, γ-butyrolactones mediate morphological changes and regulate specialized metabolism. Despite their importance, few γ-butyrolactones have been linked to their cognate biosynthetic gene clusters. A new series of γ-butyrolactones called the salinipostins was recently identified from the marine actinomycete genus Salinispora and linked to the spt biosynthetic gene cluster. Here we report the detection of spt-like gene clusters in diverse bacterial families not known for the production of this class of compounds. This finding expands the taxonomic range of bacteria that may employ this class of compounds and provides opportunities to discover new compounds associated with chemical communication.
The molecular and metabolic program for adaptation of white adipocytes to cool physiologic temperatures
Authors: Mori Hiroyuki , Dugan Colleen E. , Nishii Akira , Benchamana Ameena , Li Ziru , Cadenhead Thomas S. , Das Arun K. , Evans Charles R. , Overmyer Katherine A. , Romanelli Steven M. , Peterson Sydney K. , Bagchi Devika P. , Corsa Callie A. , Hardij Julie , Learman Brian S. , El Azzouny Mahmoud , Inoki Ken , MacDougald Ormond A.
Published: October 2020

Although visceral adipocytes located within the body’s central core are maintained at ~37°C, adipocytes within bone marrow, subcutaneous, and dermal depots are found primarily within the peripheral shell, and generally exist at cooler temperatures. Responses of brown and beige/brite adipocytes to cold stress are well-studied; however, comparatively little is known about mechanisms by white adipocytes adapt to temperatures below 37°C. Here we report that adaptation of cultured adipocytes to 31°C, the temperature at which distal marrow adipose tissues and subcutaneous adipose tissues often reside, induces extensive changes in gene expression, increased anabolic and catabolic lipid metabolism, and elevated oxygen consumption with reduced reliance on glucose and preferential use of pyruvate, glutamine and fatty acids as energy sources. Cool temperatures up-regulate stearoyl-CoA desaturase-1 expression and monounsaturated lipid levels in cultured adipocytes and distal bone marrow adipose tissues, and stearoyl-CoA desaturase-1 activity is required for acquisition of maximal oxygen consumption at 31°C.
Improved diagnostic prediction of the pathogenicity of bloodstream isolates ofStaphylococcus epidermidis
Authors: VanAken Shannon M. , Newton Duane , VanEpps J. Scott
Published: October 2020

With an estimated 440,000 active cases occurring each year, medical device associated infections pose a significant burden on the US healthcare system, costing about $9.8 billion in 2013.Staphylococcus epidermidisis the most common cause of these device-associated infections, which typically involve isolates that are multi-drug resistant and possess multiple virulence factors.S. epidermidisis also frequently a benign contaminant of otherwise sterile blood cultures. Therefore, tests that distinguish pathogenic from non-pathogenic isolates would improve the accuracy of diagnosis and prevent overuse/misuse of antibiotics. Attempts to use multi-locus sequence typing (MLST) with machine learning for this purpose had poor accuracy (~73%). In this study we sought to improve the diagnostic accuracy of predicting pathogenicity by focusing on phenotypic markers (i.e., antibiotic resistance, growth fitness in human plasma, and biofilm forming capacity) and the presence of specific virulence genes (i.e., mecA, ses1, andsdrF). Commensal isolates from healthy individuals (n=23), blood culture contaminants (n=21), and pathogenic isolates considered true bacteremia (n=54) were used. Multiple machine learning approaches were applied to characterize strains as pathogenicvsnon-pathogenic. The combination of phenotypic markers and virulence genes improved the diagnostic accuracy to 82.4% (sensitivity: 84.9% and specificity: 80.9%). Oxacillin resistance was the most important variable followed by growth rate in plasma. This work shows promise for the addition of phenotypic testing in clinical diagnostic applications.
Virus infections inVarroa destructor-resistant honeybees
Authors: Oddie Melissa A. Y. , Lanz Sandra , Dahle Bjørn , Yañez Orlando , Neumann Peter
Published: October 2020

Populations of European honeybee subspecies,Apis mellifera, have the ability to adapt naturally to the ectoparasitic mite,Varroa destructor. It is possible that a tolerance to mite-vectored viruses may contribute to colony survival. If this is the case, surviving populations should show lower virus titers and prevalence compared to susceptible populations. Here, we investigated the prevalence and titers of 10 viruses, some known to be associated withV. destructor, in adult workers and pupae as well as mites. Samples were collected from both a mite-surviving and mite-susceptible honeybee population in Norway. Surviving colonies had a lower prevalence of a key virus (DWV-A) associated withV. destructorin individual adult bees sampled, and generally lower titers of this virus in mite infested pupae and mites within the colonies when compared to sympatric, susceptible controls. However, these surviving colonies also displayed higher prevalence and titers of two viruses not associated withV. destructor(BQCV & LSV1). The results of this study therefore suggest that general tolerance to virus infections is unlikely to be a key mechanism for natural colony survival in Norway, but evidence may point to mite control as a predominant mechanism.
Remote testing of vitamin D levels across the UK MS population – a case control study
Authors: Vickaryous Nicola , Jitlal Mark , Jacobs Benjamin Meir , Middleton Rod , Chandran Siddharthan , MacDougall Niall John James , Giovannoni Gavin , Dobson Ruth
Published: October 2020

Objective

The association between vitamin D deficiency and multiple sclerosis (MS) is well described. We set out to use remote sampling to ascertain vitamin D status and vitamin D supplementation in a cross-sectional study of people with MS across the UK.

Methods

People with MS and matched controls were recruited from across the UK. 1768 people with MS enrolled in the study; remote sampling kits were distributed to a subgroup. Dried blood spots (DBS) were used to assess serum 25(OH)D in people with MS and controls.

Results

1768 MS participants completed the questionnaire; 388 MS participants and 309 controls provided biological samples. Serum 25(OH)D was higher in MS than controls (median 71nmol/L vs 49nmol/L). A higher proportion of MS participants than controls supplemented (72% vs 26%, p<0.001); people with MS supplemented at higher vD doses than controls (median 1600 vs 600 IU/day, p<0.001). People with MS who did not supplement had lower serum 25(OH)D levels than non-supplementing controls (median 38 nmol/L vs 44 nmol/L). Participants engaged well with remote sampling.

Conclusions

The UK MS population have higher serum 25(OH)D than controls, mainly as a result of vitamin D supplementation. Remote sampling is a feasible way of carrying out large studies.
Serotype has a significant impact on the virulence of 7th pandemicVibrio choleraeO1
Authors: Nordqvist Stefan L , Thorell Kaisa , Nilsson Frida , Löfstrand Madeleine , Hagelberg Arvid , Holmgren Jan , Lebens Michael R.
Published: October 2020

Of over 200 different identifiedVibrio choleraeserogroups only the O1 serogroup is consistently associated with endemic and epidemic cholera disease. The O1 serogroup has two serologically distinguishable variants, the Ogawa and Inaba serotypes, which differ only by a methyl group present on the terminal sugar of the Ogawa O-antigen but absent from Inaba strains. This methylation is catalyzed by a methyltransferase encoded by thewbeTgene, which in Inaba strains is disrupted by mutation. It is currently thought that there is little difference between the two serotypes. However, here we show, using isogenic pairs of O1 El TorV. cholerae, that Inaba strains show significantly different patterns of gene expression and are significantly less able than the corresponding Ogawa strains to cause cholera in an infant mouse infection model. Our results suggest that changes in gene expression resulting from the loss of thewbeTgene lead to reduced virulence and possibly also reduced survival fitness outside the human host.

Author Summary

The bacteriumVibrio choleraecauses the pandemic diarrheal disease cholera. Despite many identified serotypes ofV. choleraeonly one, O1, causes pandemic cholera. The O1 serotype of pandemicV. choleraehas two distinguishable variants (called Ogawa and Inaba) long considered to be clinically and epidemiologically equivalent. Cholera outbreaks consist only of one the two variants at any time. In general, Ogawa strains cause the majority of outbreaks with relatively short-lived Inaba outbreaks occurring sporadically. We have suggested earlier that Inaba outbreaks occur during periods of environmental selective pressure against the Ogawa serotype. We demonstrate here that the two variants are not clinically equivalent. The Ogawa serotype is better able to respond to infection in an animal model by up regulating the expression of virulence genes essential for disease development. We suggest that this phenomenon is the result of wider ranging differences in gene expression resulting from the mutation that converts Ogawa into Inaba strains, and may help to explain the dominance of the Ogawa serotype in nature.
Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare
Authors: Mogro E.G. , Ambrosis N. , Lozano M.J.
Published: October 2020

Motivation

Bacterial genomes are composed by a core and an accessory genome. The first composed of housekeeping and essential genes, while the second is composed, in its majority, of mobile genetic elements, including transposable elements (TEs). Insertion sequences (ISs), the smallest TEs, have an important role in genome evolution, and contribute to bacterial genome plasticity and adaptability. ISs can spread in a genome, presenting different locations in nearly related strains, and producing phenotypic variations. Few tools are available which can identify differentially located ISs (DLIS) on assembled genomes.

Results

We developed ISCompare to profile IS mobilization events in related bacterial strains using complete or draft genome assemblies. ISCompare was validated using artificial genomes with simulated random IS insertions and real sequences, achieving the same or better results than other available tools, with the advantage that ISCompare can analyse multiple ISs at the same time and outputs a list of candidate DLIS. We think that ISCompare provides an easy and straightforward approach to look for differentially located ISs on bacterial genomes.

Availability and implementation

ISCompare was implemented in python3 and its source code is freely available for download athttps://github.com/maurijlozano/ISCompare.

Supplementary information

Supplementary data are available athttps://github.com/maurijlozano/ISCompare.
Lateralized functional responses in the cortex arise from the dynamic interactions in the structural connectome
Authors: Kumar Neeraj , Jaiswal Amit Kumar , Roy Dipanjan , Banerjee Arpan
Published: October 2020

Structure-function relationships are fundamental to studies of neural systems, yet the mechanistic underpinnings of how structural networks shape hemispheric lateralization remain elusive. For instance, the asymmetric neuroanatomic embedding of primary auditory cortices was shown when connectivity with all other brain areas were considered. Concomitantly, functional lateralization e.g., left hemispheric dominance of speech processing and right hemispheric dominance of music perception, is widely acknowledged. The present article provides a parsimonious mechanistic explanation based on computational modelling and empirical recordings to demonstrate emergence of hemispheric lateralization of brain function. For validation of the model, empirical EEG recordings of auditory steady state responses (ASSR) were undertaken, and empirical findings suggest right hemispheric dominance at the level of cortical sources in binaural and monaural hearing conditions. Subsequently, we demonstrate the entrainment and phase of oscillations in connected brain regions based on a neurodynamic model constrained by empirically derived structural connectivity matrix from diffusion data. For relevance, we have taken into consideration time-delays in neural communication stemming from fibre distances and neuronal coupling arising from fibre densities. Based on relevant network parameters, we could demonstrate the emergence of right hemispheric dominance of ASSR in binaural and monaural hearing conditions when auditory cortical areas were chosen as triggers of entrained phase oscillators. Furthermore, we discovered emergence of left-lateralized functional response when bilateral Broca’s area replaced auditory areas as triggers. Hence, a single unified mechanism based on entrainment of phase oscillators in a large-scale brain network could explain both emergence of right and left hemispheric laterality.

Significance statement

The origin of hemispheric specialization of sensory processing is a fundamental question in neuroscience. For instance, speech and language are predominantly processed in the left hemispheric regions, while the right hemisphere is specialized for processing rhythmic, tonal, and melodic stimuli. Identification of the network mechanisms that give rise to such functional lateralization from structural constraints remains elusive. In the present study, we simulate neural activity observed during human EEG recordings of auditory steady-state responses from a biophysically realistic large-scale model constrained by underlying structural connectivity. Subsequently, we demonstrate how hemispheric lateralization of brain responses to sensory stimuli emerge from the time-delayed interactions among whole-brain neuronal ensembles.
The Theory and Practice of the viral dose in neutralization assay: insights on SARS-CoV-2 “doublethink” effect
Authors: Manenti Alessandro , Molesti Eleonora , Maggetti Marta , Torelli Alessandro , Lapini Giulia , Montomoli Emanuele
Published: October 2020

Due to the global spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is an urgent need for reliable high-throughput serological assays in order to evaluate the immunological responses against SARS-COV-2 virus and to enable population screening, as well as vaccines and drug’s efficacy testing. Several serological assays for SARS-CoV-2 are now becoming available in the market. However, it has also become extremely important to have well-established assays with desirable high sensitivity and specificity. To date, the micro-neutralization (MN) assay, is currently considered the gold-standard being capable of evaluating and detecting, functional neutralizing antibodies (nAbs). Several protocols exist for microneutralization assays which vary in several steps of the protocol: cell seeding conditions, number of cells seeded, virus amount used in the infection step, virus-serum-cells incubation period etc. These potential differences account for a high degree of variability and inconsistency of the results and using a harmonized protocol for the micro-neutralization assay could potentially solve this.

Given this situation, the main aim of our study was to carry out SARS-CoV-2 wild type virus MN assay in order to investigate which optimal tissue culture infective dose 50 (TCID50) infective dose in use is the most adequate choice for implementation in terms of reproducibility, standardization possibilities and comparability of results. Therefore, we assessed the MN by using two different viral infective doses: a standard dose of 100 TCID50/well and a lower dose of 25 TCID50/well. The results obtained, yielded by MN on using the lower infective dose (25 TCID50), were in line with those obtained with the standard infective dose; in some cases, however, we detected a titre that was one or two dilution steps higher, which maintained all negative samples negative. This suggesting that the lower dose can potentially have a positive impact on the detection and estimation of neutralizing antibodies present in a given sample, showing higher sensitivity but similar specificity and therefore, it would require a more accurate assessment and cross-laboratories standardisation especially when MN is employed as serological assay of choice for pre-clinical and clinical studies.
Photochemical probe identification of the small-molecule binding site in a mammalian membrane-boundO-acyltransferase
Authors: Lanyon-Hogg Thomas , Ritzefeld Markus , Zhang Leran , Pogranyi Balazs , Mondal Milon , Sefer Lea , Johnston Callum D. , Coupland Claire E. , Andrei Sebastian A. , Newington Joshua , Magee Anthony I. , Siebold Christian , Tate Edward W.
Published: October 2020

The mammalian membrane-boundO-acyltransferase (MBOAT) superfamily is involved in biological processes including growth, development and appetite sensing. MBOATs are attractive drug targets in cancer and obesity; however, information on the binding site and molecular mechanisms underlying small-molecule inhibition is elusive. This study reports development of a photochemical probe to interrogate the small-molecule binding site in the human MBOAT Hedgehog acyltransferase (HHAT) based on HHAT inhibitor RUSKI-201. Structure-activity relationship investigation identified the improved enantiomeric inhibitorIMP-1575, which is the most potent HHAT inhibitor reported to-date, and guided rational design of a photocrosslinking probe that maintained HHAT-inhibitory potency. Photocrosslinking and proteomic sequencing of HHAT delivered identification of the first small-molecule binding site in a mammalian MBOAT. Topology and homology data suggested a potential mechanism for HHAT inhibition which was confirmed via kinetic analysis. Our results provide an optimal HHAT inhibitorIMP-1575(Ki= 38 nM) and a strategy for mapping of interaction sites in MBOATs.
Knockout of zebrafish desmin genes does not cause skeletal muscle degeneration but alters calcium flux
Authors: Kurekci Gulsum Kayman , Mangit Ecem Kural , Koyunlar Cansu , Unsal Seyda , Saglam Berk , Ergin Bora , Gizer Merve , Uyanik Ismail , Düz Niloufar Boustanabadimaralan , Korkusuz Petek , Talim Beril , Purali Nuhan , Hughes Simon M. , Dincer Pervin R.
Published: October 2020

Desmin is a muscle-specific intermediate filament protein that has fundamental role in muscle structure and force transmission. Whereas human desmin protein is encoded by a single gene, two desmin paralogs (desmaanddesmb) exist in zebrafish.Desmaanddesmbshow differential spatiotemporal expression during zebrafish embryonic and larval development, being similarly expressed in skeletal muscle until hatching, after which expression ofdesmbshifts to gut smooth muscle. We generated knockout (KO) mutant lines carrying loss-of-function mutations for each gene by using CRISPR/Cas9. Mutants are viable and fertile, and lack obvious skeletal muscle, heart or intestinal defects. In contrast to morphants, knockout of each gene did not cause any overt muscular phenotype, but did alter calcium flux in myofibres. These results point to a possible compensation mechanism in these mutant lines generated by targeting nonsense mutations to the first coding exon.
Multivariate genomic analysis of 1.5 million people identifies genes related to addiction, antisocial behavior, and health
Authors: Linnér Richard Karlsson , Mallard Travis T. , Barr Peter B. , Sanchez-Roige Sandra , Madole James W. , Driver Morgan N. , Poore Holly E. , Grotzinger Andrew D. , Tielbeek Jorim J. , Johnson Emma C. , Liu Mengzhen , Zhou Hang , Kember Rachel L. , Pasman Joëlle A. , Verweij Karin J.H. , Liu Dajiang J. , Vrieze Scott ,   COGA Collaborators, Kranzler Henry R. , Gelernter Joel , Harris Kathleen Mullan , Tucker-Drob Elliot M. , Waldman Irwin , Palmer Abraham A. , Harden K. Paige , Koellinger Philipp D. , Dick Danielle M.
Published: October 2020

Behaviors and disorders related to self-regulation, such as substance use, antisocial conduct, and ADHD, are collectively referred to asexternalizingand have a shared genetic liability. We applied a multivariate approach that leverages genetic correlations among externalizing traits for genome-wide association analyses. By pooling data from ~1.5 million people, our approach is statistically more powerful than single-trait analyses and identifies more than 500 genetic loci. The identified loci were enriched for genes expressed in the brain and related to nervous system development. A polygenic score constructed from our results captures variation in a broad range of behavioral and medical outcomes that were not part of our genome-wide analyses, including traits that until now lacked well-performing polygenic scores, such as opioid use disorder, suicide, HIV infections, criminal convictions, and unemployment. Our findings are consistent with the idea that persistent difficulties in self-regulation can be conceptualized as a neurodevelopmental condition.
A pan-cancer metabolic atlas of the tumor microenvironment
Authors: Rohatgi Neha , Ghoshdastider Umesh , Baruah Probhonjon , Skanderup Anders Jacobsen
Published: October 2020

Tumors are heterogeneous cellular environments with entwined metabolic dependencies. Here, we used a tumor transcriptome deconvolution approach to profile the metabolic states of cancer and non-cancer (stromal) cells in bulk tumors of 20 solid tumor types. We identified metabolic genes and processes recurrently altered in cancer cells across tumor types, including pan-cancer upregulation of deoxythymidine triphosphate (dTTP) production. In contrast, the tryptophan catabolism rate limiting enzymes,IDO1andTDO2, were highly overexpressed in stroma, suggesting that kynurenine-mediated suppression of antitumor immunity is predominantly constrained by the stroma. Oxidative phosphorylation was unexpectedly the most upregulated metabolic process in cancer cells compared to both stromal cells and a large atlas of cancer cell lines, suggesting that the Warburg effect may be less pronounced in cancer cellsin vivo. Overall, our analysis highlights fundamental differences in metabolic states of cancer and stromal cells inside tumors and establishes a pan-cancer resource to interrogate tumor metabolism.
Mapping calcium dynamics in a developing tubular structure
Authors: Hoyer Jorgen , Saba Morsal , Dondorp Daniel , Kolar Kushal , Esposito Riccardo , Chatzigeorgiou Marios
Published: October 2020

Calcium is a ubiquitous and versatile second messenger that plays a central role in the development and function of a wide range of cell types, tissues and organs. Despite significant recent progress in the understanding of calcium (Ca2+) signalling in organs such as the developing and adult brain, we have relatively little knowledge of the contribution of Ca2+to the development of tubes, structures widely present in multicellular organisms. Here we image Ca2+dynamics in the developing notochord ofCiona intestinalis. We show that notochord cells exhibit distinct Ca2+dynamics during specific morphogenetic events such as cell intercalation, cell elongation and tubulogenesis. We used an optogenetically controlled Ca2+actuator to show that sequestration of Ca2+results in defective notochord cell intercalation, and pharmacological inhibition to reveal that stretch-activated ion channels (SACs), inositol triphosphate receptor (IP3R) signalling, Store Operated Calcium Entry (SOCE), Sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) and gap junctions are required for regulating notochord Ca2+activity during tubulogenesis. Cytoskeletal rearrangements drive the cell shape changes that accompany tubulogenesis. In line with this, we show that Ca2+signalling modulates reorganization of the cytoskeletal network across the morphogenetic events leading up to and during tubulogenesis of the notochord. We additionally demonstrate that perturbation of the actin cytoskeleton drastically remodels Ca2+dynamics, suggesting a feedback mechanism between actin dynamics and Ca2+signalling during notochord development. This work provides a framework to quantitatively define how Ca2+signalling regulates tubulogenesis using the notochord as model organ, a defining structure of all chordates.
A Simultaneous EEG-fMRI Study of Thalamic Load-Dependent Working Memory Delay Period Activity
Authors: Gomes Bernard A. , Plaska Chelsea Reichert , Ortega Jefferson , Ellmore Timothy M.
Published: October 2020

Working memory (WM) is an essential component of executive functions which depend on maintaining task-related information online for brief periods in both the presence and absence of interfering stimuli. Active maintenance occurs during the WM delay period, the time between stimulus encoding and subsequent retrieval. Previous studies have extensively documented prefrontal (PFC) and posterior parietal (PPC) cortex activity during the WM delay period, but the role of subcortical structures including the thalamus remains to be fully elucidated, especially in humans. Using simultaneous EEG-fMRI, we investigated the role of the thalamus during the WM delay period following low and high memory load encoding. During the delay, participants passively viewed scrambled images containing similar color and spatial frequency to serve as a perceptual baseline. Using individual fMRI-weighted source analyses centered around delay period onset, the effects of increased and decreased memory load on maintenance were observed bilaterally in thalamus with higher source activity evoked during low compared to high load maintenance. The main finding that thalamic activation was attenuated during high compared to low load maintenance suggesting a sensory filtering role for thalamus during consolidation of stimuli in WM where the highest evoked activity occurs when fewer stimuli need to be maintained in the presence of interfering perceptual stimuli during the delay. The results support the idea that the thalamus plays a role in short-term memory maintenance by regulating processing of interfering stimuli.
Visualization and Modeling of Inhibition of IL-1β and TNF-α mRNA Transcription at the Single-Cell Level
Authors: Kalb Daniel , Vo Huy D. , Adikari Samantha , Hong-Geller Elizabeth , Munsky Brian , Werner James
Published: October 2020

IL-1β and TNF-α are canonical immune response mediators that play key regulatory roles in a wide range of inflammatory responses to both chronic and acute conditions. Here we employ an automated microscopy platform for the analysis of messenger RNA (mRNA) expression of IL-1β and TNF-α at the single-cell level. The amount of IL-1β and TNF-α mRNA expressed in a human monocytic leukemia cell line (THP-1) is visualized and counted using single-molecule fluorescent in-situ hybridization (smFISH) following exposure of the cells to lipopolysaccharide (LPS), an outer-membrane component of Gram-negative bacteria. We show that the small molecule inhibitors MG132 (a 26S proteasome inhibitor used to block NF-κB signaling) and U0126 (a MAPK Kinase inhibitor used to block CCAAT-enhancer-binding proteins C/EBP) successfully block IL-1β and TNF-α mRNA expression. Based upon this single-cell mRNA expression data, we screened 36 different mathematical models of gene expression, and found two similar models that capture the effects by which the drugs U0126 and MG132 affect the rates at which the genes transition into highly activated states. When their parameters were informed by the action of each drug independently, both models were able to predict the effects of the combined drug treatment. From our data and models, we postulate that IL-1β is activated by both NF-κB and C/EBP, while TNF-α is predominantly activated by NF-κB. Our combined single-cell experimental modeling efforts shows the interconnection between these two genes and demonstrates how the single-cell responses, including the distribution shapes, mean expression, and kinetics of gene expression, change with inhibition.
Simplified artificial blood feeding and oral infection method for mosquitoes
Authors: Pereira Thiago Nunes , Carvalho Fabiano Duarte , da Silva Lidia Henrique , de Mendonça Silvana Faria , Moreira Luciano Andrade
Published: October 2020

Mosquitoes such asAedes aegypti, Aedes albopictus and Culex quinquefasciatusare vectors of many pathogens that greatly affect humankind. The maintenance of these mosquitoes in laboratory permit different studies that can help understanding their biology, as well as the vector-pathogen interaction. In addition to sugar meals, the blood feeding is essential for maintenance of the reproductive cycle in several vectors. The main blood sources for many mosquito colonies are direct feeding on live animal or the use of human/animal blood through artificial feeders. However, this latter process has some disadvantages, as artificial feeders can be very laborious for assembly and decontamination. Based on these observations, a simplified technique for feeding and artificial infection was developed with cotton-pads soaked (CS) and blood or blood and viral supernatant to simulate an artificial infection. The efficiency of the CS technique was investigated through the number of mosquitoes fed/infected, when compared to their respective control group. The CS technique, with blood at room temperature, promoted a feeding rate of 61.4% forAe. albopictus, 70.8% forCx. quinquefasciatusand 17% forAe. aegypti. The control group (Hemotec-feeding) presented 47.9%, 16.5% and 59.1% of feeding success, respectively. To improve the CS technique forAe. aegyptimosquitoes, the procedure was then performed with blood at 38°C, which was possible to observe a feeding rate of 47.3%, in comparison to 53.2% for the control group (Hemotec). When using the CS technique for artificial infection with Mayaro virus, more than 80% of infection was observed forAe. aegyptiand 100% forAe. albopictus. In the traditional infection technique (glass feeder), the infection rate was 90% (Ae. aegypti) and 96.6%(Ae. albopictus). ForCx. quinquefasciatus, the infection was positive only with the CS technique, resulting in 1 (5%) mosquito infected with Mayaro virus. Our results suggest that this simplified technique of low-cost feeding and easy assembly, offers good results for feeding (maintenance of colonies) and artificial infection of different species of mosquitoes.