bluuebunny/crossref_metadata_2025 huggingface dataset:
Tuberculosis causes highly conserved metabolic changes in human patients, mycobacteria-infected mice and zebrafish larvae
Authors: Ding Yi , Raterink Robert Jan , Marín-Juez Rubén , Veneman Wouter J. , Egbers Koen , van den Eeden Susan , Haks Mariëlle C. , Joosten Simone A. , Ottenhoff Tom H.M. , Harms Amy C. , Alia A. , Hankemeier Thomas , Spaink Herman P.
Published: May 2020

Tuberculosis is a highly infectious and potentially fatal disease accompanied by wasting symptoms, which cause severe metabolic changes in infected people. In this study we have compared the effect of mycobacteria infection on the level of metabolites in blood of humans and mice and whole zebrafish larvae using one highly standardized mass spectrometry pipeline, ensuring technical comparability of the results. Quantification of a range of circulating small amines showed that the levels of the majority of these compounds were significantly decreased in all three groups of infected organisms. Ten of these metabolites were common between the three different organisms comprising: methionine, asparagine, cysteine, threonine, serine, tryptophan, leucine, citrulline, ethanolamine and phenylalanine. The metabolomic changes of zebrafish larvae after infection were confirmed by nuclear magnetic resonance spectroscopy. Our study identified common biomarkers for tuberculosis disease in humans, mice and zebrafish, showing across species conservation of metabolic reprogramming processes as a result of disease. Apparently, the mechanisms underlying these processes are independent of environmental, developmental and vertebrate evolutionary factors. The zebrafish larval model is highly suited to further investigate the mechanism of metabolic reprogramming and the connection with wasting syndrome due to infection by mycobacteria.
Inversion Genotyping in theAnopheles gambiaeComplex Using High-Throughput Array and Sequencing Platforms
Authors: Love R. Rebecca , Pombi Marco , Guelbeogo Moussa W. , Campbell Nathan R. , Stephens Melissa T. , Dabire Roch K. , Costantini Carlo , della Torre Alessandra , Besansky Nora J.
Published: May 2020

Chromosomal inversion polymorphisms have special importance in theAnopheles gambiaecomplex of malaria vector mosquitoes, due to their role in local adaptation and range expansion. The study of inversions in natural populations is reliant on polytene chromosome analysis by expert cytogeneticists, a process that is limited by the rarity of trained specialists, low throughput, and restrictive sampling requirements. To overcome this barrier, we ascertained tag single nucleotide polymorphisms (SNPs) that are highly correlated with inversion status (inverted or standard orientation). We compared the performance of the tag SNPs using two alternative high throughput molecular genotyping approaches versus traditional cytogenetic karyotyping of the same 960 individualAn. gambiaeandAn. coluzziimosquitoes sampled from Burkina Faso, West Africa. We show that both molecular approaches yield comparable results, and that either one performs as well or better than cytogenetics in terms of genotyping accuracy. Given the ability of molecular genotyping approaches to be conducted at scale and at relatively low cost without restriction on mosquito sex or developmental stage, molecular genotyping via tag SNPs has the potential to revitalize research into the role of chromosomal inversions in the behavior and ongoing adaptation ofAn. gambiaeandAn. coluzziito environmental heterogeneities.
Miniaturized head-mounted device for whole cortex mesoscale imaging in freely behaving mice
Authors: Rynes Mathew L , Surinach Daniel , Linn Samantha , Laroque Michael , Rajendran Vijay , Dominguez Judith , Hadjistamolou Orestes , Navabi Zahra S , Ghanbari Leila , Johnson Gregory W , Nazari Mojtaba , Mohajerani Majid , Kodandaramaiah Suhasa B
Published: May 2020

The advent of genetically encoded calcium indicators, along with surgical preparations such as thinned skulls or refractive index matched skulls, have enabled mesoscale cortical activity imaging in head-fixed mice. Such imaging studies have revealed complex patterns of coordinated activity across the cortex during spontaneous behaviors, goal-directed behavior, locomotion, motor learning, and perceptual decision making. However, neural activity during unrestrained behavior significantly differs from neural activity in head-fixed animals. Whole-cortex imaging in freely behaving mice will enable the study of neural activity in a larger, more complex repertoire of behaviors not possible in head-fixed animals. Here we present the “Mesoscope,” a wide-field miniaturized, head-mounted fluorescence microscope compatible with transparent polymer skulls recently developed by our group. With a field of view of 8 mm x 10 mm and weighing less than 4 g, the Mesoscope can image most of the mouse dorsal cortex with resolution ranging from 39 to 56 µm. Stroboscopic illumination with blue and green LEDs allows for the measurement of both fluorescence changes due to calcium activity and reflectance signals to capture hemodynamic changes. We have used the Mesoscope to successfully record mesoscale calcium activity across the dorsal cortex during sensory-evoked stimuli, open field behaviors, and social interactions. Finally, combining the mesoscale imaging with electrophysiology enabled us to measure dynamics in extracellular glutamate release in the cortex during the transition from wakefulness to natural sleep.
Male-mediated maturation in a wild primate
Authors: Lu Amy , Feder Jacob A. , Snyder-Mackler Noah , Bergman Thore J. , Beehner Jacinta C.
Published: May 2020

In humans, a controversial hypothesis suggests that father absence promotes early puberty in daughters. Data from rodents confirm females accelerate maturation with exposure to novel males (“Vandenbergh effect”) and delay it with exposure to male relatives. Here, we report the first case of male-mediated maturation in a wild primate, geladas (Theropithecus gelada). Females were more likely to mature after a change in the reproductive male: some matured earlier than expected (Vandenbergh effect) and some later (due to father presence). Novel males stimulated a surge in estrogens for all immature females - even females too young to mature. Although male-mediated puberty accelerated first births, the effect was modest, suggesting that alternative scenarios, such as co-evolution with the Bruce effect (male-mediated fetal loss) may explain this phenomenon.

One Sentence Summary

Novel males induce an estrogen surge, male-mediated puberty, and a head-start on reproduction for immature female geladas.
Worker-behavior and behavior-behavior interaction networks in the trap-jaw antOdontomachus chelifer(Latreille, 1802) (Hymenoptera: Formicidae)
Authors: Neves Felipe Marcel , Borges Marcelo Eduardo , Pie Marcio R.
Published: May 2020

Division of labor is among the main factors to explain the evolutionary success of social systems, from the origins of multicellularity to complex animal societies. The remarkable ecological success of social insects seems to have been largely driven by ergonomic advantages stemming from the behavioral specialization of workers. However, little is known about how individuals and their corresponding behavioral repertoires are related to each other within a division of labor context, particularly by viewing such relationships as complex networks. Applications of network theory to the study of social insects are almost exclusively used to analyze behavioral interactions between individuals, rather than to the study of relations among individuals and behaviors. Here, we use an approach to the study of the organization of the behavioral repertoire of ant colonies that considers both individual-behavior interactions and behavior-behavior interactions, besides colony time budgets. Our study investigates the organization of division of labor in colonies of the trap-jaw antOdontomachus chelifer(Latreille, 1802). All the behavioral acts (including inactivity) performed within three queenright colonies of different sizes (n = 7, 30, and 60 workers) were studied under controlled laboratory conditions. Each ant was individually marked and observed by scan sampling in 10 min intervals for 10 h each (n = 5,919 behavioral acts). We describe the network topologies in terms of centrality, specialization, modularity, and nestedness. This study shows that workers ofO. cheliferare organized according to structured networks, composed of individuals exhibiting varying degrees of specialization. The observed centrality scores indicate that some behaviors could have a disproportionately larger impact on the network organization (especially self-grooming). The results underscore the potential of the use of complex networks (particularly measures of modularity and nestedness) in order to discover and study novel organizational patterns of social groups in animal behavior.
A validation of Illumina EPIC array system with bisulfite-based amplicon sequencing
Authors: Noble Alexandra , Pearson John , Boden Joseph , Horwood John , Gemmell Neil , Kennedy Martin , Osborne Amy
Published: May 2020

The Illumina Infinium® MethylationEPIC BeadChip system (hereafter EPIC array) is considered to be the current gold standard detection method for assessing DNA methylation at the genome-wide level. EPIC arrays are used for hypothesis generation or pilot studies, the natural conclusion is to validate methylation candidates and expand these in a larger cohort, in a targeted manner. As such, an accurate smaller-scale, targeted technique, that generates data at the individual CpG level that is equivalent to the EPIC array, is needed. Here, we tested an alternative DNA methylation detection technique, known as bisulfite-based amplicon sequencing (BSAS), to determine its ability to validate CpG sites detected in EPIC array studies. BSAS was able to detect differential DNA methylation at CpG sites to a degree which correlates highly with the EPIC array system. However, BSAS correlated less well with EPIC array data when the magnitude of change via EPIC array was greater than 5%, suggesting that this lower specificity at larger differential methylation values is a consequence of PCR amplification that BSAS requires. However, our data suggests that BSAS does offer advantages that the EPIC array: BSAS amplifies a region of the genome (~500bp) around a CpG of interest, allowing analyses of other CpGs in the region that may not be present on the EPIC array, aiding discovery of novel CpG sites and differentially methylated regions of interest. We conclude that BSAS offers a valid investigative tool for specific regions of the genome that are currently not contained on the array system.
Proteomic responses to ocean acidification in the brain of juvenile coral reef fish
Authors: Tsang Hin Hung , Welch Megan , Munday Philip L. , Ravasi Timothy , Schunter Celia
Published: May 2020

Elevated CO2levels predicted to occur by the end of the century can affect the physiology and behaviour of marine fishes. For one important survival mechanism, the response to chemical alarm cues from conspecifics, substantial among-individual variation in the extent of behavioural impairment when exposed to elevated CO2has been observed in previous studies. Whole brain transcriptomic data has further emphasized the importance of parental phenotypic variation in the response of juvenile fish to elevated CO2. In this study, we investigate the genome-wide proteomic responses of this variation in the brain of 5-week old spiny damselfish,Acanthochromis polyacanthus. We compared the expression of proteins in the brains of juvenileA. polyacanthusfrom two different parental behavioural phenotypes (sensitive and tolerant) that had been experimentally exposed to short-term, long-term and inter-generational elevated CO2. Our results show differential expression of key proteins related to stress response and epigenetic markers with elevated CO2exposure. Proteins related to neurological development were also differentially expressed particularly in the long-term developmental treatment, which might be critical for juvenile development. By contrast, exposure to elevated CO2in the parental generation resulted in only three differentially expressed proteins in the offspring, revealing potential for inter-generational acclimation. Lastly, we found a distinct proteomic pattern in juveniles due to the behavioural sensitivity of parents to elevated CO2, even though the behaviour of the juvenile fish was impaired regardless of parental phenotype. Our data shows that developing juveniles are affected in their brain protein expression by elevated CO2, but the effect varies with the length of exposure as well as due to variation of parental phenotypes in the population.
Experimentally-Determined Strengths of Atom-Atom (C, N, O) Interactions Responsible for Protein Self-Assembly in Water: Applications to Folding and Other Protein Processes
Authors: Cheng Xian , Shkel Irina A. , O’Connor Kevin , Record M. Thomas
Published: May 2020

Folding and other protein self-assembly processes are driven by favorable interactions between O, N, and C unified atoms of the polypeptide backbone and sidechains. These processes are perturbed by solutes that interact with these atoms differently than water does. C=O···HN hydrogen bonding and various π-system interactions have been better-characterized structurally or by simulations than experimentally in water, and unfavorable interactions are relatively uncharacterized. To address this situation, we previously quantified interactions of alkylureas with amide and aromatic compounds, relative to interactions with water. Analysis yielded strengths of interaction of each alkylurea with unit areas of different hybridization states of unified O, N, C atoms of amide and aromatic compounds. Here, by osmometry, we quantify interactions of ten pairs of amides selected to complete this dataset. A novel analysis yields intrinsic strengths of six favorable and four unfavorable atom-atom interactions, expressed per unit area of each atom and relative to interactions with water. The most favorable interactions are sp2O - sp2C (lone pair-π, presumably n-π*), sp2C - sp2C (π-π and/or hydrophobic), sp2O-sp2N (hydrogen bonding) and sp3C-sp2C (CH-π and/or hydrophobic). Interactions of sp3C with itself (hydrophobic) and with sp2N are modestly favorable, while sp2N interactions with sp2N and with amide/aromatic sp2C are modestly unfavorable. Amide sp2O-sp2O interactions and sp2O-sp3C interactions are more unfavorable, indicating the preference of amide sp2O to interact with water. These intrinsic interaction strengths are used to predict interactions of amides with proteins and chemical effects of amides (including urea, N-ethylpyrrolidone (NEP), and polyvinyl-pyrrolidone (PVP)) on protein stability.

Significance

Quantitative information about strengths of amide nitrogen-amide oxygen hydrogen bonds and π-system and hydrophobic interactions involving amide-context sp2and/or sp3carbons is needed to assess their contributions to specificity and stability of protein folds and assemblies in water, as well as to predict or interpret how urea and other amides interact with proteins and affect protein processes. Here we obtain this information from thermodynamic measurements of interactions between small amide molecules in water and a novel analysis that determines intrinsic strengths of atom-atom interactions, relative to water and per unit area of each atom-type present in amide compounds. These findings allow prediction or interpretation of effects of any amide on protein processes from structure, and may be useful to analyze protein interfaces.
Biologically excretable AIE dots for visualizing through the marmosets intravitally: horizons in future clinical nanomedicine
Authors: Feng Zhe , Bai Siyi , Qi Ji , Sun Chaowei , Zhang Yuhuang , Yu Xiaoming , Ni Huwei , Wu Di , Fan Xiaoxiao , Xue Dingwei , Liu Shunjie , Chen Ming , Gong Junyi , Wei Peifa , He Mubin , Lam Jacky W. Y. , Li Xinjian , Tang Ben Zhong , Gao Lixia , Qian Jun
Published: May 2020

Superb reliability and biocompatibility equip aggregation-induced emission (AIE) dots with tremendous potential for fluorescence bioimaging. However, there is still a chronic lack of design instructions of excretable and bright AIE emitters. Here, we designed a kind of PEGylated AIE (OTPA-BBT) dots with strong absorption and extremely high NIR-II PLQY as 13.6%, and proposed the long-aliphatic-chain design blueprint contributing to their excretion from animal body. Assisted by the OTPA-BBT dots with bright fluorescence beyond 1100 nm and even 1500 nm (NIR-IIb), large-depth cerebral vasculature (beyond 600 μm) as well as real-time blood flowing were monitored through-thinned-skull, and noninvasive NIR-IIb imaging with rich high-spatial-frequency information gave a precise presentation of gastrointestinal tract in marmosets. Importantly, after intravenous or oral administration, the definite excretion of OTPA-BBT dots from the body was demonstrated, which showed an influential evidence of bio-safety.
Anophelesmosquitoes revealed new principles of 3D genome organization in insects
Authors: Lukyanchikova Varvara , Nuriddinov Miroslav , Belokopytova Polina , Liang Jiangtao , Reijnders Maarten J.M.F. , Ruzzante Livio , Waterhouse Robert M. , Tu Zhijian , Sharakhov Igor V. , Fishman Veniamin
Published: May 2020

Chromosomes are hierarchically folded within cell nuclei into territories, domains and subdomains, but the functional importance and evolutionary dynamics of these hierarchies are poorly defined. Here, we comprehensively profiled genome organizations of fiveAnophelesmosquito species and showed how different levels of chromatin architecture influence contacts between genomic loci. Patterns observed on Hi-C maps are associated with known cytological structures, epigenetic profiles, and gene expression levels. At the level of individual loci, we identified specific, extremely long-ranged looping interactions, conserved for ~100 million years. We showed that the mechanisms underlying these looping contacts differ from previously described Polycomb-dependent interactions and clustering of active chromatin.
The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis
Authors: Scheer Hélène , de Almeida Caroline , Ferrier Emilie , Simonnot Quentin , Poirier Laure , Pflieger David , Sement François M. , Koechler Sandrine , Piermaria Christina , Krawczyk Paweł , Mroczek Seweryn , Chicher Johana , Kuhn Lauriane , Dziembowski Andrzej , Hammann Philippe , Zuber Hélène , Gagliardi Dominique
Published: May 2020

Uridylation is a widespread modification destabilizing eukaryotic mRNAs. Yet, molecular mechanisms underlying TUTase-mediated mRNA degradation remain mostly unresolved. Here, we report that theArabidopsisTUTase URT1 participates in a molecular network connecting several translational repressors/decapping activators. URT1 directly interacts with DECAPPING 5 (DCP5), theArabidopsisortholog of human LSM14 and yeast Scd6, and this interaction connects URT1 to additional decay factors like DDX6/Dhh1-like RNA helicases. Nanopore direct RNA sequencing reveals a global role of URT1 in shaping poly(A) tail length, notably by preventing the accumulation of excessively deadenylated mRNAs. Based onin vitroandin plantadata, we propose a model that explains how URT1 could reduce the accumulation of oligo(A)-tailed mRNAs both by favoring their degradation and because 3’ terminal uridines intrinsically hinder deadenylation. Importantly, preventing the accumulation of excessively deadenylated mRNAs avoids the biogenesis of illegitimate siRNAs that silence endogenous mRNAs and perturbArabidopsisgrowth and development.
Multi-contrast Anatomical Subcortical Structures Parcellation
Authors: Bazin Pierre-Louis , Alkemade Anneke , Mulder Martijn J. , Henry Amanda G. , Forstmann Birte U.
Published: May 2020

The human subcortex is comprised of more than 450 individual nuclei which lie deep in the brain. Due to their small size and close proximity, up until now only 7% have been depicted in standard MRI atlases. Thus, the human subcortex can largely be considered as terra incognita. Here we present a new open source parcellation algorithm to automatically map the subcortex. The new algorithm has been tested on 17 prominent subcortical structures based on a large quantitative MRI dataset at 7 Tesla. It has been carefully validated against expert human raters and previous methods, and can easily be extended to other subcortical structures and applied to any quantitative MRI dataset. In sum, we hope this novel parcellation algorithm will facilitate functional and structural neuroimaging research into small subcortical nuclei and help to chart terra incognita.
Reprogramming of serine metabolism is an actionable vulnerability inFLT3-ITDdriven acute myeloid leukaemia
Authors: Bjelosevic Stefan , Gruber Emily , Newbold Andrea , Kats Lev M. , Shembrey Carolyn , Abrehart Thomas C. , Todorovski Izabela , Pomilio Giovanna , Wei Andrew H. , Gregory Gareth P. , Vervoort Stephin J. , Brown Kristin K. , Johnstone Ricky W.
Published: May 2020

Activating FMS-like tyrosine kinase 3 (FLT3) mutations occur in approximately 30% of all acute myeloid leukaemias (AMLs) and are associated with poor prognosis. The limited clinical efficacy of FLT3 inhibitor monotherapy has highlighted the need for alternative therapeutic targets and treatments for FLT3-mutant AML. Using human and murine models of MLL-rearranged AML harbouring FLT3 internal tandem duplication (FLT3-ITD) and primary patient samples, we have demonstrated that FLT3-ITD promotes serine uptake and serine synthesis via transcriptional regulation of neutral amino acid transporters (SLC1A4andSLC1A5) and genes in thede novoserine synthesis pathway (PHGDHandPSAT1). Mechanistically, dysregulation of serine metabolism in FLT3-mutant AML is dependent on the mTORC1-ATF4 axis, that drives RNA-Pol II occupancy atPHGDH, PSAT1, SLC1A4andSLC1A5. Genetic or pharmacological inhibition of thede novoserine synthesis pathway selectively inhibited the proliferation of FLT3-ITD AML cells, and this was potentiated by withdrawal of exogenous serine. Purine supplementation effectively rescued the antiproliferative effect of inhibitingde novoserine synthesis, consistent with the idea that serine fuels purine nucleotide synthesis in FLT3-mutant AML. Pharmacological inhibition of the de novo serine synthesis pathway, using the PHGDH inhibitor WQ-2101, sensitises FLT3-mutant AML cells to the standard of care chemotherapy agent cytarabine via exacerbation of DNA damage. Collectively, these data reveal new insights as to how FLT3 mutations reprogram metabolism in AML, and reveal a combination therapy strategy to improve the treatment of FLT3-mutant AML.

Statement of Significance

FLT3 mutations are common in AML and are associated with poor prognosis. We show that FLT3-ITD stimulates serine metabolism, thereby rendering FLT3-ITD leukemias dependent on serine for proliferation and survival. This metabolic dependency can be exploited pharmacologically to sensitize FLT3-mutant AML to chemotherapy.
DNA polymerase epsilon is a central coordinator of heterochromatin structure and function in Arabidopsis
Authors: Bourguet Pierre , López-González Leticia , Gómez-Zambrano Ángeles , Pélissier Thierry , Hesketh Amy , Potok Magdalena E. , Pouch-Pélissier Marie-Noëlle , Perez Magali , Da Ines Olivier , Latrasse David , White Charles I. , Jacobsen Steven E. , Benhamed Moussa , Mathieu Olivier
Published: May 2020

Background

Chromatin organizes the DNA molecule and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications must be faithfully passed on to daughter strands. There is evidence that DNA polymerases play a role in transcriptional silencing, but the extent of their contribution and how it relates to heterochromatin maintenance is unclear.

Results

We isolate a strong hypomorphic Arabidopsis thaliana mutant of the POL2A catalytic subunit of DNA polymerase epsilon and show that POL2A is required to stabilize heterochromatin silencing genome wide, likely by preventing replicative stress. We reveal that POL2A inhibits DNA methylation and histone H3 lysine 9 methylation. Hence, release of heterochromatin silencing in POL2A deficient mutants paradoxically occurs in a chromatin context of increased level of these two repressive epigenetic marks. At the nuclear level, POL2A defect is associated with fragmentation of heterochromatin.

Conclusion

These results indicate that POL2A is critical to secure both heterochromatin structure and function. We also reveal that unhindered replisome progression is required for the faithful propagation of DNA methylation through the cell cycle.
A cortico-collicular circuit for accurate orientation to shelter during escape
Authors: Campagner Dario , Vale Ruben , Tan Yu Lin , Iordanidou Panagiota , Pavón Arocas Oriol , Claudi Federico , Stempel A. Vanessa , Keshavarzi Sepiedeh , Petersen Rasmus S. , Margrie Troy W. , Branco Tiago
Published: May 2020

When faced with predatorial threats, escape towards shelter is an adaptive action that offers long-term protection against the attacker. From crustaceans to mammals, animals rely on knowledge of safe locations in the environment to instinctively execute rapid shelter-directed escape actions1,2. While previous work has identified neural mechanisms of escape initiation3–5, it is not known how the escape circuit incorporates spatial information to execute rapid flights along the most efficient route to shelter. Here we show that mouse retrosplenial cortex (RSP) and superior colliculus (SC) form a circuit that encodes shelter direction vector and is specifically required for accurately orienting to shelter during escape. Shelter direction is encoded in RSP and SC neurons in egocentric coordinates and SC shelter-direction tuning depends on RSP activity. Inactivation of the RSP-SC pathway disrupts orientation to shelter and causes escapes away from the optimal shelter-directed route, but does not lead to generic deficits in orientation or spatial navigation. We find that the RSP and SC are monosynaptically connected and form a feedforward lateral inhibition microcircuit that strongly drives the inhibitory collicular network due to higher RSP input convergence and synaptic integration efficiency in inhibitory SC neurons. This results in broad shelter direction tuning in inhibitory SC neurons and sharply tuned excitatory SC neurons. These findings are recapitulated by a biologically-constrained spiking network model where RSP input to the local SC recurrent ring architecture generates a circular shelter-direction map. We propose that this RSP-SC circuit might be specialized for generating collicular representations of memorized spatial goals that are readily accessible to the motor system during escape, or more broadly, during navigation when the goal must be reached as fast as possible.
Repurposing screen identifies Amlodipine as an inducer of PD-L1 degradation and antitumor immunity
Authors: Li Chushu , Yao Han , Wang Huanbin , Fang Jing-Yuan , Xu Jie
Published: May 2020

Cancer cell expression of PD-L1 leads to T cells exhaustion by transducing co-inhibitory signal, and further understanding the regulation of PD-L1 in cancer cells may provide additional therapeutic strategies. Here by drug repurposing screen we identified amlodipine as a potent inhibitor of PD-L1 expression in cancer cells. Further survey of calcium-associated pathways revealed calpains-dependent stabilization of the PD-L1 protein. Intracellular calcium delivered an operational signal to calpain-dependent Beclin-1 cleavage, blocking autophagic degradation of PD-L1 accumulated on recycling endosome (RE). Blocking calcium flux by amlodipine depleted PD-L1 expression and increased CD8+ T cell infiltration in tumor tissues but not in myocardium, causing dose-dependent tumor suppressionin vivo. Rescuing PD-L1 expression eliminated the effects of amlodipine, suggesting the PD-L1 dependent effect of amlodipine. These results reveal a calcium-dependent mechanism controlling PD-L1 degradation, and highlight calcium flux blockade as a potential strategy for combinatorial immunotherapy.
No evidence of phago-mixotropy in Micromonas polaris, the dominant picophytoplankton species in the Arctic
Authors: Jimenez Valeria , Burns John A. , Le Gall Florence , Not Fabrice , Vaulot Daniel
Published: May 2020

In the Arctic Ocean, the small green alga Micromonas polaris dominates pico-phytoplankton during the summer months. It has been previously hypothesized to be phago-mixotrophic (capable of bacteria ingestion) based on laboratory and field experiments. Prey uptake was analysed in several M. polaris strains isolated from different regions and depths of the Arctic Ocean. Using both fluorescent beads and fluorescently labelled bacteria as prey, we found no evidence of phago-mixotrophy in any M. polaris strain by flow cytometric measurement of prey ingestion. In addition, in silico predictions reveal that members of the genus Micromonas lack a genetic signature of phagocytotic capacity.
Influenza C and D viral load in cattle correlates with bovine respiratory disease (BRD): Emerging role of orthomyxoviruses in the pathogenesis of BRD
Authors: Nissly Ruth H. , Zaman Noriza , Ibrahim Puteri Ainaa S. , McDaniel Kaitlin , Lim Levina , Kiser Jennifer N. , Bird Ian , Chothe Shubhada K. , Bhushan Gitanjali L. , Vandegrift Kurt , Neibergs Holly J. , Kuchipudi Suresh V.
Published: May 2020

Bovine respiratory disease (BRD) is the costliest disease affecting the cattle industry globally. Despite decades of research, the pathophysiology of BRD is not yet fully understood. It is widely believed that viruses predispose cattle to bacterial infection by causing direct damage to the respiratory tract and interfering with the immune system, leading to bacterial pneumonia. BRD remains a major challenge despite extensive vaccination against all major viral pathogens associated with the disease. Orthomyxoviruses (Influenza C & D viruses), have recently been found to infect cattle throughout the United States and are implicated to play a role in BRD. Here, we use the largest cohort study to date to investigate the association of influenza viruses in cattle with BRD. Cattle (n=599) from 3 locations were individually observed and scored for respiratory symptoms using the McGuirk scoring system. Deep pharyngeal and mid-nasal swabs were collected from each animal and were tested quantitatively for bovine viral diarrhea virus, bovine herpesvirus 1, bovine respiratory syncytial virus, bovine coronavirus, influenza C virus (ICV) and influenza D virus (IDV) by real-time PCR. Cattle that have higher viral loads of IDV and ICV also have greater numbers of co-infecting viruses than controls. More strikingly, in BRD-symptomatic cattle, the geometric mean of detectable IDV viral RNA was nearly 2 logs higher in co-infected animals (1.30×104) than those singly infected with IDV (2.19×102). This is strong evidence that viral coinfections can lead to higher replication of IDV. Our results strongly suggest that orthomyxoviruses may be significant contributors to BRD.
Towards the Target: Tilorone, Quinacrine and Pyronaridine Bind to Ebola Virus Glycoprotein
Authors: Lane Thomas R. , Ekins Sean
Published: May 2020

Pyronaridine, tilorone and quinacrine were recently identified by a machine learning model and demonstratedin vitroandin vivoactivity against Ebola virus (EBOV) and represent viable candidates for drug repurposing. These drugs were docked into the crystal structure of the ebola glycoprotein and then experimentally validatedin vitroto generate Kd values for tilorone (0.73 μM) pyronaridine (7.34 μM), and quinacrine (7.55 μM). These are more potent than the previously reported toremifene (16 μM).
Phenotypic changes of bacteria through opportunity and global methylation leads to antibiotic resistance
Authors: Neerathilingam Muniasamy , Mysore Sumukh , Bairy Sneha , Chandola Chetan , Varadharajan Venkadeshwari , Rajasekharan Ram
Published: May 2020

The antibiotic stress on bacteria leads to initiation of adaptive mechanisms, including exploiting the available opportunity, if any, for cell survival. In order to use the opportunity for survival while under threat, the microbe undergoes various mechanisms which are not completely known e.g. homologous recombination, horizontal gene transfer etc. Our aim is to understand the adaptive mechanism for cell survival during stress, especially antibiotic stress, inE. coliin the presence of opportunity. Understanding this mechanism in bacteria that gained resistance will help in identifying alternative survival pathways. By subjecting a recombination deficient (ΔRecA) strain of bacteria to antibiotic stress, we expected cell death, due to its inability to repair DNA damage (1, 2). Here we show that providing an opportunity in the form of an antibiotic resistance gene with homologous ends aids bacterial survival. There was 3-fold increase in cell envelope thickness along with 2.5-fold increase in phosphatidylethanolamine (PE) content, and enhanced antibiotic resistance to >4000µg/mL (Kan). We observed genome-wide alteration of methylation pattern that lead to changes in transcriptome, proteome, lipidome, and metabolite level, thus, leading to morphological and physiological changes. We prove that global methylation helps in survival of bacteria under stress that changes essential pathways like energy, cell envelope, lipids, amino acids acid, etc. leading to over production of cell wall components including synthesis of PE. By inhibiting the activity of methyltransferase, it is noticed that there is reduction in PE synthesis in agreement with demethylation. This proves that the phenotypic changes are caused due to the global methylation, and also demonstrates that demethylation could be used as a strategy to prevent antibiotic resistance in microbes.

One Sentence Summary

Global methylation determines the survival of bacteria to gain the antimicrobial resistance with an opportunity
Comparative analysis of macrophage post-translational modifications during intracellular bacterial pathogen infection
Authors: Johnson Jeffrey R. , Parry Trevor , Repasy Teresa , Geiger Kristina M. , Verschueren Erik , Budzik Jonathan M. , Jimenez-Morales David , Newton Billy W. , Powell Emma , Coscoy Laurent , Portnoy Daniel A. , Krogan Nevan J. , Cox Jeffery S.
Published: May 2020

Macrophages activate robust antimicrobial functions upon engulfing virulent bacteria, yet a wide array of pathogens paradoxically thrive within these innate immune cells. To probe the pathogen-macrophage interface, we used proteomics to comprehensively quantify changes in post-translational modifications (PTMs) of host proteins during infection with three evolutionarily diverse intracellular pathogens:Mycobacterium tuberculosis, Salmonella entericaserovar Typhimurium, andListeria monocytogenes. Comparing global phosphorylation and ubiquitylation patterns identified extensive reprogramming of cellular pathways during infection, with ubiquitylation patterns revealing unique pathogen-specific molecular response signatures undetectable by transcriptional profiling. Differential PTM changes during infection with attenuatedM. tuberculosiscells lacking the ESX-1 virulence determinant revealed extensive modification of phagosome dynamics and antiviral type I interferon activation. We found thatM. tuberculosis-mediated activation of the antiviral OASL1-IRF7 pathway promotes bacterial replication, uncovering a new mechanism of virus-bacterial synergy. Our data reveals remarkable specificity in innate cellular responses to complex stimuli and provides a resource for deeper understanding of host-pathogen interactions.
Morphological Cell Profiling of SARS-CoV-2 Infection Identifies Drug Repurposing Candidates for COVID-19
Authors: Mirabelli Carmen , Wotring Jesse W. , Zhang Charles J. , McCarty Sean M. , Fursmidt Reid , Frum Tristan , Kadambi Namrata S. , Amin Anya T. , O’Meara Teresa R. , Pretto Carla D. , Spence Jason R. , Huang Jessie , Alysandratos Konstantinos D. , Kotton Darrell N. , Handelman Samuel K. , Wobus Christiane E. , Weatherwax Kevin J. , Mashour George A. , O’Meara Matthew J. , Sexton Jonathan Z.
Published: May 2020

The global spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the associated disease COVID-19, requires therapeutic interventions that can be rapidly identified and translated to clinical care. Traditional drug discovery methods have a >90% failure rate and can take 10-15 years from target identification to clinical use. In contrast, drug repurposing can significantly accelerate translation. We developed a quantitative high-throughput screen to identify efficacious agents against SARS-CoV-2. From a library of 1,425 FDA-approved compounds and clinical candidates, we identified 17 dose-responsive compounds within vitroantiviral efficacy in human liver Huh7 cells and confirmed antiviral efficacy in human colon carcinoma Caco-2, human prostate adenocarcinoma LNCaP, and in a physiologic relevant model of alveolar epithelial type 2 cells (iAEC2s). Additionally, we found that inhibitors of the Ras/Raf/MEK/ERK signaling pathway exacerbate SARS-CoV-2 infectionin vitro.Notably, we discovered that lactoferrin, a glycoprotein classically found in secretory fluids, including mammalian milk, inhibits SARS-CoV-2 infection in the nanomolar range in all cell models with multiple modes of action, including blockage of virus attachment to cellular heparan sulfate and enhancement of interferon responses. Given its safety profile, lactoferrin is a readily translatable therapeutic option for the management of COVID-19.

IMPORTANCE

Since its emergence in China in December 2019, SARS-CoV-2 has caused a global pandemic. Repurposing of FDA-approved drugs is a promising strategy for identifying rapidly deployable treatments for COVID-19. Herein, we developed a pipeline for quantitative high-throughput image-based screening of SARS-CoV-2 infection in human cells that led to the identification of several FDA-approved drugs and clinical candidates within vitroantiviral activity.
The linear ubiquitin chain assembly complex LUBAC generates heterotypic ubiquitin chains
Authors: Carvajal Alan Rodriguez , Diaz Carlos Gomez , Vogel Antonia , Sonn-Segev Adar , Schodl Katrin , Deszcz Luiza , Orban-Nemeth Zsuzsanna , Sakamoto Shinji , Mechtler Karl , Kukura Philipp , Clausen Tim , Haselbach David , Ikeda Fumiyo
Published: May 2020

The linear ubiquitin chain assembly complex (LUBAC) is the only known ubiquitin ligase that generates linear/Met1-linked ubiquitin chains. One of the LUBAC components, HOIL-1L, was recently shown to catalyse oxyester bond formation between the C-terminus of ubiquitin and some substrates. However, oxyester bond formation in the context of LUBAC has not been directly observed. We present the first 3D reconstruction of LUBAC obtained by electron microscopy and report its generation of heterotypic ubiquitin chains containing linear linkages with oxyester-linked branches. We found that addition of the oxyester-bound branches depends on HOIL-1L catalytic activity. We suggest a coordinated ubiquitin relay mechanism between the HOIP and HOIL-1L ligases supported by cross-linking mass spectrometry data, which show proximity between the catalytic RBR domains. Mutations in the linear ubiquitin chain-binding NZF domain of HOIL-1L reduces chain branching confirming its role in the process. In cells, these heterotypic chains were induced by TNF. In conclusion, we demonstrate that LUBAC assembles heterotypic ubiquitin chains with linear and oxyester-linked branches by the concerted action of HOIP and HOIL-1L.
Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease
Authors: Douangamath Alice , Fearon Daren , Gehrtz Paul , Krojer Tobias , Lukacik Petra , Owen C. David , Resnick Efrat , Strain-Damerell Claire , Aimon Anthony , Ábrányi-Balogh Péter , Brandaõ-Neto José , Carbery Anna , Davison Gemma , Dias Alexandre , Downes Thomas D , Dunnett Louise , Fairhead Michael , Firth James D. , Jones S. Paul , Keely Aaron , Keserü György M. , Klein Hanna F , Martin Mathew P. , Noble Martin E. M. , O’Brien Peter , Powell Ailsa , Reddi Rambabu , Skyner Rachael , Snee Matthew , Waring Michael J. , Wild Conor , London Nir , von Delft Frank , Walsh Martin A.
Published: May 2020

COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments was progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.
Functional microRNA targetome undergoes degeneration-induced shift in the retina
Authors: Chu-Tan Joshua A. , Feng Zhi-Ping , Wooff Yvette , Cioanca Adrian V. , Schumann Ulrike , Aggio-Bruce Riemke , Patel Hardip , Rutar Matt , Hannan Katherine , Panov Konstantin , Provis Jan , Natoli Riccardo
Published: May 2020

MicroRNA (miRNA) play a significant role in the pathogenesis of complex neurodegenerative diseases, including age-related macular degeneration, acting as post-transcriptional gene suppressors through their association with argonaute (AGO) protein family members. However, to understand their role in disease, investigation into the regulatory nature of miRNA with their targets is required. To identify the active-miRnome-targetome interactions in the degenerating retina, AGO2 HITS-CLIP was performed using a mouse model of retinal degeneration. Analysis revealed a similar miRnome between healthy and damaged retinas, however, a shift in the active targetome was observed. This shift was also demonstrated by a change in the seed binding regions of miR-124-3p, the most abundant retinal miRNA loaded in AGO2. Following damage, AGO2 was localised to the inner retinal layers indicating a locational miRNA response to retinal damage. This study provides important insight into the alteration of miRNA regulatory activity that occurs as a response to retinal degeneration.
Osteoconductive material of a newly developed resin modified glass ionomer cement containing bioactive glasses for biomedical purposes
Authors: Ana Ika Dewi
Published: May 2020

Hybridization of resin modified- glass ionomer cement (RMGIC) and bioactive glass (BAG) may result higher mechanical strength and resistance to disintegration, while less contain of polyacrylic acid would lead to bioactivity of the cement. In the present study we investigated the effect of BAG from the CaSiO3-Ca3(PO4)2system addition to the bioactivity of RMGIC. The BAG containing 10, 15, and 20% of P2O5(denoted as CSP10, 15, and 20) were used in the study to modify the powder of RMGIC, with apatite wollastonite (AWG) was chosen for a comparison. The surface bioactivity was assessed using XRD, FT-IR, and SEM analysis after specimen immersion in the simulated body fluid (SBF). Measurement of Ca, P, F, Sr, and Al was conducted for the remaining SBF. Cells studies were done to evaluate cell attachment, proliferation, and differentiation on the RMGIC containing BAG compared to the one without BAG. Results of Sr and Al analysis lead to the conclusion that addition of BAG may not influence stability of the matrix of the cement. It was also confirmed that addition of bioactive glass was positive factor indicating excellent ions exchange in SBF and spontaneous growth of apatite by consuming the Ca and P ions in the surrounding fluid. The ability of osteoblasts differentiation on the four types of bioactive cements were higher than that of RMGIC without BAG. These results might provide novel insights into the development of a new generation of osteoconductive biomedical materials.
Defining a critical enhancer near Nanog using chromatin-focused approaches identifies RNA Pol II recruitment as required for expression
Authors: Agrawal Puja , Blinka Steven , Pulakanti Kirthi , Reimer Michael H. , Rao Sridhar
Published: May 2020

Transcriptional enhancers have been defined by their ability to operate independent of distance and orientation in plasmid-based reporter assays of gene expression. Currently, histone marks are used heavily to identify and define enhancers but both methods do not consider the endogenous role of an enhancer in the context of native chromatin. We employed a combination of genomic editing, single cell analyses, and sequencing approaches to investigate aNanog-associatedcis-regulatory element (CRE) which has been reported by others to be either an alternative promoter or a super-enhancer (SE). We first demonstrate both distance and orientation independence in native chromatin, eliminating the issues raised with plasmid-based approaches. We also demonstrate that the dominant SE modulatesNanogglobally and operates by recruiting and/or initiating RNA Polymerase II. Our studies have important implications to how transcriptional enhancers are defined and how they regulate gene expression.

AUTHOR SUMMARY

Different DNA elements help regulate the levels of gene expression. One such element are enhancers, short sequences that interact with genes to modulate levels of expression but can operate over large distances. Previously, these sequences were defined by their ability to regulate expression independent of their distance from a gene and the orientation of the sequence. However, these characteristics were found using techniques that did not recapitulate the native environment. Here, we have shown that an enhancer of one gene is indeed an enhancer by testing its distance and orientation-independence within the native environment. We also show that the mechanisms by which the enhancer is regulating expression is by controlling the levels of RNA Polymerase II at a gene. RNA Polymerase II is the protein that converts the gene sequence to a form usable by a cell, called mRNA. This is interesting because while this has been considered historically the main way enhancers operate, more recent work has focused on other, later regulatory steps involved in controlling mRNA production.
Evaluation of Antibacterial and Antioxidant activity of methanol crude extract ofAspilia africanaleaves: an in vitro approach
Authors: Oluwarinu Adepoju , Omololu-Aso
Published: May 2020

Aspilia africana(Compositae) is one of such plants considered of great importance in pharmacopeia of traditional medicine. Its leaf is widely used in ethnomedicinal practices in tropical Africa because of its ability to stop bleeding and promote rapid healing of wounds. This study was carried out on the leaf part to determine its antimicrobial and antioxidant potentials of its leaf methanol extract. The methanolic extract of the leaf was subjected to preliminary phytochemical screening and it indicated the presence of saponins, tannin, resin, phlobatannins, and phenols. Thein-vitroantibacterial test of the methanol crude extract using agar well diffusion method showed broad-spectrum activity with minimum bactericidal concentration of 30, 75 mg/mL forKlebsiella pneumonia, and Bacillus subtilisrespectively.In-vitroantioxidant activities using 2, 2–diphenyl-1-picrylhydrazyl assay indicate that the methanol leaves extract had higher activity than of 92.23 µg/mL compared to standard drugs (Ascorbic acid 1.07mg/mL) and IC50at 4.66. This study concluded thatAspilia africanamethanol crude extract exhibits dosage-dependent antioxidant potential and could be further explored if it’s are in pure form.