bluuebunny/crossref_metadata_2025 huggingface dataset:
The combined action of Esrrb and Nr5a2 is essential for naïve pluripotency
Authors: Festuccia Nicola , Owens Nick , Chervova Almira , Dubois Agnès , Navarro Pablo
Published: June 2020

The maintenance of pluripotency in mouse embryonic stem cells (ESCs) is governed by the action of an interconnected network of transcription factors. Among them, only Oct4 and Sox2 have been shown to be strictly required for the self-renewal of ESCs and pluripotency, particularly in culture conditions where differentiation cues are chemically inhibited. Here, we report that the conjunct activity of two orphan nuclear receptors, Esrrb and Nr5a2, parallels the importance of that of Oct4 and Sox2 in naïve ESCs. By occupying a large common set of regulatory elements, these two factors control the binding of Oct4, Sox2 and Nanog to DNA. Consequently, in their absence the pluripotency network collapses and the transcriptome is substantially deregulated, leading to the differentiation of ESCs. Altogether, this work identifies orphan nuclear receptors, previously thought to be performing supportive functions, as a new set of core regulators of naïve pluripotency.
Bidirectional introgression betweenBetula tianshanicaandBetula microphyllaand its implications for conservation
Authors: Ding Junyi , Hua Donglai , Borrell James S. , Buggs Richard J.A. , Wang Luwei , Wang Feifei , Li Zheng , Wang Nian
Published: June 2020

Molecular markers can allow us to differentiate species that occupy a morphological continuum, and detect patterns of allele sharing that can help us understand the dynamics of geographic zones where they meet.Betula microphyllais a declining wetland species in NW China that forms a continuum of leaf morphology with its relativeBetula tianshanica.

We use ecological niche models (ENM) to predict the distribution ofB. microphylla, B. tianshanicaand the more commonly occurringB. platyphylla. We use restriction-site associated DNA sequencing and SSRs to resolve their genetic structure and patterns of allele sharing.

ENM predicted an expansion of suitable range ofB. tianshanicaintoB. microphyllasince the Last Glacial Maximum and the contraction ofB. microphylla’srange in the future. We resolved the species identification of some intermediate morphotypes. We found signatures of bidirectional introgression betweenB. microphyllaandB. tianshanicawith SNPs showing more admixture than SSRs. Introgression fromB. microphyllaintoB. tianshanicawas greater in the Tianshan Mountains where the two species have occurred in proximity. Unexpectedly, introgression fromB. tianshanicaintoB. microphyllawas widespread in the Altay Mountains where there are no records ofB. tianshanicaoccurrence.

This presence ofB. tianshanica-derivedalleles far beyond the species’ current range could be due to unexpectedly high pollen flow, undiscovered populations ofB. tianshanicain the region, incomplete lineage sorting, or selection for adaptive introgression inB. microphylla. These different interpretations have contrasting implications for the conservation ofB. microphylla.
TheDrosophilaIndividual Activity Monitoring and Detection System (DIAMonDS)
Authors: Seong Ki-Hyeon , Matsumura Taishi , Shimada-Niwa Yuko , Niwa Ryusuke , Kang Siu
Published: June 2020

Here, we have developed DIAMonDS (DrosophilaIndividual Activity Monitoring and Detection System) comprising time-lapse imaging by a charge-coupled device (CCD) flatbed scanner and Sapphire, a novel algorithm and web application. DIAMonDS automatically and sequentially identified the transition time points of multiple life cycle events such as pupariation, eclosion, and death in individual flies at high temporal resolution and on a large scale. DIAMonDS performed simultaneous multiple scans to measure individual deaths (≤ 1,152 flies per scanner) and pupariation and eclosion timings (≤ 288 flies per scanner) under various chemical exposures, environmental conditions, and genetic backgrounds. DIAMonDS correctly identified 74–85% of the pupariation and eclosion events and ∼92% of the death events within ±10 scanning frames. This system is a powerful tool for studying the influences of genetic and environmental factors on fruit flies and efficient, high-throughput genetic and chemical screening in drug discovery.
Paternal obesity and epigenetic inheritance of breast cancer: The role of systemic effects and transmission to the second generation
Authors: Fontelles Camile C. , da Cruz Raquel Santana , Gonsiewski Alexandra K. , Barin Ersilia , Tekmen Volkan , Jin Lu , Cruz M. Idalia , Loudig Olivier , Warri Anni , de Assis Sonia
Published: June 2020

Background

While genetics explains some familial breast cancer cases, we showed that environmentally-induced epigenetic inheritance of breast cancer can also occur in rodent models. We previously reported that paternal consumption of a high-fat diet and ensuing obesity increased breast cancer susceptibility in the offspring (F1). Nevertheless, it is still unclear whether paternal-induced programming of breast cancer in daughters is associated with systemic alterations or mammary epithelium-specific factors. It also remains to be determined whether the ancestrally programmed breast cancer predisposition in F1 progeny can be transmitted to subsequent generations.

Methods

Male mice (F0) were fed either a control (CO) diet or an obesity-inducing diet (OID) for seven weeks and then mated with female mice (F0) reared on a CO diet. The resulting offspring (F1), also exclusively fed CO diet, were either used for mammary gland and tumor transplantation surgeries or to generate the F2 generation. To induce the mammary tumors, female mice were treated with 7,12 dimethylbenz[a]anthracene (DMBA). Total RNA extracted from F0 or F1 males sperm was used for small RNA-Seq analysis.

Results

Mammary glands from F1 CO female offspring exhibited enhanced development when transplanted into OID females [OID(CO-MG)], as shown by higher mammary gland area, epithelial branching and elongation, compared to CO females that received a CO mammary gland [CO(CO-MG)]. Similarly, mammary tumors from F1 CO female offspring transplanted into OID females [OID(CO.T)] displayed improved growth with a higher proliferation/apoptosis rate. We also found that granddaughters (F2) from the OID grand-paternal germline showed accelerated tumor growth compared to COxCO granddaughters (F2). Transmission of breast cancer predisposition to the F2 generation through OID male germline was associated with alterations in specific sperm tRNA fragments (tRF) in both F0 and F1 males.

Conclusions

Our findings indicate that systemic metabolic and mammary stromal alterations are the most significant contributors to paternal programming of mammary gland development and cancer predisposition in female offspring rather than mammary epithelium confined factors. Our data also show breast cancer predisposition in OID daughters can be transmitted to subsequent generations and could explain some familial cancers, if confirmed in humans.
Monocyte-specific changes in gene expression implicateLACTB2andPLIN2in Alzheimer’s disease
Authors: Harwood Janet C. , Leonenko Ganna , Sims Rebecca , Escott-Price Valentina , Williams Julie , Holmans Peter
Published: June 2020

More than 50 genetic loci have been identified as being associated with Alzheimer’s disease (AD) from genome-wide association studies (GWAS) and many of these are involved in immune pathways and lipid metabolism. Therefore, we performed a transcriptome-wide association study (TWAS) of immune-relevant cells, to study the mis-regulation of genes implicated in AD. We used expression and genetic data from naive and induced CD14+ monocytes and two GWAS of AD to study genetically controlled gene expression in monocytes at different stages of differentiation and compared the results with those from TWAS of brain and blood. We identified nine genes with statistically independent TWAS signals, seven are known AD risk genes from GWAS:BIN1, PTK2B, SPI1, MS4A4A, MS4A6E, APOEandPVRand two,LACTB2andPLIN2/ADRP, are novel candidate genes for AD. Three genes,SPI1, PLIN2andLACTB2, are TWAS significant specifically in monocytes. LACTB2 is a mitochondrial endoribonuclease and PLIN2/ADRP associates with intracellular neutral lipid storage droplets (LSDs) which have been shown to play a role in the regulation of the immune response. Notably,LACTB2andPLIN2were not detected from GWAS alone.
sPLINK: A Federated, Privacy-Preserving Tool as a Robust Alternative to Meta-Analysis in Genome-Wide Association Studies
Authors: Nasirigerdeh Reza , Torkzadehmahani Reihaneh , Matschinske Julian , Frisch Tobias , List Markus , Späth Julian , Weiß Stefan , Völker Uwe , Heider Dominik , Wenke Nina Kerstin , Kacprowski Tim , Baumbach Jan
Published: June 2020

Genome-wide association studies (GWAS) have been widely used to unravel connections between genetic variants and diseases. Larger sample sizes in GWAS can lead to discovering more associations and more accurate genetic predictors. However, sharing and combining distributed genomic data to increase the sample size is often challenging or even impossible due to privacy concerns and privacy protection laws such as the GDPR. While meta-analysis has been established as an effective approach to combine summary statistics of several GWAS, its accuracy can be attenuated in the presence of cross-study heterogeneity. Here, we presentsPLINK(safe PLINK), a user-friendly tool, which performs federated GWAS on distributed datasets while preserving the privacy of data and the accuracy of the results.sPLINKneither exchanges raw data nor does it rely on summary statistics. Instead, it performs model training in a federated manner, communicating only model parameters between cohorts and a central server. We verify that the federated results fromsPLINKare the same as those from aggregated analyses conducted withPLINK. We demonstrate thatsPLINKis robust against heterogeneous data (phenotype and confounding factors) distributions across cohorts while existing meta-analysis tools considerably lose accuracy in such scenarios. We also show thatsPLINKachieves practical runtime, in order of minutes or hours, and acceptable network bandwidth consumption for chi-square and linear/logistic regression tests. Federated analysis withsPLINK, thus, has the potential to replace meta-analysis as the gold standard for collaborative GWAS. The user-friendly, readily usablesPLINKtool is available athttps://exbio.wzw.tum.de/splink.
Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica)
Authors: Downey-Wall Alan M. , Cameron Louise P. , Ford Brett M. , McNally Elise M. , Venkataraman Yaamini R. , Roberts Steven B. , Ries Justin B. , Lotterhos Katie E.
Published: June 2020

Early evidence suggests that DNA methylation can mediate phenotypic responses of marine calcifying species to ocean acidification (OA). Few studies, however, have explicitly studied DNA methylation in calcifying tissues through time. Here, we examined the phenotypic and molecular responses in the extrapallial fluid and mantle (fluid and tissue at the calcification site) in the Eastern oyster (Crassostrea virginica) exposed to experimental OA over 80 days. Oysters were reared under three experimental pCO2treatments (‘control’, 580 μatm; ‘moderate OA’, 1000 uatm; ‘high OA’, 2800 μatm) and sampled at 6 time points (24 hours - 80 days). We found that high OA initially induced changes in the pH of the extrapallial fluid (pHEPF) relative to the external seawater, but the magnitude of this difference was highest at 9 days and diminished over time. Calcification rates were significantly lower in the high OA treatment compared to the other treatments. To explore how oysters regulate their extrapallial fluid, gene expression and DNA methylation were examined in the mantle-edge tissue of oysters from day 9 and 80 in the control and high OA treatments. Mantle tissue mounted a significant global molecular response (both in the transcriptome and methylome) to OA that shifted through time. Although we did not find individual genes that were significantly differentially expressed to OA, the pHEPFwas correlated with the eigengene expression of several co-expressed gene clusters. A small number of OA-induced differentially methylated loci were discovered, which corresponded with a weak association between OA-induced changes in genome-wide gene body DNA methylation and gene expression. Gene body methylation, however, was not significantly correlated with the eigengene expression of pHEPFcorrelated gene clusters. These results suggest that inC. virginica, OA induces a subtle response in a large number of genes, but also indicates that plasticity at the molecular level may be limited. Our study highlights the need to re-assess the plasticity of tissue-specific molecular responses in marine calcifiers, as well as the role of DNA methylation and gene expression in mediating physiological and biomineralization responses to OA.
From gas to sugar: Trehalose production inCupriavidus necatorfrom CO2and hydrogen gas
Authors: Löwe Hannes , Beentjes Marleen , Pflüger-Grau Katharina , Kremling Andreas
Published: June 2020

The paradigm of a fossil based, non-renewable economy will have to change in the future due to environmental concerns and the inevitable depletion of resources. Therefore, the way we produce and consume chemicals has to be rethought: The bio-economy offers such a concept for the sustainable production of commodity chemicals using waste streams or renewable electricity and CO2. Residual biomass or organic wastes can be gasified to energy rich mixtures that in turn can be used for synthesis gas fermentation.

Within this scope, we present a new process for the production of trehalose from gaseous substrates with the hydrogen-oxidizing bacteriumCupriavidus necatorH16. We first show thatC. necatoris a natural producer of trehalose, accumulating up to 3.6% of its cell dry weight as trehalose when stressed with 150 mM sodium chloride. Bioinformatic investigations revealed a so far unknown mode of trehalose and glycogen metabolism in this organism. Next, we evaluated different concepts for the secretion of trehalose and found that expression of the sugar efflux transporter A (setA) fromEscherichia coliwas able to lead to a trehalose-leaky phenotype. Finally, we characterized the strain under autotrophic conditions using a H2/CO2/O2-mixture and other substrates. Even without overexpressing trehalose synthesis genes, titers of 0.47 g/L and yields of around 10% were reached, which shows the great potential of this process.

Taken together, this process represents a new way to produce sugars with a higher areal efficiency than photosynthesis by crop plants. With further metabolic engineering, we anticipate an application of this technology for the renewable production of trehalose and other sugars, as well as for the synthesis of13C-labeled sugars.

Graphical abstract
Pain sensitivity does not differ between obese and healthy weight individuals
Authors: Emerson Nichole M. , Nahman-Averbuch Hadas , Coghill Robert C.
Published: June 2020

There is emerging evidence suggesting a relationship between obesity and chronic pain. We investigated whether pain-free obese individuals display altered pain responses to acute noxious stimuli, thus raising the possibility of greater pain sensitivity and potential susceptibility for chronic pain development. Psychophysical and anthropometric data were collected from 39 individuals with an obese body mass index (BMI) classification (BMI≥30) and 40 age/sex-matched individuals of a healthy BMI (BMI<24.9). Since BMI may be an inaccurate index of obesity, additional anthropometric parameters of central adiposity, and percent body fat (BF%) were examined. Pain responses to supra-threshold noxious heat and cold stimuli were examined. Subjects provided pain intensity and unpleasantness ratings to noxious heat (49°C) applied at varying durations (5s, 12s, 30s) and locations (ventral forearm/lower leg). Cold pain ratings, thresholds, and tolerances were obtained following immersion of the hand in a cold-water bath (0-2°C). Between-group differences in pain responses, as well as relationships between pain responses and obesity parameters were examined. Importantly, confounds that may influence pain such as anxiety, depression, impulsivity, sleepiness, and quality of life were assessed. No between-group differences in pain sensitivity to noxious heat and cold stimuli were found. After controlling for sex, no relationships were found between BMI, central adiposity, or BF% and pain responses to noxious heat or cold stimuli. These results indicate that obesity, BF%, and central adiposity have little influence on pain sensitivity in obese individuals. Accordingly, it is unlikely that obesity alone increases susceptibility for chronic pain development via amplification of nociceptive processes.
Structural basis of ribosomal RNA transcription regulation
Authors: Shin Yeonoh , Qayyum M. Zuhaib , Pupov Danil , Esyunina Daria , Kulbachinskiy Andrey , Murakami Katsuhiko S.
Published: June 2020

Ribosomal RNA (rRNA) is the most highly expressed gene in rapidly growing bacteria and is drastically downregulated under stress conditions by the global transcriptional regulator DksA and the alarmone ppGpp. To reveal the mechanism of highly regulated rRNA transcription, we determined cryo-electron microscopy structures of theEscherichia coliRNA polymerase (RNAP) σ70holoenzyme at different steps of rRNA promoter recognition with and without DksA/ppGpp. RNAP contacts the UP element of rRNA promoter using the dimerized α subunit carboxyl-terminal domain and scrunches the template DNA with the σfinger and β’lid to select a transcription start site favorable for rRNA expression. Promoter DNA binding to RNAP induces conformational change of the σ domain 2 that opens a gate for DNA loading and ejects σ1.1from the RNAP cleft to facilitate open complex formation. DksA/ppGpp binding to RNAP also opens the DNA loading gate, but it is not coupled to σ1.1ejection and impedes the open complex formation of the rRNA promoter due to its G+C rich discriminator sequence. Mutations in σ1.1or the β’lid stabilize the RNAP and rRNA promoter complex and decrease its sensitivity to DksA/ppGpp. These results provide a molecular basis for exceptionally active rRNA transcription and for its vulnerability to DksA/ppGpp.
An innovative approach for HLA typing, molecular tumor testing and the validation of tumor exclusive antigens
Authors: Ghosh Michael , Bichmann Leon , Scheid Jonas , Güler Gizem , Schuster Heiko , Di Marco Moreno , Marcu Ana , Beyer Meret , Nelde Annika , Freudenmann Lena K. , Mühlenbruch Lena , Löffler Markus W. , Kohlbacher Oliver , Rammensee Hans-Georg , Stevanović Stefan
Published: June 2020

Disclaimer

This manuscript has been withdrawn by the corresponding author, as it was submitted and made public in bioRxiv without knowledge and the full consent of all the authors listed. The co-authors are therefore not responsible for the contents of this manuscript. For this reason, the submitting author has chosen to withdraw this preprint as a precautionary measure and would like to state that this work should not be cited as a reference. For any related questions that may arise, please contact the corresponding author.
Overproduction of the AlgT sigma factor is lethal to mucoidPseudomonas aeruginosa
Authors: Cross Ashley R. , Raghuram Vishnu , Wang Zihuan , Dey Debayan , Goldberg Joanna B.
Published: June 2020

Pseudomonas aeruginosaisolates from chronic lung infections often overproduce alginate, giving rise to the mucoid phenotype. Isolation of mucoid strains from chronic lung infections correlates with a poor patient outcome. The most common mutation that causes the mucoid phenotype is calledmucA22and results in a truncated form of the anti-sigma factor MucA that is continuously subjected to proteolysis. When a functional MucA is absent, the cognate sigma factor, AlgT, is no longer sequestered and continuously transcribes the alginate biosynthesis operon leading to alginate overproduction. In this work, we report that in the absence of wild-type MucA, providing exogenous AlgT is toxic. This is intriguing since mucoid strains endogenously possess high levels of AlgT. Furthermore, we show that suppressors of toxic AlgT production have mutations inmucP, a protease involved in MucA degradation, and provide the first atomistic model of MucP. Our findings support a model where mutations inmucPstabilize the truncated form of MucA22 rendering it functional and therefore able to reduce toxicity by properly sequestering AlgT.

IMPORTANCE

Pseudomonas aeruginosais an opportunistic bacterial pathogen capable of causing chronic lung infections. Phenotypes important for the long-term persistence and adaption to this unique lung ecosystem are largely regulated by the AlgT sigma factor. Chronic infection isolates often contain mutations in the anti-sigma factormucAresulting in uncontrolled AlgT and continuous production of alginate, in addition to the expression of ~300 additional genes includingalgTitself. Here we report that in the absence of wild-type MucA, AlgT overproduction is lethal and that suppressors of toxic AlgT production have mutations in the MucA protease, MucP. Since AlgT contributes to the establishment of chronic infections, understanding how AlgT is regulated will provide vital information on howP. aeruginosais capable of causing long-term infections.
Comparison of different linear-combination modelling algorithms for short-TE proton spectra
Authors: Zöllner Helge J. , Považan Michal , Hui Steve C. N. , Tapper Sofie , Edden Richard A. E. , Oeltzschner Georg
Published: June 2020

Short-TE proton MRS is used to study metabolism in the human brain. Common analysis methods model the data as linear combination of metabolite basis spectra. This large-scale multi-site study compares the levels of the four major metabolite complexes in short-TE spectra estimated by three linear-combination modelling (LCM) algorithms.

277 medial parietal lobe short-TE PRESS spectra (TE = 35 ms) from a recent 3T multi-site study were pre-processed with the Osprey software. The resulting spectra were modelled with Osprey, Tarquin and LCModel, using the same three vendor-specific basis sets (GE, Philips, and Siemens) for each algorithm. Levels of total N-acetylaspartate (tNAA), total choline (tCho), myoinositol (mI), and glutamate+glutamine (Glx) were quantified with respect to total creatine (tCr).

Group means and CVs of metabolite estimates agreed well for tNAA and tCho across vendors and algorithms, but substantially less so for Glx and mI, with mI systematically estimated lower by Tarquin. The cohort mean coefficient of determination for all pairs of LCM algorithms across all datasets and metabolites was, indicating generally only moderate agreement of individual metabolite estimates between algorithms. There was a significant correlation between local baseline amplitude and metabolite estimates (cohort mean).

While mean estimates of major metabolite complexes broadly agree between linear-combination modelling algorithms at group level, correlations between algorithms are only weak-to-moderate, despite standardized pre-processing, a large sample of young, healthy and cooperative subjects, and high spectral quality. These findings raise concerns about the comparability of MRS studies, which typically use one LCM software and much smaller sample sizes.

Graphical Abstract

Three linear-combination algorithms (Osprey, Tarquin and LCMode) were used to quantify the levels of tNAA, tCho, mI, and Glx in 277 short-TE PRESS. Group means and CVs of metabolite estimates agreed well for tNAA and tCho, but substantially less so for Glx and mI with a cohort mean correlation coefficient of, indicating moderate agreement between algorithms. These findings raise concerns about the comparability of MRS studies, which typically use one LCM software and much smaller sample sizes.
Speech perception under the tent: A domain-general predictive role for the cerebellum
Authors: Skipper Jeremy I , Lametti Daniel R
Published: June 2020

The role of the cerebellum in speech perception remains a mystery. Given its uniform architecture, we tested the hypothesis that it implements a domain-general mechanism whose role in speech is determined by connectivity. We collated all neuroimaging studies reporting cerebellar activity in the Neurosynth database (n = 8,206). From this set, we found all studies involving passive speech and sound perception (n = 72, 64% speech, 12.5% sounds, 12.5% music, and 11% tones) and speech production and articulation (n = 175). Standard and coactivation neuroimaging meta-analyses were used to compare cerebellar and associated cortical activations between passive perception and production. We found distinct regions of perception-and production-related activity in the cerebellum and regions of perception-production overlap. Each of these regions had distinct patterns of cortico-cerebellar connectivity. To test for domain generality versus specificity, we identified all psychological and task-related terms in the Neurosynth database that predicted activity in cerebellar regions associated with passive perception and production. Regions in the cerebellum activated by speech perception were associated with domain-general terms related to prediction. One hallmark of predictive processing is metabolic savings (i.e., decreases in neural activity when events are predicted). To test the hypothesis that the cerebellum plays a predictive role in speech perception, we examined cortical activation between studies reporting cerebellar activation and those without cerebellar activation during speech perception. When the cerebellum was active during speech perception there was far less cortical activation than when it was inactive. The results suggest that the cerebellum implements a domain-general mechanism related to prediction during speech perception.
Protein covariance networks reveal interactions important to the emergence of SARS coronaviruses as human pathogens
Authors: Robins William P. , Mekalanos John J.
Published: June 2020

SARS-CoV-2 is one of three recognized coronaviruses (CoVs) that have caused epidemics or pandemics in the 21stcentury and that have likely emerged from animal reservoirs based on genomic similarities to bat and other animal viruses. Here we report the analysis of conserved interactions between amino acid residues in proteins encoded by SARS-CoV-related viruses. We identified pairs and networks of residue variants that exhibited statistically high frequencies of covariance with each other. While these interactions are likely key to both protein structure and other protein-protein interactions, we have also found that they can be used to provide a new computational approach (CoVariance-based Phylogeny Analysis) for understanding viral evolution and adaptation. Our data provide evidence that the evolutionary processes that converted a bat virus into human pathogen occurred through recombination with other viruses in combination with new adaptive mutations important for entry into human cells.
Allergen-induced dendritic cell migration is controlled through Substance P release by sensory neurons
Authors: Aderhold Pamela A. , Dewan Zaynah N. A. , Perner Caroline , Flayer Cameron H. , Zhu Xueping , Voisin Tiphaine , Camire Ryan B. , Chiu Isaac M. , Chow Ohn A. , Sokol Caroline L.
Published: June 2020

Dendritic cells (DCs) of the cDC2 lineage are necessary for the initiation of the allergic immune response and in the dermis are marked by their expression of CD301b. CD301b+dermal DCs respond to allergens encountered in vivo, but not in vitro. This suggests that another cell in the dermis may sense allergens and relay that information to activate and induce the migration of CD301b+DCs to the draining lymph node. Using a model of cutaneous allergen exposure, we show that allergens directly activate TRPV1+sensory neurons leading to itch and pain behaviors. Allergen-activated sensory neurons release the neuropeptide Substance P, which stimulates proximally located CD301b+DCs through MRGPRA1. Substance P induces CD301b+DC migration to the draining lymph node where they initiate Th2 differentiation. Thus, sensory neurons act as primary sensors of allergens, linking exposure to activation of allergic-skewing DCs and the initiation of the allergic immune response.
Multi-Locus Molecular Phylogeny ofSolenopsis(Hymenoptera: Formicidae)
Authors: Shreve Scott , Achury Rafael , Johnson Kevin , Suarez Andrew , Gotzek Dietrich
Published: June 2020

The myrmicine ant genusSolenopsisis species-rich, globally distributed, and is often a common and ecologically important faunal element of the leaf litter. The genus is also well-known for containing several widely distributed tramp species and some of the worst invasive species in the World (the Red Imported Fire Ant,S. invicta, and the Tropical Fire Ant,S. geminata). Although not hyper-diverse and despite its ecological and economic importance,Solenopsishas long frustrated systematists due its lack of reliable diagnostic characters and no phylogenetic hypothesis exists to date. We present a preliminary multi-locus molecular phylogenetic analysis ofSolenopsisto address this knowledge gap. Our analyses recover mostly well-supported phylogenetic hypothesis, which suggestsSolenopsisarose in the Neotropics and spread to all other continents (except Antarctica). Importantly, it demonstrates problems with current systematic understanding of the genus, but provides an evolutionary framework upon which to build future research.
Induction of RNA interference byC. elegansmitochondrial dysfunction via the DRH-1/RIG-I homologue RNA helicase and the EOL-1/RNA decapping enzyme
Authors: Mao Kai , Breen Peter , Ruvkun Gary
Published: June 2020

RNA interference (RNAi) is an antiviral pathway common to many eukaryotes that detects and cleaves foreign nucleic acids. In mammals, mitochondrially localized proteins such as MAVS, RIG-I, and MDA5 mediate antiviral responses. Here, we report that mitochondrial dysfunction inCaenorhabditis elegansactivates RNAi-directed silencing via induction of a pathway homologous to the mammalian RIG-I helicase viral response pathway. The induction of RNAi also requires the conserved RNA decapping enzyme EOL-1/DXO. The transcriptional induction ofeol-1requires DRH-1 as well as the mitochondrial unfolded protein response (UPRmt). Upon mitochondrial dysfunction, EOL-1 is concentrated into foci that depend on the transcription of mitochondrial RNAs that may form dsRNA, as has been observed in mammalian antiviral responses. The enhanced RNAi triggered by mitochondrial dysfunction contributes to the increase in longevity that is induced by mitochondrial dysfunction.
Temporal proteomic profiling reveals insight into critical developmental processes and temperature-influenced physiological response differences in a bivalve mollusc
Authors: Trigg Shelly A. , Mitchell Kaitlyn R. , Thompson Rhonda Elliott , Eudeline Benoit , Vadopalas Brent , Timmins-Schiffman Emma B. , Roberts Steven B.
Published: June 2020

Background

Protein expression patterns underlie physiological processes and phenotypic differences including those occurring during early development. The Pacific oyster (Crassostrea gigas) undergoes a major phenotypic change in early development from free-swimming larval form to sessile benthic dweller while proliferating in environments with broad temperature ranges. Despite the economic and ecological importance of the species, physiological processes occurring throughout metamorphosis and the impact of temperature on these processes have not yet been mapped out.

Results

Towards this, we comprehensively characterized protein abundance patterns for 7978 proteins throughout metamorphosis in the Pacific oyster at different temperature regimes. We used a multi-statistical approach including principal component analysis, ANOVA-simultaneous component analysis, and hierarchical clustering coupled with functional enrichment analysis to characterize these data. We identified distinct sets of proteins with time-dependent abundances generally not affected by temperature. Over 12 days, adhesion and calcification related proteins acutely decreased, organogenesis and extracellular matrix related proteins gradually decreased, proteins related to signaling showed sinusoidal abundance patterns, and proteins related to metabolic and growth processes gradually increased. Contrastingly, different sets of proteins showed temperature-dependent abundance patterns with proteins related to immune response showing lower abundance and catabolic pro-growth processes showing higher abundance in animals reared at 29°C relative to 23°C.

Conclusion

Although time was a stronger driver than temperature of metamorphic proteome changes, temperature-induced proteome differences led to pro-growth physiology corresponding to larger oyster size at 29°C, and to altered specific metamorphic processes and possible pathogen presence at 23°C. These findings offer high resolution insight into why oysters may experience high mortality rates during this life transition in both field and culture settings. The proteome resource generated by this study provides data-driven guidance for future work on developmental changes in molluscs. Furthermore, the analytical approach taken here provides a foundation for effective shotgun proteomic analyses across a variety of taxa.
Limited inhibition of multiple nodes in a driver network blocks metastasis
Authors: Yesilkanal Ali E. , Yang Dongbo , Tiwari Payal , Sabino Alan U. , Lee Jiyoung , Xie Xiao-He , Sun Siqi , Dann Christopher , Steinberg Ethan , Stuhlmiller Timothy , Frankenberger Casey , Goldsmith Elizabeth , Johnson Gary L. , Ramos Alexandre F. , Rosner Marsha R.
Published: June 2020

Metastasis suppression by high-dose, multi-drug targeting is largely unsuccessful due to network heterogeneity and compensatory network activation. Here we show that targeting driver network signaling capacity by limited inhibition of its core pathways is a more effective anti-metastatic strategy. This principle underlies the action of a physiological metastasis suppressor, Raf Kinase Inhibitory Protein, which moderately decreases stress-regulated MAP kinase network activity, reducing the output to metastatic transcription factor BACH1 and motility-related target genes. We developed a low-dose four-drug mimic that blocks metastatic colonization in mouse breast cancer models and increases survival. Experiments and network flow modeling show: 1) limited inhibition of multiple pathways is required to overcome variation in MAPK network topology and suppress signaling output across heterogeneous tumor cells, and 2) restricting inhibition of individual kinases dissipates surplus signal, preventing threshold activation of compensatory kinase networks. This low-dose multi-drug approach to decrease signaling capacity of driver networks represents a transformative, clinically-relevant strategy for anti-metastatic treatment.
Differences in metabolic and liver pathobiology induced by two dietary mouse models of nonalcoholic fatty liver disease
Authors: Zhang Hannah , Léveillé Mélissa , Courty Emilie , Gunes Aysim , Nguyen Bich , Estall Jennifer L.
Published: June 2020

Non-alcoholic fatty liver disease (NAFLD) is a growing epidemic associated with key aspects of metabolic disease such as obesity and diabetes. The first stage of NAFLD is characterized by lipid accumulation in hepatocytes, but this can further progress into non-alcoholic steatohepatitis (NASH), fibrosis or cirrhosis, and hepatocellular carcinoma (HCC). A western diet, high in fats, sugars and cholesterol is linked to NAFLD development. Murine models are often used to experimentally study NAFLD, as they can display similar histopathological features as humans; however, there remains debate on which diet-induced model most appropriately and consistently mimics both human disease progression and pathogenesis. In this study, we performed a side-by-side comparison of two popular diet models of murine NAFLD/NASH and associated HCC: a high fat diet supplemented with 30% fructose water (HFHF) and a western diet high in cholesterol (WDHC), comparing them to a common grain-based chow diet (GBD). Mice on both experimental diets developed liver steatosis, while WDHC-fed mice had greater levels of hepatic inflammation and fibrosis than HFHF-fed mice. In contrast, HFHF-fed mice were more obese and developed more severe metabolic syndrome, with less pronounced liver disease. Despite these differences, WDHC-fed and HFHF-fed mice had similar tumour burdens in a model of diet-potentiated liver cancer. Response to diet and resulting phenotypes were generally similar between sexes, albeit delayed in females. Notably, although metabolic and liver disease phenotypes are often thought to progress in parallel, this study shows that modest differences in diet can significantly uncouple glucose homeostasis and liver damage. In conclusion, long-term feeding of either HFHF or WDHC are reliable methods to induce NASH and diet-potentiated liver cancer in mice of both sexes; however, the choice of diet involves a trade-off between severity of metabolic syndrome and liver damage.
X-linked meiotic drive boosts population size and persistence
Authors: Mackintosh Carl , Pomiankowski Andrew , Scott Michael F
Published: June 2020

X-linked meiotic drivers cause X-bearing sperm to be produced in excess by male carriers, leading to female-biased sex ratios. Selection for these selfish sex chromosomes can lead to completely female populations, which cannot produce offspring and go extinct. However, at the population level, moderately female-biased sex ratios are optimal because relatively few males are required to fertilise all the females. We develop eco-evolutionary models for sex-linked meiotic drive alleles to investigate their full range of demographic effects. We find general conditions for the spread and fixation of X-drivers, accounting for transmission bias and other factors associated with the spread of X-drivers such as sperm competition and polyandry. Our results suggest driving X-alleles that do not reach fixation (or do not bias segregation excessively) will boost population sizes and persistence times by increasing population productivity, demonstrating the potential for selfish genetic elements to move sex ratios closer to the population-level optimum. We suggest that researchers should look beyond extinction risk and consider the potential for ecologically beneficial side effects of selfish genetic elements, especially in light of proposals to use meiotic drive for biological control.
Structural variation affecting DNA backbone interactions underlies adaptation of B3 DNA binding domains to constraints imposed by protein architecture
Authors: Jia Haiyan , Suzuki Masaharu , McCarty Donald R.
Published: June 2020

Functional diversification of transcription factor families through variation in modular domain architectures has played a central role in the independent evolution of gene regulatory networks underlying complex development in plants and animals. Here we show that architecture has in turn constrained evolution of B3 DNA binding domains in the B3 network regulating embryo formation in plants. B3 domains of ABI3, FUS3, LEC2 and VAL1 proteins recognize the same cis-element. ABI3 and VAL1 have complex architectures that physically integrate cis-element recognition with other signals, whereas LEC2 and FUS3 have reduced architectures conducive to their roles as pioneer activators. Qualitatively different activities of LEC2 and ABI3 B3 domains measured in vivo and in vitro are attributed in part to clade-specific substitutions in three amino acids that interact with the DNA backbone. Activities of FUS3 and VAL1 B3 domains show a similar correlation with architectural complexity. Domain-swap analyses in planta show that in a complex architecture setting the attenuated activities of ABI3 and VAL1 B3 domains are required for proper integration of ciselement recognition with hormone signalling. These results highlight modes of structural variation affecting non-specific, electrostatic interactions with the DNA backbone as a general mechanism allowing adaptation of DNA binding affinity to architectural constraints while preserving DNA sequence specificity.
Synthetic antibodies neutralize SARS-CoV-2 infection of mammalian cells
Authors: Miersch Shane , Ustav Mart , Li Zhijie , Case James B. , Ganaie Safder , Matusali Giulia , Colavita Francesca , Lapa Daniele , Capobianchi Maria R. , Novelli Giuseppe , Gupta Jang B. , Jain Suresh , Pandolfi Pier Paolo , Diamond Michael S. , Amarasinghe Gaya , Rini James M. , Sidhu Sachdev S.
Published: June 2020

Coronaviruses (CoV) are a large family of enveloped, RNA viruses that circulate in mammals and birds. Three highly pathogenic strains have caused zoonotic infections in humans that result in severe respiratory syndromes including the Middle East Respiratory Syndrome CoV (MERS), Severe Acute Respiratory Syndrome CoV (SARS), and the ongoing Coronavirus Disease 2019 (COVID-19) pandemic. Here, we describe a panel of synthetic monoclonal antibodies, built on a human IgG framework, that bind to the spike protein of SARS-CoV-2 (the causative agent of COVID-19), compete for ACE2 binding, and potently inhibit SARS-CoV-2. All antibodies that exhibited neutralization potencies at sub-nanomolar concentrations against SARS-CoV-2/USA/WA1 in Vero E6 cells, also bound to the receptor binding domain (RBD), suggesting competition for the host receptor ACE2. These antibodies represent strong immunotherapeutic candidates for treatment of COVID-19.
Phylogenetic and evolutionary analysis reveals the recent dominance of ciprofloxacin resistant S. sonnei and local persistence of S. flexneri clones in India
Authors: Sethuvel Dhiviya Prabaa Muthuirulandi , Mutreja Ankur , Pragasam Agila Kumari , Vasudevan Karthick , Murugan Dhivya , Anandan Shalini , Michael Joy Sarojini , Walia Kamini , Veeraraghavan Balaji
Published: June 2020

Shigella is the second leading cause of bacterial diarrhea worldwide. Recently S. sonnei seems to be replacing S. flexneri in low and middle-income countries undergoing economic development. Despite this, studies focusing on these species at genomic level remain largely unexplored. Here we compared the genome sequences of S. flexneri and S. sonnei isolated from India with the publically available genomes of global strains. Our analysis provide evidence for the long term persistence of all PGs of S. flexneri and the recent dominance of ciprofloxacin-resistant S. sonnei lineage in India. Within S. flexneri PGs, majority of the study isolates belonged to PG3 within the predominance of serotype 2. For S. sonnei, the current pandemic involves globally distributed MDR clones that belong to Central Asia lineage III. The presence of such epidemiologically-dominant lineages in association with stable AMR determinants results in the successful survival in the community.
Transgenic goats producing an improved version of cetuximab in milk
Authors: Laible Götz , Cole Sally , Brophy Brigid , Maclean Paul , Chen Li How , Pollock Dan P. , Cavacini Lisa , Fournier Nathalie , De Romeuf Christophe , Masiello Nicholas C. , Gavin William G. , Wells David N. , Meade Harry M.
Published: June 2020

Therapeutic monoclonal antibodies (mAbs) represent one of the most important classes of pharmaceutical proteins to treat human diseases. Most are produced in cultured mammalian cells which is expensive, limiting their availability. Goats, striking a good balance between a relatively short generation time and copious milk yield, present an alternative platform for the cost-effective, flexible, large-scale production of therapeutic mAbs. Here, we focused on cetuximab, a mAb against epidermal growth factor receptor, that is commercially produced under the brand name Erbitux and approved for anti-cancer treatments. We generated several transgenic goat lines that produce cetuximab in their milk. Two lines were selected for detailed characterization. Both showed stable genotypes and cetuximab production levels of up to 10g/L. The mAb could be readily purified and showed improved characteristics compared to Erbitux. The goat-produced cetuximab (gCetuximab) lacked a highly immunogenic epitope that is part of Erbitux. Moreover, it showed enhanced binding to CD16 and increased antibody-dependent cell-dependent cytotoxicity compared to Erbitux. This indicates that these goats produce an improved cetuximab version with the potential for enhanced effectiveness and better safety profile compared to treatments with Erbitux. In addition, our study validates transgenic goats as an excellent platform for large-scale production of therapeutic mAbs.
Exometabolite dynamics over stationary phase reveal strain-specific responses to nutrient limitation
Authors: Chodkowski John L. , Shade Ashley
Published: June 2020

Microbial exponential growth is expected to occur infrequently outside of the laboratory, in the environment. Instead, resource-limited conditions impose non-growth states for microbes. However, non-growth states are uncharacterized for the majority of environmental bacteria, especially in regard to exometabolite production. To investigate exometabolite production in response to nutrient limitation, we compared exometabolites produced over time in stationary phase across three environmental bacteria:Burkholderia thailandensisE264 (ATCC 700388),Chromobacterium violaceumATCC 31532, andPseudomonas syringaepathovartomatoDC3000 (ATCC BAA-871). We grew each strain in monoculture and investigated exometabolite dynamics over time from mid-exponential to stationary phase. We focused on exometabolites that were released into the media and accumulated over 45 hours, including approximately 20 hours of stationary phase. In concert, we analyzed transcripts (RNAseq) to inform interpretation of exometabolite output. We found that a majority of exometabolites released under these conditions were strain-specific. A subset of identified exometabolites were involved in both central and secondary metabolism. Transcript analysis supported that exometabolites were released from intact cells, as various transporters were either upregulated or consistently expressed. Interestingly, we found that all strains released succinate, and that each strain re-routed their metabolic pathways involved in succinate production during stationary phase. Overall, these results show that non-growth states can also be metabolically active and dynamic. Furthermore, they show that environmental bacteria have the capability to transform a resource-limited extracellular environment into a rich chemical milieu. This work has implications for understanding microbial community interactions via exometabolites, and within resource-limited environments.

Importance

Non-growth states are common for bacteria that live in resource-limited environments, and yet these states remain largely uncharacterized in cellular metabolism and metabolite output. Here, we investigated and compared stationary phase exometabolites and RNA transcripts for each of three environmental bacterial strains. We observed that diverse exometabolites were produced and that they collectively exhibited clear and directional dynamics over time. Additionally, each bacteria strain had a characteristic exometabolite profile and dynamic. This work affirms that stationary phase is not at all “stationary” for these bacteria, and sets the stage for understanding how individual metabolisms support interspecies interactions in resource-limited environments.