bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of cytotoxic, antiviral effect and mutagenic potential of a micronutrient combination in vitro cell culture
Authors: Matti Nazish , Ashraf Muhammad , Rasheed Muhammad Adil , Altaf Imran , Carvalho Isabel , Nadeem Muhammad Faisal
Published: June 2020

Background

Micronutrients are essential for the body to produce enzymes, hormones and other substances essential for proper growth and development. Iodine, potassium iodide and ascorbic acid are ones of the most important in global public health terms. However, their lack represents a major threat to the human and animal health.

Methodology

Antiviral, cytotoxic and mutagenic activity of commercially available micronutrient combination consisting of iodine, ascorbic acid, potassium iodide and excipients was evaluated. Commercial preparation of micronutrient combination was compared with self-prepared micronutrient preparation. MTT assay was used to evaluate the cytotoxicity of all the preparation. Confluent monolayer of Chicken Embryo Fibroblasts grown in 96-well cell culture plates were treated with ten concentrations of each preparation in triplicate manner and was used to determine the viability of the cells and cell survival percentage. Antiviral efficacy was determined against influenza virus H9N1 strain by virus infection and subsequent cell viability assay. Furthermore, mutagenicity was measured by bacterial reverse mutation analysis by Ames test using two strains ofSalmonella typhimuriumTA100 and TA 98 with and without S9. After appropriate incubation, number of revertant colonies per plate were counted in triplicate manner and MF was calculated.

Results

Our combination showed cytotoxicity at doses higher than 11.71ug/ml while showed significant antiviral efficacy at concentrations of 11.71ug/ml, 5.86ug/ml, 2.93ug/ml and 1.4ug/ml which faded away at lower dilutions. Commercially available preparation was found to be non-mutagenic in our experiment.

Conclusions

Combination consisting of iodine, ascorbic acid, potassium iodide is effective in the treatment of viral infections.
Generation and utilization of a HEK-293T murine GM-CSF expressing cell line
Authors: Robinson Elektra K. , Covarrubias Sergio , Zhou Simon , Carpenter Susan
Published: June 2020

Macrophages and dendritic cells (DCs) are innate immune cells that play a key role in defense against pathogens.In vitrocultures of bone marrow-derived macrophages (BMDMs) and dendritic cells (BMDCs) are well-established and valuable methods for immunological studies. Typically, commercially available recombinant GMCSF is utilized to generate BMDCs and is also used to culture alveolar macrophages. We have generated a new HEK-293T cell line expressing murine GM-CSF that secretes high levels of GM-CSF (∼180ng/ml) into complete media as an alternative to commercial GM-CSF. Differentiation of dendritic cells and expression of various markers were kinetically assessed using the GM-CSF HEK293T cell line, termed supGM-CSF and compared directly to purified commercial GMCSF. After 7-9 days of cell culture the supGM-CSF yielded twice as many viable cells compared to the commercial purified GM-CSF. In addition to differentiating BMDCs, the supGM-CSF can be utilized to culture alveolar macrophages without an altering inflammatory activation cascade. Collectively, our results show that supernatant from our GM-CSF HEK293T cell line supports the differentiation of mouse BMDCs or alveolar macrophage culturing, providing an economical alternative to purified GM-CSF.
Symbiotic cyanobacteria communities in hornworts across time, space, and host species
Authors: Nelson Jessica M. , Hauser Duncan A. , Li Fay-Wei
Published: June 2020

Rationale

While plant-microbe interactions have been intensively studied in mycorrhizal and rhizobial symbioses, much less is known about plant symbioses with nitrogen-fixing cyanobacteria. Here we focused on hornworts (a bryophyte lineage), and investigated the diversity of their cyanobionts and how these communities are shaped by spatial, temporal, and host factors.

Method

We carried out repeated samplings of hornwort and soil samples in upstate New York throughout the growing season. Three sympatric hornwort species were included, allowing us to directly compare partner specificity and selectivity. To profile cyanobacteria communities, we established a new metabarcoding protocol targetingrbcL-Xwith PacBio long reads.

Results

Hornwort cyanobionts have a high phylogenetic diversity, including clades that do not contain other known plant or lichen symbionts. While the sympatric hornwort species have similarly low specificity, they exhibit different preferences toward cyanobionts, although this depended on what cyanobacteria were present in the soil. Cyanobacterial communities varied spatially, even at small scales, but time did not play a major organizing role.

Conclusion.

This study highlights the importance of sampling soil and sympatric species to infer partner compatibility and preference, and marks a critical step toward better understanding the ecology and evolution of plant-cyanobacteria symbiosis.
The Mammalian Target of Rapamycin (mTOR) Kinase Mediates Haloperidol-Induced Cataleptic Behavior
Authors: Ramírez-Jarquín Uri Nimrod , Shahani Neelam , Pryor William , Usiello Alessandro , Subramaniam Srinivasa
Published: June 2020

The mammalian target of rapamycin (mTOR) is a ubiquitously expressed serine/threonine kinase protein complex (mTORC1 or mTORC2) that orchestrates diverse functions ranging from embryonic development to aging. However, its brain tissue-specific roles remain less explored. Here, we have identified that the depletion of themTORgene in the mice striatum completely prevented the extrapyramidal motor side-effects (catalepsy) induced by the dopamine 2 receptor (D2R) antagonist haloperidol, which is the most widely used typical antipsychotic drug. Conversely, a lack of striatal mTOR in mice did not affect catalepsy triggered by the dopamine 1 receptor (D1R) antagonist SCH23390. Along with the lack of cataleptic effects, the administration of haloperidol in mTOR mutants failed to increase striatal phosphorylation levels of ribosomal protein pS6 (S235/236) as seen in control animals. To confirm the observations of the genetic approach, we used a pharmacological method and determined that the mTORC1 inhibitor rapamycin has a profound influence upon post-synaptic D2R-dependent functions. We consistently found that pretreatment with rapamycin entirely prevented (in a time-dependent manner) the haloperidol-induced catalepsy in wild-type mice. Collectively, our data indicate that striatal mTORC1 blockade may offer therapeutic benefits with regard to the prevention of D2R-dependent extrapyramidal motor side-effects of haloperidol in psychiatric illness.
Pre-meiotic, 24-nt reproductive phasiRNAs are abundant in anthers of wheat and barley but not rice and maize
Authors: Bélanger Sébastien , Pokhrel Suresh , Czymmek Kirk , Meyers Blake C.
Published: June 2020

Two classes of pre-meiotic (21-nt) and meiotic (24-nt) phasiRNAs and their patterns of accumulation have been described in maize and rice anthers. Their precise function remains unclear, but some studies have shown that they support male fertility. The important role of phasiRNAs in anthers underpins our current study to their characterization in wheat and barley anthers. In this study, we staged anthers at every 0.2 mm of development for one wheat and two barley varieties. We isolated pre-meiotic (0.2 mm, 0.4 mm and 0.6 mm), meiotic (0.8 mm, 1.0 mm and 1.4 mm) and post-meiotic (1.8 mm) anthers for which we then investigated accumulation patterns of RNAs, including reproductive phasiRNAs. We annotated a total 12,821 and 2,897PHASloci in the wheat and barley genomes, respectively. When comparing the total number ofPHASloci in genomes of maize, rice, barley and wheat, we characterized an expansion of reproductivePHASloci in the genomes ofPoaceaesubfamilies fromPanicoideaetoOryzoideaeand toPoideae. In addition to the two classes of pre-meiotic (21-nt) and meiotic (24-nt) phasiRNAs, previously described in maize and rice anthers, we described a group of 24-nt phasiRNAs that accumulate in pre-meiotic anthers. The absence of pre-meiotic 24-nt phasiRNAs in maize and rice suggests a divergence in grass species of thePoideaesubfamily. Additionally, we performed a co-expression gene analysis describing the regulation of phasiRNA biogenesis in wheat and barley anthers. We highlightAGO9andAGO6as candidate binding partners of pre-meiotic and meiotic 24-nt phasiRNAs, respectively.

One sentence summary

In wheat and barley anthers, 24-nt reproductive phasiRNAs are abundant in both meiotic and pre-meiotic stages.
Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories
Authors: Melo Marcelo C. R. , Bernardi Rafael C. , de la Fuente-Nunez Cesar , Luthey-Schulten Zaida
Published: June 2020

Molecular interactions are essential for regulation of cellular processes, from the formation of multiprotein complexes, to the allosteric activation of enzymes. Identifying the essential residues and molecular features that regulate such interactions is paramount for understanding the biochemical process in question, allowing for suppression of a reaction through drug interventions, or optimization of a chemical process using bioengineered molecules. In order to identify important residues and information pathways within molecular complexes, the Dynamical Network Analysis method was developed and has since been broadly applied in the literature. However, in the dawn of exascale computing, this method is generally limited to relatively small biomolecular systems. In this work we provide an evolution of the method, application and interface. All data processing and analysis is conducted through Jupyter notebooks, providing automatic detection of important solvent and ion residues, an optimized and parallel generalized correlation implementation that is linear with respect to the number of nodes in the system, and subsequent community clustering, calculation of betweenness of contacts, and determination optimal paths. Using the popular visualization program VMD, high-quality renderings of the networks over the biomolecular structures can be produced. Our new implementation was employed to investigate three different systems, with up to 2.5 M atoms, namely the OMP-decarboxylase, the Leucyl-tRNA synthetase complexed with its cognate tRNA and adenylate, and the respiratory complex I in a membrane environment. Our enhanced and updated protocol provides the community with an intuitive and interactive interface, which can be easily applied to large macromolecular complexes.
Mechanism and inhibition of SARS-CoV-2 PLpro
Authors: Klemm Theresa , Ebert Gregor , Calleja Dale J. , Allison Cody C. , Richardson Lachlan W. , Bernardini Jonathan P. , Lu Bernadine G. C. , Kuchel Nathan W. , Grohmann Christoph , Shibata Yuri , Gan Zhong Yan , Cooney James P. , Doerflinger Marcel , Au Amanda E. , Blackmore Timothy R. , Geurink Paul P. , Ovaa Huib , Newman Janet , Riboldi-Tunnicliffe Alan , Czabotar Peter E. , Mitchell Jeffrey P. , Feltham Rebecca , Lechtenberg Bernhard C. , Lowes Kym N. , Dewson Grant , Pellegrini Marc , Lessene Guillaume , Komander David
Published: June 2020

Coronaviruses, including SARS-CoV-2, encode multifunctional proteases that are essential for viral replication and evasion of host innate immune mechanisms. The papain-like protease PLpro cleaves the viral polyprotein, and reverses inflammatory ubiquitin and anti-viral ubiquitin-like ISG15 protein modifications1,2. Drugs that target SARS-CoV-2 PLpro (hereafter, SARS2 PLpro) may hence be effective as treatments or prophylaxis for COVID-19, reducing viral load and reinstating innate immune responses3. We here characterise SARS2 PLpro in molecular and biochemical detail. SARS2 PLpro cleaves Lys48-linked polyubiquitin and ISG15 modifications with high activity. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. We further exploit two strategies to target PLpro. A repurposing approach, screening 3727 unique approved drugs and clinical compounds against SARS2 PLpro, identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non-covalent small molecule SARS PLpro inhibitors were able to inhibit SARS2 PLpro with high potency and excellent antiviral activity in SARS-CoV-2 infection models.
Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates
Authors: Savastano Adriana , de Opakua Alain Ibáñez , Rankovic Marija , Zweckstetter Markus
Published: June 2020

The etiologic agent of the Covid-19 pandemic is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The viral membrane of SARS-CoV-2 surrounds a helical nucleocapsid in which the viral genome is encapsulated by the nucleocapsid protein. The nucleocapsid protein of SARS-CoV-2 is produced at high levels within infected cells, enhances the efficiency of viral RNA transcription and is essential for viral replication. Here we show that RNA induces cooperative liquid-liquid phase separation of the SARS-CoV-2 nucleocapsid protein. In agreement with its ability to phase separate in vitro, we show that the protein associates in cells with stress granules, cytoplasmic RNA/protein granules that form through liquid-liquid phase separation and are modulated by viruses to maximize replication efficiency. Liquid-liquid phase separation generates high-density protein/RNA condensates that recruit the RNA-dependent RNA polymerase complex of SARS-CoV-2 providing a mechanism for efficient transcription of viral RNA. Inhibition of RNA-induced phase separation of the nucleocapsid protein by small molecules or biologics thus can interfere with a key step in the SARS-CoV-2 replication cycle.
Identification of a critical horseshoe-shaped region in the nsp5 (Mpro, 3CLpro) protease interdomain loop (IDL) of coronavirus mouse hepatitis virus (MHV)
Authors: Nick Benjamin C. , Pandya Mansi C. , Lu Xiaotao , Franke Megan E. , Callahan Sean M. , Hasik Emily F. , Berthrong Sean T. , Denison Mark R. , Stobart Christopher C.
Published: June 2020

Human coronaviruses are enveloped, positive-strand RNA viruses which cause respiratory diseases ranging in severity from the seasonal common cold to SARS and COVID-19. Of the 7 human coronaviruses discovered to date, 3 emergent and severe human coronavirus strains (SARS-CoV, MERS-CoV, and SARS-CoV-2) have recently jumped to humans in the last 20 years. The COVID-19 pandemic spawned by the emergence of SARS-CoV-2 in late 2019 has highlighted the importance for development of effective therapeutics to target emerging coronaviruses. Upon entry, the replicase genes of coronaviruses are translated and subsequently proteolytically processed by virus-encoded proteases. Of these proteases, nonstructural protein 5 (nsp5, Mpro, or 3CLpro), mediates the majority of these cleavages and remains a key drug target for therapeutic inhibitors. Efforts to develop nsp5 active-site inhibitors for human coronaviruses have thus far been unsuccessful, establishing the need for identification of other critical and conserved non-active-site regions of the protease. In this study, we describe the identification of an essential, conserved horseshoe-shaped region in the nsp5 interdomain loop (IDL) of mouse hepatitis virus (MHV), a common coronavirus replication model. Using site-directed mutagenesis and replication studies, we show that several residues comprising this horseshoe-shaped region either fail to tolerate mutagenesis or were associated with viral temperature-sensitivity. Structural modeling and sequence analysis of these sites in other coronaviruses, including all 7 human coronaviruses, suggests that the identified structure and sequence of this horseshoe regions is highly conserved and may represent a new, non-active-site regulatory region of the nsp5 (3CLpro) protease to target with coronavirus inhibitors.

Importance

In December 2019, a novel coronavirus (SARS-CoV-2) emerged in humans and triggered a pandemic which has to date resulted in over 8 million confirmed cases of COVID-19 across more than 180 countries and territories (June 2020). SARS-CoV-2 represents the third emergent coronavirus in the past 20 years and the future emergence of new coronaviruses in humans remains certain. Critically, there remains no vaccine nor established therapeutics to treat cases of COVID-19. The coronavirus nsp5 protease is a conserved and indispensable virus-encoded enzyme which remains a key target for therapeutic design. However, past attempts to target the active site of nsp5 with inhibitors have failed stressing the need to identify new conserved non-active-site targets for therapeutic development. This study describes the discovery of a novel conserved structural region of the nsp5 protease of coronavirus mouse hepatitis virus (MHV) which may provide a new target for coronavirus drug development.
Cryptosporulation inKurthiaspp. forces a rethinking of asporogenesis in Firmicutes
Authors: Filippidou Sevasti , Fatton Mathilda , Junier Thomas , Berge Matthieu , Poppleton Daniel , Blum Thorsten B , Kaminek Marek , Odriozola Adolfo , Blom Jochen , Johnson Shannon L , Abrahams Jan Pieter , Chain Patrick S , Gribaldo Simonetta , Tocheva Elitza I. , Zuber Benoît , Viollier Patrick H , Junier Pilar
Published: June 2020

Sporulation is a complex morphophysiological process resulting in a cellular structure that is more resistant than the vegetative form. In Firmicutes, this structure is produced within the mother cell, and is called an endospore. Endospore formation is thought to have evolved in the common ancestor of Firmicutes. However, sporulation has apparently been lost in some extant lineages that are defined asasporogenic. We isolated strain 11kri321, a representative of the genusKurthia, from an oligotrophic geothermal reservoir. WhileKurthiaspp. is considered to comprise only asporogenic species, strain 11kri321 produced spores. Genomic reconstruction of the sporulation pathway shows elements typical of sporulation in Bacilli, including the signaling for sporulation onset. However, key genes were missing, including those involved in engulfment and dipicolinic acid synthesis. Based on the results for strain 11kri321, sporulation was investigated in otherKurthiastrains. Genes involved in signaling, cell division and spore coat formation were detected in three availableKurthiagenomes. Moreover, endosporulation was clearly visualized in at least two of the four strains tested. These results show thatKurthiais an endospore-forming Firmicute lineage. However, the genetic background of sporulation in this genus deviates from the known sporulation pathway in Firmicutes and even within Bacilli, suggesting that a revision of the minimal set of genes used for genomic detection of sporulation is required. Based on our findings we propose the termcryptosporulantto refer to putative asporogenic Firmicutes for which a detailed genomic and physiological characterization of sporulating is missing.

Importance

Endospore-forming Firmicutes include many environmental and medical relevant bacterial clades. In these microorganisms, the ability to produce endospores is essential for survival in the environment and even for pathogenesis. The minimum core of genes required to produce a viable and resistant spore, the distinction between endospore-forming and asporogenic groups, as well as the evolution of sporulation have been a subject of investigation and debate for decades. Here, we demonstrate endosporulation in the genusKurthia,considered as asporogenic. Morphological, physiological and genomic analyses were undertaken to demonstrate that sporulation is not lost within this lineage. Based on our results we propose a re-examination of the minimal genetic requirements of sporulation and the use of the termcryptosporulantto describe lineages of Firmicutes that have not previously been observed to sporulate, but for which a detailed analysis is still missing.
Analysis of Gene Expression from Systemic Lupus Erythematosus Synovium Reveals a Profile of Activated Immune Cells and Inflammatory Pathways
Authors: Hubbard Erika L. , Catalina Michelle D. , Heuer Sarah , Bachali Prathyusha , Robl Robert , Geraci Nicholas S. , Grammer Amrie C. , Lipsky Peter E.
Published: June 2020

Arthritis is a common manifestation of systemic lupus erythematosus (SLE) yet understanding of the underlying pathogenic mechanisms remains incomplete. We, therefore, interrogated gene expression profiles of SLE synovium to gain insight into the nature of lupus arthritis (LA), using osteoarthritis (OA) and rheumatoid arthritis (RA) as comparators. Knee synovia from SLE, OA, and RA patients were analyzed for differentially expressed genes (DEGs) and also by Weighted Gene Co-expression Network Analysis (WGCNA) to identify modules of highly co-expressed genes. Genes upregulated and/or co-expressed in LA revealed numerous immune/inflammatory cells dominated by a myeloid phenotype, whereas OA was characteristic of fibroblasts and RA of T- and B-cells. Upstream regulator analysis identifiedCD40Land inflammatory cytokines as drivers of the LA gene expression profile. Genes governing trafficking of immune cells into the synovium by chemokines were identified, but notin situgeneration of germinal centers. GSVA confirmed activation of specific myeloid and lymphoid cell types in LA. Numerous therapies were predicted to target LA, including TNF, NFκB, MAPK, and CDK inhibitors. Detailed gene expression analysis identified a unique pattern of cellular components and physiologic pathways operative in LA, as well as drugs potentially able to target this common manifestation of SLE.
Can expectation suppression be explained by reduced attention to predictable stimuli?
Authors: Alink Arjen , Blank Helen
Published: June 2020

The expectation-suppression effect – reduced stimulus-evoked responses to expected stimuli – is widely considered to be an empirical hallmark of reduced prediction errors in the framework of predictive coding. Here we challenge this notion by proposing that that expectation suppression could be explained by a reduced attention effect. Specifically, we argue that reduced responses to predictable stimuli can also be explained by a reduced saliency-driven allocation of attention. We base our discussion mainly on findings in the visual cortex and propose that resolving this controversy requires the assessment of qualitative differences between the ways in which attention and ‘surprise’ enhance brain responses.
Ecogenomics of key prokaryotes in the arctic ocean
Authors: Royo-Llonch Marta , Sánchez Pablo , Ruiz-González Clara , Salazar Guillem , Pedrós-Alió Carlos , Labadie Karine , Paoli Lucas ,   Tara Oceans Coordinators, Chaffron Samuel , Eveillard Damien , Karsenti Eric , Sunagawa Shinichi , Wincker Patrick , Karp-Boss Lee , Bowler Chris , Acinas Silvia G
Published: June 2020

The Arctic Ocean is a key player in the regulation of climate and at the same time is under increasing pressure as a result of climate change. Predicting the future of this ecosystem requires understanding of the responses of Arctic microorganisms to environmental change, as they are the main drivers of global biogeochemical cycles. However, little is known about the ecology and metabolic potential of active Arctic microbes. Here, we reconstructed a total of 3,550 metagenomic bins from 41 seawater metagenomes collected as part of the Tara Oceans expedition, covering five different Arctic Ocean regions as well as the sub-Arctic North Atlantic Ocean and including various depths and different seasons (spring to autumn). Of these bins, 530 could be classified as Metagenome Assembled Genomes (MAGs) and over 75% of them represented novel species. We describe their habitat range and environmental preferences, as well as their metabolic capabilities, building the most comprehensive dataset of uncultured bacterial and archaeal genomes from the Arctic Ocean to date. We found a prevalence of mixotrophs, while chemolithoautotrophs were mostly present in the mesopelagic Arctic Ocean during spring and autumn. Finally, the catalogue of Arctic MAGs was complemented with metagenomes and metatranscriptomes from the global ocean to identify the most active MAGs present exclusively in polar metagenomes. These polar MAGs, which display a range of metabolic strategies, might represent Arctic sentinels of climate change and should be considered in prospective studies of the future state of the Arctic Ocean.
Transcription factor Sp1 regulates mitotic fidelity through Aurora B kinase-mediated condensin I localization
Authors: Flashner Samuel , Swift Michelle , Sowash Aislinn , Azizkhan-Clifford Jane
Published: June 2020

Mitotic chromosome assembly is essential for faithful chromosome segregation. Despite their salient role directing interphase chromatin organization, little is known about how transcription factors mediate this process during mitosis. Here, we characterize a mitosis-specific role for transcription factor specificity protein 1 (Sp1). Sp1 localizes to mitotic centromeres and auxin-induced rapid Sp1 degradation results in chromosome segregation errors and aberrant mitotic progression. These defects are driven by anomalous mitotic chromosome assembly. Sp1 degradation results in chromosome condensation defects through reduced condensin complex I localization. Sp1 also mediates the localization and activation of Aurora B kinase early in mitosis, which is essential for condensin complex I recruitment. Underscoring the clinical significance of our findings, aberrant Sp1 expression correlates with aneuploidy in several human cancers, including kidney renal papillary cell carcinoma, ovarian serous cystadenocarcinoma, mesothelioma, cholangiocarcinoma, and hepatocellular carcinoma. Our results suggest that Sp1 protects genomic integrity during mitosis by promoting chromosome assembly.
No evidence of coronaviruses or other potentially zoonotic viruses in Sunda pangolins (Manis javanica) entering the wildlife trade via Malaysia
Authors: Lee Jimmy , Hughes Tom , Lee Mei-Ho , Field Hume , Rovie-Ryan Jeffrine Japning , Sitam Frankie Thomas , Sipangkui Symphorosa , Nathan Senthilvel K.S.S. , Ramirez Diana , Kumar Subbiah Vijay , Lasimbang Helen , Epstein Jonathan H. , Daszak Peter
Published: June 2020

The legal and illegal trade in wildlife for food, medicine and other products is a globally significant threat to biodiversity that is also responsible for the emergence of pathogens that threaten human and livestock health and our global economy. Trade in wildlife likely played a role in the origin of COVID-19, and viruses closely related to SARS-CoV-2 have been identified in bats and pangolins, both traded widely. To investigate the possible role of pangolins as a source of potential zoonoses, we collected throat and rectal swabs from 334 Sunda pangolins (Manis javanica) confiscated in Peninsular Malaysia and Sabah between August 2009 and March 2019. Total nucleic acid was extracted for viral molecular screening using conventional PCR protocols used to routinely identify known and novel viruses in extensive prior sampling (>50,000 mammals). No sample yielded a positive PCR result for any of the targeted viral families – Coronaviridae, Filoviridae, Flaviviridae, Orthomyxoviridae and Paramyxoviridae. In light of recent reports of coronaviruses including a SARS-CoV-2 related virus in Sunda pangolins in China, the lack of any coronavirus detection in our ‘upstream’ market chain samples suggests that these detections in ‘downstream’ animals more plausibly reflect exposure to infected humans, wildlife or other animals within the wildlife trade network. While confirmatory serologic studies are needed, it is likely that Sunda pangolins are incidental hosts of coronaviruses. Our findings further support the importance of ending the trade in wildlife globally.
Transcriptomic signatures associated with regional cortical thickness changes in Parkinson’s disease
Authors: Keo Arlin , Dzyubachyk Oleh , van der Grond Jeroen , van Hilten Jacobus J. , Reinders Marcel J. T. , Mahfouz Ahmed
Published: June 2020

Cortical atrophy is a common manifestation in Parkinson’s disease, particularly in later disease stages. Here, we investigated patterns of cortical thickness using T1-weighted anatomical MRI data of 149 Parkinson’s disease patients and 369 controls. To elucidate the molecular underpinnings of cortical thickness changes in Parkinson’s disease, we performed an integrated analysis of brain-wide healthy transcriptomic data from the Allen Human Brain Atlas and neuroimaging features. For this purpose, we used partial least squares regression to identify gene expression patterns correlated with cortical thickness changes. In addition, we identified gene expression patterns underlying the relationship between cortical thickness and clinical domains of Parkinson’s disease. Our results show that genes whose expression in the healthy brain is associated with cortical thickness changes in Parkinson’s disease are enriched in biological pathways related to sumoylation, regulation of mitotic cell cycle, mitochondrial translation, DNA damage responses, and ER-Golgi traffic. The associated pathways were highly related to each other and all belong to cellular maintenance mechanisms. The expression of genes within most pathways was negatively correlated with cortical thickness changes, showing higher expression in regions associated with decreased cortical thickness (atrophy). On the other hand, sumoylation pathways were positively correlated with cortical thickness changes, showing higher expression in regions with increased cortical thickness (hypertrophy). Our findings suggest that alterations in the balanced interplay of these mechanisms play a role in changes of cortical thickness in Parkinson’s disease and possibly influence motor and cognitive functions.
Shortlisting genes important in seed maturation by principal component analysis of gene expression data
Authors: Pathak Ashish K , Singla Ridhima , Juneja Mamta , Tuli Rakesh
Published: June 2020

Transcriptome data are widely used for functional analysis of genes. De-novo assembly of transcriptome gives a large number of unigenes. A large proportion of them remain unannotated. Efficient computational methods are required for identifying genes and modeling those for regulatory and functional roles. Principal component analysis (PCA) was used in a novel approach to shortlist genes, independently of annotation in genome expression data, taking seed development inArabidopsis thalianaas a representative case. PCA was applied to published genome expression data from four lines of Arabidopsis, mutated in seed development. The PC separating all the developmental stages between a mutant and its respective wild type was selected for shortlisting genes as functionally more important. The shortlisted genes identified by PCA belong to a number of biological functions. The genes reported to give sensitivity to desiccation were identified in PCA analysis also in desiccation intolerant lines only. With respect to the network of 98 genes targeted by ABI3, a higher number of genes was identified as important in the mutants abi 3-5, fus 3-3 andlec 1-1 in comparison to abi 3-1. Ontological analysis and comparison with earlier studies suggest that PCA of genome expression data is useful for shortlisting functionally important genes.
Antiviral treatment of SARS-CoV-2-infected hamsters reveals a weak effect of favipiravir and a complete lack of effect for hydroxychloroquine
Authors: Kaptein Suzanne JF , Jacobs Sofie , Langendries Lana , Seldeslachts Laura , ter Horst Sebastiaan , Liesenborghs Laurens , Hens Bart , Vergote Valentijn , Heylen Elisabeth , Maas Elke , De Keyzer Carolien , Bervoets Lindsey , Rymenants Jasper , Van Buyten Tina , Thibaut Hendrik Jan , Dallmeier Kai , Boudewijns Robbert , Wouters Jens , Augustijns Patrick , Verougstraete Nick , Cawthorne Christopher , Weynand Birgit , Annaert Pieter , Spriet Isabel , Velde Greetje Vande , Neyts Johan , Rocha-Pereira Joana , Delang Leen
Published: June 2020

SARS-CoV-2 rapidly spread around the globe after its emergence in Wuhan in December 2019. With no specific therapeutic and prophylactic options available, the virus was able to infect millions of people. To date, close to half a million patients succumbed to the viral disease, COVID-19. The high need for treatment options, together with the lack of small animal models of infection has led to clinical trials with repurposed drugs before any preclinicalin vivoevidence attesting their efficacy was available. We used Syrian hamsters to establish a model to evaluate antiviral activity of small molecules in both an infection and a transmission setting. Upon intranasal infection, the animals developed high titers of SARS-CoV-2 in the lungs and pathology similar to that observed in mild COVID-19 patients. Treatment of SARS-CoV-2-infected hamsters with favipiravir or hydroxychloroquine (with and without azithromycin) resulted in respectively a mild or no reduction in viral RNA and infectious virus. Micro-CT scan analysis of the lungs showed no improvement compared to non-treated animals, which was confirmed by histopathology. In addition, both compounds did not prevent virus transmission through direct contact and thus failed as prophylactic treatments. By modelling the PK profile of hydroxychloroquine based on the trough plasma concentrations, we show that the total lung exposure to the drug was not the limiting factor. In conclusion, we here characterized a hamster infection and transmission model to be a robust model for studyingin vivoefficacy of antiviral compounds. The information acquired using hydroxychloroquine and favipiravir in this model is of critical value to those designing (current and) future clinical trials. At this point, the data here presented on hydroxychloroquine either alone or combined with azithromycin (together with previously reportedin vivodata in macaques and ferrets) provide no scientific basis for further use of the drug in humans.
Genetic architecture and gene mapping of cyanide in cassava (Manihot esculenta Crantz.)
Authors: Ogbonna Alex C , de Andrade Luciano Rogerio Braatz , Rabbi Ismail Y. , Mueller Lukas A. , de Oliveira Eder Jorge , Bauchet Guillaume J.
Published: June 2020

Cassava is a root crop originating from South America and a major staple crop in the Tropics, including marginal environments. In this study, we focused on South American and African cassava germplasm and investigated the genetic architecture of Hydrogen Cyanide (HCN), a major component of tuber quality. HCN is a plant defense component against herbivory but also toxic for human consumption. We genotyped 3,354 landraces and modern breeding lines originating from 26 Brazilian states and 1,389 individuals were phenotypically characterized across multi-year trials for HCN. All plant material was subjected to high density genotyping using Genotyping-by-sequencing (GBS). We performed genome wide association mapping (GWAS) to characterize the genetic architecture and gene mapping of HCN. Field experiment revealed strong broad and narrow-sense trait heritability (0.82 and 0.41 respectively). Two major loci were identified, encoding for an ATPase and a MATE protein and contributing up to 7% and 30% of the cyanide concentration in roots, respectively. We developed diagnostic markers for breeding applications, validated trait architecture consistency in African germplasm and investigated further evidence for domestication of sweet and bitter cassava. Fine genomic loci characterization indicate; (i) a major role played by vacuolar transporter in regulating HCN content, (ii) co-domestication of sweet and bitter cassava major alleles to be geographical zone dependant, and (ii) major loci allele for high cyanide cassava inManihot esculenta Crantzseems to originate from its ancestor,M. esculentassp.flabellifolia.Taken together these findings expand insights on cyanide in cassava and its glycosylated derivatives in plants.

One-sentence summary

Identification of an intracellular transporter gene and its allelic variation allow to point out cultivars with up to 30 percent decrease in cassava root cyanide content, toxic for human consumption.
IGF2BP1 is a targetable SRC/MAPK-dependent driver of invasive growth in ovarian cancer
Authors: Bley Nadine , Schott Annekatrin , Müller Simon , Misiak Danny , Lederer Marcell , Fuchs Tommy , Aßmann Chris , Glaß Markus , Ihling Christian , Sinz Andrea , Pazaitis Nikolaos , Wickenhauser Claudia , Vetter Martina , Ungurs Olga , Strauss Hans-Georg , Thomssen Christoph , Hüttelmaier Stefan
Published: June 2020

Epithelial-to-mesenchymal transition (EMT) is a hallmark of aggressive, mesenchymal-like high-grade serous ovarian carcinoma (HG-SOC). The SRC kinase is a key driver of cancer-associated EMT promoting adherens junction (AJ) disassembly by phosphorylation-driven internalization and degradation of AJ proteins. Here we show, that the IGF2 mRNA binding protein 1 (IGF2BP1) is up-regulated in mesenchymal-like HG-SOC and promotes SRC activation by a previously unknown protein-ligand-induced, but RNA-independent mechanism. IGF2BP1-driven invasive growth of ovarian cancer cells essentially relies on the SRC-dependent disassembly of AJs. Concomitantly, IGF2BP1 enhances ERK2 expression in a RNA-binding dependent manner. Together this reveals a post-transcriptional mechanism of interconnected stimulation of SRC/ERK signaling in ovarian cancer cells. The IGF2BP1-SRC/ERK2 axis is targetable by the SRC-inhibitor saracatinib and MEK-inhibitor selumetinib. However, due to IGF2BP1-directed stimulation only combinatorial treatment effectively overcomes the IGF2BP1-promoted invasive growth in 3D culture conditions as well as intraperitoneal mouse models. In conclusion, we reveal an unexpected role of IGF2BP1 in enhancing SRC/MAPK-driven invasive growth of ovarian cancer cells. This provides a rational for the therapeutic benefit of combinatorial SRC/MEK inhibition in mesenchymal-like HG-SOC.

Graphical Abstract
Developmental Influences on Symptom Expression in Antipsychotic-Naïve First-Episode Psychosis
Authors: Bridgwater Miranda , Bachman Peter , Tervo-Clemmens Brenden , Haas Gretchen , Hayes Rebecca , Luna Beatriz , Salisbury Dean F. , Jalbrzikowski Maria
Published: June 2020

Introduction

The neurodevelopmental model of psychosis was established over 30 years ago; however, the developmental influence on psychotic symptom expression – how a person’s age affects clinical presentation in first-episode psychosis – has not been thoroughly investigated.

Method

Using generalized additive modeling, which allows for linear and non-linear functional forms of age-related change, we leveraged symptom data from a large sample of antipsychotic-naïve individuals experiencing a first episode of psychosis (N=340, 12-40 years, 1-12 visits), collected at the University of Pittsburgh from 1990-2017. We examined relationships between age and severity of perceptual and non-perceptual positive symptoms and negative symptoms. We also tested for age-associated effects onchangein positive or negative symptom severity following baseline assessment, and explored the time-varying relationship between perceptual and non-perceptual positive symptoms across adolescent development.

Results

In the cross-sectional and longitudinal data, perceptual positive symptoms significantly decreased with increasing age (F=7.0, p=0.0007; q=0.003) while non-perceptual positive symptoms increased with increasing age (F=4.1,p=0.01,q=0.02). These relationships remained significant when SES, IQ, and illness duration were included as covariates. There were no developmental effects on change in positive or negative symptom severity (allp>0.25). Finally, an association between severity of non-perceptual and perceptual symptoms developed with increasing age, with a significant association starting at age 18.

Conclusion

These findings suggest that as cognitive maturation proceeds, perceptual symptoms attenuate while non-perceptual symptoms are enhanced, reflecting influences of developmental processes on psychosis expression. Findings underscore how pathological brain-behavior relationships vary as a function of development.
The legacy of recurrent introgression during the radiation of hares
Authors: Ferreira Mafalda S. , Jones Matthew R. , Callahan Colin M. , Farelo Liliana , Tolesa Zelalem , Suchentrunk Franz , Boursot Pierre , Mills L. Scott , Alves Paulo C. , Good Jeffrey M. , Melo-Ferreira José
Published: June 2020

Abstract

Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification ofLepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1- 4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along theLepusradiation, including recent gene flow between extant species since the last glacial maximum, but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation within and among species.
Rapid kinetics of lipid second messengers controlled by a cGMP signalling network coordinates apical complex functions inToxoplasmatachyzoites
Authors: Katris Nicholas J. , Yamaryo-Botte Yoshiki , Janouškovec Jan , Shunmugam Serena , Arnold Christophe-Sebastien , Yang Annie S. P. , Vardakis Alexandros , Stewart Rebecca J. , Sauerwein Robert , McFadden Geoffrey I. , Tonkin Christopher J. , Cesbron-Delauw Marie-France , Waller Ross. F. , Botte Cyrille Y.
Published: June 2020

Host cell invasion and subsequent egress byToxoplasmaparasites is regulated by a network of cGMP, cAMP, and calcium signalling proteins. Such eukaryotic signalling networks typically involve lipid second messengers including phosphatidylinositol phosphates (PIPs), diacylglycerol (DAG) and phosphatidic acid (PA). However, the lipid signalling network inToxoplasmais poorly defined. Here we present lipidomic analysis of a mutant of central flippase/guanylate cyclase TgGC inToxoplasma, which we show has disrupted turnover of signalling lipids impacting phospholipid metabolism and membrane stability. The turnover of signalling lipids is extremely rapid in extracellular parasites and we track changes in PA and DAG to within 5 seconds, which are variably defective upon disruption of TgGC and other signalling proteins. We then identify the position of each protein in the signal chain relative to the central cGMP signalling protein TgGC and map the lipid signal network coordinating conoid extrusion and microneme secretion for egress and invasion.
A Biodiversity Composition Map of California Derived from Environmental DNA Metabarcoding and Earth Observation
Authors: Lin Meixi , Simons Ariel Levi , Curd Emily E. , Harrigan Ryan J. , Schneider Fabian D. , Ruiz-Ramos Dannise V. , Gold Zack , Osborne Melisa G. , Shirazi Sabrina , Schweizer Teia M. , Moore Tiara N. , Fox Emma A. , Turba Rachel , Garcia-Vedrenne Ana E. , Helman Sarah K. , Rutledge Kelsi , Mejia Maura Palacios , Munguia Ramos Miroslava N. , Wetzer Regina , Pentcheff Dean , McTavish Emily Jane , Dawson Michael N. , Shapiro Beth , Wayne Robert K. , Meyer Rachel S.
Published: June 2020

Unique ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. We offer a way to use environmental DNA, community science and remote sensing together as methods to reduce the discrepancy between the magnitude of change and historical approaches to measure it. Taking advantages of modern ecological models, we integrate environmental DNA and Earth observations to evaluate regional biodiversity patterns for a snapshot of time, and provide critical community-level characterization. We collected 278 samples in Spring 2017 from coastal, shrub and lowland forest sites in California, a large-scale biodiversity hotspot. We applied gradient forest to model 915 family occurrences and community composition together with environmental variables and multi-scalar habitat classifications to produce a statewide biodiversity-based map. 16,118 taxonomic entries recovered were associated with environmental variables to test their predictive strength on alpha, beta, and zeta diversity. Local habitat classification was diagnostic of community composition, illuminating a characteristic of biodiversity hotspots. Using gradient forest models, environmental variables predicted 35% of the variance in eDNA patterns at the family level, with elevation, sand percentage, and greenness (NDVI32) as the top predictors. This predictive power was higher than we found in published literature at global scale. In addition to this indication of substantial environmental filtering, we also found a positive relationship between environmentally predicted families and their numbers of biotic interactions. In aggregate, these analyses showed that strong eDNA community-environment correlation is a general characteristic of temperate ecosystems, and may explain why communities easily destabilize under disturbances. Our study provides the first example of integrating citizen science based eDNA with biodiversity mapping across the tree of life, with promises to produce large scale, high resolution assessments that promote a more comprehensive and predictive understanding of the factors that influence biodiversity and enhance its maintenance.
Combined transient ablation and single cell RNA sequencing reveals the development of medullary thymic epithelial cells
Authors: Wells Kristen L. , Miller Corey N. , Gschwind Andreas R. , Wei Wu , Phipps Jonah D. , Anderson Mark S. , Steinmetz Lars M.
Published: June 2020

Medullary thymic epithelial cells (mTECs) play a critical role in central immune tolerance by mediating negative selection of autoreactive T cells through the collective expression of the peripheral self-antigen compartment, including tissue-specific antigens (TSAs). Recent work has shown that gene expression patterns within the mTEC compartment are remarkably heterogenous and include multiple differentiated cell states. To further define mTEC development and medullary epithelial lineage relationships, we combined lineage tracing and recovery from transientin vivomTEC ablation with single cell RNA-sequencing. The combination of bioinformatic and experimental approaches revealed a non-stem transit-amplifying population of cycling mTECs that precededAireexpression. Based on our findings, we propose a branching model of mTEC development wherein a heterogeneous pool of transit-amplifying cells gives rise toAire- andCcl21a-expressing mTEC subsets. We further use experimental techniques to show that within theAire-expressing developmental branch, TSA expression peaked asAireexpression decreased, implyingAireexpression must be established before TSA expression can occur. Collectively, these data provide a higher order roadmap of mTEC development and demonstrate the power of combinatorial approaches leveraging bothin vivomodels and high-dimensional datasets.