bluuebunny/crossref_metadata_2025 huggingface dataset:
Caenorhabditis elegans: a model to study the anthelmintic effects of polyphenolic compounds on the fertility of parasitic gastrointestinal nematodes?
Authors: Arroyo-Lopez C
Published: September 2020

We set up a Caenorhabditis elegansmodel to extrapolate anthelmintic (AH) effects of commercial polyphenols to related gastrointestinal zoonotic species. We compared the practical convenience of S liquid to solid agar Nematode grown medium in daily reproduction patterns and total brood size. Solid agar resulted a highly effective, reproducibly medium, in a less costly and rapid time manner. A minimum of three replications per monomer concentration are suggested to get a robust statistical analysis. Flavonoids Quercetin and Rutin potentially decrease brood sizes and percentage of development, with the exception of 20μM concentration. Flavanols resulted heterogeneous. In a dose-dependent manner Catechin 20μM significantly decreased egg output, and egg hatching in a 15% on respect to control values. Contrary, Epigallocatechin-gallate, seems to stimulate brood sizes and egg-hatching, however, EGCG10μM decreased reproduction but with no in a significative manner. We found a nematocidal effect on the reproductive parameters ofC. elegansexposed to the chalcones Phloretin and Phloridzin, and Flavones Flavone and Genistein. A significant general decrease on reproductive parameters were found, particularly significant for Genistein 20μM in the percentage of hatching respect to control. Effects of time schedule and monomer concentration were found for the Hydrolysable tannins Gallic and Tannic acid. Tannic acid showed effectiveness against egg-hatching. The spectrum of percentages of change compared to each blank resulted negative decreasing fertility values, but for GA5, associated with a net increase of larvae hatched.

1AH, GIN, CTS, HTs Q) Quercetin, (R) Rutin, (C) (+)-Catechin hydrate, (EGCG) (-)-Epigallocatechin Gallate, (PTN) Phloretin, (PDN) Phloridzin Dihydrate, (GE) Genistein, (FLA) Flavone, (GA) Gallic acid and (TA) Tannic acid., G1 (adult worm originally seeded per plate and monomer concentration at time 0. Two replications were performed per plate). Solvents: PBS (Phosphate Buffer Solution), CH4O (Methanol 0,002%) L3
Critical events of the origins of life
Authors: Bastian Caleb Deen , Rabitz Herschel
Published: September 2020

We discuss some critical events of the origins of life using a mathematical model and simulation studies. We find that for a replicating population of RNA molecules participating in template-directed polymerization, the hitting and establishment of a high-fidelity replicator depends critically on the polymerase fitness and sequence specificity landscapes and on genome dimension. Probability of hitting is dominated by polymerase landscape curvature, whereas hitting time is dominated by genome dimension. Surface chemistries, compartmentalization, and decay increase hitting times. These results suggest replication to be the first ‘privileged function’ marking the start of Darwinian evolution, possibly in conjunction with clay minerals or preceded by metabolism, whose dynamics evolved mostly during the final period of the search.
Control of theAzollasymbiosis sexual reproduction: ferns to shed light on the origin of floral regulation?
Authors: Dijkhuizen Laura W. , Tabatabaei Badraldin Ebrahim Sayed , Brouwer Paul , Rijken Niels , Buijs Valerie A. , Güngör Erbil , Schluepmann Henriette
Published: September 2020

Azollaferns and the filamentous cyanobacteriaNostoc azollaeconstitute a model symbiosis that enabled colonization of the water surface with traits highly desirable for development of more sustainable crops: their floating mats capture CO2and fixate N2at high rates phototrophically. Their mode of sexual reproduction is heterosporous. Regulation of the transition from vegetative to spore-forming phases in ferns is largely unknown, yet a pre-requisite forAzolladomestication, and of particular interest since ferns represent the sister lineage of seed plants.

Far-red light (FR) induced sporocarp formation inA. filiculoides. Sporocarps obtained, when crossed, verified species attribution of Netherlands strains but not Iran’s Anzali lagoon. FR-responsive transcripts included CMADS1 MIKCC-homologues and miRNA-controlled GAMYB transcription factors in the fern, transporters inN.azollae, and ycf2 in chloroplasts. Loci of conserved miRNA in the fern lineage included miR172, yet FR only induced miR529 and miR535, and reduced miR319 and miR159.

Suppression of sexual reproduction in both gametophyte and sporophyte-dominated plant lineages by red light is likely a convergent ecological strategy in open fields as the active control networks in the different lineages differ. MIKCCtranscription factor control of flowering and flower organ specification, however, likely originated from the diploid to haploid phase transition in the homosporous common ancestor of ferns and seed plants.
To rarefy or not to rarefy: Enhancing diversity analysis of microbial communities through next-generation sequencing and rarefying repeatedly
Authors: Cameron Ellen S. , Schmidt Philip J. , Tremblay Benjamin J.-M. , Emelko Monica B. , Müller Kirsten M.
Published: September 2020

Amplicon sequencing has revolutionized our ability to study DNA collected from environmental samples by providing a rapid and sensitive technique for microbial community analysis that eliminates the challenges associated with lab cultivation and taxonomic identification through microscopy. In water resources management, it can be especially useful to evaluate ecosystem shifts in response to natural and anthropogenic landscape disturbances to signal potential water quality concerns, such as the detection of toxic cyanobacteria or pathogenic bacteria. Amplicon sequencing data consist of discrete counts of sequence reads, the sum of which is the library size. Groups of samples typically have different library sizes that are not representative of biological variation; library size normalization is required to meaningfully compare diversity between them. Rarefaction is a widely used normalization technique that involves the random subsampling of sequences from the initial sample library to a selected normalized library size. Rarefying is often dismissed as statistically invalid because subsampling effectively discards a portion of the observed sequences. Nonetheless, it remains prevalent in practice. Notably, the superiority of rarefying relative to many other normalization approaches has been argued in diversity analysis. Here, repeated rarefying is proposed as a tool for diversity analyses to normalize library sizes. This enables (i) proportionate representation of all observed sequences and (ii) characterization of the random variation introduced to diversity analyses by rarefying to a smaller library size shared by all samples. While many deterministic data transformations are not tailored to produce equal library sizes, repeatedly rarefying reflects the probabilistic process by which amplicon sequencing data are obtained as a representation of the source microbial community. Specifically, it evaluates which data might have been obtained if a particular sample’s library size had been smaller and allows graphical representation of the effects of this library size normalization process upon diversity analysis results.
Integrative Analysis of Spatial and Single-Cell Transcriptomics Reveals Principles of Tissue Organization and Intercellular Communication in Mouse Olfactory Bulb
Authors: Canozo Francisco Jose Grisanti , Zuo Zhen , Martin James F. , Samee Md. Abul Hassan
Published: September 2020

Intercellular communication and spatial organization of cells are two critical aspects of a tissue’s function. Understanding these aspects requires integrating data from single-cell RNA-Seq (scRNA-seq) and spatial transcriptomics (ST), the two cutting edge technologies that offer complementary insights into tissue composition, architecture, and function. Integrating these data types is non-trivial since they differ widely in the number of profiled genes and often do not share marker genes for given cell-types. We developed STANN, a neural network model that overcomes these methodological challenges. Given ST and scRNA-seq data of a tissue, STANN models cell-types in the scRNA-seq dataset from the genes that are profiled by both ST and scRNA-seq. The trained STANN model then assigns cell-types to the ST dataset. We apply STANN to assign cell-types in a recent ST dataset (SeqFISH+) of mouse olfactory bulb (MOB). Our analysis of STANN’s assigned cell-types revealed principles of tissue architecture and intercellular communication at unprecedented detail. We find that cell-type compositions are disproportionate in the tissue, yet their relative proportions are spatially consistent within individual morphological layers. Surprisingly, within a morphological layer, there is a high spatial variation in cell-type colocalization patterns and intercellular communication mechanisms. Our analysis suggests that spatially localized gene regulatory networks may account for such variability in intercellular communication mechanisms.
Structural and dynamic characterization of the C-terminal tail of ErbB2: disordered but not random
Authors: Pinet L. , Wang Y.-H. , Deville C. , Lescop E. , Guerlesquin F. , Badache A. , Bontems F. , Morellet N. , Durand D. , Assrir N. , van Heijenoort C.
Published: September 2020

ErbB2 (or HER2) is a receptor tyrosine kinase overexpressed in some breast cancers, associated with poor prognosis. Treatments targeting the receptor extracellular and kinase domains have greatly improved disease outcome in the last twenty years. In parallel, the structures of these domains have been described, enabling better mechanistic understanding of the receptor function and targeted inhibition. However, ErbB2 disordered C-terminal cytoplasmic tail (CtErbB2) remains very poorly characterized in terms of structure, dynamics and detailed functional mechanism. Yet, it is where signal transduction is triggered, via phosphorylation of tyrosine residues, and carried out, via interaction with adaptor proteins. Here we report the first description of ErbB2 disordered tail at atomic resolution, using NMR and SAXS. We show that although no part of CtErbB2 has any stable secondary or tertiary structure, it has around 20% propensity for a N-terminal helix that is suspected to interact with the kinase domain, and many PPII stretches distributed all along the sequence, forming potential SH3 and WW domains binding sites. Moreover, we identified a long-range transient contact involving CtErbB2 termini. These characteristics suggest new potential mechanisms of auto-regulation and protein-protein interaction.

SIGNIFICANCE

We report here the first description of the receptor tyrosine kinase ErbB2 disordered tail (CtErbB2) at atomic resolution, using NMR and SAXS. We show that although CtErbB2 exhibits no stable structure, it does exhibit partial secondary and tertiary structures likely important for its function. These structural elements are consistent with an active role of the C-terminal tail in the regulation of the receptor’s activity, thanks to the presence of preformed structures for intramolecular interactions, as well as long-range contacts modulating accessibility of those sites and proline interaction sites distinct from the main tyrosine sites. Together, those results reinforce the view that disordered tails of receptors are more than random anchors for partners.
PAX8 orchestrates an angiogenic program through interaction with SOX17
Authors: Chaves-Moreira Daniele , Mitchell Marilyn A. , Arruza Cristina , Rawat Priyanka , Sidoli Simone , Nameki Robbin , Reddy Jessica , Corona Rosario I. , Ma Sisi , Winterhoff Boris , Konecny Gottfried E. , Garcia Benjamin A. , Brady Donita C. , Lawrenson Kate , Morin Patrice J. , Drapkin Ronny
Published: September 2020

Worldwide, the number of new ovarian cancer cases approaches 300,000 with more than 180,000 deaths every year. The low survival-rate reflects the limitations of current therapies and highlights the importance of identifying new therapeutic targets. Despite significant recent efforts to identify novel vulnerabilities in ovarian cancer, none have led to effective durable therapies with improvement in overall survival. PAX8, a lineage-transcription factor, whose expression is a major molecular feature of ovarian carcinomas, represents a novel therapeutic target. Herein, we have identified SOX17 as abona fidePAX8-interacting partner and elucidated the impact of this interaction on the development of ovarian cancer. Importantly, we found that PAX8 and SOX17 regulate tumor angiogenesisin vitroandin vivo. The role of PAX8 and SOX17 in the regulation of angiogenesis reveals a novel function for these factors in regulating the tumor microenvironment and highlight this pathway as a viable therapeutic target.
Pro-drug peptide and its metabolites disrupt amyloid fibrils by destabilizing salt bridge interaction and planar beta-sheet topology
Authors: Adupa Vasista , Mandal Bhubaneswar , Reddy K. Anki
Published: September 2020

The most common age-related neurodegenerative disorder, Alzheimer’s disease, is clinically characterized by continuous neuronal loss resulting in loss of memory and dementia with no cure to date. Amyloid-β(Aβ) aggregates and tau protein are believed to be the causative agents of this pathogenesis. In the present study, we have investigated the effect of the Pro-Drug peptide (PDp) and its metabolites (α-aspartyl &β-aspartyl) on the Aβaggregates using atomistic molecular dynamics simulations. One of the key findings in our work is in the presence ofα-aspartyl as a ligand, the salt bridges which hold the N-terminals together are completely disrupted, thus setting the N-terminals free and exposed entirely to the solvent which can make the aggregation of Aβless severe. The efficiency of the ligands, which are responsible for the disruption of Aβ, depends on the alignment and strength of the repulsive interactions. Besides repulsive interactions, we found that there is a need for hydrogen bonding, which acts as a support for the ligand to stay in the vicinity of the aggregate. Moreover, we have noticed that one of the metabolites, namelyβ-aspartyl, formed more hydrogen bonds with the aggregate than the other ligands and had a different mode of action with the chains of Aβdue to its unique flexible kink in the backbone.
HetF protein is a new divisome component in a filamentous and developmental cyanobacterium
Authors: Xing Wei-Yue , Liu Jing , Wang Zi-Qian , Zhang Ju-Yuan , Zeng Xiaoli , Yang Yiling , Zhang Cheng-Cai
Published: September 2020

Bacterial cell division, with a few exceptions, is driven by FtsZ through a treadmilling mechanism to remodel and constrict the rigid peptidoglycan (PG) layer. Yet, different organisms may differ in the composition of the cell-division complex (divisome). In the filamentous cyanobacteriumAnabaenaPCC 7120,hetFis required for the initiation of the differentiation of heterocysts, cells specialized in N2-fixing cells under combined nitrogen deprivation. In this study, we demonstrate thathetFis expressed in vegetative cells and necessary for cell division in a conditional manner. Under non-permissive conditions, cells of a ΔhetFmutant stop dividing, consistent with increased level of HetF under similar conditions in the wild type. Furthermore, HetF is a membrane protein located at midcell and cell-cell junctions. In the absence of HetF, FtsZ rings are still present in the elongated cells; however, PG remodelling is abolished. This phenotype is similar to that observed with the inhibition of septal PG synthase FtsI. We further reveal that HetF is recruited to or stabilized at the divisome by interacting with FtsI and this interaction is necessary for HetF function in cell division. Our results indicate that HetF is a member of the divisome, and reveal distinct features of the cell-division machinery in cyanobacteria that are of high ecological and environmental importance.

Significance Statement

Cyanobacteria shaped the Earth’s evolutionary history, and are still playing important roles for elementary cycles in different environments. They are consisted of highly diverse species with different cell shape, size and morphology. Although these properties are strongly affected by the process of cytokinesis, the mechanism remains largely unexplored. Using different approaches, we demonstrate that HetF is a new component of the cell division machinery in the filamentous cyanobacteriumAnabaenaPCC 7120. The common and diverged characteristics of cell division in prokaryotes reflect the evolutionary history of different bacteria, as an adaptive measure to proliferate under certain environmental conditions. As a protein for cell differentiation, the recruitment of HetF to the septum illustrates such an adaptive mechanism for cyanobacteria.
Visualizing and isolating iron-reducing microorganisms at single cell level
Authors: Gan Cuifen , Wu Rongrong , Luo Yeshen , Song Jianhua , Luo Dizhou , Li Bei , Yang Yonggang , Xu Meiying
Published: September 2020

Iron-reducing microorganisms (FeRM) play key roles in many natural and engineering processes. Visualizing and isolating FeRM from multispecies samples are essential to understand the in-situ location and geochemical role of FeRM. Here, we visualized FeRM by a “turn-on” Fe2+-specific fluorescent chemodosimeter (FSFC) with high sensitivity, selectivity and stability. This FSFC could selectively identify and locate active FeRM from either pure culture, co-culture of different bacteria or sediment-containing samples. Fluorescent intensity of the FSFC could be used as an indicator of Fe2+concentration in bacterial cultures. By integrating FSFC with a single cell sorter, we obtained three FSFC-labeled cells from an enriched consortia and all of them were subsequently evidenced to be capable of iron-reduction and two unlabeled cells were evidenced to have no iron-reducing capability, further confirming the feasibility of the FSFC.

Importance

Visualization and isolation of FeRM from samples containing multispecies are commonly needed by researchers from different disciplines, such as environmental microbiology, environmental sciences and geochemistry. However, no available method has been reported. In this study, we provid a solution to visualize FeRM and evaluate their activity even at single cell level. Integrating with single cell sorter, FeRM can also be isolated from samples containing multispecies. This method can be used as a powerful tool to uncover the in-situ or ex-situ role of FeRM and their interactions with ambient microbes or chemicals.
LNX1 Modulates Notch1 Signaling to Promote Expansion of the Glioma Stem Cell Population During Temozolomide Therapy in Glioblastoma
Authors: Baisiwala Shivani , Hall Robert H , Saathoff Miranda R , Shireman Jack M , Park Cheol , Warnke Louisa , Hardiman Clare , Wang Jenny Y , Goel Chirag , Budhiraja Shreya , McCortney Kathleen , Horbinski Craig M. , Ahmed Atique U.
Published: September 2020

Glioblastoma (GBM) is the most common primary brain malignancy in adults, with a 100% recurrence rate and a 21-month median survival. Our lab and others have shown that GBM contains a subpopulation of glioma stem cells (GSCs) that expand with chemotherapy, and that may contribute to therapeutic resistance and recurrence in GBM. To investigate the mechanism behind this expansion, we applied gene set expression analysis (GSEA) to patient-derived xenograft (PDX) cells in response to temozolomide (TMZ), the most commonly used chemotherapy against GBM. Results showed significant enrichment of cancer stem cell and cell cycle pathways (FDR<0.25). The ligand of numb protein 1 (LNX1), a known regulator of Notch signaling by targeting negative regulator Numb, is strongly upregulated after TMZ therapy (p<0.0001) and is negatively correlated with survival of GBM patients. LNX1 is also upregulated after TMZ therapy in multiple PDX lines with concomitant downregulations in Numb and upregulations in intracellular Notch1 (NICD). Overexpression of LNX1 results in Notch1 signaling activation and increased CSC populations. In contrast, knocking down LNX1 reverses these changes, causing a significant downregulation of NICD, eliminating induction of functional stemness after TMZ therapy, and resulting in more prolonged median survival in a mouse model. Our data indicate that removing LNX1 activity results in a less aggressive and more chemo-sensitive tumor. Based on this, we propose that during anti-GBM chemotherapy, LNX1-regulated Notch1 signaling promotes stemness and contributes to therapeutic resistance.
Radiation induced toxicity in rectal epithelial stem cell contributes to acute radiation injury in rectum
Authors: Tirado Felipe Rodriguez , Bhanja Payel , Castro-Nallar Eduardo , Olea Ximena Diaz , Salamanca Catalina , Saha Subhrajit
Published: September 2020

Background

Radiation induced rectal epithelial damage is a very common side effect of pelvic radiotherapy and often compromise the life quality and treatment outcome in patients with pelvic malignancies. Unlike small bowel and colon effect of radiation in rectal stem cells has not been explored extensively. Here we demonstrate that Lgr5 positive rectal stem cells are radiosensitive and organoid based transplantation of rectal stem cells mitigates radiation damage in rectum

Methods

C57Bl6 male mice (JAX) at 24 h was exposed to pelvic irradiation (PIR) to determine the radiation effect in pelvic epithelium. Effect PIR on Lgr5-positive rectal stem cells (RSCs) was determined in Lgr5-EGFP-Cre-ERT2 mice exposed to PIR. Effect PIR or clinically relevant fractionated PIR on regenerative response of Lgr5-positive RSCs was examined by lineage tracing assay using Lgr5-eGFP-IRES-CreERT2; Rosa26-CAG-tdTomato mice with tamoxifen administration to activate Cre recombinase and thereby marking the ISC and their respective progeny. Ex vivo three-dimensional organoid cultures were developed from Lgr5-EGFP-Cre-ERT2 mice. Organoid growth was determined by quantifying the budding crypt/total crypt ratio. Organoids from Lgr5-EGFP-ires-CreERT2-TdT mice were transplanted in C57Bl6 male mice exposed to PIR. Engraftment and repopulation of Lgr5-positive RSCs were determined after tamoxifen administration to activate Cre recombinase in recipient mice. Statistical analysis was performed using Log-rank (Mantel-Cox) test and paired two-tailttest.

Result

Exposure to pelvic irradiation significantly damaged rectal epithelium with the loss of Lgr5+ve rectal stem cells. Radio-sensitivity of rectal epithelium was also observed with exposure to clinically relevant fractionated pelvic irradiation. Regenerative capacity of Lgr5+ve rectal stem cells were compromised in response to fractionated pelvic irradiation. Ex-vivo organoid study demonstrated that Lgr5+ve rectal stem cells are sensitive to both single and fractionated radiation. Organoid based transplantation of Lgr5+ve rectal stem cells promote repair and regeneration of rectal epithelium.

Conclusion

Lgr5 positive rectal stem cells are radio-sensitive and contribute to radiation induced rectal epithelial toxicity. Transplantation of Lgr5 positive rectal stem cells mitigates radiation induced rectal injury and promote repair and regeneration process in rectum.
Conserved interactions required for in vitro inhibition of the main protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Authors: Shitrit Alina , Zaidman Daniel , Kalid Ori , Bloch Itai , Doron Dvir , Yarnizky Tali , Buch Idit , Segev Idan , Ben-Zeev Efrat , Segev Elad , Kobiler Oren
Published: September 2020

The COVID-19 pandemic caused by the SARS-CoV-2 requires a fast development of antiviral drugs. SARS-CoV-2 viral main protease (Mpro, also called 3C-like protease, 3CLpro) is a potential target for drug design. Crystal and co-crystal structures of the SARS-CoV-2 Mpro have been solved, enabling the rational design of inhibitory compounds. In this study we analyzed the available SARS-CoV-2 and the highly similar SARS-CoV-1 crystal structures. We identified within the active site of the Mpro, in addition to the inhibitory ligands’ interaction with the catalytic C145, two key H-bond interactions with the conserved H163 and E166 residues. Both H-bond interactions are present in almost all co-crystals and are likely to occur also during the viral polypeptide cleavage process as suggested from docking of the Mpro cleavage recognition sequence. We screenedin silicoa library of 6,900 FDA-approved drugs (ChEMBL) and filtered using these key interactions and selected 29 non-covalent compounds predicted to bind to the protease. Additional screen, using DOCKovalent was carried out on DrugBank library (11,414 experimental and approved drugs) and resulted in 6 covalent compounds. The selected compounds from both screens were testedin vitroby a protease activity inhibition assay. Two compounds showed activity at the 50μM concentration range. Our analysis and findings can facilitate and focus the development of highly potent inhibitors against SARS-CoV-2 infection.
Ribosome stalling caused by the Argonaute-microRNA-SGS3 complex regulates the production of secondary siRNAs in plants
Authors: Iwakawa Hiro-oki , Lam Andy Y.W. , Mine Akira , Fujita Tomoya , Kiyokawa Kaori , Yoshikawa Manabu , Takeda Atsushi , Iwasaki Shintaro , Tomari Yukihide
Published: September 2020

The path of ribosomes on mRNAs can be impeded by various obstacles. One such example is halting of ribosome movement by microRNAs, though the exact mechanism and physiological role remain unclear. Here, we find that ribosome stalling caused by the Argonaute-microRNA-SGS3 complex regulates the production of secondary small interfering RNAs (siRNAs) in plants. We show that the double-stranded RNA-binding protein SGS3 directly interacts with the 3′ end of the microRNA in an Argonaute protein, resulting in ribosome stalling. Importantly, microRNA-mediated ribosome stalling positively correlates with efficient production of secondary siRNAs from target mRNAs. Our results illustrate a role for paused ribosomes in regulation of small RNA function that may have broad biological implications across the plant kingdom.
Scribble controls social behaviors through the regulation of the ERK/Mnk1 pathway
Authors: Moreau Maïté M. , Pietropaolo Susanna , Ezan Jérôme , Robert Benjamin J.A. , Miraux Sylvain , Maître Marlène , Cho Yoon , Crusio Wim E. , Montcouquiol Mireille , Sans Nathalie
Published: September 2020

Social behavior is a basic domain affected in several neurodevelopmental disorders. Indeed, deficits in social interest, interactions and recognition represent core symptoms of Autism Spectrum Disorder but are also found associated with a heterogeneous set of neuropsychiatric and rare disorders. TheSCRIBgene that codes for the polarity protein SCRIBBLE has been identified as a risk gene for spina bifida, the most common type of open neural tube defect, found at high frequencies in autistic patients, as other congenital anomalies, while the deletions/mutations of the 8q24.3 region encompassingSCRIBgenes is associated with multisyndromic and rare disorders. Nonetheless, the potential link betweenSCRIBand ASD-relevant social phenotypes has not been investigated yet. Hence, we performed an extensive behavioral characterization of thecircletailline that carries a mutated version ofScrib. Scribcrc/+mice displayed reduced social interest, lack of preference for social novelty and social reward, and reduced social habituation while other behavioral domains were unaltered. Social deficits were associated with reduced hippocampal volume, upregulation of ERK phosphorylation in specific hippocampal regions, together with increased c-Fos activity in the same brain areas. Importantly, the social alterations were rescued by both direct and indirect pERK inhibition. These results support a specific link between polarity genes, social behaviors and hippocampal functionality, thus suggesting a role forSCRIBin the etiopathology of neurodevelopmental disorders. Furthermore, our data demonstrate the crucial role of the MAPK/ERK signaling pathway, in underlying the social deficits induced bySCRIBmutation, thus supporting its relevance as a therapeutic target.
Nicotinamide mononucleotide (NMN) deamidation by host-microbiome interactions
Authors: Kim Lynn-Jee , Chalmers Timothy J. , Madawala Romanthi , Smith Greg C. , Li Catherine , Das Abhirup , Keung Poon Eric Wing , Wang Jun , Tucker Simon P. , Sinclair David A. , Quek Lake-Ee , Wu Lindsay E.
Published: September 2020

Oral administration of nicotinamide mononucleotide (NMN) is a prominent strategy to elevate nicotinamide adenine dinucleotide (NAD+) levels to treat age-related pathologies, where it is assumed to be directly incorporated into the NAD+metabolome through the canonical recycling pathway. During oral delivery, NMN is exposed to the gut microbiome, which can modify the NAD+metabolome through enzyme activities that are not present in mammals. Here, we show that orally delivered NMN can undergo direct deamidation and incorporation in mammalian tissue via thede novopathway, and that this deamidation is reduced in animals treated with antibiotics to ablate the gut microbiome. Further, we show that antibiotics treatment increases the overall availability of NAD+metabolites in the gut epithelium, with one possibility that the gut microbiome could be in competition with the host for dietary NAD+precursors. Together, these data highlight previously undescribed interactions between orally delivered NMN and the gut microbiome.
IFT-A deficiency in juvenile mice impairs biliary development and exacerbates ADPKD liver disease
Authors: Wang Wei , Pottorf Tana S , Wang Henry H , Dong Ruochen , Kavanaugh Matthew A. , Cornelius Joseph T. , Apte Udayan , Pritchard Michele T , Sharma Madhulika , Tran Pamela V
Published: September 2020

Polycystic liver disease (PLD) is characterized by the growth of numerous biliary cysts and presents in patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD), causing significant morbidity. Interestingly, deletion of intraflagellar transport-B (IFT-B) genes in adult mouse models of ADPKD attenuates severity of PKD and PLD. Here we examine the role of deletion of IFT-A gene, Thm1, in PLD of juvenile and adult Pkd2 conditional knock-out mice. Perinatal deletion of Thm1 results in disorganized and expanded biliary regions, biliary fibrosis, shortened primary cilia on CK19+ biliary epithelial cells, and reduced Notch signaling. In contrast, perinatal deletion of Pkd2 causes PLD, with multiple CK19+ biliary epithelial cell-lined cysts, fibrosis, lengthened primary cilia, and increased Notch and ERK signaling. Perinatal deletion of Thm1 in Pkd2 conditional knock-out mice increased hepatomegaly and liver necrosis, indicating enhanced liver disease severity. In contrast to effects in the developing liver, deletion of Thm1 in adult mice, alone and together with Pkd2, did not cause a biliary phenotype nor affect Pkd2-mutant PLD, respectively. However, similar to juvenile PLD, Notch and ERK signaling were increased in adult Pkd2-mutant cyst-lining cholangiocytes. Taken together, Thm1 is required for biliary tract development, likely by enabling Notch signaling, and proper biliary development restricts PLD severity. Unlike IFT-B genes, Thm1 does not affect hepatic cystogenesis, suggesting divergent regulation of signaling and cystogenic processes in the liver by IFT-B and –A. Notably, increased Notch signaling in cyst-lining cholangiocytes may indicate that aberrant activation of this pathway promotes hepatic cystogenesis, presenting as a novel potential therapeutic target.
Diversity and dynamics of fungi during spontaneous fermentations and association with unique aroma profiles in wine
Authors: Liu Di , Legras Jean-Luc , Zhang Pangzhen , Chen Deli , Howell Kate
Published: September 2020

Microbial activity is an integral part of an agricultural ecosystem and influences the quality of agricultural commodities. Microbial ecology influences grapevine health and crop production, conversion of sugar to ethanol during fermentation, thus wine aroma and flavour. There are regionally differentiated microbial patterns in grapevines and must but how microbial patterns contribute to wine regional distinctiveness (terroir) at small scale (<100 km) is not well defined. Here we characterise fungal communities, yeast populations, andSaccharomyces cerevisiaepopulations during spontaneous fermentation using metagenomics and population genetics to investigate microbial distribution and fungal contributions to the resultant wine. We found differentiation of fungi, yeasts, andS. cerevisiaebetween geographic origins (estate/vineyard), with influences from the grape variety. Growth and dominance ofS. cerevisiaeduring fermentation reshaped the fungal community and showed geographic structure at the strain level. Associations between fungal microbiota diversity and wine chemicals suggest thatS. cerevisiaeplays a primary role in determining wine aroma profiles at a sub-regional scale. The geographic distribution at scales of less than 12 km supports that differential microbial communities, including the dominant fermentative yeastS. cerevisiaecan be distinct in a local setting. These findings provide further evidence for microbial contributions to wineterroir, and perspectives for sustainable agricultural practices to maintain microbial diversity and optimise fermentation function to craft beverage quality.
Spatial analysis of ligand-receptor interaction in skin cancer at genome-wide and single-cell resolution
Authors: Tran M , Yoon S , Teoh M , Andersen S , Lam PY , Purdue P , Raghubar A , Hanson SJ , Devitt K , Jones K , Walters S , Tuong ZK , Kulasinghe A , Monkman J , Soyer HP , Frazer I , Nguyen Q
Published: September 2020

The ability to study cancer-immune cell communication across the whole tumor section without tissue dissociation is needed for cancer immunotherapies, to understand molecular mechanisms and to discover potential druggable targets. In this work, we developed a powerful experimental and analytical toolbox to enable genome-wide scale discovery and targeted validation of cellular communication. We assessed the utilities of five sequencing and imaging technologies to study cancer tissue, including single-cell RNA sequencing and Spatial Transcriptomic (measuring over >20,000 genes), RNA In Situ Hybridization (multiplex 4-12 genes), digital droplet PCR, and Opal multiplex protein staining (4-9 proteins). To spatially integrate multimodal data, we developed a computational method called STRISH that can automatically scan across the whole tissue section for local expression of gene and/or protein markers to recapitulate an interaction landscape across the whole tissue. We evaluated the unique ability of this toolbox to discover and validate cell-cell interactionin situthrough in-depth analysis of two types of cancer, basal cell carcinoma and squamous cell carcinoma, which account for over 70% of cancer cases. We expect that the approach described here will be widely applied to discover and validate ligand receptor interaction in different types of solid cancer tumors.
R2DT: computational framework for template-based RNA secondary structure visualisation across non-coding RNA types
Authors: Sweeney Blake A. , Hoksza David , Nawrocki Eric P. , Ribas Carlos Eduardo , Madeira Fábio , Cannone Jamie J. , Gutell Robin , Maddala Aparna , Meade Caeden , Williams Loren Dean , Petrov Anton S. , Chan Patricia P. , Lowe Todd M. , Finn Robert D. , Petrov Anton I.
Published: September 2020

Non-coding RNAs (ncRNA) are essential for all life, and the functions of many ncRNAs depend on their secondary (2D) and tertiary (3D) structure. Despite proliferation of 2D visualisation software, there is a lack of methods for automatically generating 2D representations in consistent, reproducible, and recognisable layouts, making them difficult to construct, compare and analyse. Here we present R2DT, a comprehensive method for visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,632 templates representing the majority of known structured RNAs, from small RNAs to the large subunit ribosomal RNA. R2DT has been applied to ncRNA sequences from the RNAcentral database and produced >13 million diagrams, creating the world’s largest RNA 2D structure dataset. The software is freely available athttps://github.com/rnacentral/R2DTand a web server is found athttps://rnacentral.org/r2dt.
Repression by hdac3 and dax1 mediates lineage restriction of embryonic stem cells
Authors: Olivieri Daniel , Papasaikas Panagiotis , Lukonin Ilya , Rittirsch Melanie , Hess Daniel , Smallwood Sébastien A. , Stadler Michael B. , Betschinger Joerg
Published: September 2020

Mouse embryonic stem cells (mESCs) give rise to embryonic but not extraembryonic endoderm fates. Here, we identify the mechanism of this lineage barrier and report that the histone deacetylase Hdac3 and the corepressor Dax1 cooperatively restrict transdifferentiation of mESCs by silencing an enhancer of the extraembryonic endoderm-specifying transcription factor (TF) Gata6. This restriction is opposed by the pluripotency TFs Nr5a2 and Esrrb, which promote cell type conversion. Perturbation of the barrier extends mESC potency, and allows formation of 3D spheroids that mimic the spatial segregation of embryonic epiblast and extraembryonic endoderm in early embryos. Overall, this study shows that transcriptional repressors stabilize pluripotency by biasing the equilibrium between embryonic and extraembryonic lineages that is hardwired into the mESC TF network.
Peripheral microtubules ensure asymmetric furrow positioning in neural stem cells
Authors: Thomas Alexandre , Gallaud Emmanuel , Pascal Aude , Serre Laurence , Arnal Isabelle , Richard-Parpaillon Laurent , Savoian Matthew Scott , Giet Régis
Published: September 2020

Neuroblast (NB) cell division is characterized by a basal positioning of the cleavage furrow resulting in a large difference in size between the future daughter cells. In animal cells, furrow placement and assembly is governed by centralspindlin, a highly conserved complex that accumulates at the equatorial cell cortex of the future cleavage site and at the spindle midzone. In contrast to model systems studied so far, these two centralspindlin populations are spatially and temporally separated in NBs. A cortical leading pool is located at the basal cleavage furrow site and a second pool accumulates at the midzone before travelling to the site of the basal cleavage furrow during cytokinesis completion. By manipulating microtubule (MT) dynamics, we show that the cortical centralspindlin population requires peripheral astral microtubules and the Chromosome Passenger Complex (CPC) for efficient recruitment. Loss of this pool does not prevent cytokinesis but enhances centralspindlin levels at the midzone leading to furrow repositioning towards the equator and decreased size asymmetry between daughter cells. Together these data reveal that the asymmetrical furrow placement characteristic of NBs results from a competition between spatially and functionally separate centralspindlin pools in which the cortical pool is dominant and requires peripheral astral microtubules.
Engineered expression of the invertebrate-specific scorpion toxin AaHIT reduces adult longevity and female fecundity in the diamondback mothPlutella xylostella
Authors: Harvey-Samuel T.D. , Xu X. , Lovett E. , Dafa’alla T. , Walker A. , Norman V.C. , Carter R. , Teal J. , Akilan L. , Leftwich P.T. , Alphey L.
Published: September 2020

BACKGROUND

Previous Genetic Pest Management (GPM) systems in diamondback moth (DBM) have relied on expressing lethal proteins (‘effectors’) that are ‘cell-autonomous’ i.e. do not leave the cell they are expressed in. To increase the flexibility of future GPM systems in DBM, we aimed to assess the use of a non cell-autonomous, invertebrate-specific, neurotoxic effector – the scorpion toxin AaHIT. This AaHIT effector was designed to be secreted by expressing cells, potentially leading to effects on distant cells, specifically neuromuscular junctions.

RESULTS

Expression of AaHIT caused a ‘shaking/quivering’ phenotype which could be repressed by provision of an antidote (tetracycline); a phenotype consistent with the AaHIT mode-of-action. This effect was more pronounced when AaHIT expression was driven by theHr5/ie1promoter (82.44% of males, 65.14% of females) rather thanOp/ie2 (57.35% of males, 48.39% of females). Contrary to expectations, the shaking phenotype and observed fitness costs were limited to adults where they caused severe reductions in mean longevity (–81%) and median female fecundity (–93%). qPCR of AaHIT expression patterns and analysis ofpiggyBac-mediated transgene insertion sites suggest that restriction of observed effects to the adult stages may be due to influence of local genomic environment on the tetO-AaHIT transgene.

CONCLUSION

We have demonstrated the feasibility of using non cell-autonomous effectors within a GPM context for the first time in the Lepidoptera, one of the most economically damaging orders of insects. These findings provide a framework for extending this system to other pest Lepidoptera and to other secreted effectors.
The evolution of thermal performance in native and invasive populations of Mimulus guttatus
Authors: Querns Aleah , Wooliver Rachel , Vallejo-Marín Mario , Sheth Seema Nayan
Published: September 2020

1. The rise of globalization has spread organisms beyond their natural range, allowing further opportunity for species to adapt to novel environments and potentially become invaders. Yet, the role of climatic niche evolution in promoting the success of invasive species remains poorly understood. Here, we use thermal performance curves (TPCs) to test hypotheses about thermal adaptation during the invasion process. First, if novel temperature regimes impose strong selection in the introduced range, invasive populations may evolve distinct TPCs relative to native populations. Second, invasive species may not exhibit specialist-generalist tradeoffs and instead may be “masters-of-all” with high maximum performance and broad TPCs. Third, with sufficient time, standing genetic variation, and temperature-mediated selection, TPCs of native and invasive populations may show parallel evolution in response to thermal gradients.

2. To test these hypotheses, we built TPCs for 18 native (United States) and 13 invasive (United Kingdom) populations of the yellow monkeyflower, Mimulus guttatus. We grew clones of multiple genotypes per population across six temperature regimes in growth chambers.

3. Invasive populations have not evolved different thermal optima or performance breadths, providing evidence for evolutionary stasis of thermal performance between the native and invasive ranges after over 200 years post-introduction. Further, both native and invasive populations experienced similar specialist-generalist tradeoffs whereby broad TPCS come at the cost of lower peak performance. Inconsistent with the idea that the degree of thermal specialization varies across spatial or temperature gradients, native and invasive populations did not exhibit adaptive clines in thermal performance breadth with latitude or temperature seasonality. However, thermal optimum increased with mean annual temperature in the native range, indicating some adaptive differentiation among native populations

4.Synthesis: These findings suggest that thermal niches were static during the invasion process, and that general-purpose genotypes, rather than rapid evolution in the introduced range, may promote invasion.
Go Get Data (GGD): simple, reproducible access to scientific data
Authors: Cormier Michael J. , Belyeu Jonathan R. , Pedersen Brent S. , Brown Joseph , Koster Johannes , Quinlan Aaron R.
Published: September 2020

Genomics research is complicated by the inherent difficulty of collecting, transforming, and integrating the numerous datasets and annotations germane to one’s research. Furthermore, these data exist in disparate sources, and are stored in numerous, often abused formats from multiple genome builds. Since these complexities waste time, inhibit reproducibility, and curtail research creativity, we developed Go Get Data (GGD;https://gogetdata.github.io/) as a fast, reproducible approach to installing standardized data recipes.
Clinicopathologic Correlates and Natural History of Atypical Chronic Myeloid Leukemia
Authors: Montalban-Bravo Guillermo , Kanagal-Shamanna Rashmi , Sasaki Koji , Masarova Lucia , Naqvi Kiran , Jabbour Elias , DiNardo Courtney , Takahashi Koichi , Konopleva Marina , Pemmaraju Naveen , Kadia Tapan , Ravandi Farhad , Daver Naval , Borthakur Gautam , Estrov Zeev , Khoury Joseph D. , Loghavi Sanam , Soltysiak Kelly A. , Pierce Sherry , Bueso-Ramos Carlos , Patel Keyur , Verstovsek Srdan , Kantarjian Hagop , Bose Prithviraj , Garcia-Manero Guillermo
Published: September 2020

There is limited data on the clonal mechanisms underlying leukemogenesis, prognostic factors, and optimal therapy for atypical chronic myeloid leukemia (aCML). We evaluated the clinicopathological features, outcomes, and responses to therapy of 65 patients with aCML. Median age was 67 years (range 46-89). The most frequently mutated genes includedASXL1(83%),SRSF2(68%), andSETBP1(58%). Mutations inSETBP1, SRSF2, TET2, andGATA2tended to appear within dominant clones, with frequentSRSF2andSETBP1codominance, while other RAS pathway mutations were more likely to appear as minor clones. Acquisition of new, previously undetectable mutations at transformation was observed in 63% of evaluable patients, the most common involving signaling pathway mutations. Hypomethylating agents were associated with the highest response rates and duration. With a median overall survival of 25 months (95% CI 20-30), intensive chemotherapy was associated with worse OS than other treatment modalities, and allogeneic stem cell transplantation was the only therapy associated with improved outcomes (HR 0.044, 95% CI 0.035-0.593, p=0.007). Age, platelet count, BM blast percentage, and serum LDH levels were independent predictors of survival and were integrated in a multivariable model which allowed to predict 1-year and 3-year survival.
Stability of Human Serum Amyloid A Fibrils
Authors: Wang Wenhua , Hansmann Ulrich H. E.
Published: September 2020

In systemic amyloidosis, Serum amyloid A (SAA) fibril deposits cause widespread damages to tissues and organs that eventually may lead to death. A therapeutically intervention therefore has either to dissolve these fibrils or inhibit their formation. However, only recently has the human SAA fibril structure be resolved at a resolution that is sufficient for development of drug candidates. Here, we use molecular dynamic simulations to probe the factors that modulate the stability of this fibril model. Our simulations suggest that fibril formation starts with the stacking of two misfolded monomers into metastable dimers, with the stacking depending on the N-terminal amyloidogenic regions of different chains forming anchors. The resulting dimers pack in a second step into a two-fold two-layer tetramer that is stable enough to nucleate fibril formation. The stability of the initial dimers is enhanced under acidic conditions by a strong salt bridge and side-chain hydrogen bond network in the C-terminal cavity (residues 23 - 51) but not affected by the presence of the disordered C-terminal tail.

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