bluuebunny/crossref_metadata_2025 huggingface dataset:
A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes
Authors: Uengwetwanit Tanaporn , Pootakham Wirulda , Nookaew Intawat , Sonthirod Chutima , Angthong Pacharaporn , Sittikankaew Kanchana , Rungrassamee Wanilada , Arayamethakorn Sopacha , Wongsurawat Thidathip , Jenjaroenpun Piroon , Sangsrakru Duangjai , Leelatanawit Rungnapa , Khudet Jutatip , Koehorst Jasper J. , Schaap Peter J. , dos Santos Vitor Martins , Tangy Frédéric , Karoonuthaisiri Nitsara
Published: May 2020

The black tiger shrimp (Penaeus monodon) is one of the most prominent farmed crustacean species with an average annual global production of 0.5 million tons in the last decade. To ensure sustainable and profitable production through genetic selective breeding programs, several research groups have attempted to generate a reference genome using short-read sequencing technology. However, the currently available assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA in this species. Here, we report the first chromosome-level whole-genome assembly ofP. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of novel genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several gene groups involved in nutrient metabolism pathways and revealed 67 newly identified growth-associated genes. Our high-quality genome assembly provides an invaluable resource for accelerating the development of improved shrimp strain in breeding programs and future studies on gene regulations and comparative genomics.
Pituitary Tumor Transforming Gene 1orchestrates gene regulatory variation in mouse ventral midbrain during aging
Authors: Gui Yujuan , Thomas Mélanie H. , Garcia Pierre , Karout Mona , Halder Rashi , Michelucci Alessandro , Kollmus Heike , Zhou Cuiqi , Melmed Shlomo , Schughart Klaus , Balling Rudi , Mittelbronn Michel , Nadeau Joseph H. , Williams Robert W. , Sauter Thomas , Buttini Manuel , Sinkkonen Lasse
Published: May 2020

Background

Dopaminergic neurons in the midbrain are of particular interest due to their role in diseases such as Parkinson’s disease and schizophrenia. Genetic variation between individuals can affect the integrity and function of dopaminergic neurons but the DNA variants and molecular cascades modulating dopaminergic neurons and other cells types of ventral midbrain remain poorly defined. Three genetically diverse inbred mouse strains — C57BL/6J, A/J, and DBA/2J — differ significantly in their genomes (~7 million variants), motor and cognitive behavior, and susceptibility to neurotoxins.

Results

To further dissect the underlying molecular networks responsible for these variable phenotypes, we generated RNA-seq and ChIP-seq data from ventral midbrains of the 3 mouse strains. We defined 1000–1200 transcripts that are differentially expressed among them. These widespread differences may be due to altered activity or expression of upstream transcription factors. Interestingly, transcription factors were significantly underrepresented among the differentially expressed genes, and only one TF,Pttg1, showed significant differences among all strains. The changes inPttg1expression were accompanied by consistent alterations in histone H3 lysine 4 trimethylation atPttg1transcription start site. The ventral midbrain transcriptome of three-month-old C57BL/6J congenicPttg1-/-mutants was only modestly altered, but shifted towards that of A/J and DBA/2J in nine-month-old mice. Principle component analysis identified the genes underlying the transcriptome shift and deconvolution of these bulk RNA-seq changes using midbrain single cell RNA-seq data suggested that the changes were occurring in several different cell types, including neurons, oligodendrocytes, and astrocytes.

Conclusion

Taken together, our results show thatPttg1contributes to gene regulatory variation between mouse strains and influences mouse midbrain transcriptome during aging.
scRNA-seq analysis of colon and esophageal tumors uncovers abundant microbial reads in myeloid cells undergoing proinflammatory transcriptional alterations
Authors: Robinson Welles , Stone Joshua K. , Schischlik Fiorella , Gasmi Billel , Kelly Michael C. , Seibert Charlie , Dadkhah Kimia , Gertz E. Michael , Lee Joo Sang , Zhu Kaiyuan , Ma Lichun , Wang Xin Wei , Sahinalp S. Cenk , Patro Rob , Leiserson Mark D.M. , Harris Curtis C. , Schäffer Alejandro A. , Ruppin Eytan
Published: May 2020

The study of the tumor microbiome has been garnering increased attention. We developed a computational pipeline (CSI-Microbes) for identifying microbial reads from single-cell RNA sequencing (scRNA-seq) data. Using a series of controlled experiments and analyses, we performed the first systematic evaluation of the efficacy of recovering microbial UMIs by multiple scRNA-seq technologies, which identified the newer 10x chemistries (3’ v3 and 5’) as the best suited approach. Based on these findings, we analyzed patient esophageal and colorectal carcinomas and found that reads from distinct genera tend to co-occur in the same host cells, testifying to possible intracellular polymicrobial interactions. Microbial reads are disproportionately abundant within myeloid cells that upregulate proinflammatory cytokines likeIL1ΒandCXCL8and downregulate antigen processing and presentation (APP) pathways. The latter, however, are markedly upregulated in infected tumor cells. These results testify that intracellular bacteria predominately reside within co-opted myeloid cells, which inflame the tumor microenvironment and may influence immunotherapy response.
Indoleamine 2,3-dioxygenase-1 expressing aggregate bone marrow dendritic cell populations are associated with systemic T-cell compartment changes in chronic myelomonocytic leukemia
Authors: Mangaonkar Abhishek A. , Reichard Kaaren K. , Binder Moritz , Coltro Giacomo , Lasho Terra L. , Carr Ryan M. , Chiu April , Negron Vivian , Hefazi Mehrdad , Anagnostou Theodora , Villasboas Jose C , Gonsalves Wilson , Gangat Naseema , Shah Mithun , Alkhateeb Hassan B , Al-Kali Aref , Elliott Michelle A , Begna Kebede H , Wolanskyj-Spinner Alexandra P , Litzow Mark R , Hogan William J , Ansell Stephen M , Pardanani Animesh , Tefferi Ayalew , Patnaik Mrinal M.
Published: May 2020

Systemic immune tolerance is not well-characterized in chronic myelomonocytic leukemia (CMML). Due to the presence of clonal plasmacytoid dendritic cells (pDC) in CMML, and the established association of lymph node indoleamine 2,3-dioxygenase-1 (IDO1)-positive (+) DC populations (IDC) with systemic immune tolerance in other malignant contexts, we sought to determine the association of IDO1 expression and bone marrow (BM) DC populations with systemic T-cell compartment changes using primary CMML patient samples (BM, plasma, and peripheral blood mononuclear cells) via immunohistochemistry (IHC), liquid chromatography-mass spectrometry (LC-MS), and time-of-flight mass cytometry (CyTOF). Our results highlight that aggregate BM IDC (CD123 and/or CD11c positive) occur in 33% CMML patients at any disease time-point (IHC), correlate with accentuated tryptophan catabolism (LC-MS, increased kynurenine level, median 4.7 versus 3 microM, P=0.049*), systemic regulatory T-cell expansion (CyTOF, %parent cell type, 14.5 versus 4.9%, P=0.04*) and play a role in disease progression, as evidenced by a higher rate of transformation to acute myeloid leukemia (41 versus 13%, P=0.002**), when compared to CMML patients without BM IDC. Our data also highlight a perturbed immune system in CMML with specific systemic immune signatures, particularly type 1, IL-17 producing helper T, CD4 terminal effector and natural killer cell suppression.

Key Points

Aggregate IDO1+ dendritic cell populations occur in the CMML bone marrow microenvironment, and their presence correlates with disease progression.

Systemic immune microenvironment signatures in CMML indicate an altered T- and natural killer (NK)-cell balance. Specifically, suppression of type 1 helper T (Th1), IL-17 producing helper T (Th17), CD4 terminal effector and NK cells.

IDO1+ bone marrow dendritic cell populations in CMML are associated with a T-cell compartment shift towards a regulatory T cell phenotype.
SCA-1 micro-heterogeneity in the fate decision of dystrophic fibro/adipogenic progenitors
Authors: Giuliani Giulio , Vumbaca Simone , Fuoco Claudia , Gargioli Cesare , Giorda Ezio , Massacci Giorgia , Palma Alessandro , Reggio Alessio , Riccio Federica , Vinci Maria , Castagnoli Luisa , Cesareni Gianni
Published: May 2020

The term micro-heterogeneity refers to non-genetic cell to cell variability observed in a bell-shaped distribution of the expression of a trait within a population. The contribution of micro-heterogeneity to physiology and pathology remains largely uncharacterised. To address such an issue, we investigated the impact of heterogeneity in skeletal muscle fibro/adipogenic progenitors (FAPs) isolated from an animal model of Duchenne muscular dystrophy (DMD), themdxmouse. FAPs play an essential role in muscle homeostasis. However, in pathological conditions or ageing, they are the source of intramuscular infiltrations of fibrotic or adipose tissue. By applying a multiplex flow cytometry assay, we characterised and purified frommdxmuscles two FAP cell states expressing different levels of SCA-1. The two cell states are morphologically identical and repopulate each other after several growth cycles. However, they differ in theirin vitrobehaviour. Cells expressing higher levels of SCA-1 (SCA1-High-FAPs) differentiate more readily into adipocytes while, when exposed to a fibrogenic stimulation, increase the expression ofCOL1A1mRNA. In addition, SCA1-High-FAPs proliferate more extensivelyex vivoand display more proliferating cells in dystrophic muscles. Adipogenesis of FAP cell states is inhibitedin vitroby leukocytes from young dystrophic mice, while leukocytes isolated from aged dystrophic mice are less effective in limiting the adipogenesis of SCA1-High-FAPs suggesting a differential regulatory effect of the microenvironment on micro-heterogeneity. Our data suggest that FAP micro-heterogeneity is modulated in pathological conditions and that this heterogeneity in turn may impact on the behaviour of mesenchymal cells in genetic diseases.
The effect of vascular health factors on white matter microstructure mediates age-related differences in executive function performance
Authors: Hoagey David A. , Lazarus Linh T.T. , Rodrigue Karen M. , Kennedy Kristen M.
Published: May 2020

Even within healthy aging, vascular risk factors can detrimentally influence cognition, with executive functions (EF) particularly vulnerable. Fronto-parietal white matter (WM) connectivity in part, supports EF and may be particularly sensitive to vascular risk. Here, we utilized structural equation modeling in 184 healthy adults (aged 20-94 years of age) to test the hypotheses that: 1) fronto-parietal WM microstructure mediates age effects on EF; 2) higher blood pressure (BP) and white matter hyperintensity (WMH) burden influences this association. All participants underwent comprehensive cognitive and neuropsychological testing including tests of processing speed, executive function (with a focus on tasks that require switching and inhibition) and completed an MRI scanning session that included FLAIR imaging for semi-automated quantification of white matter hyperintensity burden and diffusion-weighted imaging for tractography. Structural equation models were specified with age (as a continuous variable) and blood pressure predicting within-tract WMH burden and fractional anisotropy predicting executive function and processing speed. Results indicated that fronto-parietal white matter of the genu of the corpus collosum, superior longitudinal fasciculus, and the inferior frontal occipital fasciculus (but not cortico-spinal tract) mediated the association between age and EF. Additionally, increased systolic blood pressure and white matter hyperintensity burden within these white matter tracts contribute to worsening white matter health and are important factors underlying age-brain-behavior associations. These findings suggest that aging brings about increases in both BP and WMH burden, which may be involved in the degradation of white matter connectivity and in turn, negatively impact executive functions as we age.
Expandability differences in learning transfer between computerized and non-computerized games
Authors: Shigyo Maki , Tamura Kaori , Okamoto Tsuyoshi
Published: May 2020

Computerized and non-computerized games are used in training designed to improve cognitive function. However, it is unclear which properties of the games influence the transfer of cognitive performance. This study aimed to examine the expandability of this transfer according to the properties of training tools. We introduced two training tools (virtual and standard Rubik’s Cubes) and examined bidirectional transfer between the two cube types and transfer to other cognitive tasks. The results showed that transfer from the virtual cube to the standard cube was greater relative to that observed from the standard cube to the virtual cube. Regarding transfer to other tasks, cognitive transfer did not differ significantly between the virtual and standard cubes, but the training exerted beneficial effects. These results suggest that transfer expandability differed between computerized and non-computerized games. The findings of the study could contribute to the provision of an effective cognitive training programme.
A bimodular PKS platform that expands the biological design space
Authors: Zargar Amin , Valencia Luis , Wang Jessica , Lal Ravi , Chang Samantha , Werts Miranda , Wong Andrew R. , Benites Veronica , Baidoo Edward , Katz Leonard , Keasling Jay D.
Published: May 2020

Traditionally engineered to produce novel bioactive molecules, Type I modular polyketide synthases (PKSs) could be engineered as a new biosynthetic platform for the production ofde novofuels, commodity chemicals, and specialty chemicals. Previously, our investigations manipulated the first module of the lipomycin PKS to produce short chain ketones, 3-hydroxy acids, and saturated, branched carboxylic acids. Building upon this work, we have expanded to multi-modular systems by engineering the first two modules of lipomycin to generate unnatural polyketides as potential biofuels and specialty chemicals inStreptomyces albus. First, we produce 20.6 mg/L of the ethyl ketone, 4,6 dimethylheptanone through a reductive loop exchange in LipPKS1 and a ketoreductase knockouts in LipPKS2. We then show that an AT swap in LipPKS1 and a reductive loop exchange in LipPKS2 can produce the potential fragrance 3-isopropyl-6-methyltetrahydropyranone. Highlighting the challenge of maintaining product fidelity, in both bimodular systems we observed side products from premature hydrolysis in the engineered first module and stalled dehydration in reductive loop exchanges. Collectively, our work expands the biological design space and moves the field closer to the production of “designer” biomolecules.

Highlights

Engineered lipomycin module 1 and module 2 to produce unnatural polyketides as valuable bio-based chemicals

A reductive loop swap and ketoreductase knockout used to produce 20 mg/mL of a novel ethyl ketone, a gasoline replacement

An acyltransferase swap and reductive loop swap successfully produced δ-lactone, a potential fragrant compound

Incomplete reduction and premature hydrolysis observed in engineered modules

Graphical abstract
Homology-guided identification of a conserved motif linking the antiviral functions of IFITM3 to its oligomeric state
Authors: Rahman Kazi , Coomer Charles A. , Majdoul Saliha , Ding Selena , Padilla-Parra Sergi , Compton Alex A.
Published: May 2020

The interferon-inducible transmembrane (IFITM) proteins belong to the Dispanin/CD225 family and inhibit diverse virus infections. IFITM3 reduces membrane fusion between cells and virions through a poorly characterized mechanism. We identified a GxxxG motif in many CD225 proteins, including IFITM3 and proline rich transmembrane protein 2 (PRRT2). Mutation of PRRT2, a regulator of neurotransmitter release, at glycine-305 was previously linked to paroxysmal neurological disorders in humans. Here, we show that glycine-305 and the homologous site in IFITM3, glycine-95, drive protein oligomerization from within a GxxxG motif. Mutation of glycine-95 in IFITM3 disrupted its oligomerization and reduced its antiviral activity against Influenza A and HIV-1. The oligomerization-defective variant was used to reveal that IFITM3 promotes membrane rigidity in a glycine-95-dependent manner. Furthermore, a compound which counteracts virus inhibition by IFITM3, amphotericin B, prevented the IFITM3-mediated rigidification of membranes. Overall, these data suggest that IFITM3 oligomers inhibit virus-cell fusion by promoting membrane rigidity.
Experience-dependent refinement of natural approach responses towards specific visual stimuli in mice
Authors: Procacci Nicole M. , Allen Kelsey M. , Robb Gael E. , Ijekah Rebecca , Hoy Jennifer L.
Published: May 2020

Specific features of visual objects innately draw orienting and approach responses in animals, and provide natural signals of potential reward. In addition, the rapid refinement of innate approach responses enhances the ability of an animal to effectively and conditionally forage, capture prey or initiate a rewarding social experience. However, the neural mechanisms underlying how the brain encodes naturally appetitive stimuli and conditionally transforms stimuli into approach behavior remain unclear. As a first step towards this goal, we have developed a behavioral assay to quantify innate, visually-evoked approach behaviors in freely moving mice presented with simple, computer generated stimuli of varying sizes and speeds in the lower visual field. We found that specific combinations of stimulus features selectively evoked innate approach versus freezing behavioral responses. Surprisingly, we also discovered that prey capture experience selectively modified a range of visually-guided appetitive behaviors, including increasing the probability of approach and pursuit of moving stimuli, as well as altering those visual features that evoked approach. These findings will enable the use of sophisticated genetic strategies to uncover novel neural mechanisms underlying predictive coding, innate behavioral choice, and flexible, state-dependent processing of stimuli in the mouse visual system.

Highlights

Novel stimuli with specific visual features reliably elicit an approach in C57BL/6J mice.

Introduction of motion to stimuli makes freezing the most probable behavioral response.

Spontaneous behavioral responses are tuned to size, speed and visual field location.

Prey capture experience selectively refines natural, visually-evoked approach behaviors.
Fractal Genomics ofSOD1Evolution
Authors: Saeed Mohammad
Published: May 2020

To understand the fundamental processes of gene evolution such as the impact of point mutations and segmental duplications on statistical topography, Superoxide Dismutase-1 (SOD1) orthologous sequences (n=50) were studied. These demonstrated scale invariant self-similarity patterns and long-range correlations (LRC) indicating fractal organization. Phylogenetic hierarchies changed whenSOD1orthologs were grouped according to fractal measures, indicating statistical topographies can be used to study gene evolution. Sliding window k-mer analysis showed that majority of k-mers across allSOD1orthologs were unique, with very few duplications. Orthologs from simpler species contributed minimally (<1% of k-mers) to more complex species. Both simple and complex random processes failed to produce significant matching k-mer sequences forSOD1orthologs. Point mutations causing amyotrophic lateral sclerosis did not impact the fractal organization of humanSOD1. Hence,SOD1did not evolve by a patchwork of repetitive sequences modified by point mutations. Instead, this study proposes thatSOD1gene sequences evolved by regulated interweaving of unique oligomer sequences that led to LRC, signifying convergent evolution.

Summary Statement

SOD1has long-range correlations which resulted not from point mutations, segmental duplications or patching together sequences from simpler organisms. Instead,SOD1underwent convergent evolution by repeated unique sequence assemblies.
SARS-CoV-2 transcriptome analysis and molecular cataloguing of immunodominant epitopes for multi-epitope based vaccine design
Authors: Kushwaha Sandeep Kumar , Kesarwani Veerbhan , Choudhury Samraggi , Gandhi Sonu , Sharma Shailesh
Published: May 2020

SARS-CoV-2 is a single-stranded RNA virus that has caused more than 0.29 million deaths worldwide as of May 2020, and influence of COVID-19 pandemic is increasing continuously in the absence of approved vaccine and drug. Moreover, very limited information is available about SARS-CoV-2 expressed regions and immune responses. In this paper an effort has been made, to facilitate vaccine development by proposing multiple epitopes as potential vaccine candidates by utilising SARS-CoV-2 transcriptome data. Here, publicly available RNA-seq data of SARS-CoV-2 infection in NHBE and A549 human cell lines were used to construct SARS-CoV-2 transcriptome to understand disease pathogenesis and immune responses. In the first step, epitope prediction, MHC class I and II gene identification for epitopes, population coverage, antigenicity, immunogenicity, conservation and crossreactivity analysis with host antigens were performed by using SARS-CoV-2 transcriptome, and in the second step, structural compatibility of identified T-and B-cell epitopes were evaluated with MHC molecules and B-cell receptors through molecular docking studies. Quantification of MHC gene expression was also performed that indicated high variation in allele types and expression level of MHC genes with respect to cell lines. In A549 cell line, HLA-A*30:01:01:01 and HLA-B*44:03:01:01 were highly expressed, whereas 92 variants of HLA-A*24 genes such as HLA-A*24:02:01:01, HLA-A*24:286, HLA-A*24:479Q, HLA-A*24:02:134 and HLA-A*24:02:116 were highly expressed in NHBE cell lines. Prevalence of HLA-A*24 alleles was suggested as risk factors for H1N1 infection, and associated with type-1 diabetes. HLA-C*03:03, linked with male infertility factors was also highly expressed in SARS-CoV-2 infected NHBE cell lines. Finally, three potential T-cell and five B-cell epitopes were selected for molecular docking studies with twenty-two MHC molecules and two B-cell receptors respectively. The results ofin silicoanalysis indicated that proposed epitopes have high potential to recognize immune response of SARS-CoV-2 infection. This study will facilitatein vitroandin vivovaccine related research studies.
Recommendations for sample pooling on the Cepheid GeneXpert®system using the Cepheid Xpert®Xpress SARS-CoV-2 assay
Authors: Becker Michael G. , Taylor Tracy , Kiazyk Sandra , Cabiles Dana R. , Meyers Adrienne F.A. , Sandstrom Paul A.
Published: May 2020

The coronavirus disease 2019 (Covid-19) pandemic, caused by SARS-CoV-2, has resulted in a global testing supply shortage. In response, pooled testing has emerged as a promising strategy that can immediately increase testing capacity. Here, we provide support for the adoption of sample pooling with the point-of-care Cepheid Xpert®Xpress SARS-CoV-2 molecular assay. Corroborating previous findings, the Xpert®Xpress SARS-CoV-2 assay limit of detection was comparable to central laboratory reverse-transcription quantitative PCR tests with observed SARS-CoV-2 detection below 100 copies/mL. The Xpert®Xpress assay detected SARS-CoV-2 after samples with minimum viral loads of 461 copies/mL were diluted into six sample pools. Based on these data, we recommend the adoption of pooled testing with the Xpert®Xpress SARS-CoV-2 assay where warranted by population public health needs. The suggested number of samples per pool, or pooling depth, is unique for each point-of-care test site and should be determined by assessing positive test rates. To statistically determine appropriate pooling depth, we have calculated the pooling efficiency for numerous combinations of pool sizes and test rates. This information is included as a supplemental dataset that we encourage public health authorities to use as a guide to make recommendations that will maximize testing capacity and resource conservation.
Performance assessment of Respiratory Viral ELITe MGB® assay for the quantitative detection of influenza A/B and respiratory syncytial viruses
Authors: Piralla Antonio , Giardina Federica , Fratini Alice , Sapia Davide , Rovida Francesca , Baldanti Fausto
Published: May 2020

Influenza (Flu) and respiratory syncytial virus (RSV) are responsible for lower respiratory tract infections (LRTIs) associated with significant hospitalization among young children. In the present study, the performances of a triplex PCR assay detecting Flu A/B and RSV were compared with our in-house single-plex assays using 160 stored respiratory specimens previously tested using a panel of laboratory-developed real-time RT-PCR. Of them, 61 were positive for FluA, 41 for FluB, and 58 for RSV. All samples were retrospectively quantified with Respiratory Viral (RV) ELITe MGB® Panel (ELITechGroup Molecular Diagnostics, Puteaux, France) processed using ELITe InGenius® system. Overall, the total percentage agreement observed was 93.4% (57/61) for FluA, 92.7% (38/41) for FluB, and 86.2% (50/58) for RSV. A significant correlation of VL values was observed between the two methods for FluA and RSV (ρ= 0.91 and 0.84). This finding was supported by the strength of agreement between the two methods, as showed by the linear regression analysis (R2 =0.84 and 0.80). FluB viral load values measured by RV Panel were less significantly correlated (ρ= 0.77 and R2 =0.56). The bland-Altman analysis showed how 84.2% (48/57) of FluA and 86.0% of RSV (43/50) samples fell within ±1.0 Log10 variation from our laboratory results, while only 21.1% (8/38) of FluB results fell within this range. The great majority of FluB samples (29/30) outside range had values higher than +1.0 Log10 (median +2.1 Log10 range +1.0 to +3.5 Log10). In conclusion, RV ELITe MGB® Panel constitutes a valid and robust system for simultaneous detection and quantification of Flu A/B and RSV.
Analytical and Clinical Comparison of Three Nucleic Acid Amplification Tests for SARS-CoV-2 Detection
Authors: Smith Elizabeth , Zhen Wei , Manji Ryhana , Schron Deborah , Duong Scott , Berry Gregory J.
Published: May 2020

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first identified in December 2019 and has quickly become a worldwide pandemic. In response, many diagnostic manufacturers have developed molecular assays for SARS-CoV-2 under the Food and Drug Administration (FDA) Emergency Use Authorization (EUA) pathway. This study compared three of these assays: the Hologic Panther Fusion SARS-CoV-2 assay (Fusion), the Hologic Aptima SARS-CoV-2 assay (Aptima) and the BioFire Diagnostics COVID-19 test (BioFire), to determine analytical and clinical performance, as well as workflow. All three assays showed a similar limit of detection (LOD) using inactivated virus, with 100% detection ranging from 500-1,000 genome equivalents/ml, whereas use of a quantified RNA transcript standard showed the same trend, but had values ranging from 62.5 to 125 copies/ml, confirming variability in absolute quantification of reference standards. The clinical correlation found that the Fusion and BioFire assays had a positive percent agreement (PPA) of 98.7%, followed by the Aptima assay at 94.7% when compared to the consensus result. All three assays exhibited 100% negative percent agreement (NPA). Analysis of discordant results revealed that all four samples missed by the Aptima assay had Ct values >37 on the Fusion assay.

In conclusion, while all three assays showed similar relative LODs, we showed differences in absolute LODs depending on which standard was employed. In addition, the Fusion and BioFire assays showed better clinical performance, while the Aptima assay showed a modest decrease in overall PPA. These findings should be kept in mind when making platform testing decisions.
Association of zinc-finger antiviral protein (ZAP) binding to viral genomic RNA with attenuation of replication of echovirus 7
Authors: Goonawardane Niluka , Nguyen Dung , Simmonds Peter
Published: May 2020

Previous studies have implicated both zinc finger antiviral protein (ZAP) and oligoadenylate synthetase 3 (OAS3)/RNASeL in the attenuation of RNA viruses with elevated CpG and UpA dinucleotides. Mechanisms and inter-relationships between these two pathways were investigated using an echovirus 7 (E7) replicon with compositionally modified sequences inserted into the 3’untranslated region. ZAP and OAS3 immunoprecipitation (IP) assays provided complementary data on dinucleotide composition effects on binding. Elevated frequencies of alternative pyrimidine/purine (CpA and UpG) and reversed (GpC and ApU) dinucleotides showed no attenuating effect nor specific binding to ZAP by IP. However, the bases 3’ and 5’ to CpG motifs influenced replication and ZAP binding; UCGU enhanced CpG-mediated attenuation and ZAP-binding while A residues shielded CpGs from ZAP recognition. Attenuating effects of elevated frequencies of UpA on replication occurred independently of CpG dinucleotides and bound non-competitively with CpG-enriched RNA consistent with a separate recognition site from CpG. Remarkably, immunoprecipitation with OAS3 antibody reproduced the specific binding to CpG- and UpA-enriched RNA sequences. However, OAS3 and ZAP were coimmunoprecipitated in both ZAP and OAS3 IP, and colocalised with E7 and stress granules (SGs) by confocal microscopy analysis of infected cells. ZAP’s association with larger cellular complexes may mediate the recruitment of OAS3/RNAseL, KHNYN and other RNA degradation pathways.

Importance

We have recently discovered that the OAS3/RNAseL antiviral pathway is essential for restriction of CpG- and UpA-enriched viruses, in addition to the requirement for zinc finger antiviral protein (ZAP). The current study provides evidence for the specific dinucleotide and wider recognition contexts associated with virus recognition and attenuation. It further documents the association of ZAP and OAS3 and association with stress granules and a wider protein interactome that may mediate antiviral effects in different cellular compartments. The study provides a striking re-conceptualisation of the pathways associated with this aspect of antiviral defence.
Glucocorticoid signaling in pancreatic islets modulates gene regulatory programs and genetic risk of type 2 diabetes
Authors: Aylward Anthony , Okino Mei-Lin , Benaglio Paola , Chiou Joshua , Beebe Elisha , Padilla Jose Andres , Diep Sharlene , Gaulton Kyle J
Published: May 2020

Glucocorticoids are key regulators of glucose homeostasis and pancreatic islet function, but the gene regulatory programs driving responses to glucocorticoid signaling in islets and the contribution of these programs to diabetes risk are unknown. In this study we used ATAC-seq and RNA-seq to map chromatin accessibility and gene expression from eight primary human islet samples culturedin vitrowith the glucocorticoid dexamethasone. We identified 2,838 accessible chromatin sites and 1,114 genes with significant changes in activity in response to glucocorticoids. Chromatin sites up-regulated in glucocorticoid signaling were prominently enriched for glucocorticoid receptor binding sites and up-regulated genes were enriched for ion transport and lipid metabolism, whereas down-regulated chromatin sites and genes were enriched for inflammatory, stress response and proliferative processes. Genetic variants associated with glucose levels and T2D risk were enriched in glucocorticoid-responsive chromatin sites, including fine-mapped risk variants at 54 known signals. Among fine-mapped variants in glucocorticoid-responsive chromatin, a likely casual variant at the 2p21 locus had glucocorticoid-dependent allelic effects on beta cell enhancer activity and affectedSIX2andSIX3expression. Our results provide a comprehensive map of islet regulatory programs in response to glucocorticoids through which we uncover a role for islet glucocorticoid signaling in mediating risk of type 2 diabetes.
Nutrient restriction, inducer of yeast meiosis, induces meiotic initiation in mammals
Authors: Zhang Xiaoyu , Gunewardena Sumedha , Wang Ning
Published: May 2020

From yeasts to mammals, the molecular machinery and chromosome structures carrying out meiosis are frequently conserved. However, the signal to initiate meiosis appears divergent: while nutrient restriction induces meiosis in the yeast system, retinoic acid (RA), a chordate morphogen, is necessary but not sufficient to induce meiotic initiation in mammalian germ cells via its target,Stra8. Here, using cultured mouse male germline stem cells without the support of gonadal somatic cells, we show that nutrient restriction in combination with RA robustly inducesSpo11-dependent meiotic DNA double strand breaks (DSBs) andStra8-dependent meiotic gene programs recapitulating those of early meiosisin vivo. Moreover, a distinct network of 11 nutrient restriction-upregulated transcription factor genes was identified, whose expression does not require RA and is associated with early meiosisin vivo. Thus, our study proposes a conserved model, in which nutrient restriction induces meiotic initiation by upregulating transcriptional factors for meiotic gene programs, and provides anin vitroplatform to derive haploid gametes in culture.

One Sentence Summary

nutrient restriction synergizes with retinoic acid to induce mammalian meiotic initiation
Sensing soluble uric acid by Naip1-Nlrp3 platform
Authors: Braga Tarcio Teodoro , Davanso Mariana Rodrigues , Mendes Davi , de Souza Tiago Antonio , de Brito Anderson Fernandes , Cruz Mario Costa , Hiyane Meire Ioshie , de Lima Dhemerson Souza , Nunes Vinicius , Giarola Juliana de Fátima , Souto Denio Emanuel Pires , Próchnicki Tomasz , Lauterbach Mario , Biscaia Stellee Marcela Petris , de Freitas Rilton Alves , Curi Rui , Pontillo Alessandra , Latz Eicke , Saraiva Camara Niels Olsen
Published: May 2020

The immune system can recognize microbes and sterile tissue damage. Among the damage-associated molecular patterns (DAMPs), uric acid is considered a major component which can trigger inflammation. It represents a breakpoint in the evolutionary history of humans as our ancestors lost the uricase gene, the enzyme responsible for its cleavage. High soluble uric acid (sUA) concentration is able to increase IL-1β in murine, but not human macrophages. We observed that sUA increased the mRNA expression ofNaip1in murine macrophages, and, therefore, we hypothesized that the recognition of sUA can be made by a Naip1-Nlrp3 inflammasome platform. Additionally, we used genome-wide transcriptome analysis, functional analyses and structural modeling predictions and observed that virus-transduction of murine Naip1 into human macrophages induced IL-1β after sUA stimulus, besides leading to fatty acid production and an inflammation-related response. Moreover, pharmacologic inhibition and genetic loss of Nlrp3 led to decreased IL-1β production upon sUA stimulus. Surface plasmon resonance and quartz crystal microbalance showed that sUA is able to interact with Naip1. Naip could be a lost receptor for sUA in the evolutionary process and a better understanding of the immune modulatory function of sUA could lead to design rational novel anti-hyperuricemic therapies.
Autocrine inhibition of cell motility can drive epithelial branching morphogenesis in absence of growth
Authors: Rens Elisabeth G. , Zeegers Mathé T. , Rabbers Iraes , Szabó Andras , Merks Roeland M.H.
Published: May 2020

Epithelial branching morphogenesis drives the development of organs such as the lung, salivary gland, kidney and the mammary gland. It involves cell proliferation, cell differentiation and cell migration. An elaborate network of chemical and mechanical signals between the epithelium and the surrounding mesenchymal tissues regulates the formation and growth of branching organs. Surprisingly, when cultured in isolation from mesenchymal tissues, many epithelial tissues retain the ability to exhibit branching morphogenesis even in absence of proliferation. In this work, we propose a simple, experimentally-plausible mechanism that can drive branching morphogenesis in absence of proliferation and cross-talk with the surrounding mesenchymal tissue. The assumptions of our mathematical model derive fromin vitroobservations of the behavior of mammary epithelial cells. These data show that autocrine secretion of the growth factor TGFβ1 inhibits the formation of cell protrusions, leading to curvature dependent inhibition of sprouting. Our hybrid cellular Potts and partial-differential equation model correctly reproduces the experimentally observed tissue-geometry dependent determination of the sites of branching, and it suffices for the formation of self-avoiding branching structures in absence and also in presence of cell proliferation.
Analyzing editosome function in high-throughput
Authors: Del Campo Cristian , Leeder Wolf-Matthias , Reißig Paul , Göringer H. Ulrich
Published: May 2020

Mitochondrial gene expression in African trypanosomes and other trypanosomatid pathogens requires a U-nucleotide specific insertion/deletion-type RNA-editing reaction. The process is catalyzed by a macromolecular protein complex known as the editosome. Editosomes are restricted to the trypanosomatid clade and since editing is essential for the parasites, the protein complex represents a near perfect target for drug intervention strategies. Here we report the development of an improvedin vitroassay to monitor editosome function. The test system utilizes fluorophore-labeled substrate RNAs to analyze the processing reaction by automated, high-throughput capillary electrophoresis (CE) in combination with a laser-induced fluorescence (LIF) readout. We optimized the assay for high-throughput screening (HTS)-experiments and devised a multiplex fluorophore-labeling regime to scrutinize the U-insertion/U-deletion reaction simultaneously. The assay is robust, it requires only nanogram amounts of materials and it meets all performance criteria for HTS-methods. As such the test system should be helpful in the search for trypanosome-specific pharmaceuticals.
Theory of mechano-chemical patterning and optimal migration in cell monolayers
Authors: Boocock Daniel , Hino Naoya , Ruzickova Natalia , Hirashima Tsuyoshi , Hannezo Edouard
Published: May 2020

Collective cell migration offers a rich field of study for non-equilibrium physics and cellular biology, revealing phenomena such as glassy dynamics [1], pattern formation [2] and active turbulence [3]. However, how mechanical and chemical signaling are integrated at the cellular level to give rise to such collective behaviors remains unclear. We address this by focusing on the highly conserved phenomenon of spatio-temporal waves of density [2, 4–8] and ERK/MAPK activation [9–11], which appear bothin vitroandin vivoduring collective cell migration and wound healing. First, we propose a biophysical theory, backed by mechanical and optogenetic perturbation experiments, showing that patterns can be quantitatively explained by a mechano-chemical coupling between three-dimensional active cellular tensions and the mechano-sensitive ERK/MAPK pathway. Next, we demonstrate how this biophysical mechanism can robustly induce migration in a desired orientation, and we determine a theoretically optimal pattern for inducing efficient collective migration fitting well with experimentally observed dynamics. We thereby provide a bridge between the biophysical origin of spatio-temporal instabilities and the design principles of robust and efficient long-ranged migration.
Broad sarbecovirus neutralizing antibodies define a key site of vulnerability on the SARS-CoV-2 spike protein
Authors: Wec Anna Z. , Wrapp Daniel , Herbert Andrew S. , Maurer Daniel , Haslwanter Denise , Sakharkar Mrunal , Jangra Rohit K. , Dieterle M. Eugenia , Lilov Asparouh , Huang Deli , Tse Longping V. , Johnson Nicole V. , Hsieh Ching-Lin , Wang Nianshuang , Nett Juergen H. , Champney Elizabeth , Burnina Irina , Brown Michael , Lin Shu , Sinclair Melanie , Johnson Carl , Pudi Sarat , Bortz Robert , Wirchnianski Ariel S. , Laudermilch Ethan , Florez Catalina , Fels J. Maximilian , O’Brien Cecilia M. , Graham Barney S. , Nemazee David , Burton Dennis R. , Baric Ralph S. , Voss James E. , Chandran Kartik , Dye John M. , McLellan Jason S. , Walker Laura M.
Published: May 2020

Broadly protective vaccines against known and pre-emergent coronaviruses are urgently needed. Critical to their development is a deeper understanding of cross-neutralizing antibody responses induced by natural human coronavirus (HCoV) infections. Here, we mined the memory B cell repertoire of a convalescent SARS donor and identified 200 SARS-CoV-2 binding antibodies that target multiple conserved sites on the spike (S) protein. A large proportion of the antibodies display high levels of somatic hypermutation and cross-react with circulating HCoVs, suggesting recall of pre-existing memory B cells (MBCs) elicited by prior HCoV infections. Several antibodies potently cross-neutralize SARS-CoV, SARS-CoV-2, and the bat SARS-like virus WIV1 by blocking receptor attachment and inducing S1 shedding. These antibodies represent promising candidates for therapeutic intervention and reveal a new target for the rational design of pan-sarbecovirus vaccines.
Interpretable deep learning of label-free live cell images uncovers functional hallmarks of highly-metastatic melanoma
Authors: Zaritsky Assaf , Jamieson Andrew R. , Welf Erik S. , Nevarez Andres , Cillay Justin , Eskiocak Ugur , Cantarel Brandi L. , Danuser Gaudenz
Published: May 2020

Deep convolutional neural networks have emerged as a powerful technique to identify hidden patterns in complex cell imaging data. However, these machine learning techniques are often criticized as uninterpretable “black-boxes” - lacking the ability to provide meaningful explanations for the cell properties that drive the machine’s prediction. Here, we demonstrate that the latent features extracted from label-free live cell images by an adversarial auto-encoding deep convolutional neural network capture subtle details of cell appearance that allow classification of melanoma cell states, including the metastatic efficiency of seven patient-derived xenograft models that reflect clinical outcome. Although trained exclusively on patient-derived xenograft models, the same classifier also predicted the metastatic efficiency of immortalized melanoma cell lines suggesting that the latent features capture properties that are specifically associated with the metastatic potential of a melanoma cell regardless of its origin. We used the autoencoder to generate “in-silico” cell images that amplified the cellular features driving the classifier of metastatic efficiency. These images unveiled pseudopodial extensions and increased light scattering as functional hallmarks of metastatic cells. We validated this interpretation by analyzing experimental image time-lapse sequences in which melanoma cells spontaneously transitioned between states indicative of low and high metastatic efficiency.

Together, this data is an example of how the application of Artificial Intelligence supports the identification of processes that are essential for the execution of complex integrated cell functions but are too subtle to be identified by a human expert.
IgA MAb blocks SARS-CoV-2 Spike-ACE2 interaction providing mucosal immunity
Authors: Ejemel Monir , Li Qi , Hou Shurong , Schiller Zachary A. , Wallace Aaron L. , Amcheslavsky Alla , Yilmaz Nese Kurt , Toomey Jacqueline R. , Schneider Ryan , Close Brianna J. , Chen Da-Yuan , Conway Hasahn L. , Mohsan Saeed , Cavacini Lisa A. , Klempner Mark S. , Schiffer Celia A. , Wang Yang
Published: May 2020

COVID-19 caused by SARS-CoV-2 has become a global pandemic requiring the development of interventions for the prevention or treatment to curtail mortality and morbidity. No vaccine to boost mucosal immunity or as a therapeutic has yet been developed to SARS-CoV-2. In this study we discover and characterize a cross-reactive human IgA monoclonal antibody, MAb362. MAb362 binds to both SARS-CoV and SARS-CoV-2 spike proteins and competitively blocks hACE2 receptor binding, by completely overlapping the hACE2 structural binding epitope. Furthermore, MAb362 IgA neutralizes both pseudotyped SARS-CoV and SARS-CoV-2 in human epithelial cells expressing hACE2. SARS-CoV-2 specific IgA antibodies, such as MAb362, may provide effective immunity against SARS-CoV-2 by inducing mucosal immunity within the respiratory system, a potentially critical feature of an effective vaccine.
Peptide YY: a novel Paneth cell antimicrobial peptide that maintains fungal commensalism
Authors: Pierre Joseph F. , La Torre Diana , Sidebottom Ashley , Kambal Amal , Zhu Xiaorong , Tao Yun , Cham Candace M. , Wang Ling , Harris Katharine G. , Zaborina Olga , Alverdy John , Herzog Herbert , Witchley Jessica , Noble Suzanne M. , Leone Vanessa , Chang Eugene B.
Published: May 2020

Perturbed interactions between the intestinal microbes and host correlate with emergence of fungal virulence. Here we report a previously unknown role for peptide YY (PYY), a described endocrine molecule, as an antimicrobial peptide (AMP) expressed by gut immune epithelial Paneth Cells (PC). PC-PYY differs from other AMPs, including lysozyme, because of limited antibacterial activity, packaging in discrete secretory granules, and selective antifungal activity to virulent hyphae, but not yeast forms ofCandida albicans. The latter action is through binding of cationic PC-PYY to the anionic hyphal surface, resulting in membrane disruption and killing. PC-PYY is compartmentalized to surface mucus, which optimizes activity and prevents conversion to endocrine PYY by dipeptidyl peptidase-IV (DPP-IV). We conclude PC-PYY is a unique AMP with selective antifungal activity that maintains gut fungal commensalism. Compromised PC-PYY action from PC dysfunction and/or mucus depletion in ileal Crohn’s disease may initiate or contribute to disease via fungal pathogenesis.

Highlights

⍰ Paneth Cell PYY (PC-PYY) is an antimicrobial peptide that differs from endocrine-PYY

⍰ PC-PYY is a selective anti-fungal peptide, targeting the virulent form of C.albicans

⍰ PC-PYY is separately packaged, retained by mucus, and released byC. albicanshyphae

⍰ PC-PYY is proposed as essential for maintenance of fungal commensalism in the gut

Graphical Abstract

Model for Paneth cell (PC) PYY action and regulation of fungal commensalisms and potential role in the pathogenesis of ileal Crohn’s Disease (iCD)

(A)In a healthy ileum, commensal yeast reside and do not stimulate PYY1-36release from PCs.(B)Increased virulent hyphae (purple hyphae) results in PYY1-36release from crypt PCs into the mucus. Hyphae are targeted by PYY1-36and killed (red hyphae) to manage the increased fungi community in gut.(C)In a diseased ileum such as iCD, hyphal load induces immune activation and increased inflammation through PC dysfunction (gray PCs) and decreased PYY1-36release or mucus depletion and PC dysfunction.