bluuebunny/crossref_metadata_2025 huggingface dataset:
SF3B1 mutant-induced missplicing of MAP3K7 causes anemia in myelodysplastic syndromes
Authors: Lieu Yen K. , Liu Zhaoqi , Ali Abdullah M. , Wei Xin , Penson Alex , Zhang Jian , An Xiuli , Rabadan Raul , Raza Azra , Manley James L. , Mukherjee Siddhartha
Published: June 2020

SF3B1 is the most frequently mutated RNA splicing factor in multiple neoplasms, including ~25% of myelodysplastic syndromes (MDS) patients. Mortality in MDS frequently results from severe anemia, but the underlying mechanism is largely unknown. Here we elucidate the detailed, elusive pathway by whichSF3B1mutations cause anemia. We demonstrate, in CRISPR-edited cell models, normal human primary cells, and MDS patient cells, that mutant SF3B1 induces a splicing error in transcripts encoding the kinase MAP3K7, resulting in reduced MAP3K7 protein levels and deactivation of downstream target p38 MAPK. We show that disruption of this MAP3K7-p38 MAPK pathway leads to premature downregulation of GATA1, a master regulator of erythroid differentiation, and that this is sufficient to trigger accelerated differentiation and apoptosis. As a result, the overproduced, late staged erythroblasts undergo apoptosis and are unable to mature in the bone marrow. Our findings provide a detailed mechanism explaining the origins of anemia in MDS patients harboringSF3B1mutations.
A Total-Group Phylogenetic Metatree for Cetacea and the Importance of Fossil Data in Diversification Analyses
Authors: Lloyd Graeme T. , Slater Graham J.
Published: June 2020

Abstract

Phylogenetic trees provide a powerful framework for testing macroevolutionary hypotheses, but it is becoming increasingly apparent that inferences derived from extant species alone can be highly misleading. Trees incorporating living and extinct taxa are are needed to address fundamental questions about the origins of diversity and disparity but it has proved challenging to generate robust, species–rich phylogenies that include large numbers of fossil taxa. As a result, most studies of diversification dynamics continue to rely on molecular phylogenies. Here, we extend and apply a recently developed meta–analytic approach for synthesizing previously published phylogenetic studies to infer a well–resolved set of species level, time–scaled phylogenetic hypotheses for extinct and extant cetaceans (whales, dolphins and allies). Our trees extend sampling from the ∼ 90 extant species to over 400 living and extinct species, and therefore allow for more robust inference of macroevolutionary dynamics. While the diversification scenarios we recover are broadly concordant with those inferred from molecular phylogenies they differ in critical ways, most notably in the relative contributions of extinction and speciation rate shifts in driving rapid radiations. Supertrees are often viewed as poor substitute for phylogenies inferred directly from character data but the metatree pipeline overcomes many of the past criticisms leveled at these approaches. Meta–analytic phylogenies provide the most immediate route for integrating fossils into macroevolutionary analyses, the results of which range from untrustworthy to nonsensical without them.
Optimized design of antisense oligomers for targeted rRNA depletion
Authors: Phelps Wesley A. , Carlson Anne E. , Lee Miler T.
Published: June 2020

RNA sequencing (RNA-seq) has become a standard method for quantifying gene expression transcriptome-wide. Although RNA-seq is often paired with polyadenylate (poly(A)) selection to enrich for messenger RNA (mRNA), many applications require alternate approaches to counteract the high proportion of ribosomal RNA (rRNA) in total RNA. Recently, selective rRNA digestion, using RNaseH and antisense DNA oligomers that tile the entire length of target RNAs, has emerged as an alternative to commercial rRNA depletion kits. Here, we present a streamlined, more economical RNaseH-mediated rRNA depletion method with substantially lower up-front costs, using shorter antisense oligos only sparsely tiled along the target RNA, in a digestion reaction of only 5 minutes. We introduce a novel Web tool, Oligo-ASST, that simplifies oligo design to target regions with optimal thermodynamic properties, and additionally can generate compact, common oligo pools that simultaneously target divergent RNAs, e.g. across different species. We demonstrate the efficacy of these strategies by designing oligo sets to deplete rRNA inXenopus laevisand in zebrafish, which expresses two distinct versions of rRNAs during embryogenesis. The resulting RNA-seq libraries reduce rRNA to <5% of aligned reads, on par with poly(A) selection, and also reveal expression of many non-adenylated RNA species. Oligo-ASST is freely available athttps://mtleelab.pitt.edu/oligoto design antisense oligos for any taxon or to target any abundant RNA for depletion.

Abstract Figure
An insight into transcriptome ofLlaNACGene Over-expressing Tobacco Plants
Authors: Singh Sadhana , Grover Atul
Published: June 2020

Here, we report a whole transcriptome analysis ofLlaNACgene (fromLepidium latifolium) containing transgenic tobacco line (NC10) and wild type (WT), to attain deeper knowledge into the downstream genes activated by the over-expressing transgene. Transcriptome sequencing of NC10 and WT samples generated huge data using Illumina platform. The maximum number of unigenes GO annotated were of Biological process (8988, 3209) followed by molecular function (5155, 2577) and cellular components (3826, 1583) for WT and NC10 samples respectively. KEGG Pathway analysis revealed the unigenes were enriched in different functional pathway categories. The unigenes whose products involved in carbohydrate metabolism, glycan metabolism, and secondary metabolites synthesis were more for NC10 library in comparison to WT. Greater variety of transcription factors were involved in transgenic than wild-type plants. Genes like, Copia-like retrotransposable element, Peroxidase 64-like, Peptidyl-prolyl cis-trans isomerise, Cytochrome P450, Lipoyl synthase, CBL-interacting serine/threonine-protein kinase 5-like etc. were found differentially expressed in both the samples. Promoter analysis of these differentially expressed genes have elements for defence and stress response, abscisic acid response, shoot specific expression and light response, etc. In summary this study reports the involvement of the overexpressed genes in the dual action of cold tolerance and biomass accumulation, as sugars participate in both of these activities of the cell.
Efficient precisein vivobase editing in adult dystrophic mice
Authors: Xu Li , Zhang Chen , Li Haiwen , Wang Peipei , Gao Yandi , Mohler Peter J. , Mokadam Nahush A. , Ma Jianjie , Arnold William D. , Han Renzhi
Published: June 2020

Background

Recent advances in the base editing technology have created an exciting opportunity to precisely correct disease-causing mutations. However, the large size of base editors and their inherited off-target activities pose challenges forin vivobase editing. Moreover, the requirement of a protospacer adjacent motif (PAM) sequence within a suitable window near the mutation site further limits the targeting feasibility. In this work, we rationally improved the adenine base editor (ABE) to overcome these challenges and demonstrated the exceptionally high efficiency to precisely edit the Duchenne muscular dystrophy (DMD) mutation in adult mice.

Methods

We employed a fluorescence reporter assay to assess the feasibility of ABE to correct the dystrophin mutation inmdx4cvmice. The intein protein trans-splicing (PTS) was used to split the oversized ABE into two halves for efficient packaging into adeno-associated virus 9 (AAV9). The ABE with broadened PAM recognition (ABE-NG) was rationally re-designed for improved off-target RNA editing activity and on-target DNA editing efficiency. Themdx4cvmice at the 5 weeks of age receiving intramuscular or intravenous injections of AAV9 carrying the improved ABE-NG were analyzed at 10 weeks or 10 months of age. The editing outcomes were analyzed by Sanger and deep sequencing of the amplicons, immunofluorescence staining, Western blot and contractile function measurements. The off-target activities, host immune response and long-term toxicity were analyzed by deep sequencing, ELISA and serological assays, respectively.

Results

We showed efficientin vitrobase correction of the dystrophin mutation carried inmdx4cvmice using ABE-NG. The super-fast intein-splits of ABE-NG enabled the expression of full-length ABE-NG and efficient AAV9 packaging. We rationally improved ABE-NG with eliminated off-target RNA editing activity and minimal PAM requirement, and packaged into AAV9 (AAV9-iNG). Intramuscular and intravenous administration of AAV9-iNG resulted in dystrophin restoration and functional improvement. At 10 months after AAV9-iNG treatment, a near complete rescue of dystrophin was measured inmdx4cvmouse hearts. The off-target activities remained low and no obvious toxicity was detected.

Conclusions

This study highlights the promise of permanent base editing using iABE-NG for the treatment of monogenic diseases, in particular, the genetic cardiomyopathies.
Topoisomerase IB interacts with genome segregation proteins and is involved in multipartite genome maintenance inDeinococcus radiodurans
Authors: Kota Swathi , Chaudhary Reema , Mishra Shruti , Misra Hari S.
Published: June 2020

Deinococcus radiodurans, an extremophile, resistant to many abiotic stresses including ionizing radiation, has 2 type I topoisomerases (drTopo IA and drTopo IB) and one type II topoisomerase (DNA gyrase). The role of drTopo IB in guanine quadruplex DNA (G4 DNA) metabolism was shownin vitro. Here we report thatD. radioduranscells lacking drTopo IB (ΔtopoIB) show sensitivity to G4 DNA binding drug (NMM) under normal growth conditions. The activity of G4 motif containing promoters likemutLandrecQwas reduced in the presence of NMM in mutant cells. In mutant cells, the percentage of anucleated cells was more while the ploidy numbers of genome elements were less as compared to wild type. Protein-protein interaction studies showed that drTopo IB interacts with genome segregation and DNA replication initiation (DnaA) proteins. The typical patterns of cellular localization of GFP-PprA were affected in the mutant cells. Microscopic examination ofD. radioduranscells expressing drTopo IB-RFP showed its localization on nucleoid forming a streak parallel to the old division septum and perpendicular to newly formed septum. These results together suggest the role of drTopo IB in genome maintenance in this bacterium.
Acquisition of hypoxia inducibility by oxygen sensing N-terminal cysteine oxidase in spermatophytes
Authors: Weits Daan A. , Zhou Lina , Giuntoli Beatrice , Carbonare Laura Dalle , Iacopino Sergio , Piccinini Luca , Shukla Vinay , Bui Liem T. , Novi Giacomo , van Dongen Joost T. , Licausi Francesco
Published: June 2020

N-terminal cysteine oxidases (NCOs) are enzymes that use molecular oxygen to oxidize the amino-terminal cysteine of specific proteins, thereby initiating the proteolytic N-degron pathway and thus conferring them oxygen-dependent instability. To expand the characterization of the plant family of NCOs (PCOs), we performed a phylogenetic analysis across different plant taxa in terms of sequence similarity and transcriptional regulation. Based on this survey, we propose a distinction of PCOs into two main groups: A-type and B-type sequences. A-type PCOs are conserved across all plant species and are generally unaffected at the mRNA level by oxygen availability. Instead, B-type PCOs differentiated in spermatophytes to acquire specific amino acid features and transcriptional regulation in response to hypoxia. Both groups of PCO proteins possess the ability to destabilize Cys-initiating proteins. Indeed, the inactivation of two A-type PCOs inArabidopsis thaliana, PCO4 and PCO5, is sufficient to activate, at least partially, the anaerobic response in young seedlings, whereas the additional removal of B-type PCOs leads to a stronger induction of anaerobic genes and impairs plant growth and development. Our results show that both PCO types are required to regulate the anaerobic response in angiosperm. Therefore, while it is possible to distinguish two clades within the PCO family, separated by both amino acid features and transcriptional regulation, we conclude that they both contribute to restrain the anaerobic transcriptional program in normoxic conditions and together generate a molecular switch to toggle the hypoxic response in Arabidopsis.

One sentence summary

Hypoxic induction of Plant Cysteine Oxidases has been acquired and fixed in seed plants by ancestor proteins able to initiate the proteolysis of Cys-initiating protein substrates by the Arg/N-degron pathway.
Increased baseline RASGRP1 signals Enhance Stem Cell Fitness during Native Hematopoiesis
Authors: Karra Laila , Romero-Moya Damia , Ksionda Olga , Krush Milana , Gu Zhaohui , Mues Marsilius , Depeille Philippe , Mullighan Charles , Roose Jeroen P.
Published: June 2020

Oncogenic mutations inRASgenes, likeKRASG12DorNRASG12D, trap Ras in the active state and cause myeloproliferative disorder and T cell leukemia (T-ALL) when induced in the bone marrow viaMx1CRE. The RAS exchange factor RASGRP1 is frequently overexpressed in T-ALL patients. In T-ALL cell lines overexpression of RASGRP1 increases flux through the RASGTP/RasGDP cycle. Here we expandedRASGRP1expression surveys in pediatric T-ALL and generated aRoLoRiGmouse model crossed toMx1CREto determine the consequences of induced RASGRP1 overexpression in primary hematopoietic cells. RASGRP1-overexpressing, GFP-positive cells outcompeted wild type cells and dominated the peripheral blood compartment over time. RASGRP1 overexpression bestows gain-of-function colony formation properties to bone marrow progenitors in medium containing limited growth factors. RASGRP1 overexpression enhances baseline mTOR-S6 signaling in the bone marrow, but notin vitrocytokine-induced signals. In agreement with these mechanistic findings, hRASGRP1-ires-EGFP enhances fitness of stem- and progenitor- cells, but only in the context of native hematopoiesis. RASGRP1 overexpression is distinct fromKRASG12DorNRASG12D, does not cause acute leukemia on its own, and leukemia virus insertion frequencies predict that RASGRP1 overexpression can effectively cooperate with lesions in many other genes to cause acute T cell leukemia.
Liftoff: an accurate gene annotation mapping tool
Authors: Shumate Alaina , Salzberg Steven L.
Published: June 2020

Improvements in DNA sequencing technology and computational methods have led to a substantial increase in the creation of high-quality genome assemblies of many species. To understand the biology of these genomes, annotation of gene features and other functional elements is essential; however for most species, only the reference genome is well-annotated. One strategy to annotate new or improved genome assemblies is to map or ‘lift over’ the genes from a previously-annotated reference genome. Here we describe Liftoff, a new genome annotation lift-over tool capable of mapping genes between two assemblies of the same or closely-related species. Liftoff aligns genes from a reference genome to a target genome and finds the mapping that maximizes sequence identity while preserving the structure of each exon, transcript, and gene. We show that Liftoff can accurately map 99.9% of genes between two versions of the human reference genome with an average sequence identity >99.9%. We also show that Liftoff can map genes across species by successfully lifting over 98.4% of human protein-coding genes to a chimpanzee genome assembly with 98.7% sequence identity.

Availability

The source code for Liftoff is available athttps://github.com/agshumate/Liftoff
A Synthetic Single-Stranded Dual-Template Oligonucleotide as a Reference Standard for Monochrome Multiplex qPCR Measurements of Average Telomere Length
Authors: Cawthon Richard M.
Published: June 2020

Quantitative PCR is frequently used to measure average telomere length (TL) relative to the TL of a reference DNA sample of the investigator’s choosing. This makes comparisons of TLs across studies and laboratories difficult. Here we demonstrate that a single synthetic single-stranded dual-template oligonucleotide (DTO) containing both a telomere repeat sequence (T) and a segment of the human beta-globin (HBB) single copy gene (S) can be used as a universal reference standard for monochrome multiplex quantitative PCR (MMqPCR) measurements of average TL using SYBR Green I as the only fluorescent reporter dye. A set of twelve concentrations of the DTO is prepared by serial 3-fold dilutions, to a lowest concentration of ~20 copies per μl. The 5 highest concentrations are used for the T standard curve, and the 5 lowest concentrations are used for the S standard curve. For each reaction 5 μl containing approximately 3 ng of genomic DNA (or one of the DTO dilutions) is mixed with 5 μl of a 2x MasterMix containing the primers for T and S amplification, and MMqPCR is performed. The design of the primers and thermal cycling profile allows all T amplification signals to be collected before exponential amplification of the S signal begins. Exponential amplification from S is then carried out in a temperature range that keeps the telomere product fully melted and therefore unable to influence the S amplification signal. The T value for each DNA sample is the Standard Curve DTO dilution that contains the same number of copies of the telomere sequence as the experimental sample, and the S value is the DTO dilution that contains the same number of copies of the single copy gene sequence as the experimental sample. Dividing the first dilution by the second dilution yields an absolute T/S ratio, since it is expressed relative to the fixed 1:1 T/S ratio that is built into the DTO by design. Absolute T/S ratios for average TL in 48 human DNA samples determined by this method correlated strongly with mean Terminal Restriction Fragment (mTRF) lengths for the same DNA samples determined by the Southern Blot method (R-squared = 0.801). This DTO and the accompanying protocol may facilitate the standardization of average telomere length measurements and analyses across laboratories.
Amino acid oxidation constrained protein sequences during evolution: an analysis of a model bacterium
Authors: González-Tortuero Enrique , Rodriguez-Rojas Alexandro
Published: June 2020

Within the cell, there are compartments and local conditions that may constrain amino acid sequence. Life emerged in an anoxic world but releasing a photosynthesis by-product, the molecular oxygen, forced adaptive changes to counteract its toxicity. Several mechanisms evolved to balance the intracellular redox state and maintain a reductive environment more compatible with many essential biological functions. Here, we statistically interrogate the aminoacidic composition ofE. coliproteins and investigate how the proneness or susceptibility to oxidation of amino acid biased their sequences. By sorting the proteins in five different compartments: cytoplasm, internal membrane, periplasm, outer membrane and extracellular; we found that various oxidative lesions constrain protein composition, that there is a dependency of the cellular compartments and there is an impact on the evenness distribution or frequency. This analysis is necessary from an evolutionary point of view to reflect how the oxidative atmosphere could restrict protein composition and probably imposed a trend in the codon bias.
Cyclo olefin polymer-based solvent-free mass-productive microphysiological systems
Authors: Yamanaka Makoto , Wen Xiaopeng , Imamura Satoshi , Sakai Risako , Terada Shiho , Kamei Ken-ichiro
Published: June 2020

A microphysiological system (MPS) holds a great promise for drug screening and toxicological testing as an alternative to animal models. However, this platform has several issues in terms of the materials used (e.g., polydimethylsiloxane), such as the absorbance of tested drug candidates and fluorescent dyes by the material, as well as the effect on cultured cellular status, thus misleading the results obtained from cell assays and fabrication processes. Hence, to eliminate the issues mentioned above, we developed a cyclo olefin polymer (COP)-based MPS via photobonding process using vacuum ultraviolet (VUV), named COP-VUV-MPS. COP-VUV-MPS showed better chemical resistance and avoided molecule absorption. COP-VUV-MPS could maintain the stemness of environmentally sensitive human-induced pluripotent stem cells without causing undesired cellular phenotypes and gene expression. These results suggested that COP-VUV-MPS might be broadly used for the advancement of MPS and applications in drug development and in vitro toxicological testing.
IsoMaTrix: a framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations
Authors: West Jeffrey , Ma Yongqian , Kaznatcheev Artem , Anderson Alexander R. A.
Published: June 2020

Evolutionary game theory describes frequency-dependent selection for fixed, heritable strategies in a population of competing individuals using a payoff matrix, typically described using well-mixed assumptions (replicator dynamics). IsoMaTrix is an open-source package which computes the isoclines (lines of zero growth) of matrix games, and facilitates direct comparison of well-mixed dynamics to structured populations in two or three dimensions. IsoMaTrix is coupled with a Hybrid Automata Library module to simulate structured matrix games on-lattice. IsoMaTrix can also compute fixed points, phase flow, trajectories, velocities (and subvelocities), delineated “region plots” of positive/negative strategy velocity, and uncertainty quantification for stochastic effects in structured matrix games. We describe a result obtained via IsoMaTrix’s spatial games functionality, which shows that the timing of competitive release in a cancer model (under continuous treatment) critically depends on the initial spatial configuration of the tumor.

Availability and implementation

The code is available at:https://github.com/mathonco/isomatrix.
ANALYSIS OF MICROBIAL DIVERSITY IN RAW FISH CEVICHE
Authors: Ramírez-Martínez M. E. , Rodríguez-Castillejos G. C. , Hernández-Jiménez M. C. , Ramírez-Quintanilla L. Y. , Siller-López F. , Acosta-Cruz E. , Martínez-Montoya H.
Published: June 2020

Ceviche is a traditional dish made from raw fish meat marinated in lime juice without any heat cooking step throughout its preparation process. Although the use of organic acids as antibacterial agents is well known; recent research indicates that lime juice actually can reduce the risk ofV. parahemolyticusinfections but it is ineffective against other potential pathogens. Despite the fact that fresh fish meat is safe; exposed organs including skin, gills and guts represent a potential source of bacterial contamination. In Mexico, diarrheal diseases are caused mainly by contaminated food; it is estimated that almost 67% of infections are due the presence of bacterial agents mainly in frozen and fresh fish. The main objective of this study was to estimate the taxonomic diversity of microbial species present in ready-to-eat ceviche using a metagenomic approach. Six samples of commercially available ceviche were subjected to DNA high throughput sequencing and bioinformatics analyses, we identified between 65,000 and 131,000 reads per sample. The predominant phyla identified through the samples wereProteobacteria,BacteroidetesandFirmicutes. We discuss the factors involved in the microbiological quality of this kind of raw foods and how they influence the bacterial diversity within the analyzed samples.
Evaluation of ExoU inhibitors in aPseudomonas aeruginosascratch infection assay
Authors: Foulkes Daniel M. , McLean Keri , Harris Joscelyn , Haneef Atikah S. , Fernig David G. , Winstanley Craig , Berry Neil , Kaye Stephen B.
Published: June 2020

Pseudomonas aeruginosahas recently been highlighted by the World Health Organisation (WHO) as a major threat with high priority for the development of new therapies. The type III secretion system ofP. aeruginosadelivers the toxin ExoU into the cytosol of target host cells, where its plasma membrane directed phospholipase activity induces rapid cell lysis. Therefore, inhibition of the phospholipase activity of ExoU would be an important treatment strategy inP. aeruginosainfections. We evaluated a panel of ExoU small molecule inhibitors, previously identified from high throughput cellular based assays, and analysed their inhibition of ExoU phospholipase activityin vitro. A corneal epithelial (HCE-T) scratch and infection model using florescence microscopy, and cell viability assays, were used to test the efficacy of compounds to inhibit ExoU fromP. aeruginosa. Compounds Pseudolipasin A, compound A and compound B were effective at mitigating ExoU mediated cytotoxicity after infection at concentrations as low as 0.5 μM. Importantly, by using the antimicrobials moxifloxacin and tobramycin to control bacterial load, these assays were extended from 6 h to 24 h.P. aeruginosaremained cytotoxic to HCE-T cells with moxifloxacin, present at the minimal inhibitory concentration (MIC) for 24 h, but, when used in combination with either PSA, compound A or compound B, partial scratch healing was observed. These results provide evidence that ExoU inhibitors could be used in combination with certain antimicrobials as a novel means to treat clinical infections of ExoU producingP. aeruginosa.
A Decision Analytic Approach for Social Distancing Policies During COVID-19 Pandemic
Authors: Ertem Zeynep , Araz Ozgur M. , Cruz-Aponte Mayteé
Published: June 2020

The COVID-19 pandemic has become a crucial public health issue in many countries including the United States. In the absence of the right vaccine strain and sufficient antiviral stockpiles on hand, non-pharmaceutical interventions have become valuable public health tools at the early stages of the pandemic and they are employed by many countries across the globe. These interventions are designed to increase social distancing between individuals to reduce the transmission of the virus and eventually dampen the burden on the healthcare system. The virus transmissibility is a function of the average number of contacts individuals have in their communities and it is highly dependent on population density and daily mobility patterns, along with other social factors. These show significant variation across the United States. In this article, we study the effectiveness of social distancing measures in communities with different population density. Specifically, first we show how the empirical estimation of reproduction number differs for two completely different states, thus the experience of the COVID-19 outbreak is drastically different, suggesting different outbreak growth rates in practice. Second, we develop an age-structured compartmental model for simulating the disease spread in order to demonstrate the variation in the observed outbreak characteristics. We find that early trigger and late trigger options present a trade-off between the peak magnitude and the overall death toll of the outbreak which may also vary across different populations.
Characterization of a novel, low-cost, scalable vaporized hydrogen peroxide system for sterilization of N95 respirators and other COVID-19 related personal protective equipment
Authors: Dave Nikhil , Pascavis Katie Sue , Patterson John , Wallace David , Chowdhury Abhik , Abbaszadegan Morteza , Alum Absar , Herckes Pierre , Zhang Zhaobo , Kozicki Michael , Forzani Erica , Mora S. Jimena , Chang Josh , Ewell Clinton , Smith Tyler , Naufel Mark
Published: June 2020

Due to the virulence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for the respiratory disease termed COVID-19, there has been a significant increase in demand for surgical masks and N95 respirators in medical clinics as well as within communities operating during the COVID-19 epidemic. Thus, community members, business owners, and even medical personnel have resorted to alternative methods for sterilizing face coverings and N95 respirators for reuse. While significant work has shown that vaporized hydrogen peroxide (VHP) can be used to sterilize N95 respirators, the cost and installation time for these sterilization systems limit their accessibility. To this end, we have designed and constructed a novel, cost-effective, and scalable VHP system that can be used to sterilize N95 respirators and other face coverings for clinical and community applications. N95 respirators inoculated with P22 bacteriophage showed a greater than 6-log10reduction in viral load when sterilized in the VHP system for one 60-minute cycle. Further, N95 respirators treated with 20 cycles in this VHP system showed comparable filtration efficiency to untreated N95 respirators in a 50 to 200 nanometer particulate challenge filtration test. While a 23% average increase in water droplet roll-off time was observed for N95 respirators treated with 5 cycles in the sterilization, no breakdown in fluid resistance was detected. These data suggest that our VHP system is effective in sterilizing N95 respirators and other polypropylene masks for reuse. Relating to the present epidemic, deployment of this system reduces the risk of COVID-19 community transmission while conserving monetary resources otherwise spent on the continuous purchase of disposable N95 respirators and other face coverings. In summary, this novel, scientifically validated sterilization system can be easily built at a low cost and implemented in a wide range of settings.
A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2
Authors: Maricic Tomislav , Nickel Olaf , Aximu-Petri Ayinuer , Essel Elena , Gansauge Marie , Kanis Philipp , Macak Dominik , Riesenberg Stephan , Bokelmann Lukas , Zeberg Hugo , Meyer Matthias , Borte Stephan , Pääbo Svante
Published: June 2020

SARS-CoV-2 causes substantial morbidity and mortality in elderly and immunocompromised individuals, particularly in retirement homes, where transmission from asymptomatic staff and visitors may introduce the infection. Here we present a cheap and fast approach to detect SARS-CoV-2 in single or pooled gargle lavages (“mouthwashes”). With this approach, we test all staff at a nursing home daily over a period of three weeks in order to reduce the risk that the infection penetrates the facility. This or similar approaches could be implemented to protect hospitals, nursing homes and other institutions in this and future viral epidemics.
Reproducibility in the UK Biobank of Genome-Wide Significant Signals Discovered in Earlier Genome-wide Association Studies
Authors: O’Sullivan Jack W. , Ioannidis John P. A.
Published: June 2020

With the establishment of large biobanks, discovery of single nucleotide polymorphism (SNPs) that are associated with various phenotypes has been accelerated. An open question is whether SNPs identified with genome-wide significance in earlier genome-wide association studies (GWAS) are replicated also in later GWAS conducted in biobanks. To address this question, the authors examined a publicly available GWAS database and identified two, independent GWAS on the same phenotype (an earlier, “discovery” GWAS and a later, replication GWAS done in the UK biobank). The analysis evaluated 136,318,924 SNPs (of which 6,289 had reached p<5e-8 in the discovery GWAS) from 4,397,962 participants across nine phenotypes. The overall replication rate was 85.0% and it was lower for binary than for quantitative phenotypes (58.1% versus 94.8% respectively). There was a18.0% decrease in SNP effect size for binary phenotypes, but a 12.0% increase for quantitative phenotypes. Using the discovery SNP effect size, phenotype trait (binary or quantitative), and discovery p-value, we built and validated a model that predicted SNP replication with area under the Receiver Operator Curve = 0.90. While non-replication may often reflect lack of power rather than genuine false-positive findings, these results provide insights about which discovered associations are likely to be seen again across subsequent GWAS.
Explainable CNN-attention Networks (C-Attention Network) for Automated Detection of Alzheimer’s Disease
Authors: Wang Ning , Chen Mingxuan , Subbalakshmi K.P.
Published: June 2020

Abstract

In this work we propose three explainable deep learning architectures to automatically detect patients with Alzheimer’s disease based on their language abilities. The architectures use: (1) only the part-of-speech features; (2) only language embedding features and (3) both of these feature classes via a unified architecture. We use self-attention mechanisms and interpretable 1-dimensional Convolutional Neural Network (CNN) to generate two types of explanations of the model’s action: intra-class explanation and inter-class explanation. The inter-class explanation captures the relative importance of each of the different features in that class, while the inter-class explanation captures the relative importance between the classes. Note that although we have considered two classes of features in this paper, the architecture is easily expandable to more classes because of its modularity. Extensive experimentations and comparison with several recent models show that our method outperforms these methods with an accuracy of 92.2% and F1 score of 0.952 on the DementiaBank dataset while being able to generate explanations. We show by examples, how to generate these explanations using attention values.
Modulation of ferroptosis sensitivity by TXNRD1 in pancreatic cancer cells
Authors: Cai Luke L. , Ruberto Richard A. , Ryan Matthew J. , Eaton John K. , Schreiber Stuart L. , Viswanathan Vasanthi S.
Published: June 2020

Abstract

The selenoprotein thioredoxin reductase 1 (TXNRD1) plays a central role in ameliorating oxidative stress. Inhibition of TXNRD1 has been explored as a means of killing cancer cells that are thought to develop an enhanced reliance on such antioxidant proteins. In the context of ferroptosis, a non-apoptotic form of oxidative cell death, TXNRD1 has been proposed to cooperate with the phospholipid hydroperoxidase enzyme glutathione peroxidase 4 (GPX4) to protect cells from the lethal accumulation of lipid peroxides. Here, we report our unexpected finding that in pancreatic cancer cells, CRISPR–Cas9-mediated loss of TXNRD1 confers protection from ferroptosis induced by small-molecule inhibition of GPX4. Insights stemming from mechanistic interrogation of this phenomenon suggest that loss of TXNRD1 results in increased levels of GPX4 protein, potentially by influencing availability of selenocysteine, a scarce amino acid required by both proteins for proper synthesis and function. Increased abundance of GPX4 protein, in turn, protects cells from the effects of small-molecule GPX4 inhibition. These findings implicate selenoprotein regulation in governing ferroptosis sensitivity. Furthermore, by delineating a relationship between GPX4 and TXNRD1 contrary to that observed in numerous other settings, our discoveries underscore the context-specific nature of ferroptosis circuitry and its modulators.
More than noise: Context-dependant luminance contrast discrimination in a coral reef fish (Rhinecanthus aculeatus)
Authors: van den Berg Cedric P. , Hollenkamp Michelle , Mitchell Laurie J. , Watson Erin J. , Green Naomi F. , Marshall N. Justin , Cheney Karen L.
Published: June 2020

Achromatic (luminance) vision is used by animals to perceive motion, pattern, space and texture. Luminance contrast sensitivity thresholds are often poorly characterised for individual species and are applied across a diverse range of perceptual contexts using over-simplified assumptions of an animal’s visual system. Such thresholds are often estimated using the Receptor Noise Limited model (RNL) using quantum catch values and estimated noise levels of photoreceptors. However, the suitability of the RNL model to describe luminance contrast perception remains poorly tested.

Here, we investigated context-dependent luminance discrimination using triggerfish (Rhinecanthus aculeatus)presented with large achromatic stimuli (spots) against uniform achromatic backgrounds of varying absolute and relative contrasts. ‘Dark’ and ‘bright’ spots were presented against relatively dark and bright backgrounds. We found significant differences in luminance discrimination thresholds across treatments. When measured using Michelson contrast, thresholds for bright spots on a bright background were significantly higher than for other scenarios, and the lowest threshold was found when dark spots were presented on dark backgrounds. Thresholds expressed in Weber contrast revealed increased contrast sensitivity for stimuli darker than their backgrounds, which is consistent with the literature. The RNL model was unable to estimate threshold scaling across scenarios as predicted by the Weber-Fechner law, highlighting limitations in the current use of the RNL model to quantify luminance contrast perception. Our study confirms that luminance contrast discrimination thresholds are context-dependent and should therefore be interpreted with caution.
Harvest and Culture of Porcine Adipose-Derived Mesenchymal Stem Cells for Autologous Transplantation
Authors: Sharma Ayushman , Dietz Allan B.
Published: June 2020

Importance

Transplantation of adipose-derived (mesenchymal) stem cells (ADSCs) are currently under investigation for numerous novel regenerative cell therapies of the head, neck and periphery. Critical to the development of these techniques is the availability of large-animal models that can be used to test the safety and efficacy of these approaches in a manner that provides source material (in this case MSC) analogous to those developed in humans.

Objective

To describe the surgical technique and laboratory procedures for harvesting and isolating porcine ADSCs that are functionally equivalent to human ADSCs without sacrificing the donor animal.

Methods

The reagents and methods used in the porcine model described were purposefully focused to be able to be sufficiently analogous to those used in humans such that data developed using these techniques should support the use of porcine models for regulatory submissions.

Results

We describe a method and confirm the activity of functionally analogous adipose derived porcine MSC. Two conditions were critical to move gain analogous performance: the cells needed to be incubated at porcine body temperature (39°C) and the cells were more sensitive to initial plating densities with plating densities of 20,000 cells/cm2being optimal.

Discussion

This approach will allow reproducible and predictable use of an autologous large-animal model for testing AMDSC therapies.
Intra-session test-retest reliability of functional connectivity in infants
Authors: Wang Yun , Hinds Walter , Duarte Cristiane S , Lee Seonjoo , Monk Catherine , Wall Melanie , Canino Glorisa , Milani Ana Carolina C. , Jackowski Andrea , Mamin Marina Griorgi , Foerster Bernd U. , Gingrich Jay , Weissman Myrna M , Peterson Bradley S. , Semanek David , Perez Edna Acosta , Labat Eduardo , Torres Ioannisely Berrios , Da Silva Ivaldo , Parente Camila , Abdala Nitamar , Posner Jonathan
Published: June 2020

Resting functional MRI studies of the infant brain are increasingly becoming an important tool in developmental neuroscience. Whereas the test-retest reliability of functional connectivity (FC) measures derived from resting fMRI data have been characterized in the adult and child brain, similar assessments have not been conducted in infants. In this study, we examined the intra-session test-retest reliability of FC measures from 119 infant brain MRI scans from four neurodevelopmental studies. We investigated edge-level and subject-level reliability within one MRI session (between and within runs) measured by the Intraclass correlation coefficient (ICC). First, using an atlas-based approach, we examined whole-brain connectivity as well as connectivity within two common resting fMRI networks – the default mode network (DMN) and the sensorimotor network (SMN). Second, we examined the influence of run duration, study site, and scanning manufacturer (e.g., Philips and General Electric) on ICCs. Lastly, we tested spatial similarity using the Jaccard Index from networks derived from independent component analysis (ICA). Consistent with resting fMRI studies from adults, our findings indicated poor edge-level reliability (ICC = 0.14 - 0.18), but moderate-to-good subject-level intra-session reliability for whole-brain, DMN, and SMN connectivity (ICC = 0.40 - 0.78). We also found significant effects of run duration, site, and scanning manufacturer on reliability estimates. Some ICA-derived networks showed strong spatial reproducibility (e.g., DMN, SMN, and Visual Network), and were labelled based on their spatial similarity to analogous networks measured in adults. These networks were reproducibly found across different study studies. However, other ICA-networks (e.g. Executive Control Network) did not show strong spatial reproducibility, suggesting that the reliability and/or maturational course of functional connectivity may vary by network. In sum, our findings suggest that developmental scientist may be on safe ground examining the functional organization of some major neural networks (e.g. DMN and SMN), but judicious interpretation of functional connectivity is essential to its ongoing success.

Highlights

Infant functional connectivity (FC) shows poor edge-level reliability (ICCs)

However, subject-level infant FC estimates show good-to-excellent ICCs

Spatial reproducibility is better for some resting networks (DMN, SMN) than others (ECN)

Reliability estimates differ across study site and MRI scanner

Conclusion - Infant FC can be a reliable measurement, but judicious use is needed
A multi-omic integrative scheme characterizes tissues of action at loci associated with type 2 diabetes
Authors: Torres Jason M. , Abdalla Moustafa , Payne Anthony , Fernandez-Tajes Juan , Thurner Matthias , Nylander Vibe , Gloyn Anna L. , Mahajan Anubha , McCarthy Mark I.
Published: June 2020

Resolving the molecular processes that mediate genetic risk remains a challenge as most disease-associated variants are non-coding and functional and bioinformatic characterization of these signals requires knowledge of the specific tissues and cell-types in which they operate. To address this challenge, we developed a framework for integrating tissue-specific gene expression and epigenomic maps (primarily from tissues involved in insulin secretion and action) to obtaintissue-of-action(TOA) scores for each association signal by systematically partitioning posterior probabilities from Bayesian fine-mapping. We applied this scheme to credible set variants for 380 association signals from a recent GWAS meta-analysis of type 2 diabetes (T2D) in Europeans. The resulting tissue profiles underscored a predominant role for pancreatic islets and, to a lesser extent, subcutaneous adipose and liver, that was largely attributable to enhancer elements and transcribed regions, particularly among signals with greater fine-mapping resolution. We incorporated resulting TOA scores into a rule-based classifier, and validated the tissue assignments through comparison with data fromcis-eQTL enrichment, functional fine-mapping, RNA co-expression, and patterns of physiological association. In addition to implicating signals with a single tissue-of-action, we also found evidence for signals with shared effects in multiple tissues as well as distinct tissue profiles between independent signals within heterogeneous loci. Lastly, we demonstrated that TOA scores can be directly coupled with eQTL colocalization to further resolve effector transcripts at T2D signals. This framework guides mechanistic inference by directing functional validation studies to the most relevant tissues and can gain power as fine-mapping resolution and cell-specific annotations become richer. This method is generalizable to all complex traits with relevant annotation data and is made available as an R package.
Application of Surgical Lead Management and Reconfigurable Coil Technology to Reduce RF Heating of DBS Implants during MRI at 3T Under Variant Body Compositions
Authors: Bhusal Bhumi , Elahi Behzad , Keil Boris , Rosenow Joshua , Kazemivalipour Ehsan , Golestanirad Laleh
Published: June 2020

Patients with active implants such as deep brain stimulation (DBS) devices, have limited access to magnetic resonance imaging (MRI) due to risks of RF heating. With an aging population, the prevalence of neurodegenerative and vascular disease increases; and so does the indication for MRI exams in patients with such implants. In response to this growing need for MRI, many groups have investigated strategies to mitigate the RF heating of the implants. These efforts, however, have relied either on simulations with homogenous body models or simplified phantom experiments (box shaped phantom with single tissue). It is well established, however, that the shape and heterogeneity of human body affects the distribution of MRI electric fields, which by proxy, alters the RF heating of an implant inside the body. In this contribution, we applied numerical simulations and phantom experiments to examine the effectiveness of RF heating mitigation strategies under variant patient body compositions, focusing on two recently proposed techniques: (a) surgical modification of DBS lead trajectories inside the body, and (b) use of a patient-adjustable reconfigurable MRI coil, both aiming to reduce the coupling of implanted leads and MRI electric fields. Our results demonstrated that both techniques perform well under variant body compositions.
Model-driven promoter strength prediction based on a fine-tuned synthetic promoter library inEscherichia coli
Authors: Zhao Mei , Zhou Shenghu , Wu Longtao , Deng Yu
Published: June 2020

Promoters are one of the most critical regulatory elements controlling metabolic pathways. However, in recent years, researchers have simply perfected promoter strength, but ignored the relationship between the internal sequences and promoter strength. In this context, we constructed and characterized a mutant promoter library of Ptrcthrough dozens of mutation-construction-screening-characterization engineering cycles. After excluding invalid mutation sites, we established a synthetic promoter library, which consisted of 3665 different variants, displaying an intensity range of more than two orders of magnitude. The strongest variant was 1.52-fold stronger than a 1 mM isopropyl-β-D-thiogalactoside driven PT7promoter. Our synthetic promoter library exhibited superior applicability when expressing different reporters, in both plasmids and the genome. Different machine learning models were built and optimized to explore relationships between the promoter sequences and transcriptional strength. Finally, our XgBoost model exhibited optimal performance, and we utilized this approach to precisely predict the strength of artificially designed promoter sequences. Our work provides a powerful platform that enables the predictable tuning of promoters to achieve the optimal transcriptional strength.
Structure and allosteric regulation of human IDH3 holoenzyme
Authors: Sun Pengkai , Liu Yan , Ma Tengfei , Ding Jianping
Published: June 2020

Human NAD-dependent isocitrate dehydrogenase or IDH3 catalyzes the decarboxylation of isocitrate into α-ketoglutarate in the TCA cycle. We here report the structure of the IDH3 holoenzyme, in which the αβ and αγ heterodimers assemble the α2βγ heterotetramer via their clasp domains, and two α2βγ heterotetramers assemble the (α2βγ)2heterooctamer via the β and γ subunits. The functional roles of the key residues involved in the assembly and allosteric regulation are validated by mutagenesis and kinetic studies. The allosteric site plays an important role but the pseudo allosteric site plays no role in the allosteric activation; the activation signal from the allosteric site is transmitted to the active sites of both heterodimers via the clasp domains; and the N-terminus of the γ subunit plays a critical role in the formation and function of the holoenzyme. These findings reveal the molecular mechanism of the assembly and allosteric regulation of human IDH3 holoenzyme.