bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Additions to the CRISPR Toolbox: CRISPR-CLONInG and CRISPR-CLIP for Donor Construction in Genome Editing
Authors: Shola Dorjee T.N. , Yang Chingwen , Kewaldar Vhy-Shelta , Kar Pradip , Bustos Victor 
Published: September 2019

AbstractCRISPR-Cas has proven to be the most versatile genetic tinkering system of our time, predominantly as a precision genome editing tool. Here, we demonstrate two additions to the repertoire of CRISPR’s application for constructing donor DNA templates. (i) CRISPR-CLONInG (CRISPR-Cutting & Ligation Of Nucleic acid In vitro via Gibson) was devised to enable efficient cut-and-paste of multiple complex DNA fragments by using CRISPR/Cas9 as a digestion alternative with precision and exclusivity features, followed by joining the digested products via Gibson Assembly, to rapidly construct dsDNA and AAV donor vectors without cloning scars. (ii) CRISPR-CLIP (CRISPR-Clipped Long ssDNA via Incising Plasmid) was devised as a DNA clipping tool to efficiently retrieve long single-stranded DNA (lssDNA) from plasmid, up to 3.5 kbases, which can be supplied as the donor template for creating genetically engineered mice via Easi-CRISPR. We utilized two different Cas types (Cpf1 and Cas9n) to induce two distinct incisions at the respective ends of the lssDNA cassette junctions on the plasmid, yielding three independent single-stranded DNA units of unique sizes eligible for strand separation, followed by target strand clip-out through gel extraction. The retrieval of the lssDNA donor circumvents involvements of restriction enzymes and DNA polymerase-based steps, hence not only retains sequence fidelity but carries virtually no restriction on sequence composition, further mitigating limitations on current Easi-CRISPR method. With the add-on feature of universal DNA-tag sequences of Cpf1-Cas9 duo PAM, CRISPR-CLIP can be facile and applicable to generate lssDNA templates for any genomic target of choice. Additionally, we demonstrate robust gene editing efficiencies in neuroblastoma cell line as well as in mice attained with the AAV and lssDNA donors constructed herein.
Differential gene expression and functional pathway enrichment in colon cell line CCD 841 CoN (CRL-1790) transfected with miR-mimics miR-18b, miR-142-3p, miR-155, and miR-890
Authors: Robinson JM 
Published: September 2019

AbstractThis report is a bioinformatic analysis of samples from NCBI GEO database series GS132501. It includes previously un-reported data for miR-mimic over-expression of the miRNAs miR-18b, miR-155, miR-142-3p, and miR-890 in the ATCC CRL-1790 cell line. Data analysis was performed using Nanostring nSolver 4.0 and Advanced Analysis Module 2.0 plugin (Nanostring MAN-10030-03). Bioinformatic methods utilized include pathway scoring, differential expression (DE), and gene-set enrichment (GSE) analyses. Findings, with full supplementary data, provide a community resource for effects of dysregulation of these miRNAs in a colon ‘epithelial-like’ cell line.
Disrupting the leukemia niche in the central nervous system attenuates leukemia chemoresistance
Authors: Jonart Leslie M. , Ebadi Maryam , Basile Patrick , Johnson Kimberly , Makori Jessica , Gordon Peter M. 
Published: September 2019

AbstractProtection from acute lymphoblastic leukemia (ALL) relapse in the central nervous system (CNS) is crucial to survival and quality of life for ALL patients. Current CNS-directed therapies cause significant toxicities and are only partially effective. Moreover, the impact of the CNS microenvironment on leukemia biology is poorly understood. Herein, we showed that leukemia cells associated with the meninges of xenotransplanted mice, or co-cultured with meningeal cells, exhibit enhanced chemoresistance due to effects on both apoptosis balance and quiescence. From a mechanistic standpoint, we identified that leukemia chemoresistance is primarily mediated by direct leukemia-meningeal cell interactions and overcome by detaching the leukemia cells from the meninges. Next, we used a co-culture adhesion assay to identify drugs that disrupted leukemia-meningeal adhesion. In addition to identifying several drugs that inhibit canonical cell adhesion targets we found that Me6TREN, a novel hematopoietic stem cell (HSC) mobilizing compound, also disrupts leukemia-meningeal adhesion in vitro and in vivo. Finally, Me6TREN enhanced the efficacy of cytarabine in treating CNS leukemia in xenotransplanted mice. This work demonstrates that the meninges exert a critical influence on leukemia chemoresistance, elucidates mechanisms of CNS relapse beyond the well-described role of the blood-brain barrier, and identifies novel therapeutic approaches for overcoming chemoresistance.
Predicting Adverse Drug-Drug Interactions with Neural Embedding of Semantic Predications
Authors: Burkhardt Hannah A. , Subramanian Devika , Mower Justin , Cohen Trevor 
Published: September 2019

AbstractThe identification of drug-drug interactions (DDIs) is important for patient safety; yet, compared to other pharmacovigilance work, a limited amount of research has been conducted in this space. Recent work has successfully applied a method of deriving distributed vector representations from structured biomedical knowledge, known as Embedding of Semantic Predications (ESP), to the problem of predicting individual drug side effects. In the current paper we extend this work by applying ESP to the problem of predicting polypharmacy side-effects for particular drug combinations, building on a recent reconceptualization of this problem as a network of drug nodes connected by side effect edges. We evaluate ESP embeddings derived from the resulting graph on a side-effect prediction task against a previously reported graph convolutional neural network approach, using the same data and evaluation methods. We demonstrate that ESP models perform better, while being faster to train, more re-usable, and significantly simpler.
Human oocytes harbouring damaged dna can complete meiosis-i
Authors: Rémillard-Labrosse Gaudeline , Dean Nicola , Allais Adélaïde , Mihajlović Aleksandar I. , Jin Shao Guang , Son Weon-Young , Chung Jin-Tae , Pansera Melissa , Henderson Sara , Mahfoudh Alina , Steiner Naama , Agapitou Kristy , Marangos Petros , Buckett William , Ligeti-Ruiter Jacob , FitzHarris Greg 
Published: September 2019

ABSTRACTChromosomal abnormalities such as aneuploidies and DNA damage are considered a major threat to the establishment of healthy eggs and embryos. Recent landmark studies showed that mouse oocytes with damaged DNA can resume meiosis and undergo Germinal Vesicle Breakdown (GVBD), but then arrest in metaphase of meiosis-I in a process involving Spindle Assembly Checkpoint (SAC) signalling. Such a mechanism could help prevent the generation of metaphase-II (Met-II) eggs with damaged DNA. However we report that this is not the case in the human oocyte. DNA damage prevents human oocytes from undergoing GVBD in some cases. Strikingly however, most oocytes harbouring DNA damage progress through meiosis-I and subsequently extrude the first polar body (PB1) to form a metaphase-II egg, revealing the absence of a DNA-damage-induced SAC response. Analysis of the resulting metaphase-II eggs revealed highly disorganised spindles with misaligned and heavily damaged chromosomes. Our results suggest that DNA damage accumulated in meiosis-I, such as could occur during in vitro maturation procedures, does not prevent polar body extrusion and therefore could persist in morphologically normal looking metaphase-II eggs.
Sawfish, Read in Tooth and Saw: rostral teeth as endogenous chemical records of movement and life-history in a critically endangered species
Authors: Hegg Jens C. , Graves Breanna , Fisher Chris M. 
Published: September 2019

AbstractThe ecology of endangered and rare species can be difficult to study due to their low abundances and legal limits on scientist’s ability to catch, sample, and track them. This is particularly true of sawfish (family Pristidae) whose numbers have declined precipitously, placing all five species on the IUCN Red List of Threatened Species worldwide. Best known for their distinctive, toothed rostrum, the ecology, movement, and life-history of sawfish is poorly understood.Sawfish rostral teeth are modified placoid scales, which grow continuously throughout the life of the fish. This continuous growth, combined with their stable calcified makeup, makes sawfish rostral teeth a potential source of temporal records of chemical and isotopic changes through the life of the fish.Rostral teeth are often preserved in museums and as curios, potentially providing a source of life-history data to inform conservation actions without the need for field study, or as an important compliment to it. This is the first study to recover temporally explicit chemical data from sawfish rostral teeth.Using archived samples of largetooth sawfish (Pristis pristis) we show that multiple chemical tracers can be recovered from sawfish rostral teeth, and that these tracers can be used to understand movement across salinity gradients. We further show that sawfish rostral teeth contain repeated structures and indistinct banding which could potentially be used for aging or growth analysis of fish.
Immune genes,IL1βandCasp9,show sexual dimorphic methylation patterns in the zebrafish gonads
Authors: Caballero-Huertas M. , Moraleda-Prados J. , Joly S. , Ribas L. 
Published: September 2019

AbstractThere is a crosstalk between the immune and the reproductive systems in which sexual dimorphism is a common pattern in vertebrates. In the last years, epigenetics has emerged as a way to study the molecular mechanisms involved during gonadal development, which are responsible to integrate environmental information that contributes to assign a specific sexual phenotype (either an ovary or a testis). In the fish gonads, it is known of the existence of the reproduction-immune system interactions although the epigenetic mechanisms involved are far to be elucidated. Here, we used the zebrafish (Danio rerio) as a model to study the DNA methylation patterns of two well-known innate immune genes:IL1βandCasp9. DNA methylation levels were studied by a candidate gene approach at single nucleotide resolution and further, gene expression analysis were carried out. Results showed that there was clear sexual dimorphism in the DNA methylation levels of the two immune studied genes, being significantly higher in the testes when compared to the ovaries. In summary, and although much research is needed, here we present two potential candidates as epimarkers with forthcoming applications in the livestock and fish farming production, for example, in immune fish diseases or sexual control programs.
Bioremediation of hydrocarbon contaminated soil from Carlini Station, Antarctica: effectiveness of different nutrient sources as biostimulation agents
Authors: Villalba Primitz Julia , Vázquez Susana , Ruberto Lucas , Lo Balbo Alfredo , Mac Cormack Walter 
Published: September 2019

AbstractLogistics and scientific activities carried out in Antarctic stations entail the risk of contamination by fuels. Among remediation strategies, biostimulation of chronically contaminated Antarctic soils significantly improves the efficiency of hydrocarbons (HCs) removal. The aim of this study was to evaluate the performance of different nutrient formulations as biostimulation agents, in order to improve the elimination of diesel fuel from Antarctic soils, in both oxic and anoxic conditions. A field test was performed in microcosms (15 kg of soil each) as experimental systems. Each microcosm was prepared by triplicate, sampled every 10 days over a 50-days period and sampled again one year later. Changes in bacterial communities, and qualitative and quantitative HCs analysis were determined. Our results showed that, during the early stages of the process, a multi-component commercial product like OSEII®(containing nutrients, enzymes and surfactants) determines a rapid elimination of HCs with changes in the structure of the bacterial soil community, whereas a more cost-effective slow-release fertilizer like Nitrofoska®would be efficient in a long-term bioremediation process.
Are methylation beta-values simplex distributed?
Authors: Nonell Lara , González Juan R 
Published: September 2019

AbstractDNA methylation plays an important role in the development and progression of disease. Beta-values are the standard methylation measures. Different statistical methods have been proposed to assess differences in methylation between conditions. However, most of them do not completely account for the distribution of beta-values. The simplex distribution can accommodate beta-values data. We hypothesize that simplex is a quite flexible distribution which is able to model methylation data.To test our hypothesis, we conducted several analyses using four real data sets obtained from microarrays and sequencing technologies. Standard data distributions were studied and modelled in comparison to the simplex. Besides, some simulations were conducted in different scenarios encompassing several distribution assumptions, regression models and sample sizes. Finally, we compared DNA methylation between females and males in order to benchmark the assessed methodologies under different scenarios.According to the results obtained by the simulations and real data analyses, DNA methylation data are concordant with the simplex distribution in many situations. Simplex regression models work well in small sample size data sets. However, when sample size increases, other models such as the beta regression or even the linear regression can be employed to assess group comparisons and obtain unbiased results. Based on these results, we can provide some practical recommendations when analyzing methylation data: 1) use data sets of at least 10 samples per studied condition for microarray data sets or 30 in NGS data sets, 2) apply a simplex or beta regression model for microarray data, 3) apply a linear model in any other case.
The effect of autopolyploidy on population genetic signals of hard sweeps
Authors: Monnahan Patrick , Brandvain Yaniv 
Published: September 2019

AbstractSearching for population genomic signals left behind by positive selection is a major focus of evolutionary biology, particularly as sequencing technologies develop and costs decline. The effect of the number of chromosome copies (i.e. ploidy) on the manifestation of these signals remains an outstanding question, despite a wide appreciation of ploidy being a fundamental parameter governing numerous biological processes. We clarify the principal forces governing the differential manifestation and persistence of the signal of selection by separating the effects of polyploidy on rates of fixation versus rates of diversity (i.e. mutation and recombination) with a set of coalescent simulations. We explore what the major consequences of polyploidy, such as a more localized signal, greater dependence on dominance, and longer persistence of the signal following fixation, mean for within- and across-ploidy inference on the strength and prevalence of selective sweeps. As genomic advances continue to open doors for interrogating natural systems, studies such as this aid our ability to anticipate, interpret, and compare data across ploidy levels.
Precise annotation of tick mitochondrial genomes reveals multiple STR variation and one transposon-like element
Authors: Chen Ze , Xu Xiaofeng , Yang Xiaolong , Yu Zhijun , Hu Yonghong , Wang Duo , Bu Wenjun , Liu Jingze , Gao Shan 
Published: September 2019

AbstractIn this study, we used long-PCR amplification combined with Next-Generation Sequencing (NGS) to obtain complete mitochondrial genomes of individual ticks and performed precise annotation of these genomes. These annotations were confirmed by the PacBio full-length transcriptome data to cover both entire strands of the mitochondrial genomes without any gaps or overlaps. Based on these annotations, most of our findings were consistent with those from previous studies. Moreover, two important findings were reported for the first time, contributing fundamental knowledge to mitochondrial biology. The first was the discovery of a transposon-like element that may reveal the mechanisms of mitochondrial gene order rearrangement and genomic structural variation. Another finding was that Short Tandem Repeat (STRs) are the dominant variation type causing mitochondrial sequence diversity within an individual tick, insect, mouse and human. Comparisons between interindividual and intraindividual variation showed that polynucleotides and STRs with longer repeat units had the same variation pattern. Particularly, mitochondria containing deleterious mutations can accumulate in cells and deleterious STR mutations irreversibly change the proteins made from their mRNAs. Therefore, we proposed that deleterious STR mutations in mitochondria cause aging and diseases. This finding helped to ultimately reveal the mechanisms of mitochondrial DNA variation and its consequences (e.g., aging and diseases) in animals. Our study will give rise to the reconsideration of the importance of STRs and a unified study of STR variation with longer and shorter repeat units (particularly polynucleotides) in both nuclear and mitochondrial genomes. The complete mitochondrial genome sequence of Dermacentor silvarum is available at the NCBI GenBank database under the accession number MN347015 and the raw data is available at the NCBI SRA database under the accession number SRP178347.
A simple method to quantify protein abundances from one thousand cells
Authors: Vitrinel Burcu , Iannitelli Dylan E. , Mazzoni Esteban O. , Christiaen Lionel , Vogel Christine 
Published: September 2019

AbstractThe rise of single-cell transcriptomics has created an urgent need for similar approaches that use a minimal number of cells to quantify expression levels of proteins. We integrated and optimized multiple recent developments to establish a proteomics workflow to quantify proteins from as few as 1,000 mammalian stem cells. The method uses chemical peptide labeling, does not require specific equipment other than cell lysis tools, and quantifies >2,500 proteins with high reproducibility. We validated the method by comparing mouse embryonic stem cells and in vitro differentiated motor neurons. We identify differentially expressed proteins with small fold-changes, and a dynamic range in abundance similar to that of standard methods. Protein abundance measurements obtained with our protocol compare well to corresponding transcript abundance and to measurements using standard inputs. The protocol is also applicable to other systems, such as FACS-purified cells from the tunicate Ciona. Therefore, we offer a straightforward and accurate method to acquire proteomics data from minimal input samples.
Hybrid incompatibility between D. virilis and D. lumei is stronger in the presence of transposable elements
Authors: Castillo Dean M. , Moyle Leonie C. 
Published: September 2019

AbstractMismatches between parental genomes in selfish elements are frequently hypothesized to underlie hybrid dysfunction and drive speciation. However, because the genetic basis of most hybrid incompatibilities is unknown, testing the contribution of selfish elements to reproductive isolation is difficult. Here we evaluated the role of transposable elements (TEs) in hybrid incompatibilities between Drosophila virilis and D. lummei by experimentally comparing hybrid incompatibility in a cross where active TEs are present in D. virilis (TE+) and absent in D. lummei, to a cross where these TEs are absent from both D. virilis (TE-) and D. lummei genotypes. Using genomic data, we confirmed copy number differences in TEs between the D. virilis (TE+) strain and both the D. virilis (TE-) strain and D. lummei. We observed F1 postzygotic reproductive isolation exclusively in the interspecific cross involving TE+ D. virilis but not in crosses involving TE- D. virilis. This mirrors intraspecies dysgenesis where atrophied testes only occur when TE+ D. virilis is the paternal parent. A series of backcross experiments, that accounted for alternative models of hybrid incompatibility, showed that both F1 hybrid incompatibility and intrastrain dysgenesis are consistent with the action of TEs rather than genic interactions. Thus, our data suggest that this TE mechanism manifests as two different incompatibility phenotypes. A further Y-autosome interaction contributes to additional, sex-specific, inviability in one direction of this cross combination. These experiments demonstrate that TEs that cause intraspecies dysgenesis can increase reproductive isolation between closely related lineages, thereby adding to the processes that consolidate speciation.
Putatively cancer-specific alternative splicing is shared across patients and present in developmental and other non-cancer cells
Authors: David Julianne K. , Maden Sean K. , Weeder Benjamin R. , Thompson Reid F. , Nellore Abhinav 
Published: September 2019

ABSTRACTWe compared cancer and non-cancer RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression (GTEx) Project, and the Sequence Read Archive (SRA). We found that: 1) averaging across cancer types, 80.6% of exon-exon junctions thought to be cancer-specific based on comparison with tissue-matched samples are in fact present in other adult non-cancer tissues throughout the body; 2) 30.8% of junctions not present in any GTEx or TCGA normal tissues are shared by multiple samples within at least one cancer type cohort, and 87.4% of these distinguish between different cancer types; and 3) many of these junctions not found in GTEx or TCGA normal tissues (15.4% on average) are also found in embryological and other developmentally associated cells. This study probes the distribution of putatively cancer-specific junctions across a broad set of publicly available non-cancer human RNA-seq datasets. Overall, we identify a subset of shared cancer-specific junctions that could represent novel sources of cancer neoantigens. We further describe a framework for characterizing possible origins of these junctions, including potential developmental and embryological sources, as well as cell type-specific markers particularly related to cell types of cancer origin. These findings refine the meaning of RNA splicing event novelty, particularly with respect to the human neoepitope repertoire. Ultimately, cancer-specific exon-exon junctions may affect the anti-cancer immune response and may have a substantial causal relationship with the biology of disease.