bluuebunny/crossref_metadata_2025_split huggingface dataset:
The genomes of precision edited cloned calves show no evidence for off-target events or increasedde novomutagenesis
Authors: Jivanji Swati , Harland Chad , Cole Sally , Brophy Brigid , Garrick Dorian , Snell Russell , Littlejohn Mathew , Laible Götz 
Published: January 2021

AbstractAnimal health and welfare are at the forefront of public concern and the agricultural sector is responding by prioritising the selection of welfare-relevant traits in their breeding schemes. In some cases, welfare-enhancing traits such as horn-status (i.e., polled) or diluted coat colour, which could enhance heat tolerance, may not segregate in breeds of primary interest, highlighting gene-editing tools such as the CRISPR-Cas9 technology as an approach to rapidly introduce variation into these populations. A major limitation preventing the acceptance of CRISPR-Cas9 mediated gene-editing, however, is the potential for off-target mutagenesis, which has raised concerns about the safety and ultimate applicability of this technology. Here, we present a clone-based study design that has allowed a detailed investigation of off-target andde novomutagenesis in a cattle line bearing edits in thePMELgene for diluted coat-colour. No off-target events were detected from high depth whole genome sequencing performed in precursor cell-lines and resultant calves cloned from those edited and non-edited cell lines. Long molecule sequencing at the edited site and plasmid-specific PCRs did not reveal structural variations and/or plasmid integration events in edited samples. Furthermore, an in-depth analysis ofde novomutations across samples revealed that the mutation frequency and spectra were unaffected by editing status. Cells in culture, however, had a distinct mutation signature wherede novomutations were predominantly C>A mutations, and in cloned calves they were predominantly T>G mutations, deviating from the expected excess of C>T mutations. We conclude that the gene-edited cells and calves in this study did not present a higher mutation load than unedited controls. Cell culture and somatic cell nuclear transfer cloning processes contributed the major source of contrast in mutational profile between samples.
Spatial Variability in Streambed Microbial Community Structure Across Two Watersheds
Authors: Akinwole Philips O. , Kan Jinjun , Kaplan Louis A. , Findlay Robert H. 
Published: January 2021

ABSTRACTThe spatial patterns of microbial communities are largely unknown compared to those of macro-fauna and flora. We investigated patterns of microbial community structure on streambed sediments from two watersheds across spatial scales spanning < 1m within a single stream to several hundred km between watersheds. Analyses of phospholipid fatty acids (PLFA) profiles indicated that the variations in microbial community structure were driven by increases in the relative abundance of microeukaryotic photoautotrophs and their contribution to total microbial biomass. Furthermore, streams within watersheds had similar microbial community structure, underscoring within-watershed controls of microbial communities. Moreover, bacterial community structure assayed as either polymerase chain reaction-denaturing gradient gelelectrophoresis (PCR-DGGE) fingerprints or PLFA profiles edited to remove microeukaryotes indicated a distinct watershed-level biogeography. No distinct stream order-level distributions were identified although DGGE analysis clearly indicated that there was greater variability in community structure among 1st-order streams compared to 2nd- and 3rd-order streams into which they flowed. Longitudinal gradients in microbial biomass and structure showed that the greatest variations were associated with 1st order streams within a watershed and 68% of the variation in total microbial biomass was explained by sediment C:N mass ratio, percent Carbon, sediment surface area, and percent water content. This study confirms a distinct microbial biogeography for headwater stream communities driven by environmental heterogeneity across distant watersheds and suggests that eukaryotic photoautotrophs play a key role in structuring sediment microbial communities.IMPORTANCEMicroorganisms in streams drive many biogeochemical reactions of global significance, including nutrient cycling and energy flow, yet the mechanisms responsible for the distribution and composition of streambed microbial communities are not well known. We sampled sediments from multiple streams in two watersheds; Neversink River (New York) and White Clay Creek (Pennsylvania) watersheds and measured microbial biomass, total microbial and bacterial community structures using phospholipid and molecular methods. Microbial and bacterial community structures displayed a distinct watershed-level biogeography. The smallest headwater streams within a watershed showed the greatest variation in microbial biomass, and C:N ratio, percent carbon, sediment surface area and percent water content explained 68% of the variations in microbial biomass. This study indicates a non-random distribution of microbial communities in streambeds, and that microeukaryotic photoautotrophs, environmental heterogeneity and geographical distance influence microbial composition and spatial distribution.
Movements ofMycoplasma mobilegliding machinery detected by high-speed atomic force microscopy
Authors: Kobayashi Kohei , Kodera Noriyuki , Kasai Taishi , Tahara Yuhei O , Toyonaga Takuma , Mizutani Masaki , Fujiwara Ikuko , Ando Toshio , Miyata Makoto 
Published: January 2021

ABSTRACTMycoplasma mobile, a parasitic bacterium, glides on solid surfaces, such as animal cells and glass by a special mechanism. This process is driven by the force generated through ATP hydrolysis on an internal structure. However, the spatial and temporal behaviors of the internal structures in living cells are unclear. In this study, we detected the movements of the internal structure by scanning cells immobilized on a glass substrate using high-speed atomic force microscopy (HS-AFM). By scanning the surface of a cell, we succeeded in visualizing particles, 2 nm in hight and aligned mostly along the cell axis with a pitch of 31.5 nm, consistent with previously reported features based on electron microscopy. Movements of individual particles were then analyzed by HS-AFM. In the presence of sodium azide, the average speed of particle movements was reduced, suggesting that movement is linked to ATP hydrolysis. Partial inhibition of the reaction by sodium azide enabled us to analyze particle behavior in detail, showing that the particles move 9 nm right, relative to the gliding direction, and 2 nm into the cell interior in 330 ms, then return to their original position, based on ATP hydrolysis.IMPORTANCETheMycoplasmagenus contains bacteria generally parasitic to animals and plants. SomeMycoplasmaspecies form a protrusion at a pole, bind to solid surfaces, and glide by a special mechanism linked to their infection and survival. The special machinery for gliding can be divided into surface and internal structures that have evolved from rotary motors represented by ATP synthases. This study succeeded in visualizing the real-time movements of the internal structure by scanning from the outside of the cell using an innovative high-speed atomic force microscope, and then analyzing their behaviors.
Cell lineage as a predictor of immune response in neuroblastoma
Authors: Sengupta Satyaki , Das Sanjukta , Crespo Angela , Miller Brian , Sharma Bandana , Zhang Shupei , Dries Ruben , Huang Hao , Krajewska Malgorzata , Debruyne David N. , Soriano Luigi , Cohen Malkiel A. , Versteeg Rogier , Jaenisch Rudolf , Spranger Stefani , Lieberman Judy , George Rani E. 
Published: January 2021

SUMMARYImmunotherapy for patients with neuroblastoma has met with limited success, partly due to an incomplete understanding of the mechanisms underlying immune responsiveness in this clinically and genetically heterogenic tumor. Here, we undertook an unbiased analysis using dimension reduction and UMAP visualization of transcriptional signatures derived from 498 primary neuroblastoma tumors. Four distinct clusters based on differentially expressed genes emerged, of which one, representing about 30% and comprising mainly ofMYCN-nonamplified tumors, was notable for the high expression of genes associated with both immune response activation and suppression. This capacity to elicit a productive immune response resided exclusively in tumors with dominant populations of undifferentiated, neural crest-like or mesenchymal cells; by contrast, tumors comprising primarily of committed, adrenergic neuron-like cells were less immunogenic. Mesenchymal neuroblastoma cells were enriched for innate and adaptive immune gene signatures, demonstrated engagement with cytotoxic T and natural killer cells, and induced immune cell infiltration in an immunocompetent mouse model. Transcriptional or targeted therapy-induced reprogramming of adrenergic cells to the mesenchymal state led to reactivation of tumor cell-intrinsic immune genes. Key immune response genes in adrenergic tumor cells were found to be epigenetically silenced by the PRC2 complex, and such repression could be relieved by either mesenchymal cell state reprogramming or EZH2 inhibition, leading to increased activation of natural killer cells by the tumor cells. These data identify cell lineage as a major determinant of the immunogenic potential in neuroblastoma that could be used to stratify patients who are most likely to benefit from immunotherapy.
Multi-omic Characterization of Human Tubular Epithelial Cell Response to Serum
Authors: Lidberg Kevin A. , Muthusamy Selvaraj , Adil Mohamed , Patel Ranita S. , Wang Lu , Bammler Theo K. , Reichel Jonathan , Yeung Catherine K. , Himmelfarb Jonathan , Kelly Edward J. , Akilesh Shreeram 
Published: January 2021

AbstractProteinuria, the spillage of serum proteins into the urine, is a feature of glomerulonephritides, podocyte disorders and diabetic nephropathy. However, the response of tubular epithelial cells to serum protein exposure has not been systematically characterized. Using transcriptomic profiling we studied serum-induced changes in primary human tubular epithelial cells cultured in 3D microphysiological devices. Serum proteins induced cellular proliferation, cytokine secretion and activated a coordinated stress response. We orthogonally confirmed our findings by comparing the transcriptomic and epigenomic landscapes of intact human kidney cortex and isolated tubular epithelial cells cultured in fetal bovine serum. Importantly, key transcriptomic programs in response to either type of serum exposure remained consistent, including comparisons to an established mouse model of kidney injury. This serum-induced transcriptional response was dominated by switching off of nuclear receptor-driven programs and activation of AP-1 and NF-κB signatures in the tubular epigenomic landscape. These features of active regulation were seen at canonical kidney injury genes (HAVCR1) and genes associated with COVID-19 (ACE2,IL6). Our data provide a reference map for dissecting the regulatory and transcriptional response of kidney tubular epithelial cells injury induced by serum.
Recombination and low-diversity confound homoplasy-based methods to detect the effect of SARS-CoV-2 mutations on viral transmissibility
Authors: Giorgi Elena E. , Bhattacharya Tanmoy , Fischer Will , Yoon Hyejin , Abfalterer Werner , Korber Bette 
Published: January 2021

AbstractThe SARS-CoV-2 variant carrying the Spike protein mutation G614 was first detected in late January 2020 and within a few months became the dominant form globally. In the months that followed, many studies, both in vitro and in animal models, showed that variants carrying this mutation were more infectious and more readily transmitted than the ancestral Wuhan form. Here we investigate why a recently published study by van Dorp et al. failed to detect such higher transmissibility of the G614 variant using homoplasy-based methods. We show that both low diversity and recombination confound the methods utilized by van Dorp et al. and significantly decrease their sensitivity. Furthermore, though they claim no evidence of recombination in their dataset, we and several other studies identify a subset of the sequences as recombinants, possibly enough to affect their statistic adversely.
Long-read assembly and comparative evidence-based reanalysis ofCryptosporidiumgenome sequences reveal new biological insights
Authors: Baptista Rodrigo P. , Li Yiran , Sateriale Adam , Sanders Mandy J. , Brooks Karen L. , Tracey Alan , Ansell Brendan R. E. , Jex Aaron R. , Cooper Garrett W. , Smith Ethan D. , Xiao Rui , Dumaine Jennifer E. , Berriman Matthew , Striepen Boris , Cotton James A. , Kissinger Jessica C. 
Published: January 2021

ABSTRACTCryptosporidiosis is a leading cause of waterborne diarrheal disease globally and an important contributor to mortality in infants and the immunosuppressed. Despite its importance, theCryptosporidiumcommunity still relies on a fragmented reference genome sequence from 2004. Incomplete reference sequences hamper experimental design and interpretation. We have generated a newC. parvumIOWA genome assembly supported by PacBio and Oxford Nanopore long-read technologies and a new comparative and consistent genome annotation for three closely related speciesC. parvum,C. hominisandC. tyzzeri. The newC. parvumIOWA reference genome assembly is larger, gap free and lacks ambiguous bases. This chromosomal assembly recovers 13 of 16 possible telomeres and raises a new hypothesis for the remaining telomeres and associated subtelomeric regions. Comparative annotation revealed that most “missing” orthologs are found suggesting that species differences result primarily from structural rearrangements, gene copy number variation and SNVs inC. parvum, C. hominisandC. tyzzeri. We made >1,500C. parvum annotation updates based on experimental evidence. They included new transporters, ncRNAs, introns and altered gene structures. The new assembly and annotation revealed a complete DNA methylaseDnmt2ortholog. 190 genes under positive selection including many new candidates were identified using the new assembly and annotation as reference. Finally, possible subtelomeric amplification and variation events inC. parvumare detected that reveal a new level of genome plasticity that will both inform and impact future research.
Acidovoraxpan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations
Authors: Siani Roberto , Stabl Georg , Gutjahr Caroline , Schloter Michael , Radl Viviane 
Published: January 2021

AbstractBeta-proteobacteria belonging to the genusAcidovoraxhave been described from various environments. Many strains can interact with a range of hosts, including humans and plants, forming neutral, beneficial or detrimental associations. In the frame of this study we investigated genomic properties of 52 bacterial strains of the genusAcidovorax, isolated from healthy roots ofLotus japonicus, with the intent of identifying traits important for effective plant-growth promotion. Based on single-strain inoculation bioassays withL. japonicus, performed in a gnotobiotic system, we could distinguish 7 robust plant-growth promoting strains from strains with no significant effects on plant-growth. We could show that the genomes of the two groups differed prominently in protein families linked to sensing and transport of organic acids, production of phytohormones, as well as resistance and production of compounds with antimicrobial properties. In a second step, we compared the genomes of the tested isolates with those of plant pathogens and free-living strains of the genusAcidovoraxsourced from public repositories. Our pan-genomics comparison revealed features correlated with commensal and pathogenic lifestyle. We could show that commensals and pathogens differ mostly in their ability to use plant-derived lipids and in the type of secretion-systems being present. Most free-livingAcidovoraxstrains did not harbour any secretion-systems. Overall, our data indicated thatAcidovoraxstrains undergo extensive adaptations to their particular lifestyle by horizontal uptake of novel genetic information and loss of unnecessary genes.
The recycling endosome protein Rab25 coordinates collective cell movements in the zebrafish surface epithelium
Authors: Willoughby Patrick Morley , Allen Molly , Yu Jessica , Korytnikov Roman , Chen Tianhui , Liu Yupeng , So Isis , Macpherson Neil , Mitchell Jennifer , Fernandez-Gonzalez Rodrigo , Bruce Ashley E. E. 
Published: January 2021

AbstractIn emerging epithelial tissues, cells undergo dramatic rearrangements to promote tissue shape changes. Dividing cells remain interconnected via transient cytokinetic bridges. Bridges are cleaved during abscission and currently, the consequences of disrupting abscission in developing epithelia are not well understood. We show that the Rab GTPase, Rab25, localizes near cytokinetic midbodies and likely coordinates abscission through endomembrane trafficking in the epithelium of the zebrafish gastrula during epiboly. In maternal-zygotic Rab25a and Rab25b mutant embryos, morphogenic activity tears open persistent apical cytokinetic bridges that failed to undergo timely abscission. Cytokinesis defects result in anisotropic cell morphologies that are associated with a reduction of contractile actomyosin networks. This slows cell rearrangements and alters the viscoelastic responses of the tissue, all of which likely contribute to delayed epiboly. We present a model in which Rab25 trafficking coordinates cytokinetic bridge abscission and cortical actin density, impacting local cell shape changes and tissue-scale forces.
EEG in game user analysis: A framework for expertise classification during gameplay
Authors: Hafeez Tehmina , Saeed Sanay Muhammad Umar , Arsalan Aamir , Anwar Syed Muhammad , Ashraf Muhammad Usman , Alsubhi Khalid 
Published: January 2021

AbstractVideo games have become a ubiquitous part of demographically diverse cultures. Numerous studies have focused on analyzing the cognitive aspects involved in game playing that could help provide an optimal gaming experience level by improving video game design. To this end, we present a framework for classifying the game player’s expertise level using wearable electroencephalography (EEG) headset. We hypothesize that expert/novice players’ brain activity is different, which can be classified using the frequency domain features extracted from EEG signals of the game player. A systematic channel reduction approach is presented using a correlation-based attribute evaluation method. This approach identifies two significant EEG channels, i.e., AF3 and P7, from the Emotiv EPOC headset’s fourteen channels. The features extracted from these EEG channels contribute the most to the video game player’s expertise level classification. This finding is validated by performing statistical analysis (t-test) over the extracted features. Moreover, among multiple classifiers used, K-nearest neighbor is the best classifier in classifying the game player’s expertise level with up to 98.04% classification accuracy.Author summaryTehmina Hafeez ROLES Investigation, Writing – original draft * E-mail:tehminamalik.52@gmail.comAFFILIATION Department of Computer Engineering, University of Engineering and Technology, Taxila, 47050, Pakistan.Sanay Muhammad Umar Saeed (Corresponding author) ROLES Conceptualization, Writing – review editing * E-mail:sanay.muhammad@uettaxila.edu.pkAFFILIATION Department of Computer Engineering, University of Engineering and Technology, Taxila, 47050, Pakistan.Aamir Arsalan ROLES Methodology, Writing – review editing * E-mail:aamir.arsalan@uettaxila.edu.pkAFFILIATION Department of Computer Engineering, University of Engineering and Technology, Taxila, 47050, Pakistan.Syed Muhammad Anwar ROLES Validation, Writing – review editing * E-mail:s.anwar@uettaxila.edu.pkAFFILIATION Department of Software Engineering, University of Engineering and Technology, Taxila, 47050, Pakistan.Muhammad Usman Ashraf (Corresponding author) ROLES Validation, Writing – review editing * E-mail:usman.ashraf@skt.umt.edu.pkAFFILIATION Department of Computer Science, University of management and Technology, Lahore (Sialkot), 51040, Pakistan.Khalid Alsubhi ROLES Conceptualization, Writing – review editing AFFILIATION Department of Computer Science, King Abdul Aziz University, Jeddah, Saudi Arabia.
Linear regression of sampling distributions of the mean
Authors: Torres David J , Vasilic Ana , Pacheco Jose 
Published: January 2021

AbstractWe show that the simple and multiple linear regression coefficients and the coefficient of determinationR2computed from sampling distributions of the mean (with or without replacement) are equal to the regression coefficients and coefficient of determination computed with individual data. Moreover, the standard error of estimate is reduced by the square root of the group size for sampling distributions of the mean. The result has applications when formulating a distance measure between two genes in a hierarchical clustering algorithm. We show that the Pearson R coefficient can measure how differential expression in one gene correlates with differential expression in a second gene.
Experimental and Molecular Predictions of the Adjuvanticity of Snail Mucin on Hepatitis B Vaccine in Albino Mice
Authors: Joshua Parker E. , Nwauzor Cynthia O. , Odimegwu Damian C. , Ukachukwu Uzochukwu G. , Asomadu Rita O. , Ezeorba Timothy P. C. 
Published: January 2021

AbstractAlthough aluminum-containing adjuvants are widely used in human vaccination due to their excellent safety profile, they exhibit low effectiveness with many recombinant antigens. This study investigated the adjuvanticity of snail mucin with recombinant Hepatitis B Vaccine (rHBsAg). Twenty-five (25) female mice distributed unbiasedly into 5 groups were used in the study and were administered different rHBsAg/Mucin formulation at 7 days intervals. Blood samples were collected a day following the administration for analysis. The results of liver function and body weight analysis were indications that snail mucin had no adverse effect on the mice. The treatment group (administer mucin and rHBsAg) showed significantly (P<0.05) higher mean titres of anti-HBsAg antibodies when compared with the negative controls and the positive control administered with two doses of rHBsAg. Furthermore, a comparable immune response to positive control administered with three doses rHBaAG was recorded.In silicoprediction, studies of the protein-protein interaction of a homology modelled snail mucus protein and HBsAg gave an indication of enhanced HBV antigen-antibody interaction. Therefore, this study has shown that snail mucin possesses some adjuvant properties and enhances immune response towards rHBsAg vaccine. However, there is a need for further molecular dynamics studies to understand its mechanism of action.