bluuebunny/crossref_metadata_2025_split huggingface dataset:
ENDO-Pore: High-throughput linked-end mapping of single DNA cleavage events using nanopore sequencing
Authors: Torres Montaguth Oscar E. , Cross Stephen J. , Ingram Kincaid W.A. , Lee Laura , Diffin Fiona M. , Szczelkun Mark D. 
Published: July 2021

ABSTRACTMapping the precise position of DNA cleavage events plays a key role in determining the mechanism and function of endonucleases. ENDO-Pore is a high-throughput nanopore-based method that allows the time resolved mapping single molecule DNA cleavage events in vitro. Following linearisation of a circular DNA substrate by the endonuclease, a resistance cassette is ligated recording the position of the cleavage event. A library of single cleavage events is constructed and subjected to rolling circle amplification to generate concatemers. These are sequenced and used to produce accurate consensus sequences. To identify the cleavage site(s), we developed CSI (Cleavage Site Investigator). CSI recognizes the ends of the cassette ligated into the cleaved substrate and triangulates the position of the dsDNA break. We firstly benchmarked ENDO-Pore using Type II restriction endonucleases. Secondly, we analysed the effect of crRNA length on the cleavage pattern of CRISPR Cas12a. Finally, we mapped the time-resolved DNA cleavage by the Type ISP restriction endonuclease LlaGI that introduces random double-strand breaks into its DNA substrates.
Systems Biology Analysis of Human Genomes Points to Key Pathways Conferring Spina Bifida Risk
Authors: Aguiar-Pulido Vanessa , Wolujewicz Paul , Martinez-Fundichely Alexander , Elhaik Eran , Thareja Gaurav , AbdelAleem Alice , Chalhoub Nader , Cuykendall Tawny , Al-Zamer Jamel , Lei Yunping , El-Bashir Haitham , Musser James M. , Al-Kaabi Abdulla , Shaw Gary M. , Khurana Ekta , Suhre Karsten , Mason Christopher E. , Elemento Olivier , Finnell Richard H. , Ross M. Elizabeth 
Published: July 2021

AbstractSpina bifida (SB) is a debilitating birth defect caused by multiple gene and environment interactions. Though SB shows non-Mendelian inheritance, genetic factors contribute to an estimated 70% of cases. Nevertheless, identifying human mutations conferring SB risk is challenging due to its relative rarity, genetic heterogeneity, incomplete penetrance and environmental influences that hamper GWAS approaches to untargeted discovery. Thus, SB genetic studies may suffer from population substructure and/or selection bias introduced by typical candidate gene searches. We report a population based, ancestry-matched whole-genome sequence analysis of SB genetic predisposition using a systems biology strategy to interrogate 298 case-control subject genomes (149 pairs). Genes that were enriched in likely gene disrupting (LGD), rare protein-coding variants were subjected to machine learning analysis to identify genes in which LGD variants occur with a different frequency in cases vs. controls and so discriminate between these groups. Those genes with high discriminatory potential for SB significantly enriched pathways pertaining to carbon metabolism, inflammation, innate immunity, cytoskeletal regulation and essential transcriptional regulation, indicating their impact on the pathogenesis of human SB. Additionally, interrogation of conserved non-coding sequences identified robust variant enrichment in regulatory regions of several transcription factors critical to embryonic development. This genome-wide perspective offers an effective approach to interrogation of coding and non-coding sequence variant contributions to rare complex genetic disorders.
The role of feedback in the production of skilled finger sequences
Authors: Popp Nicola J. , Hernandez-Castillo Carlos R. , Gribble Paul L. , Diedrichsen Jörn 
Published: July 2021

AbstractActions involving fine control of the hand, for example grasping an object, rely heavily on sensory information from the fingertips. While the integration of feedback during execution of individual movements is well understood, less is known about the use of sensory feedback in the control of skilled movement sequences. To address this gap, we trained participants to produce sequences of finger movements on a keyboard-like device over a four-day training period. Participants received haptic, visual, and auditory feedback indicating the occurrence of each finger press. We then either transiently delayed or advanced the feedback for a single press by a small amount of time (30 or 60 ms). We observed that participants rapidly adjusted their ongoing finger press by either accelerating or prolonging the ongoing press, in accordance with the direction of the perturbation. Furthermore, we could show that this rapid behavioural modulation was driven by haptic feedback. While these feedback-driven adjustments reduced in size with practice, they were still clearly present at the end of training. In contrast to the directionally-specific effect we observed on the perturbed press, a feedback perturbation resulted in a delayed onset of the subsequent presses irrespective of perturbation direction or feedback modality. This observation is consistent with a hierarchical organization of skilled movement sequences, with different levels reacting distinctly to sensory perturbations.
A Novel Art of Electrocardiogram Assessment in Zebrafish for Cardiovascular Disease Studies and Drug Screening
Authors: Le Tai , Zhang Jimmy , Nguyen Anh Hung , Torres Ramses Seferino Trigo , Vo Khuong , Dutt Nikil , Lee Juhyun , Ding Yonghe , Xu Xiaolei , Lau Michael P.H. , Cao Hung 
Published: July 2021

AbstractThe zebrafish (Dario rerio) has proven to be an excellent animal model for biological research owing to its small size, low cost for maintenance, short generation time, amenable genetics, and optical transparency. Zebrafish have been extensively used in cardiovascular studies in which mutant lines with cardiovascular defects were introduced and analyzed. Despite the small size, technological advances have paved the way to effectively assess cardiac functions of zebrafish. Here, we present a novel art for long-term simultaneous monitoring and analysis of electrocardiogram (ECG) in multiple zebrafish with controlled environment. The system helps minimize the effect of anesthetic drug and temperature to cardiac rhythm side effects as well as save time and efforts by 40-50 fold compared with the conventional approach. We further employed the system to study the Na+ sensitivity in the development of sinus arrest in Tg(SCN5A-D1275N) fish, a study model of the sick sinus syndrome, as well as the relationship between this variant and drug administration. The novel ECG system developed in this study holds promise to greatly accelerate other cardiovascular studies and drug screening using zebrafish.
Experimental and Bioinformatic upgrade for genome-wide mapping of nucleosomes in Trypanosoma cruzi
Authors: Beati Paula , Stepñicka Milena Massimino , Larrea Salomé Vilchez , Alonso Guillermo Daniel , Ocampo Josefina 
Published: July 2021

1AbstractIn Trypanosoma cruzi, as in every eukaryotic cell, DNA is packaged into chromatin by octamers of histone proteins that constitute nucleosomes. Besides compacting DNA, nucleosomes control DNA dependent processes by modulating the access of DNA binding proteins to regulatory elements on the DNA; or by providing the platform for additional layers of regulation given by histone variants and histone post-translational modifications. In trypanosomes, protein coding genes are constitutively transcribed as polycistronic units. Therefore, gene expression is controlled mainly post transcriptionally. However, chromatin organization and the histone code influence transcription, cell cycle progression, replication and DNA repair. Hence, determining nucleosome position is of uppermost importance to understand the peculiarities of these processes in trypanosomes. Digestion of chromatin with micrococcal nuclease followed by deep sequencing has been widely applied for genome-wide mapping of nucleosomes in several organisms. Nonetheless, this parasite presents numerous singularities. On one hand, special growth conditions and cell manipulation are required. On the other hand, chromatin organization shows some uniqueness that demands a specially designed analytical approach. An additional entanglement is given by the nature of its genome harboring a large content of repetitive sequences and the poor quality of the genome assembly and annotation of many strains. Here, we adapted this broadly used method to the hybrid reference strain, CL Brener. Particularly, we developed an exhaustive and thorough computational workflow for data analysis, highlighting the relevance of using its whole genome as a reference instead of the commonly used Esmeraldo-like haplotype. Moreover, the performance of two aligners, Bowtie2 and HISAT2 was tested to find the most appropriate tool to map any genomic read to reference genomes bearing this complexity.
Repopulation of a 3D-simulated periapical lesion cavity with triggered osteoblastic-differentiated dental pulp stem cell spheroids
Authors: Ribeiro Vítor Luís , Dernowsek Janaína A. , Fernandes Roger R. , Pitol Dimitrius L. , Issa João Paulo Mardegan , Mazzi-Chaves Jardel F. , Bombonato-Prado Karina Fittipaldi , Sousa-Neto Manoel Damião , Passos Geraldo Aleixo 
Published: July 2021

AbstractWe established a proof of concept model system for the biological repair of periapical lesions using stem cell spheroids. A mesenchymal stem cell line isolated from the dental pulp of deciduous teeth (shed cells) was cultured in a 2D monolayer and then in 3D multicellular spheroids. An image of a periapical lesion of an upper lateral incisor tooth was obtained by computed micro tomography, which was used as a model for photopolymer resin 3D printing to generate a negative frame of the lesion. The negative model served to prepare a positive model of the periapical lesion cavity in an agarose gel. Shed cells cultured in monolayers or as spheroids were seeded in the positive lesion mold before or after osteoblastic differentiation. The results showed that compared to cells cultured in monolayers, the spheroids featured uniform cellularity and had a greater viability within the lesion cavity, accompanied by a temporal reduction in the expression of mRNAs typically expressed by stem cells (Cd13, Cd29, Cd44, Cd73, and Cd90). Concomitantly, there was an increase in the expression of protein markers that characterize osteoblastic differentiation (RUNX2, ALP, and BGLAP). These results provide a new perspective for regenerative endodontics with the use of spheroids prepared with shed cells to repair periapical lesions.
Making BrainWaves: Portable Brain Technology in Biology Education
Authors: Davidesco Ido , Azeka Steven , Carter Steven , Laurent Emma , Valk Henry , Naipaul Jimmy , Dikker Suzanne , Suzuki Wendy A 
Published: July 2021

ABSTRACTNeuroscience is one of the fastest growing STEM fields, yet its presence in K-12 science education is very limited, partially due to the lack of accessible teaching materials and tools. Here, we describe a new high school neuroscience curriculum (“BrainWaves”), where students utilize recent advances in low-cost, portable Electroencephalography (EEG) technology to investigate their own brain activity. This semester-long curriculum is supported by science mentors and an educational application that guides students through the process of recording and analyzing their own brain activity. Evaluation data collected in 5 public New York City schools in 2018/19 indicate significant positive shifts in content knowledge and self-efficacy among students who participated inBrainWavescompared to students in other courses of the same teacher. The quantitative findings are supported by interviews, where students reported increased appreciation for neuroscience and college readiness and discussed the benefits of collaborating with scientists and using portable brain technology in classrooms.
APRILE: Exploring the Molecular Mechanisms of Drug Side Effects with Explainable Graph Neural Networks
Authors: Xu Hao , Sang Shengqi , Yao Herbert , Herghelegiu Alexandra I. , Lu Haiping , Yurkovich James T. , Yang Laurence 
Published: July 2021

AbstractThe majority of people over the age of 65 take two or more medications. While many individual drug side effects are known, polypharmacy side effects due to novel drug combinations poses great risk. Here, we present APRILE: an explainable artificial intelligence (XAI) framework that uses graph neural networks to explore the molecular mechanisms underlying polypharmacy side effects. Given a list of side effects and the pairs of drugs causing them, APRILE identifies a set of proteins (drug targets or non-targets) and associated Gene Ontology (GO) terms as mechanistic ‘explanations’ of associated side effects. Using APRILE, we generate such explanations for 843,318 (learned) and 93,966 (novel) side effect–drug pair events, spanning 861 side effects (472 diseases, 485 symptoms and 9 mental disorders) and 20 disease cate-gories. We show that our two new metrics—pharmacogenomic information utilization and protein-protein interaction information utilization—provide quantitative estimates of mechanism complexity. Explanations were significantly consistent with state of the art disease-gene associations for 232/239 (97%) side effects. Further, APRILE generated new insights into molecular mechanisms of four diverse categories of adverse drug reactions: infection, metabolic diseases, gastrointestinal diseases, and mental disorders, including paradoxical side effects. We demonstrate the viability of discovering polypharmacy side effect mechanisms by training an XAI framework on massive biomedical data. Consequently, it facilitates wider and more reliable use of AI in healthcare.
Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation
Authors: Di Santo Lionel N. , Hoban Sean , Parchman Thomas L. , Wright Jessica W. , Hamilton Jill A. 
Published: July 2021

AbstractUnderstanding the contribution of neutral and adaptive evolutionary processes to population differences is often necessary for better informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the world’s rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species’ evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to assess loci possibly under selection, and evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation reflecting consistently low effective population sizes across time and limited genetic differentiation suggesting maintenance of gene flow following divergence. However, genome scans identified more than 2000 SNPs candidates for divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates that natural selection has likely contributed to population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effect of rarity, divergent selection between populations indicates that genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine.
Discovery ofUPSTREAM OF FLOWERING LOCUS C(UFC) andFLOWERING LOCUS C EXPRESSOR(FLX) inGladiolus ×hybridus,G. dalenii
Authors: Aljaser Jaser A. , Anderson Neil O. , Noyszewski Andrzej 
Published: July 2021

AbstractGladiolus is a geophytic floricultural crop, cultivated for cut flower and garden ornamental uses. Ornamental geophytes such as gladiolus, lily, tulip and daffodil are examples of floral crops that are currently being investigated to understand the flowering pathway. While the environmental and hormonal factors leading to flowering are established inArabidopsis. However, the lack of genetic regulation is poorly understood. Thus, the importance of such an ornamental crop that relies on flowers (flowering) for economic purposes encourages researchers to discover the flowering genes to breed vigorous flowering cultivars. The understanding of the flowering mechanisms in the flowering pathway is also paramount. Herein we show the discovery ofUPSTREAM OF FLOWERING LOCUS C(UFC) andFLOWERING LOCUS C EXPRESSOR(FLX) genes inGladiolus ×hybridus and G. dalenii. TheUFCgene is adjacent toFLOWERING LOCUS C(FLC) which is a floral repressor in many temperate species.FLXgene upregulatesFRIGIDA(FRI) which upregulatesFLCexpression. The discovery of both genes is a step forward in finding theFLCgene in gladiolus, provided they are linked. Seventeen gladiolus genotypes, consisting of early flowering and commercial cultivars, have theUFCgene, consisting of four exons in two allelic forms. TheUFCgene sequenced when translated into amino acid sequence and set in pair-alignment to other species, has up to 57% in amino acid identity toMusa acuminata. TheUFCprotein ranges in identity with pair-alignment to other species, reaching up to 57% in amino acid identity toMusa acuminata. TheFLXgene in gladiolus has 3/5 (60%) exons in relative toAnanas comosus, i.e. lacking 2 exons and a partially complete gene sequence; the pair-alignment of the three exons shows up over all ~65% identity ofFLXtoAnanas comosus. TheUFCprotein consists of a conserved domain, DUF966, which is higher in identity and pair-alignment, with up to 86% identity inElaeis guineensis. The discoveredFLXgene in gladiolus has 3/5 (60%) exons, i.e. lacking 2 exons and a partially complete gene sequence; the pair-alignment of the 3 exons shows up to ~65% of identity ofFLXtoAnanas comosus. These discovered two genes in gladiolus provide insight to further our understanding of the flowering and vernalization response in ornamental geophytes.Summary StatementTwo gladiolus flowering genes (UFC; FLX) were discovered which will aid research in understanding flowering and vernalization in geophytes
The HAPPE plus Event-Related (HAPPE+ER) Software: A Standardized Processing Pipeline for Event-Related Potential Analyses
Authors: Monachino A.D. , Lopez K.L. , Pierce L.J. , Gabard-Durnam L.J. 
Published: July 2021

AbstractEvent-Related Potential (ERP) designs are a common method for interrogating neurocognitive function with electroencephalography (EEG). However, the gold standard of preprocessing ERP data is manual-editing – a subjective, time-consuming processes. A number of automated pipelines have recently been created to address the need for standardization, automation, and quantification of EEG data processing; however, few are optimized for ERP analyses (especially in developmental or clinical populations). To fill this need, we propose and validate the HAPPE plus Event-Related (HAPPE+ER) software, a standardized and automated processing pipeline optimized for ERP analyses in EEG data. HAPPE+ER processes event- related potential data from raw files through a series of filtering, line noise reduction, bad channel detection, artifact rejection from continuous data, segmentation, and bad segment rejection methods. HAPPE+ER also includes post-processing reports of both data quality and pipeline quality metrics to facilitate the evaluation and reporting of data processing in a standardized manner. Finally, HAPPE+ER includes a post-processing script to facilitate generating ERP figures and measures for statistical analysis. We describe multiple approaches with both adult and developmental data to optimize and validate pipeline performance. HAPPE+ER software is freely available under the terms of GNU General Public License athttps://github.com/PINE-Lab/HAPPE.
Truncation of IFT80 causes early embryonic loss in cattle
Authors: Ortega M. Sofía , Bickhart Derek M. , Lockhart Kelsey N. , Null Daniel J. , Hutchison Jana L. , McClure Jennifer C. , Cole John B. 
Published: July 2021

AbstractRecessive alleles represent a risk in populations that have undergone bottleneck events. We present a comprehensive framework for identification and validation of these genetic defects, including haplotype-based detection, variant selection from sequence data, and validation using knockout embryos. Holstein haplotype 2 (HH2), which causes embryonic death, was used to demonstrate the approach. HH2 was identified using a deficiency-of-homozygotes approach and confirmed to negatively affect conception rate and stillbirths. Five carriers were present in a group of 183 sequenced Holstein bulls selected to maximize the coverage of unique haplotypes. Three variants concordant with haplotype calls were found in HH2: a high-priority frameshift mutation resulting in a deletion, and two low-priority variants (1 synonymous variant, 1 premature stop codon). The frameshift in intraflagellar protein 80 (IFT80) was confirmed in a separate group of Holsteins from the 1000 Bull Genomes Project that shared no animals with the discovery set. IFT80-null embryos were generated by truncating the IFT80 transcript at exon 2 or 11 using a CRISPR-Cas9 system. Abattoir-derived oocytes were fertilized in vitro and embryos were injected at the one-cell stage either with CRISPR-Cas9 complex (n=100) or Cas9 mRNA (control, n=100) before return to culture, and replicated 3 times. IFT80 is activated at the 8-cell stage, and IFT80-null embryos arrested at this stage of development, which is consistent with data from mouse hypomorphs and HH2 carrier-to-carrier matings. This frameshift in IFT80 on chromosome 1 at 107,172,615 bp (p.Leu381fs) disrupts WNT and hedgehog signaling, and is responsible for the death of homozygous embryos.Significance StatementHolstein haplotype 2 is an embryonic lethal present in 1.21% of the US Holstein cattle population, and unrecognized carrier-to-carrier matings are responsible for >$2 million/year in additional breeding expenses. A high-impact frameshift mutation in exon 11 of intraflagellar protein 80 (IFT80) was identified as the putative causal variant. Biallelic IFT80 knockout embryos were produced in vitro and compared to wild-type embryos. IFT80-null embryos consistently arrested at the 8-cell stage of development. The IFT80 protein expressed in knockout embryos had substantially altered protein structure, resulting in a loss of functional domains. These results validate the putative causal mutation observed in Holsteins. This system is a good model for investigating possible causal variants that affect livestock fertility early in development.