Large-scale RNA editing profiling in different adult chicken tissues

AbstractRNA editing is a post-transcription maturation process that diversifies genomically encoded information and can lead to diversity and complexity of transcriptome, especially in the brain. Thanks to next-generation sequencing technologies, a large number of editing sites have been identified in different species, especially in human, mouse and rat. While this mechanism is well described in mammals, only a few studies have been performed in the chicken. Here, we developed a rigorous computational strategy to identify RNA editing sites in eight different tissues of the chicken (brain, spleen, colon, lung, kidney, heart, testes and liver), based on RNA sequencing data alone. We identified 68 A-to-G editing sites in 46 genes. Only two of these were previously reported in chicken. We found no C-to-U sites, attesting the lack of this type of editing mechanism in the chicken. Similar to mammals, the editing sites were enriched in non-coding regions, rarely resulted in change of amino acids, showed a critical role in nervous system and had a low guanosine level upstream of the editing site and some enrichment downstream from the site. Moreover, in contrast to mammals, editing sites were weakly enriched in interspersed repeats and the frequency and editing ratio of non-synonymous sites were higher than those of synonymous sites.Interestingly, we found several tissue-specific edited genes including GABRA3, SORL1 and HTR1D in brain and RYR2 and FHOD3 in heart that were associated with functional processes relevant to the corresponding tissue. This finding highlighted the importance of the RNA editing in several chicken tissues, especially the brain. This study extends our understanding of RNA editing in chicken tissues and establish a foundation for further exploration of this process.

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Large‐scale potential RNA editing profiling in different adult chicken tissues

Animal Genetics ◽

10.1111/age.12818 ◽

2019 ◽

Vol 50 (5) ◽

pp. 460-474 ◽

Cited By ~ 2

Author(s):

H. Shafiei ◽

M. R. Bakhtiarizadeh ◽

A. Salehi

Keyword(s):

Rna Editing ◽

Large Scale ◽

Adult Chicken ◽

Chicken Tissues

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Utilizing the VirIdAl Pipeline to Search for Viruses in the Metagenomic Data of Bat Samples

Viruses ◽

10.3390/v13102006 ◽

2021 ◽

Vol 13 (10) ◽

pp. 2006

Author(s):

Anna Y Budkina ◽

Elena V Korneenko ◽

Ivan A Kotov ◽

Daniil A Kiselev ◽

Ilya V Artyushin ◽

...

Keyword(s):

Large Scale ◽

High Throughput Sequencing ◽

Metagenomic Data ◽

Sequencing Data ◽

Viral Pathogens ◽

Genomic Databases ◽

Bioinformatic Pipeline ◽

Viral Genomes ◽

Sequencing Technologies ◽

Viral Screening

According to various estimates, only a small percentage of existing viruses have been discovered, naturally much less being represented in the genomic databases. High-throughput sequencing technologies develop rapidly, empowering large-scale screening of various biological samples for the presence of pathogen-associated nucleotide sequences, but many organisms are yet to be attributed specific loci for identification. This problem particularly impedes viral screening, due to vast heterogeneity in viral genomes. In this paper, we present a new bioinformatic pipeline, VirIdAl, for detecting and identifying viral pathogens in sequencing data. We also demonstrate the utility of the new software by applying it to viral screening of the feces of bats collected in the Moscow region, which revealed a significant variety of viruses associated with bats, insects, plants, and protozoa. The presence of alpha and beta coronavirus reads, including the MERS-like bat virus, deserves a special mention, as it once again indicates that bats are indeed reservoirs for many viral pathogens. In addition, it was shown that alignment-based methods were unable to identify the taxon for a large proportion of reads, and we additionally applied other approaches, showing that they can further reveal the presence of viral agents in sequencing data. However, the incompleteness of viral databases remains a significant problem in the studies of viral diversity, and therefore necessitates the use of combined approaches, including those based on machine learning methods.

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Embodied tactile perception and learning

Brain Science Advances ◽

10.26599/bsa.2020.9050012 ◽

2020 ◽

Vol 6 (2) ◽

pp. 132-158

Author(s):

Huaping Liu ◽

Di Guo ◽

Fuchun Sun ◽

Wuqiang Yang ◽

Steve Furber ◽

...

Keyword(s):

Large Scale ◽

Critical Role ◽

Tactile Perception ◽

Physical Interaction ◽

Actual Behavior ◽

Learning Methods ◽

Tactile Information ◽

Collaborative Interaction ◽

Array Sensing ◽

The Brain

Various living creatures exhibit embodiment intelligence, which is reflected by a collaborative interaction of the brain, body, and environment. The actual behavior of embodiment intelligence is generated by a continuous and dynamic interaction between a subject and the environment through information perception and physical manipulation. The physical interaction between a robot and the environment is the basis for realizing embodied perception and learning. Tactile information plays a critical role in this physical interaction process. It can be used to ensure safety, stability, and compliance, and can provide unique information that is difficult to capture using other perception modalities. However, due to the limitations of existing sensors and perception and learning methods, the development of robotic tactile research lags significantly behind other sensing modalities, such as vision and hearing, thereby seriously restricting the development of robotic embodiment intelligence. This paper presents the current challenges related to robotic tactile embodiment intelligence and reviews the theory and methods of robotic embodied tactile intelligence. Tactile perception and learning methods for embodiment intelligence can be designed based on the development of new large‐scale tactile array sensing devices, with the aim to make breakthroughs in the neuromorphic computing technology of tactile intelligence.

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Computational Approaches for Transcriptome Assembly Based on Sequencing Technologies

Current Bioinformatics ◽

10.2174/1574893614666190410155603 ◽

2020 ◽

Vol 15 (1) ◽

pp. 2-16

Author(s):

Yuwen Luo ◽

Xingyu Liao ◽

Fang-Xiang Wu ◽

Jianxin Wang

Keyword(s):

De Novo ◽

Transcriptome Assembly ◽

Critical Role ◽

High Sensitivity ◽

Biological Properties ◽

Sequencing Data ◽

Sequencing Technologies ◽

Long Reads ◽

Massive Sequencing ◽

Generation Sequencing

Transcriptome assembly plays a critical role in studying biological properties and examining the expression levels of genomes in specific cells. It is also the basis of many downstream analyses. With the increase of speed and the decrease in cost, massive sequencing data continues to accumulate. A large number of assembly strategies based on different computational methods and experiments have been developed. How to efficiently perform transcriptome assembly with high sensitivity and accuracy becomes a key issue. In this work, the issues with transcriptome assembly are explored based on different sequencing technologies. Specifically, transcriptome assemblies with next-generation sequencing reads are divided into reference-based assemblies and de novo assemblies. The examples of different species are used to illustrate that long reads produced by the third-generation sequencing technologies can cover fulllength transcripts without assemblies. In addition, different transcriptome assemblies using the Hybrid-seq methods and other tools are also summarized. Finally, we discuss the future directions of transcriptome assemblies.

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Haplotype tagging reveals parallel formation of hybrid races in two butterfly species

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2015005118 ◽

2021 ◽

Vol 118 (25) ◽

pp. e2015005118

Author(s):

Joana I. Meier ◽

Patricio A. Salazar ◽

Marek Kučka ◽

Robert William Davies ◽

Andreea Dréau ◽

...

Keyword(s):

Large Scale ◽

Low Cost ◽

Natural Populations ◽

Elevational Gradient ◽

Butterfly Species ◽

Hybrid Zones ◽

Sequencing Data ◽

Sequencing Technologies ◽

Linkage Information ◽

Haplotype Information

Genetic variation segregates as linked sets of variants or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. Yet, genomic data often omit haplotype information due to constraints in sequencing technologies. Here, we present “haplotagging,” a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species, the geographic clines for the major wing-pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the center of the hybrid zone. We propose that shared warning signaling (Müllerian mimicry) may couple the cline shifts seen in both species and facilitate the parallel coemergence of a novel hybrid morph in both comimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations.

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Divergent pattern of genomic variation in Plasmodium falciparum and P. vivax

F1000Research ◽

10.12688/f1000research.10255.1 ◽

2016 ◽

Vol 5 ◽

pp. 2763 ◽

Cited By ~ 1

Author(s):

Preeti Goel ◽

Gajinder Pal Singh

Keyword(s):

Plasmodium Falciparum ◽

Amino Acid ◽

Large Scale ◽

Genomic Variation ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Single Nucleotide ◽

Evolutionary Response ◽

Substitution Bias ◽

Synonymous Sites

The two main species causing malaria in humans, Plasmodium falciparum and P. vivax, differ significantly from each other in their evolutionary response to common drugs, but the reasons for this are not clear. Here we utilized the recently available large-scale genome sequencing data from these parasites and compared the pattern of single nucleotide polymorphisms, which may be related to these differences. We found that there was a five-fold higher preference for AT nucleotides compared to GC nucleotides at synonymous single nucleotide polymorphism sites in P. vivax. The preference for AT nucleotides was also present at non-synonymous sites, which lead to amino acid changes favouring those with codons of higher AT content. The substitution bias was also present at low and moderately conserved amino acid positions, but not at highly conserved positions. No marked bias was found at synonymous and non-synonymous sites in P. falciparum. The difference in the substitution bias between P. falciparum and P. vivax found in the present study may possibly contribute to their divergent evolutionary response to similar drug pressures.

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Multi-platform discovery of haplotype-resolved structural variation in human genomes

10.1101/193144 ◽

2017 ◽

Cited By ~ 32

Author(s):

Mark J.P. Chaisson ◽

Ashley D. Sanders ◽

Xuefang Zhao ◽

Ankit Malhotra ◽

David Porubsky ◽

...

Keyword(s):

Genome Sequencing ◽

Large Scale ◽

Structural Variation ◽

High Throughput Sequencing ◽

Whole Genome Sequencing Data ◽

Sequencing Data ◽

Full Spectrum ◽

Variant Discovery ◽

Sequencing Technologies ◽

Sequencing Studies

ABSTRACTThe incomplete identification of structural variants (SVs) from whole-genome sequencing data limits studies of human genetic diversity and disease association. Here, we apply a suite of long-read, short-read, and strand-specific sequencing technologies, optical mapping, and variant discovery algorithms to comprehensively analyze three human parent–child trios to define the full spectrum of human genetic variation in a haplotype-resolved manner. We identify 818,054 indel variants (<50 bp) and 27,622 SVs (≥50 bp) per human genome. We also discover 156 inversions per genome—most of which previously escaped detection. Fifty-eight of the inversions we discovered intersect with the critical regions of recurrent microdeletion and microduplication syndromes. Taken together, our SV callsets represent a sevenfold increase in SV detection compared to most standard high-throughput sequencing studies, including those from the 1000 Genomes Project. The method and the dataset serve as a gold standard for the scientific community and we make specific recommendations for maximizing structural variation sensitivity for future large-scale genome sequencing studies.

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Haplotype tagging reveals parallel formation of hybrid races in two butterfly species

10.1101/2020.05.25.113688 ◽

2020 ◽

Cited By ~ 4

Author(s):

Joana I. Meier ◽

Patricio A. Salazar ◽

Marek Kučka ◽

Robert William Davies ◽

Andreea Dréau ◽

...

Keyword(s):

Large Scale ◽

Low Cost ◽

Natural Populations ◽

Elevational Gradient ◽

Butterfly Species ◽

Hybrid Zones ◽

Sequencing Data ◽

Sequencing Technologies ◽

Sequencing Technique ◽

Large Populations

AbstractGenetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations.One-sentence summaryHaplotagging, a novel linked-read sequencing technique that enables whole genome haplotyping in large populations, reveals the formation of a novel hybrid race in parallel hybrid zones of two co-mimicking Heliconius butterfly species through strikingly parallel divergences in their genomes.

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A protocol to evaluate RNA sequencing normalization methods

BMC Bioinformatics ◽

10.1186/s12859-019-3247-x ◽

2019 ◽

Vol 20 (S24) ◽

Cited By ~ 8

Author(s):

Zachary B. Abrams ◽

Travis S. Johnson ◽

Kun Huang ◽

Philip R. O. Payne ◽

Kevin Coombes

Keyword(s):

Rna Sequencing ◽

Large Scale ◽

Systematic Evaluation ◽

Sequencing Data ◽

Data Set ◽

Standard Data ◽

Sequencing Technologies ◽

Large Scale Data ◽

Normalization Methods ◽

Rnaseq Data

Abstract Background RNA sequencing technologies have allowed researchers to gain a better understanding of how the transcriptome affects disease. However, sequencing technologies often unintentionally introduce experimental error into RNA sequencing data. To counteract this, normalization methods are standardly applied with the intent of reducing the non-biologically derived variability inherent in transcriptomic measurements. However, the comparative efficacy of the various normalization techniques has not been tested in a standardized manner. Here we propose tests that evaluate numerous normalization techniques and applied them to a large-scale standard data set. These tests comprise a protocol that allows researchers to measure the amount of non-biological variability which is present in any data set after normalization has been performed, a crucial step to assessing the biological validity of data following normalization. Results In this study we present two tests to assess the validity of normalization methods applied to a large-scale data set collected for systematic evaluation purposes. We tested various RNASeq normalization procedures and concluded that transcripts per million (TPM) was the best performing normalization method based on its preservation of biological signal as compared to the other methods tested. Conclusion Normalization is of vital importance to accurately interpret the results of genomic and transcriptomic experiments. More work, however, needs to be performed to optimize normalization methods for RNASeq data. The present effort helps pave the way for more systematic evaluations of normalization methods across different platforms. With our proposed schema researchers can evaluate their own or future normalization methods to further improve the field of RNASeq normalization.

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Nursing professionals’ attitudes toward use of physical restraints in Styrian nursing homes Austria

Pflege ◽

10.1024/1012-5302/a000649 ◽

2019 ◽

Vol 32 (1) ◽

pp. 57-63

Author(s):

Hannes Mayerl ◽

Tanja Trummer ◽

Erwin Stolz ◽

Éva Rásky ◽

Wolfgang Freidl

Keyword(s):

Nursing Homes ◽

Large Scale ◽

Critical Role ◽

Physical Restraint ◽

Care Practice ◽

Physical Restraints ◽

Convenience Sample ◽

Restraint Use ◽

Positive Attitudes ◽

Nursing Professionals

Abstract. Background: Given that nursing staff play a critical role in the decision regarding use of physical restraints, research has examined nursing professionals’ attitudes toward this practice. Aim: Since nursing professionals’ views on physical restraint use have not yet been examined in Austria to date, we aimed to explore nursing professionals’ attitudes concerning use of physical restraints in nursing homes of Styria (Austria). Method: Data were collected from a convenience sample of nursing professionals (N = 355) within 19 Styrian nursing homes, based on a cross-sectional study design. Attitudes toward the practice of restraint use were assessed by means of the Maastricht Attitude Questionnaire in the German version. Results: The overall results showed rather positive attitudes toward the use of physical restraints, yet the findings regarding the sub-dimensions of the questionnaire were mixed. Although nursing professionals tended to deny “good reasons” for using physical restraints, they evaluated the consequences of physical restraint use rather positive and considered restraint use as an appropriate health care practice. Nursing professionals’ views regarding the consequences of using specific physical restraints further showed that belts were considered as the most restricting and discomforting devices. Conclusions: Overall, Austrian nursing professionals seemed to hold more positive attitudes toward the use of physical restraints than counterparts in other Western European countries. Future nationwide large-scale surveys will be needed to confirm our findings.

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