The UniProt-GO Annotation database in 2011

AbstractRecently, minipig has been considered as an animal model that is appropriate for human disease model to study toxicology, pharmacology, and xenotransplantation. Nevertheless, minipigs are bred in various environment according to their use. Here, we suggest that minipigs used for research should be bred in well-controlled facility, comparing immune status of pigs raised in different breeding environment. DNA microarray was performed with ear skin and placenta of Landrace domestic pigs (DPs) and Minnesota germ-free minipigs (GPs). Their immune transcriptome was analyzed by gene ontology (GO) annotation database, based on criteria of |log2 fold change| ≥1 with P ≤ 0.05. As a result, we found that immune related genes in the ear skin of DPs were highly activated, compared to GPs. On the other hand, no significant s were found in the placenta. Quantitative real-time PCR (qRT-PCR) was performed in five candidate immune genes. Their fold changes were consistent with the results from DNA microarray (P ≤ 0.05). In conclusion, we experimentally proved that porcine immune system was affected by different breeding environment, suggesting the importance of controlling microbes in animal room for the qualified research.

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A novel non-invasive method allowing for discovery of pathologically relevant proteins from small airways

10.21203/rs.3.rs-78071/v2 ◽

2021 ◽

Author(s):

Jörgen Östling ◽

Marleen Van Geest ◽

Henric K Olsson ◽

Sven-Erik Dahlén ◽

Emilia Viklund ◽

...

Keyword(s):

Extracellular Proteins ◽

Small Airway ◽

Small Airways ◽

Healthy Controls ◽

Annotation Database ◽

Epithelial Lining Fluid ◽

Go Annotation ◽

Non Invasive ◽

Invasive Method ◽

Never Smokers

Abstract BackgroundBreath contains an aerosol of droplet particles, which are formed from the epithelial lining fluid when the small airways close and re-open during inhalation succeeding a full expiration. These particles can be collected by impaction using the PExA® method (Particles in Exhaled Air), and constitute a potential source of biomarkers reflecting pathological processes in the small airways.ObjectiveOur aim was to investigate if PExA method may be useful for discovery of biomarkers that reflect pathology of small airways.Methods10 healthy controls and 20 subjects with asthma, of whom 10 with small airway involvement as indicated by a high lung clearance index (LCI ≥2.9 z-score), were examined using the PExA instrument. The samples were analysed with the SOMAscan proteomics platform (SomaLogic Inc).ResultsTwo hundred-seven proteins were detected in up to 80% of the samples. Nine proteins showed differential abundance in subjects with asthma and high LCI as compared to healthy controls. Two of these were less abundant (ALDOA4, C4), and seven more abundant (FIGF, SERPINA1, CD93, CCL18, F10, IgM, IL1RAP). sRAGE levels were lower in ex-smokers (n=14) than in never smokers (n=16). Gene Ontology (GO) annotation database analyses revealed that the PEx proteome is enriched in extracellular proteins associated with extracellular exosome-vesicles and innate immunity.ConclusionThe applied analytical method was reproducible and allowed identification of pathologically interesting proteins in PEx samples from asthmatic subjects with high LCI. The results suggest that PEx based proteomics is an novel and promising approach to study respiratory diseases with small airway involvement.

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A Novel Non-invasive Method Allowing for Discovery of Pathologically Relevant Proteins From Small Airways

10.21203/rs.3.rs-78071/v1 ◽

2020 ◽

Author(s):

Jörgen Östling ◽

Marleen Van Geest ◽

Henric K Olsson ◽

Sven-Erik Dahlén ◽

Emilia Viklund ◽

...

Keyword(s):

Extracellular Proteins ◽

Small Airway ◽

Small Airways ◽

Healthy Controls ◽

Annotation Database ◽

Epithelial Lining Fluid ◽

Go Annotation ◽

Non Invasive ◽

Invasive Method ◽

Never Smokers

Abstract BackgroundBreath contains an aerosol of droplet particles, which are formed from the epithelial lining fluid when the small airways close and re-open during inhalation succeeding a full expiration. These particles can be collected by impaction using the PExA® method (Particles in Exhaled Air), and constitute a potential source of biomarkers reflecting pathological processes in the small airways.ObjectiveOur aim was to investigate if PExA method may be useful for discovery of biomarkers that reflect pathology of small airways.Methods10 healthy controls and 20 subjects with asthma, of whom 10 with small airway dysfunction (SAD), were examined using the PExA instrument. The samples were analysed with the SOMAscan proteomics platform (SomaLogic Inc). ResultsTwo hundred-seven proteins were detected in up to 80% of the samples. Nine proteins showed differential abundance in subjects with SAD as compared to healthy controls. Two of these were less abundant (ALDOA4, C4), and seven more abundant (FIGF, SERPINA1, CD93, CCL18, F10, IgM, IL1RAP). sRAGE levels were lower in ex-smokers (n=14) than in never smokers (n=16). Gene Ontology (GO) annotation database analyses revealed that the PEx proteome is enriched in extracellular proteins associated with extracellular exosome-vesicles and innate immunity.ConclusionThe applied analytical method was reproducible and allowed identification of pathologically interesting proteins in PEx samples from asthmatic subjects with small airway dysfunction. The results suggest that PEx based proteomics is an novel and promising approach to study respiratory diseases with small airway involvement.

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Global Transcriptome Characterization and Assembly of Thermophilic Ascomycete Chaetomium thermophilum

10.1101/826354 ◽

2019 ◽

Author(s):

Amit Singh ◽

Géza Schermann ◽

Sven Reislöhner ◽

Nikola Kellner ◽

Ed Hurt ◽

...

Keyword(s):

Basic Research ◽

Industrial Applications ◽

Open Reading Frames ◽

Annotation Database ◽

Go Annotation ◽

Chaetomium Thermophilum ◽

Alternatively Spliced ◽

Comprehensive Search ◽

R Packages ◽

Novel Transcripts

A correct genome annotation is fundamental for research in the field of molecular and structural biology. The annotation of the reference genome Chaetomium thermophilum has been reported previously, but it is limited to open reading frames (ORFs) of genes and contains only a few noncoding transcripts. In this study, we identified and annotated by deep RNA sequencing full-length transcripts of C.thermophilum. We annotated 7044 coding genes and a large number of noncoding genes (n=4567). Astonishingly, 23% of the coding genes are alternatively spliced. We identified 679 novel coding genes and corrected the structural organization of more than 50% of the previously annotated genes. Furthermore, we substantially extended the Gene Ontology (GO) and Enzyme Commission (EC) lists, which provide comprehensive search tools for potential industrial applications and basic research. The identified novel transcripts and improved annotation will help understanding the gene regulatory landscape in C.thermophilum. The analysis pipeline developed here can be used to build transcriptome assemblies and identify coding and noncoding RNAs of other species. The R packages for gene and GO annotation database can be found under https://www.bzh.uni-heidelberg.de/brunner/Chaetomium_thermophilum.

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A Novel Non-invasive Method Allowing for Discovery of Pathologically Relevant Proteins From Small Airways

10.21203/rs.3.rs-78071/v3 ◽

2021 ◽

Author(s):

Jörgen Östling ◽

Marleen Van Geest ◽

Henric K Olsson ◽

Sven-Erik Dahlen ◽

Emilia Viklund ◽

...

Keyword(s):

Research Question ◽

Extracellular Proteins ◽

Small Airway ◽

Small Airways ◽

Healthy Controls ◽

Cross Sectional ◽

Annotation Database ◽

Go Annotation ◽

Cross Sectional Design ◽

Never Smokers

Abstract BackgroundThere is a lack of early and precise biomarkers for personalized respiratory medicine. Breath contains an aerosol of droplet particles, which are formed from the epithelial lining fluid when the small airways close and re-open during inhalation succeeding a full expiration. These particles can be collected by impaction using the PExA® method (Particles in Exhaled Air), and are derived from an area of high clinical interest previously difficult to access, making them a potential source of biomarkers reflecting pathological processes in the small airways.Research questionOur aim was to investigate if PExA method is useful for discovery of biomarkers that reflect pathology of small airways.Methods and analysis10 healthy controls and 20 subjects with asthma, of whom 10 with small airway involvement as indicated by a high lung clearance index (LCI ≥2.9 z-score), were examined in a cross-sectional design, using the PExA instrument. The samples were analysed with the SOMAscan proteomics platform (SomaLogic Inc). ResultsTwo hundred-seven proteins were detected in up to 80% of the samples. Nine proteins showed differential abundance in subjects with asthma and high LCI as compared to healthy controls. Two of these were less abundant (ALDOA4, C4), and seven more abundant (FIGF, SERPINA1, CD93, CCL18, F10, IgM, IL1RAP). sRAGE levels were lower in ex-smokers (n=14) than in never smokers (n=16). Gene Ontology (GO) annotation database analyses revealed that the PEx proteome is enriched in extracellular proteins associated with extracellular exosome-vesicles and innate immunity.ConclusionThe applied analytical method was reproducible and allowed identification of pathologically interesting proteins in PEx samples from asthmatic subjects with high LCI. The results suggest that PEx based proteomics is a novel and promising approach to study respiratory diseases with small airway involvement.

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Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding

Nature Communications ◽

10.1038/s41467-021-24328-w ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

John T. Lovell ◽

Nolan B. Bentley ◽

Gaurab Bhattarai ◽

Jerry W. Jenkins ◽

Avinash Sreedasyam ◽

...

Keyword(s):

Tree Breeding ◽

Pathogen Resistance ◽

Perennial Crop ◽

Crop Species ◽

Annotation Database ◽

Pan Genome ◽

Genome Integration ◽

Transformative Potential ◽

Genome Assemblies ◽

Quantitative Genomics

AbstractGenome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.

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ADeditome provides the genomic landscape of A-to-I RNA editing in Alzheimer’s disease

Briefings in Bioinformatics ◽

10.1093/bib/bbaa384 ◽

2021 ◽

Author(s):

Sijia Wu ◽

Mengyuan Yang ◽

Pora Kim ◽

Xiaobo Zhou

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Rna Editing ◽

Memory Loss ◽

Brain Regions ◽

Disease Stage ◽

Mirna Regulation ◽

Annotation Database ◽

Functional Annotations ◽

Genomic Landscape

Abstract A-to-I RNA editing, contributing to nearly 90% of all editing events in human, has been reported to involve in the pathogenesis of Alzheimer’s disease (AD) due to its roles in brain development and immune regulation, such as the deficient editing of GluA2 Q/R related to cell death and memory loss. Currently, there are urgent needs for the systematic annotations of A-to-I RNA editing events in AD. Here, we built ADeditome, the annotation database of A-to-I RNA editing in AD available at https://ccsm.uth.edu/ADeditome, aiming to provide a resource and reference for functional annotation of A-to-I RNA editing in AD to identify therapeutically targetable genes in an individual. We detected 1676 363 editing sites in 1524 samples across nine brain regions from ROSMAP, MayoRNAseq and MSBB. For these editing events, we performed multiple functional annotations including identification of specific and disease stage associated editing events and the influence of editing events on gene expression, protein recoding, alternative splicing and miRNA regulation for all the genes, especially for AD-related genes in order to explore the pathology of AD. Combing all the analysis results, we found 108 010 and 26 168 editing events which may promote or inhibit AD progression, respectively. We also found 5582 brain region-specific editing events with potentially dual roles in AD across different brain regions. ADeditome will be a unique resource for AD and drug research communities to identify therapeutically targetable editing events. Significance: ADeditome is the first comprehensive resource of the functional genomics of individual A-to-I RNA editing events in AD, which will be useful for many researchers in the fields of AD pathology, precision medicine, and therapeutic researches.

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Relationship Between the Pyroptosis Pathway and Epilepsy: A Bioinformatic Analysis

Frontiers in Neurology ◽

10.3389/fneur.2021.782739 ◽

2022 ◽

Vol 12 ◽

Author(s):

Lu Xia ◽

Lu Liu ◽

Qiang Wang ◽

Jing Ding ◽

Xin Wang

Keyword(s):

Correlation Analysis ◽

Kainic Acid ◽

Sham Group ◽

Differentially Expressed Gene ◽

Bioinformatic Analysis ◽

Go Annotation ◽

Protein Levels ◽

Qrt Pcr ◽

Reverse Transcription Pcr ◽

Anti Epileptic Drug

PurposeThis study aimed to analyse the correlation between the pyroptosis pathway and epilepsy using bioinformatics analysis technology. We analyzed the expression of gasdermin D (GSDMD) and gasdermin E (GSDME), the key molecules of pyroptosis, in kainic acid-induced epileptic mice.MethodsWeighted gene co-expression network analysis (WGCNA) was used to construct a signed co-expression network from expression data to screen gene sets closely related to epilepsy. The correlation between the module and epilepsy was verified through module conservative analysis, gene ontology (GO) annotation analysis, and correlation analysis with known epilepsy genes. We obtained currently recognized pyroptosis-related molecules through literature review, and correlation analysis was used to evaluate their correlation with epilepsy. Differentially expressed gene (DEG) analysis was used to analyse expression changes of pyroptosis-related molecules at the transcriptome level, compared to the sham group. We subsequently established a kainic acid-induced status epilepticus (SE) model in mice and validated the mRNA and protein expression of GSDMD and GSDME, the key molecules of pyroptosis, by quantitative reverse transcription PCR (qRT-PCR) and western blotting (WB).ResultsUsing WGCNA, module conservative analysis, and correlation analysis with known epilepsy genes, we screened out a module (a gene set of interest) closely related to epilepsy that was prominently enriched in immune and inflammatory-related biological processes. Correlation analysis results suggest that pyroptosis-related molecules are closely related to this module, but have no obvious correlation with others. DEG analysis of molecules associated with pyroptosis suggests that most of the pyroptosis-related molecules had significantly increased expression after SE, such as IL1b, Casp1, Casp4, Pycard, Gsdmd, Nlrp3, Aim2, Mefv, Tlr2, Tlr3, and Tlr4. qRT-PCR and WB analysis confirmed that the mRNA and protein levels of GSDMD in the mouse hippocampus were significantly upregulated after SE. The mRNA expression of GSDME was not different between the epilepsy group and sham group. However, the WB results showed that the expression of full-length GSDME was decreased and GSDME-N-terminus were significantly increased after SE.ConclusionsOur study highlights that the pyroptosis pathway may be closely related to epilepsy. GSDMD and GSDME, the key executive molecules of pyroptosis, will help to understand the pathogenesis of epilepsy and aid in discovering new targets for anti-epileptic drug treatments.

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Network Pharmacology Study of The Mechanism of Anti-Pneumonia Action Mechanism of Gentiana Rhodantha Franch

10.21203/rs.3.rs-539959/v1 ◽

2021 ◽

Author(s):

Jun Luo ◽

Xiusheng Tang ◽

Guotao Shu ◽

Dongxin Tang ◽

Jia Yu ◽

...

Keyword(s):

Chinese Medicine ◽

Signaling Pathway ◽

High Throughput Sequencing ◽

Biological Information ◽

Network Pharmacology ◽

Chemical Components ◽

Sequencing Analysis ◽

Data Set ◽

Annotation Database ◽

Functional Richness

Abstract Background: Serum dragon bile is a Chinese medicine used to treat pneumonia, but its mechanism of action is not clear. Meanwhile, due to the development of microarray and RNA‐sequencing technology, high-throughput sequencing analysis is being used increasingly, and it has been applied as an indispensable tool in many medical fields. Therefore, in this article, we want to employed the bioinformatics approach to explore the relevant pharmacological mechanism of dragon serum bile in the treatment of pneumonia through network pharmacology.Methods: In this paper, the active chemical composition and action target of serum dragon bile are obtained through the pharmacology database (TCMSP) of Chinese medicine system and the literature, and the data set of the intersection of active ingredient and disease target is established, and the protein interoperability network of serum gallbladder action target and pneumonia action target is analyzed by using protein interaction network (PPI). Using the Biological Information Annotation Database (DAVID) for gene ontology (GO) functional richness analysis and based on kyoto Gene and Genomics Encyclopedia (KEGG) pathogenic rich analysis, to predict the mechanism of the role of seroclon bile against pneumonia. Results: Through the network pharmacological prediction, it is shown that the main chemical components of serum dragon bile are quercetin, isoorientin, luteolin, Stigmasterol, vanillic acid, etc, all of which have anti-pneumonia effects. The anti-pneumonia effect of serum dragon bile is mainly regulated by pathways in cancer, Bradder cancer, TNF signaling pathway, Hepatitis B and Non-small cell lung cancer, among which the TNF signaling pathway is more associated with pneumonia. Conclusions: It is concluded from the network pharmacological prediction that serum dragon bile may play an anti-pneumonia role by promoting apoptosis, survival, immunity, etc. Its anti-pneumonia path is closely related to key targets IL6, FOS, CASP3 and AKT1. This study provides theoretical support for the follow-up study of the anti-pneumonia mechanism of serum gentian bile.

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miRNAome expression profiles in the gonads of adultMelopsittacus undulatus

PeerJ ◽

10.7717/peerj.4615 ◽

2018 ◽

Vol 6 ◽

pp. e4615 ◽

Cited By ~ 5

Author(s):

Lan Jiang ◽

Qingqing Wang ◽

Jue Yu ◽

Vinita Gowda ◽

Gabriel Johnson ◽

...

Keyword(s):

Gene Expression ◽

Early Development ◽

Expression Profiles ◽

Critical Role ◽

Genomic Research ◽

Go Annotation ◽

Rna Molecules ◽

Non Coding Rna ◽

Mirnas Expression ◽

Paired End Sequencing

The budgerigar (Melopsittacus undulatus) is one of the most widely studied parrot species, serving as an excellent animal model for behavior and neuroscience research. Until recently, it was unknown how sexual differences in the behavior, physiology, and development of organisms are regulated by differential gene expression. MicroRNAs (miRNAs) are endogenous short non-coding RNA molecules that can post-transcriptionally regulate gene expression and play a critical role in gonadal differentiation as well as early development of animals. However, very little is known about the role gonadal miRNAs play in the early development of birds. Research on the sex-biased expression of miRNAs in avian gonads are limited, and little is known aboutM. undulatus. In the current study, we sequenced two small non-coding RNA libraries made from the gonads of adult male and female budgerigars using Illumina paired-end sequencing technology. We obtained 254 known and 141 novel miRNAs, and randomly validated five miRNAs. Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. In conclusion, this work is the first report of sex-biased miRNAs expression in the budgerigar, and provides additional sequences to the avian miRNAome database which will foster further functional genomic research.

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