scholarly journals Biological insight into design against crime

2008 ◽  
Author(s):  
D. E. Santos-Reyes
Keyword(s):  
Design Against Crime ◽  
Biological Insight ◽  
Insight Into

scholarly journals Gene-based analysis of ADHD using PASCAL: a biological insight into the novel associated genes

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Aitana Alonso-Gonzalez ◽  
Manuel Calaza ◽  
Cristina Rodriguez-Fontenla ◽  
Angel Carracedo
Keyword(s):  
Gene Network ◽  
Association Studies ◽  
Meta Analysis ◽  
Neurodevelopmental Disorder ◽  
Differentially Expressed Gene ◽  
Brain Regions ◽  
Genome Wide Association Studies ◽  
Summary Statistics ◽  
Biological Insight ◽  
Insight Into

Abstract Background Attention-Deficit Hyperactivity Disorder (ADHD) is a complex neurodevelopmental disorder (NDD) which may significantly impact on the affected individual’s life. ADHD is acknowledged to have a high heritability component (70–80%). Recently, a meta-analysis of GWAS (Genome Wide Association Studies) has demonstrated the association of several independent loci. Our main aim here, is to apply PASCAL (pathway scoring algorithm), a new gene-based analysis (GBA) method, to the summary statistics obtained in this meta-analysis. PASCAL will take into account the linkage disequilibrium (LD) across genomic regions in a different way than the most commonly employed GBA methods (MAGMA or VEGAS (Versatile Gene-based Association Study)). In addition to PASCAL analysis a gene network and an enrichment analysis for KEGG and GO terms were carried out. Moreover, GENE2FUNC tool was employed to create gene expression heatmaps and to carry out a (DEG) (Differentially Expressed Gene) analysis using GTEX v7 and BrainSpan data. Results PASCAL results have revealed the association of new loci with ADHD and it has also highlighted other genes previously reported by MAGMA analysis. PASCAL was able to discover new associations at a gene level for ADHD: FEZF1 (p-value: 2.2 × 10− 7) and FEZF1-AS1 (p-value: 4.58 × 10− 7). In addition, PASCAL has been able to highlight association of other genes that share the same LD block with some previously reported ADHD susceptibility genes. Gene network analysis has revealed several interactors with the associated ADHD genes and different GO and KEGG terms have been associated. In addition, GENE2FUNC has demonstrated the existence of several up and down regulated expression clusters when the associated genes and their interactors were considered. Conclusions PASCAL has been revealed as an efficient tool to extract additional information from previous GWAS using their summary statistics. This study has identified novel ADHD associated genes that were not previously reported when other GBA methods were employed. Moreover, a biological insight into the biological function of the ADHD associated genes across brain regions and neurodevelopmental stages is provided.

scholarly journals Conformation-independent structural comparison of macromolecules with ProSMART

2014 ◽  
Vol 70 (a1) ◽  
pp. C494-C494 ◽  
Author(s):  
Robert Nicholls ◽  
Marcus Fischer ◽  
Garib Murshudov
Keyword(s):  
Comparative Analysis ◽  
Structural Alignment ◽  
Structural Data ◽  
Visual Assessment ◽  
Biological Macromolecules ◽  
Rna Structures ◽  
Structural Comparison ◽  
Biological Insight ◽  
High Sequence Homology ◽  
Insight Into

Structural comparison often aids insight into the function and mechanics of biological macromolecules. To make such analyses more accessible, we present the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART), which is designed to allow fast but detailed comparative analysis of macromolecular structures despite potential dissimilarities in global arrangement, such as domain motion and distortion. Whilst obtaining a residue alignment between structures is a prerequisite for comparative analysis, conventional alignment methods may fail in cases where conformational differences are dramatic. However, ProSMART achieves a conformation-independent structural alignment by focusing purely on local dissimilarities, rather than enforcing chain/domain rigidity. This allows the sensible comparison of protein (or DNA/RNA) structures in the presence of conformational change. ProSMART allows analysis of the structural conservation of local backbone and side chains in a wide variety of scenarios - the method is sensitive enough to allow identification of subtle dissimilarities between structures sharing high sequence homology, whilst being versatile enough to allow identification of local similarities between more distantly-related structures. In addition, ProSMART can be used for the identification of conserved rigid substructures, which may or may not represent functional domains. ProSMART is also used for the generation of external restraints for use in crystallographic refinement. Results from ProSMART can be visualised in either CCP4mg or PyMOL. All residue-based scores are illustrated using intuitive colour gradients, allowing easy visual assessment of local backbone and side chain conservation. Complementary structural comparison tools such as ProSMART can help break the complexity of the constantly growing pool of available structural data into a more readily accessible form, and consequently may aid biological insight into macromolecular structures.

scholarly journals Integrated Analysis of Gene Network in Childhood Leukemia from Microarray and Pathway Databases

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Amphun Chaiboonchoe ◽  
Sandhya Samarasinghe ◽  
Don Kulasiri ◽  
Kourosh Salehi-Ashtiani
Keyword(s):  
Gene Network ◽  
Childhood Leukemia ◽  
Therapeutic Agents ◽  
Interaction Networks ◽  
Integrated Analysis ◽  
Molecular Pathways ◽  
Biological Processes ◽  
Biological Insight ◽  
Insight Into ◽  
Pathway Databases

Glucocorticoids (GCs) have been used as therapeutic agents for children with acute lymphoblastic leukaemia (ALL) for over 50 years. However, much remains to be understood about the molecular mechanism of GCs actions in ALL subtypes. In this study, we delineate differential responses of ALL subtypes, B- and T-ALL, to GCs treatment at systems level by identifying the differences among biological processes, molecular pathways, and interaction networks that emerge from the action of GCs through the use of a selected number of available bioinformatics methods and tools. We provide biological insight into GC-regulated genes, their related functions, and their networks specific to the ALL subtypes. We show that differentially expressed GC-regulated genes participate in distinct underlying biological processes affected by GCs in B-ALL and T-ALL with little to no overlap. These findings provide the opportunity towards identifying new therapeutic targets.

scholarly journals Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Sayed Mohammad Ebrahim Sahraeian ◽  
Marghoob Mohiyuddin ◽  
Robert Sebra ◽  
Hagen Tilgner ◽  
Pegah T. Afshar ◽  
...  
Keyword(s):  
Broad Spectrum ◽  
Rna Seq ◽  
Biological Insight ◽  
Insight Into

scholarly journals Gaining comprehensive biological insight into chloroplast RNA editing by performing a broad-spectrum RNA-seq analysis

2020 ◽  
Author(s):  
Aidi Zhang ◽  
Jing Fang ◽  
Xiaohan Jiang ◽  
Tengfei Wang ◽  
Xiujun Zhang
Keyword(s):  
Rna Editing ◽  
Synonymous Codon ◽  
Future Research ◽  
Rna Seq ◽  
Data Set ◽  
Angiosperm Evolution ◽  
Biological Insight ◽  
Plant Chloroplast ◽  
Codon Positions ◽  
Insight Into

AbstractBackgroundRNA editing is a post-transcriptional modification that complement variation at the DNA level. Until now, different RNA editing systems were found in the major eukaryotic lineages. However, the evolution trajectory in plant chloroplast remains unclear. To gain a better understanding of RNA editing in plant chloroplast, in this study, based on publicly available RNA-seq data across three plant lineages (fern, gymnosperm, and angiosperm), we provided a detailed analysis of RNA editing events in plant chloroplasts and discussed the evolution of RNA editing in land plants.ResultsThere were a total of 5,389 editing sites located in leaf chloroplast identified across 21 plants after rigorous screening. We found that the cluster of RNA editing sites across 21 plants complied with the phylogenetic tree based on linked protein sequences approximately, and majority (∼ 95%) of the editing events resulted in non-synonymous codon changes, RNA editing occurred in second codon position was mainly the largest. Additionally, RNA editing caused an overall increase in hydrophobicity of the resulting proteins. The analyses also revealed that there is an uneven distribution of editing sites among species, genes, and codon positions, the average RNA editing extent varied among different plant species as well as genes. Finally, we found that the loss of editing sites along angiosperm evolution is mainly occurring by reduce of cytosines content, fern plants has the highest cytosine content, with the evolution of plants, cytosine were lost in RNA edited genes.ConclusionsMany of the identified sites in our study have not been previously reported and represent a valuable data set for future research community. Our findings provide valuable information for evolution of RNA editing in plants.

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