scholarly journals Comparative Genomic Analysis of slc39a12/ZIP12: Insight into a Zinc Transporter Required for Vertebrate Nervous System Development

PLoS ONE ◽  
2014 ◽  
Vol 9 (11) ◽  
pp. e111535 ◽  
Author(s):  
Winyoo Chowanadisai
Keyword(s):  
Nervous System ◽  
System Development ◽  
Genomic Analysis ◽  
Nervous System Development ◽  
Comparative Genomic Analysis ◽  
Zinc Transporter ◽  
Comparative Genomic ◽  
Insight Into

scholarly journals Metabolic Diversity within the Globally Abundant Marine Group IIEuryarchaeaOffers Insight into Ecological Patterns

2018 ◽  
Author(s):  
Benjamin J Tully
Keyword(s):  
Organic Matter ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Metabolic Diversity ◽  
Metabolic Potential ◽  
Surface Ocean ◽  
Ecological Patterns ◽  
Reference Genomes ◽  
Insight Into

AbstractDespite their discovery over 25 years ago, the Marine Group IIEuryarchaea(MGII) have remained a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present the comparative genomic analysis of 250 MGII genomes, providing the most detailed view of these mesophilic archaea to-date. This analysis identified 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera revealed distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins common in all other subclades. This study redefines the MGII and provides an avenue for understanding the role these organisms play in the cycling of organic matter throughout the water column.

scholarly journals Comparative genomic analysis provides insight into the phylogeny and virulence of atypical enteropathogenic Escherichia coli strains from Brazil

2020 ◽  
Vol 14 (6) ◽  
pp. e0008373 ◽  
Author(s):  
Rodrigo T. Hernandes ◽  
Tracy H. Hazen ◽  
Luís F. dos Santos ◽  
Taylor K. S. Richter ◽  
Jane M. Michalski ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Enteropathogenic Escherichia Coli ◽  
Insight Into

scholarly journals Copy number variations in candidate genomic regions confirm genetic heterogeneity and parental bias in Hirschsprung disease

2019 ◽  
Vol 14 (1) ◽  
Author(s):  
Francesca Lantieri ◽  
Stefania Gimelli ◽  
Chiara Viaggi ◽  
Elissavet Stathaki ◽  
Michela Malacarne ◽  
...  
Keyword(s):  
Nervous System ◽  
Enteric Nervous System ◽  
Genetic Heterogeneity ◽  
Copy Number ◽  
System Development ◽  
Hirschsprung Disease ◽  
Copy Number Variations ◽  
Nervous System Development ◽  
Comparative Genomic ◽  
Genomic Regions

Abstract Background Hirschsprung Disease (HSCR) is a congenital defect of the intestinal innervations characterized by complex inheritance. Many susceptibility genes including RET, the major HSCR gene, and several linked regions and associated loci have been shown to contribute to disease pathogenesis. Nonetheless, a proportion of patients still remains unexplained. Copy Number Variations (CNVs) have already been involved in HSCR, and for this reason we performed Comparative Genomic Hybridization (CGH), using a custom array with high density probes. Results A total of 20 HSCR candidate regions/genes was tested in 55 sporadic patients and four patients with already known chromosomal aberrations. Among 83 calls, 12 variants were experimentally validated, three of which involving the HSCR crucial genes SEMA3A/3D, NRG1, and PHOX2B. Conversely RET involvement in HSCR does not seem to rely on the presence of CNVs while, interestingly, several gains and losses did co-occur with another RET defect, thus confirming that more than one predisposing event is necessary for HSCR to develop. New loci were also shown to be involved, such as ALDH1A2, already found to play a major role in the enteric nervous system. Finally, all the inherited CNVs were of maternal origin. Conclusions Our results confirm a wide genetic heterogeneity in HSCR occurrence and support a role of candidate genes in expression regulation and cell signaling, thus contributing to depict further the molecular complexity of the genomic regions involved in the Enteric Nervous System development. The observed maternal transmission bias for HSCR associated CNVs supports the hypothesis that in females these variants might be more tolerated, requiring additional alterations to develop HSCR disease.

scholarly journals Extracellular Matrix-Associated Protein Sc1 Is Not Essential for Mouse Development

2000 ◽  
Vol 20 (2) ◽  
pp. 656-660 ◽  
Author(s):  
Peter J. McKinnon ◽  
Susan K. McLaughlin ◽  
Manuela Kapsetaki ◽  
Robert F. Margolskee
Keyword(s):  
Extracellular Matrix ◽  
Nervous System ◽  
Gene Targeting ◽  
System Development ◽  
Nervous System Development ◽  
Mouse Development ◽  
Term Survival ◽  
Insight Into ◽  
Developing Nervous System

ABSTRACT Sc1 is an extracellular matrix-associated protein whose function is unknown. During early embryonic development, Sc1 is widely expressed, and from embryonic day 12 (E12), Sc1 is expressed primarily in the developing nervous system. This switch in Sc1 expression at E12 suggests an importance for nervous-system development. To gain insight into Sc1 function, we used gene targeting to inactivate mouse Sc1. The Sc1-null mice showed no obvious deficits in any organs. These mice were born at the expected ratios, were fertile, and had no obvious histological abnormalities, and their long-term survival did not differ from littermate controls. Therefore, the function of Sc1 during development is not critical or, in its absence, is subserved by another protein.

scholarly journals Neonatal Salivary Analysis Reveals Global Developmental Gene Expression Changes in the Premature Infant

2010 ◽  
Vol 56 (3) ◽  
pp. 409-416 ◽  
Author(s):  
Jill L Maron ◽  
Kirby L Johnson ◽  
David M Rocke ◽  
Michael G Cohen ◽  
Albert J Liley ◽  
...  
Keyword(s):  
Gene Expression ◽  
System Development ◽  
Newborn Care ◽  
Genomic Analysis ◽  
Nervous System Development ◽  
Comparative Genomic ◽  
Tissue Development ◽  
Bioinformatics Analyses ◽  
Noninvasive Technique ◽  
And Function

Abstract Background: There is an important need to develop noninvasive biomarkers to detect disease in premature neonates. Our objective was to determine if salivary genomic analysis provides novel information about neonatal expression of developmental genes. Methods: Saliva (50–200 μL) was prospectively collected from 5 premature infants at 5 time points: before, starting, and advancing enteral nutrition; at the introduction of oral feeds; and at advanced oral feeds. Salivary RNA was extracted, amplified, and hybridized onto whole-genomic microarrays. Results: Bioinformatics analyses identified 9286 gene transcripts with statistically significant gene expression changes across individuals over time. Of these genes, 3522 (37.9%) were downregulated, and 5764 (62.1%) were upregulated. Gene expression changes were highly associated with developmental pathways. Significantly downregulated expression was seen in embryonic development, connective tissue development and function, hematologic system development and function, and survival of the organism (10−14 < P < 10−3). Conversely, genes associated with behavior, nervous system development, tissue development, organ development, and digestive system development were significantly upregulated (10−11 < P < 10−2). Conclusions: Comparative genomic salivary analyses provide robust, comprehensive, real-time information regarding nearly all organs and tissues in the developing preterm infant. This innovative and noninvasive technique represents a new approach for monitoring health, disease, and development in this vulnerable patient population. By comparing these data in healthy infants with data from infants who develop medical complications, we expect to identify new biomarkers that will ultimately improve newborn care.

scholarly journals Comparative genomic analysis of Cristatella mucedo provides insights into Bryozoan evolution and nervous system function

2019 ◽  
Author(s):  
Viktor V Starunov ◽  
Alexander V Predeus ◽  
Yury A Barbitoff ◽  
Vladimir A Kutiumov ◽  
Arina L Maltseva ◽  
...  
Keyword(s):  
Nervous System ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
System Function ◽  
Nervous System Function ◽  
Cristatella Mucedo

This manuscript has been withdrawn by the authors as it was submitted without the full consent of all the authors.Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

scholarly journals Insight into Evolution of Bordetella pertussis from Comparative Genomic Analysis: Evidence of Vaccine-Driven Selection

2010 ◽  
Vol 28 (1) ◽  
pp. 707-715 ◽  
Author(s):  
Sophie Octavia ◽  
Ram P. Maharjan ◽  
Vitali Sintchenko ◽  
Gordon Stevenson ◽  
Peter R. Reeves ◽  
...  
Keyword(s):  
Bordetella Pertussis ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Insight Into

scholarly journals Comparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution

2019 ◽  
Vol 2019 ◽  
pp. 1-14
Author(s):  
Jianchao Ying ◽  
Jun Ye ◽  
Teng Xu ◽  
Qian Wang ◽  
Qiyu Bao ◽  
...  
Keyword(s):  
Core Genome ◽  
Genomic Analysis ◽  
Rhodococcus Equi ◽  
Comparative Genomic Analysis ◽  
Genomic Islands ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Niche Adaptation ◽  
Genomic Studies ◽  
Insight Into

Rhodococcus equi, a member of the Rhodococcus genus, is a gram-positive pathogenic bacterium. Rhodococcus possesses an open pan-genome that constitutes the basis of its high genomic diversity and allows for adaptation to specific niche conditions and the changing host environments. Our analysis further showed that the core genome of R. equi contributes to the pathogenicity and niche adaptation of R. equi. Comparative genomic analysis revealed that the genomes of R. equi shared identical collinearity relationship, and heterogeneity was mainly acquired by means of genomic islands and prophages. Moreover, genomic islands in R. equi were always involved in virulence, resistance, or niche adaptation and possibly working with prophages to cause the majority of genome expansion. These findings provide an insight into the genomic diversity, evolution, and structural variation of R. equi and a valuable resource for functional genomic studies.

scholarly journals Comparative genomic analysis of Mycobacterium intracellulare: implications for clinical taxonomic classification in pulmonary Mycobacterium avium-intracellulare complex disease

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yoshitaka Tateishi ◽  
Yuriko Ozeki ◽  
Akihito Nishiyama ◽  
Mari Miki ◽  
Ryoji Maekura ◽  
...  
Keyword(s):  
Complex Disease ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Mycobacterium Intracellulare ◽  
Clinical Strains ◽  
Genetic Components ◽  
Genomic Regions ◽  
Insight Into

Abstract Background Mycobacterium intracellulare is a representative etiological agent of emerging pulmonary M. avium-intracellulare complex disease in the industrialized countries worldwide. The recent genome sequencing of clinical strains isolated from pulmonary M. avium-intracellulare complex disease has provided insight into the genomic characteristics of pathogenic mycobacteria, especially for M. avium; however, the genomic characteristics of M. intracellulare remain to be elucidated. Results In this study, we performed comparative genomic analysis of 55 M. intracellulare and related strains such as M. paraintracellulare (MP), M. indicus pranii (MIP) and M. yonogonense. Based on the average nucleotide identity, the clinical M. intracellulare strains were phylogenetically grouped in two clusters: (1) the typical M. intracellulare (TMI) group, including ATCC13950 and virulent M.i.27 and M.i.198 that we previously reported, and (2) the MP-MIP group. The alignment of the genomic regions was mostly preserved between groups. Plasmids were identified between groups and subgroups, including a plasmid common among some strains of the M.i.27 subgroup. Several genomic regions including those encoding factors involved in lipid metabolism (e.g., fadE3, fadE33), transporters (e.g., mce3), and type VII secretion system (genes of ESX-2 system) were shown to be hypermutated in the clinical strains. M. intracellulare was shown to be pan-genomic at the species and subspecies levels. The mce genes were specific to particular subspecies, suggesting that these genes may be helpful in discriminating virulence phenotypes between subspecies. Conclusions Our data suggest that genomic diversity among M. intracellulare, M. paraintracellulare, M. indicus pranii and M. yonogonense remains at the subspecies or genovar levels and does not reach the species level. Genetic components such as mce genes revealed by the comparative genomic analysis could be the novel focus for further insight into the mechanism of human pathogenesis for M. intracellulare and related strains.

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