scholarly journals Genetic characterization of skull base chondrosarcomas

2015 ◽  
Vol 123 (4) ◽  
pp. 1036-1041 ◽  
Author(s):  
Hiroki Kanamori ◽  
Yohei Kitamura ◽  
Tokuhiro Kimura ◽  
Kazunari Yoshida ◽  
Hikaru Sasaki
Keyword(s):  
Skull Base ◽  
Case Series ◽  
Bone Neoplasms ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Genetic Characteristics ◽  
Genome Study ◽  
Skull Base Chordomas

OBJECT Although chondrosarcomas rarely arise in the skull base, chondrosarcomas and chordomas are the 2 major malignant bone neoplasms occurring at this location. The distinction of these 2 tumors is important, but this distinction is occasionally problematic because of radiological and histological overlap. Unlike chordoma and extracranial chondrosarcoma, no case series presenting a whole-genome analysis of skull base chondrosarcomas (SBCSs) has been reported. The goal of this study is to clarify the genetic characteristics of SBCSs and contrast them with those of chordomas. METHODS The authors analyzed 7 SBCS specimens for chromosomal copy number alterations (CNAs) using comparative genomic hybridization (CGH). They also examined IDH1 and IDH2 mutations and brachyury expression. RESULTS In CGH analyses, the authors detected CNAs in 6 of the 7 cases, including chromosomal gains of 8q21.1, 19, 2q22-q32, 5qcen-q14, 8q21-q22, and 15qcen-q14. Mutation of IDH1 was found with a high frequency (5 of 7 cases, 71.4%), of which R132S was most frequently mutated. No IDH2 mutations were found, and immunohistochemical staining for brachyury was negative in all cases. CONCLUSIONS To the best of the authors' knowledge, this is the first whole-genome study of an SBSC case series. Their findings suggest that these tumors are molecularly consistent with a subset of conventional central chondrosarcomas and different from skull base chordomas.

scholarly journals High-resolution Whole-Genome Analysis of Skull Base Chordomas Implicates FHIT Loss in Chordoma Pathogenesis

Neoplasia ◽  
2012 ◽  
Vol 14 (9) ◽  
pp. 788-IN4 ◽  
Author(s):  
Roberto Jose Diaz ◽  
Mustafa Guduk ◽  
Rocco Romagnuolo ◽  
Christian A. Smith ◽  
Paul Northcott ◽  
...  
Keyword(s):  
High Resolution ◽  
Skull Base ◽  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Skull Base Chordomas

scholarly journals Whole-Genome Analysis of Coxsackievirus B3 Reflects Its Genetic Diversity in China and Worldwide

2021 ◽  
Author(s):  
Qian Yang ◽  
Dongmei Yan ◽  
Yang Song ◽  
Shuangli Zhu ◽  
Yun He ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Foot And Mouth Disease ◽  
Coxsackievirus B3 ◽  
Whole Genome ◽  
Nucleotide Substitution Rate ◽  
Whole Genome Analysis ◽  
Genetic Characteristics ◽  
Heavy Burden ◽  
Group D

Abstract Background Coxsackievirus B3 (CVB3) has emerged as an active pathogen in myocarditis, aseptic meningitis, hand, foot, and mouth disease (HFMD), and pancreatitis, and is a heavy burden on public health. However, CVB3 has not been systematically analyzed with regard to whole-genome diversity and recombination. Therefore, this study was undertaken to systematically examine the genetic characteristics of CVB3 based on its whole genome. Methods We combined CVB3 isolates from our national HFMD surveillance and global sequences retrieved from GenBank. Phylogenetic analysis was performed to examine the whole genome variety and recombination forms of CVB3 in China and worldwide. Results Phylogenetic analysis showed that CVB3 strains isolated worldwide could be classified into groups A–E based on the sequence of the entire VP1 region. The predominant CVB3 strains in China belonged to group D, whereas group E CVB3 might be circulated globally compared to other groups. The average nucleotide substitution rate in the P1 region of CVB3 was 4.82 × 10−3 substitutions/site/year. Myocarditis was more common with group A. Groups C and D presented more cases of acute flaccid paralysis, and group D may be more likely to cause HFMD. Multiple recombination events were detected among CVB3 variants, and there were twenty-three recombinant lineages of CVB3 circulating worldwide. Conclusions Overall, this study provides full-length genomic sequences of CVB3 isolates with a wide geographic distribution over a long-term time scale in China, which will be helpful for understanding the evolution of this pathogen. Simultaneously, continuous surveillance of CVB3 is indispensable to determine its genetic diversity in China as well as worldwide.

Whole-genome analysis of Pandoraea species strains from cystic fibrosis patients

2019 ◽  
Vol 14 (16) ◽  
pp. 1357-1367
Author(s):  
Jumamurat R Bayjanov ◽  
Miquel B Ekkelenkamp ◽  
Malbert RC Rogers ◽  
Rafael Cantón ◽  
Barry J Benaissa-Trouw ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Core Genome ◽  
Genetic Characterization ◽  
Novel Species ◽  
Antibiotic Resistance Genes ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Acquired Antibiotic Resistance

Aim: Genetic characterization of Pandoraea strains recovered from cystic fibrosis patients. Materials & methods: The whole-genome sequence of 12 Pandoraea strains was determined using Illumina technology. The position of the strains within the genus Pandoraea was analyzed using selected partial gene sequences, core genome multi-locus sequence typing and average nucleotide identity analysis. Furthermore, the sequences were annotated. Results: The results show that some strains previously identified as Pandoraea pnomenusa, Pandoraea sputorum, Pandoraea oxalativorans and Pandoraea pulmonicola belong to novel species. The strains did not harbor acquired antibiotic resistance genes but encoded an OXA-type ß-lactamase. Conclusion: The taxonomy of the genus Pandoraea needs to be revised.

First isolation and characterization of Brucella suis from yak

Genome ◽  
2020 ◽  
Vol 63 (8) ◽  
pp. 397-405
Author(s):  
Xiaowen Yang ◽  
Ning Wang ◽  
Xiaofang Cao ◽  
Pengfei Bie ◽  
Zhifeng Xing ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Health And Safety ◽  
Host Cells ◽  
Whole Genome ◽  
Genetic Characteristics ◽  
Qinghai Province ◽  
Isolation And Characterization ◽  
Smooth Strain

Brucella spp., facultative intracellular pathogens that can persistently colonize animal host cells and cause zoonosis, affect public health and safety. A Brucella strain was isolated from yak in Qinghai Province. To detect whether this isolate could cause an outbreak of brucellosis and to reveal its genetic characteristics, several typing and whole-genome sequencing methods were applied to identify its species and genetic characteristics. Phylogenetic analysis based on MLVA and whole-genome sequencing revealed the genetic characteristics of the isolated strain. The results showed that the isolated strain is a B. suis biovar 1 smooth strain, and this isolate was named B. suis QH05. The results of comparative genomics and MLVA showed that B. suis QH05 is not a vaccine strain. Comparison with other B. suis strains isolated from humans and animals indicated that B. suis QH05 may be linked to specific animal and human sources. In conclusion, B. suis QH05 does not belong to the Brucella epidemic species in China, and as the first isolation of B. suis from yak, this strain expands the host range of B. suis.

Whole-genome analysis of human astrocytic tumors by comparative genomic hybridization

2000 ◽  
Vol 17 (1) ◽  
pp. 21-27 ◽  
Author(s):  
Motohiko Maruno ◽  
Hirotomo Ninomiya ◽  
A. K. M. Ghulam Muhammad ◽  
Masayuki Hirata ◽  
Amami Kato ◽  
...  
Keyword(s):  
Comparative Genomic Hybridization ◽  
Genome Analysis ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Astrocytic Tumors ◽  
Genomic Hybridization ◽  
Whole Genome Analysis

scholarly journals Evaluation of probiotic characteristics and whole genome analysis of Pediococcus pentosaceus MR001 for use as probiotic bacteria in shrimp aquaculture

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Warapond Wanna ◽  
Komwit Surachat ◽  
Panmile Kaitimonchai ◽  
Amornrat Phongdara
Keyword(s):  
Digestive Enzyme ◽  
Shrimp Aquaculture ◽  
Control Group ◽  
Immune Gene ◽  
Whole Genome ◽  
Feeding Trial ◽  
Intestinal Histology ◽  
Whole Genome Analysis ◽  
Genetic Characteristics ◽  
Pediococcus Pentosaceus

AbstractThe development of non-antibiotic and environmentally friendly agents is a key consideration for health management in shrimp aquaculture. In this study, the probiotic potential in shrimp aquaculture of Pediococcus pentosaceus MR001, isolated from Macrobrachium rosenbergii, was investigated by means of feeding trial and genetic characterization. In the feeding trial, dietary supplementation with P. pentosaceus MR001 significantly increased weight gain and digestive enzyme activity (p < 0.05) in shrimp, Litopenaeus vannamei. The intestinal histology showed that shrimp given the probiotic diet had healthier guts than the control group. Also, the immune gene expression and the survival rate in the treatment group were significantly increased when compared with the control group. The genetic characteristics of P. pentosaceus strain MR001 were explored by performing whole-genome sequencing (WGS) using the HiSeq 2500 platform and PacBio system, revealing the complete circular genome of 1,804,896 bp. We also identified 1789 coding genes and subsequently characterized genes related to the biosynthesis of bacteriocins, stress resistance, and bile tolerance. Our findings suggest that insights in the functional and genetic characteristics of P. pentosaceus strain MR001 could provide opportunities for applications of such strain in shrimp diet supplementation.

scholarly journals Identification and Characterization of Microsatellite Markers Derived from the Whole Genome Analysis of Taenia solium

2015 ◽  
Vol 9 (12) ◽  
pp. e0004316 ◽  
Author(s):  
Mónica J. Pajuelo ◽  
María Eguiluz ◽  
Eric Dahlstrom ◽  
David Requena ◽  
Frank Guzmán ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Genome Analysis ◽  
Taenia Solium ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Identification And Characterization
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