scholarly journals Exon Structure Analysis, Ortholog Identification, and SNP Candidate Screening by Mapping Mouse RIKEN Sequences to Multiple Genome Assemblies

2003 ◽  
Vol 13 (6) ◽  
pp. 1552-1553
Author(s):  
S. Batalov
Keyword(s):  
Structure Analysis ◽  
Multiple Genome ◽  
Genome Assemblies ◽  
Ortholog Identification ◽  
Exon Structure

scholarly journals Recurrent erosion of COA1/MITRAC15 exemplifies conditional gene dispensability in oxidative phosphorylation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sagar Sharad Shinde ◽  
Sandhya Sharma ◽  
Lokdeep Teekas ◽  
Ashutosh Sharma ◽  
Nagarjun Vijay
Keyword(s):  
Skeletal Muscle ◽  
Oxidative Phosphorylation ◽  
Gene Loss ◽  
Chromosomal Rearrangements ◽  
Genomic Region ◽  
Mitochondrial Translation ◽  
Closely Related Species ◽  
Genome Assemblies ◽  
Exon Structure

AbstractSkeletal muscle fibers rely upon either oxidative phosphorylation or the glycolytic pathway with much less reliance on oxidative phosphorylation to achieve muscular contractions that power mechanical movements. Species with energy-intensive adaptive traits that require sudden bursts of energy have a greater dependency on glycolytic fibers. Glycolytic fibers have decreased reliance on OXPHOS and lower mitochondrial content compared to oxidative fibers. Hence, we hypothesized that gene loss might have occurred within the OXPHOS pathway in lineages that largely depend on glycolytic fibers. The protein encoded by the COA1/MITRAC15 gene with conserved orthologs found in budding yeast to humans promotes mitochondrial translation. We show that gene disrupting mutations have accumulated within the COA1 gene in the cheetah, several species of galliform birds, and rodents. The genomic region containing COA1 is a well-established evolutionary breakpoint region in mammals. Careful inspection of genome assemblies of closely related species of rodents and marsupials suggests two independent COA1 gene loss events co-occurring with chromosomal rearrangements. Besides recurrent gene loss events, we document changes in COA1 exon structure in primates and felids. The detailed evolutionary history presented in this study reveals the intricate link between skeletal muscle fiber composition and the occasional dispensability of the chaperone-like role of the COA1 gene.

scholarly journals Progressive Cactus is a multiple-genome aligner for the thousand-genome era

Nature ◽  
2020 ◽  
Vol 587 (7833) ◽  
pp. 246-251 ◽  
Author(s):  
Joel Armstrong ◽  
Glenn Hickey ◽  
Mark Diekhans ◽  
Ian T. Fiddes ◽  
Adam M. Novak ◽  
...  
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Genome Alignment ◽  
Vertebrate Genome ◽  
Multiple Genome ◽  
Sequencing Technologies ◽  
Third Generation Sequencing ◽  
Genome Assemblies ◽  
Information Database ◽  
Generation Sequencing

AbstractNew genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies1–3. For example, the number of vertebrate genome assemblies currently in the NCBI (National Center for Biotechnology Information) database4 increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019. In addition to this influx of assemblies from different species, new human de novo assemblies5 are being produced, which enable the analysis of not only small polymorphisms, but also complex, large-scale structural differences between human individuals and haplotypes. This coming era and its unprecedented amount of data offer the opportunity to uncover many insights into genome evolution but also present challenges in how to adapt current analysis methods to meet the increased scale. Cactus6, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequences. Here we describe progressive extensions to Cactus to create Progressive Cactus, which enables the reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We describe results from an alignment of more than 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment created so far.

200kv superconducting cryo electron microscope

1987 ◽  
Vol 45 ◽  
pp. 642-643
Author(s):  
M. Iwatsuki ◽  
Y. Kokubo ◽  
Y. Harada ◽  
J. Lehman
Keyword(s):  
Electron Microscope ◽  
Structure Analysis ◽  
Organic Materials ◽  
Strong Interactions ◽  
Specimen Preparation ◽  
Great Effort ◽  
Electron Microscopic ◽  
Crystal Fields ◽  
Special Skill ◽  
Long Time

In recent years, the electron microscope has been significantly improved in resolution and we can obtain routinely atomic-level high resolution images without any special skill. With this improvement, the structure analysis of organic materials has become one of the interesting targets in the biological and polymer crystal fields.Up to now, X-ray structure analysis has been mainly used for such materials. With this method, however, great effort and a long time are required for specimen preparation because of the need for larger crystals. This method can analyze average crystal structure but is insufficient for interpreting it on the atomic or molecular level. The electron microscopic method for organic materials has not only the advantage of specimen preparation but also the capability of providing various information from extremely small specimen regions, using strong interactions between electrons and the substance. On the other hand, however, this strong interaction has a big disadvantage in high radiation damage.

RETRIEVE – a system for XRPD phase and structure analysis

2009 ◽  
Vol 2009 (30) ◽  
pp. 209-214 ◽  
Author(s):  
P. S. Dubinin ◽  
I. S. Yakimov ◽  
O. E. Piksina ◽  
Y. I. Yakimov ◽  
A. N. Zaloga
Keyword(s):  
Structure Analysis
Sign in / Sign up

Export Citation Format

Share Document