scholarly journals An approach of orthology detection from homologous sequences under minimum evolution

2008 ◽  
Vol 36 (17) ◽  
pp. e110-e110 ◽  
Author(s):  
Kyung Mo Kim ◽  
Samsun Sung ◽  
Gustavo Caetano-Anollés ◽  
Jae Yong Han ◽  
Heebal Kim
Keyword(s):  
Minimum Evolution ◽  
Homologous Sequences ◽  
Orthology Detection

A combined ultrastructural and gene molecular research for the relationship between human uterine cervical carcinoma and human papillomavirus

1990 ◽  
Vol 48 (3) ◽  
pp. 204-205
Author(s):  
Kun Lee ◽  
Jingyi Si ◽  
Ricai Han ◽  
Wei Zhang ◽  
Bingbing Tan ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Human Papillomavirus ◽  
Intraepithelial Neoplasia ◽  
Hpv Infection ◽  
Dot Blot ◽  
Homologous Sequences ◽  
Normal Cervical Epithelium ◽  
The Relationship ◽  
Chronic Cervicitis

There are more supports for the view that human papillomavirus (HPV) infection might be an etiological factor in the development of cervical cancer when the association of persistent condylomata is considered. Biopsies from 318 cases with squamous cell carcinoma of uterine cervix, 48 with cervical and vulvar condylomata, 14 with cervical intraepithelial neoplasia (CIN), 34 with chronic cervicitis and 24 normal cervical epithelium were collected from 5 geographic regions of China with different cervical cancer mortalities. All specimens were prepared for Dot blot, Southern blot and in situ DNA-DNA hybridizations by using HPV-11, 16, 18 DNA labelled with 32P and 3H as probes to detect viral homologous sequences in samples. Among them, 32 cases with cervical cancer, 27 with condyloma and 10 normal cervical epitheliums were randomly chosen for comparative EM observation. The results showed that: 1), 192 out of 318 (60.4%) cases of cervical cancer were positive for HPV-16 DNA probe (Table I)

scholarly journals A Comparison of the Structure and Function of the Highly Homologous Maize Antioxidant Cu/Zn Superoxide Dismutase Genes, sod4 and Sod4A

Genetics ◽  
1996 ◽  
Vol 144 (1) ◽  
pp. 317-328 ◽  
Author(s):  
Sheri P Kernodle ◽  
John G Scandalios
Keyword(s):  
Structure And Function ◽  
Specific Response ◽  
Stem Tissue ◽  
Mrna Accumulation ◽  
Regulatory Motifs ◽  
Homologous Sequences ◽  
Developmental Profiles ◽  
And Function ◽  
Differential Tissue ◽  
Sporophytic Development

Abstract Two highly similar cytosolic Cu/Zn Sod (Sod4 and Sod4A) genes have been isolated from maize. Sod4A contains eight exons and seven introns. The Sod4 partial sequence contains five introns. The introns in both genes are located in the same position and have highly homologous sequences in several regions. The largest intron (>1200 bp) interrupts the 5′ leader sequence. The presence of different regulatory motifs in the promoter region of each gene may indicate distinct responses to various conditions. Zymogram and RNA blot analyses show that Sod4 and Sod4A are expressed in all tissues of the maize plant. The developmental profiles of Sod4 and Sod4A mRNA accumulation differ in scutella during sporophytic development. RNA blot analysis of the respective Sod mRNAs indicates a differential, tissue-specific response of each gene to certain stressors. RNA isolated from stem tissue of ethephon-treated seedlings shows an increase in the Sod4 but not the Sod4A transcript while there is no change in transcripts of either gene in leaves or roots. There is differential mRNA accumulation between the two genes in leaf and stem tissue of paraquat-treated seedlings. Other agents that can cause oxidative stress were also tested for differential expression of the genes.

scholarly journals Deletion Formation Between the Two Salmonella typhimurium Flagellin Genes Encoded on the Mini F Plasmid: Escherichia coli ssb Alleles Enhance Deletion Rates and Change Hot-Spot Preference for Deletion Endpoints

Genetics ◽  
1997 ◽  
Vol 145 (3) ◽  
pp. 563-572 ◽  
Author(s):  
Takafumi Mukaihara ◽  
Masatoshi Enomoto
Keyword(s):  
Escherichia Coli ◽  
Salmonella Typhimurium ◽  
Hot Spots ◽  
Hot Spot ◽  
Direct Repeats ◽  
Replication Slippage ◽  
Detection Systems ◽  
Deletion Formation ◽  
Homologous Sequences ◽  
Deletion Detection

Deletion formation between the 5′-mostly homologous sequences and between the 3′-homeologous sequences of the two Salmonella typhimurium flagellin genes was examined using plasmid-based deletion-detection systems in various Escherichia coli genetic backgrounds. Deletions in plasmid pLC103 occur between the 5′ sequences, but not between the 3′ sequences, in both RecA-independent and RecA-dependent ways. Because the former is predominant, deletion formation in a recA background depends on the length of homologous sequences between the two genes. Deletion rates were enhanced 30- to 50-fold by the mismatch repair defects, mutS, mutL and uvrD, and 250-fold by the ssb-3 allele, but the effect of the mismatch defects was canceled by the ΔrecA allele. Rates of the deletion between the 3′ sequences in plasmid pLC107 were enhanced 17- to 130-fold by ssb alleles, but not by other alleles. For deletions in pLC107, 96% of the endpoints in the recA+ background and 88% in ΔrecA were in the two hot spots of the 60- and 33-nucleotide (nt) homologous sequences, whereas in the ssb-3 background >50% of the endpoints were in four- to 14-nt direct repeats dispersed in the entire 3′ sequences. The deletion formation between the homeologous sequences is RecA-independent but depends on the length of consecutive homologies. The mutant ssb allele lowers this dependency and results in the increase in deletion rates. Roles of mutant SSB are discussed with relation to misalignment in replication slippage.

scholarly journals On the Number of Ancestors to a DNA Sequence

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1459-1468 ◽  
Author(s):  
Carsten Wiuf ◽  
Jotun Hein
Keyword(s):  
Population Size ◽  
Dna Sequence ◽  
Ancestral Sequence ◽  
Ancestral Population ◽  
Homologous Sequences ◽  
Actual Size

If homologous sequences in a population are not subject to recombination, they can all be traced back to one ancestral sequence. However, the rest of our genome is subject to recombination and will be spread out on a series of individuals. The distribution of ancestral material to an extant chromosome is here investigated by the coalescent with recombination, and the results are discussed relative to humans. In an ancestral population of actual size 1.3 million a minority of <6.4% will carry material ancestral to any present human. The estimated actual population size can be even higher, 5 million, reducing the percentage to 1.7%.

When Homologous Sequences Meet Structural Decoys: Accurate Contact Prediction by tFold in CASP14

2021 ◽  
Author(s):  
Tao Shen ◽  
Jiaxiang Wu ◽  
Haidong Lan ◽  
Liangzhen Zheng ◽  
Jianguo Pei ◽  
...  
Keyword(s):  
Contact Prediction ◽  
Homologous Sequences

scholarly journals Quantum speed limit for a relativistic electron in the noncommutative phase space

2017 ◽  
Vol 32 (23n24) ◽  
pp. 1750143 ◽  
Author(s):  
Kang Wang ◽  
Yu-Fei Zhang ◽  
Qing Wang ◽  
Zheng-Wen Long ◽  
Jian Jing
Keyword(s):  
Relativistic Electron ◽  
Uniform Magnetic Field ◽  
Lorentz Invariance ◽  
Relativistic Quantum ◽  
Quantum Mechanical ◽  
Speed Limit ◽  
Speed Of Light ◽  
Minimum Evolution ◽  
Noncommutative Phase Space ◽  
Average Speed

The influence of the noncommutativity on the average speed of a relativistic electron interacting with a uniform magnetic field within the minimum evolution time is investigated. We find that it is possible for the wave packet of the electron to travel faster than the speed of light in vacuum because of the noncommutativity. It is a clear signature of violating Lorentz invariance in the noncommutative relativistic quantum mechanical region.

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