Homology Search and Multiple Alignment

ABSTRACT Homologous recombination (HR) is critical for DNA double-strand break (DSB) repair and genome stabilization. In yeast, HR is catalyzed by the Rad51 strand transferase and its “mediators,” including the Rad52 single-strand DNA-annealing protein, two Rad51 paralogs (Rad55 and Rad57), and Rad54. A Rad51 homolog, Dmc1, is important for meiotic HR. In wild-type cells, most DSB repair results in gene conversion, a conservative HR outcome. Because Rad51 plays a central role in the homology search and strand invasion steps, DSBs either are not repaired or are repaired by nonconservative single-strand annealing or break-induced replication mechanisms in rad51Δ mutants. Although DSB repair by gene conversion in the absence of Rad51 has been reported for ectopic HR events (e.g., inverted repeats or between plasmids), Rad51 has been thought to be essential for DSB repair by conservative interchromosomal (allelic) gene conversion. Here, we demonstrate that DSBs stimulate gene conversion between homologous chromosomes (allelic conversion) by >30-fold in a rad51Δ mutant. We show that Rad51-independent allelic conversion and break-induced replication occur independently of Rad55, Rad57, and Dmc1 but require Rad52. Unlike DSB-induced events, spontaneous allelic conversion was detected in both rad51Δ and rad52Δ mutants, but not in a rad51Δ rad52Δ double mutant. The frequencies of crossovers associated with DSB-induced gene conversion were similar in the wild type and the rad51Δ mutant, but discontinuous conversion tracts were fivefold more frequent and tract lengths were more widely distributed in the rad51Δ mutant, indicating that heteroduplex DNA has an altered structure, or is processed differently, in the absence of Rad51.

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In Silico Identification and Functional Characterization of Conserved miRNAs in the Genome of Cryptosporidium parvum

Bioinformatics and Biology Insights ◽

10.1177/11779322211027665 ◽

2021 ◽

Vol 15 ◽

pp. 117793222110276

Author(s):

Md. Irtija Ahsan ◽

Md. Shahidur Rahman Chowdhury ◽

Moumita Das ◽

Sharmin Akter ◽

Sawrab Roy ◽

...

Keyword(s):

Cryptosporidium Parvum ◽

Target Genes ◽

Expressed Sequence Tag ◽

Functional Characterization ◽

Childhood Mortality ◽

Homology Search ◽

Health Concern ◽

Nutrient Metabolism ◽

Screening Process ◽

Computational Screening

Cryptosporidium parvum, a predominant causal agent of a fatal zoonotic protozoan diarrhoeal disease called cryptosporidiosis, bears a worldwide public health concern for childhood mortality and poses a key threat to the dairy and water industries. MicroRNAs (miRNAs), small but powerful posttranscriptional gene silencing RNA molecules, regulate a variety of molecular, biological, and cellular processes in animals and plants. As to the present date, there is a paucity of information regarding miRNAs of C. parvum; hence, this study was used to identify miRNAs in the organism using a comprehensible expressed sequence tag–based homology search approach consisting of a series of computational screening process from the identification of putative miRNA candidates to the functional annotation of the important gene targets in C. parvum. The results revealed a conserved miRNA that targeted 487 genes in the model organism ( Drosophila melanogaster) and 85 genes in C. parvum, of which 11 genes had direct involvements in several crucial virulence factors such as environmental oocyst protection, excystation, locomotion, adhesion, invasion, stress protection, intracellular growth, and survival. Besides, 20 genes showed their association with various major pathways dedicated for the ribosomal biosynthesis, DNA repair, transportation, protein production, gene expression, cell cycle, cell proliferation, development, immune response, differentiation, and nutrient metabolism of the organism in the host. Thus, this study provides a strong evidence of great impact of identified miRNA on the biology, virulence, and pathogenesis of C. parvum. Furthermore, the study suggests that the detected miRNA could be a potential epigenomic tool for controlling the protozoon through silencing those virulent and pathway-related target genes.

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Computational study for suppression of CD25/IL-2 interaction

Biological Chemistry ◽

10.1515/hsz-2020-0326 ◽

2020 ◽

Vol 0 (0) ◽

Author(s):

Moein Dehbashi ◽

Zohreh Hojati ◽

Majid Motovali-bashi ◽

Mazdak Ganjalikhani-Hakemi ◽

Akihiro Shimosaka ◽

...

Keyword(s):

Small Molecules ◽

Cancer Progression ◽

Immune Escape ◽

De Novo ◽

Computational Study ◽

Treg Cells ◽

Homology Search ◽

Small Interfering Rnas

AbstractCancer recurrence presents a huge challenge in cancer patient management. Immune escape is a key mechanism of cancer progression and metastatic dissemination. CD25 is expressed in regulatory T (Treg) cells including tumor-infiltrating Treg cells (TI-Tregs). These cells specially activate and reinforce immune escape mechanism of cancers. The suppression of CD25/IL-2 interaction would be useful against Treg cells activation and ultimately immune escape of cancer. Here, software, web servers and databases were used, at which in silico designed small interfering RNAs (siRNAs), de novo designed peptides and virtual screened small molecules against CD25 were introduced for the prospect of eliminating cancer immune escape and obtaining successful treatment. We obtained siRNAs with low off-target effects. Further, small molecules based on the binding homology search in ligand and receptor similarity were introduced. Finally, the critical amino acids on CD25 were targeted by a de novo designed peptide with disulfide bond. Hence we introduced computational-based antagonists to lay a foundation for further in vitro and in vivo studies.

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Localization of Male-Specifically Expressed MROS Genes of Silene latifolia by PCR on Flow-Sorted Sex Chromosomes and Autosomes

Genetics ◽

10.1093/genetics/158.3.1269 ◽

2001 ◽

Vol 158 (3) ◽

pp. 1269-1277

Author(s):

Eduard Kejnovský ◽

Jan Vrána ◽

Sachihiro Matsunaga ◽

Přemysl Souček ◽

Jiří Široký ◽

...

Keyword(s):

Sex Chromosomes ◽

Silene Latifolia ◽

Homology Search ◽

X Chromosomes ◽

Dioecious Plants ◽

Flow Sorting ◽

Heteromorphic Sex Chromosomes ◽

Copy Gene ◽

Melandrium Album ◽

Pcr Products

Abstract The dioecious white campion Silene latifolia (syn. Melandrium album) has heteromorphic sex chromosomes, XX in females and XY in males, that are larger than the autosomes and enable their separation by flow sorting. The group of MROS genes, the first male-specifically expressed genes in dioecious plants, was recently identified in S. latifolia. To localize the MROS genes, we used the flow-sorted X chromosomes and autosomes as a template for PCR with internal primers. Our results indicate that the MROS3 gene is located in at least two copies tandemly arranged on the X chromosome with additional copy(ies) on the autosome(s), while MROS1, MROS2, and MROS4 are exclusively autosomal. The specificity of PCR products was checked by digestion with a restriction enzyme or reamplification using nested primers. Homology search of databases has shown the presence of five MROS3 homologues in A. thaliana, four of them arranged in two tandems, each consisting of two copies. We conclude that MROS3 is a low-copy gene family, connected with the proper pollen development, which is present not only in dioecious but also in other dicot plant species.

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Efficient alternatives to PSI-BLAST

Bulletin of the Polish Academy of Sciences Technical Sciences ◽

10.2478/v10175-012-0063-0 ◽

2012 ◽

Vol 60 (3) ◽

pp. 495-505

Author(s):

M. Startek ◽

S. Lasota ◽

M. Sykulski ◽

A. Bułak ◽

L. Noé ◽

...

Keyword(s):

Amino Acid ◽

Finite Automata ◽

Protein Family ◽

Homology Search ◽

Amino Acid Residues ◽

Protein Alignment ◽

Substitution Model ◽

Hierarchical Tree ◽

Context Specific ◽

Ncbi Blast

Abstract In this paper we present two algorithms that may serve as efficient alternatives to the well-known PSI BLAST tool: SeedBLAST and CTX-PSI Blast. Both may benefit from the knowledge about amino acid composition specific to a given protein family: SeedBLAST uses the advisedly designed seed, while CTX-PSI BLAST extends PSI BLAST with the context-specific substitution model. The seeding technique became central in the theory of sequence alignment. There are several efficient tools applying seeds to DNA homology search, but not to protein homology search. In this paper we fill this gap. We advocate the use of multiple subset seeds derived from a hierarchical tree of amino acid residues. Our method computes, by an evolutionary algorithm, seeds that are specifically designed for a given protein family. The seeds are represented by deterministic finite automata (DFAs) and built into the NCBI-BLAST software. This extended tool, named SeedBLAST, is compared to the original BLAST and PSI-BLAST on several protein families. Our results demonstrate a superiority of SeedBLAST in terms of efficiency, especially in the case of twilight zone hits. The contextual substitution model has been proven to increase sensitivity of protein alignment. In this paper we perform a next step in the contextual alignment program. We announce a contextual version of the PSI-BLAST algorithm, an iterative version of the NCBI-BLAST tool. The experimental evaluation has been performed demonstrating a significantly higher sensitivity compared to the ordinary PSI-BLAST algorithm.

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