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1

Major histocompatibility complex in Osteichthyes

100%

Stosik M., Tokarz-Deptula B., Deptula W.

Journal of Veterinary Research

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2020

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tom 64

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nr 1

2

Natural agents-mediated targeting of histone deacetylases

75%

Farooqi A. A., Kamran-ul-Hassan Naqvi S., Perk A. A., Yanar O., Tabassum S., Ahmad M. S., Mansoor Q., Ashry M. S., Ismail M., Naoum G. E., Arafat W. O.

Archivum Immunologiae et Therapiae Experimentalis

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2018

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tom 66

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nr 1

3

Sequencing and functional analysis of the yeast genome

75%

Zagulski M., Herbert C. J., Rytka J.

Acta Biochimica Polonica

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1998

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tom 45

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nr 3

The genome of the yeast Saccharomyces cerevisiae was sequenced by an international consortium of laboratories from Europe, Canada, the U.S.A. and Japan. This project is now finished and the complete sequence of the first eukaryotic genome was released to the public data bases in April 1996. An overview and preliminary analysis of the entire genome sequence was presented in a special issue of Nature in May 1997, entitled "The yeast genome directory". At its origin the Yeast Genome Sequencing Project provoked much debate and controversy; however, the final results obtained and the insights this has given us into the organisation and content of a eukaryotic genome have more than justified the expectations of the supporters of the project. The importance of genomic sequencing and analysis, especially of model organisms, is now widely accepted and this has resulted in the birth of the new science of genomics (Botstein & Cherry, Proc. Natl. Acad. Sci. U.S.A. 94, 5506, 1997). The information from gene and protein sequences ultimately lead to functional description of all genes. The main strategies describing possible ways to analyse the function of new genes that have been identified by systematic sequencing of Saccharomyces cerevisiae genome are described.

4

Use of chromosome walking in discovery of single-nucleotide polymorphism in noncoding regions of a candidate actin gene in Pinus radiata

63%

Li W., Li H., Wu H., Chen X.-Y.

Journal of Applied Genetics

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2010

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tom 51

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nr 3

Untranslated regions (UTRs) of eukaryotic mRNAs plav crucial roles in post-transcriptional regulation of gene expression via the modulation of nucleocytoplasmic mRNA transport, translation efficiency, subcellular localization, and message stability. Single-nucleotide polymorphisms (SNPs) in UTRs of a candidate gene may also change the post-transcriptional regulation of a gene or function by nucleotide mutation. For species that have not been entirely sequenced genomically, new methods need to be devised to discover SNPs in noncoding regions of candidate genes. In this study, based on the expressed sequence tag (EST) of Pinus radiata (Monterey pine), we obtained all the sequences of UTRs of the actin gene by using a chromosome walking method. We also detected all the SNPs in and around the coding region of the actin gene. In this way, the full genomie sequence (2154 bp) of the actin gene was identified, including the 5'UTR, introns, the coding sequence, and the 3'UTR. PCR amplification and DNA fragment sequencing from 200 unrelated P. radiata trees revealed a total of 21 SNPs in the actin gene, of which 3 were located in the 5'UTR, 3 in the introns, 10 in the coding sequence, and 5 in the 3'UTR. We show that chromosome walking can be used for obtaining the sequence of UTRs, and then, based on this sequence, to discover SNPs in the noncoding regions of candidate genes from this species without an entire genomic sequence.

5

Full length genome sequence of Polish isolate of Beet soil-borne virus confirms low level of genetic diversity

63%

Borodynko N., Hasiow-Jaroszewska B., Rymelska N., Pospieszny H.

Acta Biochimica Polonica

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2009

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tom 56

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nr 4

729-731

The complete nucleotide sequence of a Polish isolate of Beet soil-borne virus was determined for the first time. The genome organization was identical with those previously established for isolates from Germany and China. A comparison of the Polish isolate with others deposited in GenBank reveled high level of nucleotide identity, about 98-100%, throughout the genome analyzed. The ratio between non-synonymous and synonymous substitutions was rather low suggesting a negative selective pressure. The non-synonymous mutations were particulary frequent in triple gene block.

6

CD4plus T cell epitope discovery and rational vaccine design

63%

Rosa D. S., Ribeiro S. P., Cunha-Neto E.

Archivum Immunologiae et Therapiae Experimentalis

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2010

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tom 58

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nr 2

121-130

7

Analysis of the filamentous bacteriophage genomes integrated into Neisseria gonorrhoeae FA1090 chromosome

63%

Piekarowicz A., Majchrzak M., Klyz A., Adamczyk-Poplawska M.

Polish Journal of Microbiology

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2006

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tom 55

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nr 4

Bioinformatic analysis of the genome sequence of Neisseria gonorrhoeae revealed presence of four specific prophage islands. Based on the similarity with other DNA phage sequences they seem to belong to the filamentous ssDNA phages group. Phages belonging to this group are also present in the genome of Neisseria meningitidis. The nucleotide and amino acids sequence of NgoΦ6 and NgoΦ7 show similar genetic organization and high homology on DNA and amino acid level. The NgoΦ9 contains only part of the genomes of the NgoΦ6-8 prophages. Several functionally same genes of different origin are duplicated, with no homology to their counterparts in phages NgoΦ6, NgoΦ7 and NgoΦ9. The prophage sequences of nucleotides of NgoΦ6 and NgoΦ7 contain specific blocks of genes responsible for phage DNA replication and structural proteins. Comparative analysis at nucleotide and amino acid level suggests that these sequences can encode functionally active phages. The genetic organization of the NgoΦ6 suggests that it can serve as a prototype of filamentous phage of N. gonorrhoeae. Presence of the genomic ssDNA of these phages in the cultures of N. gonorrhoeae confirms this conclusion.

8

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Identification of candidate gene SalT and designing markers involving in salt tolerance of Vietnamese rice landraces

51%

Trung K. H., Khoa N. T., Diep N. T., Thuy T. T., Ha D. T. T., Cuong T. D., Xuan T. D., Trung D. M., Toan N. N., Quyen P. T., Linh L. H., Khanh T. D.

International Letters of Natural Sciences

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2017

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tom 63

Rice (Oryza sativa L.) is a principle crop as the main economic importance in Vietnam, providing daily food for over 90 million people in this country. However, a large rice growing areas and rice production are being seriously affected by salinity intrusion, the threats of devastation from climate change. The need to develop salinity tolerance rice varieties to cope with adverse climate change is very imperative. In this study, based on the genome sequence databases of 36 Vietnamese rice landraces, we have identified nine Vietnamese rice landraces carrying nine SalT candidate genes with the sequence similarity to O. sativa SalT (the published GenBank: Z25811.1) which have shown salinity tolerance are included: Te Nuong, Khau mac buoc, Chan thom, Khau giang, Tan ngan, Nang thom cho dao, OM5629, Hom rau and Thom Lai landraces). Amongst them, four rice landraces, Nang thom cho dao, OM5629, Hom rau and Thom lai have revealed two fragments of deletion with six and seven nucleotides which were the most identical to the SalT reference gene. Two primer pairs have been successfully designed to identify the SalT candidate genes in Vietnamese rice landraces. This study provides useful information of salinity tolerance of some Vietnamese rice landraces for breeding programs.

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