TY  - JOUR
AU  - Stamenković, Gorana
AU  - Guduric, J
AU  - Veličković, Zlate S.
AU  - Skerl, Vesna
AU  - Krtolica-Žikić, Koviljka
AU  - Velikovic, E
AU  - Dimitrijević, Bogomir B.
PY  - 2001
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/2483
AB  - Single-strand conformation polymorphism (SSCP) and low-stringency single specific primer (LSSP)-PCR in hepatitis C virus (HCV) genotyping were examined for informativeness and reliability. The analysis of HCV isolates included seven type 1 isolates, two type 2 isolates, and two type 3 isolates. We also analyzed five isolates that presented as mixed infections determined by type-specific PCR. Among mixed isolates, one isolate was 1a/1b and four isolates were 1b/3a. SSCP and LSSP-PCR were applied to the analysis of 5 non-coding region of HCV (-289 to -5) that contains genotype-specific sequences. Direct cycle sequencing of this region determined sequence divergences that define genotype and sequence alterations within the same genotype. Optimized conditions for the SSCP analysis clearly distinguished between genotypes 1, 2 and 3. In addition, the SSCP analysis detected sequence variants within the same genotype. However, the SSCP analysis and DNA sequencing did not confirm the presence of mixed infections. LSSP analysis, not previously employed in HCV genotyping, enabled clear distinction between genotypes 1, 2 and 3, however, this method did not differentiate between sequence variants within a genotype. Importantly, the LSSP profile demonstrated distinction between mixed infection isolates.
T2  - Clinical Chemistry and Laboratory Medicine
T1  - Analysis of 5 non-coding region in hepatitis C virus by single-strand conformation polymorphism and low-stringency single specific primer PCR
VL  - 39
IS  - 10
SP  - 948
EP  - 952
DO  - 10.1515/CCLM.2001.152
ER  - 

@article{
author = "Stamenković, Gorana and Guduric, J and Veličković, Zlate S. and Skerl, Vesna and Krtolica-Žikić, Koviljka and Velikovic, E and Dimitrijević, Bogomir B.",
year = "2001",
abstract = "Single-strand conformation polymorphism (SSCP) and low-stringency single specific primer (LSSP)-PCR in hepatitis C virus (HCV) genotyping were examined for informativeness and reliability. The analysis of HCV isolates included seven type 1 isolates, two type 2 isolates, and two type 3 isolates. We also analyzed five isolates that presented as mixed infections determined by type-specific PCR. Among mixed isolates, one isolate was 1a/1b and four isolates were 1b/3a. SSCP and LSSP-PCR were applied to the analysis of 5 non-coding region of HCV (-289 to -5) that contains genotype-specific sequences. Direct cycle sequencing of this region determined sequence divergences that define genotype and sequence alterations within the same genotype. Optimized conditions for the SSCP analysis clearly distinguished between genotypes 1, 2 and 3. In addition, the SSCP analysis detected sequence variants within the same genotype. However, the SSCP analysis and DNA sequencing did not confirm the presence of mixed infections. LSSP analysis, not previously employed in HCV genotyping, enabled clear distinction between genotypes 1, 2 and 3, however, this method did not differentiate between sequence variants within a genotype. Importantly, the LSSP profile demonstrated distinction between mixed infection isolates.",
journal = "Clinical Chemistry and Laboratory Medicine",
title = "Analysis of 5 non-coding region in hepatitis C virus by single-strand conformation polymorphism and low-stringency single specific primer PCR",
volume = "39",
number = "10",
pages = "948-952",
doi = "10.1515/CCLM.2001.152"
}

Stamenković, G., Guduric, J., Veličković, Z. S., Skerl, V., Krtolica-Žikić, K., Velikovic, E.,& Dimitrijević, B. B.. (2001). Analysis of 5 non-coding region in hepatitis C virus by single-strand conformation polymorphism and low-stringency single specific primer PCR. in Clinical Chemistry and Laboratory Medicine, 39(10), 948-952.
https://doi.org/10.1515/CCLM.2001.152

Stamenković G, Guduric J, Veličković ZS, Skerl V, Krtolica-Žikić K, Velikovic E, Dimitrijević BB. Analysis of 5 non-coding region in hepatitis C virus by single-strand conformation polymorphism and low-stringency single specific primer PCR. in Clinical Chemistry and Laboratory Medicine. 2001;39(10):948-952.
doi:10.1515/CCLM.2001.152 .

Stamenković, Gorana, Guduric, J, Veličković, Zlate S., Skerl, Vesna, Krtolica-Žikić, Koviljka, Velikovic, E, Dimitrijević, Bogomir B., "Analysis of 5 non-coding region in hepatitis C virus by single-strand conformation polymorphism and low-stringency single specific primer PCR" in Clinical Chemistry and Laboratory Medicine, 39, no. 10 (2001):948-952,
https://doi.org/10.1515/CCLM.2001.152 . .

TY  - JOUR
AU  - Skerl, Vesna
PY  - 1998
UR  - https://vinar.vin.bg.ac.rs/handle/123456789/2122
AB  - A pool of 110 randomly selected/generated amino acids sequences was used to perform specific local sequence similarity alignment analysis with the pool of 279 reported sequences of human T-cell receptor (TCR) V-regions. The 110 analyzed sequences were divided, according to their origin and nature, into six protein groups, as: human intracellular (hi), extracellular/transmembrane (he) and extracellular adhesive matrix (ha) proteins, average human proteins (hum), proteins of non-human origin (nhum) and randomly generated quasi-protein sequences (r). These sequences were decomposed into all their overlapping 11-mer segments, generating a total of 56 836 derived peptides (at least 8000 per group). Each derived peptide was aligned with the 279 human TCR V-regions and assigned to the category (alpha-like, beta-like, gamma-like or delta-like) corresponding to the class (V alpha, V beta, V gamma or V delta) of the V-region encompassing the most similar segment, as determined by the performed similarity-search. The six protein groups were found to differ significantly in their distribution of derived peptides among the four categories. According to the binomial tests results, human proteins from the extracellular compartment (he, ha) comprise a higher proportion of delta-like segments (P = 2.3 x 10(-2) and P LT 10(-8), respectively) than the average human proteins (hum). In addition, and in accordance with this finding, proteins that are normally not found in that topological compartment comprise a lower proportion of delta-like peptides (P = 1.4 x 10(-5) and P LT 10(-8) for groups nhum and hi, respectively) than the average human proteins (hum). In contrast, these proteins comprise a higher proportion of gamma-like segments (P = 8.3 x 10(-3), P = 1.4 x 10(-3) and P = 1.7 x 10(-4), for groups r, nhum and hi, respectively) than the average human proteins (hum). These findings indicate significant differences between proteins encountered in the extracellular compartment-that are normally immunologically tolerated-and those the presence of which is usually non-tolerated. The results suggest that the discrimination and the reaction of the human immune network to proteins found in the extracellular compartment correlate with the proteins pattern of preferential local sequence similarity with the V gamma and V delta classes of human TCR V-regions, implying a specific and an important role of gamma delta-cells in the maintenance of the immune homeostasis. Whether this implication represents a rule associated with self-tolerance, will be investigated by future analyses. (C) 1998 Elsevier Science B.V. All rights reserved.
T2  - Immunology Letters
T1  - Human extracellular proteins display a different pattern of local sequence similarity with the four classes of human T-cell receptor V regions than foreign proteins and human intracellular proteins: a preliminary report
VL  - 60
IS  - 2-3
SP  - 67
EP  - 72
DO  - 10.1016/S0165-2478(97)00139-9
ER  - 

@article{
author = "Skerl, Vesna",
year = "1998",
abstract = "A pool of 110 randomly selected/generated amino acids sequences was used to perform specific local sequence similarity alignment analysis with the pool of 279 reported sequences of human T-cell receptor (TCR) V-regions. The 110 analyzed sequences were divided, according to their origin and nature, into six protein groups, as: human intracellular (hi), extracellular/transmembrane (he) and extracellular adhesive matrix (ha) proteins, average human proteins (hum), proteins of non-human origin (nhum) and randomly generated quasi-protein sequences (r). These sequences were decomposed into all their overlapping 11-mer segments, generating a total of 56 836 derived peptides (at least 8000 per group). Each derived peptide was aligned with the 279 human TCR V-regions and assigned to the category (alpha-like, beta-like, gamma-like or delta-like) corresponding to the class (V alpha, V beta, V gamma or V delta) of the V-region encompassing the most similar segment, as determined by the performed similarity-search. The six protein groups were found to differ significantly in their distribution of derived peptides among the four categories. According to the binomial tests results, human proteins from the extracellular compartment (he, ha) comprise a higher proportion of delta-like segments (P = 2.3 x 10(-2) and P LT 10(-8), respectively) than the average human proteins (hum). In addition, and in accordance with this finding, proteins that are normally not found in that topological compartment comprise a lower proportion of delta-like peptides (P = 1.4 x 10(-5) and P LT 10(-8) for groups nhum and hi, respectively) than the average human proteins (hum). In contrast, these proteins comprise a higher proportion of gamma-like segments (P = 8.3 x 10(-3), P = 1.4 x 10(-3) and P = 1.7 x 10(-4), for groups r, nhum and hi, respectively) than the average human proteins (hum). These findings indicate significant differences between proteins encountered in the extracellular compartment-that are normally immunologically tolerated-and those the presence of which is usually non-tolerated. The results suggest that the discrimination and the reaction of the human immune network to proteins found in the extracellular compartment correlate with the proteins pattern of preferential local sequence similarity with the V gamma and V delta classes of human TCR V-regions, implying a specific and an important role of gamma delta-cells in the maintenance of the immune homeostasis. Whether this implication represents a rule associated with self-tolerance, will be investigated by future analyses. (C) 1998 Elsevier Science B.V. All rights reserved.",
journal = "Immunology Letters",
title = "Human extracellular proteins display a different pattern of local sequence similarity with the four classes of human T-cell receptor V regions than foreign proteins and human intracellular proteins: a preliminary report",
volume = "60",
number = "2-3",
pages = "67-72",
doi = "10.1016/S0165-2478(97)00139-9"
}

Skerl, V.. (1998). Human extracellular proteins display a different pattern of local sequence similarity with the four classes of human T-cell receptor V regions than foreign proteins and human intracellular proteins: a preliminary report. in Immunology Letters, 60(2-3), 67-72.
https://doi.org/10.1016/S0165-2478(97)00139-9

Skerl V. Human extracellular proteins display a different pattern of local sequence similarity with the four classes of human T-cell receptor V regions than foreign proteins and human intracellular proteins: a preliminary report. in Immunology Letters. 1998;60(2-3):67-72.
doi:10.1016/S0165-2478(97)00139-9 .

Skerl, Vesna, "Human extracellular proteins display a different pattern of local sequence similarity with the four classes of human T-cell receptor V regions than foreign proteins and human intracellular proteins: a preliminary report" in Immunology Letters, 60, no. 2-3 (1998):67-72,
https://doi.org/10.1016/S0165-2478(97)00139-9 . .