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Majchrakova Z, Hrckova Turnova E, Bielikova M, Turna J, Dudas A. The incidence of genetic disease alleles in Australian Shepherd dog breed in European countries. PLoS One 2023; 18:e0281215. [PMID: 36848350 PMCID: PMC9970066 DOI: 10.1371/journal.pone.0281215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/18/2023] [Indexed: 03/01/2023] Open
Abstract
Genetic disease control is generally not given the importance it deserves. Information about what percentage of individuals carry a disorder-causing mutation is crucial for breeders to produce healthy offspring and maintain a healthy dog population of a particular breed. This study aims to provide information about the incidence of mutant alleles for the most frequently occurring hereditary diseases in the Australian Shepherd dog breed (AS). The samples were collected during a 10-years period (2012-2022) in the European population of the AS. Mutant alleles and incidence were calculated from all the obtained data for all the diseases, specifically: collie eye anomaly (9.71%), canine multifocal retinopathy type 1 (0.53%), hereditary cataract (11.64%), progressive rod-cone degeneration (1.58%), degenerative myelopathy (11.77%) and bob-tail/short-tail (31.74%). Our data provide more information to dog breeders to support their effort to limit the spread of hereditary diseases.
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Affiliation(s)
| | | | - Marcela Bielikova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Jan Turna
- Comenius University Science Park, Bratislava, Slovakia,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Andrej Dudas
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia,* E-mail:
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2
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Van Ameringen M, Patterson B, Turna J, Lethbridge G, Goldman Bergmann C, Lamberti N, Rahat M, Sideris B, Francisco A, Fineberg N, Pallanti S, Grassi G, Vismara M, Albert U, Gedanke Shavitt R, Hollander E, Feusner J, Rodriguez C, Morgado P, Dell’Osso B. Obsessive-compulsive disorder during the COVID-19 pandemic. J Psychiatr Res 2022; 149:114-123. [PMID: 35272208 PMCID: PMC8872360 DOI: 10.1016/j.jpsychires.2022.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/07/2022] [Indexed: 01/09/2023]
Affiliation(s)
- M. Van Ameringen
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Canada,MacAnxiety Research Centre, McMaster University, Canada,Corresponding author. Dept of Psychiatry and Behavioural Neurosciences, McMaster University. MacAnxiety Research Centre, 1057 Main St. W, #L02, Hamilton, ON, L8S 1B7, Canada
| | - B. Patterson
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Canada,MacAnxiety Research Centre, McMaster University, Canada
| | - J. Turna
- MacAnxiety Research Centre, McMaster University, Canada
| | - G. Lethbridge
- MacAnxiety Research Centre, McMaster University, Canada
| | - C. Goldman Bergmann
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Canada,MacAnxiety Research Centre, McMaster University, Canada
| | - N. Lamberti
- MacAnxiety Research Centre, McMaster University, Canada
| | - M. Rahat
- MacAnxiety Research Centre, McMaster University, Canada
| | - B. Sideris
- MacAnxiety Research Centre, McMaster University, Canada
| | | | - N. Fineberg
- National Obsessive Compulsive Disorders Treatment Service, Hertfordshire Partnership NHS Foundation Trust, Queen Elizabeth II Hospital, University of Hertfordshire, Postgraduate Medical School, UK
| | - S. Pallanti
- Institute of Neuroscience, Università di Firenze, Italy
| | | | - M. Vismara
- Department of Mental Health, Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Italy
| | - U. Albert
- Università degli Studi di Torino, Dipartimento di Neuroscienze, Italy
| | - R. Gedanke Shavitt
- OCD Spectrum Disorders Program, Institute and Department of Psychiatry, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, Brazil
| | - E. Hollander
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Montefiore Medical Center, USA
| | - J. Feusner
- Department of Psychiatry University of Toronto, Canada
| | - C.I. Rodriguez
- Department of Psychiatry and Behavioural Sciences, Stanford University, USA
| | - P. Morgado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Portugal
| | - B. Dell’Osso
- Department of Mental Health, Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Italy,“Aldo Ravelli” Center for Neurotechnology and Brain Therapeutic, University of Milan, Italy
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Hrckova Turnova E, Bielikova M, Kostal V, Turna J, Dudas A. Occurrence of the dominant black K B allele of CBD103 in German Shepherd Dogs. Anim Genet 2022; 53:230-231. [PMID: 35037272 DOI: 10.1111/age.13171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 12/17/2021] [Accepted: 12/26/2021] [Indexed: 12/01/2022]
Affiliation(s)
| | - Marcela Bielikova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | | | - Jan Turna
- Comenius University Science Park, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Andrej Dudas
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
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Pecimonova M, Radvanszky J, Smolak D, Budis J, Lichvar M, Kristinova D, Rozova I, Turna J, Szemes T. Admixed phenotype of NEDD4L associated periventricular nodular heterotopia: A case report. Medicine (Baltimore) 2021; 100:e26136. [PMID: 34087865 PMCID: PMC8183750 DOI: 10.1097/md.0000000000026136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/11/2021] [Indexed: 12/04/2022] Open
Abstract
RATIONALE Periventricular nodular heterotopia-7 (PVNH7) is a neurodevelopmental disorder associated with improper neuronal migration during neurogenesis in cortex development caused by pathogenic variants in the NEDD4L gene. PATIENT CONCERNS We report the case of a polystigmatized 2-year-old boy having significant symptomatologic overlap with PVNH7, such as delayed psychomotor and mental development, seizures and infantile spasms, periventricular nodular heterotopia, polymicrogyria, cleft palate, 2 to 3 toe syndactyly, hypotonia, microretrognathia, strabismus, and absent speech and walking. The patient showed also distinct symptoms falling outside PVNH7 symptomatology, also present in the proband's older brother, such as blue sclerae, hydronephrosis, transversal palmar crease (found also in their father), and bilateral talipes equinovarus. In addition, the patient suffered from many other symptoms. DIAGNOSES The boy, his brother and their parents were subjected to whole-exome sequencing. Because of uncertainties in symptomatology and inheritance pattern, the top-down approach was hard to apply. Using the bottom-up approach, we identified a known pathogenic variant, NM_001144967.2(NEDD4L):c.2677G>A:p.Glu893Lys, in the proband's genome that absented in any other analyzed family member, suggesting its de novo origin. INTERVENTIONS AND OUTCOMES The patient was treated with Convulex 300 mg/mL for the successful seizure control and Euthyrox 25mg for the treatment of thyroid malfunction. He also took various supplements for the metabolism support and digestion regulation. Moreover, the patient underwent the corrective surgeries of cleft palate and talipes equinovarus. LESSONS We successfully identified the causative mutation NM_001144967.2(NEDD4L):c.2677G>A:p.Glu893Lys explaining symptoms overlapping those reported for PVNH7. Symptoms shared with the brother were not explained by this variant, since he was not a carrier of the pathogenic NEDD4L variant. These are most likely not extended phenotypes of PVNH7, rather an independent clinical entity caused by a yet unidentified genetic factor in the family, highlighting thus the importance of thorough evaluation of symptomatology and genomic findings in affected and unaffected family members, when such data are available.
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Affiliation(s)
- Martina Pecimonova
- Geneton Ltd
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University
| | - Jan Radvanszky
- Geneton Ltd
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences
- Comenius University Science Park
| | - David Smolak
- Geneton Ltd
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University
| | - Jaroslav Budis
- Geneton Ltd
- Comenius University Science Park
- Slovak Centre of Scientific and Technical Information
| | | | | | | | - Jan Turna
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University
- Comenius University Science Park
- Slovak Centre of Scientific and Technical Information
| | - Tomas Szemes
- Geneton Ltd
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University
- Comenius University Science Park
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Lichvariková A, Soltys K, Szemes T, Slobodnikova L, Bukovska G, Turna J, Drahovska H. Characterization of Clinical and Carrier Streptococcus agalactiae and Prophage Contribution to the Strain Variability. Viruses 2020; 12:v12111323. [PMID: 33217933 PMCID: PMC7698700 DOI: 10.3390/v12111323] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/14/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Streptococcus agalactiae (group B Streptococcus, GBS) represents a leading cause of invasive bacterial infections in newborns and is also responsible for diseases in older and immunocompromised adults. Prophages represent an important factor contributing to the genome plasticity and evolution of new strains. In the present study, prophage content was analyzed in human GBS isolates. Thirty-seven prophages were identified in genomes of 20 representative sequenced strains. On the basis of the sequence comparison, we divided the prophages into eight groups named A–H. This division also corresponded to the clustering of phage integrase, even though several different integration sites were observed in some relative prophages. Next, PCR method was used for detection of the prophages in 123 GBS strains from adult hospitalized patients and from pregnancy screening. At least one prophage was present in 105 isolates (85%). The highest prevalence was observed for prophage group A (71%) and satellite prophage group B (62%). Other groups were detected infrequently (1–6%). Prophage distribution did not differ between clinical and screening strains, but it was unevenly distributed in MLST (multi locus sequence typing) sequence types. High content of full-length and satellite prophages detected in present study implies that prophages could be beneficial for the host bacterium and could contribute to evolution of more adapted strains.
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Affiliation(s)
- Aneta Lichvariková
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 841 15 Bratislava, Slovakia; (A.L.); (K.S.); (T.S.); (J.T.)
- Comenius University Science Park, Ilkovicova 8, 841 04 Bratislava, Slovakia
| | - Katarina Soltys
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 841 15 Bratislava, Slovakia; (A.L.); (K.S.); (T.S.); (J.T.)
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 841 15 Bratislava, Slovakia
| | - Tomas Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 841 15 Bratislava, Slovakia; (A.L.); (K.S.); (T.S.); (J.T.)
- Comenius University Science Park, Ilkovicova 8, 841 04 Bratislava, Slovakia
| | - Livia Slobodnikova
- Institute of Microbiology, Medical Faculty, Comenius University in Bratislava, 813 72 Bratislava, Slovakia;
| | - Gabriela Bukovska
- Institute of Molecular Biology, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia;
| | - Jan Turna
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 841 15 Bratislava, Slovakia; (A.L.); (K.S.); (T.S.); (J.T.)
| | - Hana Drahovska
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 841 15 Bratislava, Slovakia; (A.L.); (K.S.); (T.S.); (J.T.)
- Correspondence:
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6
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Turna J, Grosman Kaplan K, Anglin R, Patterson B, Soreni N, Bercik P, Surette MG, Van Ameringen M. The gut microbiome and inflammation in obsessive-compulsive disorder patients compared to age- and sex-matched controls: a pilot study. Acta Psychiatr Scand 2020; 142:337-347. [PMID: 32307692 DOI: 10.1111/acps.13175] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/13/2020] [Accepted: 04/15/2020] [Indexed: 12/27/2022]
Abstract
OBJECTIVE To compare the gut microbiome profile (by way of taxon analysis and indices of β- and α-diversity) and inflammatory markers (C-reactive protein [CRP], interleukin-6[IL-6] and tumour necrosis factor-α [TNF-α]) of obsessive-compulsive disorder (OCD) outpatients and non-psychiatric community controls. METHODS We collected morning stool and blood samples from 21 non-depressed, medication-free OCD patients and 22 age- and sex-matched non-psychiatric community controls. Microbiota analysis was performed using Illumina sequencing of the V3 region of 16S rRNA; serum CRP samples were analysed using immunoturbidimetry and plasma IL-6/TNF-α were examined by high-sensitivity ELISA. Multiple comparisons were corrected for using the false discovery rate (α = 0.05). RESULTS Compared to controls, the OCD group presented lower species richness/evenness (α-diversity, Inverse Simpson) and lower relative abundance of three butyrate producing genera (Oscillospira, Odoribacter and Anaerostipes). Compared to controls, mean CRP, but not IL-6 and TNF-α, was elevated OCD patients. CRP revealed moderate to strong associations with psychiatric symptomatology. CONCLUSION To our knowledge, this is the first investigation of the gut microbiome in OCD. In addition, our findings lend further support for the potential association of inflammation and OCD. These results suggest the gut microbiome may be a potential pathway of interest for future OCD research.
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Affiliation(s)
- J Turna
- Neuroscience Graduate Program, McMaster University, Hamilton, Ontario, Canada.,MacAnxiety Research Centre, Hamilton, ON, Canada.,Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
| | - K Grosman Kaplan
- MacAnxiety Research Centre, Hamilton, ON, Canada.,Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
| | - R Anglin
- School of Medicine, University of Notre Dame, Fiona Stanley Hospital, University of Western Australia, Crawley, WA, Australia
| | - B Patterson
- MacAnxiety Research Centre, Hamilton, ON, Canada.,Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
| | - N Soreni
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
| | - P Bercik
- Farncombe Digestive Health Research Institute, Department of Medicine, McMaster University, Hamilton, ON, Canada.,Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - M G Surette
- Farncombe Digestive Health Research Institute, Department of Medicine, McMaster University, Hamilton, ON, Canada.,Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - M Van Ameringen
- MacAnxiety Research Centre, Hamilton, ON, Canada.,Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
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7
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Soltys K, Stuchlikova M, Hlavaty T, Gaalova B, Budis J, Gazdarica J, Krajcovicova A, Zelinkova Z, Szemes T, Kuba D, Drahovska H, Turna J, Stuchlik S. Seasonal changes of circulating 25-hydroxyvitamin D correlate with the lower gut microbiome composition in inflammatory bowel disease patients. Sci Rep 2020; 10:6024. [PMID: 32265456 PMCID: PMC7138827 DOI: 10.1038/s41598-020-62811-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/18/2020] [Indexed: 12/24/2022] Open
Abstract
Higher probability of the development of Crohn's disease (CD) and ulcerative colitis (UC) as a possible consequence of the north-south gradient has been recently suggested. Living far north or south of the equator is manifested in fluctuation of vitamin D (vitD) levels depending on the season in both healthy and affected individuals. In the present study we investigate the possible link between the seasonal serum vitD level to the microbial composition of the lower gut of Inflammatory Bowel disease (IBD) patients using 16S rRNA sequencing. Decrease of serum vitD level in winter/spring season in a cohort of 35 UC patients and 39 CD patients was confirmed. Low gut microbiota composition of patients with IBD correlated with the serum level of 25(OH)D that directly coupled to seasonal variability of the sunshine in the central European countries. It is supposed to be related to increased abundance of Actinobacteria and Proteobacteria in UC and Actinobacteria, Fusobacteria, Firmicutes and Bacteroidetes in CD. In summer/autumn period, we observed a reduction in abundance of bacterial genera typical for inflammation like Eggerthella lenta, Fusobacterium spp., Bacteroides spp., Collinsella aerofaciens, Helicobacter spp., Rhodococcus spp., Faecalibacterium prausnitzii; and increased abundance of Pediococcus spp. and Clostridium spp. and of Escherichia/Shigella spp.
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Affiliation(s)
- Katarina Soltys
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215, Bratislava, Slovakia.
- Comenius University Science Park, Comenius University in Bratislava, Ilkovicova 8, 84104, Bratislava, Slovakia.
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215, Bratislava, Slovakia.
| | - Martina Stuchlikova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215, Bratislava, Slovakia
- National Transplant Organization, Limbova 14, 83303, Bratislava, Slovakia
| | - Tibor Hlavaty
- Department of Internal Medicine, Faculty of Medicine, Division of Gastroenterology, Comenius University in Bratislava and University hospital Bratislava, Ruzinovska 6, 826 06, Bratislava, Slovakia
| | - Barbora Gaalova
- Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215, Bratislava, Slovakia
| | - Jaroslav Budis
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Mlynska dolina F1, 842 48, Bratislava, Slovakia
| | - Juraj Gazdarica
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215, Bratislava, Slovakia
| | - Anna Krajcovicova
- Department of Internal Medicine, Faculty of Medicine, Division of Gastroenterology, Comenius University in Bratislava and University hospital Bratislava, Ruzinovska 6, 826 06, Bratislava, Slovakia
| | - Zuzana Zelinkova
- Department of Gastroenterology, St Michael Hospital, Bratislava, Slovakia
| | - Tomas Szemes
- Comenius University Science Park, Comenius University in Bratislava, Ilkovicova 8, 84104, Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215, Bratislava, Slovakia
| | - Daniel Kuba
- National Transplant Organization, Limbova 14, 83303, Bratislava, Slovakia
| | - Hana Drahovska
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215, Bratislava, Slovakia
| | - Jan Turna
- Comenius University Science Park, Comenius University in Bratislava, Ilkovicova 8, 84104, Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215, Bratislava, Slovakia
| | - Stanislav Stuchlik
- Comenius University Science Park, Comenius University in Bratislava, Ilkovicova 8, 84104, Bratislava, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215, Bratislava, Slovakia
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8
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Budis J, Gazdarica J, Radvanszky J, Szucs G, Kucharik M, Strieskova L, Gazdaricova I, Harsanyova M, Duris F, Minarik G, Sekelska M, Nagy B, Turna J, Szemes T. Combining count- and length-based z-scores leads to improved predictions in non-invasive prenatal testing. Bioinformatics 2020; 35:1284-1291. [PMID: 30219853 DOI: 10.1093/bioinformatics/bty806] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/16/2018] [Accepted: 09/13/2018] [Indexed: 02/06/2023] Open
Abstract
MOTIVATION Non-invasive prenatal testing or NIPT is currently among the top researched topic in obstetric care. While the performance of the current state-of-the-art NIPT solutions achieve high sensitivity and specificity, they still struggle with a considerable number of samples that cannot be concluded with certainty. Such uninformative results are often subject to repeated blood sampling and re-analysis, usually after two weeks, and this period may cause a stress to the future mothers as well as increase the overall cost of the test. RESULTS We propose a supplementary method to traditional z-scores to reduce the number of such uninformative calls. The method is based on a novel analysis of the length profile of circulating cell free DNA which compares the change in such profiles when random-based and length-based elimination of some fragments is performed. The proposed method is not as accurate as the standard z-score; however, our results suggest that combination of these two independent methods correctly resolves a substantial portion of healthy samples with an uninformative result. Additionally, we discuss how the proposed method can be used to identify maternal aberrations, thus reducing the risk of false positive and false negative calls. AVAILABILITY AND IMPLEMENTATION The open-source code of the proposed methods, together with test data, is freely available for non-commercial users at github web page https://github.com/jbudis/lambda. SUPPLEMENTARY INFORMATION Supplementary materials are available at Bioinformatics online.
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Affiliation(s)
- Jaroslav Budis
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia.,Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | - Juraj Gazdarica
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Jan Radvanszky
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Gabor Szucs
- Department of Applied Mathematics and Statistics, Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia
| | | | - Lucia Strieskova
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Iveta Gazdaricova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Maria Harsanyova
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Frantisek Duris
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia
| | | | | | - Balint Nagy
- Department of Human Genetics, University of Debrecen, Debrecen, Hungary
| | - Jan Turna
- Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.,Comenius University Science Park, Bratislava, Slovakia
| | - Tomas Szemes
- Bratislava, Geneton s.r.o, Bratislava, Slovakia.,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.,Comenius University Science Park, Bratislava, Slovakia
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9
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Gazdarica J, Hekel R, Budis J, Kucharik M, Duris F, Radvanszky J, Turna J, Szemes T. Combination of Fetal Fraction Estimators Based on Fragment Lengths and Fragment Counts in Non-Invasive Prenatal Testing. Int J Mol Sci 2019; 20:E3959. [PMID: 31416246 PMCID: PMC6719007 DOI: 10.3390/ijms20163959] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 11/17/2022] Open
Abstract
The reliability of non-invasive prenatal testing is highly dependent on accurate estimation of fetal fraction. Several methods have been proposed up to date, utilizing different attributes of analyzed genomic material, for example length and genomic location of sequenced DNA fragments. These two sources of information are relatively unrelated, but so far, there have been no published attempts to combine them to get an improved predictor. We collected 2454 single euploid male fetus samples from women undergoing NIPT testing. Fetal fractions were calculated using several proposed predictors and the state-of-the-art SeqFF method. Predictions were compared with the reference Y-based method. We demonstrate that prediction based on length of sequenced DNA fragments may achieve nearly the same precision as the state-of-the-art methods based on their genomic locations. We also show that combination of several sample attributes leads to a predictor that has superior prediction accuracy over any single approach. Finally, appropriate weighting of samples in the training process may achieve higher accuracy for samples with low fetal fraction and so allow more reliability for subsequent testing for genomic aberrations. We propose several improvements in fetal fraction estimation with a special focus on the samples most prone to wrong conclusion.
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Affiliation(s)
- Juraj Gazdarica
- Geneton Ltd., Bratislava 84104, Slovakia.
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 84104, Slovakia.
- Slovak Centre of Scientific and Technical Information, Bratislava 81104, Slovakia.
| | - Rastislav Hekel
- Geneton Ltd., Bratislava 84104, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 84104, Slovakia
- Slovak Centre of Scientific and Technical Information, Bratislava 81104, Slovakia
| | - Jaroslav Budis
- Geneton Ltd., Bratislava 84104, Slovakia
- Slovak Centre of Scientific and Technical Information, Bratislava 81104, Slovakia
- Comenius University Science Park, Bratislava 84104, Slovakia
| | | | - Frantisek Duris
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava 84248, Slovakia
| | - Jan Radvanszky
- Geneton Ltd., Bratislava 84104, Slovakia
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava 84505, Slovakia
| | - Jan Turna
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 84104, Slovakia
- Comenius University Science Park, Bratislava 84104, Slovakia
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava 84505, Slovakia
| | - Tomas Szemes
- Geneton Ltd., Bratislava 84104, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 84104, Slovakia
- Comenius University Science Park, Bratislava 84104, Slovakia
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Gazdarica J, Budis J, Duris F, Turna J, Szemes T. Adaptable Model Parameters in Non-Invasive Prenatal Testing Lead to More Stable Predictions. Int J Mol Sci 2019; 20:ijms20143414. [PMID: 31336782 PMCID: PMC6678500 DOI: 10.3390/ijms20143414] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 12/14/2022] Open
Abstract
Recent advances in massively parallel shotgun sequencing opened up new options for affordable non-invasive prenatal testing (NIPT) for fetus aneuploidy from DNA material extracted from maternal plasma. Tests typically compare chromosomal distributions of a tested sample with a control set of healthy samples with unaffected fetuses. Deviations above certain threshold levels are concluded as positive findings. The main problem with this approach is that the variance of the control set is dependent on the number of sequenced fragments. The higher the amount, the more precise the estimation of actual chromosomal proportions is. Testing a sample with a highly different number of sequenced reads as used in training may thus lead to over- or under-estimation of their variance, and so lead to false predictions. We propose the calculation of a variance for each tested sample adaptively, based on the actual number of its sequenced fragments. We demonstrate how it leads to more stable predictions, mainly in real-world diagnostics with the highly divergent inter-sample coverage.
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Affiliation(s)
- Juraj Gazdarica
- Geneton Ltd., Bratislava 841 04, Slovakia.
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 841 04, Slovakia.
- Slovak Centre of Scientific and Technical Information, Bratislava 811 04, Slovakia.
| | - Jaroslav Budis
- Geneton Ltd., Bratislava 841 04, Slovakia
- Slovak Centre of Scientific and Technical Information, Bratislava 811 04, Slovakia
- Comenius University Science Park, Comenius University, Bratislava 841 04, Slovakia
| | | | - Jan Turna
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 841 04, Slovakia
- Slovak Centre of Scientific and Technical Information, Bratislava 811 04, Slovakia
- Comenius University Science Park, Comenius University, Bratislava 841 04, Slovakia
| | - Tomas Szemes
- Geneton Ltd., Bratislava 841 04, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 841 04, Slovakia
- Slovak Centre of Scientific and Technical Information, Bratislava 811 04, Slovakia
- Comenius University Science Park, Comenius University, Bratislava 841 04, Slovakia
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Levarská L, Levarski Z, Stuchlík S, Kormanová L, Turna J. Vibrio natriegens – an effective tool for protein production. N Biotechnol 2018. [DOI: 10.1016/j.nbt.2018.05.899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Struhárnanská E, Levarski Z, Bírová S, Stuchlík S, Turna J, Zámocký M. Purification and characterisation of thermostable catalase AfKatG produced in E. coli. N Biotechnol 2018. [DOI: 10.1016/j.nbt.2018.05.1164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Duris F, Gazdarica J, Gazdaricova I, Strieskova L, Budis J, Turna J, Szemes T. Mean and variance of ratios of proportions from categories of a multinomial distribution. J Stat Distrib App 2018. [DOI: 10.1186/s40488-018-0083-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Hrckova Turnova E, Majchrakova Z, Bielikova M, Soltys K, Turna J, Dudas A. A novel mutation in the TYRP1 gene associated with brown coat colour in the Australian Shepherd Dog Breed. Anim Genet 2017; 48:626. [PMID: 28497851 DOI: 10.1111/age.12563] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Evelina Hrckova Turnova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Zuzana Majchrakova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Marcela Bielikova
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Katarina Soltys
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Jan Turna
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
| | - Andrej Dudas
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15, Bratislava, Slovak Republic
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Radvanszky J, Hyblova M, Durovcikova D, Hikkelova M, Fiedler E, Kadasi L, Turna J, Minarik G, Szemes T. Complex phenotypes blur conventional borders between Say-Barber-Biesecker-Young-Simpson syndrome and genitopatellar syndrome. Clin Genet 2016; 91:339-343. [DOI: 10.1111/cge.12840] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/14/2016] [Accepted: 07/18/2016] [Indexed: 01/18/2023]
Affiliation(s)
- J. Radvanszky
- Institute for Clinical and Translational Research; Biomedical Research Centre, Slovak Academy of Sciences; Bratislava Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences; Comenius University; Bratislava Slovakia
- Geneton s.r.o.; Bratislava Slovakia
| | - M. Hyblova
- Department of Molecular Biology, Faculty of Natural Sciences; Comenius University; Bratislava Slovakia
- Geneton s.r.o.; Bratislava Slovakia
| | - D. Durovcikova
- Department of Medical Genetics; Slovak Medical University; Bratislava Slovakia
| | - M. Hikkelova
- Laboratory of Medical Genetics; Alphamedical s.r.o.; Bratislava Slovakia
| | - E. Fiedler
- Institut für Klinische Genetik, Leitung Microarray-Diagnostik, Klinikum Stuttgart/Olgahospital; Stuttgart Germany
| | - L. Kadasi
- Institute for Clinical and Translational Research; Biomedical Research Centre, Slovak Academy of Sciences; Bratislava Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences; Comenius University; Bratislava Slovakia
| | - J. Turna
- Department of Molecular Biology, Faculty of Natural Sciences; Comenius University; Bratislava Slovakia
| | - G. Minarik
- Department of Molecular Biology, Faculty of Natural Sciences; Comenius University; Bratislava Slovakia
- Geneton s.r.o.; Bratislava Slovakia
| | - T. Szemes
- Department of Molecular Biology, Faculty of Natural Sciences; Comenius University; Bratislava Slovakia
- Geneton s.r.o.; Bratislava Slovakia
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Firdova Z, Turnova E, Bielikova M, Turna J, Dudas A. The prevalence of ABCB1:c.227_230delATAG mutation in affected dog breeds from European countries. Res Vet Sci 2016; 106:89-92. [DOI: 10.1016/j.rvsc.2016.03.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/24/2016] [Accepted: 03/28/2016] [Indexed: 10/22/2022]
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Orieskova M, Kajsik M, Szemes T, Holy O, Forsythe S, Turna J, Drahovska H. Contribution of the thermotolerance genomic island to increased thermal tolerance in Cronobacter strains. Antonie van Leeuwenhoek 2016; 109:405-14. [DOI: 10.1007/s10482-016-0645-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/02/2016] [Indexed: 11/29/2022]
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Turkovicova L, Smidak R, Jung G, Turna J, Lubec G, Aradska J. Proteomic analysis of the TerC interactome: Novel links to tellurite resistance and pathogenicity. J Proteomics 2016; 136:167-73. [PMID: 26778143 DOI: 10.1016/j.jprot.2016.01.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/02/2015] [Accepted: 01/04/2016] [Indexed: 12/18/2022]
Abstract
The tellurite resistance gene operon (ter) is widely spread among bacterial species, particularly pathogenic species. The ter operon has been implicated in tellurite resistance, phage inhibition, colicine resistance, and pathogenicity. The TerC protein represents one of the key proteins in tellurite resistance and shows no significant homology to any protein of known function. So far, there is no experimental evidence for TerC interaction partners. In this study, proteomic-based methods, including blue native electrophoresis and co-immunoprecipitation combined with LC-MS/MS, have been used to identify TerC interaction partners and thus providing indirect evidence for tentative functions of TerC in Escherichia coli. An interactome has been constructed and robust physical interaction of integral membrane protein TerC with TerB, DctA, PspA, HslU, and RplK has been shown. The TerC-TerB complex appears to act as a central unit that may link different functional modules with biochemical activities of C4-dicarboxylate transport, inner membrane stress response (phage shock protein regulatory complex), ATPase/chaperone activity, and proteosynthesis. In previous reports, it was hypothesized that a transmembrane unit formed by TerC protein may interact with the TerD family, but herein neither TerD nor TerE proteins were identified as TerC complex components. We propose that TerD/TerE participates in tellurite resistance through TerC-independent action.
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Affiliation(s)
- L Turkovicova
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria; Department of Molecular Biology, Faculty of Natural Science, Comenius University, Bratislava, Slovakia
| | - R Smidak
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - G Jung
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - J Turna
- Department of Molecular Biology, Faculty of Natural Science, Comenius University, Bratislava, Slovakia
| | - G Lubec
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria.
| | - J Aradska
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria.
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Firdova Z, Turnova E, Bielikova M, Turna J, Dudas A. Mutation in heat shock transcription factor 4 associated with canine hereditary cataract. J Biotechnol 2015. [DOI: 10.1016/j.jbiotec.2015.06.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kajsík M, Szemes T, Orieskova M, Oslanecova L, Drahovska H, Turna J. Cronobacter spp. specific bacteriophages as a tool for food safety. J Biotechnol 2015. [DOI: 10.1016/j.jbiotec.2015.06.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Stuchlik S, Hason L, Levarski Z, Bocanova L, Jirickova K, Hopkova D, Kois P, Turna J. Expression of recombinant formate dehydrogenase in Escherichia coli and its immobilization onto magnetic nano-particles. N Biotechnol 2014. [DOI: 10.1016/j.nbt.2014.05.968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Turna J, Levarski Z, Krahulec J, Jirickova K, Hopkova D, Stuchlik S. Expression of soluble recombinant human growth hormone in Escherichia coli cultures using shake-flask, batch and fed-batch cultivation. N Biotechnol 2014. [DOI: 10.1016/j.nbt.2014.05.940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Hopkova D, Jirickova K, Levarski Z, Krahulec J, Stuchlik S, Turna J. Preparation of human growth hormone in Pichia pastoris under a constitutive promoter. N Biotechnol 2014. [DOI: 10.1016/j.nbt.2014.05.937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Krahulec J, Osadska M, Slikova E, Halaszova H, Stuchlik S, Turna J. Optimizing of heterologous expression of human recombinant His-tagged prethrombin-2 in Escherichia coli. Curr Opin Biotechnol 2013. [DOI: 10.1016/j.copbio.2013.05.357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Drahovska H, Kajsik M, Orieskova M, Oslanecova L, Kaclikova E, Turna J. Characterization of Cronobacter bacteriophages as tools in food protection. Curr Opin Biotechnol 2013. [DOI: 10.1016/j.copbio.2013.05.273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Palffy R, Gardlik R, Behuliak M, Jani P, Balakova D, Kadasi L, Turna J, Celec P. Salmonella-mediated gene therapy in experimental colitis in mice. Exp Biol Med (Maywood) 2011; 236:177-83. [PMID: 21321314 DOI: 10.1258/ebm.2010.010277] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bacterial gene therapy - bactofection is a simple and effective method to deliver plasmid DNA into target tissue. We hypothesize that oral in vivo bactofection can be an interesting approach to influence the course of inflammatory bowel diseases. The aim of this study was to prove the effects of antioxidative and anti-inflammatory bactofection in dextran sulfate sodium (DSS)-treated mice. Attenuated bacteria Salmonella Typhimurium SL7207 carrying plasmids with genes encoding Cu-Zn superoxide dismutase and an N-terminal deletion mutant of monocyte chemoattractant protein-1 were prepared. Male Balb/c mice had ad libitum access to 1% DSS solution in drinking water during 10 days (mild model of colitis). The animals were daily fed with 200 Mio bacteria via gastric gavage during the experiment. Fecal consistency, clinical status, food and water intake were monitored. After 10 days samples were taken and markers of oxidative stress and inflammatory cytokine levels were measured. Colonic tissue was scored histologically by a blinded investigator. DSS treatment significantly increased the levels of inflammatory cytokines and malondialdehyde as a marker of lipoperoxidation in the colon. Anti-inflammatory gene therapy improved the total antioxidative capacity. In comparison with the untreated group, bacterial gene therapy lowered the histological colitis score. Salmonella-mediated antioxidative and anti-inflammatory gene therapy alleviated colitis in mice. The effect seems to be mediated by increased antioxidative status. Further studies will show whether recombinant probiotics expressing therapeutic gene might be used for the therapy of inflammatory bowel diseases.
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Affiliation(s)
- Roland Palffy
- Insitute of Molecular Biomedicine, Comenius University, Bratislava, Slovak Republic
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Soltysova A, Minarik G, Dzurenkova A, Sufliarska S, Kadasi L, Turna J, Mladosievicova B. APEX microarray panel for genotyping polymorphisms in cancer chemotherapy and estimation frequencies in a Slovak population. Pharmacogenomics 2011; 12:577-92. [DOI: 10.2217/pgs.10.199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Many studies focus on monitoring response to chemotherapy, adverse effects and prediction of therapeutic effects, which depend on individual gene variability. The amount of various polymorphisms in genes involved in the folate cycle, and other metabolic pathways involved in the metabolism of chemotherapeutic drugs, are an essential topic of such studies. This work focuses on the design and establishment of a pharmacogenetically relevant panel, which could be applied to the rapid genotyping of patients treated with thiopurines, 5-fluorouracil, methotrexate, irinotecan and glucocorticoids. Materials & methods: A total of 97 variations in 36 genes associated with side effects of chemotherapeutic treatment were selected. Of these, 94 SNPs were genotyped by the arrayed primer extension (APEX; Asper Biotech Ltd) microarray method or direct sequencing. Variations of tandem repeats or gene deletions were genotyped by capillary electrophoresis and PCR detection. A total of 300 DNA samples from healthy volunteers were tested to estimate genotype frequencies for a Slovak population. All data were checked for Hardy–Weinberg equilibrium and genetic linkage between variations. Results: We designed an APEX microarray for genotyping pharmacologically relevant polymorphisms in patients undergoing chemotherapy. We estimated genotype frequencies for all 97 polymorphisms testing 300 individuals from the Slovak population, which may also serve as an estimate of central European frequencies. These data also allowed for the testing of genetic linkage between loci. Many of the determined genotype frequencies in this study were in similar ranges found in other European populations but four SNPs, rs11760837 (p = 0.018), rs1801265 (p = 0.0375), rs1801394 (p = 0.0066) and rs182455 (p = 0.0083), demonstrated stronger deviation. Conclusion: Genetic variability in genes involved in metabolic pathways of chemotherapeutic drugs, such as methotrexate, 5-fluorouracil, thiopurines or irinotecan, is responsible for individual therapy response and development of side effects. A comprehensive approach in genotyping of numerous variants is aimed to improve individual access to patients and the selection of appropriate drugs for treatment. The APEX microarray method is a valuable tool for fast, reliable and cost-effective genotyping of variants which can be used for the typing of known variants in patients prior to treatment as well as in studies searching for new genotype–phenotype associations. The opportunity of adding additional variants during the study makes the APEX microarray technology flexible and suitable for such trials. Original submitted 4 October 2010; Revision submitted 23 November 2010.
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Affiliation(s)
| | - Gabriel Minarik
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, 842 15 Bratislava 4, Slovakia
| | - Alica Dzurenkova
- Institute of Pathological Physiology, School of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia
| | - Sabina Sufliarska
- Institute of Pathological Physiology, School of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia
| | - Ludevit Kadasi
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, 842 15 Bratislava 4, Slovakia
| | - Jan Turna
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, Mlynská dolina, 842 15 Bratislava 4, Slovakia
| | - Beata Mladosievicova
- Institute of Pathological Physiology, School of Medicine, Comenius University, Sasinkova 4, 811 08 Bratislava, Slovakia
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Alekhina O, Valkovicova L, Turna J. Study of membrane attachment and in vivo co-localization of TerB protein from uropathogenic Escherichia coli KL53. Gen Physiol Biophys 2011; 30:286-92. [DOI: 10.4149/gpb_2011_03_286] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Tothova L, Celec P, Babickova J, Gajdosova J, Al-Alami H, Kamodyova N, Drahovska H, Liptakova A, Turna J, Hodosy J. Phage therapy of Cronobacter-induced urinary tract infection in mice. Med Sci Monit 2011. [DOI: 10.12659/msm.881844] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Lubomira Tothova
- Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovakia and Department of Molecular Biology, Comenius University, Bratislava, Slovakia
| | - Peter Celec
- Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovakia and Department of Molecular Biology, Comenius University, Bratislava, Slovakia and Institute of Pathophysiology, Comenius University, Bratislava, Slovakia
| | - Janka Babickova
- Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovakia
| | - Jana Gajdosova
- Department of Molecular Biology, Comenius University, Bratislava, Slovakia
| | - Hend Al-Alami
- Department of Molecular Biology, Comenius University, Bratislava, Slovakia
| | - Natalia Kamodyova
- Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovakia
| | - Hana Drahovska
- Department of Molecular Biology, Comenius University, Bratislava, Slovakia
| | - Adriana Liptakova
- Institute of Immunology, Comenius University and Ministry of Health, Bratislava, Slovakia
| | - Jan Turna
- Department of Molecular Biology, Comenius University, Bratislava, Slovakia
| | - Julius Hodosy
- Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovakia and Institute of Physiology, Comenius University, Bratislava, Slovakia
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Smidák R, Jopcík M, Kralovicová M, Gajdosíková J, Kormanec J, Timko J, Turna J. Core promoters of the penicillin biosynthesis genes and quantitative RT-PCR analysis of these genes in high and low production strain of Penicillium chrysogenum. Folia Microbiol (Praha) 2010; 55:126-32. [PMID: 20490754 DOI: 10.1007/s12223-010-0019-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 12/09/2009] [Indexed: 11/30/2022]
Abstract
The transcription start points of the penicillin biosynthesis genes from Penicillium chrysogenum were mapped using the primer extension method. For each of the three genes consensus sequences of the core promoter elements were identified, supporting the notion that the basal transcription of these genes is mediated separately. Interestingly, transcription start of the pcbC gene is located within the potential Inr element with no TATA box-like sequence being found at expected position. This is in contrast to pcbAB and penDE genes with proposed TATA boxes or even to Aspergillus nidulans ipnA (pcbC) gene indicating possible differences in basal transcription regulation. Using the quantitative RT-PCR analysis the expression of all three biosynthesis genes was monitored in both the high and low production strain of P. chrysogenum during a 3-d cultivation under production conditions. The differences were found between the strains in time regulation and transcript levels of the biosynthesis genes. Furthermore, we showed that the effect of higher gene dosage on productivity in the production strain is amplified by more efficient transcription of the biosynthesis genes with the RNA levels approximately 37- and 12-times higher, respectively, than in a low production strain.
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Affiliation(s)
- R Smidák
- Institute of Molecular Biology, Slovak Academy of Sciences, 845 51, Bratislava 45, Slovak Republic.
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Szemes T, Vlkova B, Minarik G, Tothova L, Drahovska H, Turna J, Celec P. On the origin of reactive oxygen species and antioxidative mechanisms in Enterococcus faecalis. Redox Rep 2010; 15:202-6. [PMID: 21062535 PMCID: PMC7067330 DOI: 10.1179/135100010x12826446921581] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Enterococci cause serious infections due to a number of virulence factors and wide-spread antibiotic resistance. A molecular mechanism involved in the pathogenesis of enterococcal infections is oxidative stress. Enterococcus faecalis produces a variety of antioxidative enzymes involved in the oxidative stress response, a process that is regulated by several transcriptional regulators. In addition, direct production of free radicals derived from oxygen has been proved and hypothesized, respectively, to contribute to the pathogenesis of colorectal cancer and periodontitis. The understanding of molecular mechanisms behind the production of free radicals and the antioxidative status in E. faecalis might suggest new alternatives for the treatment of enterococcal infections and related diseases.
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Pálffy R, Gardlík R, Behuliak M, Kadasi L, Turna J, Celec P. On the physiology and pathophysiology of antimicrobial peptides. Mol Med 2009; 15:51-9. [PMID: 19015736 PMCID: PMC2583110 DOI: 10.2119/molmed.2008.00087] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2008] [Accepted: 11/06/2008] [Indexed: 12/23/2022] Open
Abstract
Antimicrobial peptides (AMP) are a heterogeneous group of molecules involved in the nonspecific immune responses of a variety of organisms ranging from prokaryotes to mammals, including humans. AMP have various physical and biological properties, yet the most common feature is their antimicrobial effect. The majority of AMP disrupt the integrity of microbial cells by 1 of 3 known mechanisms--the barrel-stave pore model, the thoroidal pore model, or the carpet model. Results of growing numbers of descriptive and experimental studies show that altered expression of AMP in various tissues is important in the pathogenesis of several gastrointestinal, respiratory, and other diseases. We discuss novel approaches and strategies to further improve the promising future of therapeutic applications of AMP. The spread of antibiotic resistance increases the importance of developing a clinical role for AMP.
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Affiliation(s)
- Roland Pálffy
- BiomeD Research and Publishing Group, Bratislava, Slovak Republic
- Institute of Pathophysiology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Roman Gardlík
- BiomeD Research and Publishing Group, Bratislava, Slovak Republic
- Institute of Pathophysiology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Michal Behuliak
- BiomeD Research and Publishing Group, Bratislava, Slovak Republic
- Institute of Pathophysiology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Ludevit Kadasi
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Jan Turna
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Peter Celec
- BiomeD Research and Publishing Group, Bratislava, Slovak Republic
- Institute of Pathophysiology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
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Vavrova S, Valkova D, Drahovska H, Kokavec J, Mravec J, Turna J. Analysis of the tellurite resistance determinant on the pNT3B derivative of the pTE53 plasmid from uropathogenic Escherichia coli. Biometals 2006; 19:453-60. [PMID: 16937251 DOI: 10.1007/s10534-005-4862-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2005] [Accepted: 11/07/2005] [Indexed: 11/24/2022]
Abstract
We have found and sequenced a significant part of the previously described tellurite resistance determinant on mini-Mu derivative pPR46, named pNT3B, originally cloned from a large conjugative plasmid pTE53, found in Escherichia coli. This plasmid contains genes essential for tellurite resistance, together with the protective region bearing genes terX, Y, W, and the conserved spacing region bearing several ORFs of unknown function. Computer analysis of obtained sequence revealed a close similarity to the formerly described ter operons found on the Serratia marcescens plasmid R478 and the chromosome of Escherichia coli O157:H7. This finding confirms the presence of a whole region on the large conjugative plasmid that pTE53 originated from a uropathogenic E. coli strain, and suggests its possible role in horizontal gene transfer, resulting in the development of new pathogenic E. coli strains.
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Affiliation(s)
- Silvia Vavrova
- Department of Molecular Biology, Comenius University, Mlynská dolina B2-137, 842 15, Bratislava, Slovak Republic
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Bukovska G, Klucar L, Vlcek C, Adamovic J, Turna J, Timko J. Complete nucleotide sequence and genome analysis of bacteriophage BFK20 — A lytic phage of the industrial producer Brevibacterium flavum. Virology 2006; 348:57-71. [PMID: 16457869 DOI: 10.1016/j.virol.2005.12.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2005] [Revised: 11/14/2005] [Accepted: 12/11/2005] [Indexed: 10/25/2022]
Abstract
The entire double-stranded DNA genome of bacteriophage BFK20, a lytic phage of the Brevibacterium flavum CCM 251--industrial producer of L-lysine--was sequenced and analyzed. It consists of 42,968 base pairs with an overall molar G + C content of 56.2%. Fifty-five potential open reading frames were identified and annotated using various bioinformatics tools. Clusters of functionally related putative genes were defined (structural, lytic, replication and regulatory). To verify the annotation of structural proteins, they were resolved by 2D gel electrophoresis and were submitted to N-terminal amino acid sequencing. Structural proteins identified included the portal and major and minor tail proteins. Based on the overall genome sequence comparison, similarities with other known bacteriophage genomes include primarily bacteriophages from Mycobacterium spp. and some regions of Corynebacterium spp. genomes--possible prophages. Our results support the theory that phage genomes are mosaics with respect to each other.
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Affiliation(s)
- Gabriela Bukovska
- Institute of Molecular Biology, Centre of Excellence for Molecular Medicine, Slovak Academy of Sciences, Dubravska cesta 21, 845 51 Bratislava, Slovakia.
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Drahovská H, Slobodníková L, Kocíncová D, Seman M, Konceková R, Trupl J, Turna J. Antibiotic resistance and virulence factors among clinical and food enterococci isolated in Slovakia. Folia Microbiol (Praha) 2004; 49:763-8. [PMID: 15881416 DOI: 10.1007/bf02931562] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The resistance to antibiotics and the distribution of virulence factors in enterococci isolated from traditional Slovak sheep cheese bryndza was compared with strains from human infections. The occurrence of 4 enterococcal species was observed in 117 bryndza-cheese isolates. The majority of strains were identified as E. faecium (76 %) and E. faecalis (23 %). Several strains of E. durans and 1 strain of E. hirae were also present. More than 90 % of strains isolated from 109 clinical enterococci were E. faecalis, the rest belonged to E. faecium. The resistance to 6 antimicrobial substances (ampicillin, ciprofloxacin, higher concentration of gentamicin, nitrofurantoin, tetracycline and vancomycin) was tested in clinical and food enterococci. A higher level of resistance was found in clinical than in food strains and E. faecium had a higher resistance than E. faecalis; no resistance to vancomycin was detected. The occurrence of 3 virulence-associated genes, cylA (coding for hemolysin), gelE (coding for gelatinase) and esp (coding for surface protein) was monitored. Differences were found in the distribution of cylA gene between clinical and bryndza-cheese E. faecalis strains; in contrast to clinical strains (45 %), cylA gene was detected in 22 % of food isolates. The distribution of 2 other virulence factors, gelE and esp, was not significantly different in the two groups of E. faecalis strains. cylA and gelE genes were not detected in E. faecium but more than 70 % of clinical E. faecium were positive for esp, even thought none of the 79 E. faecium cheese isolates contained this gene.
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Affiliation(s)
- H Drahovská
- Department of Molecular Biology, Faculty of Science, Comenius University, Bratislava, Slovakia.
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Vizvariová M, Vavrová S, Turna J. Cloning of pac gene and its flanking regions using mini-Mu bacteriophage. Acta Virol 2003; 46:69-74. [PMID: 12387497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
An in vitro method for cloning and mapping Escherichia coli genes by means of mini-Mu phage and its application to the penicillin G acylase (pac) gene of E. coli PAC2 strain with its flanking regions is described. The gene was marked by insertion of a fragment bearing kanamycin resistance (Km(r)). Most of Km(r) clones obtained from mini-Mu transductants contained the whole pac gene with its flanking regions. Localization of pac gene to 98.5 min of E. coli PAC2 chromosome was confirmed by an in vivo P1 phage transduction.
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Affiliation(s)
- M Vizvariová
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
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Pangallo D, Karpísková R, Turna J, Kuchta T. Typing of food-borne Listeria monocytogenes by the optimized repetitive extragenic palindrome-based polymerase chain reaction. New Microbiol 2002; 25:449-54. [PMID: 12437224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
The repetitive extragenic palindrome-based polymerase chain reaction was optimized for typing Listeria monocytogenes by 1) using the QlAamp method to increase the reproducibility of DNA isolation, 2) running PCR with three different DNA concentrations in parallel, 3) using antibody-protected therrnostable DNA polymerase to reduce non-specific priming, and 4) using an improved temperature programme to increase the amplification yield. When applied to 42 L. monocytogenes strains isolated from food in the Czech and Slovak republics during 1999-2000, profiles of 7-15 DNA fragments of 330-3,310 bp were amplified. Based on REP-profiles, strains (serotypes 1/2 and 4) could be divided into 12 groups.
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Affiliation(s)
- D Pangallo
- Department of Microbiology and Chemistry, Food Research Institute, Bratislava, Slovakia
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Klucar L, Nováková R, Homérová D, Sevcíková B, Turna J, Kormanec J. Phylogenetic analysis of the rplA genes encoding ribosomal protein L1. Folia Microbiol (Praha) 2002; 46:99-106. [PMID: 11501409 DOI: 10.1007/bf02873585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previously we have identified the rplA gene encoding ribosomal protein L1 in Streptomyces aureofaciens. Sequence comparison of ribosomal protein L1 among several bacterial genera revealed a high level of conservation. Based on this conservation, these proteins were used as a phylogenetic tool to compare evolutionary relationships among eubacteria and archaebacteria. This phylogenetic analysis of L1 ribosomal proteins including the S. aureofaciens rplA gene product revealed, except similar bacterial groupings, some new evolutionary relationships.
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Affiliation(s)
- L Klucar
- Institute of Molecular Biology, Slovak Academy of Sciences, 842 51 Bratislava, Slovakia
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Abstract
Two DNA-based techniques were used for species identification of enterococci. PvuII digestion of the genus-specific PCR product yielded four different restriction profiles among 20 enterococcal species; one of them was species-specific for E. faecium. In the second case, 32 reference strains belonging to 20 enterococcal species were divided to 12 groups by amplification of internal transcribed spacer of rRNA operon. Interspecies and some intraspecies profile variability was determined. Both methods gave similar results.
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Affiliation(s)
- H Drahovská
- Department of Molecular Biology, Faculty of Science, Comenius University, Bratislava, Slovakia.
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Kopácek J, Kl'ucár L, Koptidesová D, Turna J, Pastorek J, Zelník V. Nucleotide sequence of the gene encoding the major capsid protein of herpesvirus of turkeys. Virus Genes 2001; 20:107-15. [PMID: 10872871 DOI: 10.1023/a:1008158228591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The gene encoding the major capsid protein (MCP) VP5 of herpesvirus of turkeys (HVT) was identified and sequenced. It has a single open reading frame of 4236 nucleotides encoding 1412 aa protein. The gene is flanked by VP23 and UL20 sequences and is localized in the unique long region (UL) within the BamHI-B fragment. Comparison of amino acid homology has shown its clear position among the alpha-herpesviruses rather than beta- or gamma-herpesviruses. The VP5 is expressed from polycistronic mRNA together with the UL20 and the VP23 genes. The 7,2 kb RNA transcript is lacking any promoter elements or polyA signal in intergenomic regions between VP5 and UL20 or VP5 and VP23 genes, respectively. Multiple alignment of known major capsid protein sequences of all herpesvirus groups revealed presence of seven highly homologous clusters suggesting-that the corresponding protein domains might play an important role in folding of MCP and assembly of herpesvirus capsid.
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Affiliation(s)
- J Kopácek
- Institute of Virology, Slovak Academy of Sciences, Bratislava Slovak Republic
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Vizváryová M, Stuchlík S, Grones J, Macor M, Turna J. Escherichia coli strain with a deletion of the chromosomal ampC gene marked with TcR, suitable for production of penicillin G acylase. Folia Microbiol (Praha) 2001; 44:625-8. [PMID: 11097022 DOI: 10.1007/bf02825651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Escherichia coli strain which contains a marker of tetracycline resistance gene (TcR) placed by P1 transduction beside the chromosomal deletion of ampC gene (delta ampC) coding for beta-lactamase was constructed. Such introduction of TcR marker permits a fast and simple selection for the transfer of delta ampC by P1 transduction into industrial E. coli strains. This approach was used for constructing an E. coli strain suitable for penicillin acylase production.
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Affiliation(s)
- M Vizváryová
- Department of Molecular Biology, Comenius University, Bratislava, Slovakia
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Kormutakova R, Klucar L, Turna J. DNA sequence analysis of the tellurite-resistance determinant from clinical strain of Escherichia coli and identification of essential genes. Biometals 2000; 13:135-9. [PMID: 11016400 DOI: 10.1023/a:1009272122989] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The tellurite-resistant Escherichia coli strain KL53 was found during testing of the group of clinical isolates for antibiotics and heavy metal ion resistance (Burian et al. 1990). Determinant of the tellurite resistance of the strain was located on the large conjugative plasmid pTE53 and cloned into pACYC184. Three different Ter clones harboring pLK2, pLK18 and pLK20 were isolated (Burian et al. 1998). The smallest functional Ter clone harboring pLK18 was chosen for further analysis. Plasmid pLK18 have been subcloned to obtain convenient DNA fragments for sequencing of tellurite-resistance determinant. Sequencing of this DNA fragments provided complete DNA sequence of the determinant, 5,250 bp in size. The sequence has been compared with nucleotide and protein databank (BLAST programs) and significant homology with the three known operons coding for tellurite resistance has been found (determinat on plasmid pR478 from Serratia marcescens, on plasmid pMER610 from Alcaligenes sp. and chromosomal tellurite resistance genes from Proteus mirabilis). We identified 5 ORFs coding for 5 genes named terB to terF. The clone harboring pLK18 was subjected to the transposition with Tn1737Km to disrupt determinant of the tellurite resistance. Plasmid DNA of several clones containing pLK18 with Tn1737Km was isolated to locate the target site of Tn1737Km. Analyses showed, the genes terB, terC, terD and terE are essential for conservation of the resistance whereas the gene terF is not important in this respect.
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Affiliation(s)
- R Kormutakova
- Department of Molecular Biology, Faculty of Natural Science, Comenius University, Bratislava, Slovak Republic
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Abstract
We have used the T7 expression system for expression of E. coli FNR protein. The fnr gene was cloned from its initiation codon ATG into the NdeI site of an expression vector and filamentous phage mGP1-2 was used as a donor of T7 RNA polymerase gene. The level of FNR expression attained by this expression arrangement was about 45% of total cell proteins.
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Affiliation(s)
- S Stuchlík
- Department of Molecular Biology, Comenius University, Bratislava, Slovakia.
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Burian J, Tu N, Kl'ucár L, Guller L, Lloyd-Jones G, Stuchlík S, Fejdi P, Siekel P, Turna J. In vivo and in vitro cloning and phenotype characterization of tellurite resistance determinant conferred by plasmid pTE53 of a clinical isolate of Escherichia coli. Folia Microbiol (Praha) 1998; 43:589-99. [PMID: 10069007 DOI: 10.1007/bf02816374] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A determinant encoding resistance against potassium tellurite (Te(r)) was discovered in a clinical isolate of Escherichia coli strain KL53. The strain formed typical black colonies on solid LB medium with tellurite. The determinant was located on a large conjugative plasmid designated pTE53. Electron-dense particles were observed in cells harboring pTE53 by electron microscopy. X-Ray identification analysis identified these deposits as elemental tellurium and X-ray diffraction analysis showed patterns typical of crystalline structures. Comparison with JCPDS 4-0554 (Joint Committee on Powder Diffraction Standards) reference data confirmed that these crystals were pure tellurium crystals. In common with other characterized Te(r) determinants, accumulation studies with radioactively labeled tellurite showed that reduced uptake of tellurite did not contribute to the resistance mechanism. Tellurite accumulation rates for E. coli strain AB1157 harboring pTE53 were twice higher than for the plasmid-free host strain. In addition, no efflux mechanism was detected. The potassium tellurite resistance determinant of plasmid pTE53 was cloned using both in vitro and in vivo techniques in low-copy-number vectors pACYC184 and mini-Mu derivative pPR46. Cloning of the functional Te(r) determinant into high-copy cloning vectors pTZ19R and mini-Mu derivatives pBEf and pJT2 was not successful. During in vivo cloning experiments, clones with unusual "white colony" phenotypes were found on solid LB with tellurite. All these clones were Mucts62 lysogens. Their tellurite resistance levels were in the same order as the wild type strains. Clones with the "white" phenotype had a 3.6 times lower content of tellurium than the tellurite-reducing strain. Transformation of a "white" mutant with a recombinant pACYC184 based Te(r) plasmid did not change the phenotype. However, when one clone was cured from Mucts62 the "white" phenotype reverted to the wild-type "black" phenotype. It was suggested that the "white" phenotype was the result of an insertional inactivation of an unknown chromosomal gene by Mucts62, which reduced the tellurite uptake.
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Affiliation(s)
- J Burian
- Department of Molecular Biology, Faculty of Science, Comenius University, Bratislava, Slovakia.
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Abstract
Xanthomonas campestris is not able to grow in lactose media. The lactose operon from Escherichia coli as part of a mini-Mu phage was integrated at random sites in the chromosome of this bacterium. Clones expressing (beta)-galactosidase were selected. The resulting strain X. campestris 204, is suitable for production of xanthan gum directly from lactose.
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Grones J, Turna J. Transformation of microorganisms with the plasmid vector with the replicon from pAC1 from Acetobacter pasteurianus. Biochem Biophys Res Commun 1995; 206:942-7. [PMID: 7832808 DOI: 10.1006/bbrc.1995.1133] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A number of gram-negative and gram-positive bacteria species was screened for the expression of the gram-negative plasmid pACK5 and pACT72 with replicon of pAC1 plasmid from Acetobacter pasteurianus. As was described previously, both plasmids were expressed in Escherichia coli, Acetobacter pasteurianus, Acetobacter aceti, Shigella spp. and Citrobacter spp. Expressions of plasmids were successful in twelve species tested, Comamonas terrigena, Salmonella typhimurium, Serratia marcescens, Bacillus cereus, Bacillus megatericum, Bacillus subtilis, Lactobacillus helveticus, Micrococcus luteus, Sarcina lutea, Staphylococcus aureus, Staphylococcus epidermidis, Streptoccocus feacalis, and the stability of plasmid DNA was tested after cultivation in non-selective conditions.
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Affiliation(s)
- J Grones
- Department of Molecular Biology, Faculty of Natural Science, Comenius University, Bratislava, Slovak Republic
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Abstract
We have constructed two new mini-Mu derivatives, pMRfP and pBEf, that combine the properties of known mini-Mu vectors and the advantages of the replication origin (orifd) of filamentous phage fd. Mini-Mu pMRfP consists of the left (850 bp) and the right (216 bp) ends of the Mu genome, orifd, packaging signal of fd, and the gene conferring resistance to chloramphenicol. The second mini-Mu, termed pBEf, carries the left end of Mu (1001 bp), which contains the so-called internal activation sequence (enhancer of transposition), required for a higher frequency of transposition, the right end (116 bp) and the gene conferring resistance to kanamycin. These new mini-Mu vectors are suitable for in vivo cloning with the ability of single-stranded DNA preparation using one of the helper phages (M13K07, rv1, IR1, R408) and with a large cloning capacity (the size of the cloned fragment can be up to 35 kb). They can also be used as the hoppers (a transposable ori that can be turned on or off depending on the presence of the fd gene 2 product). Thus, these mini-Mu derivatives can be employed as vectors for in vivo cloning, and as regulated transposons or mobile replicons.
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Affiliation(s)
- M Osuský
- Department of Biochemistry, Comenius University, Bratislava, Slovakia
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