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Open access

Svetlana Kryštofová

Abstract

Targeted genome editing using engineered nucleases such as ZFNs and TALENs has been rapidly replaced by the CRISPR/Cas9 (clustered, regulatory interspaced, short palindromic/ CRISPR-associated nuclease) system. CRISPR/Cas9 technology represents a significant improvement enabling a new level of targeting, efficiency and simplicity. Gene editing mediated by CRISPR/Cas9 has been recently used not only in bacteria but in many eukaryotic cells and organisms, from yeasts to mammals. Other modifications of the CRISPR-Cas9 system have been used to introduce heterologous domains to regulate gene expressions or label specific loci in various cell types. The review focuses not only on native CRISPR/Cas systems which evolved in prokaryotes as an endogenous adaptive defense mechanism against foreign DNA attacks, but also on the CRISPR/Cas9 adoption as a powerful tool for site-specific gene modifications in fungi, plants and mammals.

Open access

Ivana Dokupilová, Ernest Šturdík and Daniel Mihálik

, Dangl GS, Edwards KJ, Meredith CP (2004): Theor. Appl. Genet. 108: 864-872. Schneider A, Carra A, Akkak A, This P, Laucou V, Botta R (2011): Vitis 40: (4)197-203. Sefc KM, Regner F, Turetschek E, Glossl J, Steinkellner H (1999): Genome 42: 367-373. Sefc KM, Lopes MS, Lefort F, Botta R, Roubelakis-Angelakis KA, Ibanes J, Pejic I, Wagner HW, Glossl J, Steinkellner H (2000): Theor. Appl. Genet., 100: 498-505. Sefc KM, Lefort F, Grando MS, Scott KD, Steinkellner H, Thomas MR (2001): Mol. Biol. Biotech

Open access

Jana Blaškovičová and Ján Labuda

Abstract

Genomics is a branch of bioanalytical chemistry characterized as the study of the genome structure and function. Genome represents the complete set of chromosomal and extrachromosomal genes of an organism, a cell, an organelle or a virus. There are at least five from eight species of herpesviruses commonly widespread among humans, Herpes simplex virus type 1 and 2, Varicella zoster virus, Epstein-Barr virus and Cytomegalovirus. Human gammaherpesviruses can cause serious diseases including B-cell lymphoma and Kaposi’s sarcoma. Diagnostics and study of the herpesviruses is directly dependent on the development of modern analytical methods able to detect and determine the presence and evolution of herpesviral particles/ genomes. Diagnostics and genomic characterization of human herpesvirus species is based on bioanalytical methods such as polymerase chain reaction (PCR), DNA sequencing, gel electrophoresis, blotting and others. The progress in analytical approaches in the herpesvirus genomics is reviewed in this article.

Open access

Traian Tache, Răzvan Chirică, Marius-Daniel Radu, Gabriela Gegiu and Sorin Rugină

Abstract

Enterotoxins produced by Clostridium difficile cause a series of biochemical and immunological manifestations in the cascade leading to alteration of the enterocitus cytoskeleton, intestinal inflammation and diarrhea that can greatly impair the patient’s biological status. The genome of the Clostridium difficile bacterium shows a series of evolutionary adaptations that can give it a high degree of resistance or adaptability to many known pharmacological classes. Changing the diversity of intestinal microbiota induced by the use of antibiotics creates a favorable environment from all points of view for Clostridium difficile spore activity. The theme addresses in an original way but related to the epidemiological studies presented in the literature a correlative aspect between the pathological group and the infection with Clostridium difficile. From the data presented, there is a direct correlation between Clostridium difficile infection and the use of antibiotic therapy as a curative or preventive treatment. Gastrointestinal and neurological pathologies, due to the use of curative but also preventive antibiotic therapy, are at increased risk for the installation of Clostridium difficile infection. The study presented may be a first step in raising awareness of the rational use of antibiotics and avoiding non-assisted community antibiotic therapy.

Open access

Andrzej Nowak, Maciej J. Nowak and Krystyna Cybulska

, Trautmann B, et al. A High-Coverage Yersinia pestis Genome from a Sixth-Century Justinianic Plague. Victim Mol Biol Evol. 2016;33(11):2911-2923. DOI: 10.1093/molbev/msw170. [5] Achtman M, Morelli G, Peixuan Zhu, Wirth T, Diehl I, Kusecek B, et al. Microevolution and history of the plague bacillus, Yersinia pestis. PNAS. 2004;101(51):17837-17842. DOI: 10.1073/pnas.0408026101. [6] Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P, Wagner DM, et al. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nature Genetics. 2010

Open access

Elena Masarovičová, Mária Májeková and Ivana Vykouková

:537-542. DOI: 10.1016/S1360-1385(00)01797-0. [16] Miklos GLG, Rubin GM. The role of the genome project in determining gene function: insights from model organisms. Cell. 1996;86:521-529. DOI: 10.1016/S0092-8674(00)80126-9. [17] Trewavas AJ, Malhó R. Signal perception and transduction: the origin of the phenotype. Plant Cell. 1997;9:1181-1195. DOI: 10.1105/tpc.9.7.1181. [18] Schlichting CD. The evolution of phenotypic plasticity in plants. Ann Rev Ecol Syst. 1986;17:667-693. http://www.jstor.org/stable/2097012 . [19] Sultan SE. Evolutionary

Open access

Peter Pristas, Anna Vandzurova and Peter Javorsky

References ACKERMANN, H.W., KROPINSKI, A.M.: Curated list of prokaryote viruses with fully sequenced genomes. Res. Microbiol., 158, 2007, 555-566. BICKLE, T.A., KRUGER, D.H.: Biology of DNA restriction. Microbiol. Rev., 57, 1993, 434-450. BREDE, D.A., SNIPEN, L.G., USSERY, D.W., NEDERBRAGT, A.J., NES, I.F.: Complete genome sequence of the commensal Enterococcus faecalis 62, isolated from a healthy Norwegian infant. J. Bacteriol., 193, 2011, 2377-2378. DERESINSKI, S.: Bacteriophage Therapy

Open access

Olatunji M. Kolawole, Ajibola O. Ayodeji and Jeremiah I. Ogah

Abstract

Rift Valley fever virus (RVFV) is a zoonotic virus classified as category A priority pathogen. Rift Valley fever (RVF) has been poorly investigated in Nigeria with the infection among Nigerians last reported in 1996. Two hundred (200) febrile subjects with symptoms of malaria attending local hospitals in Ilorin, Nigeria were investigated for malaria, malaria positive subjects were investigated for the presence of RVF. Malaria screening was done using CarestartTM malaria HRP2(pf), while RVF antibodies were tested for using anti-RVF IgM ELISA. Molecular identification of the viral genome was carried out using RNA extraction (QIAGEN) and quantitative Polymerase Chain Reaction (qPCR). Of the 200 subjects tested for malaria infection, 93 (46.5%) were positive, while 20 (21.5%) of the 93 subjects were seropositive for RVF. RVF virus genome was found in 5 (25%) of the 20 positive subjects. The high prevalence of RVF among malaria positive subjects show that there is a risk of a RVF outbreak if its prevalence remains unchecked.

Open access

Lenka Maliničová, Peter Pristaš and Peter Javorský

Bioinformatic Analysis of Prophage Endolysins and Endolysin-Like Genes from the Order Lactobacillales

Endolysins belonging to the group of peptigoglycan hydrolases, which are able to cleave peptidoglycan in bacterial cell walls, become an extensively studied group of enzymes. Thanks to their narrow target specificity and low probability of resistance they are considered to be an appropriate alternative to conventional antibiotics. The present paper concerns the occurrence of endolysin and endolysin-like genes in genomes of bacteria belonging to the order Lactobacillales. Using bioinformatic programmes we compared and analysed protein sequences of catalytic and cell wall binding (CWB) domains of these enzymes, their preferred combinations, their phylogenetic relationship and potential occurence of natural "domain shuffling". The existence of this phenomenon in selected group of enzymes was confirmed only in limited range, so we assume that the natural trend is the distribution of "well-tried" combinations of catalytic and CWB domains of endolysin genes as a whole.

Open access

Nikola Š Šipošová, Veronika Liptáková, Simona Kvasnová, Petra Kosorínová and Peter Pristaš

, Petrenko A, Kurakov A, Beletsky A, Mardanov A, Petrova M (2016) Resistance of permafrost and modern Acinetobacter lwoffii strains to heavy metals and arsenic revealed by genome analysis. BioMed Res. Int. Article ID 3970831. Nies DH (1999) Microbial heavy-metal resistance. Appl. Microbiol. Biotechnol. 51: 730-750. Pailan S, Sengupta K, Ganguly U, Saha P (2016) Evidence of biodegradation of chlorpyrifos by a newly isolated heavy metal-tolerant bacterium Acinetobacter sp. strain MemCl4. Environ. Earth Sci. 75: 1019. Raja CE