Next-generation sequencing and its new possibilities in medicine

Next-Generation Sequencing (NGS) originally refers to high-throughput, massively parallel sequencing methods that allow the sequencing of up to billions of small (50-1000 bp), amplified DNA fragments at the same time but nowadays, there are NGS techniques that determine the sequence of long (up to 50 kbp) single molecules. Over the past years, NGS technologies become widely available with increasing throughput and decreasing sequencing costs per base making them more cost effective than the previously used capillary sequencing methods based on Sanger biochemistry. Nowadays, high-throughput DNA sequencing is routinely used on a wide range of important fields of biology and medicine enabling large-scale sequencing projects like analysis of complete genomes, disease association studies, whole transcriptomes, methylomes and provide new insights into complex biological systems. In addition, more and more NGS-based diagnostic tools are being introduced into the clinical practice, for example, on the fields of oncology, inherited and infectious diseases or pre-implantation and prenatal genetic screenings

Draft Genome Sequence of an Escherichia coli O157:H43 Strain Isolated from Cattle

Here we report the draft genome sequence of an Escherichia coli O157:H43 strain, designated T22, with an atypical virulence gene profile and isolated from healthy cattle. T22 produces cytolethal distending toxin V (CDT-V) and belongs to phylogenetic group B1 and sequence type 155 (ST155)

Complete Genome Sequence of Propionibacterium avidum Strain 44067, Isolated from a Human Skin Abscess

Propionibacterium avidum is an anaerobic Gram-positive bacterium that forms part of the normal human cutaneous microbiota, colonizing moist areas such as the vestibule of the nose, axilla, and perineum. Here we present the complete genome sequence of P. avidum strain 44067, which was isolated from a carbuncle of the trunk

Rho-típusú GTPázokat szabályozó receptor-szerű citoplazmatikus kinázok: egy új jelátviteli kapcsolat növényekben = Receptor-like cytoplasmic kinases phosphorylating Rho GTPases: a new signal transduction link in plants

A Rop GTPázok a sejten belüli jelátviteli hálózatok molekuláris kapcsolói. Alapvető szerepük számos sejtfolyamat szabályozásában, de a kapcsolódó jelátviteli mechanizmusok növényekben még alig ismertek. Kutatásaink során elsőként azonosítottunk lucernában olyan kináz fehérjéket, amelyeket a Rop GTPázok specifikusan aktiválnak. Ezek a Rop-aktivált kinázok (RLCK VI_A) és a kinázok aktiválási mechanizmusa teljesen más, mint amit élesztő vagy állati sejtekben eddig leírtak. Vizsgáltuk a kölcsönhatás specificitását és meghatároztunk olyan fehérje régiókat amelyek a kölcsönhatásban aktiválásban részt vesznek. Megvizsgáltuk az Arabidopsis RLCK VI_A kinázok génexpressziós profilját, hogy betekintést kapjunk biológiai funkcióikba. Továbbá transzgenikus növényeket hoztunk létre, amelyekben ezeket a funkciókat potntosan meghatározhassuk. Elsődleges eredményeink alapján a kinázok között vannak olyanok, amelyek a sejtek polaritását szabályozzák, amiben a Rop GTPázok szerepe is ismert. Felismertük, hogy a Rop-aktivált kinázok kölcsönhatnak a Rop GTPázokat aktiváló RopGEF fehérje faktorokkal. Így egy potenciális molekuláris szabályozó kört sikerült feltárni. Megvizsgáltuk, hogy a Rop GTPázok maguk lehetnek-e foszforilációs szabályozás alanyai. Foszforilációt mimikáló mutációkkal igazoltuk ennek a lehetőségét és potenciális biológiai jelentőségét. Ugyanakkor igazoltuk, hogy nem az RLCK VI_A kinázok azok, amelyek a Rop GTPázokat foszforilálhatják. | Rop GTPases are molecular switches involved in many basic cellular processes in plants. Despite their central role in cellular signaling, our knowledge on their signaling partners is stills scarce. We identified for the first time plant kinases (RLCK VI_A) directly activated upon binding to Rop GTPases. These kinases are different from the Rho GTPase-activated kinases of other eukariotes and their activation mechanism seems to be also unique. We investigated the specificity of the GTPase-to-kinase interaction as well as determined some regions/motifs involved in the interaction and kinase activation. Furthermore, we determined the gene expression profile of all Arabidopsis RLCK VI_A kinases in order to have an insight into their biological function. For the same aim we produced several transgenic Arabidopsis lines. Preliminary investigations indicate that at least some of these kinases has a role in polar cell growth also regulated by Rop GTPases themselves. We realized that the Rop-activated kinases also interact with the Rop-activating RopGEF protein factors. In this way we could lay down the basis of a potential regulatory protein circuit. We also investigated the potential role for Rop GTPase activity regulation by phosphorylation. A phosphomimic Rop GTPase mutation was created and its negative effect on GTP hydrolisis as well as its differential effects on protein-protein interactions was established. It could have been revealed, however, that they are not phosphorylated by the RLCK VI_A kinases in vitro

Identification of genes preferentially expressed in wheat egg cells and zygotes

Wheat genes differentially expressed in the egg cell before and after fertilization were identified. The data support zygotic gene activation before the first cell division in wheat. To have an insight into fertilization-induced gene expression, cDNA libraries have been prepared from isolated wheat egg cells and one-celled zygotes. Two-hundred and twenty-six egg cell and 253 zygote-expressed EST sequences were determined. Most of the represented transcripts were detected in the wheat egg cell or zygote transcriptome at the first time. Expression analysis of fourteen of the identified genes and three controls was carried out by real-time quantitative PCR. The preferential expression of all investigated genes in the female gametophyte-derived samples (egg cells, zygotes, two-celled proembryos, and basal ovule parts with synergids) in comparison to the anthers, and the leaves were verified. Three genes with putative signaling/regulatory functions were expressed at a low level in the egg cell but exhibited increased (2-to-33-fold) relative expression in the zygote and the proembryo. Genes with high EST abundance in cDNA libraries exhibited strong expression in the egg cell and the zygote, while the ones coding for unknown or hypothetical proteins exhibited differential expression patterns with preferential transcript accumulation in egg cells and/or zygotes. The obtained data support the activation of the zygotic genome before the first cell division in wheat

Loss of the nodule-specific cysteine rich peptide, NCR169, abolishes symbiotic nitrogen fixation in the Medicago truncatula dnf7 mutant

Host compatible rhizobia induce the formation of legume root nodules, symbiotic organs within which intracellular bacteria are present in plant-derived membrane compartments termed symbiosomes. In Medicago truncatula nodules, the Sinorhizobium microsymbionts undergo an irreversible differentiation process leading to the development of elongated polyploid noncultivable nitrogen fixing bacteroids that convert atmospheric dinitrogen into ammonia. This terminal differentiation is directed by the host plant and involves hundreds of nodule specific cysteine-rich peptides (NCRs). Except for certain in vitro activities of cationic peptides, the functional roles of individual NCR peptides in planta are not known. In this study, we demonstrate that the inability of M. truncatula dnf7 mutants to fix nitrogen is due to inactivation of a single NCR peptide, NCR169. In the absence of NCR169, bacterial differentiation was impaired and was associated with early senescence of the symbiotic cells. Introduction of the NCR169 gene into the dnf7-2/NCR169 deletion mutant restored symbiotic nitrogen fixation. Replacement of any of the cysteine residues in the NCR169 peptide with serine rendered it incapable of complementation, demonstrating an absolute requirement for all cysteines in planta. NCR169 was induced in the cell layers in which bacteroid elongation was most pronounced, and high expression persisted throughout the nitrogen-fixing nodule zone. Our results provide evidence for an essential role of NCR169 in the differentiation and persistence of nitrogen fixing bacteroids in M. truncatula