Cytotoxic activity of Enterobacter cloacae human isolates

We examined 55 Enterobacter cloacae isolates from clinical specimens for the production of cytotonic and cytotoxic toxins and the presence of the type III secretion system (TTSS). Twelve isolates (22%) revealed cytotoxic activity that caused destruction of Vero cells, whereas 28 (51%) strains induced lysis of the murine macrophage J774 cell line. TTSS genes were present in 27% of the isolates. The results indicated that these bacteria may destroy phagocytes and epithelial cells, which may lead to spread within the host.     

Correlation of the Middle and Upper Permian marine and terrestrial sedimentary sequences in Polish, German, and USA Western Interior Basins with reference to global time markers

Here we discuss the duration and position of Upper Rotliegend and Zechstein stratigraphic units in relation to the absolute time scale, and reinterpret a carbon isotope (δ¹³C) global event recorded from Late Permian (Lopingian/Guadalupian) marine deposits. Based on δ¹³C isotope correlation (chemostratigraphy) and of climatic evidence related to the end-Guadalupian global marine and terrestrial crisis, the Guadalupian/Lopingian boundary is proposed as the boundary between both the European Upper Rotliegend (URII)/Zechstein sediments and the parallel south-west USA Ochoan/Bell Canyon Formation units. The Zechstein deposition was strongly influenced by climatic oscillations, and the marine ingressions recorded in the North German Basin and North American Delaware Basin are presumed to have resulted from the same eustatic sea-level changes in western and northern coasts of the Northern Pangaea Supercontinent. Existing constraints on the age of the Upper Rotliegend II (UR II) deposits are imposed by the uncertainty of the chronostratigraphic boundary of the Kupferschiefer and by a time marker that is Illawarra, the boundary of the reversed polarity megachron (Kiaman) and mixed polarity megachron. Three options (A, B, C) have been discussed, which are connected with a time span comprising deposition of the UR II rocks, assuming that the time span needed for the Dethlingen/Lower Noteć formations and Hannover/Upper Noteć formations is about 6 myr. The time left for the deposition of the Parchim/Lower Drawa, Mirow/Upper Drawa deposits and the time hidden in the erosional gaps and hiatuses range from 1.6 myr to 4 myr or even 8 myr. These were based on the time interval related to the Kiaman Reversed Polarity megachron, which can contain more transient normal polarity zones than currently accepted. The presence and absolute dating of all such magnetozones is difficult to determine because they are represented in continental strata characterized by numerous, poorly time-constrained erosional gaps. The proposed option C is provisionally integrated with magnetostratigraphic results and shows an alternative stratigraphical scheme for the Upper Rotliegend. This alternate Upper Rotliegend stratigraphy helps correlate rocks (deposited in dry arid climatic conditions) in the lower part of the Upper Rotliegend II of the Southern Permian Basin (Havel and Drawa subgroups) with similar rocks in the Delaware Basin (attributed to formations within the Leonardian Regional Series).     

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

Background  

Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization.     

Enzymatically stable 5' mRNA cap analogs: synthesis and binding studies with human DcpS decapping enzyme

Four novel 5' mRNA cap analogs have been synthesized with one of the pyrophosphate bridge oxygen atoms of the triphosphate linkage replaced with a methylene group. The analogs were prepared via reaction of nucleoside phosphor/phosphon-1-imidazolidates with nucleoside phosphate/phosphonate in the presence of ZnCl2. Three of the new cap analogs are completely resistant to degradation by human DcpS, the enzyme responsible for hydrolysis of free cap resulting from 3' to 5' cellular mRNA decay. One of the new analogs has very high affinity for binding to human DcpS. Two of these analogs are Anti Reverse Cap Analogs which ensures that they are incorporated into mRNA chains exclusively in the correct orientation. These new cap analogs should be useful in a variety of biochemical studies, in the analysis of the cellular function of decapping enzymes, and as a basis for further development of modified cap analogs as potential anti-cancer and anti-parasite drugs.     

Genetically Modified Pigs as Organ Donors for Xenotransplantation

The growing shortage of available organs is a major problem in transplantology. Thus, new and alternative sources of organs need to be found. One promising solution could be xenotransplantation, i.e., the use of animal cells, tissues and organs. The domestic pig is the optimum donor for such transplants. However, xenogeneic transplantation from pigs to humans involves high immune incompatibility and a complex rejection process. The rapid development of genetic engineering techniques enables genome modifications in pigs that reduce the cross-species immune barrier.     

Structural characterization of the O-specific polysaccharide from the lipopolysaccharide of the fish pathogen Aeromonas bestiarum strain P1S

The O-specific polysaccharide obtained by mild-acid degradation of lipopolysaccharide of Aeromonas bestiarum P1S was studied by sugar and methylation analyses along with ¹H and ¹³C NMR spectroscopy. The sequence of the sugar residues was determined using ¹H,¹H NOESY and ¹H,¹³C HMBC experiments. The O-specific polysaccharide was found to be a high-molecular-mass polysaccharide composed of tetrasaccharide repeating units of the structureSince small amounts of a terminal Quip3N residue were identified in methylation analysis, it was assumed that the elucidated structure also represented the biological repeating unit of the O-specific polysaccharide.     

The in vitro loose dimer structure and rearrangements of the HIV-2 leader RNA

RNA dimerization is an essential step in the retroviral life cycle. Dimerization and encapsidation signals, closely linked in HIV-2, are located in the leader RNA region. The SL1 motif and nucleocapsid protein are considered important for both processes. In this study, we show the structure of the HIV-2 leader RNA (+1-560) captured as a loose dimer. Potential structural rearrangements within the leader RNA were studied. In the loose dimer form, the HIV-2 leader RNA strand exists in vitro as a single global fold. Two kissing loop interfaces within the loose dimer were identified: SL1/SL1 and TAR/TAR. Evidence for these findings is provided by RNA probing using SHAPE, chemical reagents, enzymes, non-denaturing PAGE mobility assays, antisense oligonucleotides hybridization and analysis of an RNA mutant. Both TAR and SL1 as isolated domains are bound by recombinant NCp8 protein with high affinity, contrary to the hairpins downstream of SL1. Foot-printing of the SL1/NCp8 complex indicates that the major binding site maps to the SL1 upper stem. Taken together, these data suggest a model in which TAR hairpin III, the segment of SL1 proximal to the loop and the PAL palindromic sequence play specific roles in the initiation of dimerization.     

Embryonic and adult isoforms of XLAP2 form microdomains associated with chromatin and the nuclear envelope

Laminin-associated polypeptide 2 (LAP2) proteins are alternatively spliced products of a single gene; they belong to the LEM domain family and, in mammals, locate to the nuclear envelope (NE) and nuclear lamina. Isoforms lacking the transmembrane domain also locate to the nucleoplasm. We used new specific antibodies against the N-terminal domain of Xenopus LAP2 to perform immunoprecipitation, identification and localization studies during Xenopus development. By immunoprecipitation and mass spectrometry (LC/MS/MS), we identified the embryonic isoform XLAP2??, which was downregulated during development similarly to XLAP2??. Embryonic isoforms XLAP2?? and XLAP2?? were located in close association with chromatin up to the blastula stage. Later in development, both embryonic isoforms and the adult isoform XLAP2?? were localized in a similar way at the NE. All isoforms colocalized with lamin B2/B3 during development, whereas XLAP2?? was colocalized with lamin B2 and apparently with the F/G repeat nucleoporins throughout the cell cycle in adult tissues and culture cells. XLAP2?? was localized in clusters on chromatin, both at the NE and inside the nucleus. Embryonic isoforms were also localized in clusters at the NE of oocytes. Our results suggest that XLAP2 isoforms participate in the maintenance and anchoring of chromatin domains to the NE and in the formation of lamin B microdomains.     

Transverse testicular ectopia with abnormal karyotype - a case report

OBJECTIVES: Growth disturbances and developmental malformations of external genitalia, such as hypospadias, bifid scrotum and micropenis, coexisting with non-palpable testes, may develop as a result of primary endocrinological dysfunctions as well as an effect secondary to chromosomal aberrations. Therefore, patients with these symptoms require specific diagnostic and therapeutic approaches. Design and methods: We present an example of TTE as a presentation of karyotype abnormalities. Clinical presentation - 9.5 year old boy presented with hypospadias, bilateral cryptorchidism and right inguinal hernia and short stature. Results: Endocrine test showed low testosterone levels with adequate gonadal response. Laparoscopy was performed and revealed the presence of TTE. Conclusions: The presence of mosaic karyotype with abnormal Y chromosome does not exclude a possibility of testis migration disorders, including TTE, caused by other (possibly genetic) factors. Laparoscopy is a technique of choice for diagnosis and treatment in cases of cryptorchidism.