Risk assessment of pathological conditions caused by circulating H. pylori strains

In recent years, there has been an increase in the prevalence of inflammatory and destructive diseases of the gastroduodenal zone, which is primarily explained by Helicobacter pylori (H. pylori) infection. One of the main factors of H. pylori pathogenicity is presence of cytotoxin-associated gene — CagA. It is known that CagA-positive H. pylori strains are associated with the development of atrophy, tumor invasion and rapid metastasis. A number of recently published studies have revealed that CagA is a polymorphic gene which contains a different number of repetitive sequences located in the 3’ region. Each repetitive region of CagA contains Glu-Pro-Ile-Tyr-Ala (EPIYA) profiles including tyrosine phosphorylation. Depending on the sequence of the EPIYA profile, there are 4 segments: EPIYA-A, EPIYA-B, EPIYA-C, EPIYA-D, each containing a repetitive region. Geographical features of the prevalence of H. pylori strains depending on the sequence of EPIYA have been revealed: EPIYA-A region of the western isolates of this bacterium is associated with EPIYA-A, EPIYA-B, EPIYA-C segments, while the eastern CagA-positive H. pylori isolates are characterized by the A-B-D type of the CagA gene. Data illustrating the strong correlation between the western CagA-positive H. pylori strains, which have a repeating EPIYA-C segment, and the development of precancerous states, as well as gastric cancer, are presented. H. pylori strains containing simultaneously A-B motives of EPIYA or one C-type of the CagA gene are associated with a 7-fold increase of risk of gastric cancer compared to CagA-negative strains; presence of two or more EPIYA-C motives is associated with a 30-fold increase of this risk.

Isolation and Molecular Typing of Leishmania infantum from Phlebotomus perfiliewi in a Re-Emerging Focus of Leishmaniasis, Northeastern Italy

Visceral leishmaniasis (VL) caused by Leishmania (L.) infantum is a public health threat in the Emilia-Romagna region, northeastern Italy, but its epidemiology has not been fully elucidated in this area. The objective of this study was to characterize Leishmania infection in sand flies collected in a re-emerging focus of VL in the Bologna province. During the summer of 2016, 6114 sand flies were collected, identified, and tested for Leishmania detection. Of the identified sand flies, 96.5% were Phlebotomus (P.) perfiliewi and 3.5% were P. perniciosus. Detected parasites were characterized by biomolecular methods (multilocus microsatellite typing and characterization of repetitive region on chromosome 31), and quantified by real-time PCR. The prevalence of Leishmania infection in individually-tested P. perfiliewi sand flies varied from 6% to 10% with an increasing trend during the season. Promastigotes of L. infantum were isolated by dissection in one P. perfiliewi female; the isolated strain (Lein-pw) were closely related to Leishmania parasites from VL cases in northeastern Italy, but differed from strains isolated in dogs from the same area. Our findings strongly support the vector status of P. perfiliewi for human VL in the study area.

Analysis of the Full-Length Pyriform Spidroin Gene Sequence

Spiders often produce multiple types of silk, each with unique properties suiting them to certain tasks and biological functions. Orb-weaver spiders can generate more than six types of silk fibroins, with pyriform silk used to form attachment discs, adhering silk to other surfaces and substances. The unique higher-order structuring of silk fibroins has been cited as the source of their remarkable biomechanical properties. Even so, only one full-length gene sequence of pyriform silk protein 1 (PySp1) from Argiopeargentata has been reported, and studies on the mechanical properties of natural pyriform silk fibers are also lacking. To better understand the PySp1 family of genes, we used long-distance PCR (LD-PCR) to determine the sequence of PySp1 in the Araneusventricosus species. This full-length PySp1 gene is 11,931 bp in length, encoding for 3976 amino acids residues in non-repetitive N- and C-terminal domains with a central largely repetitive region made up of sixteen remarkably homogeneous units. This was similar to the previously reported A. argentata PySp1 sequence, with PySp1 from A. ventricosus also having a long repetitive N-linker that bridges the N-terminal and repetitive regions. Predictions of secondary structure and hydrophobicity of A. ventricosus PySp1 showed the pyriform silk fiber’s functional properties. The amino acid compositions of PySp1 is obviously distinct from other spidroins. Our sequence makes an important contribution to understand pyriform silk protein structure and also provides a new template for recombinant pyriform silk proteins with attractive properties.

Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA-dominated PHAS loci

Small RNAs regulate key physiological functions in land plants. Small RNAs can be divided into two categories: microRNAs (miRNAs) and short interfering RNAs (siRNAs); siRNAs are further sub-divided into transposon/repetitive region-localized heterochromatic siRNAs and phased siRNAs (phasiRNAs). PhasiRNAs are produced from the miRNA-mediated cleavage of a Pol II RNA transcript; the miRNA cleavage site provides a defined starting point from which phasiRNAs are produced in a distinctly phased pattern. 21-22 nucleotide (nt)-dominated phasiRNA-producing loci (PHAS) are well represented in all land plants to date. In contrast, 24 nt-dominated PHAS loci are known to be encoded only in monocots and are generally restricted to male reproductive tissues. Currently, only one miRNA (miR2275) is known to trigger the production of these 24 nt-dominated PHAS loci. In this study, we use stringent methodologies in order to examine whether or not 24 nt-dominated PHAS loci also exist in Arabidopsis thaliana. We find that highly expressed heterochromatic siRNAs were consistently mis-identified as 24 nt-dominated PHAS loci using multiple PHAS-detecting algorithms. We also find that MIR2275 is not found in A. thaliana, and it seems to have been lost in the last common ancestor of Brassicales. Altogether, our research highlights the potential issues with widely used PHAS-detecting algorithms which may lead to false positives when trying to annotate new PHAS, especially 24 nt-dominated loci.

Variability and Structure of the Repetitive Region of the Major Royal Jelly Protein Gene mrjp3 in Honeybee Apis mellifera of Different Evolutionary Branches

An assessment of the genetic diversity of the microsatellite locus mrjp3 in honeybee of European Apis mellifera subspecies was conducted. Differences in the frequency of alleles for the mrjp3 locus were found in honeybees of different evolutionary branches. Allele "529" was found to be specific for the Apis mellifera mellifera, evolutionary branch M, while alleles "406", "518", and "485" were characteristic of the southern subspecies of bees (A. m. carnica, A. m. carpatica (some researchers consider this breed as a derivative of A. m. carnica), and A. m. caucasica; evolutionary branches C and O, respectively). A high correspondence of the studied nucleotide sequences (>=99% identity) with the reference sequences (Genbank) was established indicating a high conservation of the repetitive region of the mrjp3 gene in A. mellifera subspecies inhabiting different geographic regions of Europe and Siberia. Locus mrjp3 is of considerable interest for further study as a candidate marker for differentiation of bee subspecies.

Disorder drives cooperative folding in a multidomain protein

Many human proteins contain intrinsically disordered regions, and disorder in these proteins can be fundamental to their function—for example, facilitating transient but specific binding, promoting allostery, or allowing efficient posttranslational modification. SasG, a multidomain protein implicated in host colonization and biofilm formation in Staphylococcus aureus, provides another example of how disorder can play an important role. Approximately one-half of the domains in the extracellular repetitive region of SasG are intrinsically unfolded in isolation, but these E domains fold in the context of their neighboring folded G5 domains. We have previously shown that the intrinsic disorder of the E domains mediates long-range cooperativity between nonneighboring G5 domains, allowing SasG to form a long, rod-like, mechanically strong structure. Here, we show that the disorder of the E domains coupled with the remarkable stability of the interdomain interface result in cooperative folding kinetics across long distances. Formation of a small structural nucleus at one end of the molecule results in rapid structure formation over a distance of 10 nm, which is likely to be important for the maintenance of the structural integrity of SasG. Moreover, if this normal folding nucleus is disrupted by mutation, the interdomain interface is sufficiently stable to drive the folding of adjacent E and G5 domains along a parallel folding pathway, thus maintaining cooperative folding.

Research on Layout of Measurement Points in Tunnel Lighting Experiment

Based on the measured data of the tunnel lighting, this paper is focusing on the arrangement of measured points in the experiment of tunnel lighting. Through the way of changing the location of measured area and the arrangement of measured points, comparing the simulation from the software DIALUX and the actual measurement in a repetitive region, the best position of measured area and the corresponding layout mode can be found. Analysis shows that, the larger the lamp distance is, the more similar the experiment and simulation results are. Before the experiment, the analysis of the light distribution curve is required, then, the simulation of software can help to find out the best position of lamp interval, measured area and layout mode, in order to ensure the authenticity of the results and to avoid too large or too small lighting evaluation, layout mode must include the maximum measured points and the minimum measured point.