Leucine‐rich repeat receptor‐like kinase II phylogenetics reveals five main clades throughout the plant kingdom

Receptor‐like kinases (RLKs) represent the largest group of cell surface receptors in plants. The monophyletic leucine‐rich repeat (LRR)‐RLK subfamily II is considered to contain the somatic embryogenesis receptor kinases (SERKs) and NSP‐interacting kinases known to be involved in developmental processes and cellular immunity in plants. There are only a few published studies on the phylogenetics of LRR‐RLKII; unfortunately these suffer from poor taxon/gene sampling. Hence, it is not clear how many and what main clades this family contains, let alone what structure–function relationships exist. We used 1342 protein sequences annotated as ‘SERK’ and ‘SERK‐like’ plus related sequences in order to estimate phylogeny within the LRR‐RLKII clade, using the nematode protein kinase Pelle as an outgroup. We reconstruct five main clades (LRR‐RLKII 1–5), in each of which the main pattern of land plant relationships re‐occurs, confirming previous hypotheses that duplication events happened in this gene subfamily prior to divergence among land plant lineages. We show that domain structures and intron–exon boundaries within the five clades are well conserved in evolution. Furthermore, phylogenetic patterns based on the separate LRR and kinase parts of LRR‐RLKs are incongruent: whereas the LRR part supports a LRR‐RLKII 2/3 sister group relationship, the kinase part supports clades 1/2. We infer that the kinase part includes few ‘radical’ amino acid changes compared with the LRR part. Finally, our results confirm that amino acids involved in each LRR‐RLKII–receptor complex interaction are located at N‐capping residues, and that the short amino acid motifs of this interaction domain are highly conserved throughout evolution within the five LRR‐RLKII clades.     

Infection Status of Hydatid Cysts in Humans and Sheep in Uzbekistan

Uzbekistan is endemic of cystic echinococcosis (CE). In order to estimate endemicity of CE, we collected data from emergency surgery due to CE in 2002-2010 and also investigated the prevalence of hydatid cysts in the liver and lungs of sheep at an abattoir in Uzbekistan from July 2009 to June 2010. In 14 emergency hospitals, 8,014 patients received surgical removal or drainage of CE during 2002-2010, and 2,966 patients were found in 2010. A total of 22,959 sheep were grossly examined of their liver and lungs, and 479 (2.1%) and 340 (1.5%) of them were positive for the cyst in the liver and lungs, respectively. Echinococcus granulosus is actively transmitted both to humans and sheep, and CE is a zoonotic disease of public health priority in Uzbekistan.     

A 368-base-pair cis-acting HWP1 promoter region, HCR, of Candida albicans confers hypha-specific gene regulation and binds architectural transcription factors Nhp6 and Gcf1p

To elucidate the molecular mechanisms controlling the expression of the hypha-specific adhesin gene HWP1 of Candida albicans, its promoter was dissected and analyzed using a green fluorescent protein reporter gene. A 368-bp region, the HWP1 control region (HCR), was critical for activation under hypha-inducing conditions and conferred developmental regulation to a heterologous ENO1 promoter. A more distal region of the promoter served to amplify the level of promoter activation. Using gel mobility shift assays, a 249-bp subregion of HCR, HCRa, was found to bind at least four proteins from crude extracts of yeasts and hyphae with differing binding patterns dependent on cell morphology. Four proteins with DNA binding activities were identified by using sodium dodecyl sulfate-polyacrylamide gel electrophoresis after separation by anion-exchange and heparin-Sepharose chromatography. One protein with high similarity to Nhp6, an HMG1 family member in Saccharomyces cerevisiae, and another with weak similarity to an HMG-like condensation factor from Physarum polycephalum implicated changes in chromatin structure as a critical process in hypha-specific gene regulation. Proteins with strong homology to histones were also found. These studies are the first to identify proteins that bind to a DNA segment that confers developmental gene regulation in C. albicans and suggest a new model for hypha-specific gene regulation.     

Functional beta-cell maturation is marked by an increased glucose threshold and by expression of urocortin 3

Insulin-expressing cells that have been differentiated from human pluripotent stem cells in vitro lack the glucose responsiveness characteristic of mature beta cells. Beta-cell maturation in mice was studied to find genetic markers that enable screens for factors that induce bona fide beta cells in vitro. We find that functional beta-cell maturation is marked by an increase in the glucose threshold for insulin secretion and by expression of the gene urocortin 3.     

Proteomics analysis of two heat shock proteins in insects

Heat shock proteins (HSPs) are found in all living organisms, from bacteria to humans, are expressed under stress. In this study, characterization of two families of HSP including HSP60 and HSP70 protein was compared in different insect species from different orders. According to the conserved motifs analysis, none of the motifs were shared by all insects of two protein families but each family had their own common motifs. Functional and structural analyses were carried out on seven different insect species from each protein family as the representative samples. These analyses were performed via ExPASy database tools. The tertiary structure of Drosophila melanogater as the sample of each protein family were predicted by the Phyre2 and TM-score servers then their qualities were verified by SuperPose and PROCHECK. The tertiary structures were predicted through the “c4pj1E” model (PDB Accession Code: 4pj1) in HSP60 family and “c3d2fC” model (PDB Accession Code: 3d2f) in HSP70 family. The protein phylogenetic tree was constructed using the Neighbor-joining (NJ) method by Molecular Evolutionary Genetic Analysis (MEGA) 6.06. According to the results, there was a high identity of HSP60 and HSP70 families so that they should be derived from a common ancestor however they belonged to separate groups. In protein–protein interaction analysis by STRING 10.0, 10 common enriched pathways of biological process, molecular function and Kyoto Encyclopedia of Genes and Genomes (KEGG) were identified in D. melanogaster in both families. The obtained data provide a background for bioinformatic studies of the function and evolution of insects and other organisms.

Communicated by Ramaswamy H. Sarma     

Platelet-activating factor receptor agonists mediate xeroderma pigmentosum A photosensitivity

To date, oxidized glycerophosphocholines (Ox-GPCs) with platelet-activating factor (PAF) activity produced non-enzymatically have not been definitively demonstrated to mediate any known disease processes. Here we provide evidence that these Ox-GPCs play a pivotal role in the photosensitivity associated with the deficiency of the DNA repair protein xeroderma pigmentosum type A (XPA). It should be noted that XPA-deficient cells are known to have decreased antioxidant defenses. These studies demonstrate that treatment of human XPA-deficient fibroblasts with the pro-oxidative stressor ultraviolet B (UVB) radiation resulted in increased reactive oxygen species and PAF receptor (PAF-R) agonistic activity in comparison with gene-corrected cells. The UVB irradiation-generated PAF-R agonists were inhibited by antioxidants. UVB irradiation of XPA-deficient (Xpa-/-) mice also resulted in increased PAF-R agonistic activity and skin inflammation in comparison with control mice. The increased UVB irradiation-mediated skin inflammation and TNF-α production in Xpa-/- mice were blocked by systemic antioxidants and by PAF-R antagonists. Structural characterization of PAF-R-stimulating activity in UVB-irradiated XPA-deficient fibroblasts using mass spectrometry revealed increased levels of sn-2 short-chain Ox-GPCs along with native PAF. These studies support a critical role for PAF-R agonistic Ox-GPCs in the pathophysiology of XPA photosensitivity.     

Kinetics of hydrogen-dependent denitrification under varying pH and temperature conditions

It is important to determine the effect of changing environmental conditions on the microbial kinetics for design and modeling of biological treatment processes. In this research, the kinetics of nitrate and nitrite reduction by autotrophic hydrogen-dependent denitrifying bacteria and the possible role of acetogens were studied in two sequencing batch reactors (SBR) under varying pH and temperature conditions. A zero order kinetic model was proposed for nitrate and nitrite reduction and kinetic coefficients were obtained at two temperatures (25 +/- 1 and 12 +/- 1 degrees C), and pH ranging from 7 to 9.5. Nitrate and nitrite reduction was inhibited at pH of 7 at both temperatures of 12 +/- 1 and 25 +/- 1 degrees C. The optimum pH conditions for nitrate and nitrite reduction were 9.5 at 25 +/- 1 degrees C and 8.5 at 12 +/- 1 degrees C. Nitrate and nitrite reduction rates were compared, when they were used separately as the sole electron acceptor. It was shown that nitrite reduction rates consistently exceeded nitrate reduction rates, regardless of temperature and pH. The observed transitional accumulation of nitrite, when nitrate was used as an electron acceptor, indicated that nitrite reduction was slowed down by the presence of nitrate. No activity of acetogenic bacteria was observed in the hydrogenotrophic biomass and no residual acetate was detected, verifying that the kinetic parameters obtained were not influenced by heterotrophic denitrification and accurately represented autotrophic activity.     

Comparison of α- and β-mannosidase activity in the three cereal pests,Haplothrips tritici Kurdjumov (Thysanoptera: Phlaeothripidae), Rhopalosiphum padi L. (Homoptera: Aphididae) and Eurygaster integriceps Puton (Hemiptera: Scutelleridae)

The Sunn pest, Eurygaster integriceps, the bird cherry-oat aphid, Rhopalosiphum padi, and wheat thrips, Haplothrips tritici are the major pests of wheat and other cereals in a wide area of the world. All these three insect species could produce damage to the wheat to some extent. Therefore, the purpose of the present study was to determine α- and β-mannosidase of the three mentioned insect pests. These insects were collected from the wheat farm and their guts (the Sunn pest and the aphid) and salivary glands of Sunn pest were removed. However, regarding tiny body of thrips, the whole body used in order to extract the enzymes. The enzymes, including α- and β-mannosidase activity, were measured by the hydrolysis of p-nitrophenyl-α-d-mannopyranoside (pNPαGal) and p-nitrophenyl-β-d-mannopyranoside (pNPβGal), respectively, using phosphate citrate buffer (pH 5.0). Mannosidases were not active in all three tested insect species, and also there were significant differences in activities of the two enzymes in three species. The greatest activity of α-mannosidases was observed in the Sunn pest salivary glands, E. integriceps, and the least activity was found in Sunn pest midgut with no activity. However, the activity of β-mannosidase was established in Sunn pest midgut, but there was no activity in the aphid midgut, R. padi. Activities of these two enzymes were modest in the thrips, H. tritici. The greatest amount of β-mannosidases in the Sunn pest midgut makes sense, since the Sunn pest is the main pest in the wheat farm that can feed on wheat grains. In the wheat grains, the highest amount of glycoproteins and glycolipids are present. Thus, it has been known that these enzymes (α- and β-mannosidases) are active on digestion of carbohydrates.