Role of allelic genes of matrix metalloproteinases and their tissue inhibitors in the risk of peptic ulcer disease development

Peptic ulcer disease is a chronic disease of the gastrointestinal tract, mainly manifesting itself in the formation of the fairly persistent ulcer defect of the mucous membrane of the stomach and/or duodenum. Association analysis of common polymorphisms of matrix metalloproteinases genes MMP-1 (rs1799750, rs494379), MMP-2 (rs2285052), MMP-3 (rs3025058), MMP-9 (rs3918242, rs17576), and MMP-12 (rs2276109) and their tissue inhibitors TIMP-2 (rs8179090) and TIMP-3 (rs9619311) was carried out in 353 patients with a gastric ulcer or duodenal ulcer and in 325 unrelated healthy individuals from the Republic of Bashkortostan. Associations of polymorphic variants rs1799750 and rs494379 of gene MMP-1, rs3025058 of gene MMP-3, rs3918242 and rs17576 of gene MMP-9, and rs9619311 of gene TIMP-3 with the risk of peptic ulcer disease in Russians and Tatars were revealed.     

Different laboratory populations similar bacterial profile? The case of Glossina palpalis gambiensis

Background

Microbiota plays an important role in the biology, ecology and evolution of insects including tsetse flies. The bacterial profile of 3 Glossina palpalis gambiensis laboratory colonies was examined using 16S rRNA gene amplicon sequencing to evaluate the dynamics of the bacterial diversity within and between each G. p. gambiensis colony.

Results

The three G. p. gambiensis laboratory colonies displayed similar bacterial diversity indices and OTU distribution. Larval guts displayed a higher diversity when compared with the gastrointestinal tract of adults while no statistically significant differences were observed between testes and ovaries. Wigglesworthia and Sodalis were the most dominant taxa. In more detail, the gastrointestinal tract of adults was more enriched by Wigglesworthia while Sodalis were prominent in gonads. Interestingly, in larval guts a balanced co-existence between Wigglesworthia and Sodalis was observed. Sequences assigned to Wolbachia, Propionibacterium, and Providencia were also detected but to a much lesser degree. Clustering analysis indicated that the bacterial profile in G. p. gambiensis exhibits tissue tropism, hence distinguishing the gut bacterial profile from that present in reproductive organs.

Conclusions

Our results indicated that age, gender and the origin of the laboratory colonies did not significantly influence the formation of the bacterial profile, once these populations were kept under the same rearing conditions. Within the laboratory populations a tissue tropism was observed between the gut and gonadal bacterial profile.

     

Potential probiotic properties of lactic acid bacteria isolated from the intestinal mucosa of healthy piglets

In the present study, the probiotic properties of 52 lactic acid bacteria strains, isolated from the intestinal mucosa of 60-day-old healthy piglets, were evaluated in vitro in order to acquire probiotics of potential application. Based on acidic and bile salt resistance, 11 lactic acid bacteria strains were selected, among which 1 was identified as Pediococcus acidilactici, 3 as Enterococcus faecium, 3 as Lactobacillus rhamnosus, 2 as Lactobacillus brevis, and 2 as Lactobacillus plantarum by 16S rRNA gene sequencing. All selected strains were further investigated for transit tolerance in simulated upper gastrointestinal tract, for adhesion capacity to swine intestinal epithelial cells J2 (IPEC-J2), for cell surface characteristics including hydrophobicity, co-aggregation and auto-aggregation, and for antimicrobial activities. Moreover, hemolytic, bile salt hydrolase and biogenic amine-producing abilities were investigated for safety assessment. Two E. faecium (WEI-9 and WEI-10) and one L. plantarum (WEI-51) exhibited good simulated upper gastrointestinal tract tolerance, and showed high auto-aggregation and co-aggregation with Escherichia coli 1570. The strains WEI-9 and WEI-10 demonstrated the highest adherence capacity. The 11 selected strains mentioned above exhibited strong antimicrobial activity against E. coli CVCC1570, Staphylococcus aureus CVCC1882 and Salmonella pullorum AS1.1859. None of the 11 selected strains, except WEI-9 and WEI-33, exhibited bile salt hydrolase, hemolytic or biogenic amine-producing abilities. This work showed that the E. faecium WEI-10 and L. plantarum WEI-51were found to have the probiotic properties required for use as potential probiotics in animal feed supplements.     

Cathepsin <Emphasis Type="Italic">G</Emphasis> in the immune defense of the human duodenum: New sources for biosynthesis

Proteases play a key role in the physiological processes of the small intestine, supporting its normal physiological functions as a part of the digestive system, in which hydrolysis and assimilation of nutrients are implemented. A high concentration of antigens in the intestinal lumen activates immunity and stimulates a chronic weakly expressed inflammatory response in a normal gastrointestinal tract (GIT). Cathepsin G, a serine protease controlling the functional state of immune cells, directly participates in the complicated system for the regulation of balance between physiological and pathological inflammations. To determine the role of cathepsin G in the small intestine, an immunofluorescent investigation of biopsies from the human duodenal mucosa were investigated using the confocal immunofluorescence microscopy method and human antibodies to cathepsin G. It has been shown for the first time that cathepsin G, which was regarded conventionally as one of the effectors of the inflammatory process, is a constitutive enzyme of the human duodenum and is constantly present in its normal mucosa. The new cell sources for the cathepsin G biosynthesis identified: intraepithelial lymphocytes (IELs), lamina propria lymphocytes, ^CD14-positive intestinal macrophages, and Paneth cells, which are specialized epitheliocytes of intestinal glands. Our data on the cathepsin G expression by immunocytes and Paneth cells in the duodenum allow us to attribute cathepsin G to the main proteases of intestinal immunity, which indicates the important role of this enzyme in the regulation of human GIT functions.     

<Emphasis Type="Italic">Raoultella</Emphasis> spp.—clinical significance,infections and susceptibility to antibiotics

The genus Raoultella belongs to the family of Enterobacteriaceae. Raoultella spp. are Gram-negative, aerobic, non-motile rods. This genus can be distinguished from the genus Klebsiella, in that genus use histamine as the only source of carbon in the medium. Also, Raoultella grow at 4 °C and do not produce gas from lactose at 44.5 °C. Raoultella sp. is known to inhabit natural environments (water, soil, plants). The reservoir of Raoultella is the gastrointestinal tract and upper respiratory tract. Raoultella spp. are opportunistic bacteria, which usually cause infections of the biliary tract, pneumonia and bacteraemia in oncologic and with lower immunity patients. Raoultella planticola and Raoultella ornithinolytica are the most frequently encountered human pathogens among the genus Raoultella. In this review, the current knowledge on Raoultella infections is summarized.     

Integrated analysis of leaf morphological and color traits in different populations of Chinese cabbage (<Emphasis Type="Italic">Brassica rapa</Emphasis> ssp. <Emphasis Type="Italic">pekinensis</Emphasis>)

Key message

QTLs and candidate gene markers associated with leaf morphological and color traits were identified in two immortalized populations of Brassica rapa, which will provide genetic information for marker-assisted breeding.

Abstract

Brassica rapa is an important leafy vegetable consumed worldwide and morphology is a key character for its breeding. To enhance genetic control, quantitative trait loci (QTLs) for leaf color and plant architecture were identified using two immortalized populations with replications of 2 and 4 years. Overall, 158 and 80 QTLs associated with 23 and 14 traits were detected in the DH and RIL populations, respectively. Among them, 23 common robust-QTLs belonging to 12 traits were detected in common loci over the replications. Through comparative analysis, five crucifer genetic blocks corresponding to morphology trait (R, J&U, F and E) and color trait (F, E) were identified in three major linkage groups (A2, A3 and A7). These might be key conserved genomic regions involved with the respective traits. Through synteny analysis with Arabidopsis, 64 candidate genes involved in chlorophyll biosynthesis, cell proliferation and elongation were co-localized within QTL intervals. Among them, SCO3, ABI3, FLU, HCF153, HEMB1, CAB3 were mapped within QTLs for leaf color; and CYCD3;1, CYCB2;4, AN3, ULT1 and ANT were co-localized in QTL regions for leaf size. These robust QTLs and their candidate genes provide useful information for further research into leaf architecture with crop breeding.

     

Determination of Azole Resistance and TR<Subscript>34</Subscript>/L98H Mutations in Isolates of <Emphasis Type="Italic">Aspergillus</Emphasis> Section <Emphasis Type="Italic">Fumigati</Emphasis> from Turkish Cystic Fibrosis Patients

Background

Aspergillus fumigatus is the species section Fumigati most frequently isolated from the respiratory tract of cystic fibrosis (CF) patients. Recent studies suggest that mutations in the Cyp51 gene, particularly TR₃₄/L98H, are responsible for azole resistance.

Objectives and Methods

The focus of this study was on section Fumigati isolates isolated from the respiratory tract samples of CF patients. More specifically, the goal was to detect A. fumigatus isolates, test their antifungal susceptibility to itraconazole, voriconazole and posaconazole, and finally determine the presence of TR₃₄/L98H and other mutations in the isolates Cyp51A gene.

Results and Conclusions

A set of 31 isolates of Aspergillus section Fumigati were obtained from the sputum samples of 6 CF patients and subsequently identified to species level by microsatellite genotyping. All isolates were determined as A. fumigatus and involved 14 different genotypes. The minimal inhibitory concentrations to the three azoles were determined by the E-test method, and the Cyp51A gene was sequenced. One of the genotypes was found to be resistant to all azoles but no mutations were detected in the Cyp51A gene, especially the TR₃₄/L98H mutation. Therefore, mutations in genes other than Cyp51A or other distinct mechanisms may be responsible for this reported multiazole resistance found in a Turkish CF patient.

     

Mutational spectrum of the gene for 21-hydroxylase in the patients with congenital adrenal hyperplasia from Bashkortostan

Molecular genetic analysis of congenital adrenal hyperplasia (CAH) was carried out in 59 patients from the Republic of Baskortostan, which belonged to two main groups. The first group was represented by 35 patients with salt wasting form of the disease, and the second group was comprised of 24 patients with simple virilizing form. Analysis of the CYP21A2 gene in the patients with congenital adrenal hyperplasia from the Republic of Bashkortostan revealed seven different mutations on 81.58% chromosomes, including deletion/conversion delA2 or LGC gene, R356W, I2splice, I172N, Q318X, V281L, and P30L. The mutations were present on 89.71% of chromosomes from the patients with salt wasting form, and in 69.5% of chromosomes from the patients with simple virilizing form. The most frequent mutation was gene deletion/conversion, delA2 or LGC, which was found with the frequency of 30.83%. In six CAH patients the presence of three different mutation clusters on one chromosome was demonstrated: Q318X + R356W, I172N + Q318X, and delA2 or LGC + V281L. For the mutations leading to partial loss of 21-hydroxylase activity and simple virilizing form, 100% conformity of the phenotype to genotype was established.     

Hypomorphic phenotype of <Emphasis Type="Italic">Foxn1</Emphasis> gene-modified rats by CRISPR/Cas9 system

The Foxn1 gene is known as a critical factor for the differentiation of thymic and skin epithelial cells. This study was designed to examine the phenotype of Foxn1-modified rats generated by the CRISPR/Cas9 system. Guide-RNA designed for first exon of the Foxn1 and mRNA of Cas9 were co-injected into the pronucleus of Crlj:WI zygotes. Transfer of 158 injected zygotes resulted in the birth of 50 offspring (32 %), and PCR identified five (10 %) as Foxn1-edited. Genomic sequencing revealed the deletion of 44 or 60 bp from and/or insertion of 4 bp into the Foxn1 gene in a single allele. The number of T-cells in the peripheral blood lymphocytes of mutant rats decreased markedly. While homozygous deleted mutant rats had no thymus, the mutant rats were not completely hairless and showed normal performance in delivery and nursing. Splicing variants of the indel-mutation in the Foxn1 gene may cause hypomorphic allele, resulting in the phenotype of thymus deficiency and incomplete hairless. In conclusion, the mutant rats in Foxn1 gene edited by the CRISPR/Cas9 system showed the phenotype of thymus deficiency and incomplete hairless which was characterized by splicing variants.     

Probiotic Potential of Autochthonous Bacteria Isolated from the Gastrointestinal Tract of Four Freshwater Teleosts

In this study, a total of 121 bacterial strains were isolated from the gastrointestinal tract of four teleostean species, namely striped snakehead (Channa striatus), striped dwarf catfish (Mystus vittatus), orangefin labeo (Labeo calbasu) and mrigal carp (Cirrhinus mrigala), among which 8 isolates showed promising antibacterial activity against four potential fish pathogens, Aeromonas hydrophila, Aeromonas salmonicida, Aeromonas sobria and Pseudomonas fluorescens and were non-hemolytic. The isolates were further screened in response to fish bile tolerance and extracellular digestive enzyme activity. Two bacterial strains MVF1 and MVH7 showed highest tolerance and extracellular enzymes activities, and selected for further studies. Antagonistic activity of these two isolates was further confirmed by in vitro growth inhibition assay against four selected fish pathogens in liquid medium. Finally, these two bacterial strains MVF1 and MVH7 were selected as potential probiotic candidates and thus identification by partial 16S rRNA gene sequence analysis. The bacterial isolates MVF1 and MVH7 were identified as two strains of Bacillus sp.     

A first insight into the intestinal microbiota of snow trout (<Emphasis Type="Italic">Schizothorax zarudnyi</Emphasis>)

This study addresses the biodiversity profile of bacterial community in the intestinal lumen and mucosa of snow trout fish by applying 16S rRNA gene 454-pyrosequencing. A total of 209,106 sequences with average length 689 (±53) were filtered, denoised, trimmed, and then sorted into OTUs based on 97 % sequence similarity using the USEARCH software pipeline. Bacteria representing 10 phyla were found in the samples investigated. Fimicutes ribotypes were present in intestinal-mucosa and lumen in all fish and often dominated the libraries (average 43 and 38 %, respectively). Proteobacteria were also prevalent, but at a lower relative abundance, at 22 and 29 % in mucosa and lumen, respectively. The autochthonous microbiota was dominated by sequences belonging to the Bacilli (mean sequence abundance 24 %), in particular the Lactobacillaceae, with Lactobacillus and Pediococcous being the most abundant genera. Fewer Bacilli (mean sequence abundance 22 %) and Actinobacteria (2 %) were present in the lumen, and allochthonous communities consisted of a more even split among the bacterial classes, with increases in sequences assigned to members of the γ-Proteobacteria (16 %) and Fusobacteriia (8 %). The principal bacterial genera recorded in the lumen belonged to the lactic acid bacteria group, Cetobacterium, Clostridium and Synechococcus. Results obtained suggest that the lumen and mucosal layer of the snow trout intestine may host different microbial communities. Moreover, both regions harbour a diverse microbiome with a greater microbial diversity in the intestinal mucus compared with the luminal communities of the fish. Many of these microbes might be of high physiological relevance for the fish and may play key roles in the functioning of its gut.     

Low molecular weight glutenin subunit gene composition at <Emphasis Type="Italic">Glu</Emphasis>-<Emphasis Type="Italic">D3</Emphasis> loci of <Emphasis Type="Italic">Aegilops tauschii</Emphasis> and common wheat and a further view of wheat evolution

Key message

A comprehensive comparison of LMW-GS genes between Ae. tauschii and its progeny common wheat.

Abstract

Low molecular weight glutenin subunits (LMW-GSs) are determinant of wheat flour processing quality. However, the LMW-GS gene composition in Aegilops tauschii, the wheat D genome progenitor, has not been comprehensively elucidated and the impact of allohexaploidization on the Glu-D3 locus remains elusive. In this work, using the LMW-GS gene molecular marker system and the full-length gene-cloning method, LMW-GS genes at the Glu-D3 loci of 218 Ae. tauschii and 173 common wheat (Triticum aestivum L.) were characterized. Each Ae. tauschii contained 11 LMW-GS genes, and the whole collection was divided into 25 haplotypes (AeH01–AeH25). The Glu-D3 locus in common wheat lacked the LMW-GS genes D3-417, D3-507 and D3-552, but shared eight genes of identical open reading frame (ORF) sequences when compared to that of Ae. tauschii. Therefore, the allohexaploidization induces deletions, but exerts no influence on LMW-GS gene coding sequences at the Glu-D3 locus. 92.17% Ae. tauschii had 7-9 LMW-GSs, more than the six subunits in common wheat. The haplotypes AeH16, AeH20 and AeH23 of Ae. tauschii ssp. strangulate distributed in southeastern Caspian Iran were the main putative D genome donor of common wheat. These results facilitate the utilization of the Ae. tauschii glutenin gene resources and the understanding of wheat evolution.

     

Polymorphism of the human <Emphasis Type="Italic">MDR1</Emphasis> gene in Siberian and Central Asian populations

The multidrug resistance gene MDR1 (ABCB1) codes for a P-glycoprotein that acts as an ATP-dependent transporter and is involved in removing drugs, xenobiotics, and peptides from the cell. MDR1 is expressed in the brain, kidneys, liver, and gastrointestinal tract. The P-glycoprotein is thought to play a role in individual resistance to xenobiotics and infections. Several polymorphisms of MDR1 are associated with the level of its expression and resistance to various neurodegenerative and gastrointestinal diseases. The allele and haplotype frequencies, genetic differentiation, and linkage disequilibrium for five MDR1 single nucleotide polymorphisms (3435C/T, 2677G/T/A, 1236C/T, +139C/T, and ?1G/A) were studied in the Russian, Tuvinian, and northern and southern Kyrgyz populations. Significant genetic differences were observed between Russians and northern Kyrgyz and between Tuvinians and northern Kyrgyz. The linkage disequilibrium pattern was characterized by high population specificity.     

Association of GNB3 gene C825T polymorphism with coronary heart disease

The C825T polymorphism in the gene encoding the G protein beta 3 subunit (GNB3) causes enhanced G protein activation and the increased in vitro cell proliferation. We investigated the association of gene GNB3 C825T polymorphism with coronary artery disease (CAD) in the Russian population. A total of 313 patients with CAD diagnosed on the basis of clinical studies and coronary angyography were examined. The control group included 132 individuals that lacked clinical CAD symptoms and had matching profile of coronary artery disease risk factors. Blood pressure was measured using standard protocols. Increased levels of diastolic and systolic pressure was observed in both groups. The allele and genotype frequencies of this polimorphic marker were significantly higher in the CAD patients than in control. We found that the frequency of allele C and genotype CC was significantly higher in the CAD patients (OR = 1.55; P = 0.0079; OR = 1.63; P = 0.0215, respectively), which suggests higher risk of this pathology in carriers of allele C and genotype CC. Thus, in the Russian population coronary artery disease is associated with GNB3 allele C and genotype CC.     

Linkage between the <Emphasis Type="Italic">I</Emphasis>-<Emphasis Type="Italic">3</Emphasis> gene for resistance to Fusarium wilt race 3 and increased sensitivity to bacterial spot in tomato

Key message

The negative association between the I - 3 gene and increased sensitivity to bacterial spot is due to linkage drag (not pleiotropy) and may be remedied by reducing the introgression size.

Abstract

Fusarium wilt is one of the most serious diseases of tomato (Solanum lycopersicum L.) throughout the world. There are three races of the pathogen (races 1, 2 and 3), and the deployment of three single, dominant resistance genes corresponding to each of these has been the primary means of controlling the disease. The I-3 gene was introgressed from S. pennellii and confers resistance to race 3. Although I-3 provides effective control, it is negatively associated with several horticultural traits, including increased sensitivity to bacterial spot disease (Xanthomonas spp.). To test the hypothesis that this association is due to linkage with unfavorable alleles rather than to pleiotropy, we used a map-based approach to develop a collection of recombinant inbred lines varying for portions of I-3 introgression. Progeny of recombinants were evaluated for bacterial spot severity in the field for three seasons, and disease severities were compared between I-3 introgression haplotypes for each recombinant. Results indicated that increased sensitivity to bacterial spot is not associated with the I-3 gene, but rather with an upstream region of the introgression. A survey of public and private inbred lines and hybrids indicates that the majority of modern I-3 germplasm contains a similarly sized introgression for which the negative association with bacterial spot likely persists. In light of this, it is expected that the development and utilization of a reduced I-3 introgression will significantly improve breeding efforts for resistance to Fusarium wilt race 3.

     

The role of expansin genes <Emphasis Type="Italic">PtrEXPA3</Emphasis> and <Emphasis Type="Italic">PnEXPA3</Emphasis> in the regulation of leaf growth in poplar

The genes of α-expansins of woody plants are of great interest for genetic engineering, since they can potentially be used to improve the tree growth parameters. In the flora of Russia, model woody plants for plant biotechnology are aspen (Populus tremula L.) and black poplar (Populus nigra L.). The objective of this study was to determine the role of α-expansin-encoding genes, aspen PtrEXPA3 and black poplar PnEXPA3, in the regulation and maintenance of woody plant growth. To achieve this goal, the PtrEXPA3 expression level were determined upon exogenous phytohormone treatment, the action of stress factors, and constitutive expression of the PnARGOS-LIKE gene. In addition, transgenic aspen plants with constitutive expression of the black poplar PnEXPA3 gene were generated, and their morphological analysis was carried out. The highest PtrEXPA3 mRNA level was detected in young intensely growing aspen leaves, and furthermore, expression of the gene was induced by exogenous cytokinins and auxins. In response to NaCl and constitutive expression of the PnARGOS-LIKE gene, the PtrEXPA3 mRNA level decreased. Transgenic aspen plants with constitutive PnEXPA3 expression were characterized by the decreased size of leaves, petioles, and internodes, as well as the increased size of leaf epidermal cells, while the stem size remained unchanged. Taken together, the data obtained enable the suggestion that the PtrEXPA3 and PnEXPA3 genes encode cytokinin- and auxin-regulated, leaf-specific expansins that are involved in the cell expansion.     

In Silico and Experimental Data Claiming Safety Aspects and Beneficial Attributes of the Bacteriocinogenic Strain <Emphasis Type="Italic">Enterococcus faecalis</Emphasis> B3A-B3B

This study aimed at comparing the genome of Enterococcus faecalis B3A-B3B, a bacteriocinogenic strain recently isolated from a healthy Iraqi infant to those of Enterococci of clinical and beneficial grades. The putative genes gelE, cpd, efaAfm, ccf, agg, and cob coding for virulence factors were detected in B3A-B3B strain, which meanwhile resulted to be non-cytotoxic, non-hemolytic, devoid of inflammatory effects, and sensitive to most of the antibiotics tested except for clindamycin and trimethoprim, which resistance is usually ascribed to intrinsic nature. B3A-B3B strain was remarkable for its hydrophobicity, auto-aggregation, adhesion to human Caco-2 cells, and survival in simulated gastrointestinal conditions, and cholesterol assimilation fulfilling therefore key beneficial attributes.     

Identification and functional characterization of DzS3GT,a cytoplasmic glycosyltransferase catalyzing biosynthesis of diosgenin 3-<Emphasis Type="Italic">O</Emphasis>-glucoside in <Emphasis Type="Italic">Dioscorea zingiberensis</Emphasis>

Dioscorea plants produce pharmaceutical diosgenin, which usually exists in plants in the form of saponins and has been a starting material for the production of steroids over seven decades. The first step of steroidal saponin biosynthesis from the corresponding aglycone is glycosylation by 3-O-sterol glycosyltransferase (S3GT), transferring the glycosyl from a sugar donor to the 3-OH position of the aglycone. In this study, a DzS3GT gene from Dioscorea zingiberensis was cloned and expressed in Escherichia coli, and the recombinant DzS3GT protein showed 3-O-sterol glycosyltransferase activity in vitro. Subcellular localization analysis revealed that the DzS3GT protein is located in the cytoplasm in rice protoplasts. The tissue profiles of DzS3GT differ from those reported SGT genes. DzS3GT is expressed strongly in leaves and very weakly in stems. The diosgenin 3-O-glucoside (trillin) content is much higher in the leaves than in other organs. The specificity of gene expression and saponins accumulation suggest that the biosynthesis of trillin may occur mainly in the leaves of D. zingiberensis. This is the first report of the cloning and biochemical characterization of a glycosyltransferase gene involved in the biosynthesis of diosgenin 3-O-glucoside in Dioscorea plants. In addition, the study provides a potential relevance to the biosynthesis and transport mechanism of steroidal saponins in Dioscorea plants.