Determination of real-time efflux phenotypes in Escherichia coli AcrB binding pocket phenylalanine mutants using a 1,2'-dinaphthylamine efflux assay

To evaluate the importance of phenylalanine residues for substrate transport in the Escherichia coli efflux pump protein AcrB, we subjected Phe-to-Ala binding pocket mutants to a real-time efflux assay with the novel near-infrared lipophilic membrane probe 1,2'-dinaphthylamine (1,2'-DNA). All mutations, with the exception of F617A, led to considerable retardation of efflux. F610A was the point mutation with the most pronounced impact, followed by F628A, F615A, F136A, and F178A. This is the first study to demonstrate the importance of single phenylalanine residues within the AcrB binding pocket for real-time substrate transport.     

Identification and characterization of parvalbumin-like protein in Trichophyton violaceum

Parvalbumins play crucial physiological roles in neuromuscular systems of vertebrates, such as cell-cycle, development of neurons, contraction of muscles, and regulation of intracellular calcium. To perform these neuromuscular functions, parvalbumin may be in associated with other proteins including calbindin, carbonic anhydrase, and cytochrome oxidase. Humans may show an IgE-specific hypersensitivity to parvalbumins after consumption of some distinct fish species. While this protein is abundant in fish muscles, literature review of publications related to fish parvalbumins, do not point to the presence of parvalbumins in eukaryotic microbes. In this study, we propose that distantly related parvalbumins may be found in some non-fish species. Bioinformatics studies such as multiple sequence alignment (MSA), phylogenetic analysis as well as molecular-based experiments indicate that, at least two parvalbumins sequences (UniProt IDs: A0A178F775 and A0A178F7E4) with EF-hand domains and Ca²⁺-binding sites could be identified in Trichophyton violaceum, a pathogenic fungal species.It was determined that both genes consisted of a single exon and encoded for parvalbumin proteins possessing conserved amino acid motifs. Antigenicity prediction revealed antigenic sites located in both sides of the Ca²⁺-binding site of the first EF-hand domain. Our phylogenetic analysis revealed that one of parvalbumins (UniProt ID: 0A178F775) can be evolved to other parvalbumins in T. violaceum (UniProt ID: A0A178F7E4) and fish species through evolutionary phenomenon. To confirm our in-silico findings, we designed three primer pairs to detect one of the T. violaceum parvalbumins (UniProt ID: A0A178F7E4) by polymerase chain reaction (PCR); one primer pair showed a strong and specific band in agarose gel electrophoresis. To evaluate the specificity of the method, the primers were tested on extracted DNA from Trichophyton rubrum and T. mentagrophytes. The results demonstrated that the evaluated parvalbumin gene (UniProt ID: A0A178F7E4) was T. violaceum-specific and this pathogenic fungus can be differentiated from T. rubrum and T. mentagrophytes through identification of parvalbumin genes. Further studies are necessary to unravel the biochemical and physiological functions of parvalbumins in T. violaceum.     

MiRNA-615-5p Functions as a Tumor Suppressor in Pancreatic Ductal Adenocarcinoma by Targeting AKT2

Background

Aberrant microRNA (miRNA) expression is associated with tumor development. This study aimed to elucidate the role of miR-615-5p in the development of pancreatic ductal adenocarcinoma (PDAC).

Methods

Locked nucleic acid in situ hybridization (LNA-ISH) was performed to compare miR-615-5p expression in patients between PDAC and matched adjacent normal tissues. Effects of miR-615-5p overexpression on cell proliferation, apoptosis, colony formation, migration, and invasion were determined in the pancreatic cancer cell lines PANC-1 and MIA PaCa-2. Effects of miR-615-5p on AKT2 were examined by dual-luciferase reporter assay. Lentivirus expressing miR-615 was used to create stable overexpression cell lines, which were subsequently used in mouse xenograft and metastasis models to assess tumor growth, apoptosis and metastasis.

Results

miR-615-5p expression was significantly lower in PDAC than in adjacent normal tissues. Low levels of miR-615-5p were independently associated with poor prognosis (HR: 2.243, 95% CI: 1.190-4.227, P=0.013). AKT2 protein expression was inversely correlated with miR-615-5p expression (r=-0.3, P=0.003). miR-615-5p directly targeted the 3’-untranslated region of AKT2 mRNA and repressed its expression. miR-615-5p overexpression inhibited pancreatic cancer cell proliferation, migration, and invasion in vitro, and tumor growth and metastasis in vivo. Furthermore, miR-615-5p overexpression also induced pancreatic cancer cell apoptosis both in vitro and in vivo.

Conclusions

These results show that miR-615-5p inhibits pancreatic cancer cell proliferation, migration, and invasion by targeting AKT2. The data implicate miR-615-5p in the prognosis and treatment of PDAC.     

MK615 attenuates Porphyromonas gingivalis lipopolysaccharide-induced pro-inflammatory cytokine release via MAPK inactivation in murine macrophage-like RAW264.7 cells

The Japanese apricot, known as Ume in Japanese, has been a traditional Japanese medicine for centuries, and is a familiar and commonly consumed food. The health benefits of Ume are now being widely recognized and have been strengthened by recent studies showing that MK615, an extract of compounds from Ume, has strong anticancer and anti-inflammatory effects. However, the potential role of MK615 in the periodontal field remains unknown. Here, we found that MK615 significantly reduced the production of pro-inflammatory mediators (tumor necrosis factor-alpha and interleukin-6) induced by Porphyromonas gingivalis lipopolysaccharide (LPS), a major etiological agent in localized chronic periodontitis, in murine macrophage-like RAW264.7 cells. MK615 markedly inhibited the phosphorylation of ERK1/2, p38MAPK, and JNK, which is associated with pro-inflammatory mediator release pathways. Moreover, MK615 completely blocked LPS-triggered NF-κB activation. The present results suggest that MK615 has potential as a therapeutic agent for treating inflammatory diseases such as periodontitis.     

615近交系小鼠血红蛋白遗传学分析

本文对615近交系及C_37BL、昆明种小鼠血红蛋白的表型进行了分析,观察到615小鼠及C_37BL小鼠的血红蛋白的表型均为Ⅰ型,而昆明种表现具有多态性。 615小鼠与C_37BL杂交时F_1不发生血红蛋白表型的分离,而与昆明种的Ⅱ型小鼠杂交时F_1表型发生分离。 615系小鼠网织红细胞体外培育合成血红蛋白肽链的分子同末梢红细胞血红蛋白肽链是一致的。     

Haplotype variation of estrogen receptor-α (ER-α) gene exon 4 in Turkish sheep breeds

Estrogen receptor a (ER??) gene has previously been found related with sexual development and reproduction. In this study, on the basis of the sequences of human, cattle and caprine estrogen receptor ?? (ER??) genes, available in the GenBank database, sets of PCR primers were designed and used to amplify the ovine ER?? gene exon 4 region. We identified six single nucleotide polymorphisms (SNP) in the ER?? exon 4. Some variations determined for exon 4 g.43A > G, p.T43A; g.49C > T, p.L49F; g.178A > T, p.T178S led to changes in the amino acids, but no amino acid changes were determined in g.18G > C, g.27C > T, g.96G > A. These fragments were deposited in the GenBank database under accession numbers: JF262030-JF262035. It was noted in particular that White Karaman and Awassi breeds were similar to each other, whereas the Chios breed had a different variation.     

Association of allelic variation in two NPR1-like genes with Fusarium head blight resistance in wheat

Fusarium head blight (FHB) is a destructive disease of wheat and barley. In wheat it is mainly caused by the fungal pathogens Fusarium graminearum and Fusarium culmorum. We report the identification and evaluation of candidate genes for quantitative FHB resistance. These genes showed altered expression levels in the moderately resistant winter wheat genotypes Capo and SVP72017 after inoculation with F. graminearum. Amongst others, a NPR1-like gene was identified. Sequence analysis of this gene fragment revealed a high level of variation between the parents of a doubled haploid population. Single nucleotide polymorphism and polymerase chain reaction markers were developed and two homoeologous genes were mapped on the long arms of chromosomes 2A and 2D, respectively. Markers for both genes had significant effects on FHB resistance in a diverse collection of 178 European winter wheat cultivars evaluated in multi-environmental field trials after spray inoculation with F. culmorum. These results revealed that allelic variation in two homoeologous NPR1-like genes is associated with FHB resistance in European winter wheat. Markers for these genes might therefore be used for marker-assisted breeding programs.     

Structural Basis of the Divergent Oxygenation Reactions Catalyzed by the Rieske Nonheme Iron Oxygenase Carbazole 1,9a-Dioxygenase

Carbazole 1,9a-dioxygenase (CARDO), a Rieske nonheme iron oxygenase (RO), is a three-component system composed of a terminal oxygenase (Oxy), ferredoxin, and a ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy-encoding gene from Janthinobacterium sp. strain J3 generated the I262V, F275W, Q282N, and Q282Y Oxy derivatives, which showed oxygenation capabilities different from those of the wild-type enzyme. To understand the structural features resulting in the different oxidation reactions, we determined the crystal structures of the derivatives, both free and complexed with substrates. The I262V, F275W, and Q282Y derivatives catalyze the lateral dioxygenation of carbazole with higher yields than the wild type. A previous study determined the crystal structure of Oxy complexed with carbazole and revealed that the carbonyl oxygen of Gly178 hydrogen bonds with the imino nitrogen of carbazole. In these derivatives, the carbazole was rotated approximately 15, 25, and 25°, respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and the imino nitrogen of carbazole. In the crystal structure of the F275W derivative complexed with fluorene, C-9 of fluorene, which corresponds to the imino nitrogen of carbazole, was oriented close to the mutated residue Trp275, which is on the opposite side of the binding pocket from the carbonyl oxygen of Gly178. Our structural analyses demonstrate that the fine-tuning of hydrophobic residues on the surface of the substrate-binding pocket in ROs causes a slight shift in the substrate-binding position that, in turn, favors specific oxygenation reactions toward various substrates.     

Screening of a Fosmid Library of Marine Environmental Genomic DNA Fragments Reveals Four Clones Related to Members of the Order Planctomycetales

A fosmid library with inserts containing approximately 40 kb of marine bacterial DNA (J. L. Stein, T. L. Marsh, K. Y. Wu, H. Shizuya, and E. F. DeLong, J. Bacteriol. 178:591–599, 1996) yielded four clones with 16S rRNA genes from the order Planctomycetales. Three of the clones belong to the Pirellula group and one clone belongs to the Planctomyces group, based on phylogenetic and signature nucleotide analyses of full-length 16S rRNA genes. Sequence analysis of the ends of the genes revealed a consistent mismatch in a widely used bacterium-specific 16S rRNA PCR amplification priming site (27F), which has also been reported in some thermophiles and spirochetes.     

Insecticidal Activity of Bacillus laterosporus

The Bacillus laterosporus strains 921 and 615 were shown to have toxicity for larvae of the mosquitoes Aedes aegypti, Anopheles stephensi, and Culex pipiens. The larvicidal activity of B. laterosporus was associated with spores and crystalline inclusions. Purified B. laterosporus 615 crystals were highly toxic for Aedes aegypti and Anopheles stephensi.     

Structural Changes in the Cytoplasmic Domain of the Mechanosensitive Channel MscS During Opening

The bacterial mechanosensitive channel MscS forms a homoheptamer of subunits composed of a transmembrane (TM) domain and a large cytoplasmic (CP) domain. Recent studies suggest that a lateral expansion of the TM domain, structural change in the CP domain, and TM-CP interactions are essential to open the channel. However, it has not been examined whether the CP domain undergoes structural changes during channel opening. The aim of this study was to estimate structural changes in the CP domain during channel opening using fluorescence resonance energy transfer (FRET) spectroscopy. To monitor changes in the horizontal diameter of the CP domain, four point mutants (A132C, F178C, L246C, and R259C), all of which had channel activity, were created and labeled with Alexa488 and Alexa568 for FRET analysis. The FRET efficiency of these mutants decreased when lysophosphatidylcholine was applied to open the channel, suggesting that the CP domain swells up when the channel opens. The degree of the decease in FRET efficiency after lysophosphatidylcholine treatment was smaller in the D62N/F178C mutant, which was deficient in the TM-CP interactions, than in the F178C mutant. These findings provide the first, to our knowledge, experimental evidence that the CP domain swells up during channel opening, and the swelling is mediated by the TM-CP interactions.     

Use of Transposon-Transposase Complexes To Create Stable Insertion Mutant Strains of Francisella tularensis LVS

Francisella tularensis is a highly virulent zoonotic bacterial pathogen capable of infecting numerous different mammalian species, including humans. Elucidation of the pathogenic mechanisms of F. tularensis has been hampered by a lack of tools to genetically manipulate this organism. Herein we describe the use of transposome complexes to create insertion mutations in the chromosome of the F. tularensis live vaccine strain (LVS). A Tn5-derived transposon encoding kanamycin resistance and lacking a transposase gene was complexed with transposase enzyme and transformed directly into F. tularensis LVS by electroporation. An insertion frequency of 2.6 × 10⁻⁸ ± 0.87 × 10⁻⁸ per cell was consistently achieved using this method. There are 178 described Tn5 consensus target sites distributed throughout the F. tularensis genome. Twenty-two of 26 transposon insertions analyzed were within known or predicted open reading frames, but none of these insertions was associated with the Tn5 target site. Analysis of the insertions of sequentially passed strains indicated that the transposons were maintained stably at the initial insertion site after more than 270 generations. Therefore, transformation by electroporation of Tn5-based transposon-transposase complexes provided an efficient mechanism for generating random, stable chromosomal insertion mutations in F. tularensis.     

Encephalitogenicity of Murine,But Not Bovine,DM20 in SJL Mice Is Due to a Single Amino Acid Difference in the Immunodominant Encephalitogenic Epitope

Myelin proteolipid protein (PLP) contains 2 immunodominant encephalitogenic epitopes in SJL mice, namely PLP residues 139–151 and 178–191. DM20, a minor isoform of PLP, lacks residues 116–150 and consequently contains only the single major encephalitogenic epitope 178–191. However, it has been found previously that bovine DM20 is not encephalitogenic in SJL mice. Since residue 188 within peptide 178–191 is phenylalanine (F) in murine DM20 and alanine (A) in bovine DM20, we tested the effect of this difference on the immune responses and induction of EAE. SJL mice were immunized with either highly purified murine or bovine DM20. Residues 178–191 were found to be immunodominant for each, but only murine and not bovine DM20 was encephalitogenic. A synthetic peptide corresponding to the murine 178–191 sequence (F188) was also encephalitogenic, whereas the peptide corresponding to the bovine sequence (A 188) was not. Both F188 and A188 bind with high affinity to I-A^s and both are recognized by the SJL T cell repertoire. A188-specific T cell lines reacted to both A188 and F188, but F188-specific T cell lines were not stimulated by A188. F188-specific T cell lines produced mRNA for the Thl cytokines IL2 and IFN, and, in passive transfer experiments, were encephalitogenic upon stimulation with F188, but not A188. In contrast, A188-specific T cell lines produced mRNA for IL4, IL5 and IL10, in addition to IL2 and IFN, and were not encephalitogenic after stimulation with either F188 or A188. Cotransfer of A188-specific T cell lines with F188-specific T cell lines resulted in protection from EAE. Thus, A188 induces a functionally different phenotype of T cells from that induced by F188. Taken together these data suggest that the failure of bovine DM20 to induce EAE may be attributable to induction of protective rather than pathogenic T cells by the immunodominant epitope.     

Studies on the Thermal Destruction of Escherichia coli in Milk and Milk Products

Escherichia coli (ATCC no. 9637) was shown to have mean D values (slope of destruction rate curve) of 28.2, 5.1, 1.3, 0.00195, 0.00100, 0.00055, 0.00029, and 0.00016 min in milk at temperatures of 125, 130, 135, 168, 170, 172, 174, and 176 F, respectively. The mean D values for this organism in chocolate milk were 32.2, 10.4, 2.6, 0.00265, 0.00133, 0.00069, 0.00035, and 0.00028 min at respective temperatures of 125, 130, 135, 168, 170, 172, 174, and 176 F. Mean D values of 34.4, 10.0, 3.5, 0.00093, 0.00080, 0.00068, 0.00043, and 0.00036 min were found in cream for respective temperatures of 125, 130, 135, 168, 170, 172, 174, and 176 F. In ice cream mix the organism was found to have mean D values of 39.3, 15.2, 5.1, 0.00147, 0.00120, 0.00078, 0.00070, and 0.00053 min for temperatures of 125, 130, 135, 170, 172, 174, 176, and 178 F, respectively. The slopes of the thermal death time curves were found to be 10.2, 10.2, 10.0, and 10.3 F for this organism in milk, chocolate milk, 40% fat cream, and ice cream mix, respectively.     

Detection of two CSN1S1 variants in Egyptian buffalo

The present study investigates CSN1S1 casein gene polymorphism in Egyptian buffalo. CSN1S1 was analyzed in 17 unrelated Egyptian lactating buffalo. The amplified segment includes the last 43 amino acids of Exon 17 and part of Intron 17. In the present study we report for the first time the presence of 2 variants 178^Ser (TCA) and 178^Leu (TTA) in Egyptian buffalo CSN1S1 gene. The genotypic frequencies in the investigated Egyptian buffalo sample were 0.47, 0.058 and 0.47 for homozygous 178^Ser, for homozygous 178^Leu and heterozygous 178^Leu/Ser, respectively. The 178^Ser and 178^Leu variant frequencies are 0.64 and 0.36, respectively which indicates the superiority of variant 178^Ser in Egyptian buffalo. The allelic frequency in Egyptian buffalo is not much different from the corresponding allelic frequency in Italian buffalo (0.69 and 0.31 for 178^Ser and 178^Leu, respectively) as reported by Chianese et al. [3]. This is not surprising since they both belong to Mediterranean type.     

Root-favoured biomass allocation improves growth and yield of field-grown rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) plants only when the shoot sink is expandable

We tested the hypothesis that high root/shoot (R/S) in rice improves plant growth and yield when the shoot sink is expandable, and that in a genotype with exaggerated R/S ratio, the shoot growth is not limited by root resources. This study involved the three rice genotypes, Giza 178, PM12, and Moroberekan with a range of R/S ratios and shoot sink sizes. Root regrowth after trimming or high- and low-nitrogen treatments revealed that Moroberekan has consistently high root-favoured biomass partitioning than Giza 178 or PM12. Increasing the R/S ratios by detillering improved the culm growth in Giza 178 and PM12 (by 43.4 and 17.7% of control, respectively) but not Moroberekan, indicating that PM12 was closer to achieving its growth potential than Giza 178 but Moroberekan was operating at maximal shoot growth potential because of high R/S ratio and small sink size. Under drought, shoot growth, gas exchange, and grain yield correlated strongly with R/S ratio and root length density (RLD) in the droughted but not the well-watered plants. We further hypothesized that R/S ratio of Moroberekan was in excess of shoot requirement for optimum growth. Crossing Moroberekan to PM12 generated three F1 hybrids with intermediate R/S ratios but higher growth, gas exchange, and yield than either parent. We conclude that increasing the R/S ratio improved growth and yield in PM12 but not Moroberekan, because the shoot sink size was expandable in PM12. Moreover, lower R/S ratios than that of Moroberekan could support higher shoot growth if shoot sink is expandable.     

Comparative Studies of Delignification Caused by Ganoderma Species

Isolates of six species of Ganoderma in the G. lucidum complex were evaluated for their ability to decay wood of Quercus hypoleucoides A. Camus and Abies concolor (Gord. and Glend.) Lindl. ex. Hildebr. by using in vitro agar block decay tests. Morphological, ultrastructural, and chemical studies of decayed wood were used to determine the extent of delignification or simultaneous decay caused by each species of Ganoderma. All species decayed both white fir and oak wood; however, less percent weight loss (%WL) occurred in white fir than oak. In white fir, isolates of two undescribed Ganoderma species (RLG16161, RLG16162, JEA615, and JEA625) caused significantly higher%WL (21 to 26%) than that in G. colossum, G. oregonense, G. meredithiae, and G. zonatum (10 to 16%). Only Ganoderma sp. isolates JEA615 and JEA625 caused delignification, with JEA615 causing a lignin-to-glucose gram loss ratio of 1.6:1. Morphological and ultrastructural studies confirmed delignification by this fungus and showed that some delignification had occurred by all of the species, although areas of delignification were limited to small regions adjacent to simultaneously decayed cells. In oak, G. colossum caused significantly less%WL (22 to 35%) than the other species (38 to 52%). All of the species, except G. meredithiae, caused delignification with lignin-to-glucose gram loss ratios ranging from 1.4 to 4.9:1. Extensive delignification by isolates of G. colossum and G. oregonense was observed; moderate delignification was caused by the other species. Ganoderma meredithiae caused a simultaneous decay, with only small localized regions of cells delignified, while delignification by G. zonatum was irregular, with specific zones within the cell wall delignified. The thermophilic and chlamydosporic G. colossum has the capacity to cause extensive delignification and appears ideally suited for use in lignin degradation studies and biotechnological applications of lignin-degrading fungi.     

The gaf fimbrial gene cluster of Escherichia coli expresses a full-size and a truncated soluble adhesin protein

The GafD lectin of the G (F17) fimbriae of diarrhea-associated Escherichia coli was overexpressed and purified from the periplasm of E. coli by affinity chromatography on GlcNAc-agarose. The predicted mature GafD peptide comprises 321 amino acids, but the predominant form of GafD recovered from the periplasm was 19,092 Da in size and corresponded to the 178 N-terminal amino acid residues, as judged by mass spectrometry and amino acid sequencing, and was named ΔGafD. Expression of gafD from the cloned gaf gene cluster in DegP-, Lon-, and OmpT-deficient recombinant strains did not significantly decrease the formation of ΔGafD. The peptide was also detected in the periplasm of the wild-type E. coli strain from which the gaf gene cluster originally was cloned. We expressed gafD fragments encoding C-terminally truncated peptides. Peptides GafD1-252, GafD1-224, GafD1-189, and the GafD1-178, isolated from the periplasm by affinity chromatography, had apparent sizes closely similar to that of ΔGafD. Only trace amounts of truncated forms with expected molecular sizes were detected in spheroplasts. In contrast, the shorter GafD1-157 peptide was detected in spheroplasts but not in the periplasm, indicating that it was poorly translocated or was degraded by periplasmic proteases. Pulse-chase assays using gafD indicated that ΔGafD was processed from GafD and is not a primary translation product. The ΔGafD peptide was soluble by biochemical criteria and exhibited specific binding to GlcNAc-agarose. Inhibition assays with mono- and oligosaccharides gave a similar inhibition pattern in the hemagglutination by the G-fimbria-expressing recombinant E. coli strain and in the binding of [¹⁴C]ΔGafD to GlcNAc-agarose. ΔGafD bound specifically to laminin, a previously described tissue target for the G fimbria. Our results show that a soluble, protease-resistant subdomain of GafD exhibits receptor-binding specificity similar to that for intact G fimbriae and that it is formed when gafD is expressed alone or from the gaf gene cluster.