Isolation of genomic DNAs from plants, fungi and bacteria using benzyl chloride

An in planta biolistic method for stable wheat transformation

The currently favoured method for wheat (Triticum aestivum L.) transformation is inapplicable to many elite cultivars because it requires callus culture and regeneration. Here, we developed a simple, reproducible, in planta wheat transformation method using biolistic DNA delivery without callus culture or regeneration. Shoot apical meristems (SAMs) grown from dry imbibed seeds were exposed under a microscope and subjected to bombardment with different-sized gold particles coated with the GFP gene construct, introducing DNA into the L2 cell layer. Bombarded embryos were grown to mature, stably transformed T₀ plants and integration of the GFP gene into the genome was determined at the fifth leaf. Use of 0.6-µm particles and 1350-psi pressure resulted in dramatically increased maximum ratios of transient GFP expression in SAMs and transgene integration in the fifth leaf. The transgene was integrated into the germ cells of 62% of transformants, and was therefore inherited in the next generation. We successfully transformed the model wheat cultivar ‘Fielder’, as well as the recalcitrant Japanese elite cultivar ‘Haruyokoi’. Our method could potentially be used to generate stable transgenic lines for a wide range of commercial wheat cultivars.

Drug Sensitivity and Resistance Mechanism in Aspergillus Section Nigri Strains from Japan

Aspergillus niger and its related species, known as Aspergillus section Nigri, are ubiquitously distributed across the globe and are often isolated from clinical specimens. In Japan, Aspergillus section Nigri is second most often isolated from clinical specimens following Aspergillus fumigatus We determined the species of Aspergillus section Nigri isolated in Japan by DNA sequencing of partial β-tubulin genes and investigated drug susceptibility by the CLSI M38-A2 method. The collection contained 20 Aspergillus niger, 59 Aspergillus welwitschiae, and 39 Aspergillus tubingensis strains. Drug susceptibility testing revealed 30 to 55% of A. niger, 6.8 to 18.6% of A. welwitschiae, and 79.5 to 89.7% of A. tubingensis isolates to be less susceptible (so-called resistant) to itraconazole (ITC) and/or voriconazole (VRC) according to the epidemiologic cutoff values (ECVs) proposed for A. niger previously. MIC distributions of ITC or VRC showed no remarkable differences between clinical and environmental isolates. When the cyp51A sequences were compared between susceptible and resistant strains, 18 amino acid mutations were specific for resistant isolates of A. niger and A. tubingensis; however, none of them were confirmed to be associated with azole resistance. Three nonrelated A. welwitschiae isolates possessed a partial deletion in cyp51A, likely attributable to being more susceptible to azoles than other isolates. One of five ITC-resistant A. tubingensis isolates showed higher expression of cyp51A than did susceptible strains. Our results show that cyp51A point mutations may have no association with azole resistance but that in some cases the overexpression of cyp51A may lead to the azole resistance in these species.

Efficacy of free and encapsulated Bacillus lichenformis strain SL10 on degradation of phenol: A comparative study of degradation kinetics

The present study exemplifies phenol degradation efficacy of the free and encapsulated bacterial isolate, explored the degradation kinetics and storage stability in detail. In brief, isolation, identification and phenol degradation potential of the bacterial made from wastewater treated sludge samples. The organism identified as B. licheniformis demonstrates phenol degradation at a concentration more than 1500 ppm. Optimization of environmental parameters reduces the time taken for degradation considerably. The organism has further been encapsulated using whey protein and the efficacy of encapsulated species suggested that encapsulation protects the cells from high concentration of phenol and at the same time expedite the degradation of the chosen pollutant at appreciable level. The encapsulated species effectively degrade 3000 ppm concentration of phenol within 96 h of incubation. Both pH and temperature stability observed in the encapsulated species suggests the effectiveness of the encapsulation. The encapsulated cells displayed storage stability for a four week period at 4 C and reusability up to three exposures. Degradation effected through intracellular catechol 2,3 dioxygenase. In conclusion, encapsulation of B. licheniformis (i) protects the cells from direct exposure to toxic pollutants; (ii) facilitates the field scale application and (iii) eliminate the practical difficulties in handling wet biomass in field application and assures the best possible way of remediating the phenol contaminated soil.

Studies in Phylogeny, Development of Rapid IdentificationMethods, Antifungal Susceptibility, and Growth Rates of Clinical Strains of Sporothrix schenckii Complex in Japan

Sporotrichosis is a fungal infection caused by the Sporothrix species, which have distinct virulence profiles and geographic distributions. We performed a phylogenetic study in strains morphologically identified as Sporothrix schenckii from clinical specimens in Japan, which were preserved at the Medical Mycology Research Center, Chiba University. In addition, we examined the in vitro antifungal susceptibility and growth rate to evaluate their physiological features. Three hundred strains were examined using sequence analysis of the partial calmodulin gene, or polymerase chain reaction（PCR）method using newly designed species-specific primers; 291 strains were Sporothrix globosa and 9 strains were S. schenckii sensu stricto (in narrow sense, s. s.). S. globosa strains were further clustered into two subclades, and S. schenckii s. s. strains were divided into three subclades. In 38 strains of S. globosa for which antifungal profiles were determined, 4 strains (11%) showed high minimal inhibitory concentration (MIC) value for itraconazole. All tested strains of S. schenckii s. s. and S. globosa showed low sensitivity for amphotericin B. These antifungals are used for treatment of sporotrichosis when infection is severe. S. schenckii s. s. grew better than S. globosa; wherein S. globosa showed restricted growth at 35℃ and did not grow at 37℃. Our molecular data showed that S. globosa is the main causal agent of sporotrichosis in Japan. It is important to determine the antifungal profiles of each case, in addition to accurate species-level identification, to strategize the therapy for sporotrichosis.

In vitro Evaluation of the Colistin-Carbapenem Combination in Clinical Isolates of A. baumannii Using the Checkerboard, Etest, and Time-Kill Curve Techniques

The worldwide increase in the emergence of carbapenem resistant Acinetobacter baumannii (CRAB) calls for the investigation into alternative approaches for treatment. This study aims to evaluate colistin-carbapenem combinations against Acinetobacter spp., in order to potentially reduce the need for high concentrations of antibiotics in therapy. This study was conducted on 100 non-duplicate Acinetobacter isolates that were collected from different patients admitted at Saint George Hospital-University Medical Center in Beirut. The isolates were identified using API 20NE strips, which contain the necessary agents to cover a panel of biochemical tests, and confirmed by PCR amplification of bla_{OXA−51−like}. Activities of colistin, meropenem and imipenem against Acinetobacter isolates were determined by ETEST and microdilution methods, and interpreted according to the guidelines of the Clinical and Laboratory Standards Institute. In addition, PCR amplifications of the most common beta lactamases contributing to carbapenem resistance were performed. Tri locus PCR–typing was also performed to determine the international clonality of the isolates. Checkerboard, ETEST and time kill curves were then performed to determine the effect of the colistin-carbapenem combinations. The synergistic potential of the combination was then determined by calculating the Fractional Inhibitory Concentration Index (FICI), which is an index that indicates additivity, synergism, or antagonism between the antimicrobial agents. In this study, 84% of the isolates were resistant to meropenem, 78% to imipenem, and only one strain was resistant to colistin. 79% of the isolates harbored bla_{OXA−23−like} and pertained to the International Clone II. An additive effect for the colistin-carbapenem combination was observed using all three methods. The combination of colistin-meropenem showed better effects as compared to colistin-imipenem (p < 0.05). The colistin-meropenem and colistin-imipenem combinations also showed a decrease of 2.6 and 2.8-fold, respectively in the MIC of colistin (p < 0.001). Time kill assays additionally showed synergistic effects for a few isolates, and no bacterial re-growth was detected following a 24 h incubation. Our study showed that the combination of colistin with carbapenems could be a promising antimicrobial strategy in treating CRAB infections and potentially lowering colistin toxicity related to higher doses used in colistin monotherapy.

Evaluation of different PCR primers for denaturing gradient gel electrophoresis (DGGE) analysis of fungal community structure in traditional fermentation starters used for Hong Qu glutinous rice wine

Denaturing gradient gel electrophoresis (DGGE) has become a widely used tool to examine microbial community structure. However, when DGGE is applied to evaluate the fungal community of traditional fermentation starters, the choice of hypervariable ribosomal RNA gene regions is still controversial. In the current study, several previously published fungal PCR primer sets were compared and evaluated using PCR-DGGE, with the purpose of screening a suitable primer set to study the fungal community of traditional fermentation starters for Hong Qu glutinous rice wine. Firstly, different primer sets were used to amplify different hypervariable regions from pure fungal cultures. Except NS1/FR1+ and ITS1fGC/ITS4, other primer sets (NL1+/LS2R, NL3A/NL4GC, FF390/FR1+, NS1/GCFung, NS3+/YM951r and ITS1fGC/ITS2r) amplified the target DNA sequences successfully. Secondly, the selected primer sets were further evaluated based on their resolution to distinguish different fungal cultures through DGGE fingerprints. Three primer sets (NL1+/LS2R, NS1/GCFung and ITS1fGC/ITS2r) were finally selected for investigating the fungal community structure of different traditional fermentation starters for Hong Qu glutinous rice wine. The internal transcribed spacer (ITS) region amplified by ITS1fGC/ITS2r, which is more hypervariable than the 18S rRNA gene and 26S rRNA gene, provides an excellent tool to separate amplification products of different fungal species. Results indicated that PCR-DGGE profile using ITS1fGC/ITS2r showed more abundant fungal species than that using NL1+/LS2R and NS1/GCFung. Therefore, ITS1fGC/ITS2r is the most suitable primer set for PCR-DGGE analysis of fungal community structure in traditional fermentation starters for Hong Qu glutinous rice wine. DGGE profiles based on ITS1fGC/ITS2r revealed the presence of twenty-four fungal species in traditional fermentation starter. A significant difference of fungal community can be observed directly from DGGE fingerprints and principal component analysis. The statistical analysis results based on the band intensities of fungal DGGE profile showed that Saccharomyces cerevisiae, Saccharomycopsis fibuligera, Rhizopus oryzae, Monascus purpureus and Aspergillus niger were the dominant fungal species. In conclusion, the comparison of several primer sets for fungal PCR-DGGE would be useful to enrich our knowledge of the fungal community structures associated with traditional fermentation starters, which may facilitate the development of better starter cultures for manufacturing Chinese Hong Qu glutinous rice wine.

Fungal ITS1 Deep-Sequencing Strategies to Reconstruct the Composition of a 26-Species Community and Evaluation of the Gut Mycobiota of Healthy Japanese Individuals

The study of mycobiota remains relatively unexplored due to the lack of sufficient available reference strains and databases compared to those of bacterial microbiome studies. Deep sequencing of Internal Transcribed Spacer (ITS) regions is the de facto standard for fungal diversity analysis. However, results are often biased because of the wide variety of sequence lengths in the ITS regions and the complexity of high-throughput sequencing (HTS) technologies. In this study, a curated ITS database, ntF-ITS1, was constructed. This database can be utilized for the taxonomic assignment of fungal community members. We evaluated the efficacy of strategies for mycobiome analysis by using this database and characterizing a mock fungal community consisting of 26 species representing 15 genera using ITS1 sequencing with three HTS platforms: Illumina MiSeq (MiSeq), Ion Torrent Personal Genome Machine (IonPGM), and Pacific Biosciences (PacBio). Our evaluation demonstrated that PacBio's circular consensus sequencing with greater than 8 full-passes most accurately reconstructed the composition of the mock community. Using this strategy for deep-sequencing analysis of the gut mycobiota in healthy Japanese individuals revealed two major mycobiota types: a single-species type composed of Candida albicans or Saccharomyces cerevisiae and a multi-species type. In this study, we proposed the best possible processing strategies for the three sequencing platforms, of which, the PacBio platform allowed for the most accurate estimation of the fungal community. The database and methodology described here provide critical tools for the emerging field of mycobiome studies.

Transglucosidase improves the bowel movements in type 2 diabetes mellitus patients: A preliminary randomized double-blind, placebo-controlled study

BACKGROUND

Recent studies have highlighted the relationship between gut microbiota and bowel movements.

OBJECTIVE

We aimed to evaluate transglucosidase treatment efficacy for bowel movements in patients with type 2 diabetes mellitus and to clarify the relationship between bowel movements, dietary habits, gut microbiota and fecal short-chain fatty acids.

METHODS

In this randomized double-blind, placebo-controlled study, 66 patients received placebo or transglucosidase (300 or 900 mg/day) orally, for 12 weeks. Fecal bacterial communities and short-chain fatty acids were analyzed before and after the treatment.

RESULTS

Transglucosidase treatment significantly (p < 0.05) affected fecal microbiota (Prevotella spp., Bacteroides spp., Bifidobacterium spp., and Clostridium subcluster XIVa) and fecal short-chain fatty acid (acetate, valerate, succinate and lactate) content. Clostridium cluster IV, Clostridium subcluster XIVa, Clostridium cluster XVIII and fecal pH increased significantly and order Lactobacillales decreased in patients with bowel movement disorder compared with controls. Transglucosidase treatment significantly improved bowel movements compared with placebo treatment (46.2%, 95% confidence interval: 19.2-74.9% vs. 0%, 95% confidence interval: 0-33.6%, p < 0.05). This effect was not observed in patients without bowel movement disorder.

CONCLUSION

Patients with bowel movement disorder suffer from gut dysbiosis. Transglucosidase treatment alleviates bowel movement disorder symptoms in type 2 diabetes mellitus patients by increasing fecal acetate level.

The intestinal microbiota and its role in human health and disease

The role of the intestinal microbiota in human health is gaining more attention since clear changes in the composition of the intestinal bacteria or environment are seen in patients with inflammatory bowel disease, allergy, autoimmune disease, and some lifestyle-related illnesses. A healthy gut environment is regulated by the exquisite balance of intestinal microbiota, metabolites, and the host's immune system. Imbalance of these factors in genetically susceptible persons may promote a disease state. Manipulation of the intestinal microbiota with prebiotics, which can selectively stimulate growth of beneficial bacteria, might help to maintain a healthy intestinal environment or improve diseased one. In this review, analytical methods for identification of intestinal bacteria and an update on the correlation of the intestinal microbiota with human health and disease were discussed by introducing our recent studies to determine the prebiotic effects of a fiber-rich food in animal model and on healthy people and patients with ulcerative colitis (UC).

eQTLs Regulating Transcript Variations Associated with Rapid Internode Elongation in Deepwater Rice

To avoid low oxygen, oxygen deficiency or oxygen deprivation, deepwater rice cultivated in flood planes can develop elongated internodes in response to submergence. Knowledge of the gene regulatory networks underlying rapid internode elongation is important for an understanding of the evolution and adaptation of major crops in response to flooding. To elucidate the genetic and molecular basis controlling their deepwater response we used microarrays and performed expression quantitative trait loci (eQTL) and phenotypic QTL (phQTL) analyses of internode samples of 85 recombinant inbred line (RIL) populations of non-deepwater (Taichung 65)- and deepwater rice (Bhadua). After evaluating the phenotypic response of the RILs exposed to submergence, confirming the genotypes of the populations, and generating 188 genetic markers, we identified 10,047 significant eQTLs comprised of 2,902 cis-eQTLs and 7,145 trans-eQTLs and three significant eQTL hotspots on chromosomes 1, 4, and 12 that affect the expression of many genes. The hotspots on chromosomes 1 and 4 located at different position from phQTLs detected in this study and other previous studies. We then regarded the eQTL hotspots as key regulatory points to infer causal regulatory networks of deepwater response including rapid internode elongation. Our results suggest that the downstream regulation of the eQTL hotspots on chromosomes 1 and 4 is independent, and that the target genes are partially regulated by SNORKEL1 and SNORKEL2 genes (SK1/2), key ethylene response factors. Subsequent bioinformatic analyses, including gene ontology-based annotation and functional enrichment analysis and promoter enrichment analysis, contribute to enhance our understanding of SK1/2-dependent and independent pathways. One remarkable observation is that the functional categories related to photosynthesis and light signaling are significantly over-represented in the candidate target genes of SK1/2. The combined results of these investigations together with genetical genomics approaches using structured populations with a deepwater response are also discussed in the context of current molecular models concerning the rapid internode elongation in deepwater rice. This study provides new insights into the underlying genetic architecture of gene expression regulating the response to flooding in deepwater rice and will be an important community resource for analyses on the genetic basis of deepwater responses.

Comparative Study of Bacterial Communities in Nepenthes Pitchers and Their Correlation to Species and Fluid Acidity

Pitchers are specialized digestive organs of carnivorous plants which evolved for trapping prey and represent a unique environment harboring hidden diversity of unexplored microbes forming transient hydrolytic microcosms. In this study, the diversity of bacterial communities in the pitcher fluids of seven local Nepenthes found in Thailand was assessed by tagged 16S ribosomal RNA (rRNA) gene amplicon sequencing on an Ion PGM™ platform. A total of 1,101,000 filtered sequences were obtained which were taxonomically classified into 20 phyla, 48 classes, 72 orders, 153 families, and 442 genera while the remainder (1.43 %) could not be assigned to any existing taxa. Proteobacteria represented the predominant members in closed pitchers and more diversified bacterial taxa particularly Bacteriodetes and Actinobacteria, showed increasing abundance in open pitchers containing insect bodies. Principal coordinate analysis revealed that distribution of bacterial taxa was not significantly related to the Nepenthes species but strongly correlated to the pH of the pitcher fluids (pH 1.7-6.7). Acidicella was a highly dominant bacterial genus in acidic pitcher fluids while Dyella and Mycobacterium were also common genera in most pitchers. A unique microbial community structure was found in Nepenthes ampullaria which could reflect their adaptation to digest leaf litter, in addition to insect prey. The work revealed the highly unexplored nature of bacterial microcosms in Nepenthes pitcher fluids and provides insights into their community structure in this unique ecological system.

Impact of Probiotic SYNBIO(®) Administered by Vaginal Suppositories in Promoting Vaginal Health of Apparently Healthy Women

The purpose of this study was to investigate whether vaginal administration of probiotic Lactobacillus results in their colonization and persistence in the vagina and whether it promotes normalization and maintenance of pH and Nugent score. A single-arm, open-label controlled towards the baseline (pre-post) study including 35 apparently healthy women was conducted. Each woman was examined three times during the study. Women were instructed to receive daily for 7 days, the probiotic suppositories SYNBIO(®) gin (Lactobacillus rhamnosus IMC 501(®) and Lactobacillus paracasei IMC 502(®)). Vaginal swabs were collected during visit 1, 2, and 3 to determine the total lactobacilli count, the presence of the two administered bacteria, the measure of the pH, and the estimation of Nugent score. Evaluation of treatment tolerability was based on analysis of the type and occurrence of adverse events. The probiotic vaginal suppository was well tolerated and no side effects were reported. Intermediate Nugent score was registered in 40 % of women at visit 1 and these intermediate scores reverted to normal at day 7 (end of treatment) in 20 % of subjects. Administration of SYNBIO(®) gin contributed to a significant increase in the lactobacilli level at visit 2. Molecular typing revealed the presence of the two strains originating from SYNBIO(®) gin in 100 % of women at visit 2 and 34 % at visit 3. No significant changes were registered for pH between visits. The SYNBIO(®) gin product is safe for daily use in healthy women and it could be useful to restore and maintain a normal vaginal microbiota.

Multilocus sequence typing of bifidobacterial strains from infant’s faeces and human milk: are bifidobacteria being sustainably shared during breastfeeding?

Bifidobacteria are considered to be one of the most important beneficial intestinal bacteria for infants, contributing to the priming of the mucosal immune system. These microbes can also be detected in mother’s milk, suggesting a potential role of human milk in the colonisation of infant’s gut. However, little is known about the timing of bacteria appearance in human milk, and whether human milk is the first source of inoculation. Here, we investigated whether specific strains are shared sustainably between maternal milk and infant’s gut. Faecal samples and human milk were collected from 102 healthy mother-infant pairs (infant’s faeces: meconium, 7, 30 days of age; mother’s milk: once before delivery, colostrum, 7, 30 days after delivery). Bifidobacterial strains were isolated from these samples, and were discriminated by means of multilocus sequencing typing. No bifidobacteria were detected from human milk collected before delivery, or colostrum. Strains were isolated only from human milk samples obtained 7 days after birth or later. On the other hand, bifidobacterial strains were obtained from infant’s faeces throughout the study period, sometimes as early as the first day of life (meconium). We have found that bifidobacterial species belonging to Bifidobacterium bifidum, Bifidobacterium breve, and Bifidobacterium longum subsp. longum could be identified as monophyletic between infant’s faeces and their mother’s milk. These strains were confirmed to be sustainably shared between maternal milk and infant’s gut. Moreover, monophyletic strains were isolated at the same time point or earlier from infant’s faeces than from human milk, and none were isolated earlier from human milk than from infant’s faeces. Although it remains unclear whether human milk is the first source of microbes for infants, our results confirm that human milk is a reservoir of bifidobacteria, and specific strains are shared between infant’s intestine and human milk during breastfeeding.

Molecular characterisation of clinical Cryptococcus neoformans and Cryptococcus gattii isolates from Sichuan province, China

Previous reports on the molecular characteristics of clinical isolates of Cryptococcus species in China have focused on isolates from southeast China. To obtain a more detailed molecular epidemiology, a total of 92 cryptococcal isolates were collected from Sichuan province. A total of 24 isolates from 12 other provinces were collected for comparative study. Genotypes and mating types of 116 Cryptococcus isolates were determined. Among the 116 isolates, 43 isolates (19 isolates from Sichuan and 24 isolates outside of Sichuan) were analysed by multi-locus sequence typing (MLST). All 116 clinical isolates were mating type α. Most isolates (114/116) were molecular type VNI and the remaining two isolates were VGI and VGII respectively. MLST results revealed five sequence types (STs) of C. neoformans including two novel STs, with most isolates identified as ST5. The two C. gattii isolates identified in our study were ST44 and ST159. Based on our report and previous studies, there are 15 C. neoformans STs in China which can be divided into three subgroups. The C. gattii isolate from Sichuan could be a scattered subtype of VGII (ST44). Our findings demonstrated that C. neoformans isolates in Sichuan are genetically homogeneous, and ST5 is the epidemic clone of C. neoformans in China.

Analysis of microbial community adaptation in mesophilic hydrogen fermentation from food waste by tagged 16S rRNA gene pyrosequencing

Dark fermentation is an attractive process for generation of biohydrogen, which involves complex microbial processes on decomposition of organic wastes and subsequent conversion of metabolic intermediates to hydrogen. The microbes present in an upflow anaerobic sludge blanket (UASB) reactor for waste water treatment were tested for application in batch dark fermentation of food waste at varying ratios of feedstock to heat-treated microbial inoculum (F/M) of 1-8 (g TVS/g TVS). Biohydrogen yields between 0.39 and 2.68 mol H2/mol hexose were obtained, indicating that the yields were highly dependent on the starting F/M ratio. The highest H2 purity of 66% was obtained from the first 8 h of fermentation at the F/M ratio of 2, whereas the highest H2 production was obtained after 35 h of fermentation at the F/M ratio of 5. Tagged 16S rRNA gene pyrosequencing showed that the seed culture comprised largely of uncultured bacteria with various Proteobacteria, Bacteroidetes, and Firmicutes, while the starting food waste contained mainly lactic acid bacteria. Enrichment of Firmicutes, particularly Clostridia and lactic acid bacteria occurred within 8 h of the dark fermentation and the H2 producing microcosm at 35 h was dominated >80% by Clostridium spp. The major H2 producer was identified as a Clostridial strain related to Clostridium frigidicarnis. This work demonstrated the adaption of the microbial community during the dark fermentation of complex food waste and revealed the major roles of Clostridia in both substrate degradation and biohydrogen production.

QTL analysis of internode elongation in response to gibberellin in deepwater rice

Gibberellin (GA) is a plant hormone that has important roles in numerous plant developmental phases. Rice plants known as deepwater rice respond to flooding by elongating their internodes to avoid anoxia. Previous studies reported that GA is essential for internode elongation in deepwater rice. Quantitative trait locus (QTL) analyses identified QTLs regulating internode elongation in response to deepwater conditions. However, the interaction between internode elongation and regulators of GA sensitivity in deepwater rice is unknown. In this study, we applied GA to recombinant inbred lines of T65 (non-deepwater rice) and Bhadua (deepwater rice), and performed a QTL analysis of internode elongation in response to GA. GA-induced internode elongation was detected only in deepwater rice. Our QTL analysis revealed two major QTLs on chromosomes 3 and 9 regulating total internode length, lowest elongated internode and number of elongated internodes. Furthermore, the QTL on chromosome 3 acted as an enhancer of other QTLs (e.g. the QTL on chromosome 12). Nearly isogenic lines of deepwater rice carrying the QTL regions from chromosomes 3 and 12 of the deepwater rice C9285 showed internode elongation in response to GA. Thus, these QTLs may regulate GA responsiveness in deepwater rice. This study furthers our understanding of the mechanism of internode elongation in rice.

Evaluation of Bacillus sp. MZS10 for decolorizing Azure B dye and its decolorization mechanism

To evaluate decolorization and detoxification of Azure B dye by a newly isolated Bacillus sp. MZS10 strain, the cultivation medium and decolorization mechanism of the isolate were investigated. The decolorization was discovered to be dependent on cell density of the isolate and reached 93.55% (0.04 g/L) after 14 hr of cultivation in a 5 L stirred-tank fermenter at 2.0 g/L yeast extract and 6.0 g/L soluble starch and a small amount of mineral salts. The decolorization metabolites were identified with ultra performance liquid chromatography-tandem mass spectroscopy (UPLC-MS). A mechanism for decolorization of Azure B was proposed as follows: the C=N in Azure B was initially reduced to -NH by nicotinamide adenine dinucleotide phosphate (NADPH)-dependent quinone dehydrogenase, and then the -NH further combined with -OH derived from glucose to form a stable and colorless compound through a dehydration reaction. The phytotoxicity was evaluated for both Azure B and its related derivatives produced by Bacillus sp. MZS10 decolorization, indicating that the decolorization metabolites were less toxic than original dye. The decolorization efficiency and mechanism shown by Bacillus sp. MZS10 provided insight on its potential application for the bioremediation of the dye Azure B.

Influence of cell disruption and elution on cellulase release of Clostridium straminisolvens (CSK1)

Clostridium straminisolvens (CSK1) is a novel cellulolytic bacterium isolated from a cellulose-degrading bacterial community MC1. In this study, the influence of the following cell disruption and elution methods on CSK1cellulase release was investigated: (1) freezing-thawing, (2) ultrasonication, (3) elution, (4) freezing-thawing following elution, (5) ultrasonication following elution, and lastly (6) high-pressure homogenization following elution. The activity of the cellulases CMCase, β-glucosidase, Avicelase, FPase, and xylanase in crude extracts increased 81.5, 23.8, 87.7, 46.3, and 51.7 %, respectively, with an observed optimal treatment method for each cellulase type. The release of protein from CSK1 cells increased following either cell disruption or elution and was highest at 88.3 % in the homogenization high pressure following elution treatment. A newly observed protein was present following cell elution. The performance of cell elution as determined by real time-PCR indicated that the first time cell elution removed more than 90 % of the CSK1 cells from the substrate. These findings demonstrate that cell disruption and elution are effective methods for inducing cellulase release, and elution is the key step for CSK1. To our knowledge, this study presents the first evidence of optimal treatments for induction of cellulase release of Clostridium straminisolvens. This information will be of great value for use in subsequent efforts to better understand the cellulase characteristics of CSK1 and cellulose degradation mechanisms of the MC1 community.

Molecular characterization, expression pattern, and ligand-binding property of three odorant binding protein genes from Dendrolimus tabulaeformis

Odorant binding proteins (OBPs) play important roles in insect olfactory processes. The Chinese pine caterpillar moth, Dendrolimus tabulaeformis (Lepidoptera, Lasiocampidae) is a serious economic pest in China, and the pheromones of this species have been identified to monitor their presence. However, the molecular mechanisms by which D. tabulaeformis perceive pheromones and host volatiles remain unknown. In this study, we identified and characterized three new OBPs, including one pheromone binding protein (PBP1) and two general odor binding proteins (GOBPs), from antennal cDNA of D. tabulaeformis. The deduced amino acid sequences of DtabPBP1, DtabGOBP1, and DtabGOBP2 revealed mature proteins of 140, 147, and 140 amino acids, respectively. Each has six cysteine residues in conserved positions relative to other known OBPs. Amino-acid alignments indicated that the two GOBPs are more conserved (DtabGOBP1 is 52.9–67.4 % identical to orthologs from other Lepidoptera, and DtabGOBP2 is 55.2–81.8 % identical) than the PBP (32.5–46.0 %). Real-time PCR indicated tissue- and sex-specific expression patterns of the three genes. DtabPBP1 was mainly expressed in the antennae of males, whereas female antennae had only 1.09 % the expression in male antennae. Both DtabGOBP1 and DtabGOBP2 were more highly expressed in antennae than in other tissues, while DtabGOBP1 was more abundant in male antennae and DtabGOBP2 in female antennae. In addition, the binding specificities of the three proteins were investigated, and all three OBPs exhibited high binding affinities for the pheromone component (5Z,7E)-5,7-dodecadien-1-yl propionate (Z5,E7-12:OPr). This suggests a role in binding pheromone for GOBPs, as well as PBP1, in D. tabulaeformis.

Antimicrobial action of an endophytic fungi from Sophor flavescens and structure identification of its active constituent

Endophytic fungus BS002 was isolated and characterized from Sophora flavescens by plate method, which has broad antimicrobial activity. Isolation and trace of a new bioactive compound from the fungus' culture extracts with the method of column chromatography and TLC biological autoradiography was conducted. Finally, it was identified as 6,7-(2'E) dibutenyl-5,8-dihydroxy-(Z)-cyclooct-2-ene-1,4-dione by nuclear magnetic resonance, infrared and liquid chromatography-mass spectrometry. The compound presented strong antifungal activities for example: Botryosphaeria berengriana f.sp. piricola, Physalospora piricola, Cladosporium cucumerinum Ell. Arthur., Fusarium oxysporum f.sp. cucumerinum, Fusarium moniliforme. The inhibition to Physalospora piricola was the strongest with an antibacterial diameter of 45 mm. This paper is the first report of the antimicrobial activity of endophytic fungi BS002 that was the secondary metabolites extracted from the seeds of Sophora flavescens. The results provide a broad foreground for biopharmaceuticals and biopesticide.

cPPB-aE is discovered from photosynthetic benthic dinoflagellates

Although chlorophyll degradation pathways in higher plants have been well studied, little is known about the mechanisms of chlorophyll degradation in microalgae. In this article, we report the occurrence of a chlorophyll a derivative that has never been discovered in photosynthetic organisms. This chlorophyll derivative emits no fluorescence and has a peculiar absorbance peak at 425, 451, 625, and 685 nm. From these features, it was identified as 13(2) ,17(3) -cyclopheophorbide a enol (cPPB-aE), reported as a degradation product of chlorophyll a derived from prey algal cells in heterotrophic protists. We discovered cPPB-aE in six benthic photosynthetic dinoflagellates that are phylogenetically separated into four clades based on SSU rDNA molecular phylogeny. This is the first report of this chlorophyll derivative in photosynthetic organisms and we suggest that the derivative is used to quench excess light energy.

Enhancing the anaerobic digestion of lignocellulose of municipal solid waste using a microbial pretreatment method

The use of biological pretreatment in anaerobic digestion systems has some potential; however, to date, these methods have not been able to effectively increase methane production of lignocellulose of municipal solid waste (LMSW). In this study a thermophilic microbial consortium (MC1) was used as a pretreatment method in order to enhance biogas and methane production yields. The results indicated that sCOD concentration increased significantly in the early stages of pretreatment. Ethanol, acetic acid, propionic acid, and butyric acid were the predominant volatile organic products in the MC1 hydrolysate. Biogas and methane production yields of LMSW significantly increased following MC1 pretreatment. In addition, the methane production rate of the treated LMSW was greater than that observed from the untreated sample.

Inhibitory effect of cyanide on nitrification process and its eliminating method in a suspended activated sludge process

Inhibition of nitrification by four typical pollutants (acrylonitrile, acrylic acid, acetonitrile and cyanide) in acrylonitrile wastewater was investigated. The inhibitory effect of cyanide on nitrification was strongest, with a 50% inhibitory concentration of 0.218 mg·gVSS-1 being observed in a municipal activated sludge system. However, the performance of nitrification was recovered when cyanide was completely degraded. The nitrification, which had been inhibited by 4.17 mg·gVSS-1 of free cyanide for 24 h, was recovered to greater than 95% of that without cyanide after 10 days of recovery. To overcome cyanide inhibition, cyanide-degrading bacteria were cultivated in a batch reactor by increasing the influent cyanide concentration in a stepwise manner, which resulted in an increase in the average cyanide degradation rate from 0.14 to 1.01 mg CN-·gVSS-1·h-1 over 20 days. The cultured cyanide-degrading bacteria were shaped like short rods, and the dominant cyanide-degrading bacteria strain was identified as Pseudomonas fluorescens NCIMB by PCR.

G protein-coupled receptor 43 moderates gut inflammation through cytokine regulation from mononuclear cells

BACKGROUND

Short-chain fatty acids (SCFAs), which are produced by the fermentation of dietary fiber by intestinal microbiota, may positively influence immune responses and protect against gut inflammation. SCFAs bind to G protein-coupled receptor 43 (GPR43). Here, we show that SCFA-GPR43 interactions profoundly affect the gut inflammatory response.

METHODS

Colitis was induced by adding dextran sulfate sodium to the drinking water of GPR43 knockout (-/-) and wild-type mice.

RESULTS

Dextran sulfate sodium-treated GPR43 mice exhibited weight loss, increased disease activity index (a combined measure of weight loss, rectal bleeding, and stool consistency), decreased hematocrit, and colon shortening, resulting in significantly worse colonic inflammation than in wild-type mice. Tumor necrosis factor alpha and interleukin 17 protein levels in the colonic mucosa of GPR43 mice were significantly higher than in wild-type mice. Treatment of wild-type mice with 150 mM acetate in their drinking water markedly improved these disease indices, with an increase in colon length and decrease in the disease activity index; however, it had no effect on GPR43 mice. Mononuclear cell production of tumor necrosis factor alpha after lipopolysaccharide stimulation was suppressed by acetate. This effect was inhibited by anti-GPR43 antibody.

CONCLUSIONS

SCFA-GPR43 interactions modulate colitis by regulating inflammatory cytokine production in mononuclear cells.

Rapid detection for rabbit-derived dermatophytes using microsatellite-primed polymerase chain reaction

A method exhibiting high sensitivity, specificity and rapidity to detect pathogenic dermatophytes was developed using microsatellite-primed polymerase chain reaction (PCR) in combination with a clustering method. The DNA fragments of Trichophyton mentagrophyton, Microsporum gypseum and Microsporum canis were amplified by using the primer (GACA)4 to detect the DNA polymorphism fingerprints. Twenty-one clinical strains identified as T. mentagrophyton, M. gypseum or M. canis by morphological methods were distinguished according to the differences of standard stains' bands combined with NTSYS-pc2.10 software. The results showed that there were obvious and direct differences in the bands of the three pathogenic dermatophytes, and the similarity of isolated strains and standard strains were above 90%, in line with the results of morphological identification. The method is more accurate, rapid and simple, which is meaningful for the clinical diagnosis and epidemic research of the dermatophytes.