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POI recommendation has gradually become an important topic in the field of service recommendation, which is always achieved by mining user behavior patterns. However, the context information of the collaborative signal is not encoded in the embedding process of traditional POI recommendation methods, which is not enough to capture the collaborative signal among different users. Therefore, a POI recommendation algorithm is presented by using social-time context graph neural network model (GNN) in location-based social networks. First, it finds similarities between different social relationships based on the users' social and temporal behavior. Then, the similarity among different users is calculated by an improved Euclidean distance. Finally, it integrates the graph neural network, the interaction bipartite graph of users and social-time information into the algorithm to generate the final recommendation list in this paper. Experiments on real datasets show that the proposed method is superior to the state-of-the-art POI recommendation methods.

Candidate peptides with novel angiotensin-I-converting enzyme (ACE) inhibitor activity were obtained from hydrolysates of

Diatoms exhibit high solar energy harvesting efficiency due to their remarkably organized, hierarchical micro/nanoporous, light-trapping, and scattering frustules. At present, few studies focus on cosensitization of natural near-infrared dye to expand the spectral response of dye-sensitized solar cells. In this study, the diatom frustule-TiO2 (12 : 5) composite film was prepared and assembled it on the TiO2 electrode. Compared to the single TiO2 layer film, diatom frustule-TiO2 (12 : 5) composite film sensitized by diatom’s dye showed the conversion efficiency of 0.719%. To expand the light-harvesting response to near-infrared region spectra, the cosensitized dyes were used to fabricate the visible-near-infrared responsive dye-sensitized solar cells. The cosensitization diatom frustule-TiO2 (12 : 5) composite film exhibited two distinct absorption bands in the near-infrared region and reached a higher conversion efficiency of 1.321%, which was approximately 1.4 or 1.7 folds higher than that of cosensitization double-TiO2 film or single TiO2 layer film, respectively, and approximately 3.7 or 1.7 folds higher than that of the single TiO2 layer film sensitized by diatom dye or purple bacterial dye, respectively. The results showed that the combination between diatom frustule-TiO2 with cosensitization natural dyes could significantly improve the photoelectric performance of visible-near-infrared responsive dye-sensitized solar cells.

Our study aimed to develop a prediction model to predict the short-term mortality of hepatocellular carcinoma (HCC) patients with lung metastasis. The retrospective data of HCC patients with lung metastasis was from the Surveillance, Epidemiology, and End Results registration database between 2010 and 2015. 1905 patients were randomly divided into training set (n = 1333) and validation set (n = 572). There were 1092 patients extracted from the Surveillance, Epidemiology, and End Results database 2015 to 2019 as the validation set. The variable importance was calculated to screen predictors. The constructed prediction models of logistic regression, random forest, broad learning system, deep neural network, support vector machine, and naïve Bayes were compared through the predictive performance. The mortality of HCC patients with lung metastasis was 51.65% within 1 month. The screened prognostic factors (age, N stage, T stage, tumor size, surgery, grade, radiation, and chemotherapy) and gender were used to construct prediction models. The area under curve (0.853 vs. 0.771) of random forest model was more optimized than that of logistic regression model in the training set. But, there were no significant differences in testing and validation sets between random forest and logistic regression models. The value of area under curve in the logistic regression model was significantly higher than that of the broad learning system model (0.763 vs. 0.745), support vector machine model (0.763 vs. 0.689) in the validation set, and higher than that of the naïve Bayes model (0.775 vs. 0.744) in the testing model. We further chose the logistic regression prediction model and built the prognostic nomogram. We have developed a prediction model for predicting short-term mortality with 9 easily acquired predictors of HCC patients with lung metastasis, which performed well in the internal and external validation. It could assist clinicians to adjust treatment strategies in time to improve the prognosis.

The bacterium Flavobacteriaceae strain W22 was isolated from the water column of a tree hole larval habitat of the mosquito Aedes triseriatus. The draft genome contained 3,796,379 bp, a G+C content of 35.4%, and several genes encoding enzymes functioning in polysaccharide degradation, gliding motility, and the type IX protein secretion system (T9SS).

The edible straw mushroom, Volvariella volvacea, is one of the most important cultivated mushrooms in tropical and sub-tropical regions. Strain improvement for V. volvacea is difficult because of the unknown mechanisms involved in its growth regulation and substrate utilization. A comparative physiological and transcriptomic study was conducted between two commercially available straw mushroom strains (v9 and v26) to explore their fast-growth regulation mechanism(s). The physiological study showed that V. volvacea v9 had a shorter growth cycle and higher biological efficiency (4% higher) than that in v26. At least 14,556 unigenes were obtained from the four cDNA libraries (two replicates per strain). Among them, the expression of 1597 unigenes was up-regulated while 1352 were down-regulated. Four heat-shock proteins were highly expressed in v9, showing that v9 has the better ability to handle stresses and/or environmental changes. Moreover, up to 14 putative transporter genes were expressed at a higher level in v9 than those in v26, implying that v9 has a better ability to transport nutrients or export xenobiotics efficiently. Our report allows to identify the candidate genes involved in the fast growth requirement of V. volvacea, which represents a valuable resource for strain improvement in this commercially important edible mushroom.

Background: Relapse due to loss of the CD19 targeted epitope presents a therapeutic challenge of CD19 CAR-T therapy. These patients universally have poor outcomes. CD20 is a proven therapeutic target for B-Cell Non-Hodgkin Lymphomas (B-NHL), supported by previously approved and widely used monoclonal antibody therapy. C-CAR066 is a novel 2nd generation chimeric antigen receptor T (CAR-T) therapy. Preclinical studies suggest that C-CAR066 has superior anti-tumor activity compared to CAR-Ts derived from scFVs of Leu16, Rituximab, and Obinutuzumab, Methods: NCT04036019 is a single arm, single-center, non-randomized phase I clinical trial conducted at Shanghai Tongji Hospital to evaluate the safety and efficacy of C-CAR066 in subjects with r/r B cell lymphoma who were previously treated with anti-CD19 CAR-T therapy. The primary objective of the study is to evaluate incidence and severity of treatment emergent adverse events. The secondary objectives include determining overall response rate (ORR), PFS, and OS. C-CAR066 is manufactured in a serum free, semi-automated, and digitally closed system. C-CAR066 is administered to patients as a single intravenous dose after a standard 3-day cyclophosphamide/fludarabine conditioning regimen. Results: As of Aug 3, 2020, 7 patients (all DLBCL) were enrolled and infused with C-CAR066 with a dose range of 2.0 x 106 to 5.0 x 106 CAR-T cells. The manufacturing success rate was 100%. All patients had relapsed after anti-CD19 CAR-T treatment, only one of the patients had achieved CR following anti-CD-19 CAR-T therapy. C-CAR066 treatment was well tolerated with reversible grade 1~2 CRS in six patients, grade 3 CRS in another patient, and no neurotoxicity events. 6/7 patients showed clinical improvement (best overall response rate, BOR = 85.7%). The best overall responses include 3 CR and 3PR. All patients responded to C-CAR066 treatment and showed different degrees of tumor regression (45-100%). Furthermore, the expansion and proliferation of C-CAR066 CAR-T cells in the peripheral blood positively correlated with the extent of tumor regression. Conclusion: C-CAR066 has a favorable safety profile and shows promising early efficacy in patients with r/r NHL following CD19 CAR-T therapy. It confirms that C-CAR066 has a different mechanism of action compared to anti-CD-19 CAR-T therapy. These data provide strong scientific rationale to the strategy of targeting both CD20 and CD19 tumor antigens and to ask whether this leads to superior clinical benefit to targeting either CD19 or CD20 alone in NHL. Disclosures Huang: Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Zhu:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Yao:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Zhu:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Zheng:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Chen:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Lan:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Chen:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Wei:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Shu:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Ye:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Zhang:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Wang:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Hong:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Ren:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Zhang:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Humphries:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Yao:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.

Asaia bacteria commonly comprise part of the microbiome of many mosquito species in the genera Anopheles and Aedes, including important vectors of infectious agents. Their close association with multiple organs and tissues of their mosquito hosts enhances the potential for paratransgenesis for the delivery of antimalaria or antivirus effectors. The molecular mechanisms involved in the interactions between Asaia and mosquito hosts, as well as Asaia and other bacterial members of the mosquito microbiome, remain underexplored. Here, we determined the genome sequence of Asaia strain W12 isolated from Anopheles stephensi mosquitoes, compared it to other Asaia species associated with plants or insects, and investigated the properties of the bacteria relevant to their symbiosis with mosquitoes. The assembled genome of strain W12 had a size of 3.94 MB, the largest among Asaia spp. studied so far. At least 3585 coding sequences were predicted. Insect-associated Asaia carried more glycoside hydrolase (GH)-encoding genes than those isolated from plants, showing their high plant biomass-degrading capacity in the insect gut. W12 had the most predicted regulatory protein components comparatively among the selected Asaia, indicating its capacity to adapt to frequent environmental changes in the mosquito gut. Two complete operons encoding cytochrome bo3-type ubiquinol terminal oxidases (cyoABCD-1 and cyoABCD-2) were found in most Asaia genomes, possibly offering alternative terminal oxidases and allowing the flexible transition of respiratory pathways. Genes involved in the production of 2,3-butandiol and inositol have been found in Asaia sp. W12, possibly contributing to biofilm formation and stress tolerance.

Nitrogen pollution in aquaculture needs the efficient and cost-effective in-situ technology. This study aims to apply Marichromatium gracile YL28 to in-situ bioremediation and test its ability to maintain the nitrogen balance in aquaculture. In laboratory aquaculture system, approximately 99.96% of nitrite (1 mg/L) was removed within 7 d through denitrification coupled with assimilatory nitrate reduction. Ammonium (3.5 mg/L) of 95.6% was directly assimilated by YL28 within 7 d. Moreover, in zero exchange water from shrimp (Penaeus vannamei) aquaculture field trials (20 days), YL28 significantly reduced the ammonium accumulation (0.6 mg/L) and 99.3% of nitrite (1.25 mg/L). Toxicological studies with the Institute of Cancer Research (ICR) mice and Oryzias melastigma indicated that M. gracile YL28 can be safely applied in aquatic ecosystems. All results demonstrate that strain YL28 has high promise for future applications of removing inorganic nitrogen and maintaining the nitrogen balance from in-situ aquaculture.

Elizabethkingia anophelisbacteria encounter fluxes of iron in the midgut of mosquitoes, where they live as symbionts. They also establish bacteremia with severe clinical manifestations in humans, and live in water service lines in hospitals. In this study, we investigated the global gene expression responses ofE. anophelisto iron fluxes in the midgut of femaleAnopheles stephensimosquitoes fed sucrose or blood, and in iron-poor or iron-rich culture conditions. Of 3,686 transcripts revealed by RNAseq technology, 218 were upregulated while 112 were down-regulated under iron-poor conditions. Most of these differentially expressed genes (DEGs) were enriched in functional groups assigned within “biological process,” “cell component” and “molecular function” categories.E. anophelispossessed 4 iron/heme acquisition systems. Hemolysin gene expression was significantly repressed when cells were grown under iron-rich or high temperature (37°C) conditions. Furthermore, hemolysin gene expression was down-regulated after a blood meal, indicating thatE. anopheliscells responded to excess iron and its associated physiological stress by limiting iron loading. By contrast, genes encoding respiratory chain proteins were up-regulated under iron-rich conditions, allowing these iron-containing proteins to chelate intracellular free iron.In vivostudies showed that growth ofE. anopheliscells increased 3-fold in blood-fed mosquitoes over those in sucrose-fed ones. Deletion of aerobactin synthesis genes led to impaired cell growth in both iron-rich and iron-poor media. Mutants showed more susceptibility to H2O2toxicity and less biofilm formation than did wild-type cells. Mosquitoes withE. anophelisexperimentally colonized in their guts produced more eggs than did those treated with erythromycin or left unmanipulated, as controls. Results reveal thatE. anophelisbacteria respond to varying iron concentration in the mosquito gut, harvest iron while fending off iron-associated stress, contribute to lysis of red blood cells, and positively influence mosquito host fecundity.

Task appearance prediction has great potential to improve task assignment in spatial crowdsourcing platforms. The main challenge of this prediction problem is to model the spatial dependency among neighboring regions and the temporal dependency at different time scales (e.g., hourly, daily, and weekly). A recent model ST-ResNet predicts traffic flow by capturing the spatial and temporal dependencies in historical data. However, the data fragments are concatenated as one tensor fed to the deep neural networks, rather than learning the temporal dependencies in a sequential manner. We propose a novel deep learning model, called SeqST-ResNet, which well captures the temporal dependencies of historical task appearance in sequences at several time scales. We validate the effectiveness of our model via experiments on a real-world dataset. The experimental results show that our SeqST-ResNet model significantly outperforms ST-ResNet when predicting tasks at hourly intervals and also during weekday and weekends, more importantly, in regions with intensive task requests.

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (&gt, 80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the &beta, diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p &lt, 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

Background: Aiming to improve both the response rate and durability of response while limiting antigen escape of CD-19 following anti-CD-19 CAR-T therapy, C-CAR039 has been developed as a 2nd generation 4-1BB novel bi-specific chimeric antigen receptor T (CAR-T) therapy targeting both CD19 and CD20 antigens. Methods: NCT04317885 is a single arm, single-center, non-randomized phase I clinical trial designed to evaluate the safety and efficacy of C-CAR039 in treatment of relapsed or refractory NHL (r/r NHL) patients. The primary objective of the study is to evaluate incidence and severity of treatment emergent adverse events. The secondary objectives include determining overall response rate (ORR), progression-free survival, and overall survival. Results: In preclinical studies, human T cells transduced with the lentiviral vector encoding C-CAR039in vitroshowed CAR-T proliferation, cytokine production, cytotoxicity to CD19, and CD20 single positive and double positive tumor cells. C-CAR039 can eradicate CD19/CD20 positive tumor cellsin vivobased on our animal model study. A Phase 1 trial was conducted in Shanghai Tongji Hospital in patients with r/r NHL to assess the safety and efficacy of C-CAR039 (NCT04317885). Following apheresis to harvest T cells, C-CAR039 was manufactured and infused as a single intravenous dose after a standard 3-day cyclophosphamide/fludarabine conditioning regimen. C-CAR039 was manufactured in a serum free, semi-automated, and digitally closed system with median vein to vein time of 18 days. The manufacturing success rate was 100%. As of Aug 3, 2020, 16 patients were infused with C-CAR039 with a dose range of 1.0 x 106 to 5.0 x 106 CAR-T cells/kg. 14 patients had at least one-month evaluable safety data and 13 patients (11 DLBCL, 2 FL patients) had one-month or longer efficacy data. C-CAR039 treatment was well tolerated with no grade 3 or higher cytokine release syndrome(CRS) and no neurotoxicity event. Reversible grade 1~2 CRS was observed in 12 (86%) of patients. Cytopenias due to the conditioning regimen were common and reversible. At the one-month evaluation, 12/13 patients showed clinical improvement (ORR=92%) and 11/11 of DLBCL patients responded to the treatment (ORR=100%). Median follow-up was 70 days (range: 35-257 days). The best overall response (BOR) includes 10 complete responses (CRs) and 2 partial responses (PRs). Furthermore, C-CAR039 proliferation and expansion in the peripheral blood positively correlated with tumor regression. Conclusion: C-CAR039 shows promising efficacy and a favorable safety profile in the early clinical trial in patients with r/r NHL. The early clinical efficacy signal is encouraging and compares favorably to anti-CD19 CAR-T therapies. These findings need to be evaluated in more patients with longer follow-up to confirm safety, efficacy and duration of response. Disclosures Huang: Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Zhu:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Yao:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Zhu:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Zheng:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Chen:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Li:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Lan:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Chen:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Guo:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Zhang:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Zheng:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Wang:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Hong:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Ren:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Zhang:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Humphries:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.Yao:Cellular Biomedicine Group Inc:Current Employment, Current equity holder in publicly-traded company.

Lignocellulosic biomass is a promising feedstock for sustainable production of non-food building-block sugars. This bioconversion process is preferentially carried out through the whole slurry enzymatic saccharification of the pre-treated lignocellulosic substrates. However, dissolved lignin, residual lignin, and lignin-derived phenolic molecules in the pre-treated biomass slurry can all trigger the decrease in activity and stability of cellulases, as well as the unfavorable enzyme recyclability. The hydrolyzing efficiencies can be considerably hindered by the lignin-induced non-productive binding of cellulases through various mechanisms. Three major non-covalent forces, i.e., hydrophobic, electrostatic, and hydrogen bonds interactions, can occur between the amino acid residues in cellulases and the functional groups in lignin. Various strategies such as enzyme engineering, substrate modification, additive blocking have been intensively developed to minimize the cellulase-lignin interactions. To investigate the impacts and benefits of different mechanisms and processes, this paper provides a systematic overview of the current opinions about the non-productive binding of cellulase to lignin. Through better understanding of their interactions it is our hope that the enzyme binding groups in lignin could be properly quenched by using new pre-treatment methods and/or biochemical processing strategies to increase the efficiency of cellulose bioconversion. © 2016 Society of Chemical Industry and John Wiley & Sons, Ltd

A new technique for representing speech articulation with an ultrasound-driven finite element model of the tongue is presented. By using a snake contour extraction algorithm with anatomically motivated constraints and a common coordinate system between the ultrasound and the tongue model, it is possible for the first time to obtain a realistic 3D simulation of the tongue directly from a non-invasive sensor (ultrasound), without mapping through any intermediate sensor modalities, and at near real-time frame rates.

Flavobacterium spartansii strain T16T was isolated from a disease outbreak in hatchery-reared Chinook salmon (Oncorhynchus tshawytscha) fingerlings. To gain insight into its genomic content, structure and virulence pathogenesis factors, comparative genome analyses were performed using genomes from environmental and virulent Flavobacterium strains. F. spartansii shared low average nucleotide identity (ANI) to well-known fish-pathogenic flavobacteria (e.g., F. columnare, F. psychrophilum, and F. branchiophilum), indicating that it is a new and emerging fish pathogen. The genome in T16T had a length of 5,359,952 bp, a GC-content 35.7%, and 4,422 predicted protein-coding sequences. Flavobacterium core genome analysis showed that the number of shared genes decreased with the addition of input genomes and converged at 1182 genes. At least 8 genomic islands and 5 prophages were predicted in T16T. At least 133 virulence factors associated with virulence in pathogenic bacteria were highly conserved in F. spartansii T16T. Furthermore, genes linked to virulence in other bacterial species (e.g., those encoding for a type IX secretion system, collagenase and hemolysin) were found in the genome of F. spartansii T16T and were conserved in most of the analyzed pathogenic Flavobacterium. F. spartansii was resistant to ampicillin and penicillin, consistent with the presence of multiple genes encoding diverse lactamases and the penicillin-binding protein in the genome. To allow for future investigations into F. spartansii virulence in vivo, a transposon-based random mutagenesis strategy was attempted in F. spartansii T16T using pHimarEm1. Four putative gliding motility deficient mutants were obtained and the insertion sites of pHimarEm1 in the genome of these mutants were characterized. In total, study results clarify some of the mechanisms by which emerging flavobacterial fish pathogens may cause disease and also provide direly needed tools to investigate their pathogenesis.

Low-molecular-weight chitosan (LC) promoted growth in weaned piglets as an alternative to feed-grade antibiotics. To investigate the influence of LC supplementation on piglets' gut microbiome and compare the differences in community composition between LC and antibiotics with ZnO addition, we assessed the cecal microbial community by 16S rRNA gene sequencing with three treatments consisting of basal diet (CTR group), basal diet with low-molecular-weight chitosan (LC group), and basal diet with antibiotic and ZnO (AZ group). LC decreased pH more than AZ did in the cecum (both compared to CTR). Beta diversity analysis showed that community structure was distinctly different among the CTR, LC, and AZ treatments, indicating that either LC or AZ treatment modulated the piglet microbiota. Bacteroidetes, Firmicutes, and Proteobacteria dominated the community [>98% of operational taxonomic units (OTUs)] in piglet cecal contents. Compared to CTR, both LC, and AZ increased the relative abundance of Bacteroidetes while they decreased the count of Firmicutes and AZ decreased the population of Proteobacteria. In CTR the top four abundant genera were Prevotella (~10.4%), Succinivibrio (~6.2%), Lactobacillus (~5.6%), and Anaerovibrio (5.4%). Both LC and AZ increased the relative abundance of Prevotella but decreased the ratio of Lactobacillus when they compared with CTR. Moreover, LC increased the relative abundance of Succinivibrio and Anaerovibrio while AZ decreased them. The microbial function prediction showed LC enriched more pathways in the metabolism of cofactors and vitamins than CTR or AZ did. LC may potentially function as an alternative to feed-grade antibiotics in weaned piglets due to its beneficial regulation of the intestinal microbiome.

Flavobacteria (members of the family Flavobacteriaceae ) dominate the bacterial community in the Anopheles mosquito midgut. One such commensal, Elizabethkingia anophelis , is closely associated with Anopheles mosquitoes through transstadial persistence (i.e., from one life stage to the next); these and other properties favor its development for paratransgenic applications in control of malaria parasite transmission. However, the physiological requirements of E. anophelis have not been investigated, nor has its capacity to perpetuate despite digestion pressure in the gut been quantified. To this end, we first developed techniques for genetic manipulation of E. anophelis , including selectable markers, reporter systems (green fluorescent protein [GFP] and NanoLuc), and transposons that function in E. anophelis . A flavobacterial expression system based on the promoter P ompA was integrated into the E. anophelis chromosome and showed strong promoter activity to drive GFP and NanoLuc reporter production. Introduced, GFP-tagged E. anophelis associated with mosquitoes at successive developmental stages and propagated in Anopheles gambiae and Anopheles stephensi but not in Aedes triseriatus mosquitoes. Feeding NanoLuc-tagged cells to A. gambiae and A. stephensi in the larval stage led to infection rates of 71% and 82%, respectively. In contrast, a very low infection rate (3%) was detected in Aedes triseriatus mosquitoes under the same conditions. Of the initial E. anophelis cells provided to larvae, 23%, 71%, and 85% were digested in A. stephensi , A. gambiae , and Aedes triseriatus , respectively, demonstrating that E. anophelis adapted to various mosquito midgut environments differently. Bacterial cell growth increased up to 3-fold when arginine was supplemented in the defined medium. Furthermore, the number of NanoLuc-tagged cells in A. stephensi significantly increased when arginine was added to a sugar diet, showing it to be an important amino acid for E. anophelis . Animal erythrocytes promoted E. anophelis growth in vivo and in vitro , indicating that this bacterium could obtain nutrients by participating in erythrocyte lysis in the mosquito midgut.

Flavobacterium spartansii strain T16T was isolated from a disease outbreak in hatchery-reared Chinook salmon (Oncorhynchus tshawytscha) fingerlings. To gain insight into its genomic content, structure and virulence pathogenesis factors, comparative genome analyses were performed using genomes from environmental and virulent Flavobacterium strains. F. spartansii shared low average nucleotide identity (ANI) to well-known fish-pathogenic flavobacteria (e.g., F. columnare, F. psychrophilum, and F. branchiophilum), indicating that it is a new and emerging fish pathogen. The genome in T16T had a length of 5,359,952 bp, a GC-content 35.7%, and 4,422 predicted protein-coding sequences. Flavobacterium core genome analysis showed that the number of shared genes decreased with the addition of input genomes and converged at 1182 genes. At least 8 genomic islands and 5 prophages were predicted in T16T. At least 133 virulence factors associated with virulence in pathogenic bacteria were highly conserved in F. spartansii T16T. Furthermore, genes linked to virulence in other bacterial species (e.g., those encoding for a type IX secretion system, collagenase and hemolysin) were found in the genome of F. spartansii T16T and were conserved in most of the analyzed pathogenic Flavobacterium. F. spartansii was resistant to ampicillin and penicillin, consistent with the presence of multiple genes encoding diverse lactamases and the penicillin-binding protein in the genome. To allow for future investigations into F. spartansii virulence in vivo, a transposon-based random mutagenesis strategy was attempted in F. spartansii T16T using pHimarEm1. Four putative gliding motility deficient mutants were obtained and the insertion sites of pHimarEm1 in the genome of these mutants were characterized. In total, study results clarify some of the mechanisms by which emerging flavobacterial fish pathogens may cause disease and also provide direly needed tools to investigate their pathogenesis.

β-Xylosidase activity is deficient in most cellulase enzymes secreted by filamentous fungi, which limits effective enzymatic hydrolysis of hemicellulose in lignocellulose materials and resulted in accumulation of xylo-oligosaccharides that inhibit the cellulase and xylanase activitives. An endogenous β-xylosidase gene, xyl3A , was overexpressed using two types of promoters in cellulolytic P. oxalicum RE-10. The mutants RXyl, RGXyl-1 and RGXyl-2 displayed higher β-xylosidase production than native strain RE-10 besides higher cellulase and xylanase activities, especially RGXyl-1, showing the highest β-xylosidase activity of 15.05 ± 1.79 IU/mL, about 29 folds higher than native strain, more than the highest level reported by literature. Enzymatic hydrolysis results indicated the cellulase RGXyl-1 not only increased glucose and xylose yields and thus resulted in high ethanol yield during the simultaneous saccharification and fermentation, but decreased the total enzyme loading compared to starting RE-10, which indicated a good prospect of industrial application in bioconversion of lignocellulose.

Pannonibacter phragmitetus is a bioremediation reagent for the detoxification of heavy metals and polycyclic aromatic compounds (PAHs) while it rarely infects healthy populations. However, infection by the opportunistic pathogen P. phragmitetus complicates diagnosis and treatments, and poses a serious threat to immunocompromised patients owing to its multidrug resistance. Unfortunately, genome features, antimicrobial resistance, and virulence potentials in P. phragmitetus have not been reported before. A predominant colony (31801) was isolated from a liver abscess patient, indicating that it accounted for the infection. To investigate its infection mechanism(s) in depth, we sequenced this bacterial genome and tested its antimicrobial resistance. Average nucleotide identity (ANI) analysis assigned the bacterium to the species P. phragmitetus (ANI, >95%). Comparative genomics analyses among Pannonibacter spp. representing the different living niches were used to describe the Pannonibacter pan‐genomes and to examine virulence factors, prophages, CRISPR arrays, and genomic islands. Pannonibacter phragmitetus 31801 consisted of one chromosome and one plasmid, while the plasmid was absent in other Pannonibacter isolates. Pannonibacter phragmitetus 31801 may have a great infection potential because a lot of genes encoding toxins, flagellum formation, iron uptake, and virulence factor secretion systems in its genome. Moreover, the genome has 24 genomic islands and 2 prophages. A combination of antimicrobial susceptibility tests and the detailed antibiotic resistance gene analysis provide useful information about the drug resistance mechanisms and therefore can be used to guide the treatment strategy for the bacterial infection.

Onion thrips, Thrips tabaci Lindeman, is a primary insect pest of onions (Allium cepa) worldwide. Onion thrips cause feeding damage by destroying epidermal tissue. They are also vectors of Pantoea ananatis (Serrano) Mergaert, the bacteria that causes center rot. Onions with center rot develop white streaks with water-soaked margins along the onion leaves, which turn necrotic and lead to bulb rot during storage. The role of thrips feeding on the establishment and progression of bacterial infection in onions has not been investigated. Onions infested with thrips and inoculated with P. ananatis had more necrotic tissue and symptoms were more severe with increasing thrips density. We conducted a fluorescence microscopy study that examined how P. ananatis (expressing a fluorescence protein gene) colonized a control group of onions without thrips in comparison to a test group of onions with thrips. We found that P. ananatis colonized some onions in the control group because of naturally existing wounds in the epidermal tissue but more colonization was found in the thrips infested group because of the increased presence of entry points caused by thrips feeding. Overall, our results demonstrate that wounds caused by thrips feeding facilitate center rot development by providing entry sites for the bacteria into leaf tissue.

Elizabethkingia anophelis, originally discovered from Anopheles mosquito gut, is an emerging pathogen, especially in immunocompromised patients. We isolated two strains of E. anophelis from two separate patients with multiple organ dysfunction syndrome and lower respiratory tract infection. In this paper, we reviewed the status of E. anophelis infection and its antibiotics resistance from reported cases.

Dietary zinc oxide (ZnO) at pharmacological level has been widely used to prevent and treat diarrhea in weaning piglets. Despite its importance for promoting animal health and performance, the influence of microbiome profiles in intestinal tracts by ZnO needs to be comprehensively investigated. In this study, we conducted a comparative microbial community analysis in the ileum and colon of piglets fed by either control diet, high ZnO (3,000 mg/kg) supplement or antibiotics (300 mg/kg chlortetracycline and 60 mg/kg colistin sulfate) supplement. Our results showed that both high dietary ZnO and in-feed antibiotics supplementations significantly increased 5 phyla of Spirochaetes, Tenericutes, Euryarchaeota, Verrucomicrobia, TM7, and reduced 1 phyla of Chlamydiae in ileal digesta. The relative abundance of opportunistic pathogens Campylobacterales were decreased while Enterobacteriales were increased in ZnO or antibiotics-supplemented group when compared to the control. In the colon, the phyla Euryarchaeota, the genus Methanobrevibacter, and the species Methanobrevibacter smithii were drastically increased by high dietary ZnO supplementation when compared with other groups. The microbial functional prediction analysis showed that high dietary ZnO and in-feed antibiotics had a higher abundance of transporter pathway enrichment in the ileum when compared with the control. While in the colon high dietary ZnO had a higher abundant enrichment of methane metabolism involving energy supply when compared with other groups. Both high dietary ZnO and antibiotics increased the microbiota diversity of ileal digesta while they decreased the microbiota diversity of the colonic digesta. Collectively, these results suggested that dietary ZnO and in-feed antibiotics supplementations presented similar effect on ileal microbiota, and mainly affected the non-predominant microbiota.

A spectral peak at ~421 nm appeared in vivo spectrum of Rhodopseudomonas palustris CQV97 cultured in acetate-glutamate medium (M1) but not in acetate-ammonium sulfate medium (M2). However, the spectral origin of 421 nm peak was not clear and frequently attributed to carotenoid component(s). In this study, comparative analysis of the extracted components showed that magnesium protoporphyrin IX monomethylester (MPE) was accumulated as one of the predominate components in M1 culture. The amounts of bacteriochlorophyll a in M1 culture were higher than that in M2, whereas the amounts of carotenoids were nearly identical in both cultures. A simple, rapid and minimum interference with carotenoid and bacteriochlorophyll method to efficiently extract the compounds involving in the formation of 421 nm peak was developed in this study. Assembly of purified MPE with protein components from R. palustris in vitro demonstrated that MPE caused the formation of 421 nm peak. The localization analysis in vivo demonstrated it is MPE associating to protein components and accounting for the peak at ~421 nm. This work clarified the 421 nm peak in vivo mainly originated from MPE accumulation, and will be very helpful to further explore the physiological roles of MPE or its derivatives in photosynthesis.

Chemical and surface characteristics of sulfite-pretreated royal palm sheath (RPS) fibers and parenchyma cells were investigated in order to study cell-type-dependent biomass hydrolysis by cellulase. Size, chemical composition, cellulose crystallinity and the exposure of cellulose microfibrils in pretreated RPS biomass affected the enzymatic accessibility and digestibility of different cell-type substrates.

Elizabethkingia meningoseptica EM1 was isolated from a whole-blood sample from a female patient. The draft genome sequence of Em1 contains 4,038,467 bp, with a G+C content of 36.37%. A preliminary genome analysis showed that Em1 contains genes conferring resistance to β-lactams. The bacterium has hemolysin genes and a set of genes involved in heme uptake and heme utilization, showing its potential to cause bloodstream infections. A clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) system was identified. Average nucleotide identity (ANI) analysis assigned the bacterium to the species E. meningoseptica (ANI, >95%) . The annotated genome sequence provides the genetic basis for revealing its role as a pathogen in humans.

The bacteria in the midgut of Anopheles stephensi adult females from laboratory colonies were studied by sequencing the V4 region of 16S rRNA genes, with respect to three experimental factors: stable or cured Wolbachia infection; sugar or blood diet; and age. Proteobacteria and Bacteroidetes dominated the community [>90% of operational taxonomic units (OTUs)]; most taxa were in the classes Flavobacteriia, Gammaproteobacteria, and Alphaproteobacteria, and were assigned to Elizabethkingia (46.9%), Asaia (6.4%) and Pseudomonas (6.0%), or unclassified Enterobacteriaceae (37.2%). Bacterial communities were similar between Wolbachia-cured and Wolbachia-infected mosquito lines, indicating that the gut microbiota were not dysregulated in the presence of Wolbachia. The proportion of Enterobacteriaceae was higher in mosquitoes fed a blood meal compared to those provided a sugar meal. Collectively, the bacterial community had a similar structure in older Wolbachia-infected mosquitoes 8 days after the blood meal, as in younger Wolbachia-infected mosquitoes before a blood meal, except that older mosquitoes had a higher proportion of Enterobacteriaceae and lower proportion of Elizabethkingia. Consistent presence of certain predominant bacteria (Elizabethkingia, Asaia, Pseudomonas, and Enterobacteriaceae) suggests they would be useful for paratransgenesis to control malaria infection, particularly when coupled to a Wolbachia-based intervention strategy.

The draft genome sequence of Marichromatium gracile YL-28 contains 3,840,251 bp, with a G+C content of 68.84%. The annotated genome sequence provides the genetic basis for revealing its role as a purple sulfur bacterium in the harvesting of energy and the development of bioremediation applications.

The bacteria in the midgut of Anopheles stephensi adult females from laboratory colonies were studied by sequencing the V4 region of 16S rRNA genes, with respect to three experimental factors: stable or cured Wolbachia infection; sugar or blood diet; and age. Proteobacteria and Bacteroidetes dominated the community [>90% of operational taxonomic units (OTUs)]; most taxa were in the classes Flavobacteriia, Gammaproteobacteria, and Alphaproteobacteria, and were assigned to Elizabethkingia (46.9%), Asaia (6.4%) and Pseudomonas (6.0%), or unclassified Enterobacteriaceae (37.2%). Bacterial communities were similar between Wolbachia-cured and Wolbachia-infected mosquito lines, indicating that the gut microbiota were not dysregulated in the presence of Wolbachia. The proportion of Enterobacteriaceae was higher in mosquitoes fed a blood meal compared to those provided a sugar meal. Collectively, the bacterial community had a similar structure in older Wolbachia-infected mosquitoes 8 days after the blood meal, as in younger Wolbachia-infected mosquitoes before a blood meal, except that older mosquitoes had a higher proportion of Enterobacteriaceae and lower proportion of Elizabethkingia. Consistent presence of certain predominant bacteria (Elizabethkingia, Asaia, Pseudomonas, and Enterobacteriaceae) suggests they would be useful for paratransgenesis to control malaria infection, particularly when coupled to a Wolbachia-based intervention strategy.

It has been well known that laccases can directly or indirectly catalyze oxidation of a broad species of phenols, amines and many other electron donor substrates. However, laccases as biocatalyst in "green" ionic liquids (ILs) media instead of conventional solvents are less known and regarded as an innovative research direction. The presence of ILs can either inhibit or stimulate laccase activity, strongly depending on water-miscibility and kosmotropic natures of ILs. In addition, enzyme source, mediator, pH as well as water content are very important factors which influence laccase activity and stability. Therefore, elucidation of mechanisms underlying the interactions between laccases and ILs will facilitate to screen ILs with excellent laccase compatibility. Strategies based on molecular evolution, enzyme immobilization and/or ILs modification greatly increase the tolerance of laccases against specific ILs. The use of ILs can spread the laccase applications in fields of biosynthesis, biodegradation, biosensor and biofuel cells. This article summarizes the recent progress, trends and problems in this field and focuses, in particular, on the stimulation of laccase activity in aqueous ILs media.

The issues of how to quickly collect seawater samples and of how to make sure that those samples truly reflect the in-situ information on gas composition and concentration have therefore become a hot but difficult topic in the field of ocean technology. Most conventional seawater samplers only focus on collecting seawater itself, but take little consideration on gas preservation. A set of new oceanographic tools are presented for ocean resource exploration such as hydrothermal sulfide and gas hydrate, and for investigations on the processes and mechanisms of marine physical, chemical and biological evolutions. A gas-tight deep-sea water sampling system (GTWSS) is designed for the collection of deep-sea geochemical samples. This set of tools mainly consists of a conductivity temperature depth profiler (CTD), release devices and gas-tight deep-sea water samplers (GTWS). The GTWS is able to hold the gases in deep-sea water samples tightly, providing in-situ information on gas contents in the seawater samples and can be deployed on a routine wire-deployed CTD sampler for multi-layer discrete sampling of gas-tight seawater. Sea trials are performed successfully in 2008 and 2009, on a research vessel named HaiYang Si Hao in South China Sea, with the deepest trial depth 3 930 m. GTWSS is capable of quickly sampling 12 discrete gas-tight seawater samples (8.3 L per sample) during its single deployment. The head space method is employed to separate the gases from the seawater samples immediately after recovery of the seawater samples on the vessel. Field geochemical analysis is carried out by gaseous hydrocarbon sensors and an infrared gas analyzer. Results show that the concentrations of CH4 and CO2 in the seawater sampled by GTWSS are higher than those sampled by general non-gas-tight water samplers, thus confirming the gas tightness of GTWSS. Seawater samples can be collected quickly by using GTWSS, and GTWSS can keep the samples’ integrity quite well.

The model rhizobacterium Pseudomonas putida KT2440 and other fluorescent pseudomonads possess two bacterioferritins, Bfrα and Bfrβ. However, the regulatory systems controlling the expression of these genes and the roles of these proteins in iron homeostasis are ill defined. Our studies show that both bfr α and bfr β were monocistronic: promoter motifs and transcriptional start sites were identified, and Fur boxes and σ S -dependent regulatory motifs were absent. The expressions of bfr α and bfr β were enhanced by iron exposure and were maximal in cells rapidly growing in a high-iron environment. Both bfr α and bfr β were positively regulated by Fur, and both were expressed independently of adjoining, functionally related genes. The loss of Bfrα or Bfrβ individually resulted in a significant reduction (ca. 17%) in cellular iron levels, and the deletion of both bfr α and bfr β reduced cellular iron levels by 38% relative to those of the wild type. The mutants varied in their abilities to grow in low-iron medium; while growths (rate and final cell density) of single mutants and the wild type were similar, that of the double mutant was reduced significantly. Mutants lacking Bfrα and/or Bfrβ showed no change relative to the wild type in sensitivity to reactive oxygen species toxicity. Collectively, the data show that while Bfrα and Bfrβ could function independently of each other, an interaction-dependent function cannot be ruled out. Furthermore, regardless of the mechanism, a primary benefit of the bacterioferritins to P. putida KT2440 appears to be the enhancement of its survival in the environment by strengthening its tolerance to iron starvation.

Myroides odoratimimus is an important nosocomial pathogen. Management of M. odoratimimus infection is difficult owing to the multidrug resistance and the unknown pathogenesis mechanisms. Based on our previous genomic sequencing data of M. odoratimimus PR63039 (isolated from a patient with the urinary tract infection), in this study, we further performed comparative genomic analysis for 10 selected Myroides strains. Our results showed that these Myroides genome contexts were very similar and phylogenetically related. Various prophages were identified in the four clinical isolate genomes, which possibly contributed to the genome evolution among the Myroides strains. CRISPR elements were only detected in the two clinical (PR63039 and CCUG10230) isolates and two environmental (CCUG12700 and H1bi) strains. With more stringent cutoff parameters in CARD analysis, the four clinical M. odoratimimus contained roughly equal antibiotic resistance genes, indicating their similar antibiotic resistance profiles. The three clinical (CCUG10230, CCUG12901, CIP101113) and three environmental (CCUG12700, L41, H1bi) M. odoratimimus strains were speculated to carry the indistinguishable virulent factors (VFs), which may involve in the similar pathogenesis mechanism. Moreover, some VFs might confer to the high capacity of dissemination, attacking tissue cells and induction of autoimmune complications. Our results facilitate the research of antibiotic resistance and the development of therapeutic regimens for the M. odoratimimus infections.

A cluster of six genes from Flavobacterium hibernum strain W22, fus-rpsJ-rplC-rplD-rplW-rplB, was cloned and sequenced. A short fragment upstream of rplC, but not of rpsJ, showed strong promoter activity in flavobacteria. TATCTTTG and TTG motifs that are conserved in Flavobacterium promoters were found immediately upstream of the transcription start point of rplC, at the -7 and -33 positions, respectively. RT-PCR analysis of the transcripts revealed that rpsJ and rplC are expressed as separate transcriptional units, whereas rplC and rplD-rplW-rplB are cotranscribed as a single mRNA, in contrast to the situation in the Gammaproteobacteria, which have a single transcriptional unit of 11 ribosomal S10 genes.

We have isolated a laccase (lac1) from culture fluid of Volvariella volvacea, grown in a defined medium containing 150 micro m CuSO4, by ion-exchange and gel filtration chromatography. Lac1 has a molecular mass of 58 kDa as determined by SDS/PAGE and an isoelectric point of 3.7. Degenerate primers based on the N-terminal sequence of purified lac1 and a conserved copper-binding domain were used to generate cDNA fragments encoding a portion of the lac1 protein and RACE was used to obtain full-length cDNA clones. The cDNA of lac1 contained an ORF of 1557 bp encoding 519 amino acids. The amino acid sequence from Ala25 to Asp41 corresponded to the N-terminal sequence of the purified protein. The first 24 amino acids are presumed to be a signal peptide. The expression of lac1 is regulated at the transcription level by copper and various aromatic compounds. RT-PCR analysis of gene transcription in fungal mycelia grown on rice-straw revealed that, apart from during the early stages of substrate colonization, lac1 was expressed at every stage of the mushroom developmental cycle defined in this study, although the levels of transcription varied considerably depending upon the developmental phase. Transcription of lac1 increased sharply during the latter phase of substrate colonization and reached maximum levels during the very early stages (primordium formation, pinhead stage) of fruit body morphogenesis. Gene expression then declined to approximately 20-30% of peak levels throughout the subsequent stages of sporophore development.

Volvariella volvacea, strain V14, produces multiple forms of extracellular laccase when grown in submerged culture in a defined medium with glucose as sole carbon source, and on cotton waste 'compost' representative of the conditions used for industrial-scale mushroom cultivation. In liquid culture, enzyme synthesis is associated with the onset of secondary growth, and is positively regulated by copper (up to 200 microM CuSO(4)) and by various aromatic compounds. In solid-state systems, only low levels of laccase are detectable during the vegetative growth phase but enzyme activity increases sharply at the onset of fruiting and during sporophore development.

Silent Speech Interfaces (SSI) are sensor-based communication systems in which a speaker articulates normally but does not activate their vocal chords, creating a natural user interface that does not disturb the ambient audio environment or compromise private content, and may also be used in noisy environments where a clean audio signal is not available. The SSI field was launched 2010 in a special issue of Speech Communications, where systems based on ultrasound tongue imaging, electromyography, and electromagnetic articulography were proposed. Today, although ultrasound-based SSIs can achieve Word Error Rate scores rivaling those of acoustic speech recognition, they have yet to reach the marketplace due to performance stability problems. In recent years, numerous approaches have been proposed to address this issue, including better acquisition hardware; improved tongue contour tracking; Deep Learning analysis; and the association of ultrasound data with a real time 3D model of the tongue. After outlinin...

This work validates a new strategy for complete utilization of palm residues by separating fibers and parenchyma for the respective purposes of pulping and biorefining. The parenchyma cells were fractionated from royal palm sheath (RPS) after neutral sulfite semichemical (NSSC) cooking for producing fermentable sugars, leaving vascular bundles for manufacturing pulp and paper. Parenchyma cells could be readily and completely screened out prior to defibration. They were more digestible by cellulase than vascular bundles or the pulp derived from them. Cellulose enzymatic digestibility (CED) of parenchyma cells rapidly reached 82% in 12-h hydrolysis and finally up to 92%. The CEDs of parenchyma were maintained around 90% at a medium solid consistency, 12% (w/w). The average length, retention and drainability of RPS pulp were all improved without loss of physical strength after removing parenchyma. This work may help establish a new platform for maximizing the utilization efficiency of parenchyma-rich biomass.

Relevance of the retrieved documents to a query is in the sense of information retrieval a judgement of the user rather than the material implication in the sense of logic. In this paper we depart from deductive paradigm with object-oriented extensions, then relax the too strict modus ponens in the classic propositional logic by appropriate inference rules that would capture the relevance of information in the document to the information needed by the user. In such a framework, a document is relevant to a query if the latter can be deduced from the set of axioms associated with the document using inference rules. As various kinds of inference rules will be used in the deduction, we distinguish between logical, strict, and plausible rules. Answering a query in such a framework can be done either by a special query processor that supports different kinds of inference mechanisms, or by relaxing the original query so that it can be evaluated by an ordinary query processor. Instead of suggesting a new logic model, we make use of the query answering machinery of deductive and object-oriented database in this approach.

The bacterium Delftia sp. Cs1-4 produces novel extracellular structures (nanopods) in conjunction with its growth on phenanthrene. While a full genome sequence is available for Strain Cs1-4, genetic tools that could be applied to study phenanthrene degradation/nanopod production have not been reported. Thus, the objectives of this study were to establish such tools, and apply them for molecular analysis of nanopod formation and/or phenanthrene degradation. Three types of tools were developed and/or validated. First, we developed a new expression system based on a strong promoter controlling expression of a surface layer protein (NpdA) from Delftia sp. Cs1-4, which was ca. 2,500-fold stronger than the widely used lactose promoter. Second, the Cre-loxP system was validated for generation of markerless, in-frame, gene deletions, and for in-frame gene insertions. The gene deletion function was applied to examine potential roles in nanopod formation of three genes (omp32, lasI, and hcp), while the gene insertion function was used for reporter gene tagging of npdA. Lastly, pMiniHimar was modified to enhance gene recovery and mutant analysis in genome-wide transposon mutagenesis. Application of the latter to strain Cs1-4, several new genes with potential roles in phenanthrene degradation or npdA expression were identified. Collectively, the availability of these tools has opened new avenues of investigation in Delftia sp. Cs1-4 and other related genera/species with importance in environmental toxicology.

The hyperspectral remote sensing can detect the more detailed objects on earth surface for its hundreds of wave bands. This make it can be used for very detailed land cover mapping. The study area Yanhe river valley locates on the north west of China, its size of area is 7725 km2 and length 286.9km. The most objects on the area are vegetations including crops, trees, grasses, and water. For test the real accuracy of mapping with airborne hyperspectral remote sensing imagery, parts of the aerial surveying area were investigated and mapped manually during the photographing time. Because of the soil erosion and drought, the land covers are usually mixed especially the crops mixes with grasses, the tree seedling mixes with grasses and withered seedling, some fruit trees mix with crops etc. This is the big challenge of precise land cover mapping with hyperspectral remote sensing imagery. The present work focuses on the detailed vegetation classification problems especially the easy mixed classified objects. From the field investigation, some areas are not covered by single vegetation class but mixtures of multi-species of vegetation. This phenomenon may cause mixed pixel and misclassified problem or even unmixed pixel and right classified but the confused vision in map for the mixed colors in a continuous site of land cover. The general method to solve the mixed pixel problem is the spectral unmixing. But there are some questions in classical unmixing model, one of them is the equation of unmixing model is usually ill-conditioned because of the heavy correlation among hundreds of bands. The research proposed a feature subspace based spectral unmixing model. The unmixing was based on a feature subspace of full data space, the aim is to remove the amount of correlate information and get the right solution of components of endmemeber spectra. The subspace was constructed by principal component analysis(PCA) directions and the easy mixed classes oriented projection pursuit (PP) directions. For the unmixing model, the research discussed the results of unconstrained and constrained solutions. Based on the unmixing results, the land cover map was achieved and the accuracy was verified.

Strong promoters were isolated from Flavobacterium johnsoniae in a promoter-trap vector incorporating a gfp reporter system, and were used to express fluorescent protein markers (including GFP, YFP, mOrange and mStrawberry) and insecticidal protein genes in Flavobacterium strains. Sequence analysis of trapped DNA fragments showed conserved Bacteroidetes promoter motifs (TTG-N 19 -TAnnTTTG) located upstream of putative open reading frames. Plasmids harboring these genomic DNA fragments from F. johnsoniae promoted strong production of fluorescent proteins in Flavobacterium hibernum but not in Escherichia coli . The most potent promoter (P ompA ) identified in this work was cloned upstream of genes encoding fluorescent proteins, and these were co-expressed in Flavobacterium strains. The p42 and p51 genes (binary toxins from Bacillus sphaericus ) when translationally fused to the 3′-end of gfp showed strong expression. Flavobacteria expressing these genes exhibited toxicity against larvae of the mosquitoes Culex quinquefasciatus , Anopheles gambiae , and Ochlerotatus triseriatus . However, transformants with the transcriptional fusion construct between cry11A with p20 from Bacillus thuringiensis did not express Cry11A protein indicating that constitutive expression of cry11A may be problematic in Flavobacterium .

A dual luciferase reporter (DLR) system utilizing firefly and Renilla luciferases was developed and tested in a model rhizobacterium, Pseudomonas putida KT2440. The DLR was applied to simultaneously analyze expression of three putative bacterioferritin genes ( bfr α, bfr β, and bfr ) and assess the cellular iron status of strain KT2440 by monitoring expression of the Fur-regulated fepA - fes promoter. The DLR proved to be reproducible and sensitive. Expression of bfr α (PP0482) and bfr β (PP1082) was consistent with expectations for bacterioferritin and varied directly with the iron level. However, expression of bfr (PP4856) was inversely related to the iron concentration and it was thus more likely to encode a Dps-like protein rather than a bacterioferritin.

Larvae of the eastern tree hole mosquito, Ochlerotatus triseriatus (Say), and related container-breeding species are known to feed upon substrate-associated microorganisms. Although the importance of these microbial resources to larval growth has been established, almost nothing is known about the taxonomic composition and dynamics of these critical microbial food sources. We examined bacterial and fungal community compositional changes on oak leaves tethered in natural tree hole habitats of O. triseriatus. We eliminated larvae experimentally in a subset of the tree holes and examined 16S rDNA gene sequences for bacteria and ergosterol concentrations and 18S rRNA gene sequences for fungi collected from leaf material subsamples. Leaf ergosterol content varied significantly with time, but not treatment. Principal component analysis (PCA) was used to compare microbial taxonomic patterns found in leaves incubated with or without larvae present, and we found that larval presence affected both bacterial and fungal groups, either from loosely attached or strongly adherent categories. Bacterial communities generally grouped more tightly when larvae were present, and class level taxa proportions changed when larvae were present, suggesting selection by larval feeding or activities for particular taxa such as members of the Bacteroidetes, Alphaproteobacteria, and Betaproteobacteria classes. Fungal taxa composite scores also separated along PC axes related to the presence of larvae and indicated larval feeding effects on several higher taxonomic groups, including Saccharomycetes, Dothideomycetes, and Chytridiomycota. These results support the hypothesis that larval mosquito feeding and activities altered microbial communities associated with substrate surfaces, potentially leading to decreased food value of the resource and affecting decomposition of particulate matter in the system.

Sequences that mediate the initiation of transcription in Flavobacterium species are not well known. The majority of identified Flavobacterium promoter elements show homology to those of other members of the phylum Bacteroidetes , but not of proteobacteria, and they function poorly in Escherichia coli . In order to analyze the Flavobacterium promoter structure systematically, we investigated the −33 consensus element, −7 consensus element, and spacer length of the Flavobacterium ompA promoter by measuring the effects of site-directed mutations on promoter activity. The nonconserved sequences in the spacer region and in regions close to the consensus motifs were randomized in order to determine their importance for promoter activity. Most of the base substitutions in these regions caused large decreases in promoter activity. The optimal −33/−7 motifs (TTTG/TANNTTTG) were identical to Bacteroides fragilis σ ABfr consensus −33/−7 promoter elements but lacked similarity to the E. coli σ 70 promoter elements. The length of the spacer separating the −33 and −7 motifs of the ompA promoter also had a pronounced effect on promoter activity, with 19 bp being optimal. In addition to the consensus promoter elements and spacer length, the GC content of the core promoter sequences had a pronounced effect on Flavobacterium promoter activity. This information was used to conduct a scan of the Flavobacterium johnsoniae and B. fragilis genomes for putative promoters, resulting in 188 hits in B. fragilis and 109 hits in F. johnsoniae .