RESUMO
The common polyvinylidene fluoride (PVDF) membrane itself is susceptible to membrane fouling, especially biofouling, which is a serious threat. In this study, PVDF membrane was modified with ciprofloxacin (CIP) through co-blending to investigate the filtration properties, bacterial inhibition and fouling resistance. Modified membranes were prepared by adding 0.3 g (MC0.3), 0.6 g (MC0.6), 0.9 g (MC0.9) and 1.2 g (MC1.2) CIP per 100 g casting solution. Among these modified membranes, MC0.6 showed the best filtration performances, with the pure water flux stabilized at about 416.67 L/(m2·h) and bovine serum albumin (BSA) rejection of 92.0% at a trans-membrane pressure of 0.1 MPa. The pore size was reduced, the average roughness was reduced to 29.4 nm, the contact angle was lowered to 68.9°, and the hydrophilicity was greatly improved. The width of the inhibition circle produced by MC0.6 was 0.35-0.45 mm, and the modified membrane showed good inhibition of non-specific bacteria and algal removal during urban river water filtration. The rejection of BSA was increased by 16.32% compared to the base membrane and the adsorption rate for BSA was reduced by 68.45%. In addition, the removal of conventional pollutants in urban river water by the modified membranes for was also improved. Compared with that of the base membrane, the removal of TN, NH3-N, TP and COD by MC0.6 was increased by 10.58%, 12.45%, 15.44% and 13.53%. The results showed that CIP co-blending modified PVDF membrane could effectively improve membrane performances and has good value for water treatment.
Assuntos
Antibacterianos , Incrustação Biológica , Ciprofloxacina , Filtração , Membranas Artificiais , Polivinil , Purificação da Água , Polivinil/química , Ciprofloxacina/química , Ciprofloxacina/farmacologia , Filtração/métodos , Purificação da Água/métodos , Incrustação Biológica/prevenção & controle , Antibacterianos/química , Antibacterianos/farmacologia , Soroalbumina Bovina/química , Adsorção , Interações Hidrofóbicas e Hidrofílicas , Polímeros de FluorcarbonetoRESUMO
Concrete is the main ingredient in construction, but it inevitably fractures during its service life, requiring a large amount of cement and aggregate for maintenance. Concrete healing through biomineralization can repair cracks and improve the durability of concrete, which is conducive to saving raw materials and reducing carbon emissions. This paper reviews the biodiversity of microorganisms capable of precipitating mineralization to repair the concrete and their mineralization ability under different conditions. To better understand the mass transfer process of precipitates, two biomineralization mechanisms, microbially-controlled mineralization and microbially-induced mineralization, have been briefly described. The application of microorganisms in the field of healing concrete, comprising passive healing and intrinsic healing, is discussed. The key insight on the interaction between cementitious materials and microorganisms is the main approach for developing novel self-healing concrete in the future to improve the corrosion resistance of concrete. At the same time, the limitations and challenges are also pointed out.
Assuntos
Biomineralização , Carbonato de Cálcio , Materiais de Construção , Carbono , BiodiversidadeRESUMO
Most mammalian genes have mRNA variants due to alternative promoter usage, alternative splicing, and alternative cleavage and polyadenylation. Expression of alternative RNA isoforms has been found to be associated with tumorigenesis, proliferation and differentiation. Detection of condition-associated transcription variation requires association methods. Traditional association methods such as Pearson chi-square test and Fisher Exact test are single test methods and do not work on count data with replicates. Although the Cochran Mantel Haenszel (CMH) approach can handle replicated count data, our simulations showed that multiple CMH tests still had very low power. To identify condition-associated variation of transcription, we here proposed a ranking analysis of chi-squares (RAX2) for large-scale association analysis. RAX2 is a nonparametric method and has accurate and conservative estimation of FDR profile. Simulations demonstrated that RAX2 performs well in finding condition-associated transcription variants. We applied RAX2 to primary T-cell transcriptomic data and identified 1610 (16.3%) tags associated in transcription with immune stimulation at FDR < 0.05. Most of these tags also had differential expression. Analysis of two and three tags within genes revealed that under immune stimulation short RNA isoforms were preferably used.
Assuntos
Processamento Alternativo , Perfilação da Expressão Gênica/métodos , Poliadenilação , Linfócitos T CD4-Positivos/metabolismo , Linhagem Celular , Distribuição de Qui-Quadrado , Variação Genética , Genômica/métodos , Humanos , Isoformas de RNA/química , Isoformas de RNA/metabolismo , Estatísticas não Paramétricas , Transcrição GênicaRESUMO
Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.
Assuntos
Adaptação Fisiológica/genética , Evolução Molecular , Genoma , Mamíferos/genética , Substituição de Aminoácidos , Animais , Humanos , Fenótipo , Filogenia , Seleção GenéticaRESUMO
BACKGROUND: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the study of populations within and across species, and have informed the biology of humans. As only a few Metazoan genomes are approaching finished quality (human, mouse, fly and worm), there is room for improvement of most genome assemblies. The honey bee (Apis mellifera) genome, published in 2006, was noted for its bimodal GC content distribution that affected the quality of the assembly in some regions and for fewer genes in the initial gene set (OGSv1.0) compared to what would be expected based on other sequenced insect genomes. RESULTS: Here, we report an improved honey bee genome assembly (Amel_4.5) with a new gene annotation set (OGSv3.2), and show that the honey bee genome contains a number of genes similar to that of other insect genomes, contrary to what was suggested in OGSv1.0. The new genome assembly is more contiguous and complete and the new gene set includes ~5000 more protein-coding genes, 50% more than previously reported. About 1/6 of the additional genes were due to improvements to the assembly, and the remaining were inferred based on new RNAseq and protein data. CONCLUSIONS: Lessons learned from this genome upgrade have important implications for future genome sequencing projects. Furthermore, the improvements significantly enhance genomic resources for the honey bee, a key model for social behavior and essential to global ecology through pollination.
Assuntos
Abelhas/genética , Genes de Insetos , Animais , Composição de Bases , Bases de Dados Genéticas , Sequências Repetitivas Dispersas/genética , Anotação de Sequência Molecular , Fases de Leitura Aberta/genética , Peptídeos/análise , Análise de Sequência de RNA , Homologia de Sequência de AminoácidosRESUMO
Tumor-specific antigens (TSA) are central elements in the immune control of cancers. To systematically explore the TSA genome, we developed a computational technology called heterogeneous expression profile analysis (HEPA), which can identify genes relatively uniquely expressed in cancer cells in contrast to normal somatic tissues. Rating human genes by their HEPA score enriched for clinically useful TSA genes, nominating candidate targets whose tumor-specific expression was verified by reverse transcription PCR (RT-PCR). Coupled with HEPA, we designed a novel assay termed protein A/G-based reverse serological evaluation (PARSE) for quick detection of serum autoantibodies against an array of putative TSA genes. Remarkably, highly tumor-specific autoantibody responses against seven candidate targets were detected in 4% to 11% of patients, resulting in distinctive autoantibody signatures in lung and stomach cancers. Interrogation of a larger cohort of 149 patients and 123 healthy individuals validated the predictive value of the autoantibody signature for lung cancer. Together, our results establish an integrated technology to uncover a cancer-specific antigen genome offering a reservoir of novel immunologic and clinical targets.
Assuntos
Antígenos de Neoplasias/isolamento & purificação , Estudos de Associação Genética/métodos , Genômica/métodos , Imunoterapia , Terapia de Alvo Molecular , Neoplasias/terapia , Antígenos de Neoplasias/genética , Antígenos de Neoplasias/imunologia , Estudos de Casos e Controles , Feminino , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Estudo de Associação Genômica Ampla , Humanos , Imunoterapia/métodos , Masculino , Análise em Microsséries , Terapia de Alvo Molecular/métodos , Neoplasias/genética , Neoplasias/imunologia , Especificidade de Órgãos/genética , Integração de SistemasRESUMO
The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi.
Assuntos
Cromossomos Fúngicos/genética , Coprinus/genética , Evolução Molecular , Sequência de Bases , Mapeamento Cromossômico , Coprinus/citologia , Coprinus/crescimento & desenvolvimento , Sistema Enzimático do Citocromo P-450/genética , Primers do DNA/genética , Proteínas Fúngicas/genética , Duplicação Gênica , Genoma Fúngico , Meiose/genética , Dados de Sequência Molecular , Família Multigênica , Filogenia , Proteínas Quinases/genética , RNA Fúngico/genética , Recombinação Genética , Retroelementos/genéticaRESUMO
BACKGROUND: Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO) annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly. METHODS: A similarity-based (i.e., computational) GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked. RESULTS: In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO). In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57%) being annotated with 1,957 distinct and specific GO terms. Unannotated proteins were assigned to the 3 root terms. The Version 5 GO annotation is publically queryable via the GO site http://amigo.geneontology.org/cgi-bin/amigo/go.cgi. Additionally, the genome of M. oryzae is constantly being refined and updated as new information is incorporated. For the latest GO annotation of Version 6 genome, please visit our website http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html. The preliminary GO annotation of Version 6 genome is placed at a local MySql database that is publically queryable via a user-friendly interface Adhoc Query System. CONCLUSION: Our analysis provides comprehensive and robust GO annotations of the M. oryzae genome assemblies that will be solid foundations for further functional interrogation of M. oryzae.
Assuntos
Genoma Fúngico , Magnaporthe/genética , Terminologia como Assunto , Biologia Computacional , Bases de Dados de Proteínas , Proteínas Fúngicas/genética , Oryza/microbiologia , Alinhamento de Sequência , Análise de Sequência de Proteína , Vocabulário ControladoRESUMO
BACKGROUND: The Cytochrome P450 system is important in fungal evolution for adapting to novel ecological niches. To elucidate the evolutionary process of cytochrome P450 genes in fungi with different life styles, we studied the patterns of gene gains and losses in the genomes of four filamentous Ascomycetes, including two saprotrophs (Aspergillus nidulans (AN) and Neurospora crassa (NC)) and two plant pathogens (Fusarium graminearum (FG) and Magnaporthe grisea (MG)). RESULTS: A total of 376 P450 genes were assigned to 168 families according to standard nomenclature. On average, only 1 to 2 genes per family were in each genome. To resolve conflicting results between different clustering analyses and standard family designation, a higher order relationship was formulated. 376 genes were clustered into 115 clans. Subsequently a novel approach based on parsimony was developed to build the evolutionary models. Based on these analyses, a core of 30 distinct clans of P450s was defined. The core clans experienced contraction in all four fungal lineages while new clans expanded in all with exception of NC. MG experienced more genes and clans gains compared to the other fungi. Parsimonious analyses unanimously supported one species topology for the four fungi. CONCLUSION: The four studied fungi exhibit unprecedented diversity in their P450omes in terms of coding sequence, intron-exon structures and genome locations, suggesting a complicated evolutionary history of P450s in filamentous Ascomycetes. Clan classification and a novel strategy were developed to study evolutionary history. Contraction of core clans and expansion of novel clans were identified. The exception was the NC lineage, which exhibited pure P450 gene loss.
Assuntos
Ascomicetos/genética , Sistema Enzimático do Citocromo P-450/genética , Evolução Molecular , Genes Fúngicos , Filogenia , Motivos de Aminoácidos , Sequência de Aminoácidos , Ascomicetos/enzimologia , Aspergillus nidulans/enzimologia , Aspergillus nidulans/genética , Sequência Conservada , Éxons , Fusarium/enzimologia , Fusarium/genética , Duplicação Gênica , Íntrons , Magnaporthe/enzimologia , Magnaporthe/genética , Família Multigênica , Neurospora crassa/enzimologia , Neurospora crassa/genéticaRESUMO
Fungi have an astounding and diverse impact on this planet. While they are agents of human diseases and the cause of allergic reactions, factories for the conversion of carbon in environmental and industrially adapted systems, and potential biological weapons, their importance as plant pathogens is unparalleled. In plants alone, fungi cause tens of thousands of different diseases and are responsible for massive losses of food, fiber and forestry at an estimated annual cost of hundreds of billions of dollars. These losses are not only realized in the incomes of individual farmers and state economies, but contribute significantly to world hunger problems and issues relating to safeguarding a global food supply. Our collective understanding of how fungi, particularly plant pathogens, grow, reproduce, identify a host and cause disease is still at a formative stage. There is an equal lack of detailed knowledge about how a plant recognizes that it is being attacked and then mounts an adequate defense response. The advent of genomic technologies has given researchers an unprecedented opportunity to address these mysteries in a powerful and more holistic manner. Where the genetic revolution of only a few years ago allowed for the characterization of single genes, today's genomic technologies are facilitating the evaluation of the entire complement of genes in an organism and the discovery of the suites of genes that act during any one time or particular condition. This review will describe the recent development of tools for whole or partial genome analysis and multigenome comparisons. Th discussion focuses on the rice blast pathosystem as a case study.