The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records ...(http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of annotated genomic, transcript and protein sequence records derived from data in public ...sequence archives and from computation, curation and collaboration (http://www.ncbi.nlm.nih.gov/refseq/). We report here on growth of the mammalian and human subsets, changes to NCBI's eukaryotic annotation pipeline and modifications affecting transcript and protein records. Recent changes to NCBI's eukaryotic genome annotation pipeline provide higher throughput, and the addition of RNAseq data to the pipeline results in a significant expansion of the number of transcripts and novel exons annotated on mammalian RefSeq genomes. Recent annotation changes include reporting supporting evidence for transcript records, modification of exon feature annotation and the addition of a structured report of gene and sequence attributes of biological interest. We also describe a revised protein annotation policy for alternatively spliced transcripts with more divergent predicted proteins and we summarize the current status of the RefSeqGene project.
Splice site consensus sequences alone are insufficient to specify the recognition of real splice sites within large transcripts, and both pseudo splice sites with good matches to the consensus ...sequences and pseudo exons flanked by pseudo splice sites are abundant in large transcripts. Selection of the correct splice sites, and therefore real exons, from the sea of potential ones is a major open question in RNA splicing. My approach to the splice site selection problem has been to study why these pseudo exons and pseudo splice sites are not used. I first focused on analyzing the defects of splice signals flanking a pseudo exon (pseudo exon 1), identified in the intron 1 of human hprt gene (Chapter II). In order to identify elements that prevent pseudo exon 1 splicing, I systematically altered known splicing signals and adjacent flanking sequences of pseudo exon 1 and assayed splicing in transfected cells. My results pinpointed a number of defects in putative splice signals flanking pseudo exon 1. These include a defective 5′ splice site, a defective polypyrimidine tract, as well as an intronic splicing silencer. In contrast, the pseudo exon body did not exert a negative influence on splicing. My results suggest that exon-bridging enhancers are not a prerequisite for constitutive exon definition, and that intrinsic defectiveness and negative elements may play important roles in distinguishing the real from false splicing signals (Chapter II). Then, I further characterized these pseudo splice signals using in vitro splicing and spliceosome assembly. My data suggests that an exon splicing enhancer is not a prerequisite for constitutive splicing in vitro as well. Using simplified 3′ half substrates, I showed pseudo 3′ splice sites failed to direct the assembly of alpha complexes. The pseudo 5′ splice site did not promote in vitro splicing in an assay for exon definition. These in vitro results with pseudo splice sites are consistent with their lack of in vivo function and further suggest that some pseudo splice sites may indeed be intrinsically defective despite a good agreement to the consensus.
Foodborne pathogenic bacteria is a serious threat to food safety, endangers human health, and can cause huge economic losses. Thus, there is a vital need for development of novel anti-bacterial ...agents with feature of enhanced antimicrobial activity and high bio-safety, which have almost no influence on textural and flavor perspectives of foods. Polysaccharides are natural macromolecular polymers that are widespread in nature and have attracted much attention due to their significant bio-activities. Although polysaccharides have been demonstrated for their activities against foodborne pathogens, their antibacterial abilities and modes of action have not been systematically discussed. This review presented herein focuses on diverse antibacterial mechanisms of polysaccharides. Actually, their antibacterial mode of action was shown to be via damaging cellular structural and inhibiting bioenergetics metabolism. Additionally, for the higher antibacterial activity, probably also the new antibacterial mechanism of polysaccharides and the strategies should be developed. Accordingly, this review could open the door for the production and application of polysaccharides as novel antibacterial agents and green preservatives in the food field.
•Foodborne pathogenic contamination causes economic loss and public health problem.•Polysaccharides are promising preservatives against foodborne pathogens.•The possible mechanisms of polysaccharides against bacteria were summarized.•Further antibacterial mechanisms of polysaccharides are recommended.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Previously, an antioxidant xanthan-oligosaccharide (LW-XG) was successfully produced via bio-degradation of commercial xanthan. In present work, the antibacterial activity and mechanism action of ...LW-XG against Staphylococcus aureus were studied. Inhibition zone of LW-XG in agar diffusion test was evident and its minimal inhibitory concentration (MIC) against S. aureus was 0.63 mg/mL. Inhibitory mechanism investigation showed that LW-XG increased the cell membrane permeability of S. aureus. Meanwhile, we found that LW-XG could retard the formation of S. aureus biofilm and lower the transcriptional levels of genes (fnbA, fnbB and clfB) related to biofilm formation. Furthermore, LW-XG decreased the Ca2+-Mg2+-ATPase activity on S. aureus cell membrane and promoted the accumulation of calcium ions in cytoplasm. Overall, LW-XG could inhibit the growth of S. aureus and be regarded as a promising antibacterial substitute in food and pharmaceutical industries.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
GCP, a polysaccharide produced by endophytic fungus Chaetomium globosum CGMCC 6882, was found to be antibacterial against Staphylococcus aureus via disrupting cell permeability. However, the ...antibacterial mechanism of GCP has not been studied before. In present work, results showed that GCP could retard the growth of S. aureus by inducing the depolarization of cell membrane, decreasing the activity of Ca2+-Mg2+-ATPase on cell membrane, and increasing the accumulation of calcium ions in cytoplasm. Moreover, we found that GCP could also inhibit the synthesis of whole cell proteins of S. aureus. Overall, this study proved that the antibacterial mechanism of GCP could be diversified and more studies are needed in the investigation of the antibacterial mechanisms of various polysaccharides.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
This study investigated the effect of molecular weight on antibacterial activity of polysaccharides. Results showed that low molecular weight (3.105 × 104 Da) polysaccharide (GCP-2) had higher ...inhibitory effects against Escherichia coli and Staphylococcus aureus than high molecular weight (5.340 × 104 Da) polysaccharide (GCP-1). Meanwhile, antibacterial activities of GCP-2 and GCP-1 against S. aureus were higher than those of E. coli. Minimum inhibitory concentrations (MICs) of GCP-1 against E. coli and S. aureus were 2.0 mg/mL and 1.2 mg/mL, and MICs of GCP-2 against E. coli and S. aureus were 1.75 mg/mL and 0.85 mg/mL, respectively. Antibacterial mechanisms investigation revealed that GCP-2 and GCP-1 influenced cell membrane integrity, Ca2+-Mg2+-ATPase activity on cell membrane and calcium ions in cytoplasm of E. coli and S. aureus, but not cell wall. Present work provided important implications for future studies on development of antibacterial polysaccharides based on molecular weight feature.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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