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Find video protocols related to scientific articles indexed in Pubmed.
Syndrome in question.
An Bras Dermatol
PUBLISHED: 09-04-2014
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Vulvovaginal-gingival syndrome is characterized by erosions and desquamation of the vulva, vagina, and gingiva. We reported a case of a 32-year-old woman presenting with an 8-year history of damage to the vulval and perianal anatomy and limitation of mouth opening. The patient's symptoms were relieved after treatment with topical tacrolimus cream.
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[Funding for division of microbiology by National Natural Science Foundation of China in 2013].
Wei Sheng Wu Xue Bao
PUBLISHED: 05-03-2014
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We provide an overview of proposals applied and projects funded by the division of microbiology, department of life sciences, National Natural Science Foundation of China in 2013,. The traits and problems in different sub-disciplines were also analyzed, which provides reference for Chinese researchers to apply funding in microbiology next year.
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Kissing nevus of the penis. Report of two cases and review of the literature.
An Bras Dermatol
PUBLISHED: 04-29-2014
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Kissing nevus is a curious type of nevus that was first described on the eyelids and rarely described on the penis. We report two cases of kissing nevus of the penis and review previously reported cases. The lesions of the kissing nevus of the penis showed characteristic mirror-image symmetry relative to the coronal sulcus. On histopathology, the lesion showed a compound nevus.
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[Blastic plasmacytoid dendritic cell neoplasm:a clinicopathologic study of 7 cases].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 04-26-2014
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To improve the clinicopathological understanding of blastic plasmacytoid dendritic cell neoplasm (BPDCN).
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Protein Network Signatures Associated with Exogenous Biofuels Treatments in Cyanobacterium Synechocystis sp. PCC 6803.
Front Bioeng Biotechnol
PUBLISHED: 01-01-2014
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Although recognized as a promising microbial cell factory for producing biofuels, current productivity in cyanobacterial systems is low. To make the processes economically feasible, one of the hurdles, which need to be overcome is the low tolerance of hosts to toxic biofuels. Meanwhile, little information is available regarding the cellular responses to biofuels stress in cyanobacteria, which makes it challenging for tolerance engineering. Using large proteomic datasets of Synechocystis under various biofuels stress and environmental perturbation, a protein co-expression network was first constructed and then combined with the experimentally determined protein-protein interaction network. Proteins with statistically higher topological overlap in the integrated network were identified as common responsive proteins to both biofuels stress and environmental perturbations. In addition, a weighted gene co-expression network analysis was performed to distinguish unique responses to biofuels from those to environmental perturbations and to uncover metabolic modules and proteins uniquely associated with biofuels stress. The results showed that biofuel-specific proteins and modules were enriched in several functional categories, including photosynthesis, carbon fixation, and amino acid metabolism, which may represent potential key signatures for biofuels stress responses in Synechocystis. Network-based analysis allowed determination of the responses specifically related to biofuels stress, and the results constituted an important knowledge foundation for tolerance engineering against biofuels in Synechocystis.
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In vitro antifungal activity of farnesyltransferase inhibitors against clinical isolates of Aspergillus and Candida.
Ann. Clin. Microbiol. Antimicrob.
PUBLISHED: 10-30-2013
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Protein farnesylation is an important tosttranslational modification in fungi. We evaluated the antifungal activity of two farnesyltransferase inhibitors against clinical isolates of Aspergillus and Candida. Unfortunately, the MICs were vastly higher than the concentrations that inhibit the proliferation and viability of mammalian cells.
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Complementary iTRAQ proteomics and RNA-seq transcriptomics reveal multiple levels of regulation in response to nitrogen starvation in Synechocystis sp. PCC 6803.
Mol Biosyst
PUBLISHED: 08-15-2013
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Sequential adaptation to environmental stress needs complex regulation at different cellular levels in cyanobacteria. To uncover the regulatory mechanism in response to nitrogen starvation, we investigated the genome-wide correlation between protein abundance and gene expression in a model cyanobacterium Synechocystis sp. PCC 6803 using complementary quantitative iTRAQ proteomics and RNA-seq transcriptomics. Consistent with the cell growth inhibition, proteomic analysis indicated phase-dependent down-regulation of proteins related to nitrogen metabolism, ribosome complexes, glycolysis pathway and tricarboxylic acid (TCA) cycles by nitrogen starvation. Transcriptomic analysis also showed that genes related to "Photosynthesis", "Protein synthesis" and "Energy metabolism" were significantly down-regulated by nitrogen starvation. Interestingly, the concordance between protein abundances and their corresponding mRNAs exhibited a functional categories-dependent pattern, with some categories, such as "Protein synthesis" and "Energy metabolism", having a relatively high correlation, while others even with numerous discordant changes in protein-mRNA pairs, indicated divergent regulation of transcriptional and post-transcriptional processes. In particular, an increased abundance of proteins related to "Photosynthesis" upon nitrogen starvation was found to be reversely correlated with the down-regulation of their corresponding mRNAs. In addition, two metabolic modules highly correlated with nitrogen starvation were identified by a co-expression network analysis, and were found to contain mostly photosynthetic proteins and hypothetical proteins, respectively. We further confirmed the involvement of the photosynthetic genes in nitrogen starvation tolerance by constructing and analyzing the psbV gene deletion mutant.
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Draft Genome Sequence of Lactococcus lactis subsp. lactis Strain YF11.
Genome Announc
PUBLISHED: 08-10-2013
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Lactococcus lactis subsp. lactis strain YF11 is a food preservative bacterium with a high capacity to produce nisin. Here, we announce the draft genome sequence of Lactococcus lactis subsp. lactis YF11 (2,527,433 bp with a G+C content of 34.81%).
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Integrated proteomic and transcriptomic analysis reveals novel genes and regulatory mechanisms involved in salt stress responses in Synechocystis sp. PCC 6803.
Appl. Microbiol. Biotechnol.
PUBLISHED: 06-08-2013
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Salt stress is a common stress that limits growth and productivity of photosynthetic microbes in natural environments. Although cellular responses of a model cyanobacterium Synechocystis sp. PCC6803 to high and changing salt concentration have been studied, it remains undefined of the gene components and their regulation in the long-term salt acclimation networks. In this study, we performed an integrated study coupling a quantitative iTRAQ-LC-MS/MS proteomics and a next-generation sequencing-based RNA-seq transcriptomics on Synechocystis under salt stress for an extended period of time. Comparative quantification of protein abundances led to the identification of 68 and 108 proteins differentially regulated by salt treatment at 24 and 48 h, respectively. RNA-seq transcriptomic analysis showed that genes involved in energy metabolism and protein synthesis, and genes encoding hypothetical proteins responded to salt stress in a phase-dependent pattern. Notably, a gene encoding CO2-uptake-related protein (CupA) and three genes encoding hypothetical proteins were induced significantly at either transcript or protein level after long-term salt stress. Gene knockout and comparative growth analysis demonstrated that these four genes were involved in salt tolerance in Synechocystis. In addition, a complementary proteome and transcriptome analysis showed that concordance between protein abundances and their corresponding mRNAs varied significantly between various gene-protein pairs, indicating divergent regulation of transcriptional and post-transcriptional processes during salt stress adaptation in Synechocystis. The study provided new insights on genes and regulatory mechanism involved in salt stress response in Synechocystis.
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Integrated OMICS guided engineering of biofuel butanol-tolerance in photosynthetic Synechocystis sp. PCC 6803.
Biotechnol Biofuels
PUBLISHED: 04-06-2013
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Photosynthetic cyanobacteria have been recently proposed as a microbial factory to produce butanol due to their capability to utilize solar energy and CO2 as the sole energy and carbon sources, respectively. However, to improve the productivity, one key issue needed to be addressed is the low tolerance of the photosynthetic hosts to butanol.
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Metabolic engineering of Escherichia coli for production of salvianic acid A via an artificial biosynthetic pathway.
Metab. Eng.
PUBLISHED: 02-04-2013
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Salvianic acid A, a valuable derivative from L-tyrosine biosynthetic pathway of the herbal plant Salvia miltiorrhiza, is well known for its antioxidant activities and efficacious therapeutic potential on cardiovascular diseases. Salvianic acid A was traditionally isolated from plant root or synthesized by chemical methods, both of which had low efficiency. Herein, we developed an unprecedented artificial biosynthetic pathway of salvianic acid A in E. coli, enabling its production from glucose directly. In this pathway, 4-hydroxyphenylpyruvate was converted to salvianic acid A via D-lactate dehydrogenase (encoding by d-ldh from Lactobacillus pentosus) and hydroxylase complex (encoding by hpaBC from E. coli). Furthermore, we optimized the pathway by a modular engineering approach and deleting genes involved in the regulatory and competing pathways. The metabolically engineered E. coli strain achieved high productivity of salvianic acid A (7.1g/L) with a yield of 0.47mol/mol glucose.
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Flame figures associated with eosinophilic dermatosis of hematologic malignancy: is it possible to distinguish the condition from eosinophilic cellulitis in patients with hematoproliferative disease?
Int J Clin Exp Pathol
PUBLISHED: 01-01-2013
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Eosinophilic dermatosis of hematologic malignancy is a multifaceted dermatosis with a wide morphological spectrum, presenting as pruritic, erythematous, papular and occasionally vesicular, urticarial, nodular eruptions. Histopathologically eosinophil infiltration in the super and deep dermis was found. We reported a case of eosinophilic dermatosis of hematologic malignancy presented as urticarial and vesicular lesions in a patient with chronic lymphocytic leukemia. A skin biopsy revealed a prominent subepidermal blister and a diffuse infiltrate of eosinophils with flame figures in the dermis and subcutaneous tissue. Although flame figures associated with eosinophilic dermatosis of hematologic malignancy is rarely reported, we believe that it would not seem unusual to find them in this skin disease. Eosinophilic cellulitis, which share clinical and histological features with eosinophilic dermatosis of hematologic malignancy, has also been described as showing an association with hematoproliferative diseases. In order to clearly describe eosinophilic dermatosis in patients with hematologic malignancies, the terminology eosinophilic dermatosis of hematologic malignancy, instead of eosinophilic cellulitis, would be a more suitable term in patients with eosinophilic dermatosis.
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Identification of a novel nonsense mutation in POLH in a Chinese pedigree with xeroderma pigmentosum, variant type.
Int J Med Sci
PUBLISHED: 01-01-2013
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Xeroderma pigmentosum-variant (XPV) is one type of XP, a rare autosomal recessive disorder, and caused by defects in the post replication repair machinery while nucleotide-excision repair (NER) is not impaired. In the present study, we reported a Chinese family with XPV phenotype, which was confirmed by histopathological results. Genetic variants were detected by polymerase chain reaction and exon sequencing. Furthermore, the reported molecular defects in XPV patients from previous literatures were reviewed. A homozygous c.67C>T mutation in the exon 2 of DNA polymerase eta (POLH), a novel non-sense mutation in POLH, was discovered.
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Extraction, purification and antibacterial activities of a polysaccharide from spent mushroom substrate.
Int. J. Biol. Macromol.
PUBLISHED: 09-27-2011
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To contribute towards effective exploitation and utilization of spent mushroom substrate (SMS), a water-soluble polysaccharide named PL was isolated and purified from SMS. The total sugar content and monosaccharide composition were analyzed by phenol-sulfuric acid method and capillary electrophoresis, and infrared spectroscopy was also performed for structure characterization. The results showed that the total sugar content of crude polysaccharide from SMS was about 25.8%, the polysaccharide contained two fractions (PL1 and PL2), which was mainly composed of glucose, rhamnose and mannose with a molar ratio of 1:3.13:1.16. The attributions of the main absorptions of both PL1 and PL2 were characteristic of glycosidic structures, and the FT-IR spectra of PL2 and lentinan were very similar. Escherichia coli, Staphylococcus aureus and Sarcina lutea were used to study the antibacterial activity and minimal inhibitory concentrations (MICs) of the polysaccharide. The antibacterial activity of polysaccharide from SMS against E. coli was the strongest, while the weakest against S. lutea, and the MICs of PL2 were 12.5, 25 and 100 ?g/mL, respectively.
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Prediction and Characterization of Missing Proteomic Data in Desulfovibrio vulgaris.
Comp. Funct. Genomics
PUBLISHED: 03-01-2011
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Proteomic datasets are often incomplete due to identification range and sensitivity issues. It becomes important to develop methodologies to estimate missing proteomic data, allowing better interpretation of proteomic datasets and metabolic mechanisms underlying complex biological systems. In this study, we applied an artificial neural network to approximate the relationships between cognate transcriptomic and proteomic datasets of Desulfovibrio vulgaris, and to predict protein abundance for the proteins not experimentally detected, based on several relevant predictors, such as mRNA abundance, cellular role and triple codon counts. The results showed that the coefficients of determination for the trained neural network models ranged from 0.47 to 0.68, providing better modeling than several previous regression models. The validity of the trained neural network model was evaluated using biological information (i.e. operons). To seek understanding of mechanisms causing missing proteomic data, we used a multivariate logistic regression analysis and the result suggested that some key factors, such as protein instability index, aliphatic index, mRNA abundance, effective number of codons (N(c)) and codon adaptation index (CAI) values may be ascribed to whether a given expressed protein can be detected. In addition, we demonstrated that biological interpretation can be improved by use of imputed proteomic datasets.
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Multiple paraneoplastic syndromes: myasthenia gravis, vitiligo, alopecia areata, and oral lichen planus associated with thymoma.
J. Neurol. Sci.
PUBLISHED: 02-22-2011
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Thymomas are associated with paraneoplastic autoimmune diseases at a high frequency. It is rare that four paraneoplastic autoimmune disorders co-occur in a single patient. We describe a thymoma patient with diagnoses of myasthenia gravis, vitiligo, alopecia areata, and oral lichen planus associated with a thymoma. After thymectomy, the weakness, vitiligo, alopecia and mucocutaneous lesions were improving progressively, possibly implicating the thymoma in initiating these autoimmune conditions. We believe that this is the first report of this particular combination of multiple paraneoplastic syndromes associated with thymoma.
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In vitro interaction of itraconazole with amphotericin B, caspofungin, and terbinafine against clinical isolates of Trichosporon asahii.
Mycopathologia
PUBLISHED: 08-30-2010
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Treatment of disseminated trichosporosis is still challenging. Itraconazole is a widely used broad-spectrum antifungal drug. In vitro interactions of itraconazole (ICZ) with amphotericin B (AMB), caspofungin (CAS), and terbinafine (TBF) against 18 clinical isolates of Trichosporon asahii were assessed by chequerboard microdilution method. ICZ combined with CAS showed the highest percentage of synergistic effect (72.2%), followed by ICZ/AMB (11%) and ICZ/TBF (11%) combination. Antagonistic effect was not observed. This study demonstrates that itraconazole can enhance the antifungal activity of CAS against T. asahii, suggesting that this combination may be a potential strategy for treating disseminated trichosporosis.
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Truncated Afyap1 attenuates antifungal susceptibility of Aspergillus fumigatus to voriconazole and confers adaptation of the fungus to oxidative stress.
Mycopathologia
PUBLISHED: 03-21-2010
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In yeasts truncated YAP1 homologues confer antifungal resistance. Our previous work has identified Afyap1, a YAP1 homologue, in Aspergillus fumigatus and found that it is responsible for oxidative stress in vitro. In order to decipher whether truncated Afyap1 involves in antifungal resistance mechanism and in oxidative stress adaptation in A. fumigatus, we introduce a putatively hyperactive truncated Afyap1 into wild-type A. fumigatus. We found that the resulted A. fumigatus containing truncated Afyap1 attenuated susceptibility to voriconazole and resistance to various oxidants. However, the Afyap1 deletion mutant and the strain harboring multiple copies of full-length Afyap1 had voriconazole susceptibility comparable with that of a wild-type A. fumigatus strain. Our study demonstrates that the truncated Afyap1 may involve in antifungal resistance to voriconazole in A. fumigatus and that the truncated Afyap1 sufficiently confers tolerance to oxidative stress in A. fumigatus.
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Photodynamic therapy in the treatment of superficial mycoses: an evidence-based evaluation.
Mycopathologia
PUBLISHED: 02-04-2010
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Photodynamic therapy (PDT) is effective in the destruction of fungi. In order to evaluate the efficacy and safety of PDT for superficial mycoses, we performed an evidence-based review of published literature. Database of MEDLINE, EMBASE, and Cochrane Library was searched until March 2010. English-language articles evaluating the efficacy and safety of PDT for superficial mycoses were included. No randomized clinical trials were found. Seven reports described the antifungal effect of PDT against 63 superficial mycoses patients. Eight of 10 (80%) tinea cruris patients and 6 of 10 (60%) tinea pedis were led to mycological cure after 1-3 treatments. Unfortunately, only 4 (40%) tinea cruris patients and 3 (30%) tinea pedis had a persist healing at the 8-week follow-up. Six of the 9 (66.7%) foot-interdigital mycoses patients recovered clinically and microbiologically after 1 or 4 treatments. Only 2 patients (22.2%) had a persist healing at the 8-week follow-up. Eleven of 30 (36.6%) onychomycosis patients were cure for 18 months after treatment, and 3 onychomycosis patients were all cure in other 2 reports. The therapeutic effect of PDT for one pityriasis versicolor patients was well. Overall tolerability of PDT was good. Therefore, it is unclear what PDTs place for superficial mycoses will be. Further clinical trials are needed to evaluate the efficacy of PDT to treat superficial mycoses. It is also important to optimize treatment protocols in order to cope with recurrence.
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In vitro interactions of micafungin with amphotericin B, itraconazole or fluconazole against the pathogenic phase of Penicillium marneffei.
J. Antimicrob. Chemother.
PUBLISHED: 02-17-2009
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Penicillium marneffei infection is an important disease among human immunodeficiency virus patients in south-east Asia, including southern China. However, therapeutic strategies are limited. Combination regimens with synergistic drugs could provide additional options for treating penicilliosis. We evaluated the in vitro efficacy of combining micafungin with amphotericin B, itraconazole or fluconazole against the pathogenic yeast form of P. marneffei.
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Amyloidosis cutis dyschromica.
Orphanet J Rare Dis
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Amyloidosis cutis dyschromica is a rarely documented variant of cutaneous amyloidosis. To date, only 26 cases have been reported.
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Atrophic dermatofibrosarcoma protuberans: report of a case demonstrated by detecting COL1A1-PDGFB rearrangement.
Diagn Pathol
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Dermatofibrosarcoma protuberans is a locally aggressive mesenchymal neoplasm. It usually presents as an indurated plaque that protrudes above the surface of the skin. Some patients have clinically persistent plaques that might be atrophic. The atrophic variant of dermatofibrosarcoma protuberans may be confused with some common skin diseases with atrophic appearance. We reported a 40-year-old woman who had a 10-year history of an atrophic dermatofibrosarcoma protuberans. Molecular analysis showed a fusion between COL1A1 exon 31 to exon 2 of PDGFB. The lesion was totally excised, with negative margins of the resection demonstrated by CD34 immunostaining. To our knowledge, this is the second case of atrophic dermatofibrosarcoma protuberans confirmed by detection of COL1A1-PDGFB fusion gene. This appears to be the first report of a fusion between COL1A1 exon 31 to exon 2 of PDGFB in atrophic dermatofibrosarcoma protuberans.
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Whole-genome sequence of Nocardiopsis alba strain ATCC BAA-2165, associated with honeybees.
J. Bacteriol.
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The actinomycete Nocardiopsis alba was reportedly associated with honeybees in separate occurrences. We report the complete genome of Nocardiopsis alba ATCC BAA-2165 isolated from honeybee guts. It will provide insights into the metabolism and genetic regulatory networks of this genus of bacteria that enable them to live in a range of environments.
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Quantitative proteomics reveals dynamic responses of Synechocystis sp. PCC 6803 to next-generation biofuel butanol.
J Proteomics
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Butanol is a promising biofuel, and recent metabolic engineering efforts have demonstrated the use of photosynthetic cyanobacterial hosts for its production. However, cyanobacteria have very low tolerance to butanol, limiting the economic viability of butanol production from these renewable producing systems. The existing knowledge of molecular mechanism involved in butanol tolerance in cyanobacteria is very limited. To build a foundation necessary to engineer robust butanol-producing cyanobacterial hosts, in this study, the responses of Synechocystis PCC 6803 to butanol were investigated using a quantitative proteomics approach with iTRAQ - LC-MS/MS technologies. The resulting high-quality dataset consisted of 25,347 peptides corresponding to 1452 unique proteins, a coverage of approximately 40% of the predicted proteins in Synechocystis. Comparative quantification of protein abundances led to the identification of 303 differentially regulated proteins by butanol. Annotation and GO term enrichment analysis showed that multiple biological processes were regulated, suggesting that Synechocystis probably employed multiple and synergistic resistance mechanisms in dealing with butanol stress. Notably, the analysis revealed the induction of heat-shock protein and transporters, along with modification of cell membrane and envelope were the major protection mechanisms against butanol. A conceptual cellular model of Synechocystis PCC 6803 responses to butanol stress was constructed to illustrate the putative molecular mechanisms employed to defend against butanol stress.
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Systematic characterization of hypothetical proteins in Synechocystis sp. PCC 6803 reveals proteins functionally relevant to stress responses.
Gene
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We described here a global detection and functional inference of hypothetical proteins involved in stress response in Synechocystis sp. PCC 6803. In the study, we first applied an iTRAQ-LC-MS/MS based quantitative proteomics to the Synechocystis cells grown under five stress conditions. The analysis detected a total of 807 hypothetical proteins with high confidence. Among them, 480 were differentially regulated. We then applied a Weighted Gene Co-expression Network Analysis approach to construct transcriptional networks for Synechocystis under nutrient limitation and osmotic stress conditions using transcriptome datasets. The analysis showed that 305 and 467 coding genes of hypothetical proteins were functionally relevant to nutrient limitation and osmotic stress, respectively. A comparison of responsive hypothetical proteins to all stress conditions allowed identification of 22 hypothetical proteins commonly responsive to all stresses, suggesting they may be part of the core stress responses in Synechocystis. Finally, functional inference of these core stress responsive proteins using both sequence similarity and non-similarity approaches was conducted. The study provided new insights into the stress response networks in Synechocystis, and also demonstrated that a combination of experimental "OMICS" and bioinformatics methodologies could improve functional annotation for hypothetical proteins.
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Quantitative iTRAQ LC-MS/MS proteomics reveals metabolic responses to biofuel ethanol in cyanobacterial Synechocystis sp. PCC 6803.
J. Proteome Res.
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Recent progress in metabolic engineering has led to autotrophic production of ethanol in various cyanobacterial hosts. However, cyanobacteria are known to be sensitive to ethanol, which restricts further efforts to increase ethanol production levels in these renewable host systems. To understand the mechanisms of ethanol tolerance so that engineering more robust cyanobacterial hosts can be possible, in this study, the responses of model cyanobacterial Synechocystis sp. PCC 6803 to ethanol were determined using a quantitative proteomics approach with iTRAQ LC-MS/MS technologies. The resulting high-quality proteomic data set consisted of 24,887 unique peptides corresponding to 1509 identified proteins, a coverage of approximately 42% of the predicted proteins in the Synechocystis genome. Using a cutoff of 1.5-fold change and a p-value less than 0.05, 135 and 293 unique proteins with differential abundance levels were identified between control and ethanol-treated samples at 24 and 48 h, respectively. Functional analysis showed that the Synechocystis cells employed a combination of induced common stress response, modifications of cell membrane and envelope, and induction of multiple transporters and cell mobility-related proteins as protection mechanisms against ethanol toxicity. Interestingly, our proteomic analysis revealed that proteins related to multiple aspects of photosynthesis were up-regulated in the ethanol-treated Synechocystis cells, consistent with increased chlorophyll a concentration in the cells upon ethanol exposure. The study provided the first comprehensive view of the complicated molecular mechanisms against ethanol stress and also provided a list of potential gene targets for further engineering ethanol tolerance in Synechocystis PCC 6803.
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Proteomic analysis reveals resistance mechanism against biofuel hexane in Synechocystis sp. PCC 6803.
Biotechnol Biofuels
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Recent studies have demonstrated that photosynthetic cyanobacteria could be an excellent cell factory to produce renewable biofuels and chemicals due to their capability to utilize solar energy and CO2 as the sole energy and carbon sources. Biosynthesis of carbon-neutral biofuel alkanes with good chemical and physical properties has been proposed. However, to make the process economically feasible, one major hurdle to improve the low cell tolerance to alkanes needed to be overcome.
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Structure-based phylogeny of polyene macrolide antibiotic glycosyltransferases.
Gene
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Antibiotic glycosyltransferases (AGts) attach unusual deoxy-sugars to aglycons so antibiotics can exert function. It has been reported that polyene macrolide (PEM) AGts have different evolutionary origin when compared with other polyketide AGts, and our previous analysis have suggested that they could be results of horizontal gene transfer (HGT) from eukaryotes. In this paper, we compared the structures of PEM AGts with structures of eukaryotes and other AGts, and then built models of the representative PEM AGts and GT-1 glycosyltransferases. We also constructed the Neighbor-Joining (NJ) trees based on the normalized Root Mean Square (RMS) distance, the Bayesian tree guided by structural alignments, and carried out analysis on several key conserved residues in PEM AGts. The NJ tree showed a close relationship between PEM AGts and eukaryotic glycosyltransferases, and Bayesian tree further supported their affinity with UDP-glucuronosyltransferases (UGTs). Analysis on key conserved residues showed that PEM AGts may have similar interaction mechanism such as in the formation of hydrogen bonds as eukaryotic glycosyltransferases. Using structure-based phylogenetic approaches, this study further supported that PEM AGts were the result of HGT between prokaryotes and eukaryotes.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.