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Value of a newly sequenced bacterial genome

World Journal of Biological Chemistry 2014年第2期5卷 161-168页

作者： Eudes GV Barbosa flavia f aburjaile Rommel TJ Ramos Adriana R Carneiro Yves Le Loir Jan Baumbach Anderson Miyoshi Artur Silva Vasco Azevedo Laboratório de Genética Celular e Molecular Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte 31270-901 MG Brazil Department of Mathematics and Computer Science University of Southern Denmark5230 Odense Denmark INRA UMR1253 Science et Technologie du Lait et de l’uf F-35042 Rennes France Laboratório de Polimorfismo de DNA Instituto de Ciências Biológicas Univeridade Federal do Pará Belém 66075-110 Brazil

Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft(partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.

关键词： Next-generation sequencing Drafts Prokaryotic genomes Computational tools Omics

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Human leukocyte antigen compatibility and incidence of donorspecific antibodies in pediatric liver transplant recipients

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World Journal of Gastroenterology 2024年第33期30卷 3837-3845页

作者： Melina U Melere flavia H feier Jorge Neumann Antônio N Kalil Juliana de M Montagner Luiza S Nader Carolina S da Silva Marco Aurélio f Junior Gabriela P Coral Guilherme P Bobsin Cristina T ferreira Department of Hepatology and Liver Transplantation Santa Casa de Porto AlegrePorto Alegre 90050170Rio Grande do SulBrazil Department of Hepato-biliary-pancreatic Surgery and Liver Transplantation Irmandade Santa Casa de Misericórdia de Porto AlegrePorto Alegre 90020-090Rio Grande do SulBrazil Postgraduation Program in Medicine:Hepatology Federal University of Health Sciences of Porto AlegrePorto Alegre 90050-170Rio Grande do SulBrazil Laboratory of Transplantation Immunology Irmandade Santa Casa de Misericórdia de Porto AlegrePorto Alegre 90020-090Rio Grande do SulBrazil

BACKGROUND Antibody-mediated rejection following liver transplantation(LT)has been increasingly recognized,particularly with respect to the emergence of de novo donor-specific antibodies(DSAs)and their impact on graft *** substantial evidence for adult populations exists,research focusing on pediatric LT outcomes remains *** To investigate the prevalence of human leukocyte antigen(HLA)mismatches and DSA and evaluate their association with rejection episodes after pediatric *** A cohort of pediatric LT recipients underwent HLA testing at Santa Casa de Porto Alegre,Brazil,between December 2013 and December *** patients who survived for>30 days after LT with at least one DSA analysis were *** classes I and II and cross-matches were *** presence of de novo DSA(dnDSA)was evaluated at least 3 months after LT using the Luminex®single antigen bead method,with a positive reaction threshold set at 1000 *** episodes were confirmed by liver *** Overall,67 transplanted children were analyzed;61 received grafts from living donors,85%of whom were related to ***-transplant DSA(class I or II)was detected in 28.3%of patients,and dnDSA was detected in 48.4%.The median time to DSA detection after LT was 19.7[interquartile range(IQR):4.3-35.6]*** rejection occurred in 13 patients at follow-up,with C4d positivity observed in 5/13 Liver *** median time to rejection was 7.8(IQR:5.7-12.8)*** presence of dnDSA was significantly associated with rejection(36%vs 3%,Pfree survival rates at 12 and 24 months were 76%vs 100%and 58%vs 95%for patients with dnDSA anti-DQ vs those without,*** Our findings highlight the importance of incorporating DSA assessment into pre-and post-transplantation protocols for pediatric LT *** implications may include immunosuppression minimization strategies based on this analysis in pediatric LT recip

关键词： Human leukocyte antigens Donor-specific antibodies Liver transplantation Pediatric Rejection

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Evaluation of the Antibacterial and Antifungal Capacity of Nanoemulsions Loaded with Synthetic Chalcone Derivatives Di-Benzyl Cinnamaldehyde and Benzyl 4-Aminochalcone

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Journal of Renewable Materials 2024年第2期12卷 285-304页

作者： flavia Oliveira Monteiro da Silva Abreu Taysse Holanda Joice farias do Nascimento Henety Nascimento Pinheiro Rachel Menezes Castelo Hélcio Silva dos Santos Thais Benincá Patrícia da Silva Malheiros Júlio César Sousa Prado Raquel de Oliveira fontenelle Maria Madalena de Camargo forte Natural Polymers Laboratory PPGCNState University of CearáFortaleza60.714.903Brazil Polymeric Materials Laboratory PPGE3MFederal University of Rio Grande do SulPorto Alegre91501-970Brazil Natural Product Chemistry Laboratory PPGCNState University of CearáFortaleza60.714.903Brazil food Hygiene and Microbiology Laboratory PPGCTAFederal University of Rio Grande do SulPorto Alegre91501-970Brazil Microbiology Laboratory Medicine SchoolFederal University of CearáSobral62010-560Brazil

With the increase in antimicrobial resistance,it has become necessary to explore alternative approaches for combating and preventing ***-cinnamaldehyde(CNM)and Benzyl4-amino(B4AM)are bioactive compounds derived from chalcones but with restricted solubility in aqueous *** can enhance the solubility of compounds and can be a promising alternative in the development of novel antimicrobials,with reduced side effects and prolonged *** objective of this study was to evaluate the stability of oil-in-water nanoemulsions loaded with two distinct types of chalcones at two different dosages,to propose a stable formulation with antimicrobial *** showed that nanoemulsions presented high encapsulation efficiency,low polydispersity index(PDI)and particle size below 200 nm,indicating that emulsification was a suitable method for nanoemulsion *** with higher dosages exhibited significant antimicrobial effects when compared to free chalcones and positive ***,B4AM nanoemulsions at higher dosages showed expressive activity against Salmonella minnesota,with a 420%greater inhibitory response compared to the free form and showing equivalence to the positive *** nanoemulsions showed excellent inhibitory activity at the highest dosage,equivalent to the positive control against *** and Staphylococcus *** greater number of conjugated bonds in CNM increased the antimicrobial activity in comparison with B4AM,and the formation of nanometric domains enhanced the bioavailability,being a promising alternative for antimicrobial applications.

关键词： Polysaccharide nanoemulsions S.aureus S.minnesota chalcones alginate

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Consequences of Helicobacter pylori infection in children

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World Journal of Gastroenterology 2010年第41期16卷 5181-5194页

作者： Lucia Pacifico Caterina Anania John f Osborn flavia ferraro Claudio Chiesa Department of Pediatrics Sapienza University of Rome 324 I-00161 Rome Italy Department of Public Health Sciences Sapienza University of Rome I-00185 Rome Italy Department of Molecular Medicine National Research Council I-00133 Rome Italy

Although evidence is emerging that the prevalence of Helicobacter pylori (H. pylori) is declining in all age groups, the understanding of its disease spectrum continues to evolve. If untreated, H. pylori infection is lifelong. Although H. pylori typically colonizes the hu-man stomach for many decades without adverse con-sequences, children infected with H. pylori can manifest gastrointestinal diseases. Controversy persists regarding testing (and treating) for H. pylori infection in children with recurrent abdominal pain, chronic idiopathic thrombocytopenia, and poor growth. There is evidence of the role of H. pylori in childhood iron deficiency anemia, but the results are not conclusive. The possibility of an inverse relationship between H. pylori and gastroesophageal reflux disease, as well as childhood asthma, remains a controversial question. A better understanding of the H. pylori disease spectrum in childhood should lead to clearer recommendations about testing for and treating H. pylori infection in children who are more likely to develop clinical sequelae.

关键词： Helicobacter pylori Children Gastrointestinal diseases Epigastric pain Anemia Growth retardation Chronic idiopathic thrombocytopenic pupura

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Vitamin B12-induced spermatogenesis recovery in cimetidine-treated rats： effect on the spermatogonia number and sperm concentration

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Asian Journal of Andrology 2017年第5期19卷 567-572页

作者： flavia L Beltrame Estela Sasso-Cerri Department of Morphology and Genetics Federal University of Sao Paulo (UNIFESP/EPM) Sao Paulo Brazil Department of Morphology Laboratory f Histology and Embryology Dental School - Sao Paulo State University (UNESP/FOAr) Araraquara Sao Paulo Brazil

The H2-receptor antagonist cimetidine is an antiulcer drug also used for the treatment of cancer due to its antiangiogenic effect. However, this drug has caused structural changes in the seminiferous tubules. Vitamin B12 has been used as a therapeutic agent for the treatment of male infertility. The supplementation of rats with vitamin B12 during cimetidine treatment has recovered the damaged seminiferous tubules, but how this vitamin restores the seminiferous epithelium has not been clarified. In this study, we evaluated whether vitamin B12 improves the number of spermatogonia, spermatocytes, and sperm concentration in cimetidine-treated rats. Adult male rats were treated for 50 days as follows： cimetidine group received 100 mg kg^-1 b.w. of cimetidine, cimetidine-B12 group received cimetidine and 3 μg of vitamin B12-hydroxocobalamin, B12 group received only 3 μg of vitamin, and control group received saline. Sperm concentration was calculated and historesin-embedded testes sections were used for the quantitative analyses of spermatogonia （A; In/B） and spermatocytes. TUNEL method and PCNA immunofluorescence were performed. Cimetidine caused a significant reduction in sperm concentration. TUNEL-positive spermatogonia and spermatocytes were correlated to a significant reduction in the number of these cells. In cimetidine-B12 group, sperm concentration was higher than cimetidine group and a significant increase in the number of spermatogonia （stages Ⅱ-Ⅵ） was correlated to a high incidence of PCNA-immunolabeled spermatogonia and spermatocytes. The results show that the supplementation of rats with vitamin B12 during cimetidine treatment increases sperm concentration and exerts a potential effect in the recovery of spermatogonia and spermatocytes.

关键词： cimetidine fertility spermatogenesis testis vitamin B12

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Relaxant effect and possible mechanism of 17-nor-subincanadine E in rabbit corpora cavernosa

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Asian Journal of Andrology 2011年第5期13卷 747-753页

作者： Otacilio D Benvindo Nilberto Rf Nascimento Claudia f Santos Manasses C fonteles Edilberto R Silveira Daniel E Uchoa Adriana R Campos Karina MA Cunha flavia A Santos Vietla S Rao Department of Physiology and Pharmacology Faculty of Medicine Federal University of Ceara PO Box 3157 60430-270 Fortaleza CE Brazil Superior Institute of Biomedicine Caara State University Fortaleza CE Brazil Detriment of Organic and Inorganic Chemistry Federal University of Ceara 60455-760 Fortaleza CE Brazil

Compounds with dual action on cyclic adenosine monophosphate （cAMP） and cyclic guanosine monophosphate （cGMP） may be a treatment option for erectile dysfunction, as they not only promote penile erection but also prevent the upregulation of phosphodiesterase-5. In this study, we examined the possible relaxant effect and mechanism of 17-nor-subincanadine E （SEC, 0.2-200 pmol I^-1）, a plant-derived alkaloid, in rabbit corpus cavernosum （RbCC） strips that had been precontracted by exposure to phenylephrine （10 pmol I^- 1） or a high concentration of K＋（60 mmol I^- 1） in vitro. In addition to SEC＇s effect on cAMP and cGMP levels, electrical field stimulation （EfS） in phenylephrine-precontracted RbCC and calcium chloride （1-100 mmol I^-1） evoked responses in depolarized RbCC were analysed. SEC relaxed the phenylephrine-precontracted RbCCs in a concentration-dependent manner. Atropine, guanethidine and N-co-nitro-L-arginine methyl ester （L-NAME） did not have any effect on the relaxation of RBCCs. When 1H-1,2,4oxadiazole[4,3-a] quinoxalin-1-one （ODQ） was added, it effectively blocked the relaxant response of SEC. Although SEC enhanced the maximal relaxation produced by sodium nitroprusside （SNP） and forskolin in phenylephrine-precontracted cavernosal smooth muscle, it caused a decrease in the maximal contractile response induced by calcium chloride in depolarized RbCCs. The relaxant effect of SEC was paralleled by an increase in the tissue levels of the Cyclic nucleotides cAMP and cGMP. We conclude that SEC promotes the relaxation of RbCC, possibly favouring cAMP and cGMP accumulation and calcium blockade. This novel mechanism could be useful for patients who do not benefit from phosphodiesterase inhibitors and for those with endothelial and nitrergic dysfunction, such as patients with diabetes, hypertension and dyslipidaemias.

关键词： 17-nor-subincanadine E cyclic nucleotides electrical field stimulation nitric oxide rabbit corpus cavernosum smoothmuscle relaxation

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Prospects for sociogenomics in avian cooperative breeding and parental care

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Current Zoology 2020年第3期66卷 293-306页

作者： flavia TERMIGNONI-GARCIA Matthew I.M.LOUDER Christopher N.BALAKRISHNAN Lauren O’CONNELL Scott V.EDWARDS Department of Organismic and Evolutionary Biology Harvard UniversityCambridgeMA 02138USA Museum of Comparative Zoology Harvard UniversityCambridgeMA 02138USA International Research Center for Neurointelligence The University of TokyoHongoBunkyo-kuTokyo 113-0033Japan Department of Biology East Carolina UniversityGreenvilleNC 27858USA Department of Biology Stanford UniversityStanfordCA 94305USA

for the last 40 years,the study of cooperative breeding(CB)in birds has proceeded primarily in the context of discovering the ecological,geographical,and behavioral drivers of *** advent of molecular tools in the early 1990s assisted in clarifying the relatedness of helpers to those helped,in some cases,confirming predictions of kin selection *** for genome-wide analysis of sequence variation,gene expression,and epigenetics promise to add new dimensions to our understanding of avian CB,primarily in the area of molecular and developmental correlates of delayed breeding and dispersal,as well as the ontogeny of achieving parental status in ***,we outline key ways in which modern-omics approaches,in particular genome sequencing,transcriptomics,and epigenetic profiling such as ATAC-seq,can be used to add a new level of ana-lysis of avian *** on recent and ongoing studies of avian social behavior and sociogenom-ics,we review how high-throughput sequencing of a focal species or clade can provide a robust foundation for downstream,context-dependent destructive and non-destructive sampling of spe-cific tissues or physiological states in the field for analysis of gene expression and epigenetics.-Omics approaches have the potential to inform not only studies of the diversification of CB over evolutionary time,but real-time analyses of behavioral interactions in the field or *** of birds represents a new branch in the network of methods used to study CB,and can help clarify ways in which the different levels of analysis of CB ultimately interact in novel and unexpected ways.

关键词： ATAC-seq behavior convergent evolution epigenetics neurobiology phylogeny

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Morphology and Thermal Properties of Core-Shell PVA/PLA Ultrafine fibers Produced by Coaxial Electrospinning

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Materials Sciences and Applications 2015年第2期6卷 189-199页

作者： Raquel P.Goncalves flavia f.f.da Silva Paulo H.S.Picciani Marcos L.Dias Institute of Macromolecules Federal University of Rio de JaneiroRio de JaneiroBrazil

Coaxial electrospinning process was used to produce biodegradable membranes made of coreshell fibers of a poly(lactic acid) (PLA) shell and a poly(vinyl alcohol) (PVA) core. Scanning electron microscopy analyses of these structures showed that the PLA shell can present certain porosity depending on the process condition. fTIR-ATR and contact angle measurements also suggested imprisonment of the PVA core within the PLA shell. This type of structure was also confirmed by means of transmissions electron microscopy. The morphology of these fibers was dependent on the flow rate of both core and shell solutions, and homogeneous and smooth surface was only attained when the flow rate of the external PLA solution was 4 times the flow rate of the internal PVA solution. The increase in the PLA solution flow rate increases the diameter of the core-shell fiber which reaches up to 1.7 μm. Nevertheless, fibers with smaller average diameter could also be produced (200 nm). These core-shell fibers presented improved hydrophilicity as compared with monolithic PLA fibers.

关键词： Core-Shell fibers Electrospinning Poly(Lactic Acid) Poly(Vinyl Alcohol)

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Tailoring the partitioning of proteins using ionic liquids as adjuvants in polymer-polymer aqueous biphasic systems

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Green Chemical Engineering 2022年第4期3卷 328-337页

作者： flavia f.Magalhaes Matheus M.Pereira Rita de Cassia Superbi de Sousa Ana P.M.Tavares Joao A.P.Coutinho Mara G.freire CICECO-Aveiro Institute of Materials Department of ChemistryUniversity of AveiroAveiro3810-193Portugal Separation Process Laboratory(LPS) Department of Food TechnologyFederal University of Viçosa(UFV)P.H.Rolfs Av.s/n36570-000 ViçosaMGBrazil

Aqueous biphasic systems(ABS)are promising for proteins purification;however,when dealing with samples comprising several proteins,the selectivity towards a target protein is difficult to *** this work,the addition of ionic liquids(ILs)as adjuvants(5 wt%and 10 wt%)in ABS composed of polyethylene glycol(PEG)and dextran was investigated to tailor proteins partitioning between the coexisting *** liquid-liquid phase diagrams were determined at 298 K,followed by partition studies of three proteins(bovine serum albumin(BSA),immunoglobulin G(IgG),and cytochrome C(Cyt C)).Partition coefficients of IgG and BSA indicate the preference of both proteins to the dextran-rich phase,whereas Cyt C has no preferential partitioning between the *** addition of chloride-based ILs as adjuvants allows to increase or decrease the partition coefficients,thus tailoring the proteins partitioning between the *** partitioning essentially depends on the IL content in each phase,whereas Cyt C and IgG partitioning is ruled by the ILs chemical structure and established *** docking was carried out to address the ILs effect on the proteins partitioning,supporting experimental observations,while identifying the specific interactions *** partition of each protein in polymer-salt ABS with ILs as adjuvants was determined,demonstrating the higher tailoring ability of polymer-polymer ABS when adding ***,the partition of each protein in presence of the remaining ones was determined,as well as the selectivity of the studied systems to separate each pair of proteins,paving the way for their use in liquidliquid chromatography.

关键词： Aqueous biphasic systems Polymer-polymer systems Protein partition Ionic liquids Adjuvants

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Genetic diversity and population structure of Prochilodus costatus and Prochilodus argenteus preceding dam construction in the Paraopeba River,Sao francisco River Basin,Minas Gerais,Brazil

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Open Journal of Genetics 2012年第2期2卷 121-130页

作者： Tatiana M.Barroca fabio P.Arantes Barbara f.Magalhaes flavia f.Siqueira Carolina C.R.Horta Isabella f.Pena Jorge A.Dergam Evanguedes Kalapothakis Departamento de Biologia Geral Instituto de Ciencias BiologicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil Programa de Pos-Graduacao em Zoologia de Vertebrados Pontificia Universidade Catolica de Minas GeraisBelo HorizonteBrazil Departamento de Biologia Animal Centro de Ciencias Biologicas e da SaudeUniversidade Federal de VicosaVicosaBrazil

Curimat?-pioa (Prochilodus costatus) and curimat?-pacu (Prochilodus argenteus) are migratory fish species endemic to the S?o francisco River Basin in Brazil. Both species play important roles in local fisheries and ecology in the Paraopeba River. A dam was recently constructed on this river and to help in the development and conservation programs, we characterized the genetic variation of both species before dam construction. Complex hypervariable repeats micro-satellite was used to asses genetic variation for both species within and between the five collection sites in order to detect population substructuring. Nucleotide substitutions and insertion/deletion polymorphisms (indels) resulted in 35 P. costatus haplotypes (sample size = 89) and 22 P. argenteus haplotypes (sample size = 32). Significant genetic diversity and population differentiation was detected between five sampling sites for both species. Therefore, each of the five sites should be regarded as a group comprising significant genetic differences in species conservation and maintenance plans. Comparing these results to genetic diversity measures after dam construction will be critical for future management in this region.

关键词： freshwater fish Complex Hypervariable Repeats Microsatellite Genetic Diversity Population Structure

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