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Perspective on the use of synthetic biology in rudimentary food fermentations

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systems microbiology and Biomanufacturing 2023年第1期3卷 150-165页

作者： Alexander da silva Vale Gilberto Vinícius de melo Pereira Leonardo martins santana Dão pedro de carvalho Neto Brigitte sthepani Orozco Colonia Vanete Thomaz soccol Bruna Leal maske Carlos Ricardo soccol Department of Bioprocess Engineering and Biotechnology Federal University of Paraná(UFPR)CuritibaPRBrazil Department of Genetics University of São Paulo(USP)Ribeirão PretoSPBrazil Federal Institute of Education Science and Technology of Paraná(IFPR)LondrinaPRBrazil

Rudimentary food fermentation can be defined as a spontaneous process of conversion of food components through enzy-matic action.A great variety of fermented foods are produced using spontaneous approaches;however,cocoa and coffee represent the most important agricultural commodities on international *** a manner to increase the efficiency of these processes,starter cultures have been developed and applied under field *** selection process begins with the recovery of microbial strains from spontaneous fermentation through phenotypic and metabolic ***,mutation-based breeding is used to develop and improve well-adapted starter *** advances in synthetic biology,especially in the last decade,the development of robust cellular fabrications with high fermentative capacity has become easier-largely due to the development of genomic approaches,such as next-generation sequencing techniques,CRIsPR-Cas system and bioinformatics *** review brings prospects on the use of synthetic biology to design new robust strains for use in cocoa and coffee fermentations,but which can be extended to other rudimentary *** addition,metabolic traits and target genes(e.g.,UvrA,RecA,GPD1,and GPP2)are proposed as a starting point for the improvement of cocoa and coffee ***,the regulatory and safety requirements for these food crops are *** review aims to stimulate research on the process of fermentation and the associated synthetic biology tools to produce fermented food efficiently and sustainably.

关键词： Coffee fermentation Cocoa fermentation starter cultures CRIsPR-Cas synthetic promoters

Web-based system for training and dissemination of a magnification chromoendoscopy classification

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World Journal of Gastroenterology 2008年第46期14卷 7086-7092页

作者： mário Jorge Dinis-Ribeiro Ricardo Cruz Correia Cristina santos sónia Fernandes Ernesto Palhares Rui Almeida silva pedro Amaro miguel Areia Altamiro Costa-Pereira Luis moreira-Dias Gastroenterology Department Portuguese Oncology Institute Center for Research in Information systems and Health Technologies (CINTEsIs)/Department of Biostatistics and medical Informatics Porto Faculty of Medicine Gastroenterology Department Coimbra University Hospital

AIm： To evaluate the use of web-based technologies to assess the learning curve and reassess reproducibility of a simplified version of a classification for gastric magnification chromoendoscopy （mC）. mETHODs： As part of a multicenter trial, a hybrid approach was taken using a CD-ROm, with 20 films of mC lasting 5 s each and an ＂autorun＂ file triggering a local HTmL frameset referenced to a remote questionnaire through an Internet connection. Three endoscopists were asked to prospectively and independently classify 10 of these films randomly selected with at least 3 d apart. The answers were centrally stored and returned to participants together with adequate feedback with the right answer. REsULTs： For classification in 3 groups, both intra- [Cohen＇s kappa （K） = 0.79-1.00 to 0.89-1.00] and inter-observer agreement increased from 1st （moderate） to 6th observation （k = 0.94）. Also, agreement with reference increased in the last observations （0.90, 1.00 and 1.00, for observers A, B and C, respectively）. Validity of 100% was obtained by all observers at their 4th observation. When a 4th （sub）group was considered, inter-observer agreement was almost perfect （K = 0.92） at 6th observation. The relation with reference clearly improved into K （0.93-1.00） and sensitivity （75%-100%） at their 6th observations. CONCLUsION： This mC classification seems to be easily explainable and learnable as shown by excellent intra- and inter-observer agreement, and improved agreement with reference. A web system such as the one used in this study may be useful for endoscopic or other image based diagnostic procedures with respect to definition, education and dissemination.

关键词： magnification Chromoendoscopy Reproducibility Learning curve

Which metrics drive macroinvertebrate drift in neotropical sky island streams?

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Water Biology and security 2023年第1期2卷 1-8页

作者： marcos Callisto Diego m.P.Castro marden s.Linares Laryssa K.carvalho Jose E.L.Barbosa Robert m.Hughes Universidade Federal de minas Gerais Instituto de Ci^encias BiologicasDepartamento de GeneticaEcologia e Evoluç~aoLaboratorio de Ecologia de BentosCP 486Av.Ant^onio Carlos6627PampulhaBelo HorizonteMGCEP 31270-901Brazil Laboratorio de Ecologia Aquatica Departamento de BiologiaCentro de Ci^encias.Biologicas e da SaúdeUniversidade Estadual da ParaíbaAv.das Bananeiras351BodocongoCampina GrandePBCEP 58429-500Brazil Amnis Opes Institute 2895 SE GlennCorvallisOR97333-2169USA Department of Fisheries Wildlife&Conservation Sciences104 Nash HallCorvallisOR97331-3803USA Universidade Federal de Lavras Departamento de Ecologia e Conservaç~aoPrograma de Pos Graduaç~ao em Ecologia AplicadaCEP 37200-900LavrasMinas GeraisBrazil

Despite long-standing interest,the mechanisms driving aquatic macroinvertebrate drift in tropical streams remain poorly ***,the objective of this study was to evaluate which environmental metrics drive macroinvertebrate drift in neotropical sky island *** evaluated whether altitude,the abundance of food resources,and variations in water quality influenced macroinvertebrate drift density,diversity,richness,and functional feeding *** hypothesis was developed to test whether increased altitude,lower food availability(particulate organic matter),and discharge would increase the density,taxonomic richness,and diversity of drifting *** headwater stream sites were sampled in the rainy and dry seasons in the Espinhaço meridional mountain Range(EmmR)of southeast *** were collected using drift nets deployed from 5:00 *** 8:00 *** abundance of food resources was assessed through estimates of coarse(CPOm)and fine(FPOm)particulate organic matter,and primary *** availability was an important explanatory variable for Gathering-Collectors and scrapers,Altitude was important for shredders and Predators,and Filtering-Collectors were linked to water discharge,suggesting that functional group drift masses were linked to different ecosystem *** temperature,conductivity,dissolved oxygen,current velocity,FPOm biomass and microbasin elevation range exerted little influence on macroinvertebrate *** taxa composition,this study also found that Baetidae and Leptohyphidae(Ephemeroptera)and Chironomidae and simuliidae(Diptera)were the most abundant groups drifting.

关键词： Biodiversity conservation stream processes macroinvertebrate functional groups Water quality serra do espinhaço

Performance and calibration of quark/gluon-jet taggers using 140 fb^(-1) of pp collisions at √s=13 TeV with the ATLAs detector

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Chinese Physics C 2024年第2期48卷 1-25页

作者： G. Aad B. Abbott K. Abeling N.J. Abicht s.H. Abidi A. Aboulhorma H. Abramowicz H. Abreu Y. Abulaiti B.s. Acharya C. Adam Bourdarios L. Adamczyk s.V. Addepalli m.J. Addison J. Adelman A. Adiguzel T. Adye A.A. Affolder Y. Afik m.N. Agaras J. Agarwala A. Aggarwal C. Agheorghiesei A. Ahmad F. Ahmadov W.s. Ahmed s. Ahuja X. Ai G. Aielli A. Aikot m. Ait Tamlihat B. Aitbenchikh I. Aizenberg m. Akbiyik T.P.A. Åkesson A.V. Akimov D. Akiyama N.N. Akolkar K. Al Khoury G.L. Alberghi J. Albert P. Albicocco G.L. Albouy s. Alderweireldt m. Aleksa I.N. Aleksandrov C. Alexa T. Alexopoulos F. Alfonsi m. Algren m. Alhroob B. Ali H.m.J. Ali s. Ali s.W. Alibocus m. Aliev G. Alimonti W. Alkakhi C. Allaire B.m.m. Allbrooke J.F. Allen C.A. Allendes Flores P.P. Allport A. Aloisio F. Alonso C. Alpigiani m. Alvarez Estevez A. Alvarez Fernandez m. Alves Cardoso m.G. Alviggi m. Aly Y. Amaral Coutinho A. Ambler C. Amelung m. Amerl C.G. Ames D. Amidei s.P. Amor Dos santos K.R. Amos V. Ananiev C. Anastopoulos T. Andeen J.K. Anders s.Y. Andrean A. Andreazza s. Angelidakis A. Angerami A.V. Anisenkov A. Annovi C. Antel m.T. Anthony E. Antipov m. Antonelli F. Anulli m. Aoki T. Aoki J.A. Aparisi Pozo m.A. Aparo L. Aperio Bella C. Appelt A. Apyan N. Aranzabal s.J. Arbiol Val C. Arcangeletti A.T.H. Arce E. Arena J-F. Arguin s. Argyropoulos J.-H. Arling O. Arnaez H. Arnold G. Artoni H. Asada K. Asai s. Asai N.A. Asbah J. Assahsah K. Assamagan R. Astalos s. Atashi R.J. Atkin m. Atkinson H. Atmani P.A. Atmasiddha K. Augsten s. Auricchio A.D. Auriol V.A. Austrup G. Avolio K. Axiotis G. Azuelos D. Babal H. Bachacou K. Bachas A. Bachiu F. Backman A. Badea P. Bagnaia m. Bahmani A.J. Bailey V.R. Bailey J.T. Baines L. Baines O.K. Baker E. Bakos D. Bakshi Gupta V. Balakrishnan R. Balasubramanian E.m. Baldin P. Balek E. Ballabene F. Balli L.m. Baltes W.K. Balunas J. Balz E. Banas m. Bandieramonte A. Bandyopadhyay s. Bansal L. Barak m. Barakat E.L. Barberio D. Barberis m. Barbero m.Z. Barel K.N. Barends T. Barillari m-s. Barisits T. Barklow P. Baron D.A. Baron mo The ATLAs Collaboration

The identification of jets originating from quarks and gluons,often referred to as quark/gluon tagging,plays an important role in various analyses performed at the Large Hadron Collider,as standard model measurements and searches for new particles decaying to quarks often rely on suppressing a large gluon-induced *** paper describes the measurement of the efficiencies of quark/gluon taggers developed within the ATLAs Collaboration,using √s=13 TeV proton–proton collision data with an integrated luminosity of 140 fb^(-1) collected by the ATLAs *** taggers with high performances in rejecting jets from gluon over jets from quarks are studied:one tagger is based on requirements on the number of inner-detector tracks associated with the jet,and the other combines several jet substructure observables using a boosted decision tree.A method is established to determine the quark/gluon fraction in data,by using quark/gluon-enriched subsamples defined by the jet *** in tagging efficiency between data and simulation are provided for jets with transverse momentum between 500 GeV and 2 TeV and for multiple tagger working points.

关键词： ATLAs JET QUARK GLUON TAGGING

Therapeutic and prophylactic thalidomide in TNBs-induced colitis: synergistic effects on TNF-α, IL-12 and VEGF production

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World Journal of Gastroenterology 2007年第15期13卷 2166-2173页

作者： Ana Teresa carvalho Heitor souza Antonio Jose Carneiro morgana Castelo-Branco Kalil madi Alberto schanaider Flavia silva Fernando Antonio Pereira Júnior márcia G Pereira Cláudio Tortori Ilana Dines Jane carvalho Eduardo Rocha Celeste Elia Departamento de Clínica médica Hospital Universitário Clementino Fraga Filho Brazil Departamento de Histologia e Embriologia Laboratório de Imunologia Celular Instituto de Ci(e|^)ncias BiomédicasUniversidade Federal do Rio de Janeiro21941-590Brazil Laboratório multidisciplinar de Pesquisa Anatomia Patológica Hospital Universitário Clementino Fraga FilhoBrazil e Cirurgia Experimental Hospital Universitário Clementino Fraga Filho Brazil

AIm： To evaluated the therapeutic and prophylactic effect of thalidomide on 2, 4, 6-trinitrobenzene sulfonic acid （TNBs）-induced colitis. Thalidomide has been reported to downregulate the expression of tumor necrosis factor α （TNF-α）, IL-12, and vascular endothelial growth factor （VEGF）, hallmarks of intestinal inflammation in Crohn＇s disease （CD）. mETHODs： male Wistar rats were divided in five groups of ten animals each. Four groups received a rectal infusion of TNBs in ethanol. The first group was sacrificed 7 d after colitis induction. The second and third groups received either thalidomide or placebo by gavage and were sacrificed at 14 d. The fourth group received thalidomide 6 h before TNBs administration, and was sacrificed 7 d after induction. The fifth group acted as the control group and colitis was not induced. Histological inflammatory scores of the colon were performed and lamina propria CD4＋ T cells, macrophages, and VEGF＋ cells were detected by immunohistochemistry. TNF-α and IL-12 were quantified in the supernatant of organ cultures by ELIsA. REsULTs： significant reduction in the inflammatory score and in the percentage of VEGF＋ cells was observed in the group treated with thalidomide compared with animals not treated with thalidomide. Both TNF-α and IL-12 levels were significantly reduced among TNBs induced colitis animals treated with thalidomide compared with animals that did not receive thalidomide. TNF-α levels were also significantly reduced among the animals receiving thalidomide prophylaxis compared with untreated animals with TNBs-induced colitis. Intestinal levels of TNF-α and IL-12 were significantly correlated with the inflammatory score and the number of VEGF＋ cells. CONCLUsION： Thalidomide significantly attenuates TNBs-induced colitis by inhibiting the intestinal production of TNF-α, IL-12, and VEGF. This effect may support the use of thalidomide as an alternate approach in selected patients with CD.

关键词： Thalidomide Experimental colitis Inflammatory bowel disease Tumor necrosis factor α IL-12 Vascular endothelial growth factor

Fluorescence of Chlorophyll a for Discovering Inhibitors of Photosynthesis in Plant Extracts

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American Journal of Plant sciences 2016年第11期7卷 1545-1554页

作者： Ana C. de carvalho Jéssica P. salvador Thais de m. Pereira pedro Henrique A. Ferreira João Carlos s. Lira Thiago A. m. Veiga Departamento de Ciências Exatas e da Terra Universidade Federal de Sao Paulo (UNIFESP) Sao Paulo Brasil

Aims: Twelve crude extracts were prepared from different parts of Pluchea sagittalis, Cecropia palmata and Brachiaria brizantha, and their effect on the light reaction of photosynthesis. study Design: Use of fluorescence of ChL a (Chlorophyll a) to detect inhibitors of photosynthesis in plant extracts. Place and Duration of study: Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Departamento de Ciências Exatas e da Terra, Universidade Federal de sao Paulo (UNIFEsP), between July 2015 and January 2016. methodology: The samples had their effect on the light reaction of photosynthesis studied by Chlorophyll a (Chl a) fluorescence transient by the use of chloroplasts isolated from spinach leaves. As negative controls we used the same amounts of DmsO that have been employed to solubilize the samples, and as positive control we have used 10 μm of the commercial herbicide DCmU (Diuron). Results: The extracts inhibited the photosynthesis, and their inhibition sites were located in the range of electron flow from OEC complex and between Psub>680sub> to Qsub>Asub> of Ps II, and inhibited the photosystem II (Ps II) by inducing the appearance of the transient bands K and J. Conclusion: Our results suggest an indicative that the photochemical apparatus probably is failing at the donor and acceptor sides of PsII, causing damage to electron transport during the photosynthesis phenomenon.

关键词： Fluorescence of ChL a Dereplication Photosynthesis Natural Products

Enzyme from Banana(musa sp.)Extraction Procedures for sensitive Adrenaline Biosensor Construction

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American Journal of Analytical Chemistry 2013年第6期4卷 293-300页

作者： solange carvalho da silva Célio Wisniewski pedro Orival Luccas Cristiana schmidt de magalhaes Exact sciences Institute Federal University of Alfenas—Unifal-MGAlfenasBrazil Chemistry Institute Federal University of Alfenas—Unifal-MGAlfenasBrazil

For building a biosensor, at least two enzyme sources can be employed. The pure enzyme has features with better selectivity and low stability. Crude extract presents better stability and wrong selectivity. Thus, one intermediate condition can be feasible joining both benefits of crude extract and pure enzymes. For that result, several procedures of extraction and semi purification of polyphenol oxidase (PPO) enzyme from banana (musa sp.) were studied. The results showed that cleaned enzymatic extracts presented higher specific activities than crude extracts (2.8 up to 5.3 fold), despite the total protein concentration diminishing from 27% up to 72%, indicating that polyphenol oxidase (PPO) enzyme was preserved in them. The biosensors with 125 AU mL-1 containing cleaned enzymatic extracts performed better by grinding or grinding plus sonication for 30 s. They were linear over the ranges of 5.9 × 10-6 mol·L-1 to 1.4 × 10-3 mol·L-1 and 7.9 × 10-8 mol·L-1 to 4.0 × 10-3 mol·L-1, respectively. The limit of Detection (LOD) was 5.9 × 10-6 mol·L-1 and 7.9 × 10-8 mol·L-1, respectively. The LOD obtained is adequate to adrenaline determination on blood and medicinal samples, and were applied in medicinal samples with satisfactory results.

关键词： Enzymatic Extract Epinephrine Biosensor Polyphenol Oxidase

What is the value of eucalyptus monocultures for the biodiversity of the Atlantic forest? A multitaxa study in southern Bahia, Brazil

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Journal of Forestry Research 2013年第2期24卷 263-272页

作者： pedro Luís Bernardo da Rocha Blandina Felipe Viana márcio Zikán Cardoso Amada mariana Costa de melo misonete Gueidneli Cavalcanti Costa Rodrigo Nogueira de Vasconcelos Tatiana Bichara Dantas Instituto de Biologia Universidade Federal da Bahia. Rua Bar o de Jeremoabo

Eucalyptus plantations are increasing in Brazil, frequently replacing pastures, but there is still scarce information about its capacity to maintain the fauna of neighbor forest remnants. In this study, we compared descriptors of the communities of leaf litter organisms （lizards, anurans, myriapods, arachnids, orthopterans, coleopterans, and ants） between a large remnant of primary Atlantic Forest and an adjacent eucalyptus monoculture （phase 1）. Then, we compared the same descriptors for leaf litter lizards and anurans, Euglossini bees, and frugivorous butterflies among the largest remnant, small remnants at intermediate regeneration stage, and eucalyptus monocultures that were not adjacent to the largest remnant （phase 2）. monocultures were sampled immediately before logging. In phase 1, we detected significant differences in structure between the forest and the monoculture in six out of seven communities sampled. Ca. 81% of the species of the landscape were recorded in the forest, but only 54% of these were found also in the monoculture. In phase 2, the structure of two out of four forest communities was significantly different from the structure of small remnants and monocultures. On average, 76% of the species found in the whole landscape were sampled in the forest. Out of this subset, on average 74% of the species were also sampled in small remnants and 68% in monocultures. Findings of the present study point out a moderate capacity of eucalyptus monocultures to harbor species of the forest fauna even when fully grown but highlights the opportunity that they might offer for increasing connectivity in anthropogenic forest landscapes depending on their management.

关键词： Atlantic forest monoculture biodiversity

Relationship between clinical remission of perianal fistulas in Crohn’s disease and serum adalimumab concentrations:A multicenter cross-sectional study

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World Journal of Gastroenterology 2022年第9期28卷 961-972页

作者： Laura sirmai Anne-Laure Pelletier Nathalie Gault Camille Zallot Guillaume Bouguen Dominique Bouchard Pascale Roland Nicaise marine Peyneau sandrine sironneau marcelo De carvalho Bittencourt Antoine Petitcollin pedro Fernandez Xavier Roblin Laurent siproudhis Laurent Abramowitz Division of Hepato-Gastroenterology and Digestive Oncology Bichat Claude Bernard University HospitalParis 75018France Division of Hepato-Gastroenterology Hospital Croix Saint SimonParis 75020France Division of Epidemiology Biostatistics and Clinical ResearchUniversity Hospital Center BichatParis 75018France National Institute of Health and medical Research CIC-EC1425 University Hospital Center BichatParis 75018France Division of Gastroenterology Nancy Regional and University Hospital CenterNancy 54035France Imphy CIC 1414 Group and Division of Gastroenterology and Hepatology University Hospital of RennesPontchaillouRennes 35033France Division of Proctology Hospital BagatelleTalence 33400France Division of Immunology University Hospital Center BichatParis 75018France Inflammation Microbiome and ImmunosurveillanceFaculty of PharmacyUniversitéParis-SaclayChâtenay-Malabry 92290France Division of Radiology Bagatelle Hospital CenterTalence 33400France Division of Immunology Nancy Regional and University Hospital CenterNancy 54000France University of Lorraine CNRS UMR 7365IMoPANancy 54000France Antoine Petitcol Department of Clinical and Biological Pharmacology and Pharmacovigilance Pharmacoepidemiology and Drug Information CenterRennes University HospitalRennes 35700France Division of Radiology University Hospital Center BichatParis 75018France Orangerie Center Le Perreux-sur-Marne 94170France Division of Gastroenterology CHU Saint EtienneSaint-Priest-en-Jarez 42270France Division of Gastroenterology and Hepatology and Proctology University Hospital Center BichatParis 75018France Ramsay GDs Clinique Blomet Paris 75018France

BACKGROUND Crohn’s disease(CD)is complicated by perianal fistulas in approximately 20%of *** permanent fistula closure remains a challenge for *** association between serum anti-tumor necrosis factor-αconcentrations and clinical outcomes in patients with CD has been demonstrated;however,little information is available on serum adalimumab(ADA)concentrations and remission of perianal fistulas in such *** To study the relationship between serum ADA concentrations and clinical remission of CDassociated perianal *** This cross-sectional study of patients with CD-associated perianal fistulas treated with ADA was performed at four French hospitals between December 2013 and march *** the time of each serum ADA concentration measurement,we collected information about the patients and their *** primary study endpoint was clinical remission of fistulas defined as the absence of drainage(in accordance with Present’s criteria),with a PDAI≤4,absence of a seton and assessment of the overall evaluation as favorable by the proctologist at the relevant *** also assessed fistula healing[defined as being in clinical and radiological(magnetic resonance imaging,mRI)remission]and adverse *** The study cohort comprised 34 patients who underwent 56 evaluations(patients had between one and four evaluations).Fifteen patients had clinical remissions(44%),four of whom had healed fistulas on *** ADA concentrations were significantly higher at evaluations in which clinical remission was identified than at evaluations in which it was not[14(10-16)vs 10(2-15)μg/mL,P=0.01].serum ADA concentrations were comparable at the times of evaluation of patients with and without healed fistulas[11(7-14)vs 10(4-16)μg/mL,P=0.69].The adverse event rate did not differ between different serum ADA *** We found a significant association between high serum ADA concentrations and clinical remission of CD-associated

关键词： Crohn’s disease Clinical pharmacology Peri-anal disorders Adalimumab