Báo cáo khoa học: Prediction of missing enzyme genes in a bacterial metabolic network Reconstruction of the lysine-degradation pathway ofPseudomonas aeruginosa doc

... missing enzyme genes in a bacterial metabolic network Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa Yoshihiro Yamanishi1, Hisaaki Mihara2, Motoharu Osaki2, Hisashi ... eukaryotes and archaea, and thereis also variation within bacteria. We also focused on the lysine-degradation pathway because the substratesand intermediates of the pathway are structurally ... topredict the candidate genes corresponding to missing enzymes in this pathway. There are two paths froml-lysine to glutarate in the lysine-degradation pathway: l-lysine ﬁ 5-amino pentanamide ﬁ 5-amino...

Báo cáo khoa học: Metabolomics, modelling and machine learning in systems biology – towards an understanding of the languages of cells potx

... hypotheses that are consistent with the data and achieve this in a value-free manner. Much of classical biochemis-try and signalling pathway analysis has concentrated on the analyses of changes in the ... visualiz-ing, and integrating molecular pathway data. J BiomedInform 37, 43–53.306 Hoffmann R, Krallinger M, Andres E, Tamames J,Blaschke C & Valencia A (2005) Text mining for meta-bolic pathways, ... is a human being in the loop, and the number of experiments that can be evaluated is corre-spondingly small.As indicated above, active learning methods areattractive, and, in a manner related...

Báo cáo khoa học: "Prediction of Learning Curves in Machine Translation" ppt

... Since ad-hoc manual translation canrepresent a signiﬁcant investment in time andmoney, a prior assesment of the amount of training data required to achieve a satisfac-tory accuracy level can ... Linguistics Prediction of Learning Curves in Machine TranslationPrasanth Kolachina∗Nicola Cancedda†Marc Dymetman†Sriram Venkatapathy†∗ LTRC, IIIT-Hyderabad, Hyderabad, India† Xerox Research Centre ... that a given amount of additionaltraining data is more advantageous when added to a small rather than to a big amount of initial data. The last condition is related to our use of BLEU —which...

Báo cáo khoa học: "Prediction of Thematic Rank for Structured Semantic Role Labeling" doc

... referenced argument of a j, 5) a iACaj: a jis the continuation argument of a i, 6) a iCAaj: a iis the continuation argument of a j, 7) a i= a j: a iand a jare labeled as the same role label, ... automatic parsing data.2 Prediction of Thematic Rank2.1 Ranking Arguments in PropBankThere are two main problems in modeling the- matic hierarchy for SRL on PropBank. On the onehand, there is ... a iand a j in this paper include: 1) a i a j: a iis higher than a j, 2) a i≺ a j: a iis lower than a j, 3) a iARaj: a jis the referenced argument of a i, 4) a iRAaj: a iis the referenced...

Báo cáo khoa học: Prediction of coenzyme speciﬁcity in dehydrogenases ⁄ reductases A hidden Markov model-based method and its application on complete genomes doc

... groups and testing against the remaining group and a false data set. The false data setswere created by dividing the remaining sequences in the ASTRAL data set (4701 sequences) into six equally ... mem-brane-attached. The transmembrane (TM) helix can befound in either the N-terminal part of the protein, as in 11-beta hydroxysteroid dehydrogenase type 1 [11], or in the C-terminal, as in monoamine ... obtain a trustworthytest set. The selected proteins belong to the folds ‘NAD(P)-binding Rossmann-fold domain’, ‘FAD ⁄ NAD(P)-bindingdomain’ and ‘Nucleotide-binding domain’. The dataset wasscrutinized...

Tài liệu Báo cáo khoa học: Hypothalamic malonyl-CoA and CPT1c in the treatment of obesity pptx

... catalyzed by ACC – the key reg-ulatory enzyme in the pathway. Malonyl-CoA serves as the basic chain-elongating substrate for the formation of long-chain saturated fatty acids catalyzed by FAS.It ... in various organ systems. Even in organismslacking a brain, such as Caenorhabditis elegans, the nervous system plays a key role in maintaining energybalance [1–4]. In more advanced, mammalian ... chain is trans-ferred back to coenzyme A via the malonyl-CoAinsensitive CPT2 [41–45].There are at least six carnitine acyltransferases in mammals [46]. Carnitine acetyltransferase and carni-tine...

Tài liệu Báo cáo khoa học: Anaerobic sulfatase-maturating enzyme – A mechanistic link with glycyl radical-activating enzymes? docx

... 5¢-GCCGTA GCC AAC CTC GCA GCC GAA TAC GCC TATTAT-3¢ and 5¢- ATA ATA GGC GTA TTC GGC TGCGAG GTT GGC TAC GGC-3¢; for the C27 6A ⁄ C28 2A mutant, 5¢-GGC GTA GCT ACA ATG GCG AAG CATGCC GGA CAT-3¢ and ... of radical-AdoMet enzymes.AbbreviationsAdoMet, S-adenosyl-L-methionine; anSME, anaerobic sulfatase-maturating enzyme; anSMEbt, Bacteroides thetaiotaomicron anaerobicsulfatase-maturating enzyme; ... 5¢-ATG TCC GGC ATG CTTCGC CAT TGT AGC TAC GCC-3¢; and for the C33 9A ⁄ C34 2A ⁄ C34 8A mutant, 5¢- ACC CAA GCC AAGGAG GCC GAC TTT CTA TTT GCC GCC AAC GGA-3¢ and 5¢-TCC GTT GGC GGC AAA TAG AAA...

Tài liệu Báo cáo khoa học: High-afﬁnity ligand binding by wild-type/mutant heteromeric complexes of the mannose pptx

... anunexpected decrease in PMP-BSA binding. It thusappears that tethering of the C-terminal end of the ectodomain is important for both IGF-II and PMP-BSA binding. In summary, the major ﬁndings ... shown asrectangles. The shaded rectangles indicate repeats 3 and 9, towhich the main determinants of Man-6-P binding have beenmapped. The stippled rectangles represent repeat 11 containing the ... percentage of binding would follow the line displayed in the bar graph. However, the datashow that when a mutant FLAG-tagged mini-receptorserved as the ‘bait’ for immunoprecipitation, bindingof...

Tài liệu Báo cáo khoa học: 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5¢-phosphate synthases of fungi and archaea docx

... riboﬂavin biosynthetic pathway in plants is similarto that of eubacteria, rather than that in fungi andarchaea. In view of the close similarity between puta-tive plant deaminases and their apparently ... putative plant pyrimidine reductasedomains catalyse the equivalent reduction to RibDproteins. In these proteins, the associated deaminasedomains lack an invariant zinc-binding motif [18]. Ithas been ... synthases usingNADPH as cosubstrate results in progressive disap-pearance of substrate signals and the appearance of a singlet at 42 p.p.m., reﬂecting the 1¢ carbon of the ribi-tyl side chain of...

Tài liệu Báo cáo khoa học: DNA modiﬁcation with cisplatin affects sequence-speciﬁc DNA binding of p53 and p73 proteins in a target site-dependent manner pptx

... fragmentwas treated with cisplatin in the same way, the inten-sity of the R53band on the autoradiogram increasedwith the degree of DNA modiﬁcation. The increasewas already signiﬁcant at ... double-strandedDNA containing the major adduct of the anticancerdrug cisplatin. Nature 377, 649–652.29 Zlatanova J, Yaneva J & Leuba SH (1998) Proteins thatspeciﬁcally recognize cisplatin-damaged DNA: ... monofunctional adducts. It has been foundthat cisplatin cytotoxicity is related mainly to the IACsthat induce signiﬁcant changes in the DNAconformation, including bending and unwinding of the DNA double...

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