A new set of bioinformatics tools for genome projects

A new tool called System for Automated Bacterial Integrated Annotation--SABIA (SABIA being a very well-known bird in Brazil) was developed for the assembly and annotation of bacterial genomes. This system performs automatic tasks of assembly analysis, ORFs identification/analysis, and extragenic region analyses. Genome assembly and contig automatic annotation data are also available in the same working environment. The system integrates several public domains and newly developed software programs capable of dealing with several types of databases, and it is portable to other operational systems. These programs interact with most of the well-known biological database/softwares, such as Glimmer, Genemark, the BLAST family programs, InterPro, COG, Kegg, PSORT, GO, tRNAScan and RBSFinder, and can also be used to identify metabolic pathways.     

Characterization of fatty acid elongation system in porcine neutrophil microsomes

Microsomes purified from porcine neutrophils containing the fatty acid chain-elongation system for long- and very-long-chain fatty acyl-CoAs, and several enzymatic characters for the elongation of palmitoyl-CoA (16:0-CoA) and arachidoyl-CoA (20:0-CoA) were examined. The heat-inactivation profile for the elongation of 16:0-CoA was different from that of 20:0-CoA, suggesting the presence of different enzyme systems for palmitoyl-CoA and arachidoyl-CoA. Contrary to the elongation system of brain microsomes, the successive synthesis of lignoceric acid (24:0) from 20:0-CoA at 60 microM was not prominent under normal conditions in the neutrophil microsomes. The synthesis of behenic acid (22:0) was slightly inhibited by 0.5 mM N-ethylmaleimide (NEM) present in the assay mixture, whereas the pre-treatment of microsomes with 0.5 mM NEM largely inhibited the synthesis of 22:0 from 20:0-CoA. The synthesis of 24:0, however, was enhanced by 0.5 mM NEM in the elongation of 20:0-CoA and the rate of 24:0 synthesis became dominant over the synthesis of 22:0. These results suggested that the elongation enzyme for very-long-chain fatty acyl-CoA, especially for 20:0-CoA elongation to 22:0 in the neutrophil microsomes contained NEM-sensitive sulfhydryl groups in the active center and the mechanism for the synthesis of 24:0 through successive elongation from 20:0-CoA was different from that of 22:0, as the former was enhanced by NEM whereas the latter was strongly inhibited.     

Arachidonic and eicosapentaenoic acids in tissues of the firefly, Photinus pyralis (Insecta: Coleoptera)

We report on the presence of high proportions of arachidonic acid (20:4n-6) and eicosapentaenoic acid (20:5n-3) in the tissue lipids of adult fireflies, Photinus pyralis. Arachidonic acid typically occurs in very small proportions in phospholipids (PLs) of terrestrial insects, ranging from no more than traces to less than 1% of PL fatty acids, while 20:5n-3 is often missing entirely from insect lipids. Contrarily, 20:4n-6 made up approximately 21% of the PL fatty acids prepared from whole males and females, and from heads and thoraces prepared from males. Proportions of 20:4n-6 associated with PLs varied among tissues, including approximately 8% for male gut epithelia, 13% for testes, and approximately 25% for light organs and body fat from males. Substantial proportions of 20:5n-3 were also associated with PLs prepared from male firefly tissues, including 5% for body fat and 8% for light organs. Because 20:4n-6 and 20:5n-3 are precursors for biosynthesis of prostaglandins and other eicosanoids, we considered the possibility that firefly tissues might produce eicosanoids at exceptionally high rates. Preliminary experiments indicated otherwise. Hence, fireflies are peculiar among terrestrial insects with respect to maintaining high proportions of PL 20:4n-6 and 20:5n-3.     

Temperature sensitivity of cyclic-adenosine-3':5'-monophosphate-binding proteins, activity of protein kinases and the regulation of cell growth.

A clone of neuroblastoma cells has been selected for its ability to survive and multiply at 40 degrees C. This temperature-resistant clone, like clones of neuroblastoma cells selected for resistance to dibutyryladenosine 3':5'-monophosphate (Bt2-Ado-3':5'-P) showed an increased tumorogenicity in animals and an increased saturation density at 37 degrees C. The Ado-3':5'-P-binding proteins and Ado-3':5'-P-dependent protein kinases from the temperature-resistant and non-resistant cells have been partially purified by chromatography on a DEAE-cellulose column. The Ado-3':5'-P-binding proteins from temperature-resistant cells were more sensitive to temperature than the binding proteins from non-resistant cells. After incubation of binding proteins from resistant cells at 37 degrees C, the specific activity of Ado-3':5'-P-binding to proteins was decreased about 50% and the apparent association constant (Ka) for Ado-3':5-p-binding was decreased from 7.4 X 10(7)M-1 to 4.4 x 10(7)M-1. There was no such decrease with binding proteins from non-resistant cells. A decrease in the activity of binding proteins from the temperature-resistant cells, but not of those from non-resistant cells, was also found when the proteins were stored at 2 degrees C. Treatment with 2-mercaptoethanol made binding proteins from the resistant cells less temperature-sensitive. In the absence of added Ado-3:5-P the protein kinase activity from the temperature-resistant cells was about 50% of the activity from non-resistant cells. Kinase activity was increased by addition of Ado-3:5-P and there was a greater increase with kinases from resistant cells. The maximum protein kinase activity was found in the presence of 10muM Ado-3':5'-P for the temperature-resistant cells and 0.1 muM Ado-3':5'-P for the non-resistant cells. The results indicate that the temperature sensitivity of Ado-3':5'-P-binding proteins, and the activity of protein kinase from cells selected for resistance to high temperature, are similar to those of cells selected for resistance to Bt2-Ado-3':5'-P. It is suggested that the temperature sensitivity of Ado-3':5'-P-binding proteins and the activity of Ado-3':5'-P-dependent protein kinases are involved in the regulation of malignancy and of cell growth at different temperatures.     

Acylation of carcinogenic hydroxamic acids by carbamoyl phosphate to form reactive esters

Two methylated derivatives of arginine were isolated from the encephalitogenic protein of myelin from the central nervous system. Evidence is presented for the proposed structures, omega-NN'-dimethylarginine and omega-N-monomethylarginine. In the encephalitogenic protein from human brain the proportion 1:6:10 for arginine:monomethylarginine:dimethylarginine residues was found to occur at position 107. Possible roles for the methylated arginine in conformational changes and altered ion-exchange behaviour are discussed.     

Isolation and composition of oligosaccharide cores from endotoxins of two Serratia marcescens strains

The oligosaccharide cores isolated from the acetic acid hydrolysates of endotoxins from Serratia marcescens 08 and Serratia marcescens Bizio were analyzed for their sugar composition. The intact oligosaccharide core from S. marcescens 08 consisted of 2-keto-3-deoxyoctonate, d-glycero-d-mannoheptose, l-glycero-d-mannoheptose, d-glucose, d-galactose, and d-glucosamine in a molar ratio of 2:1:5:3:1:3 and that from S. marcescens Bizio consisted of the same sugar components in a molar ratio of 2:1:5:5:1:2. This result indicates that endotoxins from S. marcescens genus may contain more than one structural type of oligosaccharide core. Both oligosaccharide cores also differ in their chemical compositions from cores of other Enterobacteriaceae.     

Isolation, tissue distribution, and molecular characterization of Toxoplasma gondii from chickens in Grenada, West Indies

The prevalence of Toxoplasma gondii in free-range chickens is a good indicator of the prevalence of T. gondii oocysts in the soil because chickens feed from the ground. The prevalence of T. gondii in 102 free-range chickens (Gallus domesticus) from Grenada was determined. Antibodies to T. gondii were assayed by the modified agglutination test (MAT). Antibodies were found in 53 (52%) chickens with titers of 1:5 in 6, 1:10 in 4, 1:20 in 4, 1:40 in 4, 1:80 in 15, 1:160 in 9, 1: 320 in 5, 1:640 in 4, and 1:1,280 or greater in 2. Hearts, pectoral muscles, and brains of 43 seropositive chickens with MAT titers of 1:20 or greater were bioassayed individually in mice. Tissues of each of 10 chickens with titers of 1:5 and 1:10 were pooled and bioassayed in mice. Tissues from the remaining 49 seronegative chickens were pooled and fed to 4 T. gondii-free cats. Feces of cats were examined for oocysts; they did not shed oocysts. T. gondii was isolated from 35 of 43 chickens with MAT titers of 1:20 or greater; from the hearts, brains, and pectoral muscles of 2, hearts and brains of 20, from the hearts alone of 11, and brains alone of 2. T. gondii was isolated from 1 of 10 chickens with titers of 1:5 or 1:10. All 36 T. gondii isolates were avirulent for mice. Genotyping of these 36 isolates using polymorphisms at the SAG2 locus indicated that 29 were Type III, 5 were Type I, 1 was Type II, and 1 had both Type I and Type III. Genetically, the isolates from Grenada were different from those from the United States; Type II was the predominant type from the United States. Phenotypically, all isolates from Grenada were avirulent for mice, whereas those from Brazil were mouse-virulent. This is the first report of isolation of T. gondii from chickens from Grenada, West Indies.     

Specific biogas production and role of packing medium in the treatment of rubber thread manufacturing industry wastewater

Wastewater from three rubber thread manufacturing industries collected from three different sampling points was characterised. The acidic wastewater (pH = 3.6 to 4.7) contains high levels of COD, BOD, nitrogen and zinc. The average COD:N:P ratio was 100:3.8:0.4 whereas the BOD:N:P ratio was 100:4.5:0.4 with more than sufficient amounts of N and P for anaerobic digestion using the up-flow anaerobic filter. The specific biogas yield ranged between 0.250 to 0.069 l CH₄/g COD added when the organic loading rate was altered from 2.0 to 14.0 g COD/l/d respectively. The biogas production rate and the biogas yield rate increased from 8.2 to 42.7 l/d and 0.97 to 1.50 l CH₄/l/d respectively, for the same organic loading rate. The N and P utilised ranged between 1.53 to 1.20 and 0.3 to 0.26 mg per 100 mg COD consumed respectively when the organic loading rate was increased from 2.0 to 14.0 g COD/l/d. The optimum COD:N:P ratio obtained for steady state operation of the up-flow anaerobic filter in this study for the rubber thread manufacturing wastewater was 100:1.3:0.3. Attached biomass was responsible for the removal of more than 70% of the COD in the wastewater when PU foam was used as the packing media.     

Characteristics of the lactan gum produced from various carbon sources by Rahnella aquatilis

The characteristics of the lactan gum produced by Rahnella aquatilis varied according to the carbon sources used: the steady shear viscosity of lactan gum produced from fructose medium was higher than that produced from the other carbon sources, and furthermore the level of energy required (D H), for the degradation of lactan gum from fructose by Rahnella aquatilis was higher than that from other carbon sources. The lactan gums produced from sucrose or lactose contained mannose, galactose and galacturonic acid in the approximate molar ratio of 5:3:2. However, the lactan gum produced from galactose, glucose or fructose contained the same sugars at 2:4:4, 2:3:5 and 7:1.5:1.5 respectively.     

Estimated biological variation of the mature human milk fatty acid composition

We estimated the biological variation (CV(biol)) of 28 fatty acids (FA) in 465 mature human milk samples from The Netherlands, Caribbean, Jerusalem, Tanzania and Pakistan, by using data from the observed variation (CV(obs)) and analytical variation (CV(anal)). CV(biol) of the various regions was remarkably similar. The average CV(biol) of 455 samples, Pakistan excluded, ranged from 12.7% for 16:0 and 18.9% for 18:1 omega 9 to 68% for 22:6 omega 3 and about 100% for 20:5 omega 3. Those of 20:4 omega 6, 18:2 omega 6 and 18:3 omega 3 were 28.0, 33.0 and 37.3%, respectively. Because of the large CV(biol) and the many dietary changes in recent history, it seems impossible to consider the present human milk FA composition as the 'gold standard' for infant formula. Optimal human milk FA composition should rather derive from populations that consume traditional diets or from the scientific data that show the function of the individual FAs in neonatal development.     

Safety zones for a Sclerotinia sclerotiorum-based mycoherbicide: Accounting for regional and yearly variation in climate

Variation in the width of 'safety zones' for sheep and dairy pasture treated with a Sclerotinia sclerotiorum (Lib.) de Bary-based mycoherbicide was quantified using 10 years of climate data from each of five regions in New Zealand. Acceptable and risk-averse zones were defined as the maximum distances in any direction from a treated pasture where 'added:natural' ratios of air-borne S. sclerotiorum spores are 1:1 and 1:10, respectively. The 10-year mean 1:1 safety zone had zero width for sheep pasture at all locations, and was at most, 50 m wide for dairy pasture. The width of the 10-year mean 1:10 zone varied regionally from 314 to 443 m for sheep and from 175 to 280 m for dairy pasture, and the 90th percentile 1:10 zones were up to 41% wider. Linear relationships between safety zone width and mean wind speed were evident and these could be used to derive region-specific safety zones.     

Stoichiometry of proton release from the catalytic center in photosynthetic water oxidation. Reexamination by a glass electrode study at ph 5.5-7.2.

The catalytic center (CC) of water oxidation in photosystem II passes through four stepwise increased oxidized states (S(0)-S(4)) before O(2) evolution takes place from 2H(2)O in the S(4) --> S(0) transition. The pattern of the release of the four protons from the CC cannot be followed directly in the medium, because proton release from unknown amino acid residues also takes place. However, pH-independent net charge oscillations of 0:0:1:1 in S(0):S(1):S(2):S(3) have been considered as an intrinsic indicator for the H(+) release from the CC. The net charges have been proposed to be created as the charge difference between electron abstraction and H(+) release from the CC. Then the H(+) release from the CC is 1:0:1:2 for the S(0) --> S(1) --> S(2) --> S(3) --> S(0) transition. Strong support for this conclusion is given in this work with the analysis of the pH-dependent pattern of H(+) release in the medium measured directly by a glass electrode between pH 5.5 and 7.2. Improved and crystallizable photosystem II core complexes from the cyanobacterium Synechococcus elongatus were used as material. The pattern can be explained by protons released from the CC with a stoichiometry of 1:0:1:2 and protons from an amino acid group (pK approximately 5.7) that is deprotonated and reprotonated through electrostatic interaction with the oscillating net charges 0:0:1:1 in S(0):S(1):S(2):S(3). Possible water derivatives that circulate through the S states have been named.     

Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae)

We analyzed sequence variation for chalcone synthase (CHS:) and alcohol dehydrogenase (ADH:) loci in 28 species in the genera ARABIDOPSIS: and ARABIS: and related taxa from tribe Arabideae. CHS: was single-copy in nearly all taxa examined, while ADH: duplications were found in several species. Phylogenies constructed from both loci confirmed that the closest relatives of Arabidopsis thaliana include Arabidopsis lyrata, Arabidopsis petraea, and Arabidopsis halleri (formerly in the genus CARDAMINOPSIS:). Slightly more distant are the North American n = 7 Arabis (BOECHERA:) species. The genus ARABIS: is polyphyletic-some unrelated species appear within this taxonomic classification, which has little phylogenetic meaning. Fossil pollen data were used to compute a synonymous substitution rate of 1.5 x 10 substitutions per site per year for both CHS: and Adh. Arabidopsis thaliana diverged from its nearest relatives about 5 MYA, and from Brassica roughly 24 MYA. Independent molecular and fossil data from several sources all provide similar estimates of evolutionary timescale in the Brassicaceae.     

DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis

SUMMARY: DnaSP is a Windows integrated software package for the analysis of the DNA polymorphism from nucleotide sequence data. DnaSP version 3 incorporates several methods for estimating the amount and pattern of DNA polymorphism and divergence, and for conducting neutrality tests. AVAILABILITY: For academic uses, DnaSP is available free of charge from: http://www.bio.ub.es/julio/DnaSP.html CONTACT: julio@porthos.bio.ub.es     

Force-velocity characteristics of stomach muscle: a comparison between longitudinal and circular muscle strips

The longitudinal and circular muscle preparations from guinea pig stomach were compared in their property of shortening. The highest shortening speed was attained only for about 1 sec for longitudinal muscle and about 2 sec for circular muscle from the onset of stimulation in the course of tetanic contraction. Dynamic constants calculated from a force-velocity curve were almost independent of the muscle length, being set near its optimum length. Mean dynamic constants of the longitudinal muscle were: Vmax: 0.205 L/sec, b: 0.056 L/sec, a/Po: 0.292 and that of the circular muscle were: Vmax: 0.576 L/sec, b: 0.056 L/sec, a/Po: 0.107. The difference in Vmax of these muscles are discussed along with the difference in ultrastructure of the contractile filaments.     

Virulence markers and serotypes of Shiga toxin-producing Escherichia coli, isolated from cattle in Rio Grande do Sul, Brazil

AIMS: To determine the prevalence of Shiga toxin-producing Escherichia coli (STEC) and serotypes and virulence markers of the STEC isolates from beef and dairy cattle in Rio Grande do Sul, Brazil. METHODS AND RESULTS: Faecal samples from beef cattle were collected at slaughterhouses. The isolates were submitted to colony hybridization assay with specific DNA probes for stx1, stx2 and eae genes, and serotyped for the identification of O and H antigens. Thirty-nine per cent of beef cattle surveyed harboured at least one STEC strain. Among the distinct serotypes identified, 10 were shared by both beef and dairy cattle. Most of the strains isolated harboured stx2. Genotypic and phenotypic profiles allowed the identification of 34 and 31 STEC strains, isolated from beef and dairy cattle, respectively. Serotypes O10:H14, O15:H21, O96:H21, O119:H4, O124:H11, O128:H21, O137:H-, O141:H19, O159:H42, O160:H2 and O177:H11, identified in this study, have not been previously reported as STEC isolated from cattle. CONCLUSIONS: Cattle are an important reservoir of STEC strains associated with human diseases in South America. SIGNIFICANCE AND IMPACT OF THE STUDY: Determining the prevalence, genotypic profile and serotypes of STEC strains isolated from cattle enables the prediction of possible risk for public health.     

Effects of phospholipids on the function of (Ca2(+)-Mg2+)-ATPase.

The ATPase activity for the (Ca2(+)-Mg2+)-ATPase purified from rabbit skeletal muscle sarcoplasmic reticulum is lower when reconstituted into bilayers of dimyristoleoylphosphatidylcholine [(C14:1)PC] than when it is reconstituted into dioleoylphosphatidylcholine [(C18:1)PC]. The rate of formation of phosphoenzyme on addition of ATP is slower for (C14:1)PC-ATPase than for the native ATPase or (C18:1)PC-ATPase. The reduction in rate of phosphoenzyme formation is attributed to a reduction in the rate of a conformational change on the ATPase following binding of ATP but before phosphorylation. The level of phosphoenzyme formed from Pi is also less for (C14:1)PC-ATPase than for (C18:1)PC-ATPase. At steady state at pH 6.0 in the presence of ATP Ca2+ is released from (C18:1)PC-ATPase into the medium, but not from (C14:1)PC-ATPase. These effects of (C14:1)PC on the ATPase are reversed by addition of androstenol to a 1:1 molar ratio with (C14:1)PC. The results are interpreted in terms of a kinetic model for the ATPase.     

不同部位喉黏膜间充质细胞的分离培养

目的:探讨不同部位喉黏膜间充质细胞的分离、培养方法,为喉部组织工程提供更多的可供选择的种子细胞。方法:收集临床上喉部手术病人切下的不同部位的喉黏膜,主要是会厌的背侧黏膜和声带的黏膜,各3例,共计6例。对会厌背侧的黏膜采用消化培养的方法,对声带部位的黏膜采用组织块培养法。最后通过免疫荧光染色对两种方法所获得的细胞进行鉴定,确定其来源于喉黏膜的间充质。结果:通过两种方法均可以成功获得相应部位的细胞,免疫荧光染色vimentin均呈阳性表达且CK均呈阴性表达,证明了获得的细胞确实是来源于间充质。结论:本实验成功的培养出了喉部不同部位的间充质细胞,为喉部的组织工程提供了更多的可供选择的种子细胞。     

Membrane properties of D-erythro-N-acyl sphingomyelins and their corresponding dihydro species

We have prepared acyl chain-defined D-erythro-sphingomyelins and D-erythro-dihydrosphingomyelins and compared their properties in monolayer and bilayer membranes. Surface pressure/molecular area isotherms of D-erythro-N-16:0-sphingomyelin (16:0-SM) and D-erythro-N-16:0-dihydrosphingomyelin (16:0-DHSM) show very similar packing properties, except that the expanded-to-condensed phase transition (crystallization) occurs at a lower surface pressure for 16:0-DHSM. The measured surface potential was generally about 100 mV less for 16:0-DHSM monolayers compared to 16:0-SM monolayers. The condensed domains (crystals) that formed in 16:0-SM monolayers as a function of compression displayed star-shaped morphology when viewed under an epifluorescence microscope. 16:0-DHSM monolayers did not form similar crystals upon compression. 16:0-DHSM was degraded much faster by sphingomyelinase from Staphylococcus aureus than 16:0-SM (10-fold difference in enzyme activity needed for comparable hydrolytic rate). Cholesterol desorption from 16:0-DHSM to cyclodextrin was slightly slower (approximately 20%) than the rate measured from 16:0-SM monolayers (at 60 mol % cholesterol). The bilayer melting temperature of 16:0-DHSM was 47.7 degrees C (DeltaH 8.3 kcal/mol) whereas it was 41.2 degrees C for 16:0-SM (DeltaH 8.1 kcal/mol). Cholesterol/16:0-DHSM bilayers (15 mol % sterol) had more condensed domains than comparable 16:0-SM bilayers, as evidenced from the quenching resistance of DPH in DHSM membranes. We conclude that cholesterol interacts more favorably with 16:0-DHSM and that the membranes are more condensed than comparable 16:0-SM-containing membranes.     

Analysis of the condensation step in elongation of very-long-chain saturated and tetraenoic fatty acyl-CoAs in swine cerebral microsomes

The condensation products in the elongation of exogenous arachidoyl-CoA (20:0-CoA) and endogenous fatty acids in adult swine cerebral microsomes were isolated and purified by using HPLC and a radioanalyzer. A saponification product of the condensation reaction of 20:0-CoA with malonyl-CoA was identified by gas chromatography-mass spectrometry as 2-heneicosanone (21:0-2-one). The endogenous substrates (16:0-CoA and 20:4-CoA) were likewise identified as 2-heptadecanone (17:0-2-one) and 2-heneicosatetraenone (21:4-2-one). Quantitative analysis of condensation activity was performed using electron-impact mass fragmentography. A characteristic fragment ion (m/z 59) of 21:0-2-one was used to estimate the condensation activity for 20:0-CoA, and fragment ions at m/z 58 and 80 were monitored for the endogenous substrates (16:0-CoA and 20:4-CoA, respectively). The molecular ion for each product was detected using chemical ionization. A comparative study of the condensation of 20:0-CoA and endogenous substrates was carried out for microsomes obtained from white matter, gray matter, and isolated neuronal cells; the activity for 20:0-CoA was significantly lower in gray matter and neuronal cells than in white matter, whereas the activity for endogenous substrates was almost the same for microsomes obtained from gray and white matter. This result suggests that the condensation enzyme for 20:0-CoA may be different from that for endogenous 16:0-CoA or 20:4-CoA in swine cerebral microsomes.