Cloning, expression, and nucleotide sequence of a lipase gene from Pseudomonas fluorescens B52.

In this study, we report the cloning and expression of lipase gene from Pseudomonas fluorescens B52, a psychrotrophic spoilage bacterium isolated from refrigerated raw milk. Sequence analysis revealed one major open reading frame of 1,428 nucleotides that was predicted to encode a protein with a molecular weight of 50,241. The predicted enzyme was found to contain an amino acid sequence highly homologous to the putative substrate-binding domain present within all lipases examined to date.     

Early life stress, MAOA, and gene-environment interactions predict behavioral disinhibition in children

Several, but not all, studies have shown that the monoamine oxidase A functional promoter polymorphism ( MAOA-LPR ) interacts with childhood adversity to predict adolescent and adult antisocial behavior. However, it is not known whether MAOA-LPR interacts with early life (pre-birth–3 years) stressors to influence behavior in prepubertal children.
The Avon Longitudinal Study of Parents and Children, UK, is a community-representative cohort study of children followed from pre-birth onwards. The impact of family adversity from pre-birth to age 3 years and stressful life events from 6 months to 7 years on behavioral disinhibition was determined in 7500 girls and boys. Behavioral disinhibition measures were: mother-reported hyperactivity and conduct disturbances (Strengths and Difficulties Questionnaire) at ages 4 and 7 years.
In both sexes, exposure to family adversity and stressful life events in the first 3 years of life predicted behavioral disinhibition at age 4, persisting until age 7. In girls, MAOA-LPR interacted with stressful life events experienced from 6 months to 3.5 years to influence hyperactivity at ages 4 and 7. In boys, the interaction of MAOA-LPR with stressful life events between 1.5 and 2.5 years predicted hyperactivity at age 7 years. The low activity MAOA-LPR variant was associated with increased hyperactivity in girls and boys exposed to high stress. In contrast, there was no MAOA-LPR interaction with family adversity.
In a general population sample of prepubertal children, exposure to common stressors from pre-birth to 3 years predicted behavioral disinhibition, and MAOA-LPR – stressful life event interactions specifically predicted hyperactivity.     

The Diffusion of Oxygen, Carbon Dioxide, and Inert Gas in Flowing Blood

Measurements were made of exchange rates of oxygen, carbon dioxide, and krypton-85 with blood at 37.5°C. Gas transfer took place across a 1 mil silicone rubber membrane. The blood was in a rotating disk boundary layer flow, and the controlling resistance to transfer was the concentration boundary layer. Measured rates were compared with rates predicted from the equation of convective diffusion using velocities derived from the Navier-Stokes equations and diffusivities calculated from the theory for conduction in a heterogeneous medium. The measured absorption rate of krypton-85 was closely predicted by this model. Significant deposition of material onto the membrane surface, resulting in an increased transfer resistance, occurred in one experiment with blood previously used in a nonmembrane type artificial lung. The desorption rate of oxygen from blood at low P_o2¹ was up to four times the corresponding transfer rate of inert gas. This effect is described somewhat conservatively by a local equilibrium form of the convective diffusion equation. The carbon dioxide transfer rate in blood near venous conditions was about twice that of inert gas, a rate significantly greater than predicted by the local equilibrium theory. It should be possible to apply these theoretical methods to predict exchange rates with blood flowing in systems of other geometries.     

Cloning, sequence, and expression of bovine interferon-gamma

Bovine interferon-gamma (IFN-gamma) sequences have been isolated by screening a cDNA library with a human IFN-gamma cDNA probe. The cDNA library was constructed from RNA isolated from concanavalin A-stimulated bovine lymph node cells. The open reading frame predicts that the bovine IFN-gamma precursor is composed of 166 amino acids with a predicted m.w. of 19,393. Alignment of the amino acid sequence with human IFN-gamma indicates that mature bovine IFN-gamma is composed of 143 amino acids with a predicted m.w. of 16,858. It has an amino acid homology of 63% with human IFN-gamma, and 47% with murine IFN-gamma. Biologically active bovine IFN-gamma was synthesized in an Escherichia coli expression system.     

Mismatch Repair by Efficient Nick-Directed, and Less Efficient Mismatch-Specific, Mechanisms in Homologous Recombination Intermediates in Chinese Hamster Ovary Cells

Repair of single-base mismatches formed in recombination intermediates in vivo was investigated in Chinese hamster ovary cells. Extrachromosomal recombination was stimulated by double-strand breaks (DSBs) introduced into regions of shared homology in pairs of plasmid substrates heteroallelic at 11 phenotypically silent mutations. Recombination was expected to occur primarily by single-strand annealing, yielding predicted heteroduplex DNA (hDNA) regions with three to nine mismatches. Product spectra were consistent with hDNA only occurring between DSBs. Nicks were predicted on opposite strands flanking hDNA at positions corresponding to original DSB sites. Most products had continuous marker patterns, and observed conversion gradients closely matched predicted gradients for repair initiated at nicks, consistent with an efficient nick-directed, excision-based mismatch repair system. Discontinuous patterns, seen in ~10% of products, and deviations from predicted gradients provided evidence for less efficient mismatch-specific repair, including G-A -> G-C specific repair that may reflect processing by a homologue of Escherichia coli MutY. Mismatch repair was >80% efficient, which is higher than seen previously with covalently closed, artificial hDNA substrates. Products were found in which all mismatches were repaired in a single tract initiated from one or the other nick. We also observed products resulting from two tracts of intermediate length initiated from two nicks.     

Covalent structure, disulfide bonding, and identification of reactive surface and active site residues of human prostatic acid phosphatase

The pairing of the half-cysteine residues of human prostatic acid phosphatase was established by proteolytic digestion and analysis of the resulting peptide mixtures by fast atom bombardment mass spectrometry (FAB-MS). An independently derived, full length cDNA clone was used as the basis for the interpretation of the FAB-MS data. The sequence of the native protein is that predicted from the present cDNA sequence, except for the carboxyl-terminal end and some possible post-translational deamidations. Isolated human prostatic acid phosphatase was found to have multiple carboxyl-terminal ends, terminating in Thr, Glu, and Asp, corresponding to residues 349-351 of the 354-residue protein that is predicted from the cDNA sequence after removal of a leader peptide. The protein contains no free sulfhydryl groups. The identical monomer chains of the dimeric native enzyme are found to contain three disulfide bonds, specifically Cys-129 to Cys-340, Cys-183 to Cys-281, and Cys-315 to Cys-319. In view of the conserved positions of cysteines in the homologous human and rat liver lysosomal acid phosphatases, an identical disulfide bonding pattern may be predicted for those proteins. The location of a potential antigenic site was established by selective labeling of proximate tyrosine residues predicted to be on the surface. A conserved RHGXRXP sequence is present in the prostatic, lysosomal, Escherichia coli, and yeast acid phosphatases and is predicted to be of mechanistic significance. In addition, residue Arg-54 is shown to be an active site residue by reaction of the enzyme with phenylglyoxal. Interestingly, this residue is present in a sequence RXRY (R,H) that is also present in lysosomal phosphatase and in recently described protein tyrosine phosphatases.     

Use of a serum-based glomerular filtration rate prediction equation to assess renal function by age, sex, fasting, and health status in bottlenose dolphins (Tursiops truncatus)

Glomerular filtration rate (GFR) is a direct measurement of renal function. Although clearance tests using 24‐h urine collection or blood sample series are gold standards for measuring GFR, serum‐based prediction of GFR based upon the Modification of Diet in Renal Disease (MDRD) Study equation is acceptable for routine use in human adults. The purpose of our study was to assess the ability for a modified MDRD Study equation to predict expected changes in GFR in bottlenose dolphins (Tursiops truncatus) using a healthy dolphin population represented by 1,103 routine serum samples collected from 50 dolphins of all age groups, years 1998–2005. Predicted GFR was also calculated from serum collected from a 32‐yr‐old male dolphin with end‐stage renal disease. The dolphin‐adjusted MDRD equation predicted GFR changes in our population that paralleled what has previously been reported in other mammals, including decreasing predicted GFR with age (P < 0.01), higher predicted GFR in dolphins that had recently eaten (P < 0.01), and rapidly decreasing predicted GFR in the animal with end‐stage renal disease. We conclude that a serum‐based GFR prediction equation may be a feasible means of detecting and tracking renal function in bottlenose dolphins.     

Paracoccidioides brasiliensis presents two different cDNAs encoding homologues of the fructose 1,6-biphosphate aldolase: protein isolation, cloning of the cDNAs and genes, structural, phylogenetic, and expression analysis

A proteomic approach was used to identify a 39 kDa antigen of Paracoccidioides brasiliensis. Amino acid sequences of the N-terminal and of endoproteinase Lys-C digested peptides revealed the protein to be a fructose 1,6-biphosphate aldolase (FBA) Class II of P. brasiliensis. Two cDNA homologues, Pbfba1 and Pbfba2, were cloned and characterized. Pbfba1 encoded a predicted polypeptide of 360 amino acids that was highly homologous in the primary structure to the same enzyme from fungi and bacteria. The other DNA, Pbfba2, encoded a polypeptide predicted to be 363 amino acids. The sequence of Pbfba2 differed significantly from Pbfba1. Phylogenetic and molecular analysis supports the concept of gene duplication for FBAs in P. brasiliensis, constituting a two-member family. Expression analysis demonstrated differential expression for both fbas genes in P. brasiliensis cells.     

Comparing Observed with Predicted Weekly Influenza-Like Illness Rates during the Winter Holiday Break,United States, 2004-2013

In the United States, influenza season typically begins in October or November, peaks in February, and tapers off in April. During the winter holiday break, from the end of December to the beginning of January, changes in social mixing patterns, healthcare-seeking behaviors, and surveillance reporting could affect influenza-like illness (ILI) rates. We compared predicted with observed weekly ILI to examine trends around the winter break period. We examined weekly rates of ILI by region in the United States from influenza season 2003–2004 to 2012–2013. We compared observed and predicted ILI rates from week 44 to week 8 of each influenza season using the auto-regressive integrated moving average (ARIMA) method. Of 1,530 region, week, and year combinations, 64 observed ILI rates were significantly higher than predicted by the model. Of these, 21 occurred during the typical winter holiday break period (weeks 51–52); 12 occurred during influenza season 2012–2013. There were 46 observed ILI rates that were significantly lower than predicted. Of these, 16 occurred after the typical holiday break during week 1, eight of which occurred during season 2012–2013. Of 90 (10 HHS regions x 9 seasons) predictions during the peak week, 78 predicted ILI rates were lower than observed. Out of 73 predictions for the post-peak week, 62 ILI rates were higher than observed. There were 53 out of 73 models that had lower peak and higher post-peak predicted ILI rates than were actually observed. While most regions had ILI rates higher than predicted during winter holiday break and lower than predicted after the break during the 2012–2013 season, overall there was not a consistent relationship between observed and predicted ILI around the winter holiday break during the other influenza seasons.     

Cloning, expression, purification, and characterization of Leishmania major dihydroorotate dehydrogenase

Leishmania major Friedlin (LmjF) is a protozoan parasite whose genomic sequence has been recently elucidated. Here we have cloned, overexpressed, purified, and characterized the product of the gene from LmjF chromosome 16: LmjF16.0530, which encodes a protein with putative dihydroorotate dehydrogenase activity. Dihydroorotate dehydrogenase (DHODH) is a flavoprotein that catalyses the oxidation of L-dihydroorotate to orotate, the fourth sequential step in the de novo pyrimidine nucleotide synthesis pathway. The predicted enzyme from L. major was cloned and expressed in Escherichia coli strain BL21(DE3) as a histidine-tag fusion protein and purified to homogeneity using affinity chromatography. The final product was homogeneous in SDS-PAGE gel electrophoresis. The dihydroorotate oxidase activity has been assayed and the steady-state kinetic mechanism has been determined using fumarate as the oxidizing substrate. The catalysis by LmDHODH enzyme proceeds by a Ping-Pong Bi-Bi mechanism and the kinetic parameters Km were calculated to be 90 and 418 microM for dihydroorotate and fumarate, respectively, and Vmax was calculated to be 11 micromol min-1 mg-1. Our results confirmed that the product of the gene LmjF16.0530, whose function has previously been predicted based on homology to known proteins, can therefore be positively assigned as L. major DHODH.     

Molecular characterization of the nodulation gene, nodT, from two biovars of Rhizobium leguminosarum

DNA sequencing of the nodIJ region from Rhizobium leguminosarum biovar trifolii revealed the nodT gene immediately downstream of nodJ. DNA hybridizations using a nodT-specific probe showed that nodT is present in several R. leguminosarum strains. Interestingly, a flavonoid-inducible nodT gene homologue in R. leguminosarum bv. viciae is not in the nodABCIJ operon but is located downstream of nodMN. The sequence of the nodT gene from bv. viciae was determined and a comparison of the predicted amino-acid sequences of the two nodT genes shows them to be conserved; the predicted protein sequences appear to have a potential transit sequence typical of outer-membrane proteins. Mutations affecting nodT in either biovar had no observed effect on nodulation of the legumes tested.     

Effects of successional status, habit, sexual systems, and pollinators on flowering patterns in tropical rain forest trees

Based on data from observations of 302 tree species at La Selva, Costa Rica, we tested a range of hypotheses about the relationship between flowering parameters such as time, frequency, and duration and ecological features such as successional status, habit, sexual systems, and pollen vectors with and without considering the effect of family membership. We predicted that early successional species would flower any time of the year, but species pollinated by different vectors as well as dioecious species would flower nonrandomly across seasons. However, there was little evidence that flowering time varied with successional status, pollen vectors, and sexual systems. As we predicted, supra-annual flowering was proportionately less common in early successional species as compared to late ones, in understory species as compared to canopy species, and in dioecious species as compared to those with hermaphroditic flowers. When considering phylogeny, however, supra-annual flowering in the understory was not as rare as predicted. Our prediction of longer flowering in the early successional species as compared to late successional species was also supported. Predictions about longer flowering of dioecious species as compared to hermaphroditic species and of species pollinated by generalist vectors as compared to the specialists were not supported, though there was a trend in the expected direction.     

Molecular cloning and characterization of MACIF, an inhibitor of membrane channel formation of complement

Human erythrocytes contain a membrane protein, MACIF, which inhibits the formation of a membrane attack complex (MAC) of complement. We have cloned and sequenced the complementary DNA of MACIF messenger RNA. The amino acid sequence predicted from its nucleotide sequence consists of 128 amino acids. The amino-terminal 25 residues may correspond to a signal peptide. The carboxy-terminal sequence confirmed that MACIF is a glycosylphosphatidylinositol (GPI)-anchored protein. The amino acid sequence of MACIF was partially determined by established techniques for protein chemistry and the resultant sequence was consistent with that predicted from the nucleotide sequence. The results of sequence analyses also suggested that asparagine at the 18th position was N-glycosylated. When mRNA obtained from the MACIF cDNA clone with SP6 RNA polymerase was microinjected into Xenopus oocytes, the oocytes synthesized a product which exhibited MACIF activity and reacted with anti-MACIF antibody. Comparison of the predicted sequence revealed significant homology with mouse Ly-6 antigens.     

Potential Compounds for Oral Cancer Treatment: Resveratrol,Nimbolide, Lovastatin,Bortezomib, Vorinostat,Berberine, Pterostilbene,Deguelin, Andrographolide,and Colchicine

Oral cancer is one of the main causes of cancer-related deaths in South-Asian countries. There are very limited treatment options available for oral cancer. Research endeavors focused on discovery and development of novel therapies for oral cancer, is necessary to control the ever rising oral cancer related mortalities. We mined the large pool of compounds from the publicly available compound databases, to identify potential therapeutic compounds for oral cancer. Over 84 million compounds were screened for the possible anti-cancer activity by custom build SVM classifier. The molecular targets of the predicted anti-cancer compounds were mined from reliable sources like experimental bioassays studies associated with the compound, and from protein-compound interaction databases. Therapeutic compounds from DrugBank, and a list of natural anti-cancer compounds derived from literature mining of published studies, were used for building partial least squares regression model. The regression model thus built, was used for the estimation of oral cancer specific weights based on the molecular targets. These weights were used to compute scores for screening the predicted anti-cancer compounds for their potential to treat oral cancer. The list of potential compounds was annotated with corresponding physicochemical properties, cancer specific bioactivity evidences, and literature evidences. In all, 288 compounds with the potential to treat oral cancer were identified in the current study. The majority of the compounds in this list are natural products, which are well-tolerated and have minimal side-effects compared to the synthetic counterparts. Some of the potential therapeutic compounds identified in the current study are resveratrol, nimbolide, lovastatin, bortezomib, vorinostat, berberine, pterostilbene, deguelin, andrographolide, and colchicine.     

Adaptive energetics in house mice, Mus musculus domesticus, from the island of Porto Santo (Madeira archipelago, North Atlantic)

The bioenergetic strategies of house mice (Mus musculus domesticus) from the island of Porto Santo were investigated and compared with those of mice from mainland Portugal. Energy obtained from food ingestion was 18.2% lower in Porto Santo mice than in mainland mice (1.53 vs. 1.87 kJ/g/day). The same pattern was observed for metabolisable energy intake, which was 19.2% lower in island specimens (0.87 vs. 1.08 kJ/g/day for mainland specimens). Apparent digestibility was similar in both groups of mice. Basal metabolic rate (BMR) of Porto Santo individuals was low (1.16 ml O(2)/g/h), representing only 56% of the predicted value, based on body mass, while mainland individuals exhibited a BMR closer to the expected value, corresponding to 87% of the predicted value (1.80 ml O(2)/g/h). Thermoregulatory abilities within the range of 10-28 degrees C ambient temperature did not differ between island and mainland mice. Results suggest an adaptation of Porto Santo mice to the environmental aridity of the island of Porto Santo, leading to a conservative energetic strategy.     

Expression in Escherichia coli, refolding, and purification of human procathepsin K, an osteoclast-specific protease

We have constructed and optimized a high yielding Escherichia coli expression system to produce glycosylation-free human procathepsin K and have developed conditions for refolding this enzyme. Recombinant human procathepsin K (EC 3.4.22.38) was expressed in E. coli, refolded from inclusion bodies, and further purified by Superdex 75 size-exclusion chromatography. Purified procathepsin K had a [MH]+ of 35,063 Da which is in agreement with the predicted mass of the construct. Amino-terminal sequence analysis matched the predicted sequence with no secondary sequence detected. Purified procathepsin K activated under autocatalytic conditions to a final specific activity of 23 micromol 7-amido-4-methylcoumarin liberated/min/mg of enzyme using the fluorescent peptide substrate benzyloxycarbonyl-phenylalanine-arginine-7-amido-4-methylcoumarin. This expression and refolding procedure yielded 50 mg of purified, glycosylation-free human procathepsin K from 1 liter of E. coli cell culture and enabled the determination of the structure of human procathepsin K at 2.6 A resolution.