Characterization of heparin oligosaccharides binding specifically to antithrombin III using mass spectrometry

Heparan sulfate (HS) is a sulfated glycosaminoglycan attached to a core protein on the cell surface. Protein binding to cell surface HS is a key regulatory event for many cellular processes such as blood coagulation, cell proliferation, and migration. The concept whereby protein binding to HS is not random but requires a limited number of sulfation patterns is becoming clear. Here we describe a hydrophobic trapping assay for screening a library of heparin hexasaccharides for binders to antithrombin III (ATIII). The hexasaccharide compositions are defined with their building block content in the following format: (DeltaHexA:HexA:GlcN:SO 3:Ac). Of five initial compositions present in the library, (1:2:3:6:1), (1:2:3:7:1), (1:2:3:7:0), (1:2:3:8:0), and (1:2:3:9:0), only two are shown to bind ATIII, namely, (1:2:3:8:0) and (1:2:3:9:0). The use of amide hydrophilic interaction (HILIC) liquid chromatography-mass spectrometry permitted reproducible quantitative analysis of the composition of the initial library as well as that of the binding fraction. The specificity of the hexasaccharides binding ATIII was confirmed by assaying their ability to enhance ATIII-mediated inhibition of Factor Xa in vitro.     

Balanced intake of protein and carbohydrate maximizes lifetime reproductive success in the mealworm beetle,Tenebrio molitor (Coleoptera: Tenebrionidae)

Recent developments in insect gerontological and nutritional research have suggested that the dietary protein:carbohydrate (P:C) balance is a critical determinant of lifespan and reproduction in many insects. However, most studies investigating this important role of dietary P:C balance have been conducted using dipteran and orthopteran species. In this study, we used the mealworm beetles, Tenebrio molitor L. (Coleoptera: Tenebrionidae), to test the effects of dietary P:C balance on lifespan and reproduction. Regardless of their reproductive status, both male and female beetles had the shortest lifespan at the protein-biased ratio of P:C 5:1. Mean lifespan was the longest at P:C 1:1 for males and at both P:C 1:1 and 1:5 for females. Mating significantly curtailed the lifespan of both males and females, indicating the survival cost of mating. Age-specific egg laying was significantly higher at P:C 1:1 than at the two imbalanced P:C ratios (1:5 or 5:1) at any given age throughout their lives, resulting in the highest lifetime reproductive success at P:C 1:1. When given a choice, beetles actively regulated their intake of protein and carbohydrate to a slightly carbohydrate-biased ratio (P:C 1:1.54–1:1.64 for males and P:C 1:1.3–1:1.36 for females). The self-selected P:C ratio was significantly higher for females than males, reflecting a higher protein requirement for egg production. Collectively, our results add to a growing body of evidence suggesting the key role played by dietary macronutrient balance in shaping lifespan and reproduction in insects.     

pMAA-Red: a new pPZP-derived vector for fast visual screening of transgenic Arabidopsis plants at the seed stage

ABSTRACT: BACKGROUND: The production of transgenic plants, either for the overproduction of the protein of interest, for promoter::reporter lines, or for the downregulation of genes is an important prerequisite in modern plant research but is also very time-consuming. RESULTS: We have produced additions to the pPZP family of vectors. Vector pPZP500 (derived from pPZP200) is devoid of NotI sites and vector pPZP600 (derived from pPZP500) contains a bacterial kanamycin resistance gene. Vector pMAA-Red contains a Pdf2.1::DsRed marker and a CaMV::GUS cassette within the T-DNA and is useful for the production of promoter::GUS lines and overexpression lines. The Pdf2.1 promoter is expressed in seeds and syncytia induced by the beet cyst nematode Heterodera schachti in Arabidopsis roots. Transgenic seeds show red fluorescence which can be used for selection and the fluorescence level is indicative of the expression level of the transgene. The advantage is that plants can be grown on soil and that expression of the marker can be directly screened at the seed stage which saves time and resources. Due to the expression of the Pdf2.1::DsRed marker in syncytia, the vector is especially useful for the expression of a gene of interest in syncytia. CONCLUSIONS: The vector pMAA-Red allows for fast and easy production of transgenic Arabidopsis plants with a strong expression level of the gene of interest.     

Fidelity of the human mitochondrial DNA polymerase

We have quantified the fidelity of polymerization of DNA by human mitochondrial DNA polymerase using synthetic DNA oligonucleotides and recombinant holoenzyme and examining each of the possible 16-base pair combinations. Although the kinetics of incorporation for all correct nucleotides are similar, with an average Kd of 0.8 microM and an average k(pol) of 37 s(-1), the kinetics of misincorporation vary widely. The ground state binding Kd of incorrect bases ranges from a low of 25 microM for a dATP:A mispair to a high of 360 microM for a dCTP:T mispair. Similarly, the rates of incorporation of incorrect bases vary from 0.0031 s(-1) for a dCTP:C mispair to 1.16 s(-1) for a dGTP:T mispair. Due to the variability in the kinetic parameters for misincorporation, the estimates of fidelity range from 1 error in 3563 nucleotides for dGTP:T to 1 error in 2.3 x 10(6) nucleotides for dCTP:C. Interestingly, the discrimination against a dGTP:T mismatch is 16.5 times lower than that of a dTTP:G mismatch due to a tighter Kd for ground state binding and a faster rate of incorporation of the dGTP:T mismatch relative to the dTTP:G mismatch. We calculate an average fidelity of 1 error in 440,000 nucleotides.     

In vivo conversion of 18- and 20-C essential fatty acids in rats using the multiple simultaneous stable isotope method

An important question for mammalian nutrition is the relative efficiency of C18 versus C20 essential fatty acids (EFAs) for supporting the tissue composition of n-3 and n-6 pathway end products. One specific question is whether C22 EFAs are made available to tissues more effectively by dietary alpha-linolenic acid (18:3n-3) and linoleic acid (18:2n-6) or by dietary eicosapentaenoic acid (20:5n-3) and dihomo-gamma-linolenic acid (20:3n-6). To address this question in a direct manner, four stable isotope compounds were given simultaneously in a novel paradigm. A single oral dose of a mixture of 2H5-18:3n-3, 13C-U-20:5n-3, 13C-U-18:2n-6, and 2H5-20:3n-6 was administered to rats given a defined diet. There was a preferential in vivo conversion of arachidonic acid (20:4n-6) to docosatetraenoic acid (22:4n-6) and of 22:4n-6 to n-6 docosapentaenoic acid (22:5n-6) when the substrates originated from the C18 precursors. However, when the end products docosahexaenoic acid (22:6n-3) or 22:5n-6 were expressed as the total amount in the plasma compartment divided by the dosage, this parameter was 11-fold greater for 20:5n-3 than for 18:3n-3 and 14-fold greater for 20:3n-6 than for 18:2n-6. Thus, on a per dosage basis, the total amounts of n-3 and n-6 end products accreted in plasma were considerably greater for C20 EFA precursors relative to C18.     

Stress-activated bioluminescent Escherichia coli sensors for antimicrobial agents detection

A DNA cartridge encoding Photinus pyralis luciferase (luc), lacZ homology extensions and an excisable marker was constructed to facilitate the conversion of Escherichia coli lacZ fusions to luc fusions by lambda Red-mediated recombination. This tool was used to transform a cspA::lacZ strain into a luminescent biosensor for C-group translational inhibitors. Comparison of cspA::lacZ and cspA::luc cells showed native firefly luciferase to be a more rapid and sensitive reporter than beta-galactosidase for chloramphenicol detection. To evaluate the usefulness of a red-shifted variant of P. pyralis luciferase (LucR1) for biosensor development, a single copy translational fusion between the SOS-inducible sulA promoter and the lucR1 gene was inserted at the malP site of the E. coli chromosome. The sulA::lucR1 fusion allowed high signal detection of the quinolone ofloxacin to levels as low as 15% of the minimum inhibitory concentration and could be combined with a cspA::lacZ fusion to yield a biosensor suitable for the independent and dual detection of chloramphenicol and ofloxacin.     

Effects of duration of daily illumination on reproductive organs and fertility of the meadow vole (Microtus pennsylvanicus).

The objective of this study was to determine the optimum simple, constant photoperiod for voles in a laboratory colony. Voles from an established colony maintained at 22 degrees C with a photoperiod of 14:10 hours of light:dark were transferred at 50 days of age to a photoperiod of 12:12, 14:10, 16:8 or 18:6 hours of light:dark. From Day 96 to Day 102, the 9--10 females per treatment group were paired with a male. Body and gonadal weights, spermatogenesis, ovarian activity and pregnancy were evaluated on Day 110. Reproductive function and body weight of both male and female voles maintained on a photoperiod of 16:8 exceeded (p less than 0.05) values for voles exposed to 12:12 hours of light:dark and tended to be more favorable than for voles in the 14:10 and 18:6 groups.     

Combination system in advanced image processing for improving image contrast and a conventional row-ratio grid for an indirect flat-panel detector system: An experimental study

Conventional grids with high grid ratios are not ideal for use in bedside radiography because of the difficulty in maintaining the required alignment. To address this issue, the potential usefulness of a combination system that employs removal processing software for scattered radiation and a conventional grid with a low grid ratio (3:1) for an indirect-conversion-type flat-panel detector system was evaluated by measuring image quality and observer performance. The hypothetical grid ratios for the software were 2:1, 3:1, 6:1, 8:1, and 10:1. The scatter fraction of the combination system was lower than that of the software alone. Significant improvement was observed in the effect of scattered radiation removal up to a hypothetical software grid ratio of 6:1. However, the Wiener spectrum increased (radiographic noise degraded) with an increase in the hypothetical grid ratio. The contrast ratios of the combination system were improved compared to those of the software alone for anthropomorphic chest radiographs. An observer test was also conducted using the contrast-detail phantom. The combination system indicated higher low-contrast detectability compared to the software alone, although there were no statistical differences between the hypothetical grid ratios of 6:1, 8:1, and 10:1 in all combinations of the software alone and the combination system. We concluded that a combination system with software that uses a hypothetical grid ratio of 6:1 or more and a 3:1 conventional grid would be more useful for reducing the scattered radiation component compared to the software alone with a hypothetical higher grid ratio for thicker objects.     

Kinetic studies of chicken and turkey liver mitochondrial aspartate aminotransferase.

The kinetic behaviour of chicken liver and turkey liver aspartate aminotransferases (L-aspartate:2-oxoglutarate aminotransferase, EC 2.6.1.1) was studied. Steady-state data were obtained from a wide range of concentrations of substrates and product L-glutamate. The data were fitted by rational functions of degree 1:1, 1:2 and 2:2 with respect to substrates and 0:1, 1:1, 0:2 and 1:2 with regard to product (L-glutamate), by using a non-linear regression program that guarantees the fit. The goodness of fit was improved by the use of a computer program that combines model discrimination parameter refinement and sequential experimental design. It was concluded that aspartate aminotransferase requires a minimum velocity equation of degree 2:2 for L-aspartate, 2:2 for 2-oxoglutarate and 1:2 for L-glutamate. Finally, a plausible kinetic mechanism that justifies these experimental results is proposed.     

A preliminary assessment of intra-oral lubricating systems for dry mouth patients

Objective: To provide extended intra-oral delivery of a saliva substitute. Intervention: Three different types of prostheses containing saliva substitute were designed and assessed: a two-part device resembling a mandibular complete denture sealed by cobalt-samerium magnets, a one-part clear resin device for the edentate patients and a flexible mouth guard type of appliance containing a lubricant releasing bubble for the dentate patients. Setting: A teaching hospital Oral Medicine and Rheumatology Clinic. Subjects: 8 edentate and 3 dentate Sjogren Syndrome sufferers. Outcome measures: Subjective dryness after a week of wearing the lubricating appliance. Results: The majority of the subjects wore the appliances for 6–12 hours during each 24 hours. The initial dryness severity diminished after wearing the lubricating prosthesis. The patients preferred to wear the appliance at night. Conclusion: All criteria were fulfilled on designing a saliva substitute lubricating appliance and some of the subjects have worn this prosthesis successfully for up to 3 years. Particular benefit was obtained by night-time wear.     

The anaerobic degradability of thermoplastic starch: polyvinyl alcohol blends: potential biodegradable food packaging materials

A systematic study on the anaerobic degradability of a series of starch:polyvinyl alcohol (TPS:PVOH) blends was performed to determine their fate upon disposal in either anaerobic digesters or bioreactor landfills. The aims of the study were to measure the rate and extent of solubilisation of the plastics. The extent of substrate solubilisation on a COD basis reached 60% for a 90:10 (w/w) blend of TPS:PVOH, 40% for 75:25, 30% for 50:50 and 15% for PVOH only. The rate of substrate solubilisation was most rapid for the 90:10 blend (0.041 h(-1)) and decreased with the amount of starch in the blend in the following order 0.034 h(-1)(75:25); 0.023 h(-1)(50:50). The total solids that remained after 900 h were 10 wt.% (90:10); 23 wt.% (75:25); 55 wt.% (50:50); 90 wt.% (0:100). Starch containing substrates produced a higher concentration of volatile fatty acids (VFAs) and biogas, compared to the 0:100 substrate. The major outcome was that PVOH inhibited the degradation of the starch from the blend.     

Enhanced biological phosphorus removal for high-strength wastewater with a low rbCOD:P ratio

In order to assess the feasibility of enhanced biological phosphorus removal (EBPR) for dairy processing wastewater, which in New Zealand have rbCOD:P ratios that can be as low as 13:1, a sequencing batch reactor treating a synthetic wastewater with a COD(VFA) of 800 mg/l (representing a dissolved air flotation (DAF) treated, pre-fermented dairy wastewater with a raw COD of 3000 mg/l) was operated at COD:P ratios of 25:1, 15:1 and 10:1. Full (>99%) phosphate removal was achieved for COD:P loadings of 25:1 and 15:1. The trial using 10:1 COD:P loading showed less consistency but still achieved 82% phosphate removal. Based on further analysis of the final trial this study proposes that the minimum COD:P loading for complete phosphate removal is 13:1 indicating that EBPR could indeed be feasible for effective treatment of dairy processing wastewaters. With regard to the type of COD consumed, propionate was found to be favoured over acetate as a substrate. Further research into increasing the propionate content of pre-fermented dairy wastewaters is suggested.     

Chembench: a cheminformatics workbench

MOTIVATION: Advances in the field of cheminformatics have been hindered by a lack of freely available tools. We have created Chembench, a publicly available cheminformatics portal for analyzing experimental chemical structure-activity data. Chembench provides a broad range of tools for data visualization and embeds a rigorous workflow for creating and validating predictive Quantitative Structure-Activity Relationship models and using them for virtual screening of chemical libraries to prioritize the compound selection for drug discovery and/or chemical safety assessment. AVAILABILITY: Freely accessible at: http://chembench.mml.unc.edu CONTACT: alex_tropsha@unc.edu     

Mutations at the distal and proximal sites of cytochrome P-450d changed regio-specificity of acetanilide hydroxylations

Regio-specificities of acetanilide hydroxylations were studied for 11 distal, 9 proximal and 3 aromatic mutants of cytochrome P-450d. Ratios of turnover numbers among these products were remarkably changed depending on the mutants. For example, the ratio of turnover number, para:ortho:meta = 7:0.1:0.3 for the wild type changed to 11:4:3 for a distal mutant, Thr322Ala, or to 13:13:1 for a proximal mutant, Arg455Gly. It was suggested that regio-specificities of microsomal P-450 enzymes are controlled cooperatively by the whole structure of the protein molecules which influences the tertiary structure of the distal environment.     

Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments

ABSTRACT: BACKGROUND: The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM format, used in a wide range of genetic analyses. The SAMtools utilities are implemented in C and provide an API for programmatic access, to help make this functionality available to programmers wishing to develop in the high level Ruby language we have developed bio-samtools, a Ruby binding to the SAMtools library. RESULTS: The utility of SAMtools is encapsulated in 3 main classes, Bio::DB::Sam, representing the alignment files and providing access to the data in them, Bio::DB::Alignment, representing the individual read alignments inside the files and Bio::DB::Pileup, representing the summarised nucleotides of reads over a single point in the nucleotide sequence to which the reads are aligned. CONCLUSIONS: bio-samtools is a flexible and easy to use interface that programmers of many levels of experience can use to access the information in the popular and common SAM/BAM format.     

Induction of testicular growth and sexual activity in rams by a 'skeleton' short-day photoperiod

Eight adult rams were housed in 16L:8D for 16 weeks and then exposed to short days (8L:16D) or 'skeleton' short days (11L:1D:5L:7D) for 16 weeks before being returned to long days. The 'skeleton' treatment promoted testicular development and regression in a way similar to that occurring in 8L:16D, indicating that a change in the total quantity of light is not a prerequisite for the photoperiodic response in the ram.     

Accurate guanine:cytosine discrimination in T4 DNA ligase-based single nucleotide polymorphism analysis using an oxanine-containing ligation fragment

T4 DNA ligase-based mismatch detection methods have been proposed as useful strategies for single nucleotide polymorphism (SNP) analyses. However, there is a critical problem for cytosine/thymine (C/T) SNP analyses: guanine:thymine (G:T) mismatch is not distinguished from guanine:cytosine (G:C). Here we employed chemically modified nucleobases, such as oxanine and hypoxanthine, at the end of a ligation fragment and analyzed their influence on the ligation efficiency between G:C and G:T. Successful ligation for G:C and no ligation for G:T were observed when oxanine was employed adjacent to guanine in the ligation junction. This ligation method using an oxanine-containing fragment has strong potentials for the accurate analysis of C/T SNPs.     

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.