A novel approach for estimating growth phases and parameters of bacterial population in batch culture

Using mathematical analysis, a new method has been developed for studying the growth kinetics of bacterial populations in batch culture. First, sampling data were smoothed with the spline interpolation method. Second, the instantaneous rates were derived by numerical differential techniques and finally, the derived data were fitted with the Gaussian function to obtain growth parameters. We named this the Spline-Numerical-Gaussian or SNG method. This method yielded more accurate estimates of the growth rates of bacterial populations and new parameters. It was possible to divide the growth curve into four different but continuous phases based on changes in the instantaneous rates. The four phases are the accelerating growth phase, the constant growth phase, the decelerating growth phase and the declining phase. Total DNA content was measured by flow cytometry and varied depending on the growth phase. The SNG system provides a very powerful tool for describing the kinetics of bacterial population growth. The SNG method avoids the unrealistic assumptions generally used in the traditional growth equations.     

Flavonol glucosyltransferase activity in Bronze embryos of Zea mays

The major UDPG: flavonol glucosyltransferase (UFGT) in maize is an enzyme of strict positional specificity known to be coded by the Bz locus. In bz mature endosperms, no UFGT can be detected. However, bz embryos possess a residual flavonol glucosyltransferase activity which is independent of Bz locus control. The products of this activity have been identified as the 3′-, 7- and 3-glucosides.     

Growth parameters and photosynthetic pigments in leaf segments of Zea mays exposed to cadmium, as related to protection mechanisms

The influence of cadmium on growth parameters and photosynthetic pigment content was studied in maize leaf segments differing in tissue maturity. Experiments were carried out with maize seedlings Zea mays L. cv. Hidosil treated with 25, 50, 100, 150 and 200 microM Cd for 14 days under low light conditions. Tissue age-dependent decrease of fresh mass, dry mass and area of the leaf segments was correlated with Cd concentration in the growth medium. Cd induced changes in chlorophyll and carotenoid contents, and the specific areas and densities of the leaf segments were dependent on age and metal concentration. Results are discussed with respect to the protection mechanisms in the leaf segments.     

Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences

We derive an analytic expression for site-specific stationary distributions of amino acids from the structurally constrained neutral (SCN) model of protein evolution with conservation of folding stability. The stationary distributions that we obtain have a Boltzmann-like shape, and their effective temperature parameter, measuring the limit of divergent evolutionary changes at a given site, can be predicted from a site-specific topological property, the principal eigenvector of the contact matrix of the native conformation of the protein. These analytic results, obtained without free parameters, are compared with simulations of the SCN model and with the site-specific amino acid distributions obtained from the Protein Data Bank. These results also provide new insights into how the topology of a protein fold influences its designability, i.e., the number of sequences compatible with that fold. The dependence of the effective temperature on the principal eigenvector decreases for longer proteins, as a possible consequence of the fact that selection for thermodynamic stability becomes weaker in this case.     

2004 SIVB Congress Symposium Proceedings “Thinking Outside the Cell”: Plant Protoplast Technology: Status and Applications

Summary Plant protoplasts provide an enabling technology to underpin aspects of development, physiology, and genetics. Reliable procedures are available to isolate and culture protoplasts from monocotyledons and dicotyledons. Several parameters influence the topipotency of protoplasts and their derived cells, particularly the source tissue, culture medium, and environmental factors. Novel approaches to maximize the efficiency of protoplast-to-plant systems include techniques already established for animal and microbial cells, such as electrostimulation and exposure of protoplasts to surfactants and artificial respiratory gas carriers, especially perfluorochemicals and hemoglobin. Somatic hybridization by protoplast fusion is undergoing a resurgence of interest, since it enables nuclear and cytoplasmic genomes to be combined at the interspecific and intergeneric levels without prior knowledge of gene location, or involvement of recombinant DNA technology. DNA uptake into protoplasts has applications in transient and stable transformation, including the generation of transplastomic plants of commercial importance in molecular pharming. Other applications of isolated protoplasts are in studies of membrane function, cell structure, and longer-term toxicological assessments. Despite the century that has elased since protoplasts were first isolated, they still make a significant contribution to many aspects of modern plant biotechnology.     

Restrained molecular dynamics studies on complex of adriamycin with DNA hexamer sequence d-CGATCG

Adriamycin is an anthracycline anticancer drug used widely for solid tumors in spite of its adverse side effects. The solution structure of 2:1 adriamycin-d-(CGATCG)(2) complex has been studied by restrained molecular dynamics simulations. The restraint data set consists of several intramolecular and intermolecular nuclear Overhauser enhancement cross-peaks obtained from two-dimensional nuclear magnetic resonance spectroscopy data. The drug is found to intercalate between CG and GC base pairs at two d-CpG sites. The drug-DNA complex is stabilized via specific hydrogen bonding and van der Waal's interactions involving 4OCH(3), O5, 6OH, and NH(3)(+) moiety of daunosamine sugar, and rings A protons. The O-glycosidic bond C7-O7-C1'-C2' lies in the range 138 degrees -160 degrees during the course of simulations. The O6-H6...O5 hydrogen bond is stable while O11-H11...O12 hydrogen bond is not favored. The intercalating base pairs are buckled and minor groove is wider in the complex. The phosphate on one strand at intercalation site C1pG2 is in B(I) conformation and the phosphates directly lying on opposite strand is in B(II) conformation. The phosphorus on adjacent site G2pA3 is in B(II) conformation and hence a distinct pattern of B(I) and B(II) conformations is induced and stabilized. The role of various functional groups by which the molecular action is mediated has been discussed and correlated to the available biochemical evidence.     

Structure—chemical approach to organization of information on metabolic charts

A nontraditional approach to construction of metabolic charts is proposed. It is based on the discovery of symmetry in the structure of the network of metabolic reactions. So if compounds and reactions are located on the metabolic chart according to their chemical features, the chart structure will acquire a periodic pattern. The charts thus created have a natural two-dimensional coordinate system of the metabolic network. Points on the X-axis correspond to number of carbon atoms in the carbon skeleton of compounds in columns and points on the Y-axis correspond to number of -COOH groups in compounds filing in series of rows on the charts. As a result this coordinate system sections the field of the charts into rectangular blocks each of which containing compounds with the same numbers of carbon atoms and the same numbers of -COOH groups. The latter substantially improves the charts and makes them a more valid source of metabolic data possessing heuristic properties. The periodicity of the metabolic network structure enables us easily to remember information about biochemical reactions and their products. The charts can also be used as a universal key for any biological database information that is systematically connected with the metabolic information. The charts can be important for medicine and pharmacology because they can help to understand the metabolic processes involved in decomposition of a particular drug or to find the chain of reactions blocked or initiated by administering this drug into a living organism.Translated from Biokhimiya, Vol. 69, No. 12, 2004, pp. 1691–1699.Original Russian Text Copyright © 2004 by Malygin.     

Small-sample inference for the comparison of means of log-normal distributions

We propose a likelihood-based test for comparing the means of two or more log-normal distributions, with possibly unequal variances. A modification to the likelihood ratio test is needed when sample sizes are small. The performance of the proposed procedures is compared with the F-ratio test using Monte Carlo simulations.     

Changes in sperm parameters of sex-reversed female rainbow trout during spawning season in relation to sperm parameters of normal males

The production of all-female populations has important economic benefits in commercial rainbow trout aquaculture. The procedure commonly implemented to produce all-female stocks centers on the sex reversal of rainbow trout females via the administration of androgens in the early developmental stages, followed by the egg fertilization of normal females with semen from sex-reversed females (srf). However, there is no information regarding the quality of semen from srf rainbow trout throughout the spawning season. This information is critical because the quality of srf semen is highly variable. The aim of the study was to determine the changes in the semen parameters of srf rainbow trout throughout the duration of the spawning season. Sperm concentration, sperm motility parameters, and the biochemical parameters of seminal plasma (protein concentration, antitrypsin activity, osmolality, and lactate dehydrogenase activity) from srf were monitored during the spawning season and compared with normal male rainbow trout. The observed values of sperm, protein concentration, antitrypsin activity, osmolality, and lactate dehydrogenase activity of seminal plasma were all higher in comparison with normal males. Semen from srf was therefore characterized by a lower sperm motility during each period of the spawning season, in comparison with normal males, approximately 1.8, 1.5, and 1.7 times, respectively for the beginning, middle, and end of the spawning season. The percentage of sperm motility from srf and normal males were affected by the spawning season in the same way, as the highest values in the middle of the spawning season demonstrate (60% and 91% for srf and normal males, respectively). Spermatozoa of srf are characterized by a lower speed and a more curvilinear trajectory of movement as compared with that of normal males. The patterns of changes during the spawning season in sperm concentration, sperm motility parameters, as well as osmolality, and lactate dehydrogenase activity of the seminal plasma of srf were different in comparison with normal males. Our results could be important for fish breeders in regard to the spawning control of srf rainbow trout, as well as for the development of short- and long-term sperm storage procedures.     

Effect of mass spectrometric parameters on peptide and protein identification rates for shotgun proteomic experiments on an LTQ-orbitrap mass analyzer

The success of a shotgun proteomic experiment relies heavily on the performance and optimization of both the LC and the MS systems. Despite this, little consideration has, so far, been given to the importance of evaluating and optimizing the MS instrument settings during data‐dependent acquisition mode. Moreover, during data‐dependent acquisition, the users have to decide and choose among various MS parameters and settings, making a successful analysis even more challenging. We have systematically investigated and evaluated the effect of enabling and disabling the preview mode for FTMS scan, the number of microscans per MS/MS scan, the number of MS/MS events, the maximum ion injection time for MS/MS, and the automatic gain control target value for MS and MS/MS events on protein and peptide identification rates on an LTQ‐Orbitrap using the Saccharomyces cerevisiae proteome. Our investigations aimed to assess the significance of each MS parameter to improve proteome analysis and coverage. We observed that higher identification rates were obtained at lower ion injection times i.e. 50–150 ms, by performing one microscan and 12–15 MS/MS events. In terms of ion population, optimal automatic gain control target values were at 5×10⁵–1×10⁶ ions for MS and 3×10³–1×10⁴ ions for MS/MS. The preview mode scan had a minimal effect on identification rates. Using optimized MS settings, we identified 1038 (±2.3%) protein groups with a minimum of two peptide identifications and an estimated false discovery rate of ～1% at both peptide and protein level in a 160‐min LC‐MS/MS analysis.