Computational sequence analysis of matrix metalloproteinases

Matrix metalloproteinases (MMP) play a cardinal role in the breakdown of extracellular matrix involved in a variety of biological and pathological processes. Research on MMPs has classified and characterized these enzymes according to their matrix substrate specificity, gene and protein domain structure, and regulation of activity and expression. However, the discovery of new MMPs has introduced a need for a more comprehensive and systematic method of classification and quantitative comparison of known and newly discovered members. This study compiles a sequence alignment, constructs a dendrogram, and calculates physical data and homology percentage assignments in order to obtain further insight into MMP structure-function relationships. Thorough analysis of MMP primary sequence domains, physical data patterns, and statistical analysis of sequence homology yields higher resolution in the similarities and differences that group MMP members.     

Water and solute transport along developing maize roots

Hydraulic and osmotic properties were measured along developing maize (Zea mays L.) roots at distances between 15 and 465 mm from the root tip to quantify the effects of changes in root structure on the radial and longitudinal movement of water and solutes (ions). Root development generated regions of different hydraulic and osmotic properties. Close to the root tip, passive solute permeability (root permeability coefficient, P_sr) was high and selectivity (root reflection coefficient, _sr) low, indicative of an imperfect semipermeable root structure. Within the apical 100–150 mm, P_sr decreased by an order of magnitude and _sr increased significantly. Root hydraulic conductivity (Lp_r) depended on the nature of the force (hydrostatic and osmotic). Osmotic Lp_r was smaller by an order of magnitude than hydrostatic Lp_r and decreased with increasing distance from the root tip. Throughout the root, responses in turgor of cortical cells and late metaxylem to step changes in xylem pressure applied to the base of excised roots were measured at high spatial resolution. The resulting profiles of radial and longitudinal propagation of pressure showed that the endodermis had become the major hydraulic barrier in older parts of the root, i.e. at distances from the apex ä 150 mm. Other than at the endodermis, no significant radial hydraulic resistance could be detected. The results permit a detailed analysis of the root's composite structure which is important for its function in collecting and translocating water and nutrients.Abbreviations and Symbols CPP cell pressure probe - IT root segments with intact tips; - Lp_r root hydraulic conductivity - Lp_rh hydrostatic hydraulic conductivity of root - Lp_ro osmotic hydraulic conductivity of root - P_app hydrostatic pressure applied to cut end of root - P_c cell turgor - P_{c, cor} turgor of cortical cell - P_c,xyl turgor of late metaxylem vessel - P_ro stationary root pressure - P_r0,seal stationary root pressure of sealed root segment - P_sr solute permeability coefficient of root - RPP root pressure probe - TR root segments with tip removed - _sr reflection coefficient of root Dedicated to Professor Andreas Sievers on the occasion of his retirement     

Measurement of k(L)a by dynamic pressure method in pilot-plant fermentor

The dynamic pressure method (DPM) is used for measurement of k(L)a in a 1-m(3) pilot scale fermentor in coalescing (distilled water) and noncoalescing (0.3 M Na(2)SO(4) aqueous solution) batches. The method consists in recording oxygen concentration in a batch after a small pressure change (20 kPa) in the fermentor. The upward pressure change is brought about by temporary closing and subsequent throttling of outlet gas stream and the downward change by full reopening of the gas outlet. Absorption of pure oxygen yields the same k(L)a values as absorption of air. In noncoalescing batch, the downward k(L)a values are always higher than the upward values owing to spontaneous nucleation of bubbles. The experiments performed in a stirred cell confirm this behavior. Thus, only upward pressure change should be used for measurement. The correlation of k(L)a data measured in small (18-L) and large (1000-L) vessels based on power dissipated and superficial gas velocity are in a good agreement. Unlike the DPM, the classical dynamic methods yield, under the same conditions, excessively low values of k(L)a (the dynamic startup method) or fail to produce data at all (the dynamic method with interchange of air for N(2)). (c) 1994 John Wiley & Sons, Inc.     

Long-term responses of Melilotus segetalis to salinity. I. Growth and partitioning

Annual sweetclover plants [Melilotus segetalis (Brot) Ser.] were grown for a complete life cycle with and without saline (NaCl treatment of CE=15 dS m⁻¹). Growth and partitioning analyses were performed. Sequential harvests (every 15 d) during the life cycle, and separation of plant material into roots, stems, petioles, leaves and reproductive structures were carried out Salt treatment reduced growth during the early and middle stages of the life of the plant, but did not significantly affect RGR in the reproductive phase. The root–shoot allometric coefficient of salinized plants in the generative phase decreased more than in control plants. We suggest that salinity-induced growth reduction in M. segetalis was primarily a result of a lower unit leaf rate (ULR) despite an increased leaf area ratio (LAR). Earlier flowering, higher biomass allocation to shoot and greater reproductive investment, but similar relative growth rate (RGR), were some of the main characteristics of salt-stressed plants compared to controls during the reproductive phase, these apparently being associated with increased sink strength caused by developing flowers and fruits.     

Interaction between fatty-acid and starch synthesis in isolated amyloplasts from cauliflower floral buds

The interaction of fatty-acid synthesis with starch synthesis has been studied in intact amyloplasts isolated from floral buds of cauliflower (Brassica oleracea L.). These amyloplasts perform acetate-dependent fatty acid synthesis at maximum rates only at high external ATP concentrations. Neither pyruvate nor malate inhibit acetate-dependent fatty-acid synthesis. In contrast, acetate is inhibitory to the low pyruvate-dependent fatty acid synthesis. These observations indicate that neither pyruvate nor malate are used as natural precursors of fatty-acid synthesis. In contrast to fatty-acid synthesis, the rate of glucose-6-phosphate-dependent starch synthesis is already saturated in the presence of much lower ATP concentrations. Rising rates of starch synthesis influence negatively the process of acetate-dependent fatty acid synthesis. This inhibition appears to occur under both limiting and saturating concentrations of external ATP, indicating that the rate of ATP uptake is limiting when both biochemical pathways are active. The rate of starch synthesis is modulated specifically by the concentration of 3-phosphoglycerate in the incubation medium. This observation leads to the conclusion that the activity of ADP-glucose pyrophosphorylase is of primary importance for the control of both, starch and fatty-acid synthesis. Using the modified approach of Kacser and Burns (1973; Symp. Soc. Exp. Biol.27, 65–104) we have quantified the contribution of the rate of starch synthesis to the control of the metabolic flux through fatty-acid synthesis.Abbreviations ADPGlc-PPase ADPglucose pyrophosphorylase - Glc6P glucose-6-phosphate - PGA 3-phosphoglyceric acid     

Detection of gaps in sinusoids by frog auditory nerve fibers: importance in AM coding

Physiological studies were carried out in the frog (Rana pipiens pipiens) eighth nerve to determine: (i) whether the modulation rate or the silent gap was the salient feature that set the upper limit of time-locking to pulsed amplitude-modulated (PAM) stimuli, (ii) the gap detection capacity of individual eighth nerve fibers. Time-locked responses of 79 eighth nerve fibers to PAM stimuli (at the fiber's characteristic frequency) showed that the synchronization coefficient was a low-pass function of the modulation rate. In response to PAM stimuli having different pulse durations, a fiber gave rise to non-overlapping modulation transfer functions. The upper cut-off frequency of time locking was higher when tonepulses in PAM stimuli had shorter duration. The fact that the cut-off frequency was different for the different PAM series suggested that the AM rate was neither the sole, nor the main, determinant for the decay in time-locking at high AM rates. Gap detection capacity was determined for 69 eighth nerve fibers by assessing fiber's spiking activities to paired tone-pulses during an OFF-window and an ON-window. It was found that the minimum detectable gap of eighth nerve fibers ranged from 0.5 to 10 ms with an average of 1.23–2.16 ms depending on the duration of paired tone pulses. For each fiber, the minimum detectable gap was longer when the duration of tone pulses comprising the twin-pulse stimuli was more than four times longer. When the synchronization coefficient was plotted against the silent gap between tones pulses in the PAM stimuli, the gap response functions of a fiber as derived from multiple PAM series were equivalent to gap response functions deriving from twin-pulse series suggesting that it was the silent gap which primarily determined the upper limit of time-locking to PAM stimuli.Abbreviations MTF modulation transfer function - PAM pulse amplitude modulated - SAM sinusoidally amplitude modulated - SC synchronization coefficient - TW time window     

对似近分析的一点改进及其拓广

本文给出了似近分析一个重要的改进,并将改进的似近分析推广为m维似近分析,同时给出了两个数学定理及其证明。根据多维似近系数的数学性质,提出了一种新的聚类方法,即逐步多维聚类法。实例分析证明,这种聚类法比二维系数聚类优越,聚类功能强,所获得的结果更为客观。     

Modelling C3 photosynthesis: A sensitivity analysis of the photosynthetic carbon-reduction cycle

A model of the C ₃ photosynthetic system is developed which describes the sensitivity of the steadystate rate of carbon dioxide assimilation to changes in the activity of several enzymes of the system. The model requires measurements of the steady-state rate of carbon dioxide assimilation, the concentrations of several intermediates in the photosynthetic system, and the concentration of the active site of ribulose 1,5-bisphosphate carboxyalse/oxygenase (Rubisco). It is shown that in sunflowers (Helianthus annuus L.) at photon flux densities that are largely saturating for the rate of photosynthesis, the steady-stete rate of carbon dioxide assimilation is most sensitive to Rubisco activity and, to a lesser degree, to the activities of the stromal fructose, 6-bisphosphatase and the enzymes catalysing sucrose synthesis. The activities of sedoheptulose 1,7-bisphosphatase, ribulose 5-phosphate kinase, ATP synthase and the ADP-glucose pyrophosphorylase are calculated to have a negligible effect on the flux under the high-light conditions. The utility of this analysis in developing simpler models of photosynthesis is also discussed.Abbreviations c _i intercellular CO₂ concentration - C _infP ^supJ control coefficient for enzyme P with respect to flux J - DHAP dihydroxyacetonephosphate - E4P erythrose 4-phosphate - F6P fructose 6-phosphate - FBP fructose 1,6-bisphosphate - FBPase fructose 1,6-bisphosphatase - G3P glyceraldehyde 3-phosphate - G1P glucose 1-phosphate - G6P glucose 6-phosphate - Pi inorganic phosphate - PCR photosynthetic carbon reduction - PGA 3-phosphoglyceric acid - PPFD photosynthetically active photon flux density - R _n ^J response coefficient for effector n with respect to flux J - R5P ribose 5-phosphate - Rubisco ribulose 1,5-bisphosphate carboxylase/oxygenase - Ru5P ribulose 5-phosphate - RuBP ribulose 1,5-bisphosphate - S7P sedoheptulose 7-phosphate - SBP sedoheptulose 1,7-bisphosphate - SBPase sedoheptulose 1,7-bisphosphatase - SPS sucrose-phosphate synthase - Xu5P xylulose 5-phosphate - _n ^P elasticity coefficient for effector n with respect to the catalytic velocity of enzyme P This research was funded by an Australian Research Council grant to I.E.W. and was undertaken during a visity by K.A.M. to the James Cook University of North Queensland. The expert help of Glenys Hanley and Mick Kelly is greatly appreciated.     

The challenge of estimating kelp production in a turbid marine environment

Coastal kelp forests produce substantial marine carbon due to high annual net primary production (NPP) rates, but upscaling of NPP estimates over time and space remains difficult. We investigated the impact of variable underwater photosynthetically active radiation (PAR) and photosynthetic parameters on photosynthetic oxygen production of Laminaria hyperborea, the dominant NE-Atlantic kelp species, throughout summer 2014. Collection depth of kelp had no effect on chlorophyll a content, pointing to a high photoacclimation potential of L. hyperborea towards incident light. However, chlorophyll a and photosynthesis versus irradiance parameters differed significantly along the blade gradient when normalized to fresh mass, potentially introducing large uncertainties in NPP upscaling to whole thalli. Therefore, we recommend a normalization to kelp tissue area, which is stable over the blade gradient. Continuous PAR measurements revealed a highly variable underwater light climate at our study site (Helgoland, North Sea) in summer 2014, reflected by PAR attenuation coefficients (K_d) between 0.28 and 0.87 m⁻¹. Our data highlight the importance of continuous underwater light measurements or representative average values using a weighted K_d to account for large PAR variability in NPP calculations. Strong winds in August increased turbidity, resulting in a negative carbon balance at depths >3–4 m over several weeks, considerably impacting kelp productivity. Estimated daily summer NPP over all four depths was 1.48 ± 0.97 g C · m⁻² seafloor · d⁻¹ for the Helgolandic kelp forest, which is in the range of other kelp forests along European coastlines.     

Individual day-to-day variations in plasma amino acid levels in healthy persons

Summary Fasting plasma levels of the large neutral amino acids (LNAA;l-forms) andl-tryptophan (TRP) ratios were determined in thirteen healthy volunteers (7 males, 6 females) on five consecutive mornings, and the same procedure was repeated for each individual three months later. We found characteristic overall ranges for the parameters studied, and, in addition to certain differences between the sexes, considerable inter- and intraindividual daily variations. Although the individuals showed statistically identifiable mean levels that, in the majority of subjects, were maintained over a period of three months, it is concluded that the degree of intraindividual variability does not allow us to regard a single value as characteristic for a given individual. This should be borne in mind in particular in follow-up studies of plasma LNAA in patients with, for example, depressive disorders.