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.     

A comparative study of ciliated protozoa communities in activated-sludge plants

Abstract: Ciliated protozoa present in ten activated sludge plants at Madrid (Spain) were identified. The abundance of key groups of ciliates was determined at each plant; attached ciliates made up the most abundant and representative group. Multivariate statistical analysis was employed to study relationships between ciliates and both the physico-chemical and operational parameters of the plants. Partial correlation analysis revealed: (1) The indicator value of attached ciliates in assessing management and performance of the activated sludge process, (2) the relationship of swimming ciliates with short-aged sludges and lower quality effluents and (3) the direct association between swimming-crawling ciliates and bad settlement conditions of the sludge. Factor analysis showed the associations of the most frequent species of ciliates with the operational parameters of the plants, suggesting the indicator value of some of the species: Vorticella striata was related with poor quality of effluent; Aspidisca cicada with stable plant conditions, and Litonotus lamella with a deficiently settling sludge.     

The growth pattern of chimpanzees: Somatic growth and reproductive maturation inPan troglodytes

Growth of chimpanzees reared at the Kumamoto Primates Park of Sanwa Kagaku Kenkyusho Co. Ltd. was studied cross-sectionally from the viewpoints of somatic growth and reproductive maturation. Distance and velocity curves were expressed using spline function method. Males showed adolescent growth acceleration in body weight, with a peak at 7.86 yrs of age, but not in trunk length. Females showed continuous rapid growth from mid-juvenile to adolescent phase in both body weight and trunk length, but no isolated adolescent spurt. The Sanwa chimpanzees matured at about 12.5 yrs of age for females and 15.0 yrs for males. The mean adult weights and trunk lengths were 53.2 kg and 507.8 mm for males and 42.7 kg and 481.6 mm for females. The Sanwa chimpanzees had similar growth patterns to those of the Yerkes chimpanzees, although they showed a slight delay in infancy, and a higher growth rate from the early juvenile phase onwards. Growth patterns in these two laboratories may be regarded as “normative” for laboratory-reared chimpanzees. They matured earlier than wild chimpanzees by more than two years. The major reason for the retarded maturation in wild chimpanzees is the delay of growth from infant to the early juvenile phases (0–4 yrs of age), probably owing to a limited nutritional supply from the mother. Development of the testes comprised three phases: slow growth from infant to juvenile (until 6.4 yrs); rapid growth around adolescence (until 9.2 yrs); and adult (mean testicular volume, 187 cm³). Setting the nutritional standard at 2,000–2,600 Cal/day (= Kcal/day) per adult, calories were considered for captive chimpanzees in each age class.     

A Monte Carlo method for Bayesian analysis of linkage between single markers and quantitative trait loci. I. Methodology

A Bayesian approach to the statistical mapping of Quantitative Trait Loci (QTLs) using single markers was implemented via Markov Chain Monte Carlo (MCMC) algorithms for parameter estimation and hypothesis testing. Parameter estimators were marginal posterior means computed using a Gibbs sampler with data augmentation. Variables sampled included the augmented data (marker-QTL genotypes, polygenic effects), an indicator variable for linkage, and the parameters (allele frequency, QTL substitution effect, recombination rate, polygenic and residual variances). Several MCMC algorithms were derived for computing Bayesian tests of linkage, which consisted of the marginal posterior probability of linkage and the marginal likelihood of the QTL variance associated with the marker.     

Estimation of the position and effect of a lethal factor locus on a molecular marker linkage map

In the mapping of DNA markers the distortion of segregation of marker genotypes is often observed, which may be caused by a lethal factor acting in filial generations derived from distant crosses. A method is presented for estimating the recombination values between a lethal factor locus and neighboring molecular markers, and the relative viability or fertilization ability of gametes or zygotes affected by the lethal factor in an F₂ population using the maximum likelihood method and the expectation conditional maximization (ECM) algorithm. Three selection models of gamete or zygote were considered, and the most likely one was determined by goodness of fit of the observed frequency of the phenotypes to the expected ones under the models. The method was applied to segregation data of molecular markers of an F₂ population consisting of 144 individuals derived from a cross between an Indica and a Japonica rice variety. The presence of a lethal factor locus (L) located on chromosome III that caused partial gametic selection in both the male and female sides was suggested. The locus L was tightly linked to RFLP marker number 23 of the RFLP linkage map of Saito et al. (1991a), and the fertilization chance of a male or female gamete possessing the lethal factor was, on average, 41.5% of that of the normal gamete.     

Differences between observed and predicted energy costs at rest and during exercise in three subsistence-level populations

Estimates of daily energy expenditure are important for many areas of research in human ecology and adaptability. The most common technique for estimating human energy expenditure under field conditions, the factorial method, generally relies on activity-specific energy costs derived from published sources, based largely on North American and European subjects. There is concern that such data may not be appropriate for non-Western populations because of differences in metabolic costs. The present study addresses this concern by comparing measured vs. predicted energy costs at rest and during sub-maximal exercise in 83 subjects (52 males, 31 females) from three subsistence-level populations (Siberian herders and high-land and coastal Ecuadorian farmers). Energy costs at rest (i.e., lying, sitting and standing) and while performing a standard stepping exercise did not significantly differ among the three groups. However, resting energy costs were significantly elevated over predicted levels (+16% in men, +11% in women), whereas exercising costs were comparable to predicted values (?6% in men, +3% in women). Elevations in resting energy needs appear to reflect responses to thermal stress. These results indicate that temperature adjustments of resting energy costs are critical for accurately predicting daily energy needs among traditionally living populations. o 1996 Wiley-Liss, Inc.     

Application of radiotelemetry to the survey of acorn dispersal byApodemus mice

We examined the applicability of radiotelemetry to studies of acorn dispersal byApodemus mice and compared its efficiency with the of this spool-and-line method. Installation of a transmitter (2.2 g) onto acorns did not interfere with the transporting and feeding behavior of the mice. We were able to detect all transmitter-installed acorns and follow the daily changes in the sites in which they were hoarded, while we missed 59% of the spool-tied acorns due to mice breaking the threads. Mice carried transmitter-installed acorns farther than spool-tied ones. The radiotelemetry method is superior to the spool-and-line method and useful for the study of hoarding behavior in rodents.     

An ordination study of mangrove swamp communities in West Africa

The most important environmental gradients of Maine peatlands are geologic substrate and alkalinity. Other gradients are coastal-inland climate, moisture content of the peat, P and K concentrations, and shade. Abundance weighted means of pH, Ca, and moisture content of peat are given for the 48 most frequently occurring bryophyte and lichen species. A TWINSPAN differentiated twenty associations. Environments of the first four TWINSPAN dichotomies differed largely by pH and related variables, though Fe, %H₂O, shade, microtopography, and degree of humification were also significant. A CCA with forward selection entered pH, P, Fe, Na, %H₂O, shade, and a climate factor as the minimum number of variables which best account for the species variation. Bryophyte and lichen distributions are determined primarily by edaphic and hydrologic factors, which determine the kinds and amounts of mineral solutes in peat interstitial water. Two independent chemical gradients were identified: (1) the acidity-alkalinity gradient related to base cation concentrations, and (2) a gradient of Fe, Al, Mn, and Si related to shallowness of peat and inputs from granitic lithologies.     

Prairie plant guilds: a multivariate analysis of prairie species based on ecological and morphological traits

An ecomorphological analysis of the tallgrass prairie of central North America divided representative species of the native grassland flora into eight guilds or groups of species with similar life-form, phenology, and ecology. The guilds, segregated by multivariate analysis, are: (1) warm-season graminoids with Kranz anatomy and the Hatch-Slack photosynthetic pathway (C4 grasses); (2) cool-season graminoids without Kranz anatomy, but with the common Calvin or C3 photosynthetic pathway (C3 grasses and sedges); (3) annuals and biennial forbs; (4) ephemeral spring forbs; (5) spring forbs; (6) summer/fall forbs; (7) legumes; and (8) woody shrubs. The study was based on 158 plant species indigenous to three upland prairie sites in northeastern Kansas. Each species was scored for 32 traits which fall into five broad categories: plant habit, leaf characteristics, stem structures, root structures, and reproductive traits, including phenology. A multivariate, detrended correspondence analysis sorted the 158 species into the eight principal groups or guilds. These groups were further supported by a cluster analysis and discriminant function analysis of the same data set. The discriminant function analysis determined that 94.3% of the species were correctly classified in their respective guilds, and that the guilds were statistically different. Results indicate that guild analysis offers a basis for detailed classification of grassland vegetation that is more ecologically focused than species composition, as the myriad of species (about 1,000 prairie species on the central plains of North America) vary in presence, cover, and importance with their individualistic distribution.Abbreviations C3= C3 photosynthesis - C4= C4 photosynthesis - LSD= least significant difference     

An impedimetric method for rapid screening of cosmetic preservatives

An efficient impedance method was developed for rapid evaluation of cosmetic preservatives. The method used decimal reduction time or D-value to assess preservative efficacies. The D-value, which was calculated from the plot of Log CFU ml^–1 versus time by linear regression analysis, could be obtained within 48 h. Thus, the time required for the challenge test was reduced from 4–8 weeks with the standard procedures (eg US Pharmacopeia), to 2 days with the current method. A calibration curve (r=-0.95) was established by plotting the Log CFU ml^–1 versus capacitance detection time (DT) of 108 samples. With the calibration, CFU can be estimated directly from the impedance test without plating. Two commercial biocides and several other chemicals were evaluated in a shampoo by the impedance procedure againstPseudomonas aeruginosa. The D-values obtained from the impedance test were not significantly different from those produced by the conventional plate count method. The technique was found to be particularly useful when screening a large number of compounds to find novel preservatives and synergistic preservative combinations.