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.     

Biological evaluation of trace element data in human ovaries by statistical analysis

Analysis of variance, analysis of covariance, correlation coefficient, multiple correlation, and partial correlation coefficient statistical tests were applied to Cs, Cr, Co, Fe, Rb, Sc, Se, and Zn content in human ovaries in order to evaluate statistically the possible relationships between these trace elements at: the ovary as an organ, each ovarian phase separately, each morphological part independent of the ovarian phase, and between cortex and medulla within the ovarian phases. The element Cs seems to have a homogenous distribution between cortex and medulla within reproductive and menopausal phase. Zinc shows a trend to have an antagonistic relation with Cs, Cr, Co, and Fe during fetal and reproductive phases and not during menopausal phase. The relationship between Zn and Cs when Fe is kept constant could be used as a tool for the decontamination of the ovary from an abnormal Cs content or for the inhibition of the accumulation of the same element to the ovarian tissue.     

Cold hardiness and water relations parameters in Rhododendron cv. Catawbiense Boursault subjected to drought episodes

We determined whether increase in cold hardiness of Rhododendron cv. Catawbiense Boursault induced by water stress was correlated with changes in tissue water relations. Water content of the growing medium was either maintained near field capacity for the duration of the study or plants were subjected to drought episodes at different times between 15 July and 19 February. Watering during a drought episode was delayed until soil water content decreased below 0.4 m³ m⁻³ then watering was resumed at a level to maintain soil water content between 0.3 and 0.4 m³ m⁻³. Cold hardiness was evaluated in the laboratory with freeze tolerance tests on detached leaves. Water relations parameters were determined using pressure-volume analysis. Exposure to drought episodes increased cold hardiness during the cold acclimation stage in late summer and fall but not during the winter. When water-stressed plants were re-watered to field capacity, the previous gain in cold hardiness gradually disappeared. Water relations parameters correlating with seasonal changes of cold hardiness included dry matter content (r =−0.67). apoplastic water content (r =−0.60), and water potential at the turgor loss point (r = 0.40). Changes of cold hardiness in water-stressed plants in reference to well-watered plants were correlated with changes of all water relations parameters, except for osmotic potential at full turgor (r = 0.13). It is proposed that water stress reduced the hydration of cell walls, thereby increasing their rigidity. Increased rigidity of cell walls could result in a development of greater negative turgor pressures at subfreezing temperatures and therefore increased resistance to freeze dehydration.     

Root growth dynamics of Brussels sprouts (Brassica olearacea var.gemmifera) and leeks (Allium porrum L.) as reflected by root length,root colour and UV fluorescence

Minirhizotron observations of roots of leeks and Brussels sprouts grown in the Wageningen Rhizolab were used to study the dynamics of root length. Day of appearance and the time of decay were assessed for individual root segments visible on the minirhizotron surface.A Brussels sprouts crop produced much more root length than leeks, but the average longevity of these roots was about half that of leek roots.To investigate whether root colour or UV fluorescence could be used as a quantitative index of root functionality or root age, changes in root colour (on a scale of greys) over time were measured with interactive image analysis. In both crops a gradual change towards black was found with ageing. Measurements of the intensity of the UV fluorescence showed that leek roots fluoresced more than Brussels sprouts roots. Over time, UV fluorescence decreased in Brussels sprouts roots but increased in leek roots. It is concluded that UV fluorescence cannot be used as a universal indicator of root age or root functionality, but in some plant species it may be used to separate (transparent) roots from the background with image analysis techniques.     

Higher level relationships of Apiales (Apiaceae and Araliaceae) based on phylogenetic analysis of rbcL sequences

The two families of the order Apiales (Apiaceae and Araliaceae) represent a classic example of the difficulty in understanding evolutionary relationships between tropical-temperate family pairs. In Apiales, this problem is further compounded by phylogenetic confusion at almost every taxonomic level, including ordinal, interfamilial, and infrafamilial, due largely to difficulties in understanding trends in morphological evolution. Phylogenetic analyses of rbcL sequences were employed to resolve relationships at the ordinal and familial levels. The results of the ordinal analysis confirm the placement of Apiales in an expanded subclass Asteridae as the sister group to Pittosporaceae, and refute the traditional alliance of Apiales with Cornales and Rosidae. This study has also resolved relationships of a number of enigmatic genera, suggesting, for example, that Melanophylla, Aralidium, Griselinia, and Toricellia are close relatives of Apiales. Clarification of phylogenetic relationships has concomitantly provided insights into trends of morphological evolution, and suggests that the ancestral apialean taxon was probably bicarpellate, simple-leaved, woody, and paleotropical. Phylogenetic analysis at the family level suggests that apiaceous subfamily Hydrocotyloideae, often envisioned as an intermediate group between Apiaceae and Araliaceae, is polyphyletic, with some hydrocotyloids closely allied with Araliaceae rather than Apiaceae. With the exception of some hydrocotyloids, Apiaceae appear to be monophyletic. The relationship between Apiaceae and Araliaceae remains problematic. Although the shortest rbcL trees suggest that Apiaceae are derived from within a paraphyletic Araliaceae, this result is only weakly supported.     

Isozyme analysis of intercontinental disjuncts within Styrax (Styracaceae): implications for the Madrean —Tethyan hypothesis

Various hypotheses have been put forward to explain the presence of sclerophyllous plant disjuncts between western North America and the Mediterranean region. The Madrean–Tethyan hypothesis postulates that the two regions were floristically connected in the Early to Middle Tertiary by way of a low-latitude migration route. Others deny the possibility of such a route, and instead postulate convergence to xerophytic conditions from more widespread mesophytic ancestors, or suggest long-distance dispersal scenarios. One example of a “Madrean–Tethyan link” between the two regions is composed of four species within the genus Styrax: S. officinalis subsp. officinalis from the Mediterranean region, S. officinalis subsp. redivivus and subsp. fulvescens from California, and three closely related species in Texas and northeastern Mexico (S. texanus, S. platanifolius, and S. youngiae). This group was examined with isozymes to assess whether patterns of genetic variation are consistent with those predicted by the Madrean–Tethyan hypothesis. Ten populations from California, six from the Mediterranean region, and three from Texas were sampled. Pairwise comparisons revealed mean genetic identity (I) estimates of 0.581 between Mediterranean and California populations, 0.470 between Mediterranean and Texas populations, and 0.640 between California and Texas populations. Two populations of a species thought by many to be the closest relative of S. officinalis on morphological grounds (S. jaliscanus) exhibited low I (0.299–0.321) relative to all other group comparisons. Intercontinentally disjunct populations of S. officinalis possessed an I value that warrants species status for the Californian and Mediterranean groups. Divergence time estimates between Madrean and Tethyan Styrax range from 5.0 to 13.8 Mya, too recent to be consistent with the Madrean–Tethyan hypothesis. However, alternative explanations for this disjunction are suboptimal in that they require the invocation of either long-distance dispersal, which appears unlikely in this group, or extinction. Nonetheless, the evidence presented here and in other recent studies casts substantial doubt on the Madrean–Tethyan hypothesis as a general explanation for the presence of Madrean and Tethyan taxa similar in overall appearance. More plants with Madrean–Tethyan distributions must be sampled before definitive conclusions regarding this aspect of Madrean and Tethyan vegetation can be reached.     

Two-bond C-C spin-coupling constants in carbohydrates: effect of structure on coupling magnitude and sign

An empirical projection method is described to predict the magnitudes and signs of two-bond ¹³C-¹³C spin-coupling constants (²J_CC) in aldopyranosyl rings. The method has been applied primarily to the interpretation of ²J_CCC values, although the behavior of ²J_COC has also been examined in light of the new approach, producing results which may prove useful in the conformational analysis of O-glycosidic linkages in oligosaccharides. High-level ab initio calculations of ²J_CC values in model compounds were found to be in agreement with the predictions.     

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     

Analysis of woody vegetation of Corbett National Park,India

The heterogeneous vegetation mosaic of the South Turkana region of north Kenya is associated with diversity in the region's physical environment. The abundance and distribution of the dominant species are related to gradients in those abiotic factors that influence water availability, including precipitation, soil texture, and topographic relief. Research focused on three Acacia species that are a major component of the Turkana vegetation; A. tortilis, A. senegal, and A. reficiens. These species each exhibit a different response to variations in abiotic factors. Consequently, species abundance varies independently across the landscape, creating a continuum of intergrading populations. Community types can be identified within the mosaic of intergrading populations. Although community borders are not discrete due to continual change in species abundance, types are identifiable and are repeated in areas with similar environmental conditions. The landscape patterns are representative of Whittaker's (1953) climaxas-pattern, with communities created by individual patterns of populations responding to environmental gradients, creating a continuum of community change across the landscape.