Genetic evaluation of alternative silvicultural systems in coastal montane forests: western hemlock and amabilis fir

Genetic diversity and mating system were quantified for shelterwood, patch cut and green tree-retention silvicultural systems, and compared to adjacent old-growth. This is a component of a larger study conducted in montane old-growth forests of coastal British Columbia to evaluate the feasibility and ecological consequences of alternative silvicultural systems. The experiment includes replicated treatments representing a range of overstory removal adjacent to old-growth and clearcut areas. Based on 22 electrophoretically assayed loci, the effects of silvicultural systems on genetic parameters of amabilis fir (Abies amabilis and western hemlock (Tsuga heterophylla were assessed by comparing an average number of alleles per locus, the percent polymorphic loci, and observed and expected heterozygosity between parental populations and naturally regenerated progeny as well as among treatments. Genetic variation in natural regeneration was greater than in parental populations, especially for low-frequency alleles. Silvicultural treatments caused no significant differences in amabilis fir genetic-diversity parameters, while the shelterwood system resulted in lower observed and expected heterozygosity in western hemlock. Nei's genetic distance revealed that all parental populations were extremely similar. The two species had contrasting mating system dynamics with amabilis fir producing higher levels of correlated paternity and inbreeding with wider variation among individual tree outcrossing-rate estimates. Western hemlock had significant levels of correlated paternity only for the green tree and shelterwood treatments demonstrating family structuring inversely related to stand density. Inbreeding in western hemlock was significant but lower than that observed for amabilis fir with a J-shaped distribution for individual tree multilocus outcrossing-rate estimates. The pollination and dispersal mechanisms of the two species represent the most-likely factors causing these differences. Artificial regeneration may be utilized to augment the genetic resources of natural ingress.     

Alternative staining methods for Lowicryl sections.

A number of stains and stain combinations have been identified that, when used with the hydrophilic resin Lowicryl K11M, produce marked improvements over aqueous uranyl and lead salts (UA-Pb) in terms of low granularity, specificity, and range of components contrasted. Three test specimens, tobacco mosaic virus (TMV), starfish sperm, and cultured mouse fibroblasts, were used to evaluate stain characteristics. UA-Pb showed a preference for nuclei acids, which were stained specifically by osmium ammine-B at pH 1.5. A number of stain combinations in which UA was followed or preceded by salts containing barium, manganese, tungsten, molybdenum, and vanadium provided excellent staining of protein-containing components, each stain combination being unique in terms of the degree to which specific components were discriminated. These stains were particularly effective for visualizing internal components of the nucleus where a number of fibrillar and particulate structures not seen with UA-Pb were well contrasted.     

Surface and leaf-litter arthropods in the coastal forests of Tanzania

Surface and leaf litter arthropod assemblages of the seasonal lowland coastal forests of eastern Tanzania were investigated from eleven sites over a 3-year period (1991–93). Pit-fall trap data show that four groups comprise more than 10% of the total sample: ants (Hymenoptera: Formicidae, 31%), grasshoppers and crickets (Orthoptera, 22%), beetles (Coleoptera: 17.39%) and spiders (Araneae: 13.48%). Arthropod abundance varies considerably with season, with greater total numbers of arthropods in all groups found in wetter periods. Arthropod abundance also varies considerably according to habitat, with greatest numbers found in forests with the most intact canopy cover, and in valley-bottom forest as compared to ridge-top forest; the valleys are normally both wetter and with a more complete and taller canopy. Tullgren Funnel data show that over 50% of the leaf litter fauna comprises tiny arthropods of the groups Collembola and Acarina. Abundance of arthropods in the leaf litter of these forests varies from a maximum of ≈ 16,000 m^–2, to a minimum of 780 m^–2. Abundance is highest in wetter periods, in the forest areas with the most intact canopy cover, and in valley-bottom as opposed to ridge-top habitats.     

Alternative methods for the feeding of triatomines under laboratory conditions

In order to improve the rearing and maintenance of triatomines under laboratory conditions, two feeding systems were made, one with a natural source in which a pigeon kept alive after several blood meals in triatomines was used and another artificial system using defibrinated sheep blood. Besides these equipments being made of easily available materials and low cost, they have shown to be useful and efficient, with favourable conditions for the feeding of triatomines.     

Ultra-Structure database design methodology for managing systems biology data and analyses

Background  

Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping).     

Design methods for tubular fermentation systems

Methods for the design of tubular fermentation systems are summarized. The first part, on tubular system hydrodynamics, is concerned with the design methods for gas hold-up, pressure drop, drop-size distribution and actual interfacial area, and with non-ideal flow conditions. This being a critical review, only the more important methods have been selected. More recent design methods for the prediction of oxygen transfer coefficients in fermentation systems and methods of determining of true kinetic relations are also reviewed, accounting for the inevitable non-ideality of flow. General rules for system optimization are presented.     

Alternative methods for production and staining of Phanerochaete chrysosporium basidiospores.

Homokaryotic isolates of Phanerochaete chrysosporium are generally obtained by stimulating the production of basidiospores. The most commonly used method requires a special incubator that is maintained at 28 degrees C with continuous illumination. Here we report an alternate method which permits the production of basidiopores with common laboratory incubators and requires no special illumination conditions. This alternate method gives reproducible results and yields basidiospores that are not contaminated with conidia. We also report a detailed optimized method for staining basidiospores for visualizing nuclei.     

Two new species of Plinia (Myrtaceae) from coastal forests of Brazil

Plinia complanata andPlinia pauciflora, two new species from coastal forests of São Paulo state, southeastern Brazil, are described and illustrated.     

Calibrating the radial-growth averaging method for detecting releases in old-growth forests of coastal British Columbia,Canada

Dendroecological methods that use growth releases to reconstruct the history of canopy disturbances are most useful when calibrated for specific species in specific forest types. In this study, we calibrate the radial-growth averaging method to detect growth releases of western redcedar (Thuja plicata Donn ex D. Don), western hemlock (Tsuga heterophylla (Raf.) Sarg.), and Pacific silver fir (Abies amabilis Dougl. ex J. Forbes) following fine-scale canopy disturbances in old-growth forests of coastal British Columbia, Canada. Our goal is to establish a version of the method that will capture the full range of growth increases that occur for the study species following natural, fine-scale canopy gaps, yet will account for the effects of climatic variability on radial growth and growth increases. We used traditional dendroclimatological techniques and the radial-growth averaging method to examine how climatic and regional-scale factors contributed to radial growth and growth increases. In addition, we did a sensitivity analysis, using both ring widths and basal area increments, to explore how varying the values of three parameters of the radial-growth averaging method (threshold, moving average, and window) influenced the proportion of trees that showed a release pattern following the formation of canopy gaps of known timing of origin. Although radial growth of western redcedar and western hemlock was significantly associated with climate, percent-growth change derived from residual chronologies rarely exceeded 25%, which defined our minimum threshold for a release. For the sensitivity analysis, two general trends were common to all three species: (1) as threshold increased, the proportion of trees that showed a release pattern decreased, particularly for western redcedar and (2) a higher proportion of trees showed a release pattern using a 10-year versus a 5-year window, particularly for thresholds <100%. The greatest proportion of trees showed a release pattern using a 25% threshold, 5-year moving average, and 10-year window for both ring widths and basal area increments. Overall, a higher proportion of trees showed a release pattern using basal area increments as opposed to ring widths. Therefore, basal area increments are better suited to assess releases in these old-growth stands that have large inter- and intra-species variability in tree size. By establishing these empirically-based criteria, we have achieved the first step towards quantifying attributes of growth releases of trees in the study stands, allowing future studies to capture the variability of past disturbance events and predict changes in forest structure and composition over time.     

Alternative methods for the efficient construction of short hairpin RNA expression vectors

Short hairpin RNA (shRNA)-mediated RNA interference has become a basic technique in modern molecular biology and biochemistry for studying gene function and biological pathways. Here, we report two alternative and efficient methods to construct shRNA expression vectors based respectively on multiple-step sequential PCR and primer extension–homologous recombination (PE-HR). Neither method requires synthesizing long oligonucleotides containing hairpin sequences as used in traditional approaches. The hairpin sequences may produce mutations during oligo synthesis, pose problems in annealing, and lead to inefficient cloning. The PE-HR method further provides rapid and economical construction of shRNA expression vectors without needing the ligation procedure.     

Alternative methods of nutritional status assessment in adolescents

The main objective of this cross-sectional study was to determine the validity of the silhouette rating scale and reported values of height and weight in assessing weight status in a group of adolescents. 245 adolescents, students of the Belgrade elementary school, aged 11-14 (12.33 +/- 0.50), were involved. Weight status was assessed by anthropometry, self-reported height and weight and by figure rating scale. From the results obtained significant differences emerged as a function of weight status. The majority of normal weight adolescents were accurate in reporting their body size. The percentage of under-reporters was significantly higher in the overweight/obese group than in the normal weight group (chi2 = 9.741, p = 0.003). The correlation between BMI, both measured and self-reported, and perceived body size was positive and highly significant (p < 0.001). Self-reported weight and height appears acceptable for estimating weight status in normal weight adolescents, but not in those who are overweight or obese. This study also demonstrated that adolescents can estimate with some accuracy their body size using figure ratings scales.     

Alternative methods to limit extracellular bacterial activity for enumeration of intracellular bacteria

The gentamicin survival assay, a method routinely used to estimate bacterial infection of eukaryotic host cells, depends on the presumed limited penetration of gentamicin across the eukaryotic cell membrane. However, some studies have suggested that gentamicin may in fact enter eukaryotic cells and kill intracellular bacteria. In this study we devised alternative methods to enumerate intracellular Salmonellae using a lytic bacteriophage, SP6, and an amino acid auxotroph, Pro- mutant, which replicates selectively within host cells in the presence of its uptake inhibitor, 3,4-dehydro-L-proline. The conventional gentamicin survival assay was systematically compared with the alternative methods for the enumeration of intracellular Salmonellae. We found that gentamicin decreases the survival of intracellular Salmonellae when added to extracellular media at concentrations above 20 microg/ml. The alternative methods do not suffer from this disadvantage, suggesting that they should be used to replace the gentamicin survival assay. In addition, the proline auxotroph method could be applied to detect bacterial release from host cells.     

Intertidal pools as alternative nursery habitats for coastal fishes

Fish were sampled monthly in four tidal pools, for two years, on the west Portuguese coast. Species diversity of transient fish was higher than that found in previous studies, in other parts of the world. The transient fish population comprised six species: the white seabream, Diplodus sargus, sand smelt, Atherina spp., the thinlip grey mullet, Liza ramada, the Baillon's wrasse, Symphodus bailloni, the zebra seabream, Diplodus cervinus and the European pilchard, Sardina pilchardus. Abundance varied seasonally, yearly, and among pools, with peak numbers in spring and summer. The most abundant species in all pools, both as larvae and juveniles, was D. sargus. Diplodus sargus and Atherina spp. were present in most pools, from spring to autumn, while rare species were present mostly in the spring-summer period. Smaller mean sizes of larvae and juveniles were observed at the beginning of spring of 2011 (March–April) and at the end of spring/beginning of summer of 2012 (May–June). Mean size of larvae and juveniles often showed a continuous increase from spring to autumn in both years. The highest density peaks were due to the high number of post-larvae entering the pools in spring. In most pools, the overall condition (Fulton's K) of D. sargus increased throughout the year, in both years. The species richness, the high densities of early stages, and their continuous growth observed in tidal pools strongly emphasize the importance of these environments for larvae and juveniles of several transient marine fishes.     

Web-based applications for building, managing and analysing kinetic models of biological systems

Mathematical modelling and computational analysis play an essentialrole in improving our capability to elucidate the functionsand characteristics of complex biological systems such as metabolic,regulatory and cell signalling pathways. The modelling and concomitantsimulation render it possible to predict the cellular behaviourof systems under various genetically and/or environmentallyperturbed conditions. This motivates systems biologists/bioengineers/bioinformaticiansto develop new tools and applications, allowing non-expertsto easily conduct such modelling and analysis. However, amonga multitude of systems biology tools developed to date, onlya handful of projects have adopted a web-based approach to kineticmodelling. In this report, we evaluate the capabilities andcharacteristics of current web-based tools in systems biologyand identify desirable features, limitations and bottlenecksfor further improvements in terms of usability and functionality.A short discussion on software architecture issues involvedin web-based applications and the approaches taken by existingtools is included for those interested in developing their ownsimulation applications.