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.     

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.     

Tree and bird functional groups as indicators of recovery of regenerating subtropical coastal dune forests

Functional diversity indicators are increasingly used to monitor forest function recovery because they connect biodiversity to ecosystem functions. However, identifying which functions deviate from a reference forest has not received much attention, despite its potential to inform restoration interventions. In this study, we used functional groups to assess the recovery of ecosystem functions in regenerating coastal dune forests. We surveyed birds and trees in forest of different ages and a reference old‐growth forest in KwaZulu‐Natal, South Africa. We classified species into functional groups for each taxa based on functional traits or a priori defined categories (i.e. guilds) and quantified the number of species within functional groups as a proxy of function stability. Bird species density followed an asymptotic trajectory, reaching old‐growth forest values after 25 years. Insectivores and granivores showed saturating trajectories, whereas small frugivores and generalists increased linearly. With the exception of large frugivores, relative abundances of bird functional groups progressed towards old‐growth forest values as the forest aged. Tree species density increased linearly with forest age. In contrast to old‐growth forests, large‐canopy trees and understory shrubs were under‐represented, while mid‐canopy trees dominated regenerating forests. Our result suggests that most bird, but not tree, functions may have been restored. The trend in large frugivore numbers may warrant further investigation, as their low numbers may have hampered the recovery of tree functions. We conclude that functional group trajectories can track functions that deviate from a benchmark, and may therefore direct adaptive actions to recover the stability of regenerating forest.     

Alternative methods for determining anaerobic biodegradability: A review

The characterization of solid wastes is a necessary step before they can be used in anaerobic digestion. The quantities of different compounds (carbohydrates, proteins, lipids and fibers) and anaerobic biodegradability (capacity to produce methane) are important information required to characterize waste. The Biochemical Methane Potential (BMP) test is one of the most relevant tests for assessing the biodegradability of waste materials. The BMP test is run under anaerobic conditions, using bacteria populations, which makes it very time consuming, i.e., about 30 days. This paper presents alternative methods for determining the anaerobic biodegradability of solid waste. First, we describe the already existing tests for characterizing organic matter. Then we correlate an aerobic test with an anaerobic test in order to estimate anaerobic biodegradability and biogas production. This shortens the analysis time to 5 days. Models using physico-chemical characteristics as input data (total carbohydrate, total nitrogen, fiber, etc.) can predict the amount of methane produced by correlation. Pyrolysis is a very fast analytical test that can be used to characterize solid waste. Lastly, spectroscopy techniques seem to be useful for determining biodegradability, in particular by taking into account the interaction between different molecules in the organic matter.     

Evaluation of secondary forests as alternative habitats to primary forests for flower-visiting insects

Although primary forests are important for biological conservation, the value of secondary forests for forest-dependent organisms needs to be evaluated when habitat restoration is required. We examined whether flower-visiting insects can use secondary forests as alternative habitats to primary forests. In particular, we compared assemblages of bees (Anthophila) and flower longhorn beetles (Lepturinae: Cerambycidae) in young secondary, mature secondary, and primary forests. Our results showed that more bee species were captured in primary and mature secondary forests than in young secondary forests, and flower longhorn beetle species were captured more frequently in primary forests than in mature and young secondary forests. Ordination showed that the communities in the three forest types were not statistically identical, which indicated that secondary forests cannot provide an absolute alternative habitat to primary forests for bees and flower longhorn beetles. However, the results also suggest that as secondary forests mature, more primary forest species would be able to use secondary forests as habitats. This implies that restoration from other land uses, such as monoculture plantations, to secondary forests could help to promote the faunal biodiversity of primary forests.     

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.     

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.     

Targeting the Spleen as an Alternative Site for Hematopoiesis

Bone marrow is the main site for hematopoiesis in adults. It acts as a niche for hematopoietic stem cells (HSCs) and contains non‐hematopoietic cells that contribute to stem cell dormancy, quiescence, self‐renewal, and differentiation. HSC also exist in resting spleen of several species, although their contribution to hematopoiesis under steady‐state conditions is unknown. The spleen can however undergo extramedullary hematopoiesis (EMH) triggered by physiological stress or disease. With the loss of bone marrow niches in aging and disease, the spleen as an alternative tissue site for hematopoiesis is an important consideration for future therapy, particularly during HSC transplantation. In terms of harnessing the spleen as a site for hematopoiesis, here the remarkable regenerative capacity of the spleen is considered with a view to forming additional or ectopic spleen tissue through cell engraftment. Studies in mice indicate the potential for such grafts to support the influx of hematopoietic cells leading to the development of normal spleen architecture. An important goal will be the formation of functional ectopic spleen tissue as an aid to hematopoietic recovery following clinical treatments that impact bone marrow. For example, expansion or replacement of niches could be considered where myeloablation ahead of HSC transplantation compromises treatment outcomes.     

系统生物学中建模方法的研究现状及展望

系统生物学倡导利用系统论的思想和方法,从整体的高度分析、研究生命的复杂特性。这一点与实验生物学仅关注某一个或者某一些生物大分子是迥然不同的。系统生物学既要同时考虑多个层次、多种类型的生物信息,还要考虑时间因素。由于系统特性是由于不同组成部分、不同层次间相互作用而“涌现”出的新性质,因此,如果只是针对组成部分或单一层次的分析并不能真正准确地预测整体或高层次的行为。如何通过研究和整合去发现和理解“涌现”出的新的系统性质,是系统生物学面临的一个根本性的挑战。为了应对这一挑战,系统生物学,特别是计算系统生物学必须建立有效的方法,通过整合系统各个层次的信息,建立可反映该系统目前已知或已可测量的性质的物理、数学模型,并通过这样的模型来研究或预测目前还未知晓的系统性状。可以说：建模是系统生物学的最重要的研究手段之一。目前,生命科学的研究正逐步由对单一现象、单一过程的机械论式的描述型研究转向运用高通量实验技术获取海量生物信息,并在这些生物信息基础上建立物理、数学模型,最终通过建模与实验相接合的研究手段来定量阐述生命现象的本质规律。由于建模方法在系统生物学研究中的重要性,本文将对一些主要的建模类型,如定性建模方法;基于约束的建模方法;基于常微分/偏微分方程的定量建模和基于随机微分方程的定量建模方法等等分别予以简要介绍。