Stability of transformation systems representable by tree graphs: Extension to structures of biological importance

It is known that systems representable by tree graphs have entirely real eigenvalues near a steady state (Hyver, 1973). Here it is shown that the eigenvalues are negative, thus ensuring local stability.The method used in the proof allows some extensions which may be of considerable biological importance in certain cases, for example where linear systems containing circuits are involved, or enzymatic reactions, or autocatalytic reactions.     

Cellular systems as graphs

The definition of an (M,R) is formulated in a way that emphasizes its mathematical properties. Neglecting interactions between the components, it is shown that:

1. An (M,R) contains only one non-reestablishable component.
2. If an (M,R) contains only one non-reestablishable component, then that component is central.

Examples are given to illustrate the biological significance of these two results. The notion of “lag-independence” is introduced, and it is shown that if a system possesses only one non-reestablishable component which is “lag-independent” then all components are lag-independent. The concepts of reestablishability, centrality and lag-independence are applied in order to suggest various criteria for optimal organization of (M,R).     

Conflicting values: ecosystem services and invasive tree management

Tree species have been planted widely beyond their native ranges to provide or enhance ecosystem services such as timber and fibre production, erosion control, and aesthetic or amenity benefits. At the same time, non-native tree species can have strongly negative impacts on ecosystem services when they naturalize and subsequently become invasive and disrupt or transform communities and ecosystems. The dichotomy between positive and negative effects on ecosystem services has led to significant conflicts over the removal of non-native invasive tree species worldwide. These conflicts are often viewed in only a local context but we suggest that a global synthesis sheds important light on the dimensions of the phenomenon. We collated examples of conflict surrounding the control or management of tree invasions where conflict has caused delay, increased cost, or cessation of projects aimed at invasive tree removal. We found that conflicts span a diverse range of taxa, systems and countries, and that most conflicts emerge around three areas: urban and near-urban trees; trees that provide direct economic benefits; and invasive trees that are used by native species for habitat or food. We suggest that such conflict should be seen as a normal occurrence in invasive tree removal. Assessing both positive and negative effects of invasive species on multiple ecosystem services may provide a useful framework for the resolution of conflicts.     

Lily breeding by using molecular tools and transformation systems

In our review, we highlighted the progresses made in molecular breeding of lily’s flowering, including the ABCDE models, the gene cloning, the establishment of regeneration system, the gene transformation methods, the transgene technology application in lily. Meanwhile, questions that were met at present in molecular breeding in flowering of lily were underlined, and we provide viable solutions. Although many researches on lily literature had been published in the world, in our review, we provided a valuable and unique resource and spring-board from which to understand or further study the molecular breeding in flowering of lily.     

树鼩解剖数据的测定与分析

解剖数据是实验动物主要的生物学特性指标。该文对实验室驯养树鼩(7～9月龄)的体尺、骨骼、乳头、肠道及脏器重量与系数等解剖学数据进行了测定与分析。31项解剖数据测量结果显示雌、雄个体间体高、右耳宽、回肠及结肠差异显著(P<0.05),体斜长、胸深、躯干长、左右两前肢长、右后肢长、左右两侧耳长、左耳宽、龙骨长、左右两侧胫长、十二指肠及空肠长等差异极显著(P<0.01)。以体长为因变量,尾长、躯干长、左前肢长、右前肢长、左后肢长及右后肢长等为自变量作逐步回归分析,回归方程为:体长=13.90+尾长×0.16。37项脏器及系数测定结果:雌雄间比较,体重、心、肺、脾、左肾、右肾、膀胱、左海马、右海马、左颌下腺、左甲状腺、右甲状腺重量差异极显著(P<0.01)。小肠、右颌下腺、左肾上腺之间差异显著(P<0.05);心、肺、胃、膀胱、小肠、大肠、脑、右海马、左肾上腺系数雌雄间差异极显著(P<0.01)。右肾、左海马、左颌下腺、右肾上腺、左右两侧甲状腺系数之间达到了显著性水平(P<0.05)。以动物体重为因变量,以主要脏器指标:心脏、肺、肝、脾、左肾、右肾、脑为自变量,作逐步回归分析,回归方程为:体重=62.73+左肾×79.213+心脏×24.09。实验室驯养树鼩不同性别对体尺、脏器及系数、肠道等解剖数据有一定影响,为树鼩实验动物化及人类疾病动物模型研究提供基础数据。     

The existence of stable equilibria in Volterra predator-prey systems represented by loop graphs

Criteria for the existence of globally stable equilibria in classical Volterra predator-prey systems represented by loop graphs are provided by comparing the community matrix with a matrix belonging to matrix classS _W .     

Hierarchical graphs for rule-based modeling of biochemical systems

Background  

In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state of a component, and an edge represents a bond between components. Components of a molecule share the same color. Furthermore, graph-rewriting rules are used to represent molecular interactions. A rule that specifies addition (removal) of an edge represents a class of association (dissociation) reactions, and a rule that specifies a change of a vertex attribute represents a class of reactions that affect the internal state of a molecular component. A set of rules comprises an executable model that can be used to determine, through various means, the system-level dynamics of molecular interactions in a biochemical system.     

Best linear prediction of breeding values in a forest tree improvement program

Summary Best Linear Prediction (BLP) was used to predict breeding values for 1,396 parents from progeny test data in an operational slash pine breeding program. BLP rankings of parents were compared to rankings of averaged standard scores, a common approach in forestry. Using BLP rankings, selection of higher ranking parents tends to choose parents in a larger number of more precise progeny tests. The trend is the opposite with standard scores; higher ranking parents tend to be those in fewer, less precise tests. BLP and a related methodology, Best Linear Unbiased Prediction (BLUP), were developed by dairy cattle breeders and have not been used widely outside of animal breeding for predicting breeding values from messy progeny test data. Application of either of these techniques usually requires simplifying assumptions to keep the problem computationally tractable. The more appropriate technique for a given application depends upon which set of assumptions are better for the given problem. An assumption of homogeneous genetic and error variances and covariances, generally made by animal breeders when applying BLUP, was inappropriate for our data. We employed an approach that treated fixed effects as known and treated the same trait measured in different environments as different traits with heterogeneous variance structures. As tree improvement programs become more complex, the ease with which BLP and BLUP handle messy data and incorporate diverse sources of information should make these techniques appealing to forest tree breeders.     

Development of DNA-mediated transformation systems for plants

The genetic engineering of plants by DNA-mediated gene transfer requires that efficient transformation systems be developed. Considerable progress has been made in manipulating the Ti plasmid of Agrobacterium tumefaciens as a vehicle for delivery of foreign genes into protoplasts of dicotyle-donous plants. Part of the Ti plasmid, the T-DNA, can be incorporated into the genome of the host cell; the T-DNA can carry a foreign DNA sequence which co-integrates with it; under normal conditions, the tumorigenic-causing portion of the T-DNA can be inactivated so that transformed protoplasts can be regenerated and T-DNA with an inserted foreign gene can be stably maintained during regeneration, meiosis and gamete formation. A foreign gene has yet to be expressed in regenerated plants although a T-DNA gene for opine synthesis can function in regenerates. Developing a more ubiquitous transformation system for monocotyledons is further from fruition. Based on transformation systems for simple eukaryotic organisms, it is reasonable to expect that a DNA vector which is capable of amplifying a novel plant gene and which contains both a drug resistance marker to facilitate the selection of transformed plant protoplasts and a species-specific autonomously replicating sequence to ensure the stable maintenance of the input gene in the recipient cell can be constructed.     

Intrinsic negative feedback governs activation surge in two-component regulatory systems

1. Download : Download high-res image (175KB)
2. Download : Download full-size image

Highlights? Activation surge reconstituted in vitro with purified SK and RR ? ADP can be endogenously generated from ATP to stimulate an SK's phosphatase activity ? SK's affinity for ADP governs the switch from the kinase to phosphatase state ? Lid region of SK PhoQ controls its phosphatase activity and surge of RR PhoP     

Soil N forms and gross transformation rates in Chinese subtropical forests dominated by different tree species

Background and aims

Knowledge related to extent of differing soil N forms and N transformation rates in subtropical southern China is severely limited. Accordingly, the purpose of this study was to investigate if and how tree species of different foliage types (coniferous, deciduous, and evergreen broadleaved) influence N forms and microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) content as well as gross N transformation rates in the organic and mineral soils of three distinct subtropical forests in China.

Methods

Chloroform fumigation extraction was used to determine MBC and MBN content while ¹⁵N-isotope dilution techniques were used to measure gross N transformation rates. Canonical correspondence analysis (CCA) was used to quantify relationships between soil chemical characteristics and changes in soil N transformation rates.

Results

Soil N forms, MBC and MBN content, and N transformation rates were found to be significantly different between tree species. Deciduous forest soil exhibited the highest N transformation rates. Soil N transformation rates were closely associated with total soil C and N and MBC and MBN content.

Conclusions

Soil substrate quantity and soil microbial activity play a more important role in soil N transformation processes than does soil quality in China’s subtropical forests. Tree species type should therefore be taken into account when trying to determine ecosystem N cycling.     

PathSys: integrating molecular interaction graphs for systems biology

Background  

The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately.     

Strategies for the development of bacterial transformation systems

An effective transformation system is a prerequisite for facile genetic manipulation of bacteria. Bacteria may be naturally competent for transformation or may be treated with various agents, such as Tris buffers or divalent metal ions, to induce competence. Transformation can also be accomplished by electroporation, or by fusion of protoplasts with PEG in the presence of transforming DNA. Unfortunately, the mechanism by which cells become permeable to DNA and the process by which DNA enters the cells is frequently unknown. In order to establish a transformation system for an untransformable bacterium, recipient strains and transforming DNA must be carefully selected. Since it is impossible to predict in advance which method of transformation will be successful with a particular bacterial strain, several techniques are usually evaluated. This review describes a number of factors that appear to be critical for developing a transformation system and presents a strategy for experimentation with novel bacteria.     

Dominant tree mycorrhizal associations affect soil nitrogen transformation rates by mediating microbial abundances in a temperate forest

Biogeochemistry - Tree–fungal symbioses are increasingly recognized to affect soil nitrogen (N) transformations, yet the role of free-living soil microbes in the process is largely unclear....     

Effects of agricultural cropping systems on micronutrients transformation

Summary The effect of cropping systems of wheat-maize (WM), wheat-rice (WR), wheat-groundnut (WG), gram-bajra (GrB), potato-guara (PGu), and raya-mash (RaMa) in combination with treatments of dummy (uncultivated area) and applied Zn 0.0 (Zn₀), 2.8 (Zn₁), 5.6 (Zn₂) 11.2 (Zn₃) kg/ha was studied on the transformation of labile Zn fractions: exchangeable (Exch.), adsorbed (TAd) [weakly (WAd), moderately (MAd), strongly (SAd)], and organic matter (OM) in different layers of sandy loam soil. The added Zn stayed largely in the 0–30 cm layer and was associated with the WAd- and OM-Zn fractions. About 70% of the total labile Zn (PAv) remained in the WAd- and OM-Zn, that is, 33 and 39% in 0–15 cm layer, and 33–39% and 31–36% in 16–150 cm layer. All the Zn fractions in 0–15 cm layer, and only of WAd in 16–30 cm layer, significantly increased with rates of Zn addition. These were also significantly higher in Zn_1–3 than Zn₀ and dummy treatments because of the residual Zn. Diverse effects of cropping systems on soil properties, residual Zn, and labile Zn fractions were found. The influence was strong in 0–15 cm layer decreasing gradually with soil depth due largely to differences in Zn requirement, crop intake of various Zn fractions and the cultural practices of the systems. All the crops and rotations appreciabilly responded to Zn application. Uptake of Zn by crops markedly and successively increased with increasing rates of Zn application. The WR caused a significant increase in soil organic matter whereas WR and WM in CaCO₃. The WR, WM and GrB resulted in a decrease in pH while WG and GrB in CaCO₃. The RaMa and PGu maintained much higher residual Zn than other systems. The systems which caused the maximum decrease in Zn fractions were: cereal-cereal (WM) in Exch. legume-millet (GrB) in all the adsorbed, PAv and the Zn associated with CaCO₃, vegetable-legume (PGu) also in MAd and SAd; and cereal-legume (WG) in OM and PAv. Hence GrB, WG and WM in that order will cause the deficiency of Zn much earlier than the other systems due to greater use and or transformation of WAd- andOM-Zn. Such effects were least under RaMa because it increased the WAd-, MAd- and OM-Zn.     

Intrinsic regulation of enteroendocrine fate by Numb

How terminal cell fates are specified in dynamically renewing adult tissues is not well understood. Here we explore terminal cell fate establishment during homeostasis using the enteroendocrine cells (EEs) of the adult Drosophila midgut as a paradigm. Our data argue against the existence of local feedback signals, and we identify Numb as an intrinsic regulator of EE fate. Our data further indicate that Numb, with alpha‐adaptin, acts upstream or in parallel of known regulators of EE fate to limit Notch signaling, thereby facilitating EE fate acquisition. We find that Numb is regulated in part through its asymmetric and symmetric distribution during stem cell divisions; however, its de novo synthesis is also required during the differentiation of the EE cell. Thus, this work identifies Numb as a crucial factor for cell fate choice in the adult Drosophila intestine. Furthermore, our findings demonstrate that cell‐intrinsic control mechanisms of terminal cell fate acquisition can result in a balanced tissue‐wide production of terminally differentiated cell types.