A New Multivariate Approach to Studying Temporal Changes of Vegetation

We emphasize the necessity of a complex approach to evaluating vegetation change at various levels of abstraction. The analytical steps include comparisons at the data, derived variable, distance, ordination and classification levels. A variety of data randomization methods incorporated in testing the significance of changes in raw data are introduced and compared. It is shown that these are true alternatives to Procrustean comparisons, which offer an apparently unfortunate choice in the presence/absence case. We propose to evaluate nearest neighbor relationships among quadrats in a new method, called adjacency analysis, to detect temporal trends that may remain unrevealed, should our attention be paid to full distance structures only. As an illustration, compositional and structural changes in the rock grassland vegetation of the Sas-hegy Nature Reserve (Budapest, Hungary), intensively sampled by quadrats in 1977 and 2000, are evaluated. Permutation tests show that differences between the 2 years are much smaller than expected by chance alone. Such an overall stability in community structure, however, does not mean that minor aspects of vegetation pattern are invariant over the years. Changes in life form and seed mass spectra are explained by the fluctuation of hemicryptophytes and the slight but detectable expansion of annuals and woody species. Classification is slightly rearranged in time, with clearly detectable within-cluster changes, also depicted in ordination scattergrams.     

Simple and rapid determination of metabolite content in plant cell culture medium using an FT-IR/ATR method

A simple, rapid and accurate mid-infrared (MIR) spectroscopic method for simultaneously determining the product (ethanol) content and the nutrient (sugar) content in plant-cell culture media was developed using a Fourier transform infrared (FT-IR) spectrometer equipped with an attenuated total reflectance (ATR) accessory. We assessed the potential of this method by comparing it to a high-performance liquid chromatography (HPLC) method, and using the developed method to measure the ethanol and sugar contents simultaneously in liquid culture media with rice and tabacum cell suspensions, respectively. The experimental results suggest that the sugar consumption and ethanol production behaviors of the plant cell suspensions can be non-destructively and simultaneously monitored using the developed method. Furthermore, the spectroscopic method provided in this study could be developed into a technique that could be used to analyze the overall kinetics of the metabolism of the plant cell suspensions.     

Discovering high mobility group A molecular partners in tumour cells

DNA-based activities rely on an extremely coordinated sequence of events performed by several chromatin-associated proteins which act in concert. High Mobility Group A (HMGA) proteins are non-histone architectural nuclear factors that participate in the regulation of specific genes but they are also believed to have a more general role in chromatin dynamics. The peculiarity of these proteins is their flexibility, both in terms of DNA-binding and in protein-protein interactions. Since these proteins act as core elements in the assembly of multiprotein complexes called enhanceosomes, and have already displayed the ability to interact with several different proteins, we started a proteomic approach for the systematic identification of their molecular partners. By a combination of affinity chromatography, two-dimensional gel electrophoresis and mass spectrometry we have identified about twenty putative HMGA interactors which could be roughly assigned to three different classes: mRNA processing proteins, chromatin remodelling related factors and structural proteins. Direct HMGA interaction with some of these proteins was confirmed by glutathione-S-transferase pull-down assays and the HMGA domain involved was mapped. Blot-overlay experiments reveal that members of the HMGA family share most of their molecular partners but, interestingly, it seems that there are some cell-type specific partners. Taken together, these experimental data indicate that HMGA proteins are highly connected nodes in the chromatin protein network. Since these proteins are strongly implicated with cancer development, the identification of molecules able to perturb the HMGA molecular network could be a possible tool to interfere with their oncogenic activity.     

Determination of oxidized and reduced nicotinamide adenine dinucleotide in cell monolayers using a single extraction procedure and a spectrophotometric assay

While many investigations measuring oxidized nicotinamide adenine dinucleotide (NAD+) and reduced nicotinamide adenine dinucleotide (NADH) have been carried out on several mammalian tissues and blood cells, few reports have dealt with monolayers of cultured cells. Here we show a novel method to measure NAD+ and NADH in monolayers of a neuroblastoma cell line. The method was established by modifying a single extraction procedure originally developed for erythrocytes and an enzymatic cycling assay using a dye that absorbs in visible range. The following modifications were made. (i) Addition of 0.05% of a detergent, Triton X-100, to carbonate-bicarbonate extraction buffer enabled us to accurately measure cellular [NADH]/([NAD+]+[NADH]). (ii) Addition of N-ethyldibenzopyrazine ethyl sulfate salt (phenazine ethosulfate) immediately before the incubation suppressed the gradual decline of the sensitivity of the assay. The procedure presented here provides a simple and inexpensive measurement of NAD+ and NADH in cell monolayers.     

Neurogenesis and neuronal communication on micropatterned neurochips

Neural networks are formed by accurate connectivity of neurons and glial cells in the brain. These networks employ a three-dimensional bio-surface that both assigns precise coordinates to cells during development and facilitates their connectivity and functionality throughout life. Using specific topographic and chemical features, we have taken steps towards the development of poly(dimethylsiloxane; PDMS) neurochips that can be used to generate and study synthetic neural networks. These neurochips have micropatterned structures that permit adequate cell positioning and support cell survival. Within days of plating, cells differentiate into neurons displaying excitability and communication, as evidenced by intracellular calcium oscillations and action potentials. The structural and functional capacities of such simple neural networks open up new opportunities to study synaptic communication and plasticity.     

Polymorphism of monolayer lipid membrane structures made from unsymmetrical bolaamphiphiles

The crystal structures of synthetic unsymmetrical 1-glucosamide- and 1-galactosamide bolaamphiphiles, 13-[(beta-d-glucopyranosyl)carbamoyl]tridecanoic acid (1) and 15-[(beta-d-galactopyranosyl)carbamoyl]pentadecanoic acid (2), respectively, were elucidated by single-crystal X-ray analysis. The space group for 1 is P2(1), Z=2 with cell dimensions: a=8.6816(9), b=4.8578(5), c=26.250(3)A, beta=91.460(2) degrees ; that for 2P2(1), Z=2 with cell dimensions: a=4.90(1), b=40.139(1), 6.289(1)A, beta=106.48(1) degrees . The glucopyranosyl and galactopyranosyl rings in 1 and 2, respectively, take a (4)C(1) chair conformation. In the crystal lattice, the 1-glucosamide 1 forms a symmetrical monolayer lipid membrane (MLM) structure in which the molecules are packed in an antiparallel fashion, while 1-galactosamide 2 has an unsymmetrical MLM with parallel molecular packing. The stereochemistry of the sugar hydroxy group proved to affect their hydrogen-bonding networks and induce the polymorphism of the MLM.     

Plasmodium falciparum: discovery of peroxidase active organelles

Staining with 3,3' diaminobenzidine tetrahydrochloride (DAB) is a common method used for the detection of peroxidases. Using this histochemical staining method in conjunction with transmission electron microscopy, we observed oxidation of DAB that was localized to a discrete set of organelles displaying morphological similarity to small (75-90 nm diameter) versions of higher eukaryotic microbodies or peroxisomes. These single membrane bounded organelles were characterized by an asymmetrical matrix capable of oxidizing DAB to an electron dense inclusion. Oxidation of DAB was further found to be dependent upon hydrogen peroxide (H2O2) as a substrate. Given a lack of peroxisomal import proteins and enzymes, it is unlikely that these represent conventional peroxisomes. Rather, they likely represent specialized organelles containing endogenous peroxidase or pseudo-peroxidase activity.     

Pathway information for systems biology

Pathway information is vital for successful quantitative modeling of biological systems. The almost 170 online pathway databases vary widely in coverage and representation of biological processes, making their use extremely difficult. Future pathway information systems for querying, visualization and analysis must support standard exchange formats to successfully integrate data on a large scale. Such integrated systems will greatly facilitate the constructive cycle of computational model building and experimental verification that lies at the heart of systems biology.     

Modelling gene networks at different organisational levels

Approaches to modelling gene regulation networks can be categorized, according to increasing detail, as network parts lists, network topology models, network control logic models, or dynamic models. We discuss the current state of the art for each of these approaches. There is a gap between the parts list and topology models on one hand, and control logic and dynamic models on the other hand. The first two classes of models have reached a genome-wide scale, while for the other model classes high throughput technologies are yet to make a major impact.     

The integrated development of network complexity modulates the diverse evolutionary mutation rates of individual proteins

The rate of evolution-related mutation varies widely among proteins while the unity of the organism implies an integrated evolution of its protein network. Focusing on the yeast interactome, we monitored the structural impact of amino acid substitution on yeast proteins with reported structure. The impact of mutation in creating or deleting structural markers for interactivity varies across proteins and modulates the evolutionary rates, yielding a unified kinetic law of accumulation of connectivities consistent with an integrated evolution of the interactome.