Molecular and functional diversity of maize

Over the past 10,000 years, man has used the rich genetic diversity of the maize genome as the raw material for domestication and subsequent crop improvement. Recent research efforts have made tremendous strides toward characterizing this diversity: structural diversity appears to be largely mediated by helitron transposable elements, patterns of diversity are yielding insights into the number and type of genes involved in maize domestication and improvement, and functional diversity experiments are leading to allele mining for future crop improvement. The development of genome sequence and germplasm resources are likely to further accelerate this progress.     

Food-derived carbohydrates--structural complexity and functional diversity

Carbohydrates are biomolecules abundantly available in nature. They are found in bewildering types ranging from simple sugars through oligo- and polysaccharides to glycoconjugates and saccharide complexes, each exhibiting characteristic bio-physiological and/or nutritional functions both in in vivo and in vitro systems. For example, their presence or inclusion in food dictates the texture (body) and gives desirable customer appeal (satisfaction), or their inclusion in the diet offers beneficial effects of great therapeutic value. Thus, carbohydrates are integrally involved in a multitude of biological functions such as regulation of the immune system, cellular signaling (communication), cell malignancy, antiinfection responses, host-pathogen interactions, etc. If starch is considered the major energy storage carbohydrate, the gums/mucilages and other non-starch carbohydrates are of structural significance. The most investigated properties of starch are its gelatinization and melting behavior, especially during food processing. This has led to the development of the food polymer science approach, which has enabled a new interpretive and experimental frame work for the study of the plasticizing influence of simple molecules such as water, sugars, etc. on food systems that are kinetically constrained. Starch, although considered fully digestible, has been challenged, and starch is found to be partly indigestible in the GI tract of humans. This fraction of starch-resisting digestion in vivo is known as resistant starch (RS). The latter, due to its excellent fermentative capacity in the gut, especially yielding butyric acid is considered a new tool for the creation of fiber-rich foods, which are of nutraceutical importance. By a careful control of the processing conditions the content of RS, a man-made fiber, can be increased to as high as 30%. Arabinoxylans are the major endospermic cell wall polysaccharides of cereals. In wheat they are found complexed with ferulic acid esters, which after oxidative coupling in vivo mediated by H2O2 and peroxidases or even by photochemical means give cross linked diferuloyl derivatives. The latter confer strength and extensibility to the cell wall and offer resistance for digestibility by ruminants. They also help blocking of the ingress of pathogens. The ester bound ferulic acid after oxidation in vivo generates reactive oxygen species that contribute to the fragmentation of non-starch polysaccharides (hemicelluloses), and thereby reduces the product viscosity, a property seen during long-term storage of rice. In plant tissues, the arabinogalactans are implicated in such diverse functions as cell-cell adhesion, nutrition of growing pollen tubes, response to microbial infections, and also as markers of identity expressed in the terminal sequences of saccharide chains.     

Plant functional group diversity promotes soil protist diversity

We tested whether effects of plant diversity can propagate through food webs, down to heterotrophic protists not linked directly to plants. To this end we synthesised grassland ecosystems with varying numbers of plant functional groups (FGN) and assessed corresponding changes in testate amoebae communities. The number of plant species was kept constant. When FGN was increased from 1 to 3, species number and total community density of live testate amoebae were enhanced according to a linear and a saturating function, respectively. From FGN 1 to 2, the appearance of new testate amoebae species did not affect the presence of the resident species, whereas, from FGN 2 to 3 about one quarter of the resident testate amoebae species was replaced, without altering the total species number. Overall, density by species increased, while evenness of the testate amoebae community was not affected by FGN; although Trinema lineare, one of the most common species, became more abundant. The observed relationship between plant functional group diversity and testate amoebae diversity could shed new light on the biogeographical distribution patterns of protists.     

Structural type diversity: measuring structuredness of communities by type diversity

Recently, the notion of diversity, which is directed towards (effective) numbers of types (states of a trait such as species and genotypes), is increasingly used as an umbrella term akin to “variation”, thus including classical metrics of dispersion among others. This is probably due to the growing interest in functional aspects of variation which involve variable differences between types. Though the traditional notion of diversity does not cover these aspects, it shows up in many interpretations. To overcome this ambiguity, the traditional notion of diversity is extended in this paper to include variable differences with emphasis on their general significance as structuring features. For this purpose, structure is conceived to be captured by the representation of types via variable differences and abundances. Structural diversity then results from application of traditional measures of diversity to the relative structural representations of types in addition to their relative abundances. Since diversity as effective number of types alone provides no information about their mutual distinctness and the range covered by them, connections to measures of dispersion are indispensable. This is considered via two approaches that rely on dispersion characteristics and one approach that allows for an assessment of structural diversity for controlled levels of type distinctness. Effects of structure on dispersion and diversity are analyzed. The use of the approaches for discovering rarely considered characteristics of phylogenetic structure is demonstrated.     

Structural and functional diversity of viral IRESes

Some 20 years ago, the study of picornaviral RNA translation led to the characterization of an alternative mechanism of initiation by direct ribosome binding to the 5′ UTR. By using a bicistronic vector, it was shown that the 5′ UTR of the poliovirus (PV) or the Encephalomyelitis virus (EMCV) had the ability to bind the 43S preinitiation complex in a 5′ and cap-independent manner. This is rendered possible by an RNA domain called IRES for Internal Ribosome Entry Site which enables efficient translation of an mRNA lacking a 5′ cap structure. IRES elements have now been found in many different viral families where they often confer a selective advantage to allow ribosome recruitment under conditions where cap-dependent protein synthesis is severely repressed. In this review, we compare and contrast the structure and function of IRESes that are found within 4 distinct family of RNA positive stranded viruses which are the (i) Picornaviruses; (ii) Flaviviruses; (iii) Dicistroviruses; and (iv) Lentiviruses.     

Wheat root diversity and root functional characterization

Background and Aims

Under limited moisture conditions, roots can play an outstanding role with respect to yield stability by effective absorption of water from soil. A targeted integration of root traits into plant breeding programs requires knowledge on the existing root diversity and access to easy and cost-effective methods. This study aimed to assess wheat root diversity, root properties in relation to water regime, and the efficiency of root capacitance for in situ screening.

Methods

Root morphological, anatomical properties and root capacitance of wheat species from different ploidy levels were studied under field conditions in 2 years contrasting in water regime. Soil water content was weekly measured.

Results

Significant genotypic differences were observed for most root traits. The investigated genotypes exploited different strategies to maximize soil water depletion, e.g. high topsoil root length density, low tissue mass density, high specific root length, deep rooting and looser xylem vessels. Multivariate statistics of root traits revealed an acceptable genotypic differentiation according to regional origin, genetics and capacity to extract soil water.

Conclusions

Under supply-driven environments, dehydration avoidance via water uptake maximization can be achieved through high topsoil rooting density. In this regard, root capacitance can be useful for in situ screening.     

Structural conservation and functional diversity of V-ATPases

The vacuolar system of eukaryotic cells contains a large number of organelles that are primary energized by an H⁺-ATPase that was named V-ATPase. The structure and function of V-ATPases from various sources was extensively studied in the last few years. Several genes encoding subunits of the enzyme were cloned and sequenced. The sequence information revealed the relations between V-ATPases and F-ATPases that evolved from common ancestral genes. The two families of proton pumps share structural and functional similarity. They contain distinct peripheral catalytic sectors and hydrophobic membrane sectors. Genes encoding subunits of V-ATPase in yeast cells were interrupted to yield mutants that are devoid of the enzyme and are sensitive to pH and calcium concentrations in the medium. The mutants were used to study structure, function, molecular biology, and biogenesis of the V-ATPase. They also shed light on the functional assembly of the enzyme in the vacuolar system.     

Evolution and functional diversity of jellyfish opsins

Cnidaria are the most basal animal phylum possessing complex eyes [1]. Their eyes predominantly use ciliary photoreceptor cells (c-PRCs) like vertebrates, whereas insect eyes use rhabdomeric photoreceptor cells (r-PRCs) [1-4]. These two cell types show not only different cytoarchitectures but distinct phototransduction cascades, which are triggered by the respective types of opsins (e.g., [5]), ciliary opsins (c-opsins) and rhabdomeric opsins (r-opsins) [6]. Recent reports suggested that the c- and r-PRCs and their respective opsins diverged at least before the deuterostome-protostome split [7-9]. To study the earlier evolution of animal PRCs and opsins, we investigated two hydrozoan jellyfishes. We report here the first-characterized cnidarian opsins. Molecular phylogeny revealed that the cloned 20 jellyfish opsins, together with all the opsins from a hydra and some from a sea anemone, are more closely related to the c-opsins than to any other major opsin subfamily, indicating that the divergence of c- and r-opsins antedates the Cnidaria-Bilateria split. Possible scenarios of animal PRC evolution are discussed. Furthermore, Cladonema opsins show several distinct tissue- and stage-specific expression patterns. The expression of specific opsins in the eyes suggests a role in vision, whereas that in the gonads suggests a role in light-controlled release of gametes.     

Molecular and functional diversity in soil micro-organisms

Traditional approaches to the study of microbial diversity have relied on laboratory cultivation of isolates from natural environments and identification by classical techniques, including analysis of morphology, physiological characteristics and biochemical properties. These approaches provide information on fine-scale diversity but suffer from bias, resulting from the media and cultivation conditions employed, and from the inability to grow and isolate significant proportions of natural communities in the laboratory. An alternative approach is the amplification of ribosomal RNA and functional genes from nucleic acids extracted directly from environmental samples, with subsequent analysis by `fingerprinting' methods or by sequencing and phylogenetic analysis. This approach avoids the need for laboratory cultivation and has provided major insights into species and functional diversity of bacterial and archaeal populations. This article reviews molecular approaches to the characterisation of prokaryote diversity in natural environments, their more recent application to fungal diversity and the advantages and limitations of molecular analyses.     

Extinction and the loss of functional diversity

Although it is widely thought to influence ecosystem processes, there is little consensus on an appropriate measure of functional diversity. The two major perspectives, to date, are to assume that every species is functionally unique, or to assume that some species are functionally identical, such that functional groups exist. Using a continuous measure of functional diversity (FD) derived from the quantitative functional traits of species, we show that the loss of functional diversity from six natural assemblages was rapid compared with rates of loss from comparable simulated assemblages. Loss of FD occurred faster than loss of functional-group diversity in four of the six natural assemblages. Patterns of functional-group diversity loss depended on the number of functional groups and the number of species in an assemblage. Extinctions that occurred first for species with particular traits (e.g. low leaf nitrogen concentration, deep roots and large body size) caused greater loss of FD than expected by chance in four of the six natural assemblages. In two real assemblages, these trait-dependent extinctions had more severe effects on FD than our simulated worst-case extinction scenario. These data suggest that conserving a large proportion of the functional traits of species requires conserving a large proportion of all species.     

Structural and functional diversity of Nudix fold

Nudix hydrolases catalyze the hydrolysis of nucleoside diphosphates linked to other moieties X, and contain the sequence motif or Nudix box, GX5EX7REUXEEXGU. The mechanisms of Nudix hydrolases are highly diverse in the position on the substrate. In this paper, we examined the sequences and structures of the MutT/Nudix superfamily. And two recent developed methods were employed for data analyses of the superfamily. One is QH method evaluating the similarities among structures for structural phylogeny. The other method is clustering analysis by using the CLANS program that could analysis thousands of sequences of the full dataset rather than the representative sequences of the superfamily. Finally, we proposed a more objective classification of the MutT/Nudix superfamily members based on detailed sequence and structure analyses.     

On dendrogram-based measures of functional diversity

Euclidean distance is commonly involved in calculating functional diversity (FD), for example, in measures based on dendrogram branch lengths. We point out that this function is inappropriate in many cases and that the choice of clustering method is more crucial than earlier thought. Gower's formula and UPGMA clustering are suggested here as a standard combination of techniques for calculating FD. The advantage of Gower's measure is its suitability to a mixture of scale types and its tolerance to missing values. Examples demonstrate that UPGMA clustering is more robust and has a better goodness of fit to dissimilarities than complete and single linkage classifications. In addition, we propose that the effect of individual species on FD is best evaluated by species removals and subsequent comparisons of tree length values. The influence of each functional trait is optimally judged by considering both dendrogram length and topological changes.     

Viral glycoprotein heterogeneity-enhancement of functional diversity

Variations in the amino acid sequence of RNA virus envelope glycoproteins can cause changes in their antigenicity and can alter the host-cell tropism of the virus and the degree of virulence which it exhibits. Such changes may alter the course and outcome of viral diseases, either directly because of changes in the biological properties of the glycoproteins or indirectly through effects on immune surveillance and vaccine efficacy. The nature and extent of glycosylation of the surface glycoproteins of RNA viruses have also been implicated in such phenotypic alterations. It follows therefore that the 'plasticity' of the viral genome and the host-encoded glycosylation machinery combine to create populations of highly diverse viruses. This diversity is considered to be responsible for survival of these viruses in a variety of biological niches and for their ability to overcome the inhibitory effects of neutralizing antibodies and antiviral agents. In this article we discuss the implications of the inter-relationship between these two mechanisms for the generation of diversity.     

Functional richness, functional evenness and functional divergence: the primary components of functional diversity

Functional diversity is hypothesised as being beneficial for ecosystem functions, such as productivity and resistance to invasion. However, a precise definition of functional diversity, and hence a framework for its quantification, have proved elusive. We present a definition based on the analogy of the components of species diversity – richness, evenness and divergence. These concepts are applied to functional characters to give three components of functional diversity – functional richness, functional evenness and functional divergence. We demonstrate how each of these components may be calculated. It is hoped that our definition of functional diversity and its components will aid in elucidation of the mechanisms behind diversity/ecosystem-function relationships.     

Beta propellers: structural rigidity and functional diversity

Recently solved structures and proposed models have helped to reveal the structural characteristics of the beta-propeller fold, as well as the features that contribute to its high rigidity and stability. Possible strategies for identifying beta-propeller proteins in newly characterised sequences are helping to overcome the problems of predicting the beta-propeller fold from amino acid sequences.