Biochemical Descriptors Research Articles

Using molecular markers, nutritional traits and field performance data to characterize cultivated cardoon germplasm resources

Eight cardoon cultivars (six Spanish, one French and one Italian) were characterized by molecular, morphological and biochemical traits, thus exploiting the complementary nature of these methodological approaches. Molecular analysis was carried out using the inter-simple sequence repeat (ISSR) technique with twenty primers. Out of these, ten were polymorphic, producing a total of 98 DNA bands. A dendrogram, drawn on the basis of a genetic similarity matrix using the UPGMA algorithm, revealed that the 40 samples (5 plants per cultivar) could be classified into two major clusters with a Jaccard's index of 0.48. The morphological trait analysis showed that the quantitative morphological characters differed significantly among the eight cultivars and that they were influenced by environmental factors. Principal component analysis for qualitative morphological characteristics showed that a reduced number of descriptors could be used efficiently to discriminate among cultivars. The biochemical traits analysis showed that only seven compounds were able to establish differences among the analysed cardoon cultivars. The cultivars fell into different clusters when different characterization methods were used. Although the morphological and biochemical descriptors do not fully comply with the requirements needed for a reliable cultivar description, they can complete a molecular analysis obtained by ISSR markers for selecting cardoon cultivars.

PQM-1: A newly developed superior clone of pineapple for northeastern India as evident through phenotype, fruit quality and DNA polymorphism

Queen is the most preferred table purpose variety in India. However, small fruit size, deep set eyes in large numbers and weak fruit stalk make this less preferred in processing industries. A completely different plant type with distinct fruit character was identified from a clonal population of Queen which seems to be a natural mutant. The identified mutant was maintained and multiplied through vegetative propagation at Lembucherra farm of ICAR Research Complex, Tripura centre. The present study clearly established the fact that this new clone (PQM-1) is distinct from ‘queen’ and other cultivars of Tripura. Distinctness of this new clone was confirmed on the basis of standard morphological and biochemical descriptors as well as through DNA polymorphism. It was observed that PQM-1 diverged from Queen in respect of pattern of vegetative growth, leaf shape, size and colour, flowering time, fruit shape, size and colour, eye shape, fruit weight, juice content, total soluble solid (TSS) and acidity. PQM-1 was found uniform at DNA level and complement the information of phenotypic and quality parameters by showing stable differences with Queen in ISSR banding pattern. Natural mutation in DNA level might be the probable cause of its origin. It could be empathetically stated that PQM-1 would have certain competitive advantage over all existing cultivars in this region due to its late maturity, fruit quality and usefulness in both canning and fresh consumption. This certainly would emerge as new alternative to pineapple growers of this region.

Estimativa da diversidade genética de germoplasma de cebola via descritores morfológicos, agronômicos e bioquímicos

A divergência genética de 64 acessos de cebola (Allium cepa L.) tropicais e subtropicais do banco de germoplasma da Embrapa Hortaliças foi avaliada utilizando 23 descritores morfológicos, bioquímicos e agronômicos. A distância generalizada de Mahalanobis (D²) foi usada como medida de dissimilaridade e os métodos de otimização de Tocher e hierárquico do Vizinho mais Próximo foram empregados para o agrupamento dos acessos. O germoplasma de cebola avaliado apresentou base genética relativamente ampla. As cultivares EX 3000 e Régia foram os acessos geneticamente mais similares. A maior distância genética estimada foi entre os acessos VAL 14 e Beta Cristal. O método de otimização de Tocher proporcionou a formação de treze grupos, enquanto o procedimento hierárquico do vizinho mais próximo possibilitou a formação de doze grupos (corte com 43% de dissimilaridade) A maioria dos acessos dos tipos Grano e Granex, agronomicamente considerados de dias curtos e com ciclo de maturação precoce, se concentraram em mesmo grupo de similaridade genética. À exceção do acesso Tampico White, os demais acessos de bulbos brancos do tipo indústria (Beta Cristal; Dehydrator # 8; Dehydrator # 6; Primero e White Creole) exibiram estreito relacionamento. Os acessos TX 24, Baia Periforme Super Precoce, EX 3001, Excel, Red Creole, H 688, Franciscana IPA 10 e Roxa IPA 3 exibiram alta dissimilaridade genética. Os caracteres teor de açúcares totais, comprimento de bulbo, número de dias para a colheita, porcentagem de bulbos com diâmetro entre 70 e 90 mm e massa média de bulbos foram responsáveis por 58% de toda a variabilidade genética observada entre os acessos. O estudo da divergência entre acessos é importante subsídio na escolha de parentais divergentes e complementares a fim de desenvolver populações segregantes com ampla base genética em programas de melhoramento genético de cebolas tropicais.

Exercise function and biochemical properties of β-adrenergic receptors of canine heart

We tested the hypothesis that the biochemical properties of cardiac beta-adrenergic receptors (βAR), as determined by standard in vitro methods, limit physiological responsiveness of dogs to PAR stimulation during peak exercise. Accordingly, we measured oxygen consumption, left ventricular dP/dt at 40 mmHg developed pressure, heart rate, and cardiac output during maximal dynamic exercise in 13 adult mongrel dogs. These studies were followed by biochemical analysis of PAR in membrane homogenates of left ventricle from the same animals using saturation binding and agonist competition curves for [125I] cyanopindolol. There was a substantial range in both biochemical and physiological variables within this population of normal dogs. However, there were no significant correlations between biochemical descriptors of cardiac PAR and any physiological variables measured during exercise. These results suggest that receptor-effector coupling and maximal cardiac performance during intense sympathetic stimulation of peak exercise are limited by factors other than the biochemical properties of cardiac PAR.

PostDOCK: A Structural, Empirical Approach to Scoring Protein Ligand Complexes

In this work we introduce a postprocessing filter (PostDOCK) that distinguishes true binding ligand-protein complexes from docking artifacts (that are created by DOCK 4.0.1). PostDOCK is a pattern recognition system that relies on (1) a database of complexes, (2) biochemical descriptors of those complexes, and (3) machine learning tools. We use the protein databank (PDB) as the structural database of complexes and create diverse training and validation sets from it based on the "families of structurally similar proteins" (FSSP) hierarchy. For the biochemical descriptors, we consider terms from the DOCK score, empirical scoring, and buried solvent accessible surface area. For the machine-learners, we use a random forest classifier and logistic regression. Our results were obtained on a test set of 44 structurally diverse protein targets. Our highest performing descriptor combinations obtained approximately 19-fold enrichment (39 of 44 binding complexes were correctly identified, while only allowing 2 of 44 decoy complexes), and our best overall accuracy was 92%.

Protein linear indices of the ‘macromolecular pseudograph α-carbon atom adjacency matrix’ in bioinformatics. Part 1: Prediction of protein stability effects of a complete set of alanine substitutions in Arc repressor

A novel approach to bio-macromolecular design from a linear algebra point of view is introduced. A protein’s total (whole protein) and local (one or more amino acid) linear indices are a new set of bio-macromolecular descriptors of relevance to protein QSAR/QSPR studies. These amino-acid level biochemical descriptors are based on the calculation of linear maps on R n [ f k ( x m i ) : R n → R n ] in canonical basis. These bio-macromolecular indices are calculated from the k th power of the macromolecular pseudograph α-carbon atom adjacency matrix. Total linear indices are linear functional on R n . That is, the k th total linear indices are linear maps from R n to the scalar R [ f k ( x m ) : R n → R ] . Thus, the k th total linear indices are calculated by summing the amino-acid linear indices of all amino acids in the protein molecule. A study of the protein stability effects for a complete set of alanine substitutions in the Arc repressor illustrates this approach. A quantitative model that discriminates near wild-type stability alanine mutants from the reduced-stability ones in a training series was obtained. This model permitted the correct classification of 97.56% (40/41) and 91.67% (11/12) of proteins in the training and test set, respectively. It shows a high Matthews correlation coefficient (MCC = 0.952) for the training set and an MCC = 0.837 for the external prediction set. Additionally, canonical regression analysis corroborated the statistical quality of the classification model ( R canc = 0.824). This analysis was also used to compute biological stability canonical scores for each Arc alanine mutant. On the other hand, the linear piecewise regression model compared favorably with respect to the linear regression one on predicting the melting temperature ( t m) of the Arc alanine mutants. The linear model explains almost 81% of the variance of the experimental t m ( R = 0.90 and s = 4.29) and the LOO press statistics evidenced its predictive ability ( q 2 = 0.72 and s cv = 4.79). Moreover, the TOMOCOMD- CAMPS method produced a linear piecewise regression ( R = 0.97) between protein backbone descriptors and t m values for alanine mutants of the Arc repressor. A break-point value of 51.87 °C characterized two mutant clusters and coincided perfectly with the experimental scale. For this reason, we can use the linear discriminant analysis and piecewise models in combination to classify and predict the stability of the mutant Arc homodimers. These models also permitted the interpretation of the driving forces of such folding process, indicating that topologic/topographic protein backbone interactions control the stability profile of wild-type Arc and its alanine mutants.

Relationship between sedimentary organic matter and benthic fauna within the Gulf of Lion: synthesis on the identification of new biochemical descriptors of sedimentary organic nutritional value

The abilities of several biochemical characteristics of sedimentary organic matter to describe quantitative changes in benthic fauna were assessed based on several surveys carried out within the Gulf of Lion during the last decade. Two sets of high frequency samplings were carried out both inshore and offshore, together with an assessment of seasonal variability along a depth gradient, and a synoptic assessment of mesoscale spatial variability. The considered biochemical parameters were: total organic matter, organic carbon, nitrogen, total proteins, available proteins, carbohydrates, lipids, total and available amino acids. The considered faunal parameters were the abundance and the biomass of both meio- and macrofauna. Our results contribute to unravel the relative importance of food digestibility and composition in controlling particulate organic matter nutritional value. Spectra of both total and available amino acids were almost constant irrespective of the seasons and/or the environments, which were studied during these surveys. This underlines the role of particulate organic matter digestibility relative to its ability to meet specific nutritional requirements in controlling benthic fauna. Multivariate analysis used to relate biochemical and faunal parameters suggest that available amino acids and lipids are the best descriptors of food nutritional value. In contrast with carbohydrates, these two parameters are both associated with the most labile fraction of particulate organic matter. This result suggests that the use of the sum of proteins, carbohydrates and lipids as a proxy for labile organic matter is precluded at least in areas similar to the Gulf of Lion.

Enzymatically hydrolyzable protein and carbohydrate sedimentary pools as indicators of the trophic state of detritus sink systems: A case study in a Mediterranean coastal lagoon

In order to classify the trophic state of detritus sink systems, instead of the conventional indicators based on inorganic nutrient availability and algal biomass and productivity in the water column, we used new biochemical descriptors based on the amount of sedimentary organic carbon (C) and nitrogen (N) potentially available to heterotrophs. We investigated spatial and temporal changes in microphytobenthic biomass, organic matter biochemical composition, and enzymatically hydrolyzable protein and carbohydrate pools along a north-south transect in the Marsala lagoon (Mediterranean Sea, Italy) at three stations characterized by different hydrodynamic conditions and organic matter content in the sediment. In the Marsala lagoon water currents decreased from north to south and this pattern was reflected by organic matter distribution and composition. Sediment organic matter concentrations were among the highest reported in the literature and, in the central area where large meadows of the seagrassPosidonia oceanica were present, display a strong dominance of highly refractory carbohydrates. The protein to carbohydrate ratio was always < 1, indicating the dominance of aged organic detritus. Microphytobenthic biomass displayed an increasing pattern southward, and its contribution to the biopolymeric C pools ranged from negligible in the central sector of the lagoon to 50% in its northern part, indicating that sources of sediment organic C also changed along the hydrodynamic gradient. The percentage contribution of the enzymatically hydrolyzable fraction of proteins and carbohydrates was inversely related to total protein and total carbohydrate concentrations, respectively, suggesting that bioavailability of organic C and N increased with decreasing organic matter content in the sediment and with increasing hydrodynamic regime. Microphytobenthic contribution to biopolymeric C (as a proxy of autotrophic organic C) and the ratio of the enzymatically digestible fraction to biopolymeric C (as an indicator of organic matter liability) were significantly correlated, suggesting that chlorophylla sediment content might be used as an indicator of food promptly available to consumers. The present study also highlighted that the ratio of labile (i.e., enzymatically digestible) versus biopolymeric organic C in the sediments tends to decrease with increasing organic matter content, due to the increase of the refractory fraction of organic C.

Relationships between sedimentary organics and benthic meiofauna on the continental shelf and the upper slope of the Gulf of Lions (NW Mediterranean)

The relationships between the biochemical characteristics of sedimentary organics and benthic meiofauna in the Gulf of Lions were assessed based on samples collected at 19 sites during June 1998. We measured sediment granulometry, organic matter, organic carbon, nitrogen, carbohy- drate, lipid, total hydrolyzable amino acid (THAA) and enzymatically hydrolyzable amino acid (EHAA) concentrations together with C/N and EHAA/THAA ratios. Meiofauna abundance and nematode biomass were also analyzed. All biochemical parameters showed the same pattern of change relative to depth, with a decrease between 0 and 175 m, a subsequent increase between 175 and 900 m and a final decrease at greater depths. This pattern was linked to sediment granulometry and more specifically to the occurrence of coarser sediments near the edge of the continental shelf. In contrast, meiofauna abundance and nematode biomass constantly decreased with depth. This suggests that organic matter availability does not control the quantitative characteristics of benthic meiofauna over the whole range of sampled depths. The relationships between biochemical de- scriptors of sedimentary organics and quantitative characteristics of benthic meiofauna were assessed in the 0 to 175 m depth range. Lipids and to a lesser extent EHAA correlated better with meiofauna abundance and nematode biomass than nitrogen, carbohydrates and organic contents. These results are discussed in view of the identification of biochemical descriptors of the nutritive value of sedimentary particulate organic matter.

Organic matter cycling in grassland soils of the Swiss Jura mountains: biodiversity and strategies of the living communities

Several characteristics of the soils of three nutrient-poor grasslands, pertaining to their biological activity, have been measured three times during the vegetation cycle of 1994 in the Swiss Jura. Properties measured were: abundances of the faunal groups Collembola (Insecta), Oribatida, Gamasida and Actinedida (Acarina); PLFA richness, abundance and diversity (indicating microbial diversity); ATP content (an index of soil biomass), soil respiration (CO 2 production); and alkaline phosphatase, urease, chitinase, xylanase and laminarinase activities, as biochemical tracers of biotic activity. Most of these variables showed significant differences from site to site. In particular, the biochemical descriptors ATP content and phosphatase and urease activities varied in accordance with the amount of the clay-humic complex. The soils showed two strategies of litter degradation: (a) an enzymatic strategy, prevailing at the end of winter, when the edaphic climate is unfavourable; (b) a biotic strategy, based upon the work of the whole living community (fauna and microflora), at its maximum at the end of summer. Diversity of the microbial communities (as estimated by the PLFA richness) was highest in spring, when the carbon sources are complex (young litter), and subsequently decreased in inverse relationship with the specific activity of the biomass (viz. CO 2 production-to-ATP ratio). This behaviour is attributed to an increase of the amount of simple organic compounds resulting from enzymatic activity and also to the activity of microphytophagous microarthropods.

Temporal and spatial variation in the epilithic biofilm of an acid stream

Summary1. The extent of spatial and temporal variation, and the taxonomic and biochemical composition of epilithic biofilm were determined in a first‐order, acidic stream in the Ashdown Forest, southern England.2. The biofilm had an autotrophic component consisting of acidobiontic diatoms, small coccoid green algae, zygnematacean filamentous green algae, and a heterotrophic component of bacteria. Fungi were absent.3. Diatoms were the dominant algal group in spring. These were succeeded by coccoid green algae in summer. Synchronous variation existed between algae and bacteria, suggesting a strong link between the two groups.4. Quantitative community descriptors (algal and bacterial densities, chlorophyll, ash‐free dry matter) and biochemical descriptors (protein, lipid and carbohydrate content) of biofilm presented a consistent temporal pattern in which biofilm biomass peaked in spring and early summer and decreased subsequently.5. Stepwise multiple regression revealed that temporal variation in the quantity of biofilm coating substrata was primarily associated with photosynthetically active radiation. The quantity of biofilm coating the upper surfaces of substrata increased with substratum particle size (small stones, large stones and bedrock). Smothering of algae by fine particulate organic matter, proximal shading by bed sediments, and physical disturbance are proposed as mechanisms that brought about the pattern.

Analysis of the discriminating power of agro/morphological and biochemical descriptors in a sample of the Spanish collection of barley (Hordeum vulgare L.)

A sample representative of the national collection of barley (Hordeum vulgare L) has been evaluated with different agro/morphological and biochemical descriptors in order to determine their usefulness for discriminating accessions. Multivariate analysis performed on three sets of traits (agro/morphological traits, biochemical traits and agro/morphological plus biochemical traits) showed that, in general, the relationships between agro/morphological and biochemical descriptors were low. Cluster analysis revealed that the classification of the accessions by the agro/morphological data was different from the classification obtained according to the biochemical data, indicating that the two types of markers reflect different patterns of diversity. However, neither agro/morphological nor biochemical characters identified all the accessions as unique phenotypes. Conversely, all the accessions were individually separated using a combination of agro/morphological and biochemical traits since t he two types of markers provided complementary information.

Proposed Biochemical Descriptors for Amino Acids to Evaluate Grape Germplasm.

Amino acid profiles in juice were determined by using 259 grape germplasm including 169 cultivars, 81 breeder's lines, 5 rootstocks and 4 clones of wild species. Amino acid contents of cultivars and breeder's lines were higher than those of rootstocks and wild species. For amino acid composition, arginine (Arg), alanine (Ala) and glutamic acid (Glu) were predominant compared with asparatic acid (Asp), threonine (Thr), serine (Ser), valine (Val), methionine (Met), isoleucine (Ile), and leucine (Leu). Based on the primary amino acids, the grape accessions could be classified into the following five types: Glu, Arg, Ala, Arg+Ala and Ala+ Arg. Furthermore, to evaluate amino acid composition easi-ly, a new biochemical descriptor designated as γ ratio= [Thr+Ser+ Ala] /([Asp+Glu] + [Val + Met + Ile + Leu + Arg] ) was introduced. The variation in γ ratio is significantly associated with both use and species parentage, indicating that genetic differentiation for amino acid composition exists among grape germplasm. In addition, as the biochemical descriptor, amino acid profiles in grape germplasm were defined as 3 classes of amino acid content (3 : ?? 1.00 mmol ; 5 : 1.012.00 mmol ; 7 : 2.01 mmol ??, class interval= 1.0 mmol/100 ml equivalent), and 5 classes of γ ratio (1 : ?? 0.50 ; 3 : 0.511.00 ; 5 : 1.011.50 ; 7 : 1.512.00 ; 9 : 2.01 ??, class interval=0.5), respectively.

Genetic differentiation of cocoa (Theobrotna cacao L.) populations revealed by RAPD analysis

In order to preserve and exploit the valuable genetic resources of tropical forest trees, such as cocoa, a systematic assessment of the available genetic variability is necessary. The approach we have used is based on a simple mini-prep DNA extraction procedure together with a polymerase-chain-reaction- (PCR)-based polymorphic assay procedure (RAPD). Twenty-five cocoa accessions: IMCs and PAs collected from Peru and LCTEENs collected from Ecuador, which are difficult to distinguish using morphological or biochemical descriptors, were uniquely fingerprinted using a minimum of three oligonucleotide primers. Analysis of the variability detected using RAPDs clearly discriminated between the geographical origin of the three cocoa populations. Partitioning of variability into within and between population components revealed that most variation was detected within a population. The potential of RAPD analysis to facilitate the rationalization of field gene banks and provide accurate estimates of diversity to allow optimization of collecting strategies is discussed.

Drugs: Guide and caveats to explanatory and descriptive approaches—II. Drugs in psychiatric research

Over the last two decades animal models, mediators and drugs have produced a mass of experimental data difficult to relate to the epidemiological and clinical side of psychiatric disorders. Antidrepressant drugs are chosen as a model case to describe a more general scene: far from being a specific tool—a guide—in a complex situation, these drugs are acquiring a role which must be interpreted with caution (a caveat), in view of ample clinical evidence of responders to placebo, responders to any drugs, responders to many drugs, etc. Studies of biochemical descriptors of drug action as a marker of the disease and its outcome have drawn puzzling pictures, often contradictory and unstable in terms of the populations to whom they can be applied. Controlled clinical trials with antidepressant drugs over the last ten years have persisted in looking for short-term pharmacological effects rather than the medium-or long-term impact of medication in large populations. To establish a positive role for antidepressant drugs, they must be studied in a “natural” context where depressed patients are treated with all necessary follow-up.

Left Ventricular Performance in the Hypertensive Patient: Exercise-Mediated Noninvasive Separation of Loading Influences From Intrinsic Muscle Dysfunction

Patients with systemic arterial hypertension are classified primarily on the basis of the severity of arterial pressure elevation and often, as well, on the basis of biochemical descriptors such as plasma renin activity. However, while such classification is useful for prognostic and therapeutic purposes,1,2 accurate, precise prediction of the clinical outcome in the individual hypertensive patient cannot be achieved by this approach. Since the left ventricle can be considered an “end organ,” the function of which reflects the results of hypertension, it is not unreasonable to hypothesize that assessment of left ventricular performance, and particularly of the load-independent alterations in left ventricular function, may be valuable adjuncts in the determination of risk and evaluation of therapy in the hypertensive patient.