Rareza y Diversidad de Hormigas en Fragmentos de Bosque Seco Colombianos y sus Matrices1

Dry forests in middle Cauca River valley (southwest Colombia) almost have been eliminated from the region and the last remnants are seriously threatened. This study shows the biological value of seven forest fragments, comparing their ant diversity with that of their surrounding matrices. Two intensive ant surveys were made in each forest fragment and its matrix between August 1994 and February 1995. Sampling effort was the same in each of the seven sites. We found that: (1) forest fragments are richer and more diverse than their respective matrices; (2) forests preserve a larger number of rare ant species than the matrices; and (3) the richer the forest, the larger the number of exclusive ant species it preserves. Therefore, these forests must be preserved to maintain regional biodiversity.     

Decision matrices: Tools to enhance middle school engineering instruction

Decision matrices are valuable engineering tools. They allow engineers to objectively examine solution options. Decision matrices can be incorporated in K-12 classrooms to support authentic engineering instruction. In this article we provide examples of how decision matrices have been incorporated into 6th and 7th grade classrooms as part of an innovative NGSS-aligned curriculum. The article also provides guidelines and examples for how to scaffold decision matrices to support student and teacher confidence and use.     

Discrete molecular weight components of the organic matrices of mollusc shells

Discrete molecular weight components form part of the soluble fraction of the organic matrices of mollusc shells. The number of these components, their relative migration distances and concentrations vary greatly in the specimens analysed. The discrete molecular weight constituents from the organic matrices of species of the same genus are most similar. The presence of these components shows that organic matrices are heterogeneous and presumably capable of performing diverse functions.     

Mineralizing matrices in the skeletal axes of two Corallium species (Alcyonacea)

Soluble organic matrices extracted from the axial part of the skeletons of two Corallium species (Coralliidae, Alcyonacea) were analysed using FTIR spectrometry, HPLC, IEF, 2-D gel electrophoresis and XANES. All these methods show that the main characteristics of the two matrices are similar, but not identical. Both matrices are composed of proteins and sugars; they are acidic with poorly separated molecular masses. The sugar contents are low, and the matrices do not seem highly glycosylated. The differences and similarities of these matrices are also observed in the minor element contents and in the micro- and nanostructures of the samples. These results confirm the control of the morphology and the chemical composition of calcitic biocrystals. Biomineralisation processes in Coralliidae are taxonomically significant, and differ from those of Scleractinia skeletons.     

Analyse formelle de circuits de régulation génétique: le contrôle de l'immunité chez les bactériophages lambdoïdes

This paper is an attempt to describe and analyze in formal terms a genetic circuit which is rather complex and reasonably well disentangled: the control of immunity in lambdoid bacteriophages. Known models are expressed as logic equations, which relate the stade of activity of genes to variables of three kinds: genetic variables which describe the genotype of the organism, environmental variables like temperature and memorization variables. The value of each memorization variable (presence or absence of a gene product) is related to the value of the corresponding function (operation or not of the gene) by two characteristic time delays, an «establishment delay and a «decay delay.From the equations, one can derive matrices which facilitate comparison between models by showing which stable states are predicted by each model. Implications of current models, which had apparently remained cryptic, have been realized and experimentally tested.From the matrices, one can derive graphs which show the pathways (sequences of states) consistent with each model. These graphs are frequently branched and in these cases one has to analyze which conditions determine that one pathway rather than another one, is followed.     

Transforming growth factor beta stimulates fibroblast-collagen matrix contraction by different mechanisms in mechanically loaded and unloaded matrices

Studies were carried out to test the idea that transforming growth factor beta (TGFbeta) stimulated fibroblast contraction of collagen matrices by different mechanisms depending on mechanical loading on the cells and matrix. Under mechanically unloaded conditions (floating matrices), TGFbeta stimulated contraction directly as an agonist and indirectly by preactivating cells to express the myofibroblast phenotype. Increased contraction of floating matrices by preactivated cells appeared to result in part from an autocrine mechanism. Under mechanically loaded conditions (stressed matrices), TGFbeta had no direct agonist effect on contraction. Fibroblasts preactivated to become myofibroblasts showed increased ability to transfer tension to stressed matrices, and tension persisted even after the cells' actin cytoskeleton was disrupted. Our findings are consistent with the idea that fibroblasts activated to become myofibroblasts in vitro have increased contractile activity and indicate that multiple mechanisms that differ depending on mechanical loading on the cells and matrix are involved.     

Isolation and Quantification of Botulinum Neurotoxin From Complex Matrices Using the BoTest Matrix Assays

Accurate detection and quantification of botulinum neurotoxin (BoNT) in complex matrices is required for pharmaceutical, environmental, and food sample testing. Rapid BoNT testing of foodstuffs is needed during outbreak forensics, patient diagnosis, and food safety testing while accurate potency testing is required for BoNT-based drug product manufacturing and patient safety. The widely used mouse bioassay for BoNT testing is highly sensitive but lacks the precision and throughput needed for rapid and routine BoNT testing. Furthermore, the bioassay''s use of animals has resulted in calls by drug product regulatory authorities and animal-rights proponents in the US and abroad to replace the mouse bioassay for BoNT testing. Several in vitro replacement assays have been developed that work well with purified BoNT in simple buffers, but most have not been shown to be applicable to testing in highly complex matrices. Here, a protocol for the detection of BoNT in complex matrices using the BoTest Matrix assays is presented. The assay consists of three parts: The first part involves preparation of the samples for testing, the second part is an immunoprecipitation step using anti-BoNT antibody-coated paramagnetic beads to purify BoNT from the matrix, and the third part quantifies the isolated BoNT''s proteolytic activity using a fluorogenic reporter. The protocol is written for high throughput testing in 96-well plates using both liquid and solid matrices and requires about 2 hr of manual preparation with total assay times of 4-26 hr depending on the sample type, toxin load, and desired sensitivity. Data are presented for BoNT/A testing with phosphate-buffered saline, a drug product, culture supernatant, 2% milk, and fresh tomatoes and includes discussion of critical parameters for assay success.     

Pivotal roles for Streptomyces cell surface polymers in morphological differentiation,attachment and mycelial architecture

Cells that are part of a multicellular structure are typically embedded in an extracellular matrix, which is produced by the community members. These matrices, the composition of which is highly diverse between different species, are typically composed of large amounts of extracellular polymeric substances, including polysaccharides, proteins, and nucleic acids. The functions of all these matrices are diverse: they provide protection, mechanical stability, mediate adhesion to surfaces, regulate motility, and form a cohesive network in which cells are transiently immobilized. In this review we discuss the role of matrix components produced by streptomycetes during growth, development and attachment. Compared to other bacteria it appears that streptomycetes can form morphologically and functionally distinct matrices using a core set of building blocks.     

Tyrosination-detyrosination of tubulin and microtubules during the development of chick erythrocytes

The protein composition of nuclear matrices containing different amount of DNA was examined. It was found that, in matrices containing 2% to 80% of total DNA, the quantity of DNA-bound proteins remains relatively constant varying from 10% to 15% of total nuclear proteins. Electrophoretic patterns do not differ substantially, but autoradiograms with in vitro ¹²⁵I labelled proteins show quantitative variations in the actin content. Application of radioimmunoassay (RIA) enabled to determine the exact content of actin in GAT nuclei and nuclear matrices – 5 g/ml in nuclei, of which 50% are bound to DNA and 3001o being a component of the protein part of the nuclear matrix. These results are supported by electron microscopic data, where immunogold technique was performed on thin sections and spread material. The applied methods suggest that part of the nuclear actin is tightly bound (resistant to 2 M NaCI) to DNA and represents a component of the internal nuclear matrix.     

Interactions between chondroitin sulfate proteoglycan, fibronectin, and collagen

A proteoglycan isolated from a rat yolk sac tumor and characterized as a chondroitin sulfate proteoglycan with a smaller amount of dermatan sulfate was studied with respect to complex formation with collagen and fibronectin. The proteoglycan co-precipitated with native collagen from neutral salt solutions at 6 degrees C and 37 degrees C. Addition of fibronectin in such precipitation mixtures resulted in incorporation of fibronectin to the precipitate. Treatment of the proteoglycan with alkali to separate the glycosaminoglycan chains from the protein part and digestion of the protein part with papain greatly reduced the capacity of the proteoglycan to precipitate collagen and fibronectin. A defined extracellular matrix as represented by the complexes of collagen, proteoglycan, and fibronectin constructed here may be useful for studies on the biological effects of extracellular matrices. The multiple interactions of matrix macromolecules exemplified by these results may play a role in the formation of extracellular matrices and in the maintenance of their integrity.     

Recognition of ill-defined signals in nucleic acid sequences

A set of programs has been developed for the definition andhandling of nucleic acid sequence consensus information. Thesequences of known genetic control signals are combined in amatrix. The origins and positions of the signals are recorded.Old matrices can be updated dynamically: new signals are includedand obsolete ones deleted. Matrices of several different typesare computed optionally. Several of these matrices can be combinedto find possible new signals. The use of matrices allows theexact quantification of signal qualities. The described programsare part of a program library named GENEXPERT. Application examplesgiven are the search for tRNA genes and the search for promotersin the bacteriophage genome. Received on July 22, 1987; accepted on October 5, 1987     

Cancer de la prostate : les niveaux de preuve des biomarqueurs de la détection précoce

As part of an overall review on the role of PSA and other emerging biomarkers in the detection, diagnosis and treatment of prostate cancer, we present here a part of a review of the literature made by the working group Biologie de la Prostate (AFU, CNBH, SFBC, SFMN) on the use of PSA and other biomarkers in the early detection of prostate cancer with an assessment of the level of evidence.     

Mimicking dynamic in vivo environments with stimuli-responsive materials for cell culture

Traditional synthetic substrates and matrices for cell culture have proven to be of only limited utility in efforts to understand and control cell behavior, in large part because they fail to capture the multifarious biochemical, mechanical, geometric and dynamic characteristics of in vivo environments. However, recent advances in materials chemistry and engineering have begun to provide researchers with a toolbox to mimic the complex characteristics of natural extracellular matrices (ECMs), providing new pathways to explore cell-matrix interactions and direct cell fate under physiologically realistic conditions. In this review, we describe recent developments in stimuli-responsive materials as dynamic substrates and matrices for cell culture, and highlight their use in furthering our understanding of how cells respond to temporal variations in their environment.     

Disentangling community patterns of nestedness and species co-occurrence

Two opposing patterns of meta‐community organization are nestedness and negative species co‐occurrence. Both patterns can be quantified with metrics that are applied to presence‐absence matrices and tested with null model analysis. Previous meta‐analyses have given conflicting results, with the same set of matrices apparently showing high nestedness (Wright et al. 1998) and negative species co‐occurrence (Gotelli and McCabe 2002). We clarified the relationship between nestedness and co‐occurrence by creating random matrices, altering them systematically to increase or decrease the degree of nestedness or co‐occurrence, and then testing the resulting patterns with null models. Species co‐occurrence is related to the degree of nestedness, but the sign of the relationship depends on how the test matrices were created. Low‐fill matrices created by simple, uniform sampling generate negative correlations between nestedness and co‐occurrence: negative species co‐occurrence is associated with disordered matrices. However, high‐fill matrices created by passive sampling generate the opposite pattern: negative species co‐occurrence is associated with highly nested matrices. The patterns depend on which index of species co‐occurrence is used, and they are not symmetric: systematic changes in the co‐occurrence structure of a matrix are only weakly associated with changes in the pattern of nestedness. In all analyses, the fixed‐fixed null model that preserves matrix row and column totals has lower type I and type II error probabilities than an equiprobable null model that relaxes row and column totals. The latter model is part of the popular nestedness temperature calculator, which detects nestedness too frequently in random matrices (type I statistical error). When compared to a valid null model, a matrix with negative species co‐occurrence may be either highly nested or disordered, depending on the biological processes that determine row totals (number of species occurrences) and column totals (number of species per site).     

Synaptonemal complexes are integral components of the isolated mouse spermatocyte nuclear matrix

Synaptonemal complexes (SCs) have been isolated as integral components of the nuclear matrix from purified mouse pachytene spermatocytes. These nuclear synaptonemal complex-matrices are prepared by extracting Triton X-100-treated nuclei with low (0.2 M) and high (1.0 or 2.0 M) NaCl, DNase I, and RNase A to remove 85% of the nuclear proteins, 97% of the RNA, and 99% of the DNA. Studies with the light and electron microscopes indicate that these matrices, while lacking a distinct lamina, contain nuclear pores interconnected by a fiber network, residual nucleoli, and interchromatin fibers. In addition, the pachytene spermatocyte matrices contain residual XY heterochromatin and the principal components of the SCs, including two lateral elements, a central element, a presumptive centromere, and attachment plaques. These SCs are preserved within the matrix and retain their structural association with the pore-fiber complex, even when subjected to strong dissociating conditions. Nuclear matrices from pachytene spermatocytes and spermatids (steps 1-8), when analyzed by SDS PAGE, contain an array of polypeptides distinct from those of mouse liver nuclear matrices. Proteins of spermatogenic matrices range in Mr from 8,000 to approximately 150,000. The prominent lamina proteins (Mr approximately 60,000-70,000) of somatic nuclear matrices are either absent or represent only a minor part of the spermatogenic matrix. The polypeptide composition of the pachytene spermatocyte and spermatid matrices are similar, although minor quantitative and qualitative differences are evident. These observations suggest that the SC constituents may consist of a heterogeneous group of proteins present in low proportion relative to total matrix proteins, or they may be retained, but in a different form, within the spermatid matrix.     

Transport de l'auxine-14C en provenance de jeunes gousses de Vicia faba L.

Summary After the injection of [¹⁴C]indole acetic acid (IAA) into very young pods of broad-bean (Vicia faba L.) the movement of the ¹⁴C in the peduncle and stem was followed by autoradiography. In samples with only one young pod the basipetal transport was always clearly dominant. Most of the radioactivity was found in the bundles, particularly in the outer region of the bundle and also in the inner region (protoxylem parenchyma). The progression of the tracer was relatively complex. The rate of movement of the radioactive «front» could be as much as 2 cm·h^-1 but most of the ¹⁴C moved towards the base at rates clearly less than that of the «front». Chromatograms with several solvent systems showed that IAA was the main or the only mobile radioactive substance. During transport, a part of IAA was converted into indole-3-aldehyde (IAld) and indole-3-acetyl-aspartic acid (IAAsp). IAAsp and possibly also IAld, which were found mainly near the donor pod, seemed immobile. This work is part of a study on the interchange of phytohormones between fruit and plant.

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Abréviations AIA acide indolyl-acétique - AIAsp acide indolyl-acetyl-aspartique - IAld indolyl-aldéhyde     

Biodistance analysis of the Moche sacrificial victims from Huaca de la Luna plaza 3C: Matrix method test of their origins

The purpose of this study is to test two competing models regarding the origins of Early Intermediate Period (AD 200-750) sacrificial victims from the Huacas de Moche site using the matrix correlation method. The first model posits the sacrificial victims represent local elites who lost competitions in ritual battles with one another, while the other model suggests the victims were nonlocal warriors captured during warfare with nearby polities. We estimate biodistances for sacrificial victims from Huaca de la Luna Plaza 3C (AD 300-550) with eight previously reported samples from the north coast of Peru using both the mean measure of divergence (MMD) and Mahalanobis' distance (d2). Hypothetical matrices are developed based upon the assumptions of each of the two competing models regarding the origins of Moche sacrificial victims. When the MMD matrix is compared to the two hypothetical matrices using a partial-Mantel test (Smouse et al.: Syst Zool 35 (1986) 627-632), the ritual combat model (i.e. local origins) has a low and nonsignificant correlation (r = 0.134, P = 0.163), while the nonlocal origins model is highly correlated and significant (r = 0.688, P = 0.001). Comparisons of the d2 results and the two hypothetical matrices also produced low and nonsignificant correlation for the ritual combat model (r = 0.210, P = 0.212), while producing a higher and statistically significant result with the nonlocal origins model (r = 0.676, P = 0.002). We suggest that the Moche sacrificial victims represent nonlocal warriors captured in territorial combat with nearby competing polities.     

Provably sensitive indexing strategies for biosequence similarity search.

Fast algorithms for pairwise biosequence similarity search frequently use filtering and indexing strategies to identify potential matches between a query sequence and a database. For the most part, these strategies are not informed by the substitution score matrices commonly used by comparison algorithms to assign numerical scores to pairs of aligned residues. Consequently, although many filtering strategies offer strong formal guarantees about their ability to detect pairs of sequences differing by few substitutions, these methods can make no guarantee of detecting pairs with high similarity scores. We describe a general technique, score simulation, to help resolve the tension between existing filtering techniques and the use of score matrices. Score simulation, using score matrices, maps ungapped similarity search problems to the simpler problem of finding pairs of strings that differ by few substitutions. Score simulation leads to indexing schemes for biosequences that permit efficient ungapped similarity search with arbitrary score matrices while maintaining strong formal guarantees of sensitivity. We introduce the LSH-ALL-PAIRS-SIM algorithm for finding local similarities in large biosequence collections and show that it is both computationally feasible and sensitive in practice.     

Investigation of mechanisms of interaction between inulinase from Kluyveromyces marxianus and the matrices of ion-exchange resins and fiber

It is established that ion exchange resins AV-17-2P, KU-2, AV-16-GS, AM 21A, IMAC-HP, PUROLITE and fiber VION KN-1 can be applied as carriers for inulinase immobilization. The analysis of IR spectra for an enzyme, carriers and heterogeneous enzyme preparations showed that inulinase binding to matrices of various carriers occurs in general through electrostatic interactions. It is assumed that the mechanisms of interaction between inulinase from Kluyveromyces marxianus and the matrices of cation and anion exchange polymers differ essentially from each other: different sites of protein molecule take part in adsorption that causes various conformational reorganizations in an enzyme molecule.     

Chronostratigraphie de la fin de la derniere glaciation,a la lumiere des resultats de l'etude lithostratigraphique et palynologique du site de Maisieres-Canal (Belgique)

The upper part of the palaeoclimatic sequence of Maisières-Canal shows a succession of four mild episodes at thetransition between the Pleniglacial and the Late-Glacial. Those four mild fluctuations are respectively correlated with Langerie, Lascaux, Angles-sur-l'Anglin and Pré-Bölling oscillations.