Evidence against the use of surrogates for biomonitoring of Neotropical floodplains

1. Community concordance measures the level of association between the compositional patterns shown by two groups of organisms. If strong community concordance occurs, one group could be used as a surrogate for another in conservation planning and biodiversity monitoring. In this study, we evaluated the variability in the strength of community concordance, the likely mechanisms underlying community concordance and the degree to which one community can predict another in a set of Neotropical floodplain lakes (Upper Paraná River floodplain, Brazil). 2. We used a data set including six aquatic communities: fish, macrophytes, benthic macroinvertebrates, zooplankton, phytoplankton and periphyton. We used Mantel and PROTEST approaches to evaluate the levels of community concordance in up to four sampling periods. Also, we used partial Mantel test and information about biotic interactions to investigate reasons for observed patterns of concordance. Finally, we used co‐correspondence analysis to evaluate the performance of one taxonomic group in predicting the structures of other communities. 3. The levels of community concordance varied over time for almost all cross‐taxa comparisons. Concordance between phytoplankton and periphyton probably resulted from similar responses to environmental gradients, whereas other patterns of concordance were likely generated by interactions among groups. However, the levels of predictability were low, and no particular taxonomic group significantly predicted all other groups. 4. The low and temporally variable levels of community concordance cast doubts on the use of surrogate groups for biodiversity management in Neotropical floodplains.     

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring

Background

Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families.

Results

The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function.

Conclusions

Our results demonstrate that the method we present here using a k- modes site clustering algorithm based on interdependency evaluation among sites obtained from a sequence alignment of homologous proteins can provide significant insights into the complex, hierarchical inter-residue structural relationships within the 3D structure of a protein family.

     

Changing concepts in plant hormone action

Summary A plant hormone is not, in the classic animal sense, a chemical synthesized in one organ, transported to a second organ to exert a chemical action to control a physiological event. Any phytohormone can be synthesized everywhere and can influence different growth and development processes at different places. The concept of physiological activity under hormonal control cannot be dissociated from changes in concentrations at the site of action, from spatial differences and changes in the tissue's sensitivity to the compound, from its transport and its metabolism, from balances and interactions with the other phytohormones, or in their metabolic relationships, and in their signaling pathways as well. Secondary messengers are also involved. Hormonal involvement in physiological processes can appear through several distinct manifestations (as environmental sensors, homeostatic regulators and spatio-temporal synchronizers, resource allocators, biotime adjusters, etc.), dependent on or integrated with the primary biochemical pathways. The time has also passed for the hypothesized ‘specific’ developmental hormones, rhizocaline, canlocaline, and florigen: root, stem, and flower formation result from a sequential control of specific events at the right places through a coordinated control by electrical signals, the known phytohormones and nonspecific molecules of primary and secondary metabolism, and involve both cytoplasmic and apoplastic compartments. These contemporary views are examined in this review.     

An easy and reliable method for establishment and maintenance of leaf and root cell cultures ofArabidopsis thaliana

Cell suspension cultures are useful for a wide range of biochemical and physiological studies, yet their production can be technically demanding and often unreliable. Here we describe a protocol for producing Arabidopsis cell suspension cultures that is reliable and easy to use.     

Recovery in aqueous two-phase systems of lutein produced by the green microalga Chlorella protothecoides

The objective of this study was to develop a chromatographic method for the analysis of the anti-androgen vinclozolin (V) and its metabolites 2-[[(3,5-dichlorophenyl)-carbamoyl]oxy]-2-methyl-3-butenoic acid (M1), 3',5'-dichloro-2-hydroxy-2-methylbut-3-enanilide (M2) and 3,5-dichloroaniline (M3) in rat serum. V, M1-M3 were resolved using an HPLC gradient program with a mobile phase consisting of 60-75% methanol:acetonitrile (70:30) and 0.05 M monobasic sodium phosphate buffer pH 3.3 at 1 ml/min, a C18 column, and monitored at 212 nm. Incubates of 0.01 M monobasic potassium phosphate buffer (PB) pH 7.4 and rat serum were spiked with V and its metabolites and processed by diluting samples (1:4) with 0.1M PB pH 3.3, to limit methodological hydrolysis of analytes, followed by addition of acetonitrile. Recoveries of V, M1 and M2 ranged from 85 to 105%, whereas recovery of M3 was <25%. V was hydrolyzed to M1 and M2 after incubation in PB pH 7.4 and rat serum, with M1 the predominant metabolite. This method was successfully applied in the analysis of V and its metabolites in the serum of a male rat after oral administration of V (100 mg/kg).     

Spatial distribution of sharks captures in the Pacific of Nicaragua and its relationship with several oceanographic variables

Between August 1995 and August 1997 long line fishing techniques and a bathythermograph were used to correlate some physical variables with the spatial distribution of four shark species in 26 fishing cruises off the Nicaraguan Pacific Coast. They were the thresher (Alopias vulpinus), blue (Prionace glaucea), gray (Carcharhinus falciformis) and hammer (Sphyra lewini). All species concentrated in the southeastern Nicaraguan Pacific, at the seasonal upwelling area of Papagayo Gulf. The range of sea surface temperatures in which the sharks were captured was 25-28 degrees C. We could clearly associate this physical parameter with shark availability. The vertical distribution of the captured sharks suggests that they occupy termocline levels above the 15 degrees C isotherm. Although these species are oceanic, the blue shark was captured in ocean waters over the 1800 m isobar, while the grey and thresher sharks where close to the continental shelf. Body length in decreasing order are: thresher (210-290 cm, SN = 21), blue (60-240 cm, SN = 13) and gray (80-200 cm, SN = 17).     

The variability of the hepatitis B virus genome: statistical analysis and biological implications

A statistical analysis of the nucleotide sequence variability in 14 published hepatitis B virus (HBV) genomes was carried out using parametric and nonparametric methods. A parametric statistical model revealed that the different regions of the genome differed significantly in their variability. The conclusion was supported by a nonparametric kernel-density model of the HBV genome. Genes S, C, and P, region X, the precore region, and the pre-S2/pre-S1 regions were ranked in order of increasing variability. In many instances, conserved regions of the genome identified with sequences of known function in HBV biology. However, other characterized regions (such as pre-S) showed much variability despite the involvement of their encoded peptides in specific functions. Point mutations that may result in the formation of stop codons and amino acid changes may affect the clinical picture of HBV infection and may be reflected in atypical serological patterns.      

Sequence, organization, and evolution of the A+T region of Drosophila melanogaster mitochondrial DNA

The long (4.6-kb) A+T region of Drosophila melanogaster mitochondrial DNA has been cloned and sequenced. The A+T region is organized in two large arrays of tandemly repeated DNA sequence elements, with nonrepetitive intervening and flanking sequences comprising only 22% of its length. The first repeat array consists of five repeats of 338-373 bp. The second consists of four intact 464-bp repeats and a fifth partial repeat of 137 bp. Three DNA sequence elements are found to be highly conserved in D. melanogaster and in several Drosophila species with short A+T regions. These include a 300-bp DNA sequence element that overlaps the DNA replication origin and two thymidylate stretches identified on opposite DNA strands. We conclude that the length heterogeneity observed in the A+T regulatory region in mitochondrial DNAs from the genus Drosophila results from the expansion (and contraction) of the number of repeated DNA sequence elements. We also propose that the 300-bp conserved DNA sequence element, in conjunction with another primary sequence determinant, perhaps the adjacent thymidylate stretch, functions in the regulation of mitochondrial DNA replication.      

Changes in Stream Primary Producer Communities Resulting from Large-Scale Catastrophic Amphibian Declines: Can Small-Scale Experiments Predict Effects of Tadpole Loss?

Global declines of amphibian populations are well documented, yet effects of these declines on freshwater ecosystem structure and function are poorly understood. Here we examine responses of algal primary producers to tadpole extirpation over differing spatial and temporal scales. We experimentally excluded tadpoles from artificial substrata within localized areas (0.25 m²) of two streams. One stream had an intact community of frogs (frog stream), and the other had recently experienced a catastrophic decline (frogless stream), leaving virtually no tadpoles. In the frog stream, there were significantly greater levels of chlorophyll a (+111%, P = 0.009), ash-free dry mass (AFDM) (+163%, P = 0.02), inorganic sediments (+114%, P = 0.001), and higher mean algal cell biovolume in tadpole exclusion treatments than in the tadpole access treatments. Correspondingly, overall AFDM-specific net primary production (NPP) increased by 38% (P = 0.001) and chlorophyll a-specific NPP increased by 29% (P = 0.001) in tadpole access treatments compared to tadpole exclusion treatments. Areal-specific NPP did not differ between treatments. There were no significant differences in chlorophyll a, AFDM, inorganic sediments, algal cell biovolume, or biomass-specific NPP between treatments in the frogless stream. Fifteen months after our experiments, a massive amphibian decline associated with a fungal pathogen occurred in the frog stream, resulting in the extirpation of over 90% of tadpoles. This extirpation was followed by significant increases in levels of chlorophyll a (269%, P = 0.001), AFDM (+220%, P < 0.001), and inorganic sediments (+140%, P = 0.001). Reach-scale NPP increased from −1587 to −810 mg DO m⁻² d⁻¹. Additionally, algal community composition shifted from a dominance of small adnate diatoms (pre-decline) to a dominance of large upright algal species (post-decline). Our experimental results, combined with algal monitoring at the reach scale, indicate that over the course of our study catastrophic amphibian losses have significant effects on stream ecosystem structure and function. Ecosystem-level impacts of tadpole extirpations were more dramatic than results from our small-scale, short-term experiments, which predicted the direction of change in response variables but underestimated the magnitude. However, the long-term stream ecosystem responses remain unknown. Author Contributions: S.C., C.M.P., M.R.W., K.R.L., and S.K. designed the study, S.C., C.M.P., R.B., M.R.W., K.R.L., and A.D.H. performed research, S.C., C.M.P., R.J.B., M.R.W., and A.D.H. analyzed data. S.C., C.M.P., and R.J.B. wrote the paper.     

The use and limits of AFLP data in the taxonomy of polyploid wild potato species in Solanum series Conicibaccata

Solanum sect. Petota (tuber-bearing wild and cultivated potatoes) are a group of approximately 190 wild species distributed throughout the Americas from the southwestern United States south to Argentina, Chile, and Uruguay. Solanum series Conicibaccata are a group of approximately 40 species within sect. Petota, distributed from central Mexico to central Bolivia, composed of diploids (2n = 2x = 24), tetraploids (2n = 4x = 48) and hexaploids (2n = 6x = 64); the polyploids are thought to be polysomic polyploids. This study initially was designed to address species boundaries of the four Mexican and Central American species of series Conicibaccata with AFLP data with the addition of first germplasm collections of one of these four species, Solanum woodsonii, as a follow-up to prior morphological, chloroplast DNA, and RAPD studies; and additional species of series Conicibaccata from South America. AFLP data from 12 primer combinations (1722 polymorphic bands) are unable to distinguish polyploid species long thought to be distinct. The data suggest a complex reticulate history of the tetraploids or the need for a broad downward reevaluation of the number of species in series Conicibaccata, a trend seen in other series of sect. Petota. Separately, through flow cytometry, we report the first ploidy level of S. woodsonii, as tetraploid (2n = 48). The U.S. Government’s right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.