Conservation Index Research Articles

Highly Tolerated Amino Acid Substitutions Increase the Fidelity of Escherichia coli DNA Polymerase I

Fidelity of DNA synthesis, catalyzed by DNA polymerases, is critical for the maintenance of the integrity of the genome. Mutant polymerases with elevated accuracy (antimutators) have been observed, but these mainly involve increased exonuclease proofreading or large decreases in polymerase activity. We have determined the tolerance of DNA polymerase for amino acid substitutions in the active site and in different segments of E. coli DNA polymerase I and have determined the effects of these substitutions on the fidelity of DNA synthesis. We established a DNA polymerase I mutant library, with random substitutions throughout the polymerase domain. This random library was first selected for activity. The essentiality of DNA polymerases and their sequence and structural conservation suggests that few amino acid substitutions would be tolerated. However, we report that two-thirds of single base substitutions were tolerated without loss of activity, and plasticity often occurs at evolutionarily conserved regions. We screened 408 members of the active library for alterations in fidelity of DNA synthesis in Escherichia coli expressing the mutant polymerases and carrying a second plasmid containing a beta-lactamase reporter. Mutation frequencies varied from 1/1000- to 1000-fold greater compared with wild type. Mutations that produced an antimutator phenotype were distributed throughout the polymerase domain, with 12% clustered in the M-helix. We confirmed that a single mutation in this segment results in increased base discrimination. Thus, this work identifies the M-helix as a determinant of fidelity and suggests that polymerases can tolerate many substitutions that alter fidelity without incurring major changes in activity.

Formyl Peptide Receptors on Immune and Nonimmune Cells: Analysis of Sequence Conservation in FPR Genes

Formyl peptides are oligopeptides released by Gram-negative bacteria. So far, specific formyl peptide receptors (FPRs) have been described in mammals only. FPRs are seven-transmembrane G-coupled molecules and make up a relatively homogeneous group, although exhibiting different levels of affinity for the ligands. We examined the patterns of conservation/mutation within the FPR group of genes, as studied in 16 mRNAs from different species. Following alignment of the coding sections, those nucleotides identical in at least 15 sequences were assigned a “conservation index” 2; those with 8–14 identities an index 1; those with less than 8 identities an index zero. The cumulative average conservation index was 1.36. The autocorrelation function and the power spectrum of the whole series of indexes demonstrated a 3-unit periodicity. This periodicity is explained by the fact that the average conservation indexes of the first, second and third nucleotides of the coding triplets were 1.46, 1.55 (both above the mean), and 1.06 (below the mean), respectively, so that correlations at lag 3 tend to be all positive. In mRNAs, regardless of the position in the coding triplets, T is significantly more frequently conserved (average index = 1.60) than A, C, and G (1.21 – 1.38). In the nucleotides with conservation index 1 or zero, we recorded the two more frequently represented bases. In 35% of mRNA nucleotides the two more frequently represented bases were C and T; in 28% of cases the two more frequently represented bases were A and G; other couples occurred with lower frequencies. Both mutations may arise following C methylation with subsequent transformation into T (by deamination), either in the template or the coding DNA strand. Thus, we hypothesized that in FPR mRNAs there is an evolutionary trend of transformation from G to A and from C to T, the latter being the more stable of the bases.

Measurement of Horizontal Inequity in Health Care Utilisation Using European Panel Data

Measurement of inequity in health care delivery has focused on the extent to which health care utilization is or is not distributed according to need, irrespective of income. Studies using cross-sectional data have proposed various ways of measuring and standardizing for need, but inevitably much of the inter-individual variation in needs remains unobserved in cross-sections. This paper exploits panel data methods to improve the measurement by including the time-invariant part of unobserved heterogeneity into the need-standardization procedure. Using latent class hurdle models for GP and specialist visits estimated on 8 annual waves of the European Community Household Panel we compute indices of horizontal equity that partition total income-related variation in use into a need- and a non-need related part, not only for the observed but also for the unobserved but time-invariant component. We also propose and compare a more conservative index of horizontal inequity to the conventional statistic. We find that many of the cross-country comparative results appear fairly robust to the panel data test, although the panel based methods lead to higher estimates of horizontal inequity for most countries. This confirms that better estimation and control for need often reveals more pro-rich distributions of utilization.

Analysis of disease-associated ND4 mutations: How do we know which mutation is pathogenic?

It is not uncommon to identify more than one mtDNA replacement mutations in the specimens from patients. However, we usually do not know if the identified mtDNA mutation is pathogenic or not. Even functional assays are available to use, we would not know which mutation(s) is to be tested. To provide a rapid method for initial evaluation for the pathogenicity of the replacement mutation, we compared three evolutional analyses: primate conservation index (PCI), mammalian conservation index (MCI), and conservation index across a wide spectrum of species (CI). After analyzing 35 so-called diseases-associated replacement mutations of ND4, we found 8 pathogenic mutations, 15 nonpathogenic mutations, and 12 mutations of undetermined significance. The MCI classification appears to be the best one among the three systems. This study demonstrates that evolutional analysis can serve as a rapid evaluation for the pathogenicity of mtDNA replacement mutations.

Geological, geochemical and mineralogical features of some bauxite deposits from Nurra (Western Sardinia, Italy): insights on conditions of formation and parental affinity

Bauxite deposits are widespread in NW Sardinia. They formed during the middle Cretaceous, in consequence of a period of emergence of the Mesozoic carbonate shelf. In the Nurra area the geometries derived by the Middle Cretaceous tectonic phases controlled the ore typologies. Two bauxite profiles, laying on different bedrocks, were sampled. The bauxitization proceeded from the surface downward, with the accumulation of Al2O3 and residual ‘immobile’ elements (Al, Ti, HFSE), and corresponding mobility and loss of SiO2 and Fe2O3. Epigenetic kaolinite formed close to faults and joints, probably as a result of silicification, introduced by low temperature hydrothermal solutions. Rare earth elements, especially LREE, are concentrated in Fe-rich bauxite horizons, probably due to scavenging by goethite. REE-enrichment is not observed in the boehmite-rich horizons. Very high REE contents are observed in a Fe-depleted horizon due to the occurrence of REE accessory minerals, probably of the bastnasite group. Conservative indices, including TiO2/Al2O3 and Ti/Cr ratios, and Eu anomalies (Eu/Eu*), suggest that the deposits formed by weathering of sediments derived from mafic rocks of the Hercynian basement. This, in turn, implies that the basement was exposed during middle Cretaceous.

Urban seagrass: Status of Posidonia oceanica facing the Genoa city waterfront (Italy) and implications for management

A system of five adjacent Posidonia oceanica meadows facing the waterfront of Genoa city (Ligurian Sea, NW Mediterranean) was investigated over different spatial scales (meters–kilometers) using three environmental indices: conservation index (CI), substitution index (SI) and phase-shift index (PSI). CI revealed differences mostly at large spatial scale, distinguishing the poor condition of the meadows closest to Genoa centre and harbour from the comparatively healthy condition of the farthest meadows. SI showed differences mostly at small spatial scale (i.e., within meadows), suggesting the influence of local factors in the re-colonisation of regressed meadows by the seagrass Cymodocea nodosa and/or the invasive alga Caulerpa racemosa. Mapping of PSI showed that the meadows closest to Genoa centre and harbour have undergone a nearly total phase shift and have no real potential for recovery: attempts to re-establish P. oceanica there might be a waste of time and money. On the contrary, the meadows farthest from Genoa centre and harbour showed a comparatively low level of phase shift and could still fully recover given specific management actions.

Evidence for adaptive selection acting on the tRNA and rRNA genes of human mitochondrial DNA

In order to identify putative adaptive human mitochondrial DNA (mtDNA), transfer RNA (tRNA), and ribosomal RNA (rRNA) variants, we assembled a sequential mutational tree from 2,460 human mtDNA coding sequences, thus providing the relative age of all mtDNA sequence variants. Deleterious mutations affect evolutionarily conserved nucleotides and have been eliminated from the older internal branches of the tree by purifying selection, while beneficial mutations also alter conserved nucleotides but have been enriched in the internal branches of the tree by adaptive selection. Neutral polymorphisms alter poorly conserved nucleotides and are distributed throughout the tree. Stem nucleotides are more constrained than loop nucleotides. The functional importance of both types of nucleotide variants was assessed by comparison to the average evolutionary conservation index (CI) of all known pathogenic tRNA mutations, thus permitting discrimination between internal branch neutral and adaptive tRNA variants. This revealed that 19% of the stem and 13% of the loop internal branch tRNA variants were potentially adaptive. Since few pathogenic rRNA mutations are known, evidence for adaptive rRNA variation was revealed by higher stem to loop variant ratios and elevated CIs in the internal branches vs. external branches. Moreover, variants among stem noncanonical apposition bases predominantly created new Watson-Crick (WC) base pairs, thus also suggesting adaptive selection. Among the putative adaptive tRNA and rRNA polymorphisms, a number were found to occur at the base of the branches of the tree, to have recurred multiple times, and to be associated with altered human phenotypes. Therefore, a significant portion of ancient tRNA and rRNA polymorphisms appear to have been adaptive, and these are affecting human health today.

Anchoring damage on Posidonia oceanica meadow cover: A case study in Prelo cove (Ligurian Sea, NW Mediterranean)

Among the various types of human activities, the mechanical damages resulting from uncontrolled pleasure boats anchoring in shallow coastal waters would appear to be responsible for localized regressions of Posidonia oceanica meadows. This paper aims to describe and quantify the impacts of a large anchoring chains system on the structure of the P. oceanica meadow of Prelo cove (Ligurian Sea, NW Mediterranean). In this study, we provide evidence that this chains system had a negative effect on the meadow cover, generating dead ‘matte’ areas within the meadow. Meadow structure mapping, combined with the use of an environmental index (Conservation Index), which is linked to the proportional abundance of dead matte relative to living P. oceanica, underpins significant differences in the cover and in the conservation status of the meadow between areas characterized by the presence of the chains and areas without the chains. We also show that the chains affected the meadow in different ways according to P. oceanica cover. The approach proposed here, based on thematic mapping and a simple environmental index, provides relevant information for management actions on the conservation of Posidonia oceanica meadows.

RESIDUE CONSERVATION INFORMATION FOR GENERATING NEAR-NATIVE STRUCTURES IN PROTEIN–PROTEIN DOCKING

Protein-protein docking algorithms typically generate large numbers of possible complex structures with only a few of them resembling the native structure. Recently (Duan et al., Protein Sci, 14:316-218, 2005), it was observed that the surface density of conserved residue positions is high at the interface regions of interacting protein surfaces, except for antibody-antigen complexes, where a lesser number of conserved positions than average is observed at the interface regions. Using this observation, we identified putative interacting regions on the surface of interacting partners and significantly improved docking results by assigning top ranks to near-native complex structures. In this paper, we combine the residue conservation information with a widely used shape complementarity algorithm to generate candidate complex structures with a higher percentage of near-native structures (hits). What is new in this work is that the conservation information is used early in the generation stage and not only in the ranking stage of the docking algorithm. This results in a significantly larger number of generated hits and an improved predictive ability in identifying the native structure of protein-protein complexes. We report on results from 48 well-characterized protein complexes, which have enough residue conservation information from the same 59 benchmark complexes used in our previous work. We compute conservation indices of residue positions on the surfaces of interacting proteins using available homologous sequences from UNIPROT and calculate the solvent accessible surface area. We combine this information with shape-complementarity scores to generate candidate protein-protein complex structures. When compared with pure shape-complementarity algorithms, performed by FTDock, our method results in significantly more hits, with the improvement being over 100% in many instances. We demonstrate that residue conservation information is useful not only in refinement and scoring of docking solutions, but also helpful in enrichment of near-native-structures during the generation of candidate geometries of complex structures.

Establishing a multi-stakeholder value index in medicinal plants—an economic study on selected plants in Kerala and Tamilnadu States of India

In India, medicinal plants are valued for cultural reasons, non-monetary utilitarian purposes (food and medicine), industrial demand, and as a subset of the national biodiversity wealth. National policies to regulate the access and use in medicinal plants are to be framed in line with international regulations like Intellectual property rights and the Convention on Biodiversity. This requires prioritising between the numerous species using relevant indicators that may be market or non-market based. In this study, an attempt is made to prioritise between 18 medicinal plants selected on the basis of economic importance and endemicity in the states of Kerala and Tamilnadu. The prioritisation is done through a Value Index. Data was collected (for the year 2001) through personal interviews using individual questionnaires for the different stakeholders identified as those who gain utilitarian value from medicinal plants (tribal communities, vaidyas (shamans/native healers), Ayurvedic pharmacies, non-governmental and government organizations, exporters). The value index was developed based on scores assigned for different factors influencing the value of medicinal plants related to the different stakeholders. The factors are categorized into domestic and international variables, like domestic and international market demand, non-monetary factors and impact of benefit sharing. The contingency table of the scores for different species, analysed using Simple Correspondence Analysis provided positive (for international variables) and negative (for domestic variables) weights for different variables, indicating the contrasting variables that influence the value of a medicinal plant. In order to highlight the predominant utilities of the selected medicinal plants, the value index is decomposed into market and conservation index values. Results indicated that inclusion of perceptions of different stakeholders helps to prioritise investment decisions on medicinal plants, based on whether State desires to promote species in demand in the domestic market, international market or development of novel products based on use of medicinal plant species in indigenous communities. In addition, including benefit-sharing mechanisms into the frame of reference for the selected plants also highlights the utility of benefit sharing in sustaining indigenous traditions (by increasing value perception) through economic options.

Biodiversity Hotspots and Conservation Priorities in the Campo-Ma’an Rain Forests, Cameroon

Until recently, patterns of species richness and endemism were based on an intuitive interpretation of distribution maps with very limited numerical analyses. Such maps based solely on taxonomic collections tend to concentrate on collecting efforts more than biodiversity hotspots, since often the highest diversity is found in well-collected areas. During the last decades, there has been an overwhelming concern about the loss of tropical forest biological diversity, and an emphasis on the identification of biodiversity hotspots in an attempt to optimise conservation strategies. Furthermore, the concept of sites of high diversity, or hotspots, has attracted the attention of conservationists as a tool for conservation priority settings. With the development of GIS tools, geostatistics, phytosociological and multivariate analysis software packages, more rigorous numerical analyses of distributional and inventory data can be used for assessing conservation priorities. In the Campo-Ma’an rain forest, inventory data from 147 plots of 0.1 ha each and 7137 taxonomic collections were used to examine the distribution and convergence patterns of strict and narrow endemic species. We analysed the trends in endemic and rare species recorded, using quantitative conservation indices such as Genetic Heat Index (GHI) and Pioneer Index (PI), together with geostatistic techniques that help to evaluate and identify potential areas of high conservation priority. The results showed that the Campo-Ma’an area is characterised by a rich and diverse flora with 114 endemic plant species, of which 29 are restricted to the area, 29 also occur in southwestern Cameroon, and 56 others that are also found in other parts of Cameroon. Although most of the forest types rich in strict and narrow endemic species occur in the National Park, there are other biodiversity hotspots in the coastal zone and in areas such as Mont d’Elephant and Massif des Mamelles that are located outside the National Park. Unfortunately, these areas, supporting 17 strict endemic species that are not found in the park, are under serious threat and do not have any conservation status for the moment. Taking into consideration that with the growing human population density, pressure on these hotspots will increase in the near future, it is suggested that priority be given to the conservation of these areas and that a separate management strategy be developed to ensure their protection.

Industrial Research Institute's R&D Trends Forecast for 2006

As IRI member continue to invest more in and to expand growth opportunities through and external collaboration, this year's trends look even better than last year's. Despite high fuel costs, the annual Trends Forecast for conducting U.S.-based looks more favorable than it has for the past three years. Although the 2006 trends were being collected while the dollar hit a 25-month high against the euro and the yen, gas prices topped $3 a gallon and Hurricane Katrina blasted New Orleans and other Gulf cities, the results reveal a general shift to higher spending on with even more emphasis on new and less on supporting existing business. Total company expenditures (Q1) is expected to increase again, though it may not be keeping pace fully with revenue growth. Of the member responding, 25% expect their intensity (Your targeted R&D/sales ratio, Q9a) to decrease and 57% expect it to remain flat for 2006. Investment in new-business projects (Q3c) continues to accelerate at what seems to be the expense of of existing business (Q3a). The 2006 forecast continues to show more willing to make larger overhead commitments by increasing the R&D professional personnel (Q4) and hiring new graduates (Q5). Possibly this is in anticipation of the upcoming retirement bubble as baby boomers look to retire in the next few years, or more likely to meet the current needs for growth and innovation. There continues to be an emphasis on increasing university research, both in participation in consortia for precompetitive university research (Q9e) as well as grants, contracts, etc. for university research (Q9b). Outsourcing to other companies (Q6) also continues to show strong growth. Trends Analysis-Looking to 2006 This is the 22nd year for the IRI Trends Forecast. It is based on 103 surveys collected from 196 member companies, of which 93 have in the United States. The first part of this paper will focus on only the U.S. surveys, which asked the to estimate the relative change in their level of: expenditures, effort allocation, personnel, etc. between what they have done in 2005 and what they plan to do in 2006. The data for the survey were collected during August and September 2005. Being a voluntary survey, the mix of shifts from year to year, reducing the significance of any comparative statistics. Even though the mix of that participate in the survey changes somewhat each year, a chi-squared analysis was conducted comparing the 2006 survey results to the 2005 results (1). Based on a 99% confidence limit, percentages for each interval are statistically different from the prior year and as we examine the data we see expectations increasing during 2006 for: * spending to support (Q3c), and * Participation in consortia for pre-competitive university (Q9c), and slightly down from 2005 for: * spending to support existing (Q3a). Lowering the confidence limit to 95% showed additional expectations increasing during 2006 for: * spending to support directed basic (Q3b), * professional personnel level (Q4), and * Licensing technology from others (dollar volume) (Q7), and flattening from 2005 for: * Spin-offs based on developed technology (Q9g). The Sea Change Index, which was started in 2000, is calculated by taking the difference between the percentage of predicting no change to a decrease and the percentage of predicting a 5% or greater increase in the coming year. This is a rather conservative index in that it excludes the number of forecasting an increase of up to but not including 5%. …

수자원의 지속가능성 평가 지수 개발과 구성 요소의 중요도 평가

지속가능한 수자원 이용과 관리를 위해서는 유역 내에서 진행되고 있는 수자원과 관련된 활동들이 지속가능한 개발의 개념에 부합하는지 여부를 판단해야 한다. 이를 위해서는 유역의 수자원 이용과 관리에 영향을 미치는 수문, 수질, 사회, 경제 및 환경 요인을 고려한 평가지수가 필요하다. 본 연구에서는 수자원의 지속가능성을 평가할 수 있는 지표들을 선정하고 이들을 통합한 수자원 지속가능성 지수(Water Resources Sustainability Index, WRSI)를 개발하였다. WRSI를 구성하는 구성요소의 중요도(Weight)는 계층적 분석기법(Analytic Hierarchy Process, AHP)을 사용하여 결정하였다 수자원의 지속가능성을 세부적으로 평가하기 위하여 WRSI를 경제적 효율성, 사회적 공평성, 환경적 보전성, 유지관리능력 등 4개 세부기준으로 구분하였다. 세부지수의 구성 지표는 유역조사, 사회 및 경제 통계, 여론조사 및 관련된 선행 연구결과를 분석하고 적합성을 평가한 후 선정하였다. WRSI 구성요소들의 중요도는 127명의 전문가들을 대상으로 설문조사를 실시하여 결정하였다. 세부지수와 구성 지표의 중요도 분석결과는 수자원의 지속 가능한 이용을 위해서 수자원 이용의 효율성과 공평성 증대, 하천 수질을 향상시켜 친수 기능의 복원이 중요하다는 것을 나타냈다. 또한, 수자원 분야에 지속적으로 적정 재원의 투입이 필요하며, 수자원 정책 결정에 대한 주민들의 참여가 필요하다는 것을 나타냈다. To assess the water resources sustainability, many indicators and methodologies have been suggested by international organizations and developed in other countries. However, in the previous studies, some of indicators were unsuitable for assessing the sustainability of water use and management in Korea. Thus, in this study nSl(Water Resources Sustainability Index), a multi-variable index, was created by consideration of environmental, social, and economical criteria. Relative weights for components, indicators and sub-indexes, were determined by employing the Analytic Hierarchy Process. In order to extract the indicators related with water resources sustainability, the data related with water resources and indicators suggested in various field were compared and thoroughly reviewed. These indicators were classified into four groups; Economic Efficiency Index, Social Equity Index, Environmental Conservation Index, and Maintenance Capability Index. The weight of each component were decided by the survey of 127 specialists in water resources and sustainability. The result of survey represented that efficiency and equity of water use and water quality for river restoration are major issues in enhancing the water resources sustainability In addition, it was found that investment and public participation should be considered for sustainable water use.

A QUANTITATIVE ANALYSIS OF INTERFACIAL AMINO ACID CONSERVATION IN PROTEIN-PROTEIN HETERO COMPLEXES

A long-standing question in molecular biology is whether interfaces of protein-protein complexes are more conserved than the rest of the protein surfaces. Although it has been reported that conservation can be used as an indicator for predicting interaction sites on proteins, there are recent reports stating that the interface regions are only slightly more conserved than the rest of the protein surfaces, with conservation signals not being statistically significant enough for predicting protein-protein binding sites. In order to properly address these controversial reports we have studied a set of 28 well resolved hetero complex structures of proteins that consists of transient and non-transient complexes. The surface positions were classified into four conservation classes and the conservation index of the surface positions was quantitatively analyzed. The results indicate that the surface density of highly conserved positions is significantly higher in the protein-protein interface regions compared with the other regions of the protein surface. However, the average conservation index of the patches in the interface region is not significantly higher compared with other surface regions of the protein structures. This finding demonstrates that the number of conserved residue positions is a more appropriate indicator for predicting protein-protein binding sites than the average conservation index in the interacting region. We have further validated our findings on a set of 59 benchmark complex structures. Furthermore, an analysis of 19 complexes of antigen-antibody interactions shows that there is no conservation of amino acid positions in the interacting regions of these complexes, as expected, with the variable region of the immunoglobulins interacting mostly with the antigens. Interestingly, antigen interacting regions also have a higher number of non-conserved residue positions in the interacting region than the rest of the protein surface.

Examining Flake Production Strategies: Examples from the Middle Paleolithic of Southwest Asia

Recent studies of Middle Paleolithic technology suggests that raw material resource constraints are visible in the morphological variation of stone tool assemblages. This study focuses on five Middle Paleolithic assemblages (Warwasi Rocksheiter, Bisitun Cave, Tabun Cave, Skuhl Cave, and Ksar Akil Rockshelter) from two regions (Zagros and Levant), which have previously shown substantial technological differences suggesting a disparity in raw material availability. Differences in raw material availability will be emphasized through the identification of changes in blank production that may be sensitive to resource constraints. A conservation index is developed to investigate possible behavioral responses to raw material scarcity. The conservative nature of blank production is highlighted as well as the effect of different patterns of blank production on resource use. Finally, the investigation of innovative blank production strategies and core reduction sequences may reflect a conscious effort by Middle Paleolithic flintknappers to economize resources in the face of lithic resource constraints.

An Automated System for the Analysis of G Protein-Coupled Receptor Transmembrane Binding Pockets: Alignment, Receptor-Based Pharmacophores, and Their Application

G protein-coupled receptors (GPCRs) share a common architecture consisting of seven transmembrane (TM) domains. Various lines of evidence suggest that this fold provides a generic binding pocket within the TM region for hosting agonists, antagonists, and allosteric modulators. Here, a comprehensive and automated method allowing fast analysis and comparison of these putative binding pockets across the entire GPCR family is presented. The method relies on a robust alignment algorithm based on conservation indices, focusing on pharmacophore-like relationships between amino acids. Analysis of conservation patterns across the GPCR family and alignment to the rhodopsin X-ray structure allows the extraction of the amino acids lining the TM binding pocket in a so-called ligand binding pocket vector (LPV). In a second step, LPVs are translated to simple 3D receptor pharmacophore models, where each amino acid is represented by a single spherical pharmacophore feature and all atomic detail is omitted. Applications of the method include the assessment of selectivity issues, support of mutagenesis studies, and the derivation of rules for focused screening to identify chemical starting points in early drug discovery projects. Because of the coarseness of this 3D receptor pharmacophore model, however, meaningful scoring and ranking procedures of large sets of molecules are not justified. The LPV analysis of the trace amine-associated receptor family and its experimental validation is discussed as an example. The value of the 3D receptor model is demonstrated for a class C GPCR family, the metabotropic glutamate receptors.

Developing a Conservation Index for lakes in India

Developing a Conservation Index for lakes in India

Gene Expression Evolves Faster in Narrowly Than in Broadly Expressed Mammalian Genes

Despite much recent interest, it remains unclear what determines the rate of evolution of gene expression. To study this issue we develop a new measure, called "Expression Conservation Index" (ECI), to quantify the degree of tissue-expression conservation between two homologous genes. Applying this measure to a large set of gene expression data from human and mouse, we show that tissue expression tends to evolve rapidly for genes that are expressed in only a limited number of tissues, whereas tissue expression can be conserved for a long time for genes expressed in a large number of tissues. Therefore, expression breadth is an important determinant for evolutionary conservation of tissue expression. In addition, we find a rapid decrease in ECI with the synonymous divergence between duplicate genes, suggesting fast divergence in tissue expression between duplicate genes.

A novel approach to assess the impact of landuse activity on chemical and biological parameters in river catchments

Summary1. Natural variation in environmental parameters, as well as practical constraints in study design and sampling methodology, often pose difficulties in treating impact assessments in river catchments as controlled field experiments. It is frequently impossible to develop robust relationships between reference and test stations prior to the onset of an impact and the range of statistical tools which can be adopted in data analysis to detect a change or disturbance is limited.2. In an attempt to overcome these problems we introduce a novel disturbance index to assess the impact of landuse activities on river systems. The index identifies differences in hydrochemical parameters and macroinvertebrate community metrics between reference and test stations (at a set level of significance). This approach allows for objective assessment of the occurrence and direction of change as well as the duration of an impact. The disturbance index can be applied at different scales – for a single stream, a catchment or a region.3. In this paper we describe the derivation of the index and illustrate its utility through worked examples. We use the index to assess impact of clearfelling on hydrochemical parameters such as hydrogen ion concentration, total hardness, suspended solids, conductivity and nitrate concentration as well as on macroinvertebrate parameters including abundance, richness, reciprocal of Simpson's diversity index, evenness, Ephemeroptera/Plecoptera/Trichoptera (EPT) richness and percentage of EPT taxa.4. The sensitivity of the disturbance index changes with scale of application however, and the clearfelling (CF) index has proven sensitive to the detection of even quite small changes, although in these cases ecological significance should be considered. We show that the CF index, particularly when derived from a regional scale, is a conservative index but is very robust to variation in the number of samples used in its derivation. The application of the index corresponded very well with the application of more standard statistical approaches. We believe that the index can thus be applied to other impact studies with similar project design.

Effect of Nitrogen Supply on the Nitrogen Use Efficiency of an Annual Herb, Helianthus annuus L.

Abstract: Nitrogen use efficiency (NUE) is the product of nitrogen productivity (NP) and the mean residence time of nitrogen (MRT). Theory suggests that there should be a trade-off between both components, but direct experimental evidence is still scarce. To test this hypothesis, we analyzed the effect of varying nitrogen supply levels on NUE and its two components (NP, MRT) in Helianthus annuus L., an annual herb. The plants investigated were subjected to six nitrogen levels (0, 2, 4, 8, 16, and 32 g N/m2). Total plant production increased substantially with increasing nitrogen supply. Nitrogen uptake and loss also increased with nitrogen supply. Nitrogen influx (rin) and outflux (rout) were defined as the rates of nitrogen uptake and loss per unit aboveground nitrogen, respectively. Both rm and rout increased with increasing nitrogen supply. In addition, rm was far higher than rout. Consequently, the relative rate of nitrogen increment (rin-rout) also increased with nitrogen supply. There were marked differences between treatments with respect to parameters related to the stress resistance syndrome: nitrogen pool size, leaf nitrogen concentration, and net aboveground productivity increased with nitrogen supply. Plants at high nitrogen levels showed a higher NP (the growth rate per unit aboveground nitrogen) and a shorter MRT (the inverse of rout), whereas plants at low nitrogen levels displayed the reverse pattern. Shorter MRT for plants at high nitrogen levels was caused by the abscission of leaves that contained relatively large fractions of total plant nitrogen. We found a negative relationship between NP and MRT, the components of NUE, along the gradient of nitrogen availability, suggesting that there was a trade-off between NP and MRT. The NUE increased with increasing nitrogen availability, up to a certain level, and then decreased. These results offer support for the hypothesis that adaptation to infertile habitats involves a low nitrogen loss (long MRT in the plant) rather than a high NUE per se. The higher NUE at the plant level was a result, in part, of greater nitrogen resorption during senescence. We suggest that a long MRT (an index of nitrogen conservation) is a potentially successful strategy in nitrogen-poor environments. (Managing editor: Ya-Qin HAN)