How Common Are Intragene Windows with <Emphasis Type="Italic">K</Emphasis><Subscript>A</Subscript> > <Emphasis Type="Italic">K</Emphasis><Subscript>S</Subscript> Owing to Purifying Selection on Synonymous Mutations?

One method for diagnosing the mode of sequence evolution considers the ratio of nonsynonymous substitutions per nonsynonymous site (K _A) to the corresponding figure for synonymous substitutions (K _S). A ratio (K _A/K _S) greater than unity is taken as evidence for positive selection. This, however, need not necessarily be the case. Notably, there is one instance of a high intragenic K _A/K _S peak, revealed by sliding window analysis and observed in two pairwise comparisons, better accounted for by localised purifying selection on synonymous mutations that affect splicing. Is this example exceptional? To address this we isolate intragenic domains with K _A/K _S > 1 from more than 1000 long mouse-rat orthologues. Approximately one K _A/K _S > 1 peak is found per 12–15 kb of coding sequence. Surprisingly, low synonymous substitution rates underpin more incidences than do high nonsynonymous rates. Several reasons, however, prevent us from supposing that the low synonymous rates reflect purifying selection on synonymous mutations. First, for many peaks, the null that the peak is no higher than expected given the underlying rates of evolution, cannot be rejected. Second, of 18 statistically significant incidences with unusually low K _S values, only 3 are repeatable across independent comparisons. At least two of these are within alternatively spliced exons. We conclude that repeatable statistically significant intragenic domains of low intragenic K _S are rare. As so few K _A/K _S peaks reflect increased rates of protein evolution and so few hold statistical support, we additionally conclude that sliding window analysis to infer domains of positive selection is highly error-prone.     

Serology and gene sequence analysis of rare subgroup A3 blood group

To investigate the serological phenotypic characteristics and possible mechanism of subgroup A₃, a blood donor's ABO phenotypes were detected by the conventional microcolumn gel method and classic tube method. N-acetylgalactosaminyl transferase activity was detected by the non-radioactive phosphate coupling method. ABO subtype genotyping was determined by PCR-SSP and exons 1-7 of ABO gene were analyzed by Sanger sequencing. The donor's blood type was subgroup A₃ as evaluated by serological test. There was no N-acetylgalactosaminyl transferase activity in the red blood cells and weak N-acetylgalactosaminyl transferase activity in the plasma. The ABO blood group genotyping result was ABO*AO1, and the gene sequencing result was confirmed as A221/O01. Sequencing results showed two mutations, 467C>T and 607G>A in exon 7 in ABO*A allele. In conclusion, it is suggested that the ABO blood group of the donor be subgroup A₃, which may be induced by mutations 467C>T and 607G>A, and led to a decrease in N-acetylgalactosaminyl transferase activity and resulted in weakened A antigen.     

The adaptive evolution database (TAED)

Background

The Master Catalog is a collection of evolutionary families, including multiple sequence alignments, phylogenetic trees and reconstructed ancestral sequences, for all protein-sequence modules encoded by genes in GenBank. It can therefore support large-scale genomic surveys, of which we present here The Adaptive Evolution Database (TAED). In TAED, potential examples of positive adaptation are identified by high values for the normalized ratio of nonsynonymous to synonymous nucleotide substitution rates (K_A/K_S values) on branches of an evolutionary tree between nodes representing reconstructed ancestral sequences.

Results

Evolutionary trees and reconstructed ancestral sequences were extracted from the Master Catalog for every subtree containing proteins from the Chordata only or the Embryophyta only. Branches with high K_A/K_S values were identified. These represent candidate episodes in the history of the protein family when the protein may have undergone positive selection, where the mutant form conferred more fitness than the ancestral form. Such episodes are frequently associated with change in function. An unexpectedly large number of families (between 10% and 20% of those families examined) were found to have at least one branch with high K_A/K_S values above arbitrarily chosen cut-offs (1 and 0.6). Most of these survived a robustness test and were collected into TAED.

Conclusions

TAED is a raw resource for bioinformaticists interested in data mining and for experimental evolutionists seeking candidate examples of adaptive evolution for further experimental study. It can be expanded to include other evolutionary information (for example changes in gene regulation or splicing) placed in a phylogenetic perspective.     

Different alternative splicing patterns are subject to opposite selection pressure for protein reading frame preservation

Background  

Alternative splicing (AS) has been regarded capable of altering selection pressure on protein subsequences. Particularly, the frequency of reading frame preservation (FRFP), as a measure of selection pressure, has been reported to be higher in alternatively spliced exons (ASEs) than in constitutively spliced exons (CSEs). However, recently it has been reported that different ASE types – simple and complex ASEs – may be subject to opposite selection forces. Therefore, it is necessary to re-evaluate the evolutionary effects of such splicing patterns on frame preservation.     

Size-dependent variability of leaf and shoot hydraulic conductance in silver birch

Variation in leaf and shoot hydraulic conductance was examined on detached shoots of silver birch (Betula pendula Roth), cut from the lower third (shade leaves) and upper third of the crown (sun leaves) of large trees growing in a natural temperate forest stand. Hydraulic conductances of whole shoots (K _S), leaf blades (K _lb), petioles (K _P) and branches (i.e. leafless stem; K _B) were determined by water perfusion using a high-pressure flow meter in quasi-steady state mode. The shoots were exposed to irradiance of photosynthetic photon flux density of 200–250 μmol m⁻² s⁻¹, using different light sources. K _lb depended significantly (P < 0.001) on light quality, canopy position and leaf blade area (A _L). K _lb increased from crown base to tree top, in parallel with vertical patterns of A _L. However, the analysis of data on shade and sun leaves separately revealed an opposite trend: the bigger the A _L the higher K _lb. Leaf anatomical study of birch saplings revealed that this trend is attributable to enhanced vascular development with increasing leaf area. Hydraulic traits (K _S, K _B, K _lb) of sun shoots were well co-ordinated and more strongly correlated with characteristics of shoot size than those of shade shoots, reflecting their greater evaporative load and need for stricter adjustment of hydraulic capacity with shoot size. K _S increased with increasing xylem cross-sectional area to leaf area ratio (Huber value; P < 0.01), suggesting a preferential investment in water-conducting tissue (sapwood) relative to transpiring tissue (leaves), and most likely contributing to the functional stability of the hydraulic system, essential for fast-growing pioneer species.     

Independent effects of alternative splicing and structural constraint on the evolution of mammalian coding exons

Alternative splicing (AS) is known to significantly affect exon-level protein evolutionary rates in mammals. Particularly, alternatively spliced exons (ASEs) have a higher nonsynonymous-to-synonymous substitution rate (dN/dS) ratio than constitutively spliced exons (CSEs), possibly because the former are required only occasionally for normal biological functions. Meanwhile, intrinsically disordered regions (IDRs), the protein regions lacking fixed 3D structures, are also reported to have an increased evolutionary rate due to lack of structural constraint. Interestingly, IDRs tend to be located in alternative protein regions. Yet which of these two factors is the major determinant of the increased dN/dS in mammalian ASEs remains unclear. By comparing human-macaque and human-mouse one-to-one orthologous genes, we demonstrate that AS and protein structural disorder have independent effects on mammalian exon evolution. We performed analyses of covariance to demonstrate that the slopes of the (dN/dS-percentage of IDR) regression lines differ significantly between CSEs and ASEs. In other words, the dN/dS ratios of both ASEs and CSEs increase with the proportion of IDR (PIDR), whereas ASEs have higher dN/dS ratios than CSEs when they have similar PIDRs. Since ASEs and IDRs may less frequently overlap with protein domains (which also affect dN/dS), we also examined the correlations between dN/dS ratio and exon type/PIDR by controlling for the density of protein domain. We found that the effects of exon type and PIDR on dN/dS are both independent of domain density. Our results imply that nature can select for different biological features with regard to ASEs and IDRs, even though the two biological features tend to be localized in the same protein regions.     

Structural elucidation, modification and characterization of seed gum from Cassia javahikai seeds: A non-traditional source of industrial gums

A water-soluble seed gum was isolated from seed endosperm of Cassia javahikai. The acid-catalyzed fragmentation, methylation, selective enzymatic degradation and periodate oxidation suggested a heteropolymeric structure for the polysaccharide. The polysaccharide was shown to have a linear chain of β(1 → 4) linked d-mannopyranosyls units with side chains of α(1 → 6) d-galactopyranosyl units. Grafting of polyacrylamide onto the gum was performed using K₂S₂O₈/ascorbic acid redox system in presence of Ag⁺ as catalyst at 35 ± 2 °C. The viscosity of the gum solution increased on grafting and the grafted gum was observed to resist biodegradation for more than 256 h. Thermogravimetric analysis revealed that grafted gum was more thermally stable than native gum.     

Using ESTs to improve the accuracy of de novo gene prediction

Background  

ESTs are a tremendous resource for determining the exon-intron structures of genes, but even extensive EST sequencing tends to leave many exons and genes untouched. Gene prediction systems based exclusively on EST alignments miss these exons and genes, leading to poor sensitivity. De novo gene prediction systems, which ignore ESTs in favor of genomic sequence, can predict such "untouched" exons, but they are less accurate when predicting exons to which ESTs align. TWINSCAN is the most accurate de novo gene finder available for nematodes and N-SCAN is the most accurate for mammals, as measured by exact CDS gene prediction and exact exon prediction.     

Hydraulic adjustment of maple saplings to canopy gap formation

The leaf-specific hydraulic conductivity (K _L) of plant stems can control leaf water supply. This property is influenced by variation in leaf/sapwood area ratio (A _L/A _S) and the specific hydraulic conductivity of xylem tissue (K _S). In environments with high atmospheric vapor pressure deficit (VPD), K _L may increase to support higher transpiration rates. We predicted that saplings of Acerrubrum and A.pensylvanicum grown in forest canopy gaps, under high light and VPD, would have higher K _L and lower A _L/A _S than similar sized saplings in the understory. Leaf-specific hydraulic conductivity and K _S increased with sapling size for both species. In A. rubrum, K _S did not differ between the two environments but lower A _L/A _S (P=0.05, ANCOVA) led to higher K _L for gap-grown saplings (P < 0.05, ANCOVA). In A. pensylvanicum, neither K _S, A _L/A _S, nor K_L differed between environments. In a second experiment, we examined the impact of sapling size on the water relations and carbon assimilation of A.pensylvanicum. Maximum stomatal conductance for A.pensylvanicum increased with K _L (r ²=0.75, P < 0.05). A hypothetical large A. pensylvanicum sapling (2 m tall) had 2.4 times higher K _L and 22 times greater daily carbon assimilation than a small (1 m tall) sapling. Size-related hydraulic limitations in A.pensylvanicum caused a 68% reduction in daily carbon assimilation in small saplings. Mid-day water potential increased with A.pensylvanicum sapling size (r ²=0.69, P < 0.05). Calculations indicated that small A.pensylvanicum saplings (low K _L) could not transpire at the rate of large saplings (high K _L) without reaching theoretical thresholds for xylem embolism induction. The coordination between K _L and stomatal conductance in saplings may prevent xylem water potential from reaching levels that cause embolism but also limits transpiration. The K _S of the xylem did not vary across environments, suggesting that altering biomass allocation is the primary mechanism of increasing K _L. However, the ability to alter aboveground biomass allocation in response to canopy gaps is species-specific. As a result of the increase in K _L and K _S with sapling size for both species, hydraulic limitation of water flux may impose a greater restriction on daily carbon assimilation for small saplings in the gap environment. Received: 18 February 1997 / Accepted: 23 June 1997     

Recent improvements in the development of A2B adenosine receptor agonists

Adenosine is known to exert most of its physiological functions by acting as local modulator at four receptor subtypes named A₁, A_2A, A_2B and A₃ (ARs). Principally as a result of the difficulty in identifying potent and selective agonists, the A_2B AR is the least extensively characterised of the adenosine receptors family. Despite these limitations, growing understanding of the physiological meaning of this target indicates promising therapeutic perspectives for specific ligands. As A_2B AR signalling seems to be associated with pre/postconditioning cardioprotective and anti-inflammatory mechanisms, selective agonists may represent a new therapeutic group for patients suffering from coronary artery disease. Herein we present an overview of the recent advancements in identifying potent and selective A_2B AR agonists reported in scientific and patent literature. These compounds can be classified into adenosine-like and nonadenosine ligands. Nucleoside-based agonists are the result of modifying adenosine by substitution at the N ⁶-, C²-positions of the purine heterocycle and/or at the 5′-position of the ribose moiety or combinations of these substitutions. Compounds 1-deoxy-1-{6-[N′-(furan-2-carbonyl)-hydrazino]-9H-purin-9-yl}-N-ethyl-β-D-ribofuranuronamide (19, hA₁ K _i = 1050 nM, hA_2A K _i = 1550 nM, hA_2B EC₅₀ = 82 nM, hA₃ K _i > 5 μM) and its 2-chloro analogue 23 (hA₁ K _i = 3500 nM, hA_2A K _i = 4950 nM, hA_2B EC₅₀ = 210 nM, hA₃ K _i > 5 μM) were confirmed to be potent and selective full agonists in a cyclic adenosine monophosphate (cAMP) functional assay in Chinese hamster ovary (CHO) cells expressing hA_2B AR. Nonribose ligands are represented by conveniently substituted dicarbonitrilepyridines, among which 2-[6-amino-3,5-dicyano-4-[4-(cyclopropylmethoxy)phenyl]pyridin-2-ylsulfanyl]acetamide (BAY-60–6583, hA₁, hA_2A, hA₃ EC₅₀ > 10 μM; hA_2B EC₅₀ = 3 nM) is currently under preclinical-phase investigation for treating coronary artery disorders and atherosclerosis. This article has previously been published in issue 4/4, under doi:.     

Recent improvements in the development of A<Subscript>2B</Subscript> adenosine receptor agonists

Adenosine is known to exert most of its physiological functions by acting as local modulator at four receptor subtypes named A₁, A_2A, A_2B and A₃ (ARs). Principally as a result of the difficulty in identifying potent and selective agonists, the A_2B AR is the least extensively characterised of the adenosine receptors family. Despite these limitations, growing understanding of the physiological meaning of this target indicates promising therapeutic perspectives for specific ligands. As A_2B AR signalling seems to be associated with pre/postconditioning cardioprotective and anti-inflammatory mechanisms, selective agonists may represent a new therapeutic group for patients suffering from coronary artery disease. Herein we present an overview of the recent advancements in identifying potent and selective A_2B AR agonists reported in scientific and patent literature. These compounds can be classified into adenosine-like and nonadenosine ligands. Nucleoside-based agonists are the result of modifying adenosine by substitution at the N ⁶-, C²-positions of the purine heterocycle and/or at the 5′-position of the ribose moiety or combinations of these substitutions. Compounds 1-deoxy-1-{6-[N′-(furan-2-carbonyl)-hydrazino]-9H-purin-9-yl}-N-ethyl-β-D-ribofuranuronamide (19, hA₁ K _i = 1050 nM, hA_2A K _i = 1550 nM, hA_2B EC₅₀ = 82 nM, hA₃ K _i > 5 μM) and its 2-chloro analogue 23 (hA₁ K _i = 3500 nM, hA_2A K _i = 4950 nM, hA_2B EC₅₀ = 210 nM, hA₃ K _i > 5 μM) were confirmed to be potent and selective full agonists in a cyclic adenosine monophosphate (cAMP) functional assay in Chinese hamster ovary (CHO) cells expressing hA_2B AR. Nonribose ligands are represented by conveniently substituted dicarbonitrilepyridines, among which 2-[6-amino-3,5-dicyano-4-[4-(cyclopropylmethoxy)phenyl]pyridin-2-ylsulfanyl]acetamide (BAY-60–6583, hA₁, hA_2A, hA₃ EC₅₀ > 10 μM; hA_2B EC₅₀ = 3 nM) is currently under preclinical-phase investigation for treating coronary artery disorders and atherosclerosis.     

A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes

Background  

Jumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequence S to the multiple alignment or profile as a whole, S is compared and aligned to individual sequences from A. Within this alignment, S can jump between different sequences from A, so different parts of S can be aligned to different sequences from the input multiple alignment. This approach is particularly useful for dealing with recombination events.     

Complete cDNA Sequence, Genomic Structure, and Chromosomal Localization of the LPA Receptor Gene,lpA1/vzg-1/Gpcr26

Thelp_A1/Gpcr26locus encodes the first cloned and identified G-protein-coupled receptor that specifically interacts with lysophosphatidic acid. A murine full-length cDNA of size consistent with that seen on Northern blots (3.7 kb) was determined using 3′ rapid amplification of cDNA ends. Analysis of genomic clones revealed that the gene is divided into five exons, with one intron inserted in the coding region for transmembrane domain VI and one exon encoding the divergent 5′ sequence in another published cDNA clone variant (orphan receptor mrec1.3). This structure differs from the intronless coding region for a homologous receptor,Edg1,but is identical to another more similar orphan receptor (lp_A2) that has been deposited with GenBank. Using backcross analysis, both exons 1 and 4 mapped to a proximal region of murine Chromosome 4 indistinguishable from the vacillans gene. Exon 4 also mapped to a second locus on proximal Chromosome 6 inMus spretus,and this partial duplication was confirmed by Southern blot. The genomic structure indicates a distinct, divergent evolutionary lineage for thevzg-1/lp_A1subfamily of receptors compared to those of homologous orphan receptor genes.     

Evolutionary Patterns and Selective Pressures of Odorant/Pheromone Receptor Gene Families in Teleost Fishes

Background

Teleost fishes do not have a vomeronasal organ (VNO), and their vomeronasal receptors (V1Rs, V2Rs) are expressed in the main olfactory epithelium (MOE), as are odorant receptors (ORs) and trace amine-associated receptors (TAARs). In this study, to obtain insights into the functional distinction among the four chemosensory receptor families in teleost fishes, their evolutionary patterns were examined in zebrafish, medaka, stickleback, fugu, and spotted green pufferfish.

Methodology/Principal Findings

Phylogenetic analysis revealed that many lineage-specific gene gains and losses occurred in the teleost fish TAARs, whereas only a few gene gains and losses have taken place in the teleost fish vomeronasal receptors. In addition, synonymous and nonsynonymous nucleotide substitution rate ratios (K_A/K_S) in TAARs tended to be higher than those in ORs and V2Rs.

Conclusions/Significance

Frequent gene gains/losses and high K_A/K_S in teleost TAARs suggest that receptors in this family are used for detecting some species-specific chemicals such as pheromones. Conversely, conserved repertoires of V1R and V2R families in teleost fishes may imply that receptors in these families perceive common odorants for teleosts, such as amino acids. Teleost ORs showed intermediate evolutionary pattern between TAARs and vomeronasal receptors. Many teleost ORs seem to be used for common odorants, but some ORs may have evolved to recognize lineage-specific odors.     

Of mice and mammoths: generality and antiquity of the island rule

Aim

We assessed the generality of the island rule in a database comprising 1593 populations of insular mammals (439 species, including 63 species of fossil mammals), and tested whether observed patterns differed among taxonomic and functional groups.

Location

Islands world‐wide.

Methods

We measured museum specimens (fossil mammals) and reviewed the literature to compile a database of insular animal body size (S_i = mean mass of individuals from an insular population divided by that of individuals from an ancestral or mainland population, M). We used linear regressions to investigate the relationship between S_i and M, and ANCOVA to compare trends among taxonomic and functional groups.

Results

S_i was significantly and negatively related to the mass of the ancestral or mainland population across all mammals and within all orders of extant mammals analysed, and across palaeo‐insular (considered separately) mammals as well. Insular body size was significantly smaller for bats and insectivores than for the other orders studied here, but significantly larger for mammals that utilized aquatic prey than for those restricted to terrestrial prey.

Main conclusions

The island rule appears to be a pervasive pattern, exhibited by mammals from a broad range of orders, functional groups and time periods. There remains, however, much scatter about the general trend; this residual variation may be highly informative as it appears consistent with differences among species, islands and environmental characteristics hypothesized to influence body size evolution in general. The more pronounced gigantism and dwarfism of palaeo‐insular mammals, in particular, is consistent with a hypothesis that emphasizes the importance of ecological interactions (time in isolation from mammalian predators and competitors was 0.1 to > 1.0 Myr for palaeo‐insular mammals, but < 0.01 Myr for extant populations of insular mammals). While ecological displacement may be a major force driving diversification in body size in high‐diversity biotas, ecological release in species‐poor biotas often results in the convergence of insular mammals on the size of intermediate but absent species.     

Autotrophic and heterotrophic respiration in needle fir and Quercus-dominated stands in a cool-temperate forest, central Korea

To investigate annual variation in soil respiration (R _S) and its components [autotrophic (R _A) and heterotrophic (R _H)] in relation to seasonal changes in soil temperature (ST) and soil water content (SWC) in an Abies holophylla stand (stand A) and a Quercus-dominated stand (stand Q), we set up trenched plots and measured R _S, ST and SWC for 2 years. The mean annual rate of R _S was 436 mg CO₂ m⁻² h⁻¹, ranging from 76 to 1,170 mg CO₂ m⁻² h⁻¹, in stand A and 376 mg CO₂ m⁻² h⁻¹, ranging from 82 to 1,133 mg CO₂ m⁻² h⁻¹, in stand Q. A significant relationship between R _S and its components and ST was observed over the 2 years in both stands, whereas a significant correlation between R _A and SWC was detected only in stand Q. On average over the 2 years, R _A accounted for approximately 34% (range 17–67%) and 31% (15–82%) of the variation in R _S in stands A and Q, respectively. Our results suggested that vegetation type did not significantly affect the annual mean contributions of R _A or R _H, but did affect the pattern of seasonal change in the contribution of R _A to R _S.     

Interactive effects of elevated CO2 and temperature on water transport inponderosa pine

Many studies report that water flux through trees declines in response to elevated CO₂, but this response may be modified by exposure to increased temperatures. To determine whether elevated CO₂ and temperature interact to affect hydraulic conductivity, we grew ponderosa pine seedlings for 24 wk in growth chambers with one of four atmospheric CO₂ concentrations (350, 550, 750, and 1100 ppm) and either a low (15°C nights, 25°C days) or high (20°C nights, 30°C days) temperature treatment. Vapor pressure deficits were also higher in the elevated temperature treatment. Seedling biomass increased with CO₂ concentration but was not affected by temperature. Root : shoot ratio was unaffected by CO₂ and temperature. Leaf : sapwood area ratio (A_L/A_S) declined in response to elevated temperature but was not influenced by CO₂. Larger tracheid diameters at elevated temperature caused an increase in xylem-specific hydraulic conductivity (K_S). The increase in K_S and decrease in A_L/A_S led to higher leaf-specific hydraulic conductivity (K_L) at elevated temperature. Stomatal conductance (g_S) was correlated with K_L across all treatments. Neither K_S, K_L, nor g_S were affected by elevated CO₂ concentrations. High K_L in response to elevated temperature may support increased transpiration or reduce the incidence of xylem cavitation in ponderosa pine in future, warmer climates.