Significance of Population Size on the Fixation of Nonsynonymous Mutations in Genes Under Varying Levels of Selection Pressure

Previous studies observed a higher ratio of divergences at nonsynonymous and synonymous sites (ω = d_N/d_S) in species with a small population size compared to that estimated for those with a large population size. Here we examined the theoretical relationship between ω, effective population size (N_e), and selection coefficient (s). Our analysis revealed that when purifying selection is high, ω of species with small N_e is much higher than that of species with large N_e. However the difference between the two ω reduces with the decline in selection pressure (s → 0). We examined this relationship using primate and rodent genes and found that the ω estimated for highly constrained genes of primates was up to 2.9 times higher than that obtained for their orthologous rodent genes. Conversely, for genes under weak purifying selection the ω of primates was only 17% higher than that of rodents. When tissue specificity was used as a proxy for selection pressure we found that the ω of broadly expressed genes of primates was up to 2.1-fold higher than that of their rodent counterparts and this difference was only 27% for tissue specific genes. Since most of the nonsynonymous mutations in constrained or broadly expressed genes are deleterious, fixation of these mutations is influenced by N_e. This results in a higher ω of these genes in primates compared to those from rodents. Conversely, the majority of nonsynonymous mutations in less-constrained or tissue-specific genes are neutral or nearly neutral and therefore fixation of them is largely independent of N_e, which leads to the similarity of ω in primates and rodents.     

The Genomic Selfing Syndrome Accompanies the Evolutionary Breakdown of Heterostyly

The evolutionary transition from outcrossing to selfing can have important genomic consequences. Decreased effective population size and the reduced efficacy of selection are predicted to play an important role in the molecular evolution of the genomes of selfing species. We investigated evidence for molecular signatures of the genomic selfing syndrome using 66 species of Primula including distylous (outcrossing) and derived homostylous (selfing) taxa. We complemented our comparative analysis with a microevolutionary study of P. chungensis, which is polymorphic for mating system and consists of both distylous and homostylous populations. We generated chloroplast and nuclear genomic data sets for distylous, homostylous, and distylous–homostylous species and identified patterns of nonsynonymous to synonymous divergence (d_N/d_S) and polymorphism (π_N/π_S) in species or lineages with contrasting mating systems. Our analysis of coding sequence divergence and polymorphism detected strongly reduced genetic diversity and heterozygosity, decreased efficacy of purifying selection, purging of large-effect deleterious mutations, and lower rates of adaptive evolution in samples from homostylous compared with distylous populations, consistent with theoretical expectations of the genomic selfing syndrome. Our results demonstrate that self-fertilization is a major driver of molecular evolutionary processes with genomic signatures of selfing evident in both old and relatively young homostylous populations.     

Structural and dielectric properties of synthetic glycolipids in mixtures with water

Three synthetically produced glycolipids, N-(β-D-glucopyranosyl)-N-octadecyl-stearoylamide (OSGA), N-(β-D-glucopyranosyl-N-octadecyl-oleoylamide (OOGA), N-(β-D-galactopyranosyl)-N-octadecyl-lauroylamide (OLGA) have been studied in different mixtures with water by x-ray diffraction and dielectric measurements with microwaves at 9.4 GHz. The measurements were performed in the temperature range -50-70°C. X-Ray diffraction revealed a direct L_β' → H transition at 20°C, 60°C, and 45°C depending on the glycolipid species but nearly not on the water content. The hexagonal phases are saturated at a water content of ≈20 wt%. The lamellar phase absorbs even less water (< 10 wt%). The dielectric data show that in the H phase the binding of water is stronger than in the L_β' phase. In the temperature range below 0°C, OSGA and OOGA show a “subzero transition” due to the freeze-out of water in a separate ice phase. This transition can be seen in an abrupt decrease of the dielectric function because the dielectric response of ice is much smaller at microwave frequencies. OLGA does not show the subzero transition but an additional transition, hexagonal → distorted hexagonal at 60°C.     

The unstructured C-terminus of the tau subunit of Escherichia coli DNA polymerase III holoenzyme is the site of interaction with the alpha subunit

The τ subunit of Escherichia coli DNA polymerase III holoenzyme interacts with the α subunit through its C-terminal Domain V, τ_C16. We show that the extreme C-terminal region of τ_C16 constitutes the site of interaction with α. The τ_C16 domain, but not a derivative of it with a C-terminal deletion of seven residues (τ_C16Δ7), forms an isolable complex with α. Surface plasmon resonance measurements were used to determine the dissociation constant (K_D) of the α−τ_C16 complex to be ~260pM. Competition with immobilized τ_C16 by τ_C16 derivatives for binding to α gave values of K_D of 7μM for the α−τ_C16Δ7 complex. Low-level expression of the genes encoding τ_C16 and τ_C167, but not τ_C16Δ11, is lethal to E. coli. Suppression of this lethal phenotype enabled selection of mutations in the 3′ end of the τ_C16 gene, that led to defects in α binding. The data suggest that the unstructured C-terminus of τ becomes folded into a helix–loop–helix in its complex with α. An N-terminally extended construct, τ_C24, was found to bind DNA in a salt-sensitive manner while no binding was observed for τ_C16, suggesting that the processivity switch of the replisome functionally involves Domain IV of τ.     

Interactions between the 2.4 and 4.2 regions of sigmaS, the stress-specific sigma factor of Escherichia coli, and the -10 and -35 promoter elements

The σ^s subunit of Escherichia coli RNA polymerase holoenzyme (Eσ^S) is a key factor of gene expression upon entry into stationary phase and in stressful conditions. The selectivity of promoter recognition by Eσ^S and the housekeeping Eσ⁷⁰ is as yet not clearly understood. We used a genetic approach to investigate the interaction of σ^S with its target promoters. Starting with down-promoter variants of a σ^S promoter target, osmEp, altered in the –10 or –35 elements, we isolated mutant forms of σ^S suppressing the promoter defects. The activity of these suppressors on variants of osmEp and ficp, another target of σ^S, indicated that σ^S is able to interact with the same key features within a promoter sequence as σ⁷⁰. Indeed, (i) σ^S can recognize the –35 element of some but not all its target promoters, through interactions with its 4.2 region; and (ii) amino acids within the 2.4 region participate in the recognition of the –10 element. More specifically, residues Q152 and E155 contribute to the strong preference of σ^S for a C in position –13 and residue R299 can interact with the –31 nucleotide in the –35 element of the target promoters.     

Mandarin Speech Perception in Combined Electric and Acoustic Stimulation

For deaf individuals with residual low-frequency acoustic hearing, combined use of a cochlear implant (CI) and hearing aid (HA) typically provides better speech understanding than with either device alone. Because of coarse spectral resolution, CIs do not provide fundamental frequency (F0) information that contributes to understanding of tonal languages such as Mandarin Chinese. The HA can provide good representation of F0 and, depending on the range of aided acoustic hearing, first and second formant (F1 and F2) information. In this study, Mandarin tone, vowel, and consonant recognition in quiet and noise was measured in 12 adult Mandarin-speaking bimodal listeners with the CI-only and with the CI+HA. Tone recognition was significantly better with the CI+HA in noise, but not in quiet. Vowel recognition was significantly better with the CI+HA in quiet, but not in noise. There was no significant difference in consonant recognition between the CI-only and the CI+HA in quiet or in noise. There was a wide range in bimodal benefit, with improvements often greater than 20 percentage points in some tests and conditions. The bimodal benefit was compared to CI subjects’ HA-aided pure-tone average (PTA) thresholds between 250 and 2000 Hz; subjects were divided into two groups: “better” PTA (<50 dB HL) or “poorer” PTA (>50 dB HL). The bimodal benefit differed significantly between groups only for consonant recognition. The bimodal benefit for tone recognition in quiet was significantly correlated with CI experience, suggesting that bimodal CI users learn to better combine low-frequency spectro-temporal information from acoustic hearing with temporal envelope information from electric hearing. Given the small number of subjects in this study (n = 12), further research with Chinese bimodal listeners may provide more information regarding the contribution of acoustic and electric hearing to tonal language perception.     

Stacking Interactions of nucleobases: NMR-Investigations I. Selfassociation of N6,N9-Dimethyladenine and N6-Dimethyl-N9-Ethyladenine

The selfassociation of N⁶,N⁹-dimethyladenine and N⁶-dimethyl-N⁹-ethyladenine has been studied by means of NMR technique. The thermodynamic quantities have been calculated using an isodesmic NMR model with three NMR parameters (the monomer shift _M and two complex shifts ₂ and ₃).The dependence of the thermodynamic quantities on the NMR parameters is discussed. Special attention is given to the determination of _M and its temperature dependence.Calculations with ₃=2· ₂ and _M taken independently of temperature result in an average entropy _S =–17.9±1.8 e.u. for N⁶,N⁹-dimethyladenine and _S =–16.7±1.7 e.u. for N⁶-dimethyl-N⁹-ethyladenine and in an average enthalpy _H=–7.2±0.6 kcal· mol^–1 for both substances investigated.Part of the Ph.D. Theses of W. Schimmack and H. Sapper.Dedicated to Professor Dr. A. Schraub on the occasion of his 65th birthday.     

Influence of Transepithelial Potential Difference on the Sodium Uptake at the Outer Surface of the Isolated Frog Skin

The unidirectional uptake of sodium across the outer surface of the isolated frog skin (J₁₂^Na) was measured in the presence of transepithelial potential difference (Δ_ψ) ranging from +100 to -100 mV. With a sodium concentration of 115 mM in the bathing solutions J₁₂^Na increases significantly when the spontaneous Δ_ψ is reduced to zero by short-circuiting the skin. With an Na concentration of 6 mM a progressive increase J₁₂^Na can be observed when Δ_ψ is decreased in several steps from +100 to -100 mV (serosal side positive and negative, respectively). The observed change J₁₂^Na amounts to a fraction only of that predicted from the shift in Δ_ψ. The results suggest that under open circuit conditions the potential step across the outside surface is at most one half of Δ_ψ and that the resistance across the outside and inside barrier of the skin is ohmic. This is in agreement with measurements of intracellular potentials in the frog skin and with resistance measurements carried out in the toad skin. The data strongly support the view that the saturating component of J_ψ proceeds via a charged carrier system. Exposure to negative values of Δ_ψ of 50 mV or more for times of 24 min or more result in a marked reduction of J₁₂^Na which shows only partial or no reversibility.     

Low Level of Sequence Diversity at Merozoite Surface Protein-1 Locus of Plasmodium ovale curtisi and P. ovale wallikeri from Thai Isolates

Background

The merozoite surface protein-1 (MSP-1) is a candidate target for the development of blood stage vaccines against malaria. Polymorphism in MSP-1 can be useful as a genetic marker for strain differentiation in malarial parasites. Although sequence diversity in the MSP-1 locus has been extensively analyzed in field isolates of Plasmodium falciparum and P. vivax, the extent of variation in its homologues in P. ovale curtisi and P. ovale wallikeri, remains unknown.

Methodology/Principal Findings

Analysis of the mitochondrial cytochrome b sequences of 10 P. ovale isolates from symptomatic malaria patients from diverse endemic areas of Thailand revealed co-existence of P. ovale curtisi (n = 5) and P. ovale wallikeri (n = 5). Direct sequencing of the PCR-amplified products encompassing the entire coding region of MSP-1 of P. ovale curtisi (PocMSP-1) and P. ovale wallikeri (PowMSP-1) has identified 3 imperfect repeated segments in the former and one in the latter. Most amino acid differences between these proteins were located in the interspecies variable domains of malarial MSP-1. Synonymous nucleotide diversity (π_S) exceeded nonsynonymous nucleotide diversity (π_N) for both PocMSP-1 and PowMSP-1, albeit at a non-significant level. However, when MSP-1 of both these species was considered together, π_S was significantly greater than π_N (p<0.0001), suggesting that purifying selection has shaped diversity at this locus prior to speciation. Phylogenetic analysis based on conserved domains has placed PocMSP-1 and PowMSP-1 in a distinct bifurcating branch that probably diverged from each other around 4.5 million years ago.

Conclusion/Significance

The MSP-1 sequences support that P. ovale curtisi and P. ovale wallikeri are distinct species. Both species are sympatric in Thailand. The low level of sequence diversity in PocMSP-1 and PowMSP-1 among Thai isolates could stem from persistent low prevalence of these species, limiting the chance of outcrossing at this locus.     

Estimating Orientation Factors in the FRET Theory of Fluorescent Proteins: The TagRFP-KFP Pair and Beyond

The orientation factor κ², one of the key parameters defining Förster resonance energy transfer efficiency, is determined by the transition dipole moment orientations of the donor and acceptor species. Using the results of quantum chemical and quantum mechanical/molecular mechanical calculations for the chromophore-containing pockets in selected colored proteins of the green fluorescent protein family, we derived transition dipole moments corresponding to the S_0,min → S₁ excitation for green fluorescent protein, red fluorescent protein (TagRFP), and kindling fluorescent protein, and the S_1,min → S₀ emission for TagRFP. These data allowed us to estimate κ² values for the TagRFP-linker-kindling fluorescent protein tetrameric complex required for constructing novel sensors.     

Audiovisual Speech Perception at Various Presentation Levels in Mandarin-Speaking Adults with Cochlear Implants

Objectives

(1) To evaluate the recognition of words, phonemes and lexical tones in audiovisual (AV) and auditory-only (AO) modes in Mandarin-speaking adults with cochlear implants (CIs); (2) to understand the effect of presentation levels on AV speech perception; (3) to learn the effect of hearing experience on AV speech perception.

Methods

Thirteen deaf adults (age = 29.1±13.5 years; 8 male, 5 female) who had used CIs for >6 months and 10 normal-hearing (NH) adults participated in this study. Seven of them were prelingually deaf, and 6 postlingually deaf. The Mandarin Monosyllablic Word Recognition Test was used to assess recognition of words, phonemes and lexical tones in AV and AO conditions at 3 presentation levels: speech detection threshold (SDT), speech recognition threshold (SRT) and 10 dB SL (re:SRT).

Results

The prelingual group had better phoneme recognition in the AV mode than in the AO mode at SDT and SRT (both p = 0.016), and so did the NH group at SDT (p = 0.004). Mode difference was not noted in the postlingual group. None of the groups had significantly different tone recognition in the 2 modes. The prelingual and postlingual groups had significantly better phoneme and tone recognition than the NH one at SDT in the AO mode (p = 0.016 and p = 0.002 for phonemes; p = 0.001 and p<0.001 for tones) but were outperformed by the NH group at 10 dB SL (re:SRT) in both modes (both p<0.001 for phonemes; p<0.001 and p = 0.002 for tones). The recognition scores had a significant correlation with group with age and sex controlled (p<0.001).

Conclusions

Visual input may help prelingually deaf implantees to recognize phonemes but may not augment Mandarin tone recognition. The effect of presentation level seems minimal on CI users'' AV perception. This indicates special considerations in developing audiological assessment protocols and rehabilitation strategies for implantees who speak tonal languages.     

Kinetics and mechanism of catalysis by proteolytic enzymes. A comparison of the kinetics of hydrolysis of synthetic substrates by bovine α- and β-trypsin

Several esters of the α-N-toluene-p-sulphonyl and α-N-benzoyl derivatives of S-(3-aminopropyl)-l-cysteine and the methyl ester of S-(4-aminobutyl)-N-toluene-p-sulphonyl-l-cysteine were synthesized. The kinetics of hydrolysis of these and esters of the α-N-toluene-p-sulphonyl and α-N-benzoyl derivatives of l-arginine, l-lysine, S-(2-aminoethyl)-l-cysteine and esters of γ-guanidino-l-α-toluene-p-sulphonamidobutyric acid and α-N-toluene-p-sulphonyl-l-homoarginine by α- and β-trypsin were compared. On the basis of values of the specificity constants (k_cat./K_m), the two enzymes display similar catalytic efficiency towards some substrates. In other cases α-trypsin is less efficient than β-trypsin. It is possible that α-trypsin possesses greater molecular flexibility than β-trypsin.     

Osmotic adjustment in sorghum: I. Mechanisms of diurnal osmotic potential changes

Osmotic adjustment, defined as a lowering of osmotic potential (ψ_π) due to net solute accumulation in response to water stress, has been considered to be a beneficial drought tolerance mechanism in some crop species. The objective of this experiment was to determine the relative contribution of passive versus active mechanisms involved in diurnal ψ_π changes in sorghum (Sorghum bicolor L. Moench) leaf tissue in response to water stress. A single sorghum hybrid (cv AT×623 × RT×430) was grown in the field under variable water supplies. Water potential, ψ_π, and relative water content were measured diurnally on expanding and the uppermost fully expanded leaves before flowering and on fully expanded leaves during the grain-filling period. Diurnal changes in total osmotic potential (Δψ_π) in response to water stress was 1.1 megapascals before flowering and 1.4 megapascals during grain filling in comparison with 0.53 megapascal under well-watered conditions. Under water-stressed conditions, passive concentration of solutes associated with dehydration accounted for 50% (0.55 megapascal) of the diurnal Δψ_π before flowering and 47% (0.66 megapascal) of the change during grain filling. Net solute accumulation accounted for 42% (0.46 megapascal) of the diurnal Δψ_π before flowering and 45% (0.63 megapascal) of the change during grain filling in water-stressed leaves. The relative contribution of changes in nonosmotic volume (decreased turgid weight/dry weight) to diurnal Δψ_π was less than 8% at either growth stages. Water stress did not affect leaf tissue elasticity or partitioning of water between the symplasm and apoplasm.     

Implicit Target Substitution and Sequencing for Lexical Tone Production in Chinese: An fMRI Study

In this study, we examine the neural substrates underlying Tone 3 sandhi and tone sequencing in Mandarin Chinese using fMRI. Tone 3 sandhi is traditionally described as the substitution of Tone 3 with Tone 2 when followed by another Tone 3 (i.e., 33→23). According to current speech production models, target substitution is expected to engage the posterior inferior frontal gyrus. Since Tone 3 sandhi is, to some extent, independent of segments, which makes it more similar to singing, right-lateralized activation in this region was predicted. As for tone sequencing, based on studies in sequencing, we expected the involvement of the supplementary motor area. In the experiments, participants were asked to produce twelve four-syllable sequences with the same tone assignment (the repeated sequences) or a different tone assignment (the mixed sequences). We found right-lateralized posterior inferior frontal gyrus activation for the sequence 3333 (Tone 3 sandhi) and left-lateralized activation in the supplementary motor area for the mixed sequences (tone sequencing). We proposed that tones and segments could be processed in parallel in the left and right hemispheres, but their integration, or the product of their integration, is hosted in the left hemisphere.     

Binding of Imidazole to the Heme of Cytochrome c1 and Inhibition of the bc1 Complex from Rhodobacter sphaeroides: I. EQUILIBRIUM AND MODELING STUDIES*

We have used imidazole (Im) and N-methylimidazole (MeIm) as probes of the heme-binding cavity of membrane-bound cytochrome (cyt) c₁ in detergent-solubilized bc₁ complex from Rhodobacter sphaeroides. Imidazole binding to cyt c₁ substantially lowers the midpoint potential of the heme and fully inhibits bc₁ complex activity. Temperature dependences showed that binding of Im (K_d ≈ 330 μm, 25 °C, pH 8) is enthalpically driven (ΔH⁰ = −56 kJ/mol, ΔS⁰ = −121 J/mol/K), whereas binding of MeIm is 30 times weaker (K_d ≈ 9.3 mm) and is entropically driven (ΔH⁰ = 47 kJ/mol, ΔS⁰° = 197 J/mol/K). The large enthalpic and entropic contributions suggest significant structural and solvation changes in cyt c₁ triggered by ligand binding. Comparison of these results with those obtained previously for soluble cyts c and c₂ suggested that Im binding to cyt c₁ is assisted by formation of hydrogen bonds within the heme cleft. This was strongly supported by molecular dynamics simulations of Im adducts of cyts c, c₂, and c₁, which showed hydrogen bonds formed between the N_δH of Im and the cyt c₁ protein, or with a water molecule sequestered with the ligand in the heme cleft.     

High Vascular Tone of Mouse Femoral Arteries In Vivo Is Determined by Sympathetic Nerve Activity Via α1A- and α1D-Adrenoceptor Subtypes

Background and purpose

Determining the role of vascular receptors in vivo is difficult and not readily accomplished by systemic application of antagonists or genetic manipulations. Here we used intravital microscopy to measure the contributions of sympathetic receptors, particularly α₁-adrenoceptor subtypes, to contractile activation of femoral artery in vivo.

Experimental approach

Diameter and intracellular calcium ([Ca²⁺]_i) in femoral arteries were determined by intravital fluorescence microscopy in mice expressing a Myosin Light Chain Kinase (MLCK) based calcium-calmodulin biosensor. Pharmacological agents were applied locally to the femoral artery to determine the contributions of vascular receptors to tonic contraction and [Ca²⁺]_i,.

Key results

In the anesthetized animal, femoral arteries were constricted to a diameter equal to 54% of their passive diameter (i.e. tone = 46%). Of this total basal tone, 16% was blocked by RS79948 (0.1 µM) and thus attributable to α₂-adrenoceptors. A further 46% was blocked by prazosin (0.1 µM) and thus attributable to α₁-adrenoceptors. Blockade of P_2X and NPY₁ receptors with suramin (0.5 mM) and BIBP3226 (1.0 µM) respectively, reduced tone by a further 22%, leaving 16% of basal tone unaffected at these concentrations of antagonists. Application of RS100329 (α_1A-selective antagonist) and BMY7378 (α_1D-selective) decreased tone by 29% and 26%, respectively, and reduced [Ca²⁺]_i. Chloroethylclonidine (1 µM preferential for α_1B-) had no effect. Abolition of sympathetic nerve activity (hexamethonium, i.p.) reduced basal tone by 90%.

Conclusion and Implications

Tone of mouse femoral arteries in vivo is almost entirely sympathetic in origin. Activation of α_1A- and α_1D-adrenoceptors elevates [Ca²⁺]_i and accounts for at least 55% of the tone.     

Removal of organic pollutants and analysis of MLSS–COD removal relationship at different HRTs in a submerged membrane bioreactor

In order to investigate the influence of hydraulic retention time (HRT) on organic pollutant removal in a submerged membrane bioreactor (SMBR), a laboratory-scale experiment was conducted using domestic sewage as influent. The dissolved oxygen (DO) concentration was controlled at 2.0– during the experimental period. The experiments demonstrated that when HRT was 3, 2 and 1 h, the reduction of chemical oxygen demand (COD) was 89.3–97.2, 88.5–97.3 and 80–91.1%, and the effluent COD was 38.9–11.2, 41.6–10.8 and 63.4–, respectively. It is suggested that an HRT of 1 h could meet the normal standard of discharged domestic sewage, and an HRT of 2 h could meet that of water reclamation. In addition, we use mathematical software MATLAB to analyse the relation of mixed liquor suspended solids (MLSS) and COD removal. The results showed that the optimum MLSS concentration should be maintained at around in the SMBR. The results also showed that the COD removal was related to HRT (τ), influent concentration (S₀) and sludge loading rate for COD removal (N_S). Moreover, the high COD removal could be achieved through adjusting τ, S₀ and N_S.     

siRNA screening identifies METTL9 as a histidine Nπ-methyltransferase that targets the proinflammatory protein S100A9

Protein methylation is one of the most common post-translational modifications observed in basic amino acid residues, including lysine, arginine, and histidine. Histidine methylation occurs on the distal or proximal nitrogen atom of its imidazole ring, producing two isomers: Nτ-methylhistidine or Nπ-methylhistidine. However, the biological significance of protein histidine methylation remains largely unclear owing in part to the very limited knowledge about its contributing enzymes. Here, we identified mammalian seven-β-strand methyltransferase METTL9 as a histidine Nπ-methyltransferase by siRNA screening coupled with methylhistidine analysis using LC–tandem MS. We demonstrated that METTL9 catalyzes Nπ-methylhistidine formation in the proinflammatory protein S100A9, but not that of myosin light chain kinase MYLK2, in vivo and in vitro. METTL9 does not affect the heterodimer formation of S100A9 and S100A8, although Nπ-methylation of S100A9 at His-107 overlaps with a zinc-binding site, attenuating its affinity for zinc. Given that S100A9 exerts an antimicrobial activity, probably by chelation of zinc essential for the growth of bacteria and fungi, METTL9-mediated S100A9 methylation might be involved in the innate immune response to bacterial and fungal infection. Thus, our findings suggest a functional consequence for protein histidine Nπ-methylation and may add a new layer of complexity to the regulatory mechanisms of post-translational methylation.