High rates of molecular evolution in hantaviruses

Hantaviruses are rodent-borne Bunyaviruses that infect the Arvicolinae, Murinae, and Sigmodontinae subfamilies of Muridae. The rate of molecular evolution in the hantaviruses has been previously estimated at approximately 10(-7) nucleotide substitutions per site, per year (substitutions/site/year), based on the assumption of codivergence and hence shared divergence times with their rodent hosts. If substantiated, this would make the hantaviruses among the slowest evolving of all RNA viruses. However, as hantaviruses replicate with an RNA-dependent RNA polymerase, with error rates in the region of one mutation per genome replication, this low rate of nucleotide substitution is anomalous. Here, we use a Bayesian coalescent approach to estimate the rate of nucleotide substitution from serially sampled gene sequence data for hantaviruses known to infect each of the 3 rodent subfamilies: Araraquara virus (Sigmodontinae), Dobrava virus (Murinae), Puumala virus (Arvicolinae), and Tula virus (Arvicolinae). Our results reveal that hantaviruses exhibit short-term substitution rates of 10(-2) to 10(-4) substitutions/site/year and so are within the range exhibited by other RNA viruses. The disparity between this substitution rate and that estimated assuming rodent-hantavirus codivergence suggests that the codivergence hypothesis may need to be reevaluated.     

High rates of protein synthesis by isolated chloroplasts

Improvements are described in the preparation and in vitro conditions of an intact pea (Pisum sativum Progress No. 9) chloroplast system which provides high efficiency for translation of endogenous messenger RNA, using light as an energy source. High rates result in the incorporation into protein of up to 100 nanomoles tritiated leucine per milligram chlorophyll. These rates suggest extensive reinitiation, and repeated utilization of the messenger RNA that code for thylakoid proteins. Up to 39 radioactive thylakoid peptide bands were detected by fluorography after labeling with tritiated leucine.     

High rates of neural tube defects in Ukraine

BACKGROUND: Oral consumption of synthetic folic acid can prevent neural tube defects (NTDs), which are some of the most severe congenital anomalies. The prevalence of NTDs in Ukraine and other countries of the former U.S.S.R. has not been well studied. We determined the prevalence of NTD-affected pregnancies in Northwestern Ukraine as background for policy decisions related to flour fortification in this country. METHODS: The Ukrainian-American Birth Defects Program was established in 1999 and conducts population- based surveillance of birth defects in several oblasts (states) of Ukraine. We determined the prevalence of NTDs in the Volyn and Rivne oblasts of Northwestern Ukraine for three years, 2000-2002. RESULTS: There were 75,928 births in the two oblasts in 2000-2002. There were 159 cases of NTDs among live births, stillbirths, and induced abortions. The prevalence of NTDs in the two oblasts in Northwestern Ukraine is 2.1 per 1000 births. CONCLUSIONS: The prevalence of NTD-affected pregnancies we found in Northwestern Ukraine is almost four times what it should be. This prevalence suggests that population folate deficiency is widespread in Ukraine. Universal folic acid fortification of flour milled in Ukraine is urgently needed to end this epidemic of birth defects. Such fortification would be expected to prevent folate deficiency anemia, heart attacks, and strokes.     

High genome-wide mutation rates in vegetatively propagated bermudagrass

A cascade DNA amplification strategy that generates arbitrary signatures from amplification profiles (ASAP) was used to measure genome-wide mutation rates in bermudagrass (Cynodon). ASAP quantified nucleotide changes that were induced by irradiation, genetic instabilities and normal vegetative growth of cultivars and accessions of sterile interspecific hybrids. DNA sequence divergence between cultivar ‘Tifway’ and its γ radiation-induced mutant ‘Tifway II’ (0.70 ± 0.66%) was comparable to estimates in radiation-induced mutants and spontaneous sports of chrysanthemum (Chrysanthemum morifolium Ramat.). A similar divergence in sequence (0.95 ± 0.20%) was observed in the pairwise comparison of 17 nondisjunctive ‘Tifgreen’ and ‘Tifdwarf’ accessions. Mutation during normal Tifdwarf vegetative growth was evaluated by planting sprigs and sampling their offspring. Somatic sequence divergence levels (0.004 ± 0.007%) resulted in a mutation rate of 1.05 × 10^?8 per nucleotide per generation, assuming that a bermudagrass sprig constitutes a generation of growth. These rates were comparable to those found in germinal cells and individuals of either human or Drosophila melanogaster, supporting the notion that eukaryotic evolution is generation rather than time dependent. The high accumulation of somatic mutations (10 per triploid genome) is consistent with a model whereby mutation load in a population exhibiting obligate vegetative reproduction is substantially higher than in a population under sexual or asexual reproduction. These constraints could be the cause of reported genetic instabilities in the Tifgreen–Tifdwarf complex. Finally, a long-term rate measured across accessions and indicative of the accumulation of mutations in 17 Tifgreen–Tifdwarf populations (µ = 1.02 × 10^?8 per nucleotide per generation) was strikingly congruent with the bermudagrass vegetative mutation rate, suggesting absence of evolutionary constraints in the sampled genomic regions. Mutation rates calculated from across-accesions divergence estimates (5.18 ± 0.53%) indicated that plant material was evolving 100 times faster (3.8 × 10^?7 changes per nucleotide per year) than a molecular clock rate estimate for grasses, probably resulting from the compound effect of clonal growth and life span of the hybrid plant material.     

High viral infection rates in Antarctic and Arctic bacterioplankton

The frequency of visibly phage-infected bacterial cells (FVIB) and the average number of phages per cell [i.e. burst size (BS)] were determined in Antarctic and Arctic ultra-oligotrophic freshwater environments. Water samples were collected from two Antarctic freshwater lakes and cryoconite holes from a glacier in the Arctic. Data from this bipolar study show the highest FVIB (average 26.1%, range 5.1% to 66.7%) and the lowest BS (average 4, range 2-15) ever reported in the literature. The bacterial density is low in these ultra-oligotrophic freshwater environments but a large proportion of the bacteria are visibly infected. Our results suggest that a constant virioplankton population can be maintained in these extreme environments even though host density is low and often slow growing.     

High mutation rates in human and ape pseudoautosomal genes

It has been suggested that recombination may be mutagenic, which, if true, would inflate intraspecies diversity and interspecies silent divergence in regions of high recombination. Here, we test this hypothesis comparing human/orangutan genome-wide non-coding divergence (K) to that in the pseudoautosomal genes which were reported to recombine much more frequently than the rest of the genome. We demonstrate that, compared to the average human/orangutan non-coding divergence (K=3%), the substitution rate is significantly elevated in the introns of SHOX (K=5.7%), PPP2R3L (K=8.7%) and ASMT (K=6.5%) genes located in the human and orangutan Xp/Yp pseudoautosomal region (p-PAR), where recombination is over 20-fold higher than the genomic average. On the other hand, human/orangutan non-coding divergence at the Xp/Yp pseudoautosomal boundary (K=3.5%) and in the SYBL1 gene (K=2.7%), located in the human Xq/Yq pseudoautosomal region (q-PAR), where recombination is known to be less frequent than in p-PAR, was not significantly higher than the genome average. The data are consistent with the hypothesis that recombination may be mutagenic.     

High identification rates of endogenous neuropeptides from mouse brain

Mass spectrometry-based neuropeptidomics is one of the most powerful approaches for identification of endogenous neuropeptides in the brain. Until now, however, the identification rate of neuropeptides in neuropeptidomics is relatively low and this severely restricts insights into their biological function. In the present study, we developed a high accuracy mass spectrometry-based approach to enhance the identification rates of neuropeptides from brain tissue. Our integrated approach used mixing on column for loading aqueous and organic extracts to reduce the loss of peptides during sample treatment and used charge state-directed tandem mass spectrometry to increase the number of peptides subjected to high mass accuracy fragmentation. This approach allowed 206 peptides on average to be identified from a single mouse brain sample that was prepared using 15 μL of solutions per 1 mg of tissue. In total, we identified more than 500 endogenous peptides from mouse hypothalamus and whole brain samples. Our identification rate is about two to four times higher compared to previously reported studies conducted on mice or other species. The hydrophobic peptides, such as neuropeptide Y and galanin, could be presented and detected with hydrophilic peptides in the same LC-MS run, allowing a high coverage of peptide characterization over an organism. This will advance our understanding of the roles of diverse peptides and their links in the brain functions.     

High cancer mortality rates in the elderly in the UK

Introduction: Cancer is largely a disease of older individuals. We compared UK cancer mortality rates with those for other countries to assess progress. Methods: Death details were obtained from the WHO Mortality Database for the UK, the USA and 11 European countries. Mortality rates were calculated for the age groups 55–64, 65–74, 75–84 and ≥85 years. Trends between 1995–97 and 2003–05 were determined. The number of excess cancer deaths in the UK was calculated by applying the age-specific mortality rates observed in other regions to the UK. Results: For all cancers combined, UK rates for 2003–05 in those aged ≥75 years were 11–31% higher than in other regions. From 1995–97 to 2003–05, UK rates decreased by 16–17% in those aged <75 years, but increased by 2% in those ≥85 years compared with decreases of 4–16% for the other geographic areas. More than 14,000 cancer deaths in the UK in those aged ≥75 years would be avoided each year if UK mortality rates were identical to those in the USA. Conclusion: The UK is making poor progress in controlling cancer in older age groups. The gap in mortality rates between the UK and other countries and between old and young in the UK is widening.     

High mutation rates in the mitochondrial genomes of Daphnia pulex

Despite the great utility of mitochondrial DNA (mtDNA) sequence data in population genetics and phylogenetics, key parameters describing the process of mitochondrial mutation (e.g., the rate and spectrum of mutational change) are based on few direct estimates. Furthermore, the variation in the mtDNA mutation process within species or between lineages with contrasting reproductive strategies remains poorly understood. In this study, we directly estimate the mtDNA mutation rate and spectrum using Daphnia pulex mutation-accumulation (MA) lines derived from sexual (cyclically parthenogenetic) and asexual (obligately parthenogenetic) lineages. The nearly complete mitochondrial genome sequences of 82 sexual and 47 asexual MA lines reveal high mtDNA mutation rate of 1.37 × 10(-7) and 1.73 × 10(-7) per nucleotide per generation, respectively. The Daphnia mtDNA mutation rate is among the highest in eukaryotes, and its spectrum is dominated by insertions and deletions (70%), largely due to the presence of mutational hotspots at homopolymeric nucleotide stretches. Maximum likelihood estimates of the Daphnia mitochondrial effective population size reveal that between five and ten copies of mitochondrial genomes are transmitted per female per generation. Comparison between sexual and asexual lineages reveals no statistically different mutation rates and highly similar mutation spectra.     

High count rates with total internal reflection fluorescence correlation spectroscopy

We have modeled the structure of KirBac1.1 in an open state using as a starting point the structure of KirBac1.1 in its closed conformation (Protein Data Bank 1P7B). To test the validity of the open-state model, molecular dynamics simulations in octane, a lipid bilayer mimetic, were carried out. Simulations of the closed conformer were used for comparison purposes. The total simulation time was approximately 138 ns. The initial open model was refined by using projection maps obtained from electron microscopy experiments on two-dimensional crystals of the inwardly rectifying K+ channel KirBac3.1 from Magentospirillum magnetotacticum captured in its open state (C. Vénien-Bryan, unpublished data). Significant movements of the outer helices take place in going from the closed to the open model in agreement with structural and biochemical data in potassium channels, which suggests that gating is accomplished by a conformational change that takes place in the transmembrane domain upon an external stimulus. The motion of the inner helices is mainly achieved by bending at conserved glycine residues that have been previously reported to act as molecular hinges. Overall, these simulations suggest that the open conformer is stable, providing a plausible all-atom model that will enable the study of potential gating mechanisms in more detail.     

High mitochondrial mutation rates estimated from deep-rooting Costa Rican pedigrees

Estimates of mutation rates for the noncoding hypervariable Region I (HVR-I) of mitochondrial DNA vary widely, depending on whether they are inferred from phylogenies (assuming that molecular evolution is clock-like) or directly from pedigrees. All pedigree-based studies so far were conducted on populations of European origin. In this article, we analyzed 19 deep-rooting pedigrees in a population of mixed origin in Costa Rica. We calculated two estimates of the HVR-I mutation rate, one considering all apparent mutations, and one disregarding changes at sites known to be mutational hot spots and eliminating genealogy branches which might be suspected to include errors, or unrecognized adoptions along the female lines. At the end of this procedure, we still observed a mutation rate equal to 1.24 × 10(-6) , per site per year, i.e., at least threefold as high as estimates derived from phylogenies. Our results confirm that mutation rates observed in pedigrees are much higher than estimated assuming a neutral model of long-term HVRI evolution. We argue that until the cause of these discrepancies will be fully understood, both lower estimates (i.e., those derived from phylogenetic comparisons) and higher, direct estimates such as those obtained in this study, should be considered when modeling evolutionary and demographic processes.     

High regeneration rates in anther culture of interspecific sunflower hybrids

Optimization of anther culture with regard to the induction of callus formation and direct embryogenesis was obtained for interspecific hybrids ofH. annuus withH. tuberosus, H. laetiflorus, andH. resinosus by investigating six different induction media and four regeneration media. One media combination (MS-13, MS-R3 and MS-R4) used under different culture conditions (30°C / 35°C and different dark treatments) gave up to 92.7% embryogenic anthers with an average of 8.5 embryos per anther. However, direct embryogenesis as well as callus formation showed a strong genotypec and treatment specific reaction. From 5,600 anthers of the four investigated genotypes more than 2,000 plants could be regenerated. Regenerants were characterized by morphological traits and isozyme analyses to prove their androgenetic origin.     

High algal production rates achieved in a shallow outdoor flume

A mass culture of Tetraselmis suecica grown in seawater enriched with only inorganic nutrients and CO(2) in a shallow outdoor flume containing foil arrays to effect systematic vertical mixing achieved average daily production rates of over 40 g ash-free dry wt (AFDW)/m(2) over periods as long as one month when grown on a three-day dilution cycle. Photosynthetic efficiencies associated with these high production rates averaged 8-11% based on visible irradiance. Operation of the system in a one-, two-, or four-day dilution cycle resulted in lower photosynthetic efficiencies of 6-7%. A remarkable feature of the three-day dilution cycle results was the fact that production on the third day after dilution averaged 60-70 g AFDW/m(2), and corresponding photosynthetic efficiencies averaged 13-19%. The high production rates and photosynthetic efficiencies achieved on the third day after dilution may have reflected the nonequilibrium nature of the production cycle and, in particular, the fact that the adaptation of the cells to changing light condition lagged behind light condition in the culture.     

High survival and stability rates of Escherichia coli dried in hydroxyectoine

The tetrahydropyramidine hydroxyectoine acts as an osmolyte in a range of bacterial species, but its use as a desiccation protectant is less well explored. Recently, it was demonstrated that hydroxyectoine provides effective stabilisation of the Gram-negative species Pseudomonas putida, which is only relatively poorly preserved by the better-characterised protectant, trehalose. It is now shown that hydroxyectoine also protects the paradigmatic bacterium, Escherichia coli: osmotically-preconditioned E. coli dried in hydroxyectoine exhibited a high degree of desiccation tolerance, similar to that achieved using trehalose in this species. Hydroxyectoine is apparently accumulated from hypersaline medium in preference to trehalose biosynthesis, but E. coli loaded with hydroxyectoine in this way showed reduced stability in the dry state. This suggests that, although both hydroxyectoine and trehalose perform equally well as extracellular protectants, trehalose is preferred for intracellular protection.     

High rates of denitrification and nitrate removal in cold seep sediments

We measured denitrification and nitrate removal rates in cold seep sediments from the Gulf of Mexico. Heterotrophic potential denitrification rates were assayed in time-series incubations. Surficial sediments inhabited by Beggiatoa exhibited higher heterotrophic potential denitrification rates (32 μ N reduced day⁻¹) than did deeper sediments (11 μ N reduced day⁻¹). Nitrate removal rates were high in both sediment horizons. These nitrate removal rates translate into rapid turnover times (<1 day) for the nitrate pool, resulting in a faster turnover for the nitrate pool than for the sulfate pool. Together, these data underscore the rigorous nature of internal nitrogen cycling at cold seeps and the requirement for novel mechanisms to provide nitrate to the sediment microbial community.     

High rates of calcium-free diffusion in the cytosol of living cells

Calcium (Ca²⁺) is a universal second messenger that participates in the regulation of innumerous physiological processes. The way in which local elevations of the cytosolic Ca²⁺ concentration spread in space and time is key for the versatility of the signals. Ca²⁺ diffusion in the cytosol is hindered by its interaction with proteins that act as buffers. Depending on the concentrations and the kinetics of the interactions, there is a large range of values at which Ca²⁺ diffusion can proceed. Having reliable estimates of this range, particularly of its highest end, which corresponds to the ions free diffusion, is key to understand how the signals propagate. In this work, we present the first experimental results with which the Ca²⁺-free diffusion coefficient is directly quantified in the cytosol of living cells. By means of fluorescence correlation spectroscopy experiments performed in Xenopus laevis oocytes and in cells of Saccharomyces cerevisiae, we show that the ions can freely diffuse in the cytosol at a higher rate than previously thought.     

High base pair opening rates in tracts of GC base pairs

Sequence-dependent structural features of the DNA double helix have a strong influence on the base pair opening dynamics. Here we report a detailed study of the kinetics of base pair breathing in tracts of GC base pairs in DNA duplexes derived from 1H NMR measurements of the imino proton exchange rates upon titration with the exchange catalyst ammonia. In the limit of infinite exchange catalyst concentration, the exchange times of the guanine imino protons of the GC tracts extrapolate to much shorter base pair lifetimes than commonly observed for isolated GC base pairs. The base pair lifetimes in the GC tracts are below 5 ms for almost all of the base pairs. The unusually rapid base pair opening dynamics of GC tracts are in striking contrast to the behavior of AT tracts, where very long base pair lifetimes are observed. The implication of these findings for the structural principles governing spontaneous helix opening as well as the DNA-binding specificity of the cytosine-5-methyltransferases, where flipping of the cytosine base has been observed, are discussed.     

High recombination rates and hotspots in a Plasmodium falciparum genetic cross

Background

The human malaria parasite Plasmodium falciparum survives pressures from the host immune system and antimalarial drugs by modifying its genome. Genetic recombination and nucleotide substitution are the two major mechanisms that the parasite employs to generate genome diversity. A better understanding of these mechanisms may provide important information for studying parasite evolution, immune evasion and drug resistance.

Results

Here, we used a high-density tiling array to estimate the genetic recombination rate among 32 progeny of a P. falciparum genetic cross (7G8 × GB4). We detected 638 recombination events and constructed a high-resolution genetic map. Comparing genetic and physical maps, we obtained an overall recombination rate of 9.6 kb per centimorgan and identified 54 candidate recombination hotspots. Similar to centromeres in other organisms, the sequences of P. falciparum centromeres are found in chromosome regions largely devoid of recombination activity. Motifs enriched in hotspots were also identified, including a 12-bp G/C-rich motif with 3-bp periodicity that may interact with a protein containing 11 predicted zinc finger arrays.

Conclusions

These results show that the P. falciparum genome has a high recombination rate, although it also follows the overall rule of meiosis in eukaryotes with an average of approximately one crossover per chromosome per meiosis. GC-rich repetitive motifs identified in the hotspot sequences may play a role in the high recombination rate observed. The lack of recombination activity in centromeric regions is consistent with the observations of reduced recombination near the centromeres of other organisms.