A testis‐specific gene within a widely expressed gene: Contrasting evolutionary patterns of two differentially expressed mammalian proteins encoded by a single gene,CAMK4

Understanding the patterns of genetic variations within fertility‐related genes and the evolutionary forces that shape such variations is crucial in predicting the fitness landscapes of subsequent generations. This study reports distinct evolutionary features of two differentially expressed mammalian proteins [CaMKIV (Ca²⁺/calmodulin‐dependent protein kinase IV) and CaS (calspermin)] that are encoded by a single gene, CAMK4. The multifunctional CaMKIV, which is expressed in multiple tissues including testis and ovary, is evolving at a relatively low rate (0.46–0.64 × 10^?9 nucleotide substitutions/site/year), whereas the testis‐specific CaS gene, which is predominantly expressed in post‐meiotic cells, evolves at least three to four times faster (1.48–1.98 × 10^?9 substitutions/site/year). Concomitantly, maximum‐likelihood‐based selection analyses revealed that the ubiquitously expressed CaMKIV is constrained by intense purifying selection and, therefore, remained functionally highly conserved throughout the mammalian evolution, whereas the testis‐specific CaS gene is under strong positive selection. The substitution rates of different mammalian lineages within both genes are positively correlated with GC content, indicating the possible influence of GC‐biased gene conversion on the estimated substitution rates. The observation of such unusually high GC content of the CaS gene (≈74%), particularly in the lineage that comprises the bovine species, suggests the possible role of GC‐biased gene conversion in the evolution of CaS that mimics positive selection.     

Serum metabonomics study of pregnant women with gestational diabetes mellitus based on LC-MS

ObjectiveThrough metabolomics method, the objective of the paper is to differentially screen serum metabolites of GDM patients and healthy pregnant women, to explore potential biomarkers of GDM and analyze related pathways, and to explain the potential mechanism and biological significance of GDM.MethodsThe serum samples from 30 GDM patients and 30 healthy pregnant women were selected to conduct non-targeted metabolomics study by liquid chromatography-mass spectrometry. The differential metabolites between the two groups were searched and the metabolic pathway was analyzed by KEGG database.ResultsMultivariate statistical analysis found that serum metabolism in GDM patients was different significantly from healthy pregnant women, 36 differential metabolites and corresponding metabolic pathways were identified in serum, which involved several metabolic ways like, fatty acid metabolism, butyric acid metabolism, bile secretion, and amino acid metabolism.ConclusionThe discovery of these biomarkers provided a new theoretical basis and experimental basis for further study of the early diagnosis and pathogenesis of GDM. At the same time, LC-MS-based serum metabolomics methods also showed great application values in disease diagnosis and mechanism research.     

Comparisons of Some Chi-Squared Goodness-of-Fit Test Statistics in Sparse One-Way Multinomials

The behavior of Pearson's X² test, the likelihood ratio test Y² and the two of its derivatives, G² and G_k², the Freeman-Tukey test (FT) and the Cressie and Read test Statistic I(2/3) are examined in this study. Estimated attained α levels based on 1000 simulated samples when the approximating distribution is χ_k-1², are computed for these tests for the various values of k, n and seven null hypotheses. Results from estimated power computations indicate that none of the test statistics has a clear advantage over any others, and that the choice of which test to use must therefore rest mainly on the performances with regards to the attained α levels when the χ² approximation is invoked. In this respect, the log-normal approximation proposed by Lawal and Upton (1980) is strongly recommended. This is closely followed by the I(2/3).     

Lasioseius Fimetorum: a soil-dwelling predator of glasshouse pests?

Female lifespan and reproduction, in terms of numberof larvae produced, of the soil-dwelling predatorymite Lasioseius fimetorum Karg (Acari:Podocinidae) fed on mould mites (Tyrophagusputrescentiae [Schrank] [Acarina: Acaridae]) wereinvestigated by laboratory experiments at 20 °C,as were the mite's consumption rates of various prey.After a preoviposition period of 10.7 days, L.fimetorum produced progeny at a daily rate of 0.7.The oviposition period lasted 23.6 days and a total of19.4 progeny were produced per female. Females livedfor 38.6 days. Eggs of the Collembola Isotomurusspp. (Collembola: Isotomidae) were consumed in thelargest amount by L. fimetorum followed by mouldmite nymphs, larvae and pupae of thrips (Frankliniella occidentalis [Pergande] [Thysanoptera:Thripidae]), eggs of the Collembola Micrisotomaspp. (Collembola: Isotomidae), Isotomurus spp.nymphs and sciarid larvae (Bradysia pauperaTuomikoski and B. tritici (Coquillet) [Diptera:Sciaridae]). Immature drain flies (Psychoda spp.[Diptera: Psychodidae]) were not consumed by L.fimetorum. The suitability of L. fimetorum forbiological control of glasshouse pests withsoil-dwelling stages is discussed in comparison withanother predatory mite Hypoaspis miles Berlese(Acarina: Hypoaspididae).     

The role of nutrition on epigenetic modifications and their implications on health

Nutrition plays a key role in many aspects of health and dietary imbalances are major determinants of chronic diseases including cardiovascular disease, obesity, diabetes and cancer. Adequate nutrition is particularly essential during critical periods in early life (both pre- and postnatal). In this regard, there is extensive epidemiologic and experimental data showing that early sub-optimal nutrition can have health consequences several decades later.     

Curiously Modern DNA for a ``250 Million-Year-Old' Bacterium

Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected) and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the ∼59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies. Received: 12 April 2001 / Accepted: 9 June 2001     

Analysis of distributions of mutants in clones of plant-cell aggregates

Summary The organization of plant cells (or any other genetic elements, such as organelles) into aggregates modifies the expected distribution of mutants in clones. The reason for the modification, and its effect on the use of the Luria-Delbrück fluctuation test, are discussed. The Luria-Delbriick test was used to show that the trait for chlorate resistance in cultured rose-cell aggregates appeared spontaneously and in the absence of chlorate ion.     

Patch area, population density and the scaling of migration rates: the resource concentration hypothesis revisited

Empirical research has for a long time observed that animal densities may both increase and decrease with patch size, and these variable responses have been difficult to explain using the current theoretical framework. The most influential hypothesis, the resource concentration hypothesis, predicts only positive density–area relations, as a consequence of different emigration and immigration rates in small and large patches, and empirical deviations have inspired a flurry of alternative explanations. In this paper, we use realistic rules for the relationship between patch size and migration rates and show a wider predictive range for density–area relations than previously believed. Comparisons with published data suggest that observed density–area relations may easily fit in a framework based on a minimum set of behavioural and population processes. This does not imply that other mechanisms are unimportant, but merely that their quantitative importance can only be evaluated relative to patch geometry and local growth.     

Kinetic Basis for the Conjugation of Auxin by a GH3 Family Indole-acetic Acid-Amido Synthetase

The GH3 family of acyl-acid-amido synthetases catalyze the ATP-dependent formation of amino acid conjugates to modulate levels of active plant hormones, including auxins and jasmonates. Initial biochemical studies of various GH3s show that these enzymes group into three families based on sequence relationships and acyl-acid substrate preference (I, jasmonate-conjugating; II, auxin- and salicylic acid-conjugating; III, benzoate-conjugating); however, little is known about the kinetic and chemical mechanisms of these enzymes. Here we use GH3-8 from Oryza sativa (rice; OsGH3-8), which functions as an indole-acetic acid (IAA)-amido synthetase, for detailed mechanistic studies. Steady-state kinetic analysis shows that the OsGH3-8 requires either Mg²⁺ or Mn²⁺ for maximal activity and is specific for aspartate but accepts asparagine as a substrate with a 45-fold decrease in catalytic efficiency and accepts other auxin analogs, including phenyl-acetic acid, indole butyric acid, and naphthalene-acetic acid, as acyl-acid substrates with 1.4–9-fold reductions in k_cat/K_m relative to IAA. Initial velocity and product inhibition studies indicate that the enzyme uses a Bi Uni Uni Bi Ping Pong reaction sequence. In the first half-reaction, ATP binds first followed by IAA. Next, formation of an adenylated IAA intermediate results in release of pyrophosphate. The second half-reaction begins with binding of aspartate, which reacts with the adenylated intermediate to release IAA-Asp and AMP. Formation of a catalytically competent adenylated-IAA reaction intermediate was confirmed by mass spectrometry. These mechanistic studies provide insight on the reaction catalyzed by the GH3 family of enzymes to modulate plant hormone action.