Fitness variation in response to artificial selection for reduced cell area,cell number and wing area in natural populations of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

Background

Genetically based body size differences are naturally occurring in populations of Drosophila melanogaster, with bigger flies in the cold. Despite the cosmopolitan nature of body size clines in more than one Drosophila species, the actual selective mechanisms controlling the genetic basis of body size variation are not fully understood. In particular, it is not clear what the selective value of cell size and cell area variation exactly is. In the present work we determined variation in viability, developmental time and larval competitive ability in response to crowding at two temperatures after artificial selection for reduced cell area, cell number and wing area in four different natural populations of D. melanogaster.

Results

No correlated effect of selection on viability or developmental time was observed among all selected populations. An increase in competitive ability in one thermal environment (18°C) under high larval crowding was observed as a correlated response to artificial selection for cell size.

Conclusion

Viability and developmental time are not affected by selection for the cellular component of body size, suggesting that these traits only depend on the contingent genetic makeup of a population. The higher larval competitive ability shown by populations selected for reduced cell area seems to confirm the hypothesis that cell area mediated changes have a relationship with fitness, and might be the preferential way to change body size under specific circumstances.

     

拐芹根化学成分研究Ⅱ

从伞型科当归属植物拐芹(Angelica polymorpha Maxim)的根及根茎中又分得4个结晶性化合物。经物理常数测定、光谱分析,分别鉴定为欧前胡素Ⅰ,异氧化前胡内酯Ⅱ,Pabulenol Ⅲ,Phellopterin Ⅳ。     

The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster

In a recent study, we reported that the combined average mutation rate of 10 di-, 6 tri-, and 8 tetranucleotide repeats in Drosophila melanogaster was 6.3 x 10(-6) mutations per locus per generation, a rate substantially below that of microsatellite repeat units in mammals studied to date (range = 10(-2)-10(-5) per locus per generation). To obtain a more precise estimate of mutation rate for dinucleotide repeat motifs alone, we assayed 39 new dinucleotide repeat microsatellite loci in the mutation accumulation lines from our earlier study. Our estimate of mutation rate for a total of 49 dinucleotide repeats is 9.3 x 10(-6) per locus per generation, only slightly higher than the estimate from our earlier study. We also estimated the relative difference in microsatellite mutation rate among di-, tri-, and tetranucleotide repeats in the genome of D. melanogaster using a method based on population variation, and we found that tri- and tetranucleotide repeats mutate at rates 6.4 and 8.4 times slower than that of dinucleotide repeats, respectively. The slower mutation rates of tri- and tetranucleotide repeats appear to be associated with a relatively short repeat unit length of these repeat motifs in the genome of D. melanogaster. A positive correlation between repeat unit length and allelic variation suggests that mutation rate increases as the repeat unit lengths of microsatellites increase.      

Population structure of the Japanese eel, Anguilla japonica

Mitochondrial DNA (mtDNA) sequences that include (a) a part of the cytochrome b gene, (b) two tRNA genes, and (c) a part of the noncoding D-loop region of 31 Anguilla japonica (Japanese eel) and 1 A. marmorata collected from Taiwan, Japan, and mainland China were determined to evaluate the population structure of Japanese eel. Among 30 genotypes identified from the 31 Japanese eel mtDNAs sequenced, there are 58 variable sites, predominantly clustered at the D-loop region. The phylogenetic tree constructed by the unweighted pair-group method with arithmetic mean shows neither significant genealogical branches nor geographic clusters. Furthermore, the sequence-statistics test reveals little, if any, significant genetic differentiation. These results indicate that the 31 Japanese eels might come from a single population. Analysis of sequence variation in mtDNA by using the relationship between the number of segregating sites and the average number of nucleotide differences under the neutral mutation hypothesis reveals that neutral mutation acts as a major factor influencing the evolutionary divergence of the Japanese eel mitochondrial genome sequenced, especially in the noncoding region.      

Characterization and potential evolutionary impact of transposable elements in the genome of Cochliobolus heterostrophus

Background

Cochliobolus heterostrophus is a dothideomycete that causes Southern Corn Leaf Blight disease. There are two races, race O and race T that differ by the absence (race O) and presence (race T) of ~ 1.2-Mb of DNA encoding genes responsible for the production of T-toxin, which makes race T much more virulent than race O. The presence of repetitive elements in fungal genomes is considered to be an important source of genetic variability between different species.

Results

A detailed analysis of class I and II TEs identified in the near complete genome sequence of race O was performed. In total in race O, 12 new families of transposons were identified. In silico evidence of recent activity was found for many of the transposons and analyses of expressed sequence tags (ESTs) demonstrated that these elements were actively transcribed. Various potentially active TEs were found near coding regions and may modify the expression and structure of these genes by acting as ectopic recombination sites. Transposons were found on scaffolds carrying polyketide synthase encoding genes, responsible for production of T-toxin in race T. Strong evidence of ectopic recombination was found, demonstrating that TEs can play an important role in the modulation of genome architecture of this species. The Repeat Induced Point mutation (RIP) silencing mechanism was shown to have high specificity in C. heterostrophus, acting only on transposons near coding regions.

Conclusions

New families of transposons were identified. In C. heterostrophus, the RIP silencing mechanism is efficient and selective. The co-localization of effector genes and TEs, therefore, exposes those genes to high rates of point mutations. This may accelerate the rate of evolution of these genes, providing a potential advantage for the host. Additionally, it was shown that ectopic recombination promoted by TEs appears to be the major event in the genome reorganization of this species and that a large number of elements are still potentially active. So, this study provides information about the potential impact of TEs on the evolution of C. heterostrophus.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-536) contains supplementary material, which is available to authorized users.     

Predicting phenotypes of asthma and eczema with machine learning

Background

There is increasing recognition that asthma and eczema are heterogeneous diseases. We investigated the predictive ability of a spectrum of machine learning methods to disambiguate clinical sub-groups of asthma, wheeze and eczema, using a large heterogeneous set of attributes in an unselected population. The aim was to identify to what extent such heterogeneous information can be combined to reveal specific clinical manifestations.

Methods

The study population comprised a cross-sectional sample of adults, and included representatives of the general population enriched by subjects with asthma. Linear and non-linear machine learning methods, from logistic regression to random forests, were fit on a large attribute set including demographic, clinical and laboratory features, genetic profiles and environmental exposures. Outcome of interest were asthma, wheeze and eczema encoded by different operational definitions. Model validation was performed via bootstrapping.

Results

The study population included 554 adults, 42% male, 38% previous or current smokers. Proportion of asthma, wheeze, and eczema diagnoses was 16.7%, 12.3%, and 21.7%, respectively. Models were fit on 223 non-genetic variables plus 215 single nucleotide polymorphisms. In general, non-linear models achieved higher sensitivity and specificity than other methods, especially for asthma and wheeze, less for eczema, with areas under receiver operating characteristic curve of 84%, 76% and 64%, respectively. Our findings confirm that allergen sensitisation and lung function characterise asthma better in combination than separately. The predictive ability of genetic markers alone is limited. For eczema, new predictors such as bio-impedance were discovered.

Conclusions

More usefully-complex modelling is the key to a better understanding of disease mechanisms and personalised healthcare: further advances are likely with the incorporation of more factors/attributes and longitudinal measures.

     

Molecular evolution of the period gene in Drosophila athabasca

We measured nucleotide variability within and between the three semispecies of the Drosophila athabasca complex, at the period (per) gene by using a polymerase chain reaction-based four-cutter restriction- enzyme analysis. The levels of polymorphism varied considerably between the three semispecies. Our results for per, combined with previous data for X-linked allozymes, suggest that the X chromosome in the western- northern semispecies is less variable than expected under an equilibrium-neutral model. Both the pattern of divergence between the semispecies and a cladistic clustering of per haplotypes support the previously hypothesized grouping of eastern A and eastern B as the two most recently diverged semispecies. A 21-bp in-frame segment in the region of per which shares sequence similarity with the neuronal development gene single minded is deleted in all eastern A and eastern B flies examined but is present in all of the western-northern flies and all other published per sequences. Despite these hints that there may be significant differences at the per gene between the semispecies, especially the western-northern group versus the two eastern groups, there is no compelling evidence that per is involved in the mating song differences between the semispecies.      

Mitochondrial DNA differentiation during the speciation process in Peromyscus

We address the problem of the possible significance of biological speciation to the magnitude and pattern of divergence of asexually transmitted characters in bisexual species. The empirical data for this report consist of restriction endonuclease site variability in maternally transmitted mitochondrial DNA (mtDNA) isolated from 82 samples of Peromyscus polionotus and P. leucopus collected from major portions of the respective species' ranges. Data are analyzed together with previously published information on P. maniculatus, a sibling species to polionotus. Maps of restriction sites indicate that all of the variation observed can be reasonably attributed to base substitutions leading to loss or gain of particular recognition sites. Magnitude of mtDNA sequence divergence within polionotus (maximum approximately equal to 2%) is roughly comparable to that observed within any of five previously identified mtDNA assemblages in maniculatus. Sequence divergence within leucopus (maximum approximately equal to 4%) is somewhat greater than that within polionotus. Consideration of probable evolutionary links among mtDNA restriction site maps allowed estimation of matriarchal phylogenies within polionotus and leucopus. Clustering algorithms and qualitative Wagner procedures were used to generate phenograms and parsimony networks, respectively, for the between-species comparisons. Three simple graphical models are presented to illustrate some conceivable relationships of mtDNA differentiation to speciation. In theoretical case I, each of two reproductively defined species (A and B) is monophyletic in matriarchal genealogy; the common female ancestor of either species can either predate or postdate the speciation. In case II, neither species is monophyletic in matriarchal genotype. In case III, species B is monophyletic but forms a subclade within A which is thus paraphyletic with respect to B. The empirical results for mtDNA in maniculatus and polionotus appear to conform closely to case III. These theoretical and empirical considerations raise a number of questions about the general relationship of the speciation process to the evolution of uniparentally transmitted traits. Some of these considerations are presented, and it is suggested that the distribution patterns of mtDNA sequence variation within and among extant species should be of considerable relevance to the particular demographies of speciation.      

MiR‐29 coordinates age‐dependent plasticity brakes in the adult visual cortex

The authors regret having omitted grant attributions in the original publication. The funding section is herewith updated to reflect the change. “Funding attributed to Tommaso Pizzorusso was provided by EPIGEN Flagship project and PRIN2017HM8FA, funding attributed to Alessandro Cellerino was provided by Fondazione Pisa ETHERNA project, funding attributed to Pierre Baldi was provided by NIH (grant NIH {"type":"entrez-nucleotide","attrs":{"text":"GM123558","term_id":"221306858","term_text":"GM123558"}}GM123558), funding attributed to Jessica Kwok was provided by the Leverhulme Trust project grant (RPG‐2018‐100).”