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Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome ( approximately 702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immune-deficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods.

Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome (∼702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immunedeficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods., La lista completa de autores que integran el documento puede consultarse en el archivo, Este documento tiene una corrección (ver documento relacionado)., Centro Regional de Estudios Genómicos, Instituto de Investigaciones Bioquímicas de La Plata

We present a theoretical study about hydrogen complexes formed by acetylene and hydrofluoric acid using B3LYP/6-311++G(d,p) calculations and topological parameters of the atoms in molecules theory. In the C 2 H 2 2(HF) hydrogen bonded complex, besides the well-known (π⋯H) interaction formed between the hydrofluoric acid and the C C bond of the acetylene, as well as the (F d ⋯H e ) hydrogen bond in the 2(HF) dimer within the ternary hydrogen complex, the topological parameters identified a bond critical point proceeding from interaction between the fluoride atom (F f ) of the second HF molecule and the hydrogen atom (H b ) of the acetylene, characterizing then a new hydrogen bond, (F f ⋯H b ). Moreover, the AIM calculations discovered an important aspect relative to the (π⋯H) interaction, which is not linked in the midpoint of the C C bond of the acetylene but formed directly by the interaction between the hydrogen atom (H c ) of the first HF molecule and the C 2 atom of the acetylene in the C 2 H 2 2(HF) complex. In this sense, the C 2 H 2 2(HF) hydrogen bonded complex can be considered an intramolecular system constituted of three hydrogen bonds.

Theoretical investigations concerning the formation of hydrogen bonds in both homomeric, (HCN)n, and heteromeric clusters of the type (HCN)nHF (n = 1, 2, and 3) have been performed through ab initio molecular orbital calculations at the second-order Moller–Plesset (MP2) and density functional theory (DFT)/B3LYP levels, with the 6-311++G(d,p) basis set. The formation of hydrogen bonds is investigated in terms of changes in structural, electronic, and vibrational parameters of the free species. Important parameters include the increment in the distance of the HF proton donor species, the increment in the HC distance of HCN moiety, and the amount of intermolecular charge transfer between the HCN species in the (HCN)n group. It is interesting to point out the different behavior in the HC distance as HCN acts simultaneously as a proton acceptor, proton donor, and a proton donor and acceptor. Other important results concern the cooperative effect (CE) in terms of the stabilization energy and dipole moment. Both CEs increase with cluster size and are more pronounced for the heteroclusters. The HF stretching frequency is red-shifted on going in the direction (HCN)HF → (HCN)2HF → (HCN)3HF. This trend is in agreement with the following order of stabilization energies: ΔEHCN…HF < ΔE < ΔE. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

We present a theoretical study through MP2 ab initio molecular orbital calculations and B3LYP density functional theory with the 6-311++G(d,p) basis set of the heterocyclic hydrogen complexes, CnHmY-HX, where CnHmY = C2H4O, C2H5N and C2H4S, and X=F or Cl. This study aided in the elucidation the main changes in the structural, electronic and the vibrational properties in isolated species, due the hydrogen complexes formation, CnHmY-HX, revealing systematic tendencies in these chemical systems studied. The complexes has CS symmetry, with the HX subunit lying in the plane perpendicular to that of CYC nuclei of heterocyclic and acting as proton donor in forming a hydrogen bond to the heteroatom, Y. A weak secondary interaction between the CH2 groups of heterocyclics and the X atoms in HX causes a significant nonlinearity of the primary hydrogen bond. The hydrogen bond linearity deviations in these complexes due to secondary interactions are represented by theta angle. The MP2 intermolecular distances of complexes C2H5N-HF, C2H4O-HF and C2H4S-HF correspond the 1.652, 1.671 and 2.164 A, respectively, these results are in excellent agreement with experimental results of 1.700 and 2.193 A found for the last two complexes. In the same way, the MP2 values to theta angle, 14.7, 19.1 and 16.8 degrees, has a better reproduction in the experimental results of 16.5, 21.0 and 16.8 degrees, get to the C2H4O-HCl, C2H4S-HCl and C2H4S-HF complexes, respectively.

Whole genome shotgun assemblies have proven remarkably successful in reconstructing the bulk of euchromatic genes, with the only limit appearing to be determined by the sequencing depth. For genes imbedded in heterochromatin, however, the low cloning efficiency of repetitive sequences, combined with the computational challenges, demand that additional clues be used to annotate the sequences. One approach that has proven very successful in identifying protein coding genes in Y-linked heterochromatin of Drosophila melanogaster has been to make a BLASTable database of the small, unmapped contigs and fragments leftover at the end of a shotgun assembly, and to attempt to capture these by blasting with an appropriate query sequence. This approach often yields a staggered alignment of contigs from the unmapped set to the query sequence, as though the disjoint contigs represent small portions of the gene. Further inspection frequently shows that the contigs are broken by very large, heterochromatic introns. Methods of this sort are being expanded to make best use of all available clues to determine which unmapped contigs are associated with genes. These include use of EST libraries, and, in the case of the Y chromosome, testing of male specific genes and reduced shotgun depth of relevant contigs. It appears much more hopeful than anyone would have imagined that whole genome shotgun assemblies can recover the great bulk of even heterochromatic genes.

Three recent findings are making a deep impact on our understanding of the Drosophila Y. First, the sequencing of the Drosophila genome and the development of proper computational methods increased the number of known single-copy Y-linked genes from 1 to 16, and revealed a chromosome packed with genes acquired from the autosomes. Second, this, coupled with the finding that B-chromosomes are able to show very regular segregation from the X chromosome, reinforce the hypothesis that the Drosophila Y is a specialized B-chromosome, instead of a degenerated homologue of the X. Third and finally, Y chromosomes seem to have a strong effect on male fitness.

Y chromosomes, with their reduced effective population size, lack of recombination, and male-limited transmission, present a unique collection of constraints for the operation of natural selection. Male-limited transmission may greatly increase the efficacy of selection for male-beneficial mutations, but the reduced effective size also inflates the role of random genetic drift. Together, these defining features of the Y chromosome are expected to influence rates and patterns of molecular evolution on the Y as compared with X-linked or autosomal loci. Here, we use sequence data from 11 genes in 9 Drosophila species to gain insight into the efficacy of natural selection on the Drosophila Y relative to the rest of the genome. Drosophila is an ideal system for assessing the consequences of Y-linkage for molecular evolution in part because the gene content of Drosophila Y chromosomes is highly dynamic, with orthologous genes being Y-linked in some species whereas autosomal in others. Our results confirm the expectation that the efficacy of natural selection at weakly selected sites is reduced on the Y chromosome. In contrast, purifying selection on the Y chromosome for strongly deleterious mutations does not appear to be compromised. Finally, we find evidence of recurrent positive selection for 4 of the 11 genes studied here. Our results thus highlight the variable nature of the mode and impact of natural selection on the Drosophila Y chromosome.

The molecular identity and function of the Drosophila melanogaster Y-linked fertility factors have long eluded researchers. Although the D. melanogaster genome sequence was recently completed, the fertility factors still were not identified, in part because of low cloning efficiency of heterochromatic Y sequences. Here we report a method for iterative blast searching to assemble heterochromatic genes from shotgun assemblies, and we successfully identify kl-2 and kl-3 as 1β- and γ-dynein heavy chains, respectively. Our conclusions are supported by formal genetics with X-Y translocation lines. Reverse transcription–PCR was successful in linking together unmapped sequence fragments from the whole-genome shotgun assembly, although some sequences were missing altogether from the shotgun effort and had to be generated de novo . We also found a previously undescribed Y gene, polycystine-related ( PRY ). The closest paralogs of kl-2 , kl-3 , and PRY (and also of kl-5 ) are autosomal and not X-linked, suggesting that the evolution of the Drosophila Y chromosome has been driven by an accumulation of male-related genes arising de novo from the autosomes.

SR chromosomes are the best-known case of sex chromosome meiotic drive. These X chromosomes cause the production of female-biased progenies in several Drosophila species. Due to their meiotic drive advantage, they are expected to spread and become fixed, resulting in population extinction due to the lack of males. However, this apparently does not occur: SR chromosomes are maintained in balanced polymorphisms, resulting from the equilibrium between their meiotic drive advantage and deleterious fitness effects. In this paper we review the current explanations for their deleterious effects and we argue that it is highly improbable that all newly emerged SR are sufficiently deleterious to avoid fixation. Unbalanced SR almost certainly arise and go unnoticed because of three possible outcomes: (i) fixation followed by extinction of the population or species; (ii) fixation followed by the emergence and fixation of drive suppressors, restoring the normal 1:1 sexual proportion; or (iii) transformation into balanced SR due to partial suppression. If these outcomes really occur, then extant cases of sex-chromosome meiotic drive such as SR, causing small deviations on the population sexual proportion, are only the tip of the iceberg and strong sexual proportion shifts (possibly followed by extinction) are a more common feature of species evolution than is usually assumed.

Chromosomal organization is sufficiently evolutionarily stable that large syntenic blocks of genes can be recognized even between species as distantly related as mammals and puffer fish (450 million years (Myr) of divergence). In Diptera, the gene content of the X chromosome and the autosomes is well conserved: in Drosophila more than 95% of the genes have remained on the same chromosome arm in the 12 sequenced species (63 Myr of divergence, traversing 400 Myr of evolution), and the same linkage groups are clearly recognizable in mosquito genomes (260 Myr of divergence). Here we investigate the conservation of Y-linked gene content among the 12 sequenced Drosophila species. We found that only a quarter of the Drosophila melanogaster Y-linked genes (3 out of 12) are Y-linked in all sequenced species, and that most of them (7 out of 12) were acquired less than 63 Myr ago. Hence, whereas the organization of other Drosophila chromosomes traces back to the common ancestor with mosquitoes, the gene content of the D. melanogaster Y chromosome is much younger. Gene losses are known to have an important role in the evolution of Y chromosomes, and we indeed found two such cases. However, the rate of gene gain in the Drosophila Y chromosomes investigated is 10.9 times higher than the rate of gene loss (95% confidence interval: 2.3-52.5), indicating a clear tendency of the Y chromosomes to increase in gene content. In contrast with the mammalian Y chromosome, gene gains have a prominent role in the evolution of the Drosophila Y chromosome.

The Y chromosome and other heterochromatic regions present special challenges for genome sequencing and for the annotation of genes. Here we describe two new genes (ARY and WDY) on the Drosophila melanogaster Y, bringing its number of known single-copy genes to 12. WDY may correspond to the fertility factor kl-1.

Most sexually reproducing species have sexual proportions around 1:1. This major biological phenomenon remained unexplained until 1930, when Fisher proposed that it results from a mechanism of natural selection. Here we report the first experimental test of his model that obeys all its assumptions. We used a naturally occurring X-Y meiotic drive system—the sex-ratio trait of Drosophila mediopunctata—to generate female-biased experimental populations. As predicted by Fisher, these populations evolved toward equal sex proportions due to natural selection, by accumulation of autosomal alleles that direct the parental reproductive effort toward the rare sex. Classical Fisherian evolution is a rather slow mechanism: despite a very large amount of genetic variability, the experimental populations evolved from 16% of males to 32% of males in 49 generations and would take 330 generations (29 years) to reach 49%. This slowness has important implications for species potentially endangered by skewed sexual proportions, such as reptiles with temperature sex determination.

Heritability of sexual proportion in experimental sex-ratio populations of Drosophila mediopunctata

We explore the notion of two-sided limit shadowing property introduced by Pilyugin \cite{P1}. Indeed, we characterize the $C^1$-interior of the set of diffeomorphisms with such a property on closed manifolds as the set of transitive Anosov diffeomorphisms. As a consequence we obtain that all codimention-one Anosov diffeomorphisms have the two-sided limit shadowing property. We also prove that every diffeomorphism $f$ with such a property on a closed manifold has neither sinks nor sources and is transitive Anosov (in the Axiom A case). In particular, no Morse-Smale diffeomorphism have the two-sided limit shadowing property. Finally, we prove that $C^1$-generic diffeomorphisms on closed manifolds with the two-sided limit shadowing property are transitive Anosov. All these results allow us to reduce the well-known conjecture about the transitivity of Anosov diffeomorphisms on closed manifolds to prove that the set of diffeomorphisms with the two-sided limit shadowing property coincides with the set of Anosov diffeomorphisms., Comment: 10 pages

EPICS is used worldwide to build distributed control systems for scientific experiments. The EPICS software suite is based around the Channel Access (CA) network protocol that allows the communication of different EPICS clients and servers in a distributed architecture. Servers are called Input/Output Controllers (IOCs) and perform real-world I/O or local control tasks. EPICS IOCs were originally designed for VxWorks to meet the demanding real-time requirements of control algorithms and have lately been ported to different operating systems. The MARTe framework has recently been adopted to develop an increasing number of hard real-time systems in different fusion experiments. MARTe is a software library that allows the rapid and modular development of stand-alone hard real-time control applications on different operating systems. MARTe has been created to be portable and during the last years it has evolved to follow the multi-core evolution.In this paper we review several implementation differences between EPICS IOC and MARTe. We dissect their internal data structures and synchronization mechanisms to understand what happens behind the scenes. Differences in the component based approach and in the concurrent model of computation in EPICS IOC and MARTe are explained. Such differences lead to distinct time models in the computational blocks and distinct real-time capabilities of the two frameworks that a developer must be aware of.

Classically, Y chromosomes are thought to originate from X chromosomes through a process of degeneration and gene loss. Now, the availability of 12 Drosophila genomes provides an opportunity to study the origin and evolution of Y chromosomes in an informative phylogenetic context. Surprisingly, the majority of Drosophila Y-linked genes are recent acquisitions from autosomes and Y chromosome gene gains are more frequent than gene losses. Moreover, the Drosophila pseudoobscura Y chromosome lacks homology with the Y of most Drosophila species. Thus, the Drosophila Y has a different evolutionary history from canonical Y chromosomes (such as the mammalian Y) and it also might have a different origin.

We present a theoretical study of solvent effect on C2H5N···HF hydrogen-bonded complex through the application of the AGOA methodology. By using the TIP4P model to orientate the configuration of water molecules, the hydration clusters generated by AGOA were obtained through the analysis of the molecular electrostatic potential (MEP) of solute (C2H5N···HF). Thereby, it was calculated the hydration energies on positive and negative MEP fields, which are maxima (PEMmax) and minima (PEMmin) when represent the -CH2- methylene groups and hydrofluoric acid, respectively. By taking into account the higher and lower hydration energy values of -370.6 kJ mol-1 and -74.3 kJ mol-1 for PEMmax and PEMmin of the C2H5N···HF, our analysis shows that these results corroborate the open ring reaction of aziridine, in which the preferential attack of water molecules occurs at the methylene groups of this heterocyclic.

B3LYP/6-311++G(d,p) calculations were used to predict some molecular properties of the C2H6N+⋯BeH2, C2H6N+⋯MgH2, C3H8N+⋯BeH2 and C3H8N+⋯MgH2 dihydrogen-bonded complexes. In these systems, it was demonstrated that the C2H6N+ and C3H8N+ protonated rings are potential candidates to bind with protonic hydrogens derived from alkaline earth metal compounds, BeH2 and MgH2. In terms of structural parameters and quantification of the dihydrogen bond energies, we should mention that the C2H6N+ three-membered ring provides the formation of stronger bound systems, which are 4.0 kJ mol−1 more stables than C3H8N+ four-membered ones. As complement, the analysis of the infrared spectrum indicated that red-shifts and blue-shifts are occurring in the N–H bonds of both C2H6N+ and C3H8N+ cationic rings. However, these two vibrational shifts were also verified on BeH2 and MgH2, what lead us to affirm that cationic compounds derived from small nitrogen rings and earth alkaline molecules are able to form unusual dihydrogen-bonded complexes by means of distinct spectroscopic phenomena, the red-shits and blue-shifts.

We presents a chemometrical study of the intermolecular properties of the C(2)H(4)O...HX and C(2)H(5)N... HX hydrogen-bonded complexes with X = F, CN, NC, and CCH. Through the MP2 perturbation theory and B3LYP hybrid functional, as well as modifications on 6-31ijGk basis sets with i = triple-zeta, j = diffuse and k = polarization functions, systematic tendencies in the R((n...HX)) hydrogen bond distances and upsilon((n...HX)) stretch frequencies were determined by the hierarchical cluster analysis, two level factorial designs and principal component analysis. Based on well-fitted math models, not only because polarization functions provide a great variance on statistical analysis, but this basis set reproduces more efficiently the available experimental results. Moreover, independent of whether the quality on basis set is increased, the effects yielded by both DFT and MP2 were not considered important in the statistical analysis.

Affiliations des auteurs : cf page 216 de l'article; International audience; Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

The geometries of three isomers of the C2H4O...2HF tri-molecular heterocyclic hydrogen-bonded complex were examined through B3LYP/aug-cc-pVDZ calculations. Analysis of structural parameters, determination of CHELPG (charge electrostatic potential grid) intermolecular charge transfer, interpretation of infrared stretching modes, and Bader's atoms in molecules (AIM) theory calculations was carried out in order to characterize the hydrogen bonds in each isomer of the C2H4O...2HF complex. The most stable structure was determined through the identification of hydrogen bonds between C2H4O and HF, (O...H), as well as in the hydrofluoric acid dimer, (HF(D-R)...HF(D)). However, the existence of a tertiary interaction (F(lambda)...H(alpha)) between the fluoride of the second hydrofluoric acid and the axial hydrogen atoms of C2H4O was decisive in the identification of the preferred configuration of the C2H4O...2HF system.

B3LYP/6-31G(d,p) calculations were used to determine the optimized geometries of the C2H4O-C2H2 and C2H4S-C2H2 heterocyclic hydrogen-bonded complexes. Results of structural, rotational, electronic and vibrational parameters indicate that the hydrogen bonding is non-linear due to the pi bond of the acetylene interacting with the hydrogen atoms of the methyl groups of the three-membered rings. Moreover, the theoretical investigation showed that the non-linearity is much more intriguing, since there is a structural disjunction on the acetylene within the heterocyclic system.

CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO Utilizada por Nietzsche em momentos diversos de sua obra, a expressão grande política revela uma perspectiva diferenciada sobre os problemas de natureza política, radicalmente divergente do aporte crítico da modernidade política. O objetivo desta dissertação é analisar a grande política, a partir de quatro hipóteses complementares. Em primeiro lugar, supomos que a grande política deva ser analisada estritamente no campo de problemas do pensamento nietzscheano, e não à contra- luz do aporte da modernidade política e filosófica. Em segundo lugar, sendo a grande política um produto da crítica dos valores morais, sua análise exige, preliminarmente, uma discussão acerca dos temas e peculiaridades concernentes a esta crítica. Em terceiro lugar, definida como um conhecimento das condições e circunstâncias nas quais [os valores] nasceram, sob as quais se desenvolveram e se modificaram, a crítica dos valores morais, entretanto, está fincada sobre uma concepção muito específica do ser e da existência, a ontologia de Nietzsche. A análise desta ontologia é, portanto, indispensável para acessar a crítica e, consequentemente, a grande política. Em qua rto e último lugar, a grande política representa o corolário das pesquisas que Nietzsche desenvolve a partir de Verdade e mentira no sentido extra-moral (1873), acerca da gênese e desenvolvimento dos valores morais, figurando portanto como expressão fundamental de seu pensamento. Used by Nietzsche in many moments of his work, the expression great politics reveals a perspective on problems of political nature radically different from the modernity theorical political critique. The aim of this work is to justify an analysis of the great politics, from four complementary hypotheses. First of all, we assume that the great politics must strictly be analyzed inside nietzschean`s thought, and not from any values related to philosophical modernity and politics. Secondly, the expression is a product of the critique of moral values (kritik der moralischen werte), and its analysis demands, preliminarily, a discussion concerning those themes related to this critique. In third place, defined as the knowledge of the conditions and circumstances in which they [the values] grew, under which they evolved and changed`, the critique of moral values, however, is sticked on a very specific conception of the being and the existence. Therefore, it`s our hypotheses that the analysis of Nietzsche`s onthology is indispensable to access the critique and, consequently, the great politics. At last, the great politics represents a corollary of Nietzsche`s researchs developed from Truth and lie in the direction extra-moral (1873) that concerns the genesis and development of moral values and, therefore, figures as a fundamental expression of his thought.

B3LYP/6-311+G(d,p) calculations were used to explore the geometry, intermolecular energy and the vibrational harmonic spectrum of heterocyclic complexes formed between 2,5-dihydrofuran and thiophene cyclic ethers and the HCl and HF acids. The simulated structures of these hydrogen complexes are discussed in terms of the linearity deviation of the n⋯HX hydrogen bond. Theoretical results are satisfactory as compared to the experimental equilibrium structure. The energies of the hydrogen bonds were determinate through the difference between the complex and its correspondent isolated monomers. Moreover, to obtain the correct energies of the hydrogen bonds, it was included the values of the zero point vibrational energy and the basis set superposition error. The infrared spectra reveal the direct relationship between the distance of the hydrogen bond and its stretching frequencies, as well as a good interpretation of the bathochromic effect of the HCl and HF stretching modes from intermolecular charge transfer.

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We report a genome-wide search of Y-linked genes in Drosophila pseudoobscura . All six identifiable orthologs of the D. melanogaster Y-linked genes have autosomal inheritance in D. pseudoobscura . Four orthologs were investigated in detail and proved to be Y-linked in D. guanche and D. bifasciata , which shows that less than 18 million years ago the ancestral Drosophila Y chromosome was translocated to an autosome in the D. pseudoobscura lineage. We found 15 genes and pseudogenes in the current Y of D. pseudoobscura , and none are shared with the D. melanogaster Y. Hence, the Y chromosome in the D. pseudoobscura lineage appears to have arisen de novo and is not homologous to the D. melanogaster Y.

The sex-ratio trait is the production of female-biased progenies due to X-linked meiotic drive in males of several Drosophila species. The driving X chromosome (called SR) is not fixed due to at least two stabilizing factors: natural selection (favoring ST, the nondriving standard X) and drive suppression by either Y-linked or autosomal genes. The evolution of autosomal suppression is explained by Fisher's principle, a mechanism of natural selection that leads to equal proportion of males and females in a sexually reproducing population. In fact, sex-ratio expression is partially suppressed by autosomal genes in at least three Drosophila species. The population genetics of this system is not completely understood. In this article we develop a mathematical model for the evolution of autosomal suppressors of SR (sup alleles) and show that: (i) an autosomal suppressor cannot invade when SR is very deleterious in males (c < ⅓, where c is the fitness of SR/Y males); (ii) “SR/ST, sup/+” polymorphisms occur when SR is partially deleterious (∼0.3 < c < 1); while (iii) SR neutrality (c = 1) results in sup fixation and thus in total abolishment of drive. So, surprisingly, as long as there is any selection against SR/Y males, neutral autosomal suppressors will not be fixed. In that case, when a polymorphic equilibrium exists, the average female proportion in SR/Y males' progeny is given approximately by (ac+1−a+a2(c+1)2+1−4ac)∕4ac, where a is the fitness of SR/ST females.

Ab initio calculations are performed at the MP2/6-311++G(d,p) and DFT/B3LYP/6-311++G(d,p) theoretical levels to obtain geometries, H-bond energies and harmonic infrared vibrational properties for the C s symmetry structures of heterocyclic hydrogen-bonded complexes, C n H m Y–HX. The H-bond lengths in DFT/B3LYP calculation level are in better agreement with the experimental values than the MP2 results. The geometry optimization are interpreted in terms of hydrogen bond nonlinearity represented by θ and ϕ angles, once the hydrogen bond is formed among n -electrons pairs of the heteroatom in heterocyclic and the hydrogen atom in HX. The hydrogen bond energy after of the zero-point vibrational energy (ZPE) and basis set superposition error (BSSE) corrections are overestimated at DFT/B3LYP, whereas the MP2 BSSE corrections are very large than corresponding DFT/B3LYP. For example, the BSSE corrections for the C 2 H 4 S–HNC complex are 7.60 and 0.09 kJ mol −1 in MP2 and DFT/B3LYP calculations levels, respectively. The new vibrational modes in infrared harmonic spectrum arising from complexation show several interesting features, especially the intermolecular stretching mode.

Whole genome shotgun assemblies have proven remarkably successful in reconstructing the bulk of euchromatic genes, with the only limit appearing to be determined by the sequencing depth. For genes imbedded in heterochromatin, however, the low cloning efficiency of repetitive sequences, combined with the computational challenges, demand that additional clues be used to annotate the sequences. One approach that has proven very successful in identifying protein coding genes in Y-linked heterochromatin of Drosophila melanogaster has been to make a BLASTable database of the small, unmapped contigs and fragments leftover at the end of a shotgun assembly, and to attempt to capture these by blasting with an appropriate query sequence. This approach often yields a staggered alignment of contigs from the unmapped set to the query sequence, as though the disjoint contigs represent small portions of the gene. Further inspection frequently shows that the contigs are broken by very large, heterochromatic introns. Methods of this sort are being expanded to make best use of all available clues to determine which unmapped contigs are associated with genes. These include use of EST libraries, and, in the case of the Y chromosome, testing of male specific genes and reduced shotgun depth of relevant contigs. It appears much more hopeful than anyone would have imagined that whole genome shotgun assemblies can recover the great bulk of even heterochromatic genes.

Annotation of an improved whole-genome shotgun assembly of the Drosophila melanogaster genome predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Fluorescence in situ hybridization was used to correlate the genomic sequence with the cytogenetic map; the annotated euchromatic sequence extends into the centric heterochromatin on each chromosome arm., Background Most eukaryotic genomes include a substantial repeat-rich fraction termed heterochromatin, which is concentrated in centric and telomeric regions. The repetitive nature of heterochromatic sequence makes it difficult to assemble and analyze. To better understand the heterochromatic component of the Drosophila melanogaster genome, we characterized and annotated portions of a whole-genome shotgun sequence assembly. Results WGS3, an improved whole-genome shotgun assembly, includes 20.7 Mb of draft-quality sequence not represented in the Release 3 sequence spanning the euchromatin. We annotated this sequence using the methods employed in the re-annotation of the Release 3 euchromatic sequence. This analysis predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Bacterial artificial chromosome (BAC)-based fluorescence in situ hybridization analysis was used to correlate the genomic sequence with the cytogenetic map in order to refine the genomic definition of the centric heterochromatin; on the basis of our cytological definition, the annotated Release 3 euchromatic sequence extends into the centric heterochromatin on each chromosome arm. Conclusions Whole-genome shotgun assembly produced a reliable draft-quality sequence of a significant part of the Drosophila heterochromatin. Annotation of this sequence defined the intron-exon structures of 30 known protein-coding genes and 267 protein-coding gene models. The cytogenetic mapping suggests that an additional 150 predicted genes are located in heterochromatin at the base of the Release 3 euchromatic sequence. Our analysis suggests strategies for improving the sequence and annotation of the heterochromatic portions of the Drosophila and other complex genomes.

The heterochromatic state of the Drosophila Y chromosome has made the cloning and identification of Y-linked genes a challenging process. Here, we report application of a procedure to identify Y-linked gene fragments from the unmapped residue of the whole genome sequencing effort. Previously identified Y-linked genes appear in sequenced scaffolds as individual exons, apparently because many introns have become heterochromatic, growing to enormous size and becoming virtually unclonable. A TBLASTN search using all known proteins as query sequences, tested against a blastable database of the unmapped fragments, produced a number of matches consistent with this scenario. Reverse transcription–PCR and genetic methods were used to confirm those that are expressed, Y-linked genes. The five genes reported here include three protein phosphatases ( Pp1-Y1 , Pp1-Y2 , and PPr-Y ), an occludin-related gene ( ORY ), and a coiled-coils gene ( CCY ). This brings the total to nine protein-coding genes identified on the Drosophila Y chromosome. ORY and CCY may correspond, respectively, to the fertility factors ks-1 and ks-2 , whereas the three protein phosphatases represent novel genes. There remains a strong functional coherence to male function among the genes on the Drosophila Y chromosome.

Intron sizes vary widely among different genes and among homologous genes of different species. The distribution of intron sizes may be maintained in a steady state, reflecting the processes of insertion and deletion of gene sequences, or it may be that the distribution is constrained by natural selection1,2,3. If intron size is governed by natural selection, there should be a statistical association between this size and the rate of recombination per map unit of the genome, assuming that natural selection is less effective in genomic regions of low recombination4,5,6. Here we show that larger introns of Drosophila melanogaster occur preferentially in regions of low recombination, which is consistent with large introns having a deleterious effect. The association is significant (P=40.001, linear regression), despite the fact that no effort was made to stratify the data by other factors that affect intron size, such as the size of the associated coding region7 or the presence of regulatory sequences inside the intron.

In several Drosophila species there is a trait known as “sex-ratio”: males carrying certain X chromosomes (called “SR”) produce female biased progenies due to X-Y meiotic drive. In Drosophila mediopunctata this trait has a variable expression due to Y-linked suppressors of sex-ratio expression, among other factors. There are two types of Y chromosomes (suppressor and nonsuppressor) and two types of SR chromosomes (suppressible and unsuppressible). Sex-ratio expression is suppressed in males with the SRsuppressible/Ysuppressor genotype, whereas the remaining three genotypes produce female biased progenies. Now we have found that ∼10–20% of the Y chromosomes from two natural populations 1500 km apart are suppressors of sex-ratio expression. Preliminary estimates indicate that Ysuppressor has a meiotic drive advantage of 6% over Ynonsuppressor. This Y polymorphism for a nonneutral trait is unexpected under current population genetics theoly. We propose that this polymorphism is stabilized by an equilibrium between meiotic drive and natural selection, resulting from interactions in the population dynamics of X and Y alleles. Numerical simulations showed that this mechanism may stabilize nonneutral Y polymorphisms such as we have found in D. mediopunctata.

Many organisms have sexual recombination, yet its advantages are not fully understood. A new study of the fruit fly Drosophila miranda shows that recombination is essential for removing deleterious mutations from the genome and for allowing beneficial mutations to be incorporated.

Background: Most eukaryotic genomes include a substantial repeat-rich fraction termed heterochromatin, which is concentrated in centric and telomeric regions. The repetitive nature of heterochromatic sequence makes it difficult to assemble and analyze. To better understand the heterochromatic component of the Drosophila melanogaster genome, we characterized and annotated portions of a whole-genome shotgun sequence assembly. Results: WGS3, an improved whole-genome shotgun assembly, includes 20.7 Mb of draft-quality sequence not represented in the Release 3 sequence spanning the euchromatin. We annotated this sequence using the methods employed in the re-annotation of the Release 3 euchromatic sequence. This analysis predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Bacterial artificial chromosome (BAC)-based fluorescence in situ hybridization analysis was used to correlate the genomic sequence with the cytogenetic map in order to refine the genomic definition of the centric heterochromatin; on the basis of our cytological definition, the annotated Release 3 euchromatic sequence extends into the centric heterochromatin on each chromosome arm. Conclusions: Whole-genome shotgun assembly produced a reliable draft-quality sequence of a significant part of the Drosophila heterochromatin. Annotation of this sequence defined the intron-exon structures of 30 known protein-coding genes and 267 protein-coding gene models. The cytogenetic mapping suggests that an additional 150 predicted genes are located in heterochromatin at the base of the Release 3 euchromatic sequence. Our analysis suggests strategies for improving the sequence and annotation of the heterochromatic portions of the Drosophila and other complex genomes.