Re-analysis of the larval testis data on meiotic sex chromosome inactivation revealed evidence for tissue-specific gene expression related to the drosophila X chromosome

<p>Abstract</p> <p>Background</p> <p>Meiotic sex chromosome inactivation (MSCI) during spermatogenesis has been proposed as one of the evolutionary driving forces behind both the under-representation of male-biased genes on, and the gene movement out of, the X chromosome in <it>Drosophila</it>. However, the relevance of MSCI in shaping sex chromosome evolution is controversial. Here we examine two aspects of a recent study on testis gene expression (Mikhaylova and Nurminsky, <it>BMC Biol </it>2011, <b>9:</b>29) that failed to support the MSCI in <it>Drosophila</it>. First, Mikhaylova and Nurminsky found no differences between X-linked and autosomal genes based on the transcriptional profiling of the early testis development, and thus concluded that MSCI does not occur in <it>D. melanogaster</it>. Second, they also analyzed expression data from several <it>D. melanogaster </it>tissues and concluded that under-representation on the X chromosome is not an exclusive property of testis-biased genes, but instead, a general property of tissue-specific genes.</p> <p>Results</p> <p>By re-analyzing the Mikhaylova and Nurminsky's testis data and the expression data on several <it>D. melanogaster </it>tissues, we made two major findings that refuted their original claims. First, the developmental testis data has generally greater experimental error than conventional analyses, which reduced significantly the power to detect chromosomal differences in expression. Nevertheless, our re-analysis observed significantly lower expression of the X chromosome in the genomic transcriptomes of later development stages of the testis, which is consistent with the MSCI hypothesis. Second, tissue-specific genes are also in general enriched with genes more expressed in testes than in ovaries, that is testis-biased genes. By completely excluding from the analyses the testis-biased genes, which are known to be under-represented in the X, we found that all the other tissue-specific genes are randomly distributed between the X chromosome and the autosomes.</p> <p>Conclusions</p> <p>Our findings negate the original study of Mikhaylova and Nurminsky, which concluded a lack of MSCI and generalized the pattern of paucity in the X chromosome for tissue-specific genes in <it>Drosophila</it>. Therefore, MSCI and other selection-based models such as sexual antagonism, dosage compensation, and meiotic-drive continue to be viable models as driving forces shaping the genomic distribution of male-related genes in <it>Drosophila</it>.</p

Adaptive Evolution and the Birth of CTCF Binding Sites in the Drosophila Genome

Changes in the physical interaction between cis-regulatory DNA sequences and proteins drive the evolution of gene expression. However, it has proven difficult to accurately quantify evolutionary rates of such binding change or to estimate the relative effects of selection and drift in shaping the binding evolution. Here we examine the genome-wide binding of CTCF in four species of Drosophila separated by between ~2.5 and 25 million years. CTCF is a highly conserved protein known to be associated with insulator sequences in the genomes of human and Drosophila. Although the binding preference for CTCF is highly conserved, we find that CTCF binding itself is highly evolutionarily dynamic and has adaptively evolved. Between species, binding divergence increased linearly with evolutionary distance, and CTCF binding profiles are diverging rapidly at the rate of 2.22% per million years (Myr). At least 89 new CTCF binding sites have originated in the Drosophila melanogaster genome since the most recent common ancestor with Drosophila simulans. Comparing these data to genome sequence data from 37 different strains of Drosophila melanogaster, we detected signatures of selection in both newly gained and evolutionarily conserved binding sites. Newly evolved CTCF binding sites show a significantly stronger signature for positive selection than older sites. Comparative gene expression profiling revealed that expression divergence of genes adjacent to CTCF binding site is significantly associated with the gain and loss of CTCF binding. Further, the birth of new genes is associated with the birth of new CTCF binding sites. Our data indicate that binding of Drosophila CTCF protein has evolved under natural selection, and CTCF binding evolution has shaped both the evolution of gene expression and genome evolution during the birth of new genes

Power balance control strategy for staircase modulation based on improved particle swarm optimization algorithm

In view of problem of unbalanced output power of each H-bridge for staircase modulation of cascaded multilevel inverter, a power balance control strategy for staircase modulation of adjusting pulse switching angle was proposed, which realized power balance in one output cycle through interchanging output voltage of the H-bridge each 1/4 output cycle. Meanwhile, an improved particle swarm optimization algorithm based on dynamic change of inertia weight was applied into solution of switching angles of power balance control strategy for staircase modulation, which could get the optimal solution of switching angle quickly and efficiently by dynamically decreasing inertia weight with increase of evolution algebra without initial value. The simulation results verify feasibility and validity of power balance control strategy for staircase modulation based on improved particle swarm optimization algorithm

Modified Modulation Strategy of 1: 1: 2 Asymmetric Nine-Level Inverter and Its Power Balance Method

The three unit nine-level inverter can output more voltage levels with fewer h-bridge units, while having better output waveform quality. However, in the conventional hybrid frequency modulation strategy, only one low-voltage unit adopts pulse width modulation (PWM), which causes the problem of switching loss and uneven heat distribution between the two low-voltage units. At the same time, the output power of the conventional modulation strategy is unbalanced. Aiming to resolve the above problems, a modified hybrid modulation strategy and a power balance control method under the strategy is proposed in this paper. The modulation strategy achieves output power balance between the three units and an even distribution of switching losses between the two low voltage units while maintaining the same output power quality. Simulation and experimental results verify the feasibility of the modulation strategy

Multiband SHEPWM Control Technology Based on Walsh Functions

The drawback of modulation ratio limitation in selective harmonic elimination pulse width modulation (SHEPWM) technology based on Walsh function transformation. In order to solve this problem, a multiband SHEPWM control technology method for a multilevel inverter based on Walsh functions is proposed. By analyzing multiband SHEPWM for multilevel inverter voltage waveforms under a Fourier series transform, the unified nonlinear multiband SHEPWM equations for a multilevel inverter with a modulation index varying from 0 to 1 can be generalized. The equations can be solved by Walsh function transform. In this way, the difficulties faced in expanding the modulation index, online calculation, and real-time control are resolved simultaneously. A seven-level inverter is taken as the example, for which the piecewise linear equations of Walsh functions under different bands and the trajectories of switching angles are given. Meanwhile, the conditions for multiple sets of solutions at such a point where the modulation index is switched over are also taken into account. The feasibility of the proposed method is verified by simulation based on MATLAB and SIMULINK. Finally, the feasibility of the practical application is proved by the experiment based on Digital Signal Processor (DSP)

Research on Modified Hybrid Frequency Modulation Technology of Type-III Asymmetric CHB Multilevel Inverters

Asymmetric Cascaded H-bridge (ACHB) level inverters can output more voltage waveforms with fewer cascaded units while ensuring the quality of output voltage waveforms, so they have attracted more and more attention. Taking the topology of Type-III asymmetric CHB multilevel inverters as the research object, a Modified Hybrid Frequency Pulse Width Modulation (MHF-PWM) strategy is proposed in this paper. This modulation strategy overcomes the local overshoot of low-voltage unit in the presence of traditional Hybrid Frequency Pulse Width Modulation (HF-PWM), thus completely eliminating the low frequency harmonics in the output voltage waveform of Type-III ACHB nine-level inverters, and the Total Harmonic Distortion (THD) of output line voltage of the modulation strategy is lower than that of PS-PWM strategy in the whole modulation degree, which effectively improves the quality waveform of the output line voltage. At the same time, the strategy can also improve the problems of current backflow and energy feedback caused by the high-voltage unit pouring current to the low-voltage unit, thereby reducing the imbalance of the output power of the high-voltage and low-voltage units. Finally, the Matlab/Simulink simulation model and experimental platform are established to verify the validity and practicality of the modulation strategy

The DDX23 Negatively Regulates Translation and Replication of Foot-and-Mouth Disease Virus and Is Degraded by 3C Proteinase

DEAD-box helicase 23 (DDX23) is a host nuclear helicase, which is a part of the spliceosomal complex and involved in pre-mRNA splicing. To investigate whether DDX23, an internal ribosomal entry sites transacting factor (ITAF) affects foot-and-mouth disease virus (FMDV) replication and translation through internal ribosome entry site (IRES)-dependent manner. For this, we utilized a pull-down assay, Western blotting, quantitative real-time PCR, confocal microscopy, overexpression and small interfering RNA knockdown, as well as the median tissue culture infective dose. Our findings showed that FMDV infection inhibited DDX23 expression and the overexpression of DDX23 reduced viral replication, however, CRISPR Cas9 knockout/small interfering RNA knockdown increased FMDV replication. FMDV IRES domain III and IV interacted with DDX23, whereas DDX23 interacted with FMDV 3C proteinase and significantly degraded. The enzymatic activity of FMDV 3C proteinase degraded DDX23, whereas FMDV degraded DDX23 via the lysosomal pathway. Additionally, IRES-driven translation was suppressed in DDX23-overexpressing cells, and was enhanced in DDX23 knocked down. Collectively, our results demonstrated that DDX23 negatively affects FMDV IRES-dependent translation, which could be a useful target for the design of antiviral drugs

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

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