Genome-scale analysis and comparison of gene expression profiles in developing and germinated pollen in Oryza sativa

<p>Abstract</p> <p>Background</p> <p>Pollen development from the microspore involves a series of coordinated cellular events, and the resulting mature pollen has a specialized function to quickly germinate, produce a polar-growth pollen tube derived from the vegetative cell, and deliver two sperm cells into the embryo sac for double fertilization. The gene expression profiles of developing and germinated pollen have been characterised by use of the eudicot model plant <it>Arabidopsis</it>. Rice, one of the most important cereal crops, has been used as an excellent monocot model. A comprehensive analysis of transcriptome profiles of developing and germinated pollen in rice is important to understand the conserved and diverse mechanism underlying pollen development and germination in eudicots and monocots.</p> <p>Results</p> <p>We used Affymetrix GeneChip^®Rice Genome Array to comprehensively analyzed the dynamic changes in the transcriptomes of rice pollen at five sequential developmental stages from microspores to germinated pollen. Among the 51,279 transcripts on the array, we found 25,062 pollen-preferential transcripts, among which 2,203 were development stage-enriched. The diversity of transcripts decreased greatly from microspores to mature and germinated pollen, whereas the number of stage-enriched transcripts displayed a "U-type" change, with the lowest at the bicellular pollen stage; and a transition of overrepresented stage-enriched transcript groups associated with different functional categories, which indicates a shift in gene expression program at the bicellular pollen stage. About 54% of the now-annotated rice F-box protein genes were expressed preferentially in pollen. The transcriptome profile of germinated pollen was significantly and positively correlated with that of mature pollen. Analysis of expression profiles and coexpressed features of the pollen-preferential transcripts related to cell cycle, transcription, the ubiquitin/26S proteasome system, phytohormone signalling, the kinase system and defense/stress response revealed five expression patterns, which are compatible with changes in major cellular events during pollen development and germination. A comparison of pollen transcriptomes between rice and <it>Arabidopsis </it>revealed that 56.6% of the rice pollen preferential genes had homologs in <it>Arabidopsis </it>genome, but 63.4% of these homologs were expressed, with a small proportion being expressed preferentially, in <it>Arabidopsis </it>pollen. Rice and <it>Arabidopsis </it>pollen had non-conservative transcription factors each.</p> <p>Conclusions</p> <p>Our results demonstrated that rice pollen expressed a set of reduced but specific transcripts in comparison with vegetative tissues, and the number of stage-enriched transcripts displayed a "U-type" change during pollen development, with the lowest at the bicellular pollen stage. These features are conserved in rice and <it>Arabidopsis</it>. The shift in gene expression program at the bicellular pollen stage may be important to the transition from earlier cell division to later pollen maturity. Pollen at maturity pre-synthesized transcripts needed for germination and early pollen tube growth. The transcription regulation associated with pollen development would have divergence between the two species. Our results also provide novel insights into the molecular program and key components of the regulatory network regulating pollen development and germination.</p

Assessment of changes in lipid profile and related enzymes in children with asthma

Purpose: To investigate the influence of the lipid profile and related parameters on the development of asthma in children aged 10 to 15 years.Methods: Peripheral blood samples were collected from a group diagnosed with asthma as well as from a healthy control group. The lipid profile parameters measured were total cholesterol (TC), triglycerides (TG), low-density lipoprotein (LDL), very-low-density lipoprotein (VLDL), high-density lipoprotein (HDL), serum total antioxidant capacity (TAC), reduced glutathione (GSH), and malondialdehyde (MDA), and the activities of lecithin–cholesterol acyltransferase (LCAT) and cholesteryl ester transfer protein (CETP).Results: TC, TG, LDL, and VLDL levels were significantly (p ≤ 0.05) higher in the asthma group compared with the controls, while HDL level was lower. Total TAC and GSH were lower in the asthma group, while MDA level, and LCAT and CETP activities were higher.Conclusion: There is a link between an elevated lipid profile and increased antioxidant capacity in asthmatic children

Deficiency of Mkrn2 causes abnormal spermiogenesis and spermiation, and impairs male fertility.

Although recent studies have shed insights on some of the potential causes of male infertility, new underlining molecular mechanisms still remain to be elucidated. Makorin-2 (Mkrn2) is an evolutionarily conserved gene whose biological functions are not fully known. We developed an Mrkn2 knockout mouse model to study the role of this gene, and found that deletion of Mkrn2 in mice led to male infertility. Mkrn2 knockout mice produced abnormal sperms characterized by low number, poor motility, and aberrant morphology. Disruption of Mkrn2 also caused failure of sperm release (spermiation failure) and misarrangement of ectoplasmic specialization (ES) in testes, thus impairing spermiogenesis and spermiation. To understand the molecular mechanism, we found that expression of Odf2, a vital protein in spermatogenesis, was significantly decreased. In addition, we found that expression levels of Odf2 were decreased in Mkrn2 knockout mice. We also found that MKRN2 was prominently expressed in the sperm of normal men, but was significantly reduced in infertile men. This result indicates that our finding is clinically relevant. The results of our study provided insights into a new mechanism of male infertility caused by the MKRN2 downregulation

Enhancing 1α-Hydroxylase Activity with the 25-Hydroxyvitamin D-1α-Hydroxylase Gene in Cultured Human Keratinocytes and Mouse Skin

1α,25-Dihydroxyvitamin D3 (1α,25(OH)2D3) and its analogs are used to treat psoriasis because of their potent antiproliferative activity. They have the potential for causing hypercalcemia, however, and patients often become resistant to the drug. We examined the feasibility of enhancing the cutaneous production of 1α,25(OH)2D3 using a human 25-hydroxyvitamin D-1α-hydroxylase (1α-OHase) plasmid. The 1α-OHase gene was fused to the green fluorescent protein gene (1α-OHase-GFP) driven by the cytomegalovirus promoter. Transfection of cultured normal human keratinocytes with the 1α-OHase-GFP plasmid resulted in a marked increase in the expression of 1α-OHase-GFP in the mitochondria. Transfection of keratinocytes with 1α-OHase-GFP or 1α-OHase plasmids in vitro enhanced the 1α-OHase activity substantially and increased the sensitivity of the keratinocytes to the antiproliferative effect of 25(OH)D3. The 1α-OHase-GFP plasmid was topically applied to shaved C57/BL6 mice. Twenty-four hours after topical application, immunohistochemical analysis of the skin for 1α-OHase-GFP revealed the presence of 1α-OHase-GFP in the epidermis and epidermal appendages including the hair follicles. The results from this study offer a unique new approach for the topical treatment of hyperproliferative disorders such as psoriasis and skin cancer using the 1α-OHase gene that could locally increase the production of 1α,25(OH)2D3 without causing hypercalcemia or resistance

Complete mitochondrial genomes of Taenia multiceps, T. hydatigena and T. pisiformis: additional molecular markers for a tapeworm genus of human and animal health significance

<p>Abstract</p> <p>Background</p> <p>Mitochondrial genomes provide a rich source of molecular variation of proven and widespread utility in molecular ecology, population genetics and evolutionary biology. The tapeworm genus <it>Taenia </it>includes a diversity of tapeworm parasites of significant human and veterinary importance. Here we add complete sequences of the mt genomes of <it>T. multiceps</it>, <it>T. hydatigena </it>and <it>T. pisiformis</it>, to a data set of 4 published mtDNAs in the same genus. Seven complete mt genomes of <it>Taenia </it>species are used to compare and contrast variation within and between genomes in the genus, to estimate a phylogeny for the genus, and to develop novel molecular markers as part of an extended mitochondrial toolkit.</p> <p>Results</p> <p>The complete circular mtDNAs of <it>T. multiceps</it>, <it>T. hydatigena </it>and <it>T. pisiformis </it>were 13,693, 13,492 and 13,387 bp in size respectively, comprising the usual complement of flatworm genes. Start and stop codons of protein coding genes included those found commonly amongst other platyhelminth mt genomes, but the much rarer initiation codon GTT was inferred for the gene <it>atp</it>6 in <it>T. pisiformis</it>. Phylogenetic analysis of mtDNAs offered novel estimates of the interrelationships of <it>Taenia</it>. Sliding window analyses showed <it>nad</it>6, <it>nad</it>5, <it>atp</it>6, <it>nad</it>3 and <it>nad</it>2 are amongst the most variable of genes per unit length, with the highest peaks in nucleotide diversity found in <it>nad</it>5. New primer pairs capable of amplifying fragments of variable DNA in <it>nad</it>1, <it>rrn</it>S and <it>nad</it>5 genes were designed <it>in silico </it>and tested as possible alternatives to existing mitochondrial markers for <it>Taenia</it>.</p> <p>Conclusions</p> <p>With the availability of complete mtDNAs of 7 <it>Taenia </it>species, we have shown that analysis of amino acids provides a robust estimate of phylogeny for the genus that differs markedly from morphological estimates or those using partial genes; with implications for understanding the evolutionary radiation of important <it>Taenia</it>. Full alignment of the nucleotides of <it>Taenia </it>mtDNAs and sliding window analysis suggests numerous alternative gene regions are likely to capture greater nucleotide variation than those currently pursued as molecular markers. New PCR primers developed from a comparative mitogenomic analysis of <it>Taenia </it>species, extend the use of mitochondrial markers for molecular ecology, population genetics and diagnostics.</p

Target Deletion of the Cytoskeleton-Associated Protein Palladin Does Not Impair Neurite Outgrowth in Mice

Palladin is an actin cytoskeleton–associated protein which is crucial for cell morphogenesis and motility. Previous studies have shown that palladin is localized to the axonal growth cone in neurons and may play an important role in axonal extension. Previously, we have generated palladin knockout mice which display cranial neural tube closure defect and embryonic lethality before embryonic day 15.5 (E15.5). To further study the role of palladin in the developing nervous system, we examined the innervation of palladin-deficient mouse embryos since the 200 kd, 140 kd, 90–92 kd and 50 kd palladin isoforms were undetectable in the mutant mouse embryo brain. Contrary to the results of previous studies, we found no inhibition of the axonal extension in palladin-deficient mouse embryos. The cortical neurons derived from palladin-deficient mice also showed no significant difference in neurite outgrowth as compared with those from wild-type mice. Moreover, no difference was found in neurite outgrowth of neural stem cell derived-neurons between palladin-deficient mice and wild-type mice. In conclusion, these results suggest that palladin is dispensable for normal neurite outgrowth in mice

Identifying Modules of Coexpressed Transcript Units and Their Organization of Saccharopolyspora erythraea from Time Series Gene Expression Profiles

BACKGROUND: The Saccharopolyspora erythraea genome sequence was released in 2007. In order to look at the gene regulations at whole transcriptome level, an expression microarray was specifically designed on the S. erythraea strain NRRL 2338 genome sequence. Based on these data, we set out to investigate the potential transcriptional regulatory networks and their organization. METHODOLOGY/PRINCIPAL FINDINGS: In view of the hierarchical structure of bacterial transcriptional regulation, we constructed a hierarchical coexpression network at whole transcriptome level. A total of 27 modules were identified from 1255 differentially expressed transcript units (TUs) across time course, which were further classified in to four groups. Functional enrichment analysis indicated the biological significance of our hierarchical network. It was indicated that primary metabolism is activated in the first rapid growth phase (phase A), and secondary metabolism is induced when the growth is slowed down (phase B). Among the 27 modules, two are highly correlated to erythromycin production. One contains all genes in the erythromycin-biosynthetic (ery) gene cluster and the other seems to be associated with erythromycin production by sharing common intermediate metabolites. Non-concomitant correlation between production and expression regulation was observed. Especially, by calculating the partial correlation coefficients and building the network based on Gaussian graphical model, intrinsic associations between modules were found, and the association between those two erythromycin production-correlated modules was included as expected. CONCLUSIONS: This work created a hierarchical model clustering transcriptome data into coordinated modules, and modules into groups across the time course, giving insight into the concerted transcriptional regulations especially the regulation corresponding to erythromycin production of S. erythraea. This strategy may be extendable to studies on other prokaryotic microorganisms

Challenges and recent advancements of functionalization of two-dimensional nanostructured molybdenum trioxide and dichalcogenides

Atomically-thin two-dimensional (2D) semiconductors are the thinnest functional semiconducting materials available today. Among them, both molybdenum trioxide and chalcogenides (MT&Ds) represent key components within the family of the different 2D semiconductors for various electronic, optoelectronic and electrochemical applications due to their unique electronic, optical, mechanical and electrochemical properties. However, despite great progress in research dedicated to the development and fabrication of 2D MT&Ds observed within the last decade, there are significant challenges affected their charge transport behavior, fabrication on a large scale as well as high dependence of the carrier mobility on thickness. In this article, we review the recent progress on the carrier mobility engineering of 2D MT&Ds and elaborate devised strategies dedicated to the optimization of MT&Ds properties. Specifically, the latest physical and chemical methods towards the surface functionalization and optimization of the major factors influencing the extrinsic transport at the electrode-2D semiconductor interface are discusse