Identification and characterization of satellite DNAs in Poa L.

Background Poa L. is a large genus of grass in Gramineae, among which P. pratensis is widely cultivated as turf and forage. Satellite DNA is the main components of the plant genome. Information of satellites will helpful for dissection the genome composition and definition of the phylogeny relationship of these species. However, the knowledge about the satellites in genus Poa is still limited. Results Four satellite DNAs were identified using the Repeat Explorer pipeline in HiSeq Illumina reads from diploid plants in P. malaca (2n = 26). Two satellites showed high similarity with the previously identified PpTr-1 and PpTr-3, whereas two others are newly identified with the monomer of 326 bp (Poa-326) and 353 bp (Poa-353) respectively. The clone DNAs of PpTr-1 and PpTr-3, and oligonucleotides designed representing satellites Poa-326 and Poa-353 were probed to test on chromosomes across 13 Poa speceis with different polyploidy level by fluorescent in situ hybridization (FISH). PpTr-1, PpTr-3, and Poa-362 were stably positioned in the subtelomeric regions in nearly all species with the variation of hybridization sites number. However, Poa-353 showed different FISH patterns of multiple regions with the variation of hybridization intensity and distribution sites across species. In addition, 5S rDNA and 45S rDNA were used to characterize the genome of the Poa species. Four rDNA FISH patterns were revealed in the tested species. Conclusion Four identified satellite were high conservable across Poa species. Genome distribution of these satellites can be characterized by FISH. The variation of satellite DNAs and rDNA chromosomal distributions between species provide useful information for phylogenetic analysis in genus Poa.

Identification and Characterization of Satellite DNAs in Poa L.

BackgroundPoa L is a large genus of grass in Gramineae, among which P. pratensis is widely cultivated as turf and forage. Satellite DNA is the main components of the plant genome. Information of satellites will helpful for dissection the genome composition and definition of the phylogeny relationship of these species. However, the knowledge about the satellites in genus Poa is still limited.ResultsFour satellite DNAs were identified using the Repeat Explorer pipeline in HiSeq Illumina reads from diploid plants in P. malaca (2n = 26). Two satellites showed high similarity with the previously identified PpTr-1 and PpTr-3, whereas two others are newly identified with the monomer of 326bp (Poa-326) and 353bp (Poa-353) respectively. The clone DNAs of PpTr-1 and PpTr-3, and oligonucleotides designed representing satellites Poa-326 and Poa-353 were probed to test on chromosomes across 13 Poa speceis with different polyploidy level by fluorescent in situ hybridization (FISH). PpTr-1, PpTr-3, and Poa-362 were stably positioned in the subtelomeric regions in nearly all species with the variation of hybridization sites number. However, Poa-353 showed different FISH patterns of multiple regions with the variation of hybridization intensity and distribution sites across species. In addition, 5S rDNA and 45S rDNA were used to characterize the genome of the Poa species. Four rDNA FISH patterns were revealed in the tested species.ConclusionFour identified satellite were high conservable across Poa species. Genome distribution of these satellites can be characterized by FISH. The variation of satellite DNAs and rDNA chromosomal distributions between species provide useful information for phylogenetic analysis in genus Poa.

MicroRNA Expression Profiling of Epithelial Ovarian Cancer Identifies New Markers of Tumor Subtype

Background: Epithelial ovarian cancer (EOC) is often challenging to diagnose, even though histological examination. microRNA (miRNA or miRNA) is bound to the target messenger RNA (mRNA) and causing the mRNA molecules are silenced. The identification of miRNA expression-based EOC subtypes is considered a critical means of prognostication. So far, the studies on EOC subtypes have not been well characterized. Objective: This study aimed to confirm the existence of miRNAs in EOC and to assess their potential as clinical biomarkers for EOC. Methods: We sampled 25 ovarian tumor tissues from patients with human ovarian tumors (17 malignant; 12 serous EOC, five non-serous EOC, and eight benign ovarian tumors). miRNA microarray detection was performed to identify EOC miRNAs. Real-time PCR was adapted for the validation of differentially expressed miRNAs detected by microarray analysis was related to hybridization intensity. Results: The results confirmed that miRNAs exist in EOC, relative expression of EOC miRNAs demonstrated that upregulation of miR-483-5p, and downregulation of miR-127-3p, and miR-532-5p were significantly expressed in the malignant group than in the benign group at p ' 0.05. Besides, miR-483-5p could also distinguish EOC subtypes between serous EOC and non-serous EOC, with a p ' 0.05. Conclusion: A comprehensive miRNA expression profiling can help to refine subtype classification in EOC, opening new opportunities for identifying clinically applicable markers for improved stratification and diagnostics of ovarian tumors.

Hybridization of ODNs with the Core-Shell Structure of Fe3O4 Nanoparticles and CS/ALG Composite Structure

This study develops a nanocomposite structure with magnetism and biocompatibility. Composite structures with magnetism can be applied for biomarkers, specific tissue cell detection and targeted drug therapy. This study adopts a chemical disposition method to prepare Fe3O4 magnetic nanoparticles with the average size of 20-25nm. The complex biocompatible chitosan-alginate membrane covers Fe3O4 magnetic nanoparticles and the thickness of the complex membrane is controlled at 50-80nm. The efficiency of the oligonucleotide (ODN) combination is increased through the high biocompatibility of this composite film. Two groups of different sequences of ODNs and a bridge ODN undergo hybridization. The results show that the intensity at which the Fe3O4 is covered by chitosan-alginate composite film conjugated with ODNs is 2300nN. Furthermore, Fe3O4 covered by complex membrane of chitosan-alginate hybridized with 30 μM ODNs to yield the optimum hybridization intensity of 4528 nN, and the average hybridization intensity of ODNs with different concentration is 3971 nN.

The Geometric and Electronic Structures of Fen-1Si(n=2-7) Clusters

The geometric structures and electronic properties of Si doped Fen (n=2-7) clusters have been systematically studied at the BPW91 level in density-functional theory (DFT). Calculated results show that an Si impurity does not change the ground-state structure of small iron clusters and prefers to occupy surface site bonding with iron atoms as many as possible. The second-order energy difference and the vertical ionization potential show that n=4 and 6 are magic numbers within the size range studied, but the maximum value occurs at n=4 for the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital(LUMO). It is found that the hybridization intensity between Si and Fe atoms is relevant to the stability of clusters.

Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays

ABSTRACT In April 2009, a new influenza A (H1N1 2009) virus emerged that rapidly spread around the world. While current variants of this virus have caused widespread disease, particularly in vulnerable groups, there remains the possibility that future variants may cause increased virulence, drug resistance or vaccine escape. Early detection of these virus variants may offer the chance for increased containment and potentially prevention of the virus spread. We have developed and field-tested a resequencing kit that is capable of interrogating all eight segments of the 2009 influenza A(H1N1) virus genome and its variants, with added focus on critical regions such as drug-binding sites, structural components and mutation hotspots. The accompanying base-calling software (EvolSTAR) introduces novel methods that utilize neighbourhood hybridization intensity profiles and substitution bias of probes on the microarray for mutation confirmation and recovery of ambiguous base queries. Our results demonstrate that EvolSTAR is highly accurate and has a much improved call rate. The high throughput and short turn-around time from sample to sequence and analysis results (30 h for 24 samples) makes this kit an efficient large-scale evolutionary biosurveillance tool.

Expression Quantitative Trait Locus Mapping of Toxoplasma Genes Reveals Multiple Mechanisms for Strain-Specific Differences in Gene Expression

ABSTRACT Toxoplasma gondii is an intracellular parasite with a significant impact on human health, especially in cases where individuals are immunocompromised (e.g., due to human immunodeficiency virus/AIDS). In Europe and North America, only a few clonal genotypes appear to be responsible for the vast majority of Toxoplasma infections, and these clonotypes have been intensely studied to identify strain-specific phenotypes that may play a role in the manifestation of more-severe disease. To identify and genetically map strain-specific differences in gene expression, we have carried out expression quantitative trait locus analysis on Toxoplasma gene expression phenotypes by using spotted cDNA microarrays. This led to the identification of 16 Toxoplasma genes that had significant and mappable strain-specific variation in hybridization intensity. While the analysis should identify both cis- and trans-mapping hybridization profiles, we identified only loci with strain-specific hybridization differences that are most likely due to differences in the locus itself (i.e., cis mapping). Interestingly, a larger number of these cis-mapping genes than would be expected by chance encode either confirmed or predicted secreted proteins, many of which are known to localize to the specialized secretory organelles characteristic of members of the phylum Apicomplexa. For six of the cis-mapping loci, we determined if the strain-specific hybridization differences were due to true transcriptional differences or rather to strain-specific differences in hybridization efficiency because of extreme polymorphism and/or deletion, and we found examples of both scenarios.

Gonadotropin requirements for dominant follicle selection in GnRH agonist-treated cows

A study was conducted to examine the effects of gonadotropins on ovarian follicular development and differentiation in GnRH agonist (GnRHa)-treated cattle. Holstein cows were allotted into two pre-treatment groups: controls (n = 5) and GnRHa-treated (n = 9). Ovaries were removed from control cows on day 5 following a synchronized estrus. Treatment with GnRHa resulted in follicular arrest at <5 mm. Following follicular arrest, GnRHa-treated cows received a constant infusion of FSH for 96 h (GnRHa/FSH), with a randomly selected subset receiving hourly pulses of LH in addition to FSH during the last 48 h of infusion (GnRHa/FSH + LH). At the end of infusion, ovaries were removed, follicles were counted and measured, and follicular fluid samples were collected from large follicles (>10 mm). Differences in expression of mRNA for LH receptor, FSH receptor, cytochrome P450 side-chain cleavage, 3β-hydroxysteroid dehydrogenase, cytochrome P450 17α-hydroxylase (P450c17) and cytochrome P450 aromatase were determined in large follicles using in situ hybridization. The number of large follicles did not differ between GnRHa/FSH-treated and GnRHa/FSH + LH-treated cows (P = 0.64), but was greater than control animals (P ≤ 0.004). Follicular fluid concentrations of estradiol-17β and androstenedione were highest in GnRHa/FSH + LH-treated cows (P ≤ 0.04), intermediate in control cows, and lowest in GnRHa/FSH-treated cows. Hybridization intensity of P450c17 was greater in GnRHa/FSH + LH-treated versus control or GnRHa/FSH-treated cows (P ≤ 0.03). These results indicate that while FSH can support bovine follicular growth >10 mm, LH increases androgen production and expression of P450c17.

Identification and Characteristics of a Novel E1 Like Gene nUBE1L in Human Testis

A gene, presumably involved in spermatogenesis, was identified and characterized by using cDNA microarray. Hybridization intensity was 2.13 fold higher in adult testis than that in fetal testis. The full length of this gene was 4288 bp and it encoded a 578 amino acid protein. Conserved structure and amino acid sequence analysis revealed that the protein contained 1 Thif-domain, 2 UBACT-domains, and a functional active site cysteine lay upstream of UBACT domain, all of them also existed in ubiquitin-activating enzyme E1 and E1 like proteins. So we named this gene as a novel ubiquitin-activating enzyme E1 like gene (nUBE1L). Expression profile showed that nUBE1L was predominantly expressed in testis. Comparison of the expression of nUBE1L in different developmental stages of testis indicated that it was highly expressed in adult testis. In conclusion, nUBE1L is a novel human E1 like gene highly expressed in adult testis, which plays key role in ubiquitin system, and accordingly influences spermatogenesis and male fertility.

The expression and regulation of Bcl-2-related ovarian killer (Bok) mRNA in the developing and adult rat testis

OBJECTIVE: To study the role of Bcl-2-related ovarian killer (Bok) in the regulation of apoptosis in the testis of developing and adult rat. METHODS: Bok mRNA expression was analyzed by Northern hybridization before and after culturing rat seminiferous tubules in vitro. Seminiferous tubules were cultured with different hormones and growth factors. Changes in the expression level of Bok mRNA during testicular development was analyzed by Northern hybridization. Localization of Bok mRNA was verified by in situ hybridization. RESULTS: Bok mRNA was highly expressed in the rat testis, varying during development. Highest expression levels were found in immature rats. Highest hybridization intensity appeared to be in spermatogonia, pachytene spermatocytes and Sertoli cells. Treatment with FSH was able to inhibit spontaneous increase of Bok mRNA expression that occurred in the defined stages of the rat seminiferous epithelium. CONCLUSIONS: FSH protects germ cells from apoptosis and this protective effect may at least partly be due to the inhibition of Bok gene expression. The amount of apoptosis varies during testicular development and highest expression of Bok mRNA occurs at the time of apoptosis, suggesting a possible role for Bok in its regulation.