Comparative transcriptome analysis of self-incompatible flower stigmas and self-compatible bud stigmas following self-pollination in broccoli.

DH07 is a DH line of Class I S-haplotype in broccoli (Brassica oleracea var. italica), in which stigmas of flowers show self-incompatibility (SI) and stigmas of buds show self-compatibility (SC). The molecular mechanisms that lead to stigmas at different developmental stages having different responses to self-pollination are yet unknown. In the present study, comparative transcriptome profiling of the stigmas of flowers and buds before and after self-pollination was performed by RNA-sequencing using an Illumina HiSeqTM 2000. A total of 80,102,897 reads were generated for further analysis in four libraries. Comparisons of the transcriptome profiles before and after self-pollination revealed 579 differentially expressed genes (DEGs) in the stigmas of buds (SBs); of these, 431 DEGs showed increased and 148 DEGs showed decreased transcript abundance after self-pollination in SBs. There were a total of 686 DEGs between unpollinated stigmas of flowers (SFs) and pollinated SFs, among which, 517 DEGs were up regulated and 169 DEGs were down regulated. Following the self-pollination, 379 identified DEGs were common in both SBs and SFs. It was found that ARR7-like and oxysterol-binding family protein related DEGs could play key roles in SI or SC signal transduction. The results obtained in this study would form the foundation for further studies on investigating the molecular mechanisms of SI and SC in Brassica.

In-depth analysis of internal control genes for quantitative real-time PCR in Brassica oleracea var. botrytis.

Quantitative reverse-transcription PCR (qRT-PCR) is a versatile technique for the analysis of gene expression. The selection of stable reference genes is essential for the application of this technique. Cauliflower (Brassica oleracea L. var. botrytis) is a commonly consumed vegetable that is rich in vitamin, calcium, and iron. Thus far, to our knowledge, there have been no reports on the validation of suitable reference genes for the data normalization of qRT-PCR in cauliflower. In the present study, we analyzed 12 candidate housekeeping genes in cauliflower subjected to different abiotic stresses, hormone treatment conditions, and accessions. geNorm and NormFinder algorithms were used to assess the expression stability of these genes. ACT2 and TIP41 were selected as suitable reference genes across all experimental samples in this study. When different accessions were compared, ACT2 and UNK3 were found to be the most suitable reference genes. In the hormone and abiotic stress treatments, ACT2, TIP41, and UNK2 were the most stably expressed. Our study also provided guidelines for selecting the best reference genes under various experimental conditions.

Roles of oxidative DNA damage of bone marrow hematopoietic cells in steroid-induced avascular necrosis of femoral head.

An animal model of steroid-induced avascular necrosis of femoral head (SANFH) was established to investigate the role of oxidative DNA damage of bone marrow hematopoietic cells in SANFH. Forty-five-month-old Japanese white rabbits (male or female, 2.5 ± 0.5 kg) were randomly divided into groups A (methylprednisolone + Escherichia coli endotoxin), B (methylprednisolone alone), C (E. coli endotoxin alone), and D (blank control). The animals were sacrificed two and four weeks after administration of the last dose (N = 5 each group and each time). Left and right femoral heads were fixed and decalcified. Empty lacunae were counted by hematoxylin and eosin staining and oxidative DNA damage of bone marrow hematopoietic cells was detected by immunohistochemistry. At week 2, the rate of oxidative DNA damage in bone marrow hematopoietic cells was significantly higher in group A than in groups B, C, and D (P < 0.01), while there was no significant difference between groups B, C, and D. At week 4, the rate of oxidative DNA damage in bone marrow hematopoietic cells was significantly higher in group A than in groups B, C, and D (P < 0.01), while there was no significant difference among groups B, C, and D. Thus, oxidative DNA damage of bone marrow hematopoietic cells appears to play an important role in SANFH.

Desmoglein 4 diversity and correlation analysis with coat color in goat.

Desmoglein 4 (DSG4) has an important role in the development of wool traits in domestic animals. The full-length DSG4 gene, which contains 3918 bp, a complete open-reading-frame, and encodes a 1040-amino acid protein, was amplified from Liaoning cashmere goat. The sequence was compared with that of DSG4 from other animals and the results show that the DSG4 coding region is consistent with interspecies conservation. Thirteen single-nucleotide polymorphisms (SNPs) were identified in a highly variable region of DSG4, and one SNP (M-1, G>T) was significantly correlated with white and black coat color in goat. Haplotype distribution of the highly variable region of DSG4 was assessed in 179 individuals from seven goat breeds to investigate its association with coat color and its differentiation among populations. However, the lack of a signature result indicates DGS4 haplotypes related with the color of goat coat.

Brief Note Low diversity of the major histocompatibility complex class II DRA gene in domestic goats (Capra hircus) in Southern China.

DRA encodes the alpha chain of the DR heterodimer, is closely linked to DRB and is considered almost monomorphic in major histocompatibility complex region. In this study, we identified the exon 2 of DRA to evaluate the immunogenetic diversity of Chinese south indigenous goat. Two single nucleotide polymorphisms in an untranslated region and one synonymous substitution in coding region were identified. These data suggest that high immunodiversity in native Chinese population.

Association of CD14 G(-1145)A and C(-159)T polymorphisms with reduced risk for tuberculosis in a Chinese Han population.

Although the role of CD14 in mediating signals from Toll-like receptors to recognize Mycobacterium tuberculosis is known, how polymorphisms in this gene affect the susceptibility to develop tuberculosis are still not clear. We examined whether single nucleotide polymorphisms at positions -1145 and -159 in the promoter region of the CD14 gene are associated with tuberculosis in a Chinese Han population in a case-control study of 432 Chinese patients with tuberculosis and 404 ethnically matched healthy controls. Genotyping was performed to identify polymorphisms of the CD14 gene by PCR-DNA sequencing. Both the frequency of allele T in the C(-159)T polymorphism (odds ratio (OR) = 1.4; 95% confidence interval (95%CI) = 1.148-1.708) and allele G in the G(-1145)A polymorphism (OR = 1.512; 95%CI = 1.236- 1.849) were significantly more frequent in cases than in controls. The frequencies of genotypes CC and CT in the C(-159)T polymorphism, as well as the frequencies of genotypes AA and AG, were lower in cases than in controls. Based on our results, we conclude that G(-1145)A and C(-159)T polymorphisms of CD14 are associated with decreased risk for the development of tuberculosis in the Chinese Han population.

Lack of association between MD-2 promoter gene variants and tuberculosis.

Myeloid differentiation-2 (MD-2) is an essential component of the CD14-TLR4/MD-2 receptor complex involved in microbial cell wall component recognition during infection. Genetic variations in the MD-2 gene may influence human susceptibility to infectious diseases. To date, a predisposition of MD-2 gene variants to contract tuberculosis has not been reported. We investigated whether MD-2 gene polymorphisms were associated with the development of tuberculosis in a Chinese population. The six common polymorphisms (rs11465996, rs1809442, rs1809441, rs1809440, rs16938754, and rs7842342) within the MD-2 gene promoter region were all detected in 259 patients with tuberculosis and 276 healthy control subjects by DNA sequencing. None of the allelic frequencies, haplotype patterns or genotype distributions of the assayed polymorphisms was found to be significantly different between patients and controls (P > 0.05). We conclude that these gene variants in the MD-2 gene promoter region are not associated with tuberculosis, and apparently do not play a role in susceptibility to tuberculosis in the Chinese population.