Smoking, aging, and expression of proteins related to the FOXO3 signaling pathway in lung tissues

We investigated the effects of smoking and aging on proteins involved in the forkhead box O3 (FOXO3) signaling pathways in the lungs. Sixteen senescence-accelerated mouse-resistant 1 (SAMR1) and senescence-accelerated mouse-prone 8 (SAMP8) mice at 3 months of age were divided into a normally aged, smoke-exposed group (4 SAMR1 mice), a normally aged, air-exposed group (4 SAMR1 mice), an aging-accelerated, smoke-exposed group (4 SAMP8 mice), and an aging-accelerated, air-exposed group (4 SAMP8 mice). Expression of genes and proteins related to the FOXO3 signaling pathways in each group was examined by western blot analysis and immunohistochemistry. FOXO3a expression was significantly increased in the normally aged, air-exposed group compared with the aging-accelerated, air-exposed group. FOXO3a expression was significantly reduced in the aging-accelerated, smoke-exposed group compared with the aging-accelerated, air-exposed group. Sirtuin 1, manganese superoxide dis-mutase, and phosphatidylinositol 3-kinase (PI3K)/Akt expression decreased significantly in the smoke-exposed groups compared with the air-exposed groups and in the aging-accelerated groups compared with the normally aged groups. Signal transduction pathways mediated by the transcription factor FOXO3a (such as the PI3K/Akt pathway) may be involved in the accelerated aging of lung tissues in chronic obstructive pulmonary disease. Smoking inactivates the transcription factor FOXO3, thus accelerating lung tissue aging during chronic obstructive pulmonary disease.

Development of EST-SSR and TRAP markers from transcriptome sequencing data of the mango

Mango is one of the most commercially important fruit crops in tropical and subtropical regions. To increase the efficiency of breeding strategies, two EST-derived marker systems were developed in the present study using information from the mango fruit transcriptome. Using simple sequence repeats, 218 of 230 primer pairs showed stable amplification for 7 mango genotypes with amplicons ranging from 84 to 160 bp; 93 of the primer pairs yielded polymorphic products. The proportion of polymorphic bands ranged from 16.67 to 100%, with a mean of 55.64%. In contrast, 86 primer pairs exhibited good amplification with clear bands for target region amplification polymorphism analysis, and a total of 66 primer combinations were polymorphic. These two novel sets of EST-derived markers will be of use in future studies of genetic diversity, genetic map construction, and marker-assisted selection in mango.

Involvement of the mitfa gene in the development of pigment cell in Japanese ornamental (Koi) carp (Cyprinus carpio L.)

A colored phenotype is an important feature of ornamental fish. In mammals, microphthalmia-associated transcription factor (MITF) was found to regulate the development of melanocytes. In this study, the mitfa cDNA was first cloned from the Japanese ornamental (Koi) carp (Cyprinus carpio L.), an important ornamental freshwater fish. The full-length cDNA of the mitfa gene contains 1634 bp, coding for 412 amino acids in Koi. The identity degree of mitfa amino acid sequences between the Koi carp and zebrafish is 92.9%. We tested the expression of the mitfa gene in several varieties of Koi using reverse transcription-polymerase chain reaction and found that the mitfa gene is highly expressed in the skin tissues of the Taisho sanke and the Procypris merus. Interestingly, the mitfa gene was also expressed in the Kohaku and Yamabaki ogon, although melanocytes were not observed in the skin. Koi carp embryos were transparent and colorless, while after hatching, different types of pigment cells successively emerged in a fixed order. In Taisho sanke, melanocytes first appeared in the trunk at approximately 12 days of age. Subsequently, there was a large area of melanocytes by 30 days of age. The expression level of the mitfa mRNA was low in early embryos and newly hatched larvae, and increased to high levels in 30-day-old fry. The results show that the mitfa gene is involved in regulating fish body color in the development of both melanocytes and pigment cells.

Association of single nucleotide polymorphisms in the microRNA miR-1596 locus with residual feed intake in chickens

MicroRNAs are an abundant class of small non-coding RNAs that regulate gene expression. Genetic variations in microRNA sequences may be associated with phenotype differences by influencing the expression of microRNAs and/or their targets. This study identified two single nucleotide polymorphisms (SNPs) in the genomic region of the microRNA miR-1596 locus of chicken. Of the two SNPs, one was 95 bp upstream of miR-1596 (g.5678784A>T) and the other was in the middle of the sequence producing the mature microRNA gga-miR-1596-3p (g.5678944A>G). Genotypic distribution of the two SNPs had large differences among 12 chicken breeds (lines), especially between the fast-growing commercial lines and the slow-growing Chinese indigenous breeds for the g.5678784A>T SNP. Only the g.5678784A>T SNP was significantly associated with residual feed intake (RFI) in the F2 population derived from a fast-growing and a slow-growing broiler as well as in the pure Huiyang bearded chicken. The birds with the AA genotype of the g.5678784A>T SNP had lower RFI and higher expression of the mature gga-miR-1596-3p microRNA of miR-1596 than did those with the other genotypes of the same SNP. We also found that the expression of the mature gga-miR-1596-3p microRNA of miR-1596 was significantly associated with RFI. These findings suggest that miR-1596 can become a candidate gene related to RFI, and its genetic variation may contribute to changes in RFI by altering expression levels of the mature gga-miR-1596-3p microRNA in chicken.

Annexin A5 promotes macrophage activation and contributes to pulmonary fibrosis induced by silica particles

OBJECTIVE

To investigate the contributions and underlying molecular mechanisms of annexin A5 toward silica-induced pulmonary fibrosis.

METHODS

Male C57BL/6 mice were randomly divided into three groups and instilled intratracheally with silica, saline, or air. Mice were euthanized at 3, 7, 14, or 28 days following treatment. Annexin A5 levels in serum and lung tissues were detected by enzyme-linked immunosorbant assay (ELISA) assays or Western blots. The association of annexin A5 levels with silica-induced lung fibrosis was further investigated in the macrophage cell line, RAW264.7. Following exposure of these cells to silica at a concentration of 200 μg/ml for 6 or 12 h, the expression levels of transforming growth factor β1 (TGF-β1), interleukin 1α (IL-1α), Fas ligand (FasL), and their downstream targets were evaluated by Western blots. Furthermore, annexin A5 and FasL were knocked down by small interfering ribonucleic acid (siRNA) and TGF-β1 secretion into the cell culture medium was measured by ELISA assays or Western blots.

RESULTS

Mice treated with silica demonstrated lung fibrosis at 28 days following exposure, whereas, in controls, only mild and transient inflammation was evident at day 3 and day 7 postinstillation and was not present at day 14. Furthermore, silica-exposed mice exhibited significantly (p < 0.05) elevated levels of annexin A5 in serum and lung tissues, relative to control groups. Consistent with these findings, silica exposure of RAW264.7 cells for 6 or 12 h, led to an annexin A5-dependent increase in the expression levels of TGF-β1, IL-1α, FasL, and their downstream target molecules. These silica-induced changes were reversed by siRNA-mediated knockdown of annexin A5, but downregulation of FasL led to increased annexin A5 expression and reduced levels of TGF-β1, IL-1α, and FasL downstream target molecules.

CONCLUSIONS

These findings define a role of annexin A5 in promoting macrophage activation via Fas/FasL pathways in silica-induced lung fibrosis.

Scoring Functions Based on Second Level Score for k-SAT with Long Clauses

It is widely acknowledged that stochastic local search (SLS) algorithms can efficiently find models for satisfiable instances of the satisfiability (SAT) problem, especially for random k-SAT instances. However, compared to random 3-SAT instances where SLS algorithms have shown great success, random k-SAT instances with long clauses remain very difficult. Recently, the notion of second level score, denoted as "score_2", was proposed for improving SLS algorithms on long-clause SAT instances, and was first used in the powerful CCASat solver as a tie breaker. In this paper, we propose three new scoring functions based on score_2. Despite their simplicity, these functions are very effective for solving random k-SAT with long clauses. The first function combines score and score_2, and the second one additionally integrates the diversification property "age". These two functions are used in developing a new SLS algorithm called CScoreSAT. Experimental results on large random 5-SAT and 7-SAT instances near phase transition show that CScoreSAT significantly outperforms previous SLS solvers. However, CScoreSAT cannot rival its competitors on random k-SAT instances at phase transition. We improve CScoreSAT for such instances by another scoring function which combines score_2 with age. The resulting algorithm HScoreSAT exhibits state-of-the-art performance on random k-SAT (k>3) instances at phase transition. We also study the computation of score_2, including its implementation and computational complexity.

Short communication: development and characterization of novel transcriptome-derived microsatellites for genetic analysis of persimmon

Oriental persimmon (Diospyros kaki Thunb.) (2n = 6x = 90) is a major commercial and deciduous fruit tree that is believed to have originated in China. However, rare transcriptomic and genomic information on persimmon is available. Using Roche 454 sequencing technology, the transcriptome from RNA of the flowers of D. kaki was analyzed. A total of 1,250,893 reads were generated and 83,898 unigenes were assembled. A total of 42,711 SSR loci were identified from 23,494 unigenes and 289 polymerase chain reaction primer pairs were designed. Of these 289 primers, 155 (53.6%) showed robust PCR amplification and 98 revealed polymorphism between 15 persimmon genotypes, indicating a polymorphic rate of 63.23% of the productive primers for characterization and genotyping of the genus Diospyros. Transcriptome sequence data generated from next-generation sequencing technology to identify microsatellite loci appears to be rapid and cost-efficient, particularly for species with no genomic sequence information available.

Accumulation of melanin in the peritoneum causes black abdomens in broilers

A suspected case of localized visceral hyperpigmentation was described for a breed of broiler in China. Using optical microscopy, the accumulation of pigments in the abdominal skin and visceral peritoneum was observed. Electron microscopy was used to further study the ultrastructure of the pigmented peritoneum, and pigment granules resembling melanosomes at different stages were found, and melanocytes were present in this tissue. Infrared spectroscopy was used to analyze the physical-chemical properties of pigments extracted from these broilers. Using synthetic melanin as a reference and the melanin from the peritoneum of Silkie fowls as a control, the pigments in the peritonea of these broilers were found to be melanin, and it had a chemical structure similar to that of melanin from the Silkie fowl peritoneum. In this way, the black abdomens of these broilers were found to have been caused by accumulation of melanin produced by melanocytes in visceral peritonea.

AKT2 expression in histopathologic grading and recurrence of meningiomas

BACKGROUND

AKT2 (protein kinase B), an important protein in PI3K signaling pathway, is overexpressed in a variety of malignant tumors. However, in patients with meningiomas, the potential correlation between AKT2 and clinical outcome remains unknown.

METHODS

The expression of AKT2 and Ki-67 in meningioma tissues were evaluated immunohistochemically in 94 patients with meningiomas. The correlation of AKT2 immunoreactivity with clinicopathological features and the prognostic value of AKT2 in patients were also analyzed.

RESULTS

In this study, we examined the expression of AKT2 in meningiomas and unveiled its possible relationship with the clinical outcome. Immunohistochemical analysis revealed high AKT2 expression in 46 patients (46/94, 48.9%) and low AKT2 expression in the remaining 48 patients (48/94, 51.1%). There was a positive correlation between AKT2 and Ki-67 immunoreactivity (r = 0.35, P = 0.01). Clinicopathological evaluation suggested that AKT2 expression was associated with pathological grade and recurrence (P < 0.05). Univariate and Cox analysis indicated a significant correlation between high levels of AKT2 immunoreactivity and high rates of tumor recurrence (P < 0.05).

CONCLUSIONS

We conclude that AKT2 may play an important role in the development of meningioma. High AKT2 labeling index indicates higher grade of meningioma, and therefore AKT2 may be a useful molecular marker for predicting the prognosis of meningioma.

195 EFFECTS OF GSK3 INHIBITOR ON THE PLURIPOTENCY MAINTENANCE OF BUFFALO EMBRYONIC STEM-CELL-LIKE CELLS

In this study, to explore the effects and mechanism of Wnt/β-catenin signalling pathway on the maintenance of pluripotency of buffalo embryonic stem-cell-like cells (buffalo ESC-like cells), the GSK3 inhibitors BIO and CHIR99021 were added throughout the experiment – i.e. from buffalo inner cell mass (ICM) culture to ESC-like line generation. The buffalo ICM were respectively cultured in the medium containing 0.5 μg mL–1 BIO and 5 mmol L–1 CHIR99021. The percentage of ICMs attachment and primary colony formation were observed, and found that there was no significant difference in the ICMs attachment rate among of the BIO, CHIR99021, and the control groups (91.18% and 92.98% v. 94.59%; P > 0.05). Treating ICMs with CHIR99021 resulted in more primary colony formation rate compared with the control group (77.71% v. 55.41%; P < 0.05). The proliferation rate of primary colonies of buffalo ESC-like cells was detected by bromodeoxyuridine immunofluorescence techniques. The results show that the proliferation rate of primary colonies in the group of buffalo ESC-like cells treated with CHIR99021 was significantly higher than that of the control group on Day 1, Day 3, Day 4, and Day 5 (P < 0.05), and it was also evidently higher than that of control group only on Day 1 (P < 0.05) in the group of BIO, but there was no significant difference in other days (P > 0.05). The mRNA expression level of proliferation marker PCNA of ESC-like cells was significantly up-regulated in both CHIR99021 and BIO treatment groups (P < 0.05), however, treating buffalo ESC-like cells with CHIR99021 significantly up-regulated the expression of pluripotent gene Oct4 and Sox2 (P < 0.05), but had no effect on pluripotent gene Nanog expression (P > 0.05). Oct4 expression was significantly increased (P < 0.05), and the expression of Sox2 and Nanog were significantly decreased (P < 0.05) in the group of BIO treatment. Furthermore, the relative protein level of β-catenin (the downstream effector of Wnt/β-catenin signalling pathway) and the mRNA expression level of c-Myc (the downstream target gene of Wnt/β-catenin signalling pathway) were significantly increased when buffalo ESC-like cells respectively treated with CHIR99021 and BIO (P < 0.05). In conclusion, treating buffalo ESC-like cells with GSK3 inhibitors CHIR99021 can promote proliferation of buffalo ESC-like cells, maintain their undifferentiated state, and up-regulate the expression levels of β-Catenin and c-Myc in buffalo ESC-like cells. These results indicate that Wnt/β-catenin signalling pathway plays an important role in regulation of self-renewal of buffalo ESC-like cells. This work was funded by the China High Technology Development Program (2011AA100607), China Natural Science Foundation (31072033), and Guangxi Science Foundation (2012GXNSFFA060004).

NuMVC: An Efficient Local Search Algorithm for Minimum Vertex Cover

The Minimum Vertex Cover (MVC) problem is a prominent NP-hard combinatorial optimization problem of great importance in both theory and application. Local search has proved successful for this problem. However, there are two main drawbacks in state-of-the-art MVC local search algorithms. First, they select a pair of vertices to exchange simultaneously, which is time-consuming. Secondly, although using edge weighting techniques to diversify the search, these algorithms lack mechanisms for decreasing the weights. To address these issues, we propose two new strategies: two-stage exchange and edge weighting with forgetting. The two-stage exchange strategy selects two vertices to exchange separately and performs the exchange in two stages. The strategy of edge weighting with forgetting not only increases weights of uncovered edges, but also decreases some weights for each edge periodically. These two strategies are used in designing a new MVC local search algorithm, which is referred to as NuMVC. We conduct extensive experimental studies on the standard benchmarks, namely DIMACS and BHOSLIB. The experiment comparing NuMVC with state-of-the-art heuristic algorithms show that NuMVC is at least competitive with the nearest competitor namely PLS on the DIMACS benchmark, and clearly dominates all competitors on the BHOSLIB benchmark. Also, experimental results indicate that NuMVC finds an optimal solution much faster than the current best exact algorithm for Maximum Clique on random instances as well as some structured ones. Moreover, we study the effectiveness of the two strategies and the run-time behaviour through experimental analysis.