Regulation of Pax6 by CTCF during induction of mouse ES cell differentiation

Pax6 plays an important role in embryonic cell (ES) differentiation during embryonic development. Expression of Pax6 undergoes from a low level to high levels following ES cell differentiation to neural stem cells, and then fades away in most of the differentiated cell types. There is a limited knowledge concerning how Pax6 is regulated in ES cell differentiation. We report that Pax6 expression in mouse ES cells was controlled by CCCTC binding factor (CTCF) through a promoter repression mechanism. Pax6 expression was significantly enhanced while CTCF activity was kept in the constant during ES cell differentiation to radial glial cells. Instead, the interaction of CTCF with Pax6 gene was regulated by decreased CTCF occupancy in its binding motifs upstream from Pax6 P0 promoter following the course of ES cell differentiation. Reduced occupancy of CTCF in the binding motif region upstream from the P0 promoter was due to increased DNA methylations in the CpG sites identified in the region. Furthermore, changes in DNA methylation levels in vitro and in vivo effectively altered methylation status of these identified CpG sites, which affected ability of CTCF to interact with the P0 promoter, resulting in increases in Pax6 expression. We conclude that there is an epigenetic mechanism involving regulations of Pax6 gene during ES cell differentiation to neural stem cells, which is through increases or decreases in methylation levels of Pax6 gene to effectively alter the ability of CTCF in control of Pax6 expression, respectively.     

Multicolor combinatorial probe coding for real-time PCR

The target volume of multiplex real-time PCR assays is limited by the number of fluorescent dyes available and the number of fluorescence acquisition channels present in the PCR instrument. We hereby explored a probe labeling strategy that significantly increased the target volume of real-time PCR detection in one reaction. The labeling paradigm, termed "Multicolor Combinatorial Probe Coding" (MCPC), uses a limited number (n) of differently colored fluorophores in various combinations to label each probe, enabling one of 2(n)-1 genetic targets to be detected in one reaction. The proof-of-principle of MCPC was validated by identification of one of each possible 15 human papillomavirus types, which is the maximum target number theoretically detectable by MCPC with a 4-color channel instrument, in one reaction. MCPC was then improved from a one-primer-pair setting to a multiple-primer-pair format through Homo-Tag Assisted Non-Dimer (HAND) system to allow multiple primer pairs to be included in one reaction. This improvement was demonstrated via identification of one of the possible 10 foodborne pathogen candidates with 10 pairs of primers included in one reaction, which had limit of detection equivalent to the uniplex PCR. MCPC was further explored in detecting combined genotypes of five β-globin gene mutations where multiple targets were co-amplified. MCPC strategy could expand the scope of real-time PCR assays in applications which are unachievable by current labeling strategy.     

蛇足石杉COBRA基因家族的分子生物信息学及表达分析

为探明蛇足石杉COBRA基因家族成员分子生物信息学特征及组织表达规律,该文基于蛇足石杉的全长转录组数据,通过生物信息学技术对该家族成员(HsCOBRAs)的理化性质、结构域、保守基序、顺式作用元件、基因表达量等进行分析。结果表明:(1)在蛇足石杉全长转录组中共筛选出24个HsCOBRAs家族成员,其中酸性蛋白9个,稳定蛋白11个,疏水性蛋白5个,具有跨膜结构的蛋白7个,具有信号肽的蛋白3个。(2)亚细胞定位在细胞壁、叶绿体、细胞核、细胞膜上。(3)结构分析发现HsCOBRAs有7种结构域和6种保守基序,部分成员具有高度保守的CCVS结构。(4)HsCOBRAs具有CAAT-box、TATA-box等45种顺式作用元件。(5)HsCOBRA2在叶、孢子、茎、芽胞中的表达量均最高。该研究结果可为HsCOBRAs的进一步研究及生物学功能验证等提供理论依据。     

Adenosine induces ATP release via an inositol 1,4,5-trisphosphate signaling pathway in MDCK cells

ATP is released into extracellular space as an autocrine/paracrine molecule by mechanical stress and pharmacological-receptor activation. Released ATP is partly metabolized by ectoenzymes to adenosine. In the present study, we found that adenosine causes ATP release in Madin-Darby canine kidney cells. This release was completely inhibited by CPT (an A1 receptor antagonist), U-73122 (a phospholipase C inhibitor), 2-APB (an inositol 1,4,5-trisphosphate (Ins(1,4,5)P3) receptor blocker), thapsigargin (a Ca2+-ATPase inhibitor), and BAPTA/AM (an intracellular Ca2+ chelator), but not by DMPX (an A2 receptor antagonist). However, forskolin, epinephrine, and isoproterenol, inducers of cAMP accumulation, failed to release ATP. Adenosine increased intracellular Ca2+ concentrations that were strongly blocked by CPT, U-73122, 2-APB, and thapsigargin. Moreover, adenosine enhanced accumulations of Ins(1,4,5)P3 that were significantly reduced by U-73122 and CPT. These data suggest that adenosine induces the release of ATP by activating an Ins(1,4,5)P3 sensitive-Ca2+ pathway through the stimulation of A1 receptors.     

Atorvastatin-induced cardioprotection is mediated by increasing inducible nitric oxide synthase and consequent S-nitrosylation of cyclooxygenase-2

We determined the effects of cyclooxygenase-1 (COX-1; SC-560), COX-2 (SC-58125), and inducible nitric oxide synthase (iNOS; 1400W) inhibitors on atorvastatin (ATV)-induced myocardial protection and whether iNOS mediates the ATV-induced increases in COX-2. Sprague-Dawley rats received 10 mg ATV.kg(-1).day(-1) added to drinking water or water alone for 3 days and received intravenous SC-58125, SC-560, 1400W, or vehicle alone. Anesthesia was induced with ketamine and xylazine and maintained with isoflurane. Fifteen minutes after intravenous injection rats underwent 30-min myocardial ischemia followed by 4-h reperfusion [infarct size (IS) protocol], or the hearts were explanted for biochemical analysis and immunoblotting. Left ventricular weight and area at risk (AR) were comparable among groups. ATV reduced IS to 12.7% (SD 3.1) of AR, a reduction of 64% vs. 35.1% (SD 7.6) in the sham-treated group (P < 0.001). SC-58125 and 1400W attenuated the protective effect without affecting IS in the non-ATV-treated rats. ATV increased calcium-independent NOS (iNOS) [11.9 (SD 0.8) vs. 3.9 (SD 0.1) x 1,000 counts/min; P < 0.001] and COX-2 [46.7 (SD 1.1) vs. 6.5 (SD 1.4) pg/ml of 6-keto-PGF(1alpha); P < 0.001] activity. Both SC-58125 and 1400W attenuated this increase. SC-58125 did not affect iNOS activity, whereas 1400W blocked iNOS activity. COX-2 was S-nitrosylated in ATV-treated but not sham-treated rats or rats pretreated with 1400W. COX-2 immunoprecipitated with iNOS but not with endothelial nitric oxide synthase. We conclude that ATV reduced IS by increasing the activity of iNOS and COX-2, iNOS is upstream to COX-2, and iNOS activates COX-2 by S-nitrosylation. These results are consistent with the hypothesis that preconditioning effects are mediated via PG.     

A new approach for the determination of oligosaccharide structures

A new method for the determination of oligosaccharide chains, known as the D60 one-dimensional TOCSY method is introduced in this paper. The results show that the use of this method enables a more effective coherent long-range magnetic relay transfer compared with that of existing DIPSI-2 and MMDY methods. Further, the method is easy to use and is not sensitive to the error of the pulse width. Without complex z-filtering steps, the high-quality sub-spectrum of pure absorption can be quickly obtained, which facilitates sub-spectroscopy detection for the existence of weak spin-coupling sugar components in the saccharide ring. Glycosides are taken as examples to discuss the characteristics of this method and its application in the determination of oligosaccharides in spectrum peak height.     

Non-linear response of stomata in Pinus koraiensis to tree age and elevation

Knowledge on variations in stomata is useful in reflecting leaf physiological characteristics of CO₂ uptake and water transpiration, and predicting the responses of plants to future climate change. Stomatal density and number of stomatal rows (current-year, 1- and 2-year-old needles) in relation to tree age (ranging from 25 to 320 years old), elevation (ranging from 738 to 1,380 m a.s.l.), and sun exposure (sun and shade exposure) were investigated in Pinus koraiensis trees. Stomatal density and number of stomatal rows in relation to tree age and elevation showed a humped curve with the maximum values at intermediate levels of tree age (210 years old) and elevation (1,050 m a.s.l.), respectively. Needle age but not sun exposure significantly affected the stomatal density across tree ages and elevations. Our results suggest that variations in stomatal density of Pinus koraiensis needles are related to ontogenetic growth and environmental factors.