Isocitrate dehydrogenase 1 R132C mutation occurs exclusively in microsatellite stable colorectal cancers with the CpG island methylator phenotype

The CpG Island Methylator Phenotype (CIMP) is fundamental to an important subset of colorectal cancer; however, its cause is unknown. CIMP is associated with microsatellite instability but is also found in BRAF mutant microsatellite stable cancers that are associated with poor prognosis. The isocitrate dehydrogenase 1 (IDH1) gene causes CIMP in glioma due to an activating mutation that produces the 2-hydroxyglutarate oncometabolite. We therefore examined IDH1 alteration as a potential cause of CIMP in colorectal cancer. The IDH1 mutational hotspot was screened in 86 CIMP-positive and 80 CIMP-negative cancers. The entire coding sequence was examined in 81 CIMP-positive colorectal cancers. Forty-seven cancers varying by CIMP-status and IDH1 mutation status were examined using Illumina 450K DNA methylation microarrays. The R132C IDH1 mutation was detected in 4/166 cancers. All IDH1 mutations were in CIMP cancers that were BRAF mutant and microsatellite stable (4/45, 8.9%). Unsupervised hierarchical cluster analysis identified an IDH1 mutation-like methylation signature in approximately half of the CIMP-positive cancers. IDH1 mutation appears to cause CIMP in a small proportion of BRAF mutant, microsatellite stable colorectal cancers. This study provides a precedent that a single gene mutation may cause CIMP in colorectal cancer, and that this will be associated with a specific epigenetic signature and clinicopathological features.     

三种兰科植物的保护遗传学研究初探

采用随机扩增多态 DNA(RAPD)分析研究了中国3种珍稀濒危兰科植物硬叶兜兰(Paphiopedilum micranthum Tang et Wang)、麻栗坡兜兰(P. malipoense S.C.Chen et Tsi)和独花兰(Changnienia amoena Chien)的遗传多样性与群体遗传结构.12个RAPD引物在2种兜兰中共扩增出131条带.对4个硬叶兜兰群体的检测表明其物种水平的多态条带百分率(PPB)为 71.6%,Nei 的基因多样度(h)为 0.217 1,Shannon多样性指数 (I) 为 0.330 1;4个群体的平均多样性水平为 PPB = 45.2%,h = 0.145 7,I = 0.220 4,低于远交兰花的平均水平.在总遗传变异中,群体间遗传变异占20.31%,略高于远交物种的平均水平.在物种水平上,麻栗坡兜兰的PPB为49.5%,h为0.117 4,I为0.176 4,均大大低于硬叶兜兰.对11个独花兰群体采用16个RAPD引物共扩增出119条带.物种水平PPB=76.5%,h=0.194 1,I=0.305 8;在群体水平上,上述3个指标的平均值则分别为37.2%、0.119 7和0.181 0,均低于远交兰花的平均水平.群体间的遗传变异占45.27%,遗传分化明显高于远交物种的平均水平.导致3个物种遗传多样性偏低而群体间遗传分化较高的主要原因在于人为的过度采挖和生境的片断化.研究结果为兰花保护策略和措施的制定提供了理论基础.     

柠檬酸合酶的分子生物学研究进展

柠檬酸合酶（citrate synthase,CS）是细胞内多种重要代谢途径的关键酶。CS可催化草酰乙酸和乙酰辅酶A之间的缩合反应生成柠檬酸和辅酶A。通常革兰氏阳性细菌、古菌以及真核细胞的CS为同源二聚体,而革兰氏阴性细菌的CS为同源六聚体。根据其在细胞内的定位不同,CS可分为线粒体CS、乙醛酸循环体CS、过氧化物酶体CS。这些同工酶在能量代谢、植物脂肪的代谢、脂肪酸的氧化及细胞解毒过程中起着重要作用。不同来源的CS空间结构、催化机制和动力学性质十分相似。针对其生化特性、空间结构特点、催化机制以及分子进化等研究进展进行综述。     

Characterisation of Structures in Salivary Secretion Film Formation. An Experimental Study with Atomic Force Microscopy

The purpose of the present study was to characterise the structure dynamics of pure salivary secretions retained on controlled surfaces with different surface energies in the early stage of salivary film formation. Germanium prisms prepared to have either low surface energy or medium surface energy were incubated in fresh secretions of either human parotid saliva (HPS) or human submandibular/sublingual saliva (HSMSLS) for 15, 90, and 180 min. After controlled rinsing with distilled water, the surfaces were air dried and thereafter imaged with atomic force microscopy (AFM). The amount of adsorbed material and the size of the structures detected increased with increased saliva exposure time. The film thicknesses varied from 10 to 150 nm, and both HPS and HSMSLS films contained structures with diameters varying from 40 nm to 2 μm. Some of these were clustered into special formations. The HPS films exhibited a more granular morphology than the HSMSLS films. Furthermore, branched lines were detected on the low surface energy germanium prisms incubated in saliva. The results indicate that exposure time, surface energy, and type of salivary secretion all are factors affecting the adsorption characteristics of salivary films.     

Calcium-dependent translocation of calbindin-D28k from intestine to blood

Calbindin-D (vitamin D-induced calcium-binding protein; CaBP) is known to be present in blood at concentrations which vary directly with levels in the intestinal mucosa. Employing a sensitive radioimmunoassay and sampling mesentery venous blood, the present experiments demonstrated a direct relationship between intestinal calcium absorption and serum CaBP. Solutions containing 150 mM NaCl and 45Ca-labeled calcium chloride (5 or 20 mM) were placed in the lumen of ligated duodenal preparations in situ and mesentery venous blood sampled with time. The concentration of absorbed 45Ca in serum was maximal at 5 min, followed by a significant increase in mesentery CaBP maximizing at 15-20 min. Elevation of serum CaBP was not observed when calcium in the dosing solution was omitted or replaced by either glucose or glycine. The possible transfer of absorbed calcium from the enterocyte to the circulation as a CaBP complex was ruled out by calculations revealing that considerably more calcium was transferred than could be accounted for by the low and high affinity binding sites on the protein. It is proposed that vitamin D-dependent enhanced transcellular calcium transport constitutes a stimulus for the increased release of intestinal CaBP into the circulation.     

Transfer of adenine nucleotides between the releasable and nonreleasable compartments of rabbit blood platelets

The metabolic pool of adenine nucleotides in platelets can be labeled by incubating platelets for 1 h in vitro with [14C]adenosine or [32P]orthophosphate. When these platelets are treated with thrombin, the adenine nucleotides released are not labeled. Because of this, Holmsen's suggestion of a metabolically inert pool of granule nucleotides has been generally accepted. We have found that upon incubation of labeled rabbit platelets for longer times (up to 6 h) in vitro, or upon reinjection and reharvesting at times up to 66 h, the releasable pool of adenine nucleotides becomes labeled. Because the rates of 32p and 14C incorporation into this releasable pool are similar, it seems likely that these labels enter the granules as ATP. Equilibrium between the metabolic and granule pools is complete by 18 h. When rabbit platelets are labeled in vivo by intravenous injection of [32P]orthophosphate, peak labeling occurs between 60 and 70 h; this corresponds to their maturation time. The platelets probably incorporate 32P during their production in the megakaryocytes. The specific radioactivity of the adenine nucleotides in the releasable (granule) pool of these platelets is the same as the specific radioactivity in the nonreleasable (metabolic) pool. Since inorganic phosphate in platelets (and undoubtedly in the megakaryocytes) exchanges with inorganic phosphate in plasma, and since the radioactivity of the latter decreases rapidly, the adenine nucleotides in the two pools must exchange to maintain the same specific radioactivity. Transfer of adenine nucleotides into storage granules may represent a general phenomenon because it has been observed in the chromaffin cells of the adrenal medulla also.     

Effects of reproductive state on concentrations of thyroxine, 3,5,3'-triiodothyronine and cortisol in serum of dogs

Reproductive state of animals frequently is overlooked when examining endocrine functions of the thyroid gland and adrenal cortex. This experiment was done to determine effects of reproductive state on basal and stimulated concentrations of thyroxine (total T4), 3,5,3'-triiodothyronine (total T3) and cortisol in serum of adult Beagle dogs. Five male, 5 anestrous, 5 proestrous, 5 diestrous, 5 pregnant and 5 lactating dogs were fasted for 18 h before each dog received 5 IU of thyrotropic hormone (TSH) i.v. and 2.2 IU/kg of body weight of adrenocorticotropic hormone (ACTH) i.m. Blood samples were collected via jugular cannulas or by jugular venipuncture at 60, 45, 30, 15 and 1 min before and 0.5, 1, 2, 3, 4, 5, 8, 12 and 24 h after injection. Concentrations of T4 were similar in serum from diestrous and pregnant bitches but were greater (P less than 0.025) than those in dogs of other reproductive states before and after treatment with TSH. Concentrations of T3 were greater (P less than 0.005) in serum from diestrous bitches before and after TSH injection than in serum from dogs of all other reproductive states. Concentrations of T3 in males, anestrus, proestrus, pregnancy and lactation did not differ. Basal concentrations of cortisol did not differ consistently among reproductive states. However, concentrations post-ACTH were different (P less than 0.05) with anestrus = diestrus greater than lactation = pregnancy = male greater than proestrus. These results indicate that reproductive state of experimental animals must be considered when studying thyroidal and adrenal functions.     

The LeFE algorithm: embracing the complexity of gene expression in the interpretation of microarray data

Interpretation of microarray data remains a challenge, and most methods fail to consider the complex, nonlinear regulation of gene expression. To address that limitation, we introduce Learner of Functional Enrichment (LeFE), a statistical/machine learning algorithm based on Random Forest, and demonstrate it on several diverse datasets: smoker/never smoker, breast cancer classification, and cancer drug sensitivity. We also compare it with previously published algorithms, including Gene Set Enrichment Analysis. LeFE regularly identifies statistically significant functional themes consistent with known biology.