Lattices for ab initio protein structure prediction

In the study of the protein folding problem with ab initio methods, the protein backbone can be built on some periodic lattices. Any vertex of these lattices can be occupied by a "ball," which can represent the mass center of an amino acid in a simplified coarse-grained model of the protein. The backbone, at a coarse-grained level, can be constituted of a No Reverse Self Avoiding Walk, which cannot intersect itself and cannot go back on itself. There is still much debate between those who use lattices to simplify the study of the protein folding problem and those preferring to work by using an off-lattice approach. Lattices can help to identify the protein tertiary structure in a computational less-expensive way, than off-lattice approaches that have to consider a potentially infinite number of possible structures. However, the use of a lattice, constituted of insufficiently accurate direction vectors, constrains the predictive ability of the model. The aim of this study is to perform a systematic screening of 7 known classic and 11 newly proposed lattices in terms of predictive power. The crystal structures of 42 different proteins (14 mainly alpha helical, 14 mainly beta sheet and 14 mixed structure proteins) were compared to the most accurate simulated models for each lattice. This strategy defines a scale of fitness for all the analyzed lattices and demonstrates that an increase in the coordination number and in the degrees of freedom is necessary but not sufficient to reach the best result. Instead, the introduction of a good set of direction vectors, as developed and tested in this study, strongly increases the lattice performance.     

Early changes in pancreatic acinar cell calcium signaling after pancreatic duct obstruction

Intracellular Ca(2+)-changes not only participate in important signaling pathways but have also been implicated in a number of disease states including acute pancreatitis. To investigate the underlying mechanisms in an experimental model mimicking human gallstone-induced pancreatitis, we ligated the pancreatic duct of Sprague-Dawley rats and NMRI mice for up to 6 h and studied intrapancreatic changes including the dynamics of [Ca(2+)](i) in isolated acini. In contrast to bile duct ligation, pancreatic duct obstruction induced intra-pancreatic trypsinogen activation, leukocytosis, hyperamylasemia, and pancreatic edema and increased lung myeloperoxidase activity. Although resting [Ca(2+)](i) in isolated acini rose by 45% to 205 +/- 7 nmol, the acetylcholine- and cholecystokinin (CCK)-stimulated calcium peaks as well as the amylase secretion declined, but neither the [Ca(2+)](i)-signaling pattern nor the amylase output in response to the Ca(2+)-ATPase inhibitor thapsigargin nor the secretin-stimulated amylase release were impaired by pancreatic duct ligation. On the single cell level pancreatic duct ligation reduced the percentage of cells in which submaximal secretagogue stimulation was followed by a physiological response (i.e. Ca(2+) oscillations) and increased the percentage of cells with a pathological response (i.e. peak plateau or absent Ca(2+) signal). Moreover, it reduced the frequency and amplitude of Ca(2+) oscillation as well as the capacitative Ca(2+) influx in response to secretagogue stimulation. Serum pancreatic enzyme elevation as well as trypsinogen activation was significantly reduced by pretreatment of animals with the calcium chelator BAPTA-AM. These experiments suggest that pancreatic duct obstruction rapidly changes the physiological response of the exocrine pancreas to a Ca(2+)-signaling pattern that has been associated with premature digestive enzyme activation and the onset of pancreatitis, both of which can be prevented by administration of an intracellular calcium chelator.     

Male preponderance in early diagnosed type 2 diabetes is associated with the ARE insertion/deletion polymorphism in the <Emphasis Type="Italic">PPP1R3A</Emphasis> locus

Background  

The ARE insertion/deletion polymorphism of PPP1R3A has been associated with variation in glycaemic parameters and prevalence of diabetes. We have investigated its role in age of diagnosis, body weight and glycaemic control in 1,950 individuals with type 2 diabetes in Tayside, Scotland, and compared the ARE2 allele frequencies with 1,014 local schoolchildren.     

东南沿海部队皮肤浅部真菌病的调查研究

目的了解东南沿海部队官兵近年真菌菌种构成情况及调查浅部真菌病非高发季节的患病率。方法于11月对浙江地区和福建地区某部队官兵共324人进行浅部真菌病患病情况调查,通过临床检查确定皮肤病种类和感染人(次),对于临床诊断为浅部真菌病的官兵进行真菌镜检证实后明确诊断,并留菌种进行真菌培养。结果真菌感染性疾病患病率为55.2%(324人中179人发病),其中手足癣158人次(48.8%),体股癣35人次(10.8%),花斑癣24人次(7.4%),马拉色菌毛囊炎18人次(5.6%),甲癣5人次(1.5%)。真菌镜检阳性率为76.36%,首位致病菌为红色毛癣菌71株,占84.5%。结论部队尤其是亚热带地区部队,浅部真菌病的患病率较高,不同驻地官兵患皮肤浅部真菌病有差异,而服役年限及兵源与患皮肤浅部真菌病之间无显著差异。     

Vasoactive Intestinal Polypeptide-Expressing Interneurons in the Hippocampus Support Goal-Oriented Spatial Learning

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Separating Recognition Processes of Declarative Memory via Anodal tDCS: Boosting Old Item Recognition by Temporal and New Item Detection by Parietal Stimulation

There is emerging evidence from imaging studies that parietal and temporal cortices act together to achieve successful recognition of declarative information; nevertheless, the precise role of these regions remains elusive. To evaluate the role of these brain areas in declarative memory retrieval, we applied bilateral tDCS, with anode over the left and cathode over the right parietal or temporal cortices separately, during the recognition phase of a verbal learning paradigm using a balanced old-new decision task. In a parallel group design, we tested three different groups of healthy adults, matched for demographic and neurocognitive status: two groups received bilateral active stimulation of either the parietal or the temporal cortex, while a third group received sham stimulation. Accuracy, discriminability index (d’) and reaction times of recognition memory performance were measurements of interest. The d’ sensitivity index and accuracy percentage improved in both active stimulation groups, as compared with the sham one, while reaction times remained unaffected. Moreover, the analysis of accuracy revealed a different effect of tDCS for old and new item recognition. While the temporal group showed enhanced performance for old item recognition, the parietal group was better at correctly recognising new ones. Our results support an active role of both of these areas in memory retrieval, possibly underpinning different stages of the recognition process.     

Lung injury after ozone exposure is iron dependent

We tested the hypothesis that oxidative stress and biological effect after ozone (O3) exposure are dependent on changes in iron homeostasis. After O3 exposure, healthy volunteers demonstrated increased lavage concentrations of iron, transferrin, lactoferrin, and ferritin. In normal rats, alterations of iron metabolism after O3 exposure were immediate and preceded the inflammatory influx. To test for participation of this disruption in iron homeostasis in lung injury following O3 inhalation, we exposed Belgrade rats, which are functionally deficient in divalent metal transporter 1 (DMT1) as a means of iron uptake, and controls to O3. Iron homeostasis was disrupted to a greater extent and the extent of injury was greater in Belgrade rats than in control rats. Nonheme iron and ferritin concentrations were higher in human bronchial epithelial (HBE) cells exposed to O3 than in HBE cells exposed to filtered air. Aldehyde generation and IL-8 release by the HBE cells was also elevated following O3 exposure. Human embryonic kidney (HEK 293) cells with elevated expression of a DMT1 construct were exposed to filtered air and O3. With exposure to O3, elevated DMT1 expression diminished oxidative stress (i.e., aldehyde generation) and IL-8 release. We conclude that iron participates critically in the oxidative stress and biological effects after O3 exposure.     

Aflatoxin contamination of rice in the United Arab Emirates

Many people in the United Arab Emirates store rice in large quantities for long periods of time before use. Five hundred samples of rice were collected from households in Al-Ain city during the summers of 1992-1994. Aflatoxin B₁ was detected in 160 samples (64%) of long grain rice and 81 Samples (32%) of short grain rice at levels ranging from 1.2 to 16.5 μg/kg. The moisture content of samples varied between 5.7% and 15.3%. Species ofAspergillus andPenicillium (includingA. flavus andA. parasiticus) were isolated from discoloured, broken and insect damaged grain and it was confirmed that at least two of the isolates ofA. flavus were aflatoxigenic. These findings demonstrate that rice may contribute to dietary exposure to aflatoxins which are known to be carcinogenic and immunosuppressive.     

鸡PPARγ基因的表达特性及其对脂肪细胞增殖分化的影响

为分析鸡PPARγ基因的组织表达特性及其在脂肪细胞增殖和分化过程中的功能,文章以东北农业大学高、低腹脂双向选择品系肉鸡为实验材料,利用Western blotting方法,检测PPARγ基因的组织表达特性及其在高、低脂系肉鸡腹部脂肪组织间的表达差异;采用RNAi技术,在鸡原代脂肪细胞中抑制PPARγ基因的表达后,通过MTT和油红O提取比色的方法,研究鸡PPARγ基因对脂肪细胞增殖和分化的调控作用;利用Real-timePCR和Western blotting技术,分析PPARγ基因表达下调后,其他脂肪细胞分化转录因子以及与脂肪细胞分化相关的重要基因的表达变化情况。结果表明,PPARγ基因在7周龄高脂系肉鸡腹部脂肪组织、肌胃、脾脏、肾脏组织中表达量较高,在心脏中表达量较低,在肝脏、胸肌、腿肌、十二指肠中未检测到表达信号;与高脂系相比,PPARγ基因在5和7周龄低脂系肉鸡腹部脂肪组织中的表达量较低(P<0.05);PPARγ基因的表达量下降后,鸡脂肪细胞的增殖能力增强,分化能力减弱;同时,C/EBPα、SREBP1、A-FABP、Perilipin1、LPL、IGFBP-2基因的表达量均下降(P<0.05)。由此可见,PPARγ基因的表达可能与肉鸡腹部脂肪的沉积有一定的关系,该基因可能是调控鸡脂肪细胞增殖与分化的关键因子。