Prediction of "hot spots" of aggregation in disease-linked polypeptides

Background  

The polypeptides involved in amyloidogenesis may be globular proteins with a defined 3D-structure or natively unfolded proteins. The first class includes polypeptides such as β2-microglobulin, lysozyme, transthyretin or the prion protein, whereas β-amyloid peptide, amylin or α-synuclein all belong to the second class. Recent studies suggest that specific regions in the proteins act as "hot spots" driving aggregation. This should be especially relevant for natively unfolded proteins or unfolded states of globular proteins as they lack significant secondary and tertiary structure and specific intra-chain interactions that can mask these aggregation-prone regions. Prediction of such sequence stretches is important since they are potential therapeutic targets.     

Mucopolysaccharidosis type II (Hunter syndrome): mutation "hot spots" in the iduronate-2-sulfatase gene.

Mucopolysaccharidosis type II (MPS II, Hunter syndrome) is an X-chromosomal storage disorder due to deficiency of the lysosomal enzyme iduronate-2-sulfatase (IDS). We have identified IDS mutations in a total of 31 families/patients with MPS II, of which 20 are novel and unique and a further 1 is novel but has been found in 3 unrelated patients. One of the mutations detected is of special interest as an AG-->G substitution in an intron, far apart from the coding region, is deleterious by creating a new 5''-splice-donor site that results in the inclusion of a 78-bp intronic sequence. While the distribution of gene rearrangements (deletions, insertions, and duplications) of <20 bp seems to be random over the IDS gene, the analysis of a total of 101 point mutations lying within the coding region shows that they tend to be more frequent in exons III, VIII, and IX. Forty-seven percent of the point mutations are at CpG dinucleotides, of which G:C-to-A:T transitions constitute nearly 80%. Almost all recurrent point mutations involve CpG sites. Analysis of a collective of 50 families studied in our laboratory, to date, revealed that mutations occur more frequently in male meioses (estimated male-to-female ratio between 3.76 and 6.3).     

基于MODIS卫星火点的浙江省林火季节变化及驱动因子

研究林火变化趋势和驱动因子,可为林火预防和管理提供科学依据。本研究基于MODIS卫星火点数据,结合气象(日平均风速、日平均温度、日相对湿度、气温日较差、日累计降水)、人为(到公路距离、到铁路距离、到居民点距离、人口密度、人均GDP)、地形和植被因素(高程、坡度、植被覆盖度),运用趋势分析法、Logistic回归模型,对浙江省2001—2016年林火变化趋势和驱动因子进行研究。结果表明: 浙江省春、夏季林火呈显著上升趋势,秋、冬季林火呈先上升后下降趋势,秋季下降趋势显著。浙江省各季节林火预测模型拟合度均较高,模型预测准确率分别为75.8%(春季)、79.1%(夏季)、74.7%(秋季)和79.6%(冬季)。浙江省春、夏季林火发生与变化受气象、人为、地形和植被因素的显著影响;秋、冬季林火发生与变化主要受气象因素影响。在影响因素复杂、高火险区域分散的春、夏季,林火管理应重点加强人为活动管理和防火宣传教育;在秋、冬季,可通过在高火险区集中分布的西南地区增设瞭望塔和监控设备进行监测和管理。     

The role of interleukin-33 in pathogenesis of bronchial asthma. New experimental data

Interleukin-33 (IL-33) belongs to the IL-1 cytokine family and plays an important role in modulating immune system by inducing Th2 immune response via the ST2 membrane receptor. Epithelial cells are the major producers of IL-33. However, IL-33 is also secreted by other cells, e.g., bone marrow cells, dendritic cells, macrophages, and mast cells. IL-33 targets a broad range of cell types bearing the ST2 surface receptor. Many ST2-positive cells, such as Th2 cells, mast cells, basophils, and eosinophils, are involved in the development of allergic bronchial asthma (BA). This suggests that IL-33 directly participates in BA pathogenesis. Currently, the role of IL-33 in pathogenesis of inflammatory disorders, including BA, has been extensively investigated using clinical samples collected from patients, as well as asthma animal models. In particular, numerous studies on blocking IL-33 and its receptor by monoclonal antibodies in asthma mouse model have been performed over the last several years; IL-33-and ST2-deficient transgenic mice have also been generated. In this review, we summarized and analyzed the data on the role of IL-33 in BA pathogenesis and the prospects for creating new treatments for BA.     

Prediction of 'hot spots' in SV40 enhancer and relation with experimental data

A theoretical method for prediction of the points in the sequence which are relevant for its biological function, the so-called 'hot spots', is presented. This method is based on significant correlation between the spectrum of numerical presentation of any genetic sequence and its biological function. One number corresponds to the particular nucleotide, thus forming a numerical sequence. The 'hot spot' prediction has been tested on the SV40 enhancer as a model system. The SV40 enhancer was chosen because of existing detailed data about activities of systematically obtained mutants. These results have been compared with results obtained theoretically.     

Model of mammalian cell reproductive death II. Comparison with experimental data and discussion

A general equation for mammalian cell survival has been derived in the previous paper. This paper presents the results of comparison of theoretical evaluations with survival data available from the literature, including different cell lines, variations in linear energy transfer, dose rate and dose fractionation effects and the effects of ultrasoft X-rays and superheavy ions. Merits and demerits of the model are considered in comparison with other models of radiation-induced killing of mammalian cells published in the literature.     

The effect of interleukin-2 on parasitemia and myocarditis in experimental Chagas' disease

Previous investigations showed that interleukin-2 (IL-2) administered in vivo into mice infected with Trypanosoma cruzi reduced levels of parasitemia and increased longevity. Present experiments examined the effect of administration of different doses of IL-2 at different times during infection in mice on parasitemia and histopathology of heart tissue. Two different doses of IL-2 (1,500 or 10,000 U) given at 3 different times during infection were equivalent in reducing parasitemia. All of the IL-2 treated groups of mice had significantly lower numbers of circulating trypomastigotes as compared with controls not receiving this lymphokine. This IL-2 treatment of T. cruzi-infected mice resulted also in lower numbers of pseudocysts in all 4 ventricular regions in the hearts. This was particularly evident in the more severely infected right ventricular wall; however, a similar decrease was not as apparent in the less severely infected left ventricular wall. The IL-2 treated, infected mice showed minimal or no effect in reducing inflammation of myocardial cells. However, the mildest inflammation of ventricular wall tended to occur in mice receiving IL-2 treatment either as a low dose (1,500 U) or a high dose (10,000 U) at 5, 7 and 9 days after infection as compared with mice treated later on. It was concluded that IL-2 treatment of infected mice produced a significant decrease in parasitemia and decreased infection of myocardial cells.     

基于Sentinel-2的丛生竹林信息提取方法比较及分布特征

滇西南地区拥有丰富的丛生竹林景观和珍稀特有竹种资源,但竹资源分布储量不清、监测技术缺乏等问题很大程度限制了竹资源开发与利用。基于Sentinel-2A影像数据,采用反向传播神经网络、支持向量机、随机森林三种机器学习分类方法进行沧源县丛生竹林信息提取及精度评价,利用Google Earth影像和DEM数据对竹资源分布的空间和地形特征进行了分析。结果表明,随机森林分类精度优于支持向量机和反向传播神经网络,分类总体精度达90%,Kappa系数达0.87,竹林用户精度达81%。沧源县共有竹林138.07 km2,主要分布于城镇村庄、道路、水系和耕地周边,以四旁竹和防护竹林为主,采用Sentinel-2A10 m的分辨率很好地提取了空间上分布分散的丛生竹林。沧源县竹林主要分布在海拔900～2000 m,坡度范围大都位于缓坡和斜坡。研究结果可为沧源县竹资源开发利用提供数据支持,研究方法可作为大型丛生竹遥感监测的参考。     

Finite volume analysis of temperature effects induced by active MRI implants: 2. Defects on active MRI implants causing hot spots

Background

Active magnetic resonance imaging implants, for example stents, stent grafts or vena cava filters, are constructed as wireless inductively coupled transmit and receive coils. They are built as a resonator tuned to the Larmor frequency of a magnetic resonance system. The resonator can be added to or incorporated within the implant. This technology can counteract the shielding caused by eddy currents inside the metallic implant structure. This may allow getting diagnostic information of the implant lumen (in stent stenosis or thrombosis for example). The electro magnetic rf-pulses during magnetic resonance imaging induce a current in the circuit path of the resonator. A by material fatigue provoked partial rupture of the circuit path or a broken wire with touching surfaces can set up a relatively high resistance on a very short distance, which may behave as a point-like power source, a hot spot, inside the body part the resonator is implanted to. This local power loss inside a small volume can reach ¼ of the total power loss of the intact resonating circuit, which itself is proportional to the product of the resonator volume and the quality factor and depends as well from the orientation of the resonator with respect to the main magnetic field and the imaging sequence the resonator is exposed to.

Methods

First an analytical solution of a hot spot for thermal equilibrium is described. This analytical solution with a definite hot spot power loss represents the worst case scenario for thermal equilibrium inside a homogeneous medium without cooling effects. Starting with this worst case assumptions additional conditions are considered in a numerical simulation, which are more realistic and may make the results less critical. The analytical solution as well as the numerical simulations use the experimental experience of the maximum hot spot power loss of implanted resonators with a definite volume during magnetic resonance imaging investigations. The finite volume analysis calculates the time developing temperature maps for the model of a broken linear metallic wire embedded in tissue. Half of the total hot spot power loss is assumed to diffuse into both wire parts at the location of a defect. The energy is distributed from there by heat conduction. Additionally the effect of blood perfusion and blood flow is respected in some simulations because the simultaneous appearance of all worst case conditions, especially the absence of blood perfusion and blood flow near the hot spot, is very unlikely for vessel implants.

Results

The analytical solution as worst case scenario as well as the finite volume analysis for near worst case situations show not negligible volumes with critical temperature increases for part of the modeled hot spot situations. MR investigations with a high rf-pulse density lasting below a minute can establish volumes of several cubic millimeters with temperature increases high enough to start cell destruction. Longer exposure times can involve volumes larger than 100 mm³. Even temperature increases in the range of thermal ablation are reached for substantial volumes. MR sequence exposure time and hot spot power loss are the primary factors influencing the volume with critical temperature increases. Wire radius, wire material as well as the physiological parameters blood perfusion and blood flow inside larger vessels reduce the volume with critical temperature increases, but do not exclude a volume with critical tissue heating for resonators with a large product of resonator volume and quality factor.

Conclusion

The worst case scenario assumes thermal equilibrium for a hot spot embedded in homogeneous tissue without any cooling due to blood perfusion or flow. The finite volume analysis can calculate the results for near and not close to worst case conditions. For both cases a substantial volume can reach a critical temperature increase in a short time. The analytical solution, as absolute worst case, points out that resonators with a small product of inductance volume and quality factor (Q V_ind < 2 cm³) are definitely save. Stents for coronary vessels or resonators used as tracking devices for interventional procedures therefore have no risk of high temperature increases. The finite volume analysis shows for sure that also conditions not close to the worst case reach physiologically critical temperature increases for implants with a large product of inductance volume and quality factor (Q V_ind > 10 cm³). Such resonators exclude patients from exactly the MRI investigation these devices are made for.     

Nuclear factors interacting with an interleukin-6 responsive element of rat alpha 2-macroglobulin gene.

During acute inflammation, a group of liver-derived plasma proteins, acute phase proteins (APPs), increase in concentration. Interleukin-6 (IL-6) is responsible for this increase via the induction of APP gene expression. We have identified an IL-6 responsive cis-acting element (IL-6RE) of gene encoding a typical APP, rat alpha 2-macroglobulin (alpha 2M). The IL-6RE contains a sequence that is conserved among the 5'-flanking regions of various APP genes. Introduction of mutations into the conserved sequence revealed that the sequence, termed IL-6RE core, is a critical and essential component of IL6-RE. Nuclear factors binding to the IL-6RE core were identified in livers of normal and inflamed rats. Mobility shift pattern and DNase I footprinting profile indicated that the factors from normal and inflamed stages recognized the same sequence but were distinct from each other. These results suggested that the regulation of alpha 2M gene expression may involve mutually exclusive interaction of stage-specific trans-acting factors.     

Principal causes of hot spots for cytosine to thymine mutations at sites of cytosine methylation in growing cells. A model, its experimental support and implications.

In Escherichia coli and human cells, many sites of cytosine methylation in DNA are hot spots for C to T mutations. It is generally believed that T.G mismatches created by the hydrolytic deamination of 5-methylcytosines (5meC) are intermediates in the mutagenic pathway. A number of hypotheses have been proposed regarding the source of the mispaired thymine and how the cells deal with the mispairs. We have constructed a genetic reversion assay that utilizes a gene on a mini-F to compare the frequency of occurrence of C to T mutations in different genetic backgrounds in exponentially growing E. coli. The results identify at least two causes for the hot spot at a 5meC: (1) the higher rate of deamination of 5meC compared to C generates more T.G than uracil.G (U.G) mismatches, and (2) inefficient repair of T.G mismatches by the very short-patch (VSP) repair system compared to the repair of U. G mismatches by the uracil-DNA glycosylase (Ung). This combination of increased DNA damage when the cytosines are methylated coupled with the relative inefficiency in the post-replicative repair of T.G mismatches can be quantitatively modeled to explain the occurrence of the hot spot at 5meC. This model has implications for mutational hot and cold spots in all organisms.     

基于MODIS数据的天山区域地表温度时空特征

基于2001-2013年MODIS地表温度产品及TM影像遥感解译的土地利用类型数据,对天山区域地表温度时空特征进行分析.结果表明: 2001-2013年,研究区地表平均温度达1.73 ℃,呈东高西低的特点,西北部分地区的地表温度年际变化幅度明显高于其他地区,局部地区在0.55 ℃以上;地表温度呈逐年缓慢增加趋势,增加率为0.147 ℃·a^-1,季节性差异明显,冬季地表温度波动幅度较大,变异系数达12.7%,地表温度的差异白天大于夜晚,夏季明显高于其他季节;不同土地利用类型的地表温度之间存在差异,与对应像元的归一化植被指数之间存在不同的拟合效果.随着植被盖度的增加,林地、草地地表温度下降明显,归一化植被指数每下降0.1时,林地和草地的地表温度降幅为3.74、5.04 ℃;受人为活动影响较多的城镇用地和农地的地表温度与归一化植被指数之间的敏感性高于其他土地利用类型.     

A kinetic model for lipoxygenases based on experimental data with the lipoxygenase of reticulocytes

A comprehensive kinetic model for lipoxygenase catalysis is proposed which includes the simultaneous occurrence of dioxygenase and hydroperoxidase activities and is based on the assumption of a single binding site for substrate fatty acid and product. The aerobic reaction of purified lipoxygenase from rabbit reticulocytes with 9,12(Z,Z)-octadecadienoic acid (linoleic acid) as substrate was studied. The rate constants and the dissociation constants of this enzyme were calculated for the model from progress curves; the model describes correctly the experimental data. The following kinetic features of the reticulocyte enzyme are assumed to apply generally to lipoxygenases. (a) The enzyme shows autoactivation by its product. (b) The rate-limiting step is the hydrogen abstraction. (c) Both substrate fatty acid and its product are competitive inhibitors of the lipoxygenase. (d) Lowering the oxygen concentration enhances the degree of substrate inhibition, whereas product inhibition is not influenced. (e) If substrate is in excess the oxygen concentration determines the share of dioxygenase and hydroperoxidase activities of the enzyme. As predicted from the model it was found that at low concentrations of oxygen the regio- and stereo-specificities of the dioxygenation are diminished. During the autoactivation phase the steady-state approximation does not hold.     

Effect of interleukin-1beta and interleukin-4 on serum albumin parameters in rats with various behavioural characteristics

We studied the effects of pro-inflammatory cytokine interleukin-1beta and antiinflammatory cytokine interleukin-4 on serum albumin parameters in rats with various behavioural characteristics in the open-field test. Under control conditions, the total concentration of serum albumin in active animals was higher than in passive those. However, the ratio of the effective-to-total concentration of albumin (i.e., binding capacity of this protein) was greater in passive rats. Administration of interleukins was accompanied by a decrease in the total content and effective concentration of albumin in passive and, particularly, in active rats. The initial intergroup differences in the ratio of the effective-to-total concentration of albumin were not found after injection of immunomodulating agents. It was mainly related to a more significant increase in this parameter in active animals. An increase in the binding capacity of albumin after cytokine treatment could be associated with conformational changes in the protein molecule. We believe that interleukin-1b and interleukin-4 exert similar effects on the properties of binding sites of serum albumin in rats with various behavioural characteristics.     

The effect of recombinant interleukin-2 on the course of experimental staphylococcal peritonitis in mice]

The effect of RIL-2 on the survival of mice with S. aureus--induced peritonitis was studied. Animals received bacterial suspension and RIL-2 as following: bacteria--on days 0, +2, RIL-2--day 0 (group 1); bacteria--days 0, +4, RIL-2--days 0, +2 (group 2); bacteria--days 0, +6, RIL-2--days 0, +2, +4 (group 3). RIL-2 exerted no protective effect in group 1. However, in groups 2 and 3, where the control animals survival was, resp., 56% and 38%, the RIL-2 treatment increased survival up to, resp., 84% and 70%. Antibiotics given instead of RIL-2 in analogous regimen decreased the survival in group 3 to the level of 25%. Thus, RIL-2 proved to be a potent therapeutic agent in the 2nd of 3d studied models of S. aureus--induced peritonitis in mice. The perspectives of RIL-2 use in the treatment of bacterial peritonitis, including porous ones, and of the immunodepression--aggravated conditions are discussed.     

Comparison of two CD40-ligand/interleukin-2 vaccines in patients with chronic lymphocytic leukemia

Background aimsSeveral studies have demonstrated that the immunogenicity of chronic lymphocytic leukemia (CLL) cells can be increased by manipulation of the CD40/CD40-ligand (CD40L) pathway. Although immunologic, and perhaps clinical, benefits have been obtained with an autologous CLL tumor vaccine obtained by transgenic expression of CD40L and interleukin (IL)-2, there is little information about the optimal gene transfer strategies.MethodsWe compared two different CLL vaccines prepared by adenoviral gene transfer and plasmid electroporation, analyzing their phenotype and immunostimulatory activity.ResultsWe found that higher expression of transgenic CD40L was mediated by adenoviral gene transfer than by plasmid transduction, and that adenoviral transfer of CD40L was associated with up-regulation of the co-stimulatory molecules CD80 and CD86 and adhesion molecule CD54. In contrast, transgenic IL-2 secretion was greater following plasmid transduction. These phenotypic differences in the vaccines were associated with different functionality, both ex vivo and following administration to patients. Thus adenoviral vaccines induced greater activation of leukemia-reactive T cells ex vivo than plasmid vaccines. In treated patients, specific T-cell (T helper 1 (Th1) and T helper 2 (Th2)) and humoral anti-leukemia responses were detected following administration of the adenoviral vaccine (n = 15), while recipients of the plasmid vaccine (n = 9) manifested only a low-level Th2 response. Progression-free survival at 2 years was 46.7% in the adenoviral vaccine recipients, versus 11.1 % in those receiving plasmid vaccine.ConclusionsCLL vaccines expressing the same transgenes but produced by distinct methods of gene transfer may differ in the polarity of the immune response they induce in patients.     

基于“二类调查”的三峡库区重点生态恢复县森林资源空间特征的遥感分析

以高分辨率SPOT-5影像为基础数据源,结合1∶1万地形图计算地形位综合指数,利用ArcGIS的空间叠加和缓冲分析功能,识别三峡库区重点生态恢复县不同地形位与不同道路、水体和聚落缓冲半径下的林地分布特征.结果表明： 研究区林地资源总量丰富,且以乔木林和灌木林地为主,受地形制约和林地自然基础影响,林地主要分布在“两山”(方斗山、七曜山)区;林地地形位分布指数随地形位梯度的增大而呈整体上升趋势,乔木林和灌木林地表现尤为明显,其他林地类型则相反;不同缓冲半径内林地面积占缓冲范围面积的比例在道路、水体和聚落周围随缓冲半径的变化,与林地地形位分布指数有很强的相似性;不同缓冲半径内各林地类型占样区相应林地面积的比例仅在聚落周围呈现竹林、疏林地和未成林造林地高于乔木林和灌木林地;样区林地分布首先受以山地为特征的大地貌格局所左右,而不同地形位以及不同道路、水体和聚落缓冲半径下的林地分布则主要受大地貌格局主导下样区人为活动的胁迫所驱动.