FoldMiner: structural motif discovery using an improved superposition algorithm

We report an unsupervised structural motif discovery algorithm, FoldMiner, which is able to detect global and local motifs in a database of proteins without the need for multiple structure or sequence alignments and without relying on prior classification of proteins into families. Motifs, which are discovered from pairwise superpositions of a query structure to a database of targets, are described probabilistically in terms of the conservation of each secondary structure element's position and are used to improve detection of distant structural relationships. During each iteration of the algorithm, the motif is defined from the current set of homologs and is used both to recruit additional homologous structures and to discard false positives. FoldMiner thus achieves high specificity and sensitivity by distinguishing between homologous and nonhomologous structures by the regions of the query to which they align. We find that when two proteins of the same fold are aligned, highly conserved secondary structure elements in one protein tend to align to highly conserved elements in the second protein, suggesting that FoldMiner consistently identifies the same motif in members of a fold. Structural alignments are performed by an improved superposition algorithm, LOCK 2, which detects distant structural relationships by placing increased emphasis on the alignment of secondary structure elements. LOCK 2 obeys several properties essential in automated analysis of protein structure: It is symmetric, its alignments of secondary structure elements are transitive, its alignments of residues display a high degree of transitivity, and its scoring system is empirically found to behave as a metric.     

Hydrodynamics-Based Transfer of Human Apolipoprotein A-I Gene to Mice: Study of Factors Affecting the Efficiency and Duration of Gene Expression in the Mouse Liver

Human apolipoprotein A-I gene (apoA-I) inserted into a plasmid expression vector was transferred in vivo into C57Bl/6 mice using hydrodynamic injections into the tail vein. Two types of plasmid expression vectors were used: (1) pCMVcapoAI which contained cDNA of apoA-I driven by the human cytomegalovirus (CMV) early gene promoter and (2) pAlg, which contained a genomic locus of intron-containing apoA-I driven by its own extended 5-regulatory region (APOAI). Hydrodynamic intravenous injections of both expression vectors led to the appearance of human apoA-I mRNA in the liver and human ApoA-I protein in the serum of injected mice. The dynamics of human ApoA-I content in the sera of mice injected with pCMVcapoAI and pAlg were different. When pCMVcapoAI was used, the concentration of human ApoA-I in mouse serum was maximal one day after injection and decreased to zero within the next two weeks. In the case of pAlg, the content of human ApoA-I in serum was maximal (up to 20 g/ml) on days 5–7 after injection and then gradually decreased for several months (six months after injection, for example, it decreased to 25% of the maximal value). Experiments on saved pAlg plasmid isolated from the nuclei of hepatocytes 50 days after injection showed that the plasmid was retained for a long time in the form of an episome. A significant content of human ApoA-I in serum and its long-term persistence after injecting mice with pAlg may be accounted for by the properties of APOAI and/or the exon–intron structure of the apoA-I gene. Injecting mice with different variants of APOAI coupled with the luciferase gene did not lead to long-term expression of luciferase in the liver. It is concluded that the presence of introns in the apoA-I gene is required for its efficient and long-term expression after transfer to mice by means of hydrodynamic injections.     

山东平邑第四纪裂隙中哺乳动物群及其生态学意义

平邑动物群产自4个地点（裂隙）、3个层位,由14属15种（分属食虫类、翼手类、兔形类、啮齿类、食肉类和偶蹄类）构成。这些化石反映出该地中更新世期间有一个从温暖的森林环境向干冷的荒漠草原环境又向温暖的灌丛草原环境转化的过程。     

国产打碗花属植物的花粉形态及其分类学意义

本文采用光学显微镜及扫描电子显微镜系统观察了国产５种１变种打碗花属（ＣａｌｙｓｔｅｇｉａＲ．Ｂｒ．）植物的花粉．该属植物的花粉呈球形,具散孔。覆盖层具穿孔．孔圆形、椭圆形或不规则,通常５或４个一组,至五边形或四边形排列,具孔膜,凹陷,少数突出,具５－２０个不规则颗粒状突起．花粉外壁分两层,内层厚约０．５μ,外层厚薄不一,趋向萌发孔变薄,覆盖层表面具小刺状突起、小凹陷及穿孔．观察结果说明,打碗花属为一个自然分类群,其可能起源于旋花属中具散沟的类群,或与之具有共同的祖先．本文观察到有些种的部分萌发孔间具有通道,这可能是该属花粉的一种返祖现象．另外一份毛打碗花的花粉标本,其花粉外壁天覆盖层,上部２－３次分枝的基柱明显可见,这种罕见的花粉可能是由于某种突变造成的．     

白内障患者术后感染性眼内炎的病原菌分布及CD64指数、血清sTREM1、HMGB1表达的临床意义

摘要 目的：分析白内障患者术后感染性眼内炎（IE）的病原菌分布并探讨分化簇64（CD64）指数、血清可溶性髓系细胞触发受体1（sTREM1）、高迁移率族蛋白1（HMGB1）表达的临床意义。方法：选取2018年1月～2022年7月济南市人民医院眼科收治的125例（125眼）白内障术后IE患者为IE组,选取同期150例（150眼）白内障术后无术后IE患者为非IE组。分析术后IE患者病原菌分布,计算CD64指数和检测血清sTREM1、HMGB1表达。采用多因素Logistic回归分析白内障患者术后IE的影响因素,采用受试者工作特征（ROC）曲线分析CD64指数、血清sTREM1、HMGB1表达对白内障患者术后IE的诊断价值。结果：125例术后IE患者房水或玻璃原液中检测出138株病原菌,革兰氏阳性菌、革兰氏阴性菌、真菌分别占比81.88%（113/138）、16.67%（23/138）、1.45%（2/138）。与非IE组比较,IE组糖尿病、玻璃体溢出比例、CD64指数和血清sTREM1、HMGB1水平升高,手术时间更长（P＜0.05）。多因素Logistic回归分析显示,糖尿病、玻璃体溢出、手术时间延长和CD64指数、sTREM1、HMGB1升高为白内障患者术后IE的独立危险因素（P＜0.05）。ROC曲线分析显示,CD64指数与血清sTREM1、HMGB1联合预测白内障患者术后IE的曲线下面积显著高于单独预测。结论：白内障患者术后IE的病原菌以革兰氏阳性菌为主,CD64指数和血清sTREM1、HMGB1表达与白内障患者术后IE独立相关,可能成为白内障患者术后IE的辅助诊断指标,且三指标联合具有较高的预测价值。     

新疆若干植物群落对土壤和地下水指示性的初步研究

本文对北疆玛纳斯河流域和南疆策勒河流域共10种植物群落与土壤和地下水的关系进行了初步研究,分析了一些植物的指示意义。1．多枝柽柳是一种富Cl和S的植物,它所生长的土壤中Cl-和SO42-的含量较高．生长多枝柽柳群落的土壤盐化类型一般为氮化物、硫酸盐型1）。2．梭梭和白梭梭的化学元素类型很相似,它们都是富Na植物．土壤中Na+离子的相对含量一般在50%以上。3．琵琶柴在南疆多分布在砾质戈壁上,在北疆则多出现于黄土状母质上。一般说来,琵琶柴生长地段0—30cm土层内的盐分平均含量不超过1%。4．花花柴是一种潜水指示植物,它的地下水深度一般不超过3m。花花柴也是一种富S植物,土壤中SO42-离子的相对含量较高。5．疏叶骆驼刺是一种淡水指示植物。在南疆多生长在沙丘间低地和平沙地上．地下水深多在5m以下,土壤盐渍化较弱。6．铃铛刺也是潜水植物,在玛纳斯河流域它一般指示地下水深度在2—4m左右．该植物体内的低灰分含量与土壤弱盐渍化程度相联系。7．膜果麻黄生长在砾沙质的棕色荒漠土上,土体中有明显的石膏淀积层。8．黑刺是典型盐土植物,所在土壤0—30cm平均含盐量大于2%,黑刺是富Na和富Cl植物,土壤中Na+离子和Cl-离子的相对含量也较高。 9．昆仑蒿总是与昆仑黄土相联系,它是一种富K植物,可用来指示土壤中K的较高含量。     

Pollen Morphology and Its Taxonomic Significance of Caragana Fabr. (Fabaceae) from China

Pollen grains of thirty one species and two varieties of the genus Caragana Fabr. were observed under LM and SEM.The results revealed that the pollen exine ornamentation of the species examined could be divided into two types: perforate and reticulate.The later type consists of two subtypes according to lumina size and muri width. In the first subtype the lumina is round with d iameter equal to muri width,and the exine is perforate in two polar areas,while in the second subtype lumina is irregular or polygonal,with diameter sm aller than muri width.The pollen volume was divided into four types.The genus Caragana is a natural group which was indicated by the general resemblance of pollen morphology. In this genus the pollen morphological classification was not in concordance with the arrangement of the sections and series except Ser.Pygmeae and some species. The pollen variation at infraspecific level was obvious,especially the species distributed in Qinghai Xizang Plateau, such as C.jubata, C.bicolor and C. erinacea . The evolutionary trend of pollen morphology is from perforate to reticulate, which is congruous with the evolution from the pinnate leaf group to the almate leaf group in the genus.     

Pigmented eyes,photoreceptor‐like sense organs and central nervous system in the polychaete Scoloplos armiger (Orbiniidae,Annelida) and their phylogenetic importance

The phylogenetic position of Orbiniidae within Annelida is unresolved. Conflicting hypotheses place them either in a basal taxon Scolecida, close to Spionida, or in a basal position in Aciculata. Because Aciculata have a specific type of eye, the photoreceptive organs in the orbiniid Scoloplos armiger were investigated to test these phylogenetic hypotheses. Two different types of prostomial photoreceptor‐like sense organs were found in juveniles and one additional in subadults. In juveniles there are four ciliary photoreceptor‐like phaosomes with unbranched cilia and two pigmented eyes. The paired pigmented eyes lie beside the brain above the circumoesophageal connectives. Each consists of one pigmented cell, one unpigmented supportive cell and three everse rhabdomeric sensory cells with vestigial cilia. During development the number of phaosomes increases considerably and numerous unpigmented sense organs appear consisting of one rhabdomeric photoreceptor cell and one supportive cell. The development and morphology of the pigmented eyes of S. armiger suggest that they represent miniaturized eyes of the phyllodocidan type of adult eye rather than persisting larval eyes resulting in small inverse eyes typical of Scolecida. Moreover, the structure of the brain indicates a loss of the palps. Hence, a closer relationship of Orbiniidae to Phyllodocida is indicated. Due to a still extensive lack of ultrastructural data among polychaetes this conclusion cannot be corroborated by considering the structure of the unpigmented ciliary and rhabdomeric photoreceptor‐like sense organs. J. Morphol., 2009. © 2009 Wiley‐Liss, Inc.