De novo RNA synthesis and homology modeling of the classical swine fever virus RNA polymerase

Classical swine fever virus (CSFV) non-structural protein 5B (NS5B) encodes an RNA-dependent RNA polymerase (RdRp), a key enzyme which initiates RNA replication by a de novo mechanism without a primer and is a potential target for anti-virus therapy. We expressed the NS5B protein in Escherichia coli. The rGTP can stimulate de novo initiation of RNA synthesis and mutation of the GDD motif to Gly-Asp-Asp (GAA) abolishes the RNA synthesis. To better understand the mechanism of viral RNA synthesis in CSFV, a three-dimensional model was built by homology modeling based on the alignment with several virus RdRps. The model contains 605 residues folded in the characteristic fingers, palm and thumb domains. The fingers domain contains an N-terminal region that plays an important role in conformational change. We propose that the experimentally observed promotion of polymerase efficiency by rGTP is probably due to the conformational changes of the polymerase caused by binding the rGTP. Mutation of the GDD to GAA interferes with the interaction between the residues at the polymerase active site and metal ions, and thus renders the polymerase inactive. (c) 2005 Elsevier B.V. All rights reserved.

Heating characteristics of blunt swept fin-induced shock wave turbulent boundary layer interaction

An experimental study was conducted on shock wave turbulent boundary layer interactions caused by a blunt swept fin-plate configuration at Mach numbers of 5.0, 7.8, 9.9 for a Reynolds number range of (1.0.similar to 4.7) x 10(7)/m. Detailed heat transfer and pressure distributions were measured at fin deflection angles of up to 30 degrees for a sweepback angle of 67.6 degrees. Surface oil flow patterns and liquid crystal thermograms as well as schlieren pictures of fin shock shape were taken. The study shows that the flow was separated at deflection of 10 degrees and secondary separation were detected at deflection of theta greater than or equal to 20 degrees. The heat transfer and pressure distributions on flat plate showed an extensive plateau region followed by a distinct dip and local peak close to the fin foot. Measurements of the plateau pressure and heat transfer were in good agreement with existing prediction methods, but pressure and heating peak measurements at M greater than or equal to 6 were significantly lower than predicted by the simple prediction techniques at lower Mach numbers.

Tuning The Geometrical Parameters Of Biomimetic Fibrillar Structures To Enhance Adhesion

Fibrillar structures are common features on the feet of many animals, such as geckos, spiders and flies. Theoretical analyses often use periodical array to simulate the assembly, and each fibril is assumed to be of equal load sharing (ELS). On the other hand, studies on a single fibril show that the adhesive interface is flaw insensitive when the size of the fibril is not larger than a critical one. In this paper, the Dugdale Barenblatt model has been used to study the conditions of ELS and how to enhance adhesion by tuning the geometrical parameters in fibrillar structures. Different configurations in an array of fibres are considered, such as line array, square and hexagonal patterns. It is found that in order to satisfy flaw-insensitivity and ELS conditions, the number of fibrils and the pull-off force of the fibrillar interface depend significantly on the fibre separation, the interface interacting energy, the effective range of cohesive interaction and the radius of fibrils. Proper tuning of the geometrical parameters will enhance the pull-off force of the fibrillar structures. This study may suggest possible methods to design strong adhesion devices for engineering applications.

Non-Slipping Jkr Model For Transversely Isotropic Materials

A generalized plane strain JKR model is established for non-slipping adhesive contact between an elastic transversely isotropic cylinder and a dissimilar elastic transversely isotropic half plane, in which a pulling force acts on the cylinder with the pulling direction at an angle inclined to the contact interface. Full-coupled solutions are obtained through the Griffith energy balance between elastic and surface energies. The analysis shows that, for a special case, i.e., the direction of pulling normal to the contact interface, the full-coupled solution can be approximated by a non-oscillatory one, in which the critical pull-off force, pull-off contact half-width and adhesion strength can be expressed explicitly. For the other cases, i.e., the direction of pulling inclined to the contact interface, tangential tractions have significant effects on the pull-off process, it should be described by an exact full-coupled solution. The elastic anisotropy leads to an orientation-dependent pull-off force and adhesion strength. This study could not only supply an exact solution to the generalized JKR model of transversely isotropic materials, but also suggest a reversible adhesion sensor designed by transversely isotropic materials, such as PZT or fiber-reinforced materials with parallel fibers. (c) 2007 Elsevier Ltd. All rights reserved.

Switch Region for Pathogenic Structural Change in Conformational Disease and Its Prediction

Many diseases are believed to be related to abnormal protein folding. In the first step of such pathogenic structural changes, misfolding occurs in regions important for the stability of the native structure. This destabilizes the normal protein conformation, while exposing the previously hidden aggregation-prone regions, leading to subsequent errors in the folding pathway. Sites involved in this first stage can be deemed switch regions of the protein, and can represent perfect binding targets for drugs to block the abnormal folding pathway and prevent pathogenic conformational changes. In this study, a prediction algorithm for the switch regions responsible for the start of pathogenic structural changes is introduced. With an accuracy of 94%, this algorithm can successfully find short segments covering sites significant in triggering conformational diseases (CDs) and is the first that can predict switch regions for various CDs. To illustrate its effectiveness in dealing with urgent public health problems, the reason of the increased pathogenicity of H5N1 influenza virus is analyzed; the mechanisms of the pandemic swine-origin 2009 A(H1N1) influenza virus in overcoming species barriers and in infecting large number of potential patients are also suggested. It is shown that the algorithm is a potential tool useful in the study of the pathology of CDs because: (1) it can identify the origin of pathogenic structural conversion with high sensitivity and specificity, and (2) it provides an ideal target for clinical treatment.

根据花粉分析推论东北长白山西麓一万年来植被与环境

通过对长白山西麓山间沼泽分地钻孔沉积物孢粉的定量分析，结合对长白山植被与现代表土花粉关系的研究以及对当地现代沼泽体空间分布的调查的结果，认为该地区一万余年以来植被和环境经历了以下五个发展阶段，（1）约10300-1000年BP，森林植被为云冷杉林，洼地积水形成浅水湖泊，气候寒冷潮湿;（2）10000-9000年BP，以桦木林为主，并混生有一定数量的阔叶树，湖泊演化形成沼泽，低位苔草沼泽和中位落叶松-藓类沼泽发育，气候逐渐转暖;（3）9000-2900年BP，落叶阔叶林和阔叶红松林繁盛，落叶松—藓类沼泽进一步发育，气候温暖;（4）2900-950年BP，以阔叶红松林和红松云冷杉林为主，沼泽演化形成高位落叶松—狭叶杜香—泥炭藓沼泽，气候温凉潮湿;（5）950-0年BP，森林逐渐演化形成今日之阔叶红松林，沼泽退化为中低位苔草—藓类沼泽，气候温凉略干。

猪粪农用的生态风险——以东北黑土为例

集约化养殖大量使用铜(Cu)作为饲料添加剂会在养殖废物的排放和利用中导致一定的环境问题。随着东北老工业基地产业结构的调整，畜牧业作为东北地区二次振兴的主要产业得到迅速发展，由此会产生大量的畜禽粪便用于农业土壤施肥。而东北地区又是我国重要的农副产品生产基地，研究畜禽粪便农用的健康及环境风险就显得殊为必要。黑土是东北地区最主要的土壤类型，本文以东北黑土为供试材料，通过在盆栽实验中添加不同Cu浓度的猪粪来模拟施肥年限不同的菜园土，研究土壤中Cu累积对小白菜(Brassica chinensis L.)地上部分生物量与Cu含量、土壤微生物生物量和土壤酶(脱氢酶、脲酶、酸性磷酸酶)活性、微生物群落功能多样性以及对土壤功能微生物——氨氧化古菌(AOA)和氨氧化细菌(AOB)等的影响，从而实现含Cu猪粪农用对食物链途径的健康风险以及土壤生态系统的生态风险的综合评价。 研究结果表明，施用猪粪显著地改善了土壤的pH，增加了小白菜地上部分生物量，对其体内Cu浓度则没有显著影响;小白菜地上部分Cu浓度与土壤全Cu和水溶态Cu浓度显著正相关(P<0.01)，而地上生物量与土壤全Cu浓度显著负相关(P<0.05)。当土壤全Cu浓度达到300 mg kg-1后，小白菜地上部分生物量受到强烈抑制。 猪粪的施用在一定时期内显著地促进了脱氢酶和脲酶的活性，但随土壤Cu浓度的增加，脱氢酶、脲酶和酸性磷酸酶的活性逐渐受到抑制。当土壤全Cu浓度达到300 mg kg-1后，微生物生物量、脱氢酶、脲酶、酸性磷酸酶等均受到强烈抑制。 施加猪粪提高了土壤微生物群落功能多样性，当土壤Cu浓度达到170 mg kg-1后，显著地抑制了微生物群落功能多样性。种植小白菜后，各处理间微生物群落功能多样性没有显著差异，意味着植物能够维持微生物群落功能多样性。主成分分析(PCA)结果显示，当土壤全Cu浓度达到300 mg kg-1后，微生物群落功能多样性与其它处理显著不同。 猪粪显著地促进了土壤的硝化潜势速率(PNR)。随着Cu浓度的增加，硝化潜势速率逐渐受到抑制，当土壤全Cu浓度达到170 mg kg-1后，即与对照无显著差异。植物在维持硝化速率方面也起到重要作用。古菌amoA基因在每克干土中的拷贝数在9.4*106~2.59*107，细菌amoA基因在每克干土中的拷贝数约为1.48*106~1.41*107。猪粪在一定时期内显著地增加了AOA和AOB的数量，当土壤Cu浓度达到300 mg kg-1后，AOA和AOB的数量显著下降，并且AOA与AOB amoA基因拷贝数的比值增加，在小白菜栽种前(B1)和小白菜收获后(B2)分别为2.33和9.26，这意味着在高Cu浓度胁迫下，AOA的耐受性更强。古菌与细菌的amoA拷贝数与PNR之间则没有显著的相关关系，意味着AOA和AOB种群结构以及其中某些种群的活性可能发生了变化。 本文通过对东北黑土菜地土壤中Cu在作物体内的迁移积累及其对土壤微生物学指标(微生物生物量、酶活性、微生物群落功能多样性及功能微生物)的影响的综合研究，揭示了含Cu猪粪农用所造成的健康和生态风险，为建立适宜的土壤环境质量标准提供了一定的科学依据。通过本研究得出，黑土蔬菜种植中Cu浓度的阈值在170-300 mg kg-1之间。

Refined genome-wide comparative map of the domestic horse, donkey and human based on cross-species chromosome painting: insight into the occasional fertility of mules

We have made a complete set of painting probes for the domestic horse by degenerate oligonucleotide-primed PCR amplification of flow-sorted horse chromosomes. The horse probes, together with a full set of those available for human, were hybridized onto metaphase chromosomes of human, horse and mule. Based on the hybridization results, we have generated genome-wide comparative chromosome maps involving the domestic horse, donkey and human. These maps define the overall distribution and boundaries of evolutionarily conserved chromosomal segments in the three genomes. Our results shed further light on the karyotypic relationships among these species and, in particular, the chromosomal rearrangements that underlie hybrid sterility and the occasional fertility of mules.

SLA 的分型与检测

:传统的强调抗原多态性的SLA 分型方法主要是血清学、细胞学和生物化学的方法,随着分子生物学技术发 展,各具特点的SLA 分型技术不断涌现,如PCR2RFL P 法、PCR2SSCP 法、微卫星(MS) 法、DNA 序列的测定等,基于 强调SLA 的抗原多态性的分型和强调抗原保守性的功能学上的新分型技术(如SLA 超型和超基序) 进行了详细探 讨,比较了各类方法的优缺点,指明了未来SLA 分型的发展趋势。此外还指出了现行参考教材血清学SLA 单倍型 的编写错误以及重点强调了SL A2DQB 基因的准确分型技术必须借鉴于克隆测序。

Characterization of Sarcocystis species in domestic animals using a PCR-RFLP analysis of variation in the 18S rRNA gene: a cost-effective and simple technique for routine species identification

Thirteen restriction endonucleases were used to investigate nucleotide sequence variation in the 18S rRNA DNA of 88 individuals from ten Sarcocystis taxa collected as cysts from their intermediate hosts, swine, cattle and water buffalo. A DNA sequence of

Both stress experience and age determine the impairment or enhancement effect of stress on spatial memory retrieval

It has been documented that stress or glucocorticoids have conflicting effects on memory under different conditions. However, it is not fully understood why stress can either impair or enhance memory. Here, we have examined the performance of six age groups of Wistar rats in a water maze spatial task to evaluate the effects of stress under different conditions. We found that the impairment or enhancement effect of an 'elevated platform' (EP) stress on memory was dependent on previous stress experience and on age. EP stress impaired memory retrieval in water maze naive animals. but enhanced rather than impaired memory retrieval in young water maze stress-experienced animals. Furthermore, exogenously applied corticosterone or foot shock stress before water maze training prevented the impairment of memory retrieval that should be induced by treatment with corticosterone or foot shock before the 'probe trial'. Again, memory retrieval was enhanced in young animals under these conditions, and this enhancement can be prevented by the glucocorticoid receptor antagonist RU 38486. Thus, glucocorticoid receptor activation not only induced impairment of memory but also increased the capacity of young animals to overcome a later stress. The present findings suggest that the effect of stress on memory can be switched from impairment to enhancement dependent on both stress experience and age.

Effects of Abnormal Early Rearing Environments on Fear Memory in Adult Rats

为了探讨早期饲养环境对成年后大鼠条件化恐惧的影响,实验采用巴氏恐惧条件化的方法对不同饲养环境下的大鼠进行了行为检测.具体操作为:把断奶后的大鼠饲养在3个不同的人工控制的环境中(丰富环境、社群环境和贫瘠环境);8周后进行恐惧条件化训练和测试(指标为僵直百分比),以及检测不同饲养环境下的大鼠的体重、自发活动和足部电击敏感性.结果显示:与社群组相比,丰富组的大鼠条件化僵直水平明显增加,而贫瘠组的明显减少;丰富和贫瘠环境明显的影响了大鼠的体重;不同环境对自发活动和足部电击敏感性没有影响.这些结果说明幼年期的丰富环境能提高成年后大鼠的由声音诱发的条件化恐惧反应,而贫瘠环境则削弱了这种反应.

The stress experience dependent long-term depression disassociated with stress effect on spatial memory task

Behavioral stress can either block or facilitate memory and affect the induction of long-term potentiation (LTP) and long-term depression (LTD). However, the relevance of the stress experience-dependent long-term depression (SLTD) to spatial memory task is unknown. Here we have investigated the effects of acute and sub-acute elevated platform (EP) and foot shock (FS) stress on LTD induction in CA1 region of the hippocampus of anesthetized rats and spatial memory in Morris water maze. We found that LTD was facilitated by acute EP stress, but not by sub-acute EP stress that may be due to the fast adaptation of the animals to this naturalistic mild stress. However, FS stress, an inadaptable strong stress, facilitated LTD induction both in acute and sub-acute treatment. In addition, with the same stress protocols, acute EP stress impaired spatial memory but the sub-acute EP stressed animals performed the spatial memory task as well as the controls, may due to the same reason of adaptation. However, acute FS stress slightly impaired learning but sub-acute FS even enhanced memory retrieval. Our results showed that SLTD was disassociated with the effect of stress on memory task but might be related to stress experience-dependent form of aberrant memory. (C) 2003 Elsevier Science Ireland Ltd. and the Japan Neuroscience Society. All rights reserved.

Effects of unconditioned and conditioned aversive stimuli in an intense fear conditioning paradigm on synaptic plasticity in the hippocampal CA1 area in vivo

Repeated vivid recalls or flashbacks of traumatic memories and memory deficits are the cardinal features of post-traumatic stress disorder (PTSD). The underlying mechanisms are not fully understood yet. Here, we examined the effects of very strong fear conditioning (20 pairings of a light with a 1.5-mA, 0.5-s foot shock) and subsequent reexposure to the conditioning context (chamber A), a similar context (chamber B), and/or to the fear conditioned stimulus (CS) (a light) on synaptic plasticity in the hippocampal CA1 area in anesthetized Sprague-Dawley rats. The conditioning procedure resulted in very strong conditioned fear, as reflected by high levels of persistent freezing, to both the contexts and to the CS, 24 h after fear conditioning. The induction of long-term potentiation ON was blocked immediately after fear conditioning. It was still markedly impaired 24 h after fear conditioning; reexposure to the conditioning chamber A (CA) or to a similar chamber 13 (CB) did not affect the impairment. However, presentation of the CS in the CA exacerbated the impairment of LTP, whereas the CS presentation in a CB ameliorated the impairment so that LTP induction did not differ from that of control groups. The induction of long-term depression (LTD) was facilitated immediately, but not 24 h, after fear conditioning. Only reexposure to the CS in the CA, but not reexposure to either chamber A or B alone, or the CS in chamber B, 24 h after conditioning, reinstated the facilitation of LTD induction. These data demonstrate that unconditioned and conditioned aversive stimuli in an intense fear conditioning paradigm can have profound effects on hippocampal synaptic plasticity, which may aid to understand the mechanisms underlying impairments of hippocampus-dependent memory by stress or in PTSD. (c) 2005 Wiley-Liss, Inc.

Fridericia liangi sp nov (Enchytraeidae, Oligochaeta) from Changbaishan Mountain, China

We describe one new enchytraeid species, Fridericia liangi sp. nov., from Mt. Changbaishan, Jilin Province, northeastern China. It was collected from soils at the foot of Changbaishan Mountain and is distinguished from all known congeners by the following combination of characters: 1) no lateral chaetae, only ventral chaetae throughout, 2) a maximum of four chaetae in ventral preclitellar bundles, 3) one chaeta in ventral postclitellar bundles, 4) dorsal pores from VII on, 5) esophageal appendages unbranched, 6) coelomocytes without refractile vesicles, 7) clitellum girdle shaped, well developed, 8) no subneural glands, and 9) spermathecae simple.