A combined statistical model for multiple motifs search

Transcription factor binding sites (TFBS) play key roles in genebior 6.8 wavelet expression and regulation. They are short sequence segments with de¯nite structure and can be recognized by the corresponding transcription factors correctly. From the viewpoint of statistics, the candidates of TFBS should be quite di®erent from the segments that are randomly combined together by nucleotide. This paper proposes a combined statistical model for ¯nding over- represented short sequence segments in di®erent kinds of data set. While the over-represented short sequence segment is described by position weight matrix, the nucleotide distribution at most sites of the segment should be far from the background nucleotide distribution. The central idea of this approach is to search for such kind of signals. This algorithm is tested on 3 data sets, including binding sites data set of cyclic AMP receptor protein in E.coli, PlantProm DB which is a non-redundant collection of proximal promoter sequences from di®erent species, collection of the intergenic sequences of the whole genome of E.Coli. Even though the complexity of these three data sets is quite di®erent, the results show that this model is rather general and sensible.

细胞外信号调节蛋白激酶-cAMP反应元件结合蛋白信号通路在应激所致抑郁行为障碍中的作用

Stress is the most important factor in the vulnerability to depression and other behavioral disorders, but the mechanisms that stress signals are transferred into depression are far from understanding. To date, the neurotransmitters, neurotrophins and signal pathway have been concerned in the topic focusing on the pathophysiology of depression, but there are still many puzzles. Increasing evidence has indicated that the alteration in neuronal plasticity is the “trace” of stress-induced damages. The extracellular signal-regulated protein kinase(ERK)-cyclic-AMP-responsive element（CRE）-binding protein(CREB)signal pathway is a powerful intracellular signal transduction pathway participating in neuronal plasticity which is involved in higher brain cognitive functions such as learning and memory. However, so far, little is known about the role of the ERK-CREB signal pathway in response to stress and emotional modulations. Thus the aim of the study was to systematically investigate the role of the ERK-CEB signal pathway in depressive-like behaviors induced by stress. Depression animal models, antidepressant agent treatment and disruption of signal pathway in specific brain regions were applied. In the present study, three experiment sessions were designed to make sure whether the ERK-CREB signal pathway was indeed one of pathophysiological mechanisms of depressive-like behaviors induced by stress. In experiment one, two different stress animal models were applied, chronic forced swim stress and chronic empty water bottle stress. After stress, all animals were tested behaviorally using open-field, elevated-plus maze and saccharine preference test, and brain samples were processed for determination of ERK, P-ERK, CREB and P-CREB using western blot. The relationships between the proteins of ERK, P-ERK, CREB and P-CREB in the brain and the behavioral variables were also analyzed. In experiment two, rats were treated with antidepressant agent fluoxetine once a day for 21 consecutive days, then the brain levels of ERK, P-ERK, CREB and P-CREB was determined, the depressive-like behaviors were also examined. In experiment three, mitogen activated extracellular-signal-regulated kinase kinase (MEK) inhibitor U0126 was administrated to inhabit the activation of ERK in the hippocampus and prefrontal cortex respectively, then behavioral measurements and protein detection were conducted. The main results of the study were as the following: (1) Chronic forced swim stress induced animals to suffer depression and disrupted the ERK-CREB signal pathway in hippocampus and prefrontal cortex. There were significant correlations between P-ERK2, P-CREB and multiple variables of depressive-like behaviors. (2) Chronic empty water bottle stress did not induce depressive-like behaviors. Such stress decreased the brain level of P-ERK2 in hippocampus and prefrontal cortex, but the level of P-CREB in the hippocampus was increased. (3) The antidepressant agent fluoxetine relieved depressive-like behaviors and increased the activities of the ERK-CREB signal pathway in stressed animals. (4) Animals treated with U0126 injection into hippocampus showed decreased activities of the ERK-CREB signal pathway in the hippocampus, and suffered depression comorbid with anxiety. (5) Animals treated with U0126 injection into prefrontal cortex showed decreased activities of the ERK-CREB signal pathway in the prefrontal cortex, and exhibited depressive-like behaviors. In conclusion, The ERK-CREB signal pathway in the hippocampus and prefrontal cortex was involved in stress responses and significantly correlated with depressive-like behaviors; The ERK-CREB signal pathway in the hippocampus and prefrontal cortex participated in the mechanism that fluoxetine reversed stress-induced behavioral disorders, and might be the target pathway of the therapeutic action of antidepressants; The disruption of the ERK-CREB signal pathway in the hippocampus or prefrontal cortex led to depressive-like behaviors in animals, suggesting that disruption of ERK-CREB pathway in the hippocampus or prefrontal cortex was involved in the pathophysiology of depression, and might be at least one of the mechanisms of depression induced by stress.

Use of lanthanide metal complexes for the hydrolysis of 3 ',5 '- and 2 ',3 ' cyclic nucleotides

Lutetium(III) and lanthanum(III) complexes of 2-carboxyethylgermanium sesquioxide (Ge-132) can hydrolyze the phosphodiester linkage of 3',5'-cyclic adenosine monophosphate (cAMP), 3',5'-cyclic deoxyadenosine monophosphate (dcAMP) and 2',3'-cyclic adenosine monophosphate (2',3'-cAMP). Both cAMP and dcAMP are hydrolyzed with high selectivity, yielding predominantly 3'-monophosphates. 2',3'-cAMP is converted to 3'-AMP and 2'-AMP, the ratio of 3'-AMP to 2'-AMP produced being 1.4.

Efficient cleavage of ribonucleoside 3',5'-cyclic phosphates and deoxyribonucleoside 3',5'-cyclic phosphate by lanthanides

The cleavage of 3',5'-cAMP, 3',5'-cGMP and 3',5'-dcAMP by lanthanides has been investigated by HPLC and H-1 NMR. Rapid cleavage of cAMP, cGMP and dcAMP by Ce(III) under air at pH 8 and 37 degrees C has been observed. Regioselective cleavage of P-O(5') bond in cAMP, cGMP and dc;aMP tu give the corresponding 3'-AMP, 3'-GMP and 3'-dAMP by lanthanide chlorides has been achieved, and 3'-AMP and 3'-GMP are cleaved to adenosine(A) and guanosine(CT) more slowly, respectively, The notable difference in reactivity between Ce(III) and the other lanthanide ions under air has also been studied. The cleavage is enhanced with the increase in the molar fraction of Ce(IV). The fast cleavage of cAMP by Ce(III) under air at pH 8 is ascribed to the resultant Ce(IV) in the reaction mixture.

On The Cyclic Bending Behaviour Of A Hard Coating On A Ductile Substrate With Periodic Surface Hardened Regions

A cyclic bending experiment is designed to investigate the interface fracture behaviour of a hard chromium coating on a ductile substrate with periodic surface hardened regions. The unique deflection pattern of the vertical cracks after they run through the coating and impinge at the interface is revealed experimentally. A simple double-layer elastic beam model is adopted to investigate the interfacial shear stresses analytically. A FE model is employed to compute the stresses of the tri-phase structure under a single round of bending, and to investigate the effect of the loading conditions on the deflection pattern of the vertical cracks at the interface. (C) 2008 Elsevier Ltd. All rights reserved.

Stability Of Adhesion Clusters And Cell Reorientation Under Lateral Cyclic Tension

This work is motivated by experimental observations that cells on stretched substrate exhibit different responses to static and dynamic loads. A model of focal adhesion that can consider the mechanics of stress fiber, adhesion bonds, and substrate was developed at the molecular level by treating the focal adhesion as an adhesion cluster. The stability of the cluster under dynamic load was studied by applying cyclic external strain on the substrate. We show that a threshold value of external strain amplitude exists beyond which the adhesion cluster disrupts quickly. In addition, our results show that the adhesion cluster is prone to losing stability under high-frequency loading, because the receptors and ligands cannot get enough contact time to form bonds due to the high-speed deformation of the substrate. At the same time, the viscoelastic stress fiber becomes rigid at high frequency, which leads to significant deformation of the bonds. Furthermore, we find that the stiffness and relaxation time of stress fibers play important roles in the stability of the adhesion cluster. The essence of this work is to connect the dynamics of the adhesion bonds (molecular level) with the cell's behavior during reorientation (cell level) through the mechanics of stress fiber. The predictions of the cluster model are consistent with experimental observations.

Centrifuge modeling of suction bucket foundations for platforms under ice-sheet-induced cyclic lateral loadings

This paper presents the results of a series of centrifuge model tests performed to study the behavior of suction bucket foundations for a tension leg platform in the Bohai Bay, China. The target lateral loadings were from ice-sheet-induced structural vibrations at a frequency of 0.8-1.0 Hz. The results indicate that excess pore water pressures reach the highest values within a depth of 1.0-1.5 in below the mud line. The pore pressures and the induced settlement and lateral displacement increase with the amplitude of the cyclic loading. Two failure modes were observed: liquefaction in early excitations and settlement-induced problems after long-term excitations. (c) 2006 Elsevier Ltd. All rights reserved.

Fracture behavior of axisymmetrical bars under high triaxial stress and large strain cyclic loading

Axisymmetric notched bars with notch roots of large and small radii were tested under large strain cyclic loading. The main attention is focused on the fracture behaviour of steels having cycles to failure within the range 1-100. Our study shows that a gradual transition from a static ductile nature to one of fatigue cleavage can be observed and characterized by the Coffin-Manson formula in a generalized form. Both the triaxial tensile stress within the central region of specimens and static damage caused by the first increasing load have effects on the final failure event. A generalized cyclic strain range parameter DELTAepsilon is proposed as a measure of the numerous factors affecting behaviour. Fractographs are presented to illustrate the behaviour reported in the paper.

Post-cyclic Strength Degradation of Undisturbed and Remolded Marine Silty Clay

A series of static and cyclic-static tri-axial compression tests under consolidated-undrained conditions are carried out to study the characteristics of post-cyclic strength of the undisturbed and the remolded samples of marine silty clay. It is found that the post-cyclic monotonic strength decreases if the cyclic strain or pore pressure is over a certain value. The maximum degradation is 10% for undisturbed samples while 70% for remolded ones. The relationship between normalized undrained shear strength and apparent overconsolidation ratio, which is determined by the excess pore pressure induced by cyclic loading, is also established. Static consolidated-undrained tests on overconsolidated remolded samples are also performed. It is proposed that the static consolidated-undrained tests may be substituted for the cyclic-static consolidated-undrained tests if the post-cyclic strength degradation of remolded silty clay is needed to be evaluated simply.

Cyclic Deformation Of Nanocrystalline And Ultrafine-Grained Nickel

The cyclic deformation behavior Of ultrafine-grained (UFG) Ni samples synthesized by the electrodeposition method was studied. Different from those made by severely plastic deformation, the UFG samples used in this study are characterized by large-angle grain boundaries. Behaviors from nanocrystalline Ni and coarse-grained Ni samples were compared with that Of Ultrafine-grained Ni. With in situ neutron diffraction. unusual evolutions of residual lattice strains as well as cyclic hardening and softening behavior were demonstrated during the cyclic deformation. The microstructural changes investigated by TEM are discussed with respect to the unusual lattice strain and cyclic hardening/softening. (C) 2008 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Study on the Capacity Degradation of Bucket Foundation in Liquefied Sand Layer under Cyclic Loads

The capacity degradation of bucket foundation in liquefied sand layer under cyclic loads such as equivalent dynamic ice-induced loads is studied. A simplified numerical model of liquefied sand layer has been presented based on the dynamic centrifuge experiment results. The ice-induced dynamic loads are modeled as equivalent sine cyclic loads, the liquefaction degree in different position of sand layer and effects of main factors are investigated. Subsequently, the sand resistance is represented by uncoupled, non-linear sand springs which describe the sub-failure behavior of the local sand resistance as well as the peak capacity of bucket foundation under some failure criterion. The capacity of bucket foundation is determined in liquefied sand layer and the rule of capacity degradation is analyzed. The capacity degradation in liquefied sand layer is analyzed comparing with that in non-liquefied sand layer. The results show that the liquefaction degree is 0.9 at the top and is only 0.06 at the bottom of liquefied sand layer. The numerical results are agreement well with the centrifugal experimental results. The value of the degradation of bucket capacity is 12% in numerical simulating whereas it is 17% in centrifugal experiments.