Molecular cloning and characterization of a putative lipopolysaccharide-induced TNF-alpha factor (LITAF) gene homologue from Zhikong scallop Chlamys farreri

LPS-induced TNF-alpha factor (LITAF) is a novel transcriptional factor that was first discovered in LPS-stimulated human macrophage cell line THP-1. LITAF can bind to TNF-a promoter to regulate its expression. The first scallop LITAF (named as CfLITAF) was cloned from Zhikong scallop Chlamys farreri by Expressed Sequence Tag (EST) and Polymerase Chain Reaction (PCR) techniques. The cDNA of CfLITAF was of 1240 bp and consisted of a 5' untranslated region (UTR) of 112 bp, a 3' UTR of 678 bp and an open reading frame (ORF) of 450 bp encoding a polypeptide of 149 amino acids with an estimated molecular mass of 16.08 kDa and theoretical isoelectric point of 6.77. A typical conserved LITAF-domain was identified in CfLITAF by SMART analysis. Homology analysis of the deduced amino acid sequence of CfLITAF with other known sequences by using the BLAST program revealed that CfLITAF was homologous to the LITAF from human and rat (Identity = 46%), cattle, horse, mouse and chicken (Identity = 48%), western clawed frog (Identity = 42%), and zebrafish (Identity = 50%). The mRNA expression of CfLITAF in different tissues including haemocytes, muscle, mantle, heart, gill and gonad, and the temporal expression in haemocytes challenged by LPS or peptidoglycan (PGN) were measured by Real-time RT-PCR. CfLITAF mRNA transcripts could be detected in all tissues examined and be up-regulated in haemocytes after LPS challenge. No significant changes were observed after PGN stimulation. All these data indicated the existence of LITAF in scallop and also provided clue on the presence of TNF-alpha-like molecules in invertebrates. (C) 2007 Elsevier Ltd. All rights reserved.

The cDNA cloning and mRNA expression of a potential selenium-binding protein gene in the scallop Chlamys farreri

Selenium binding proteins (SeBP) represent a family of proteins that are believed to be involved in controlling the oxidation/reduction in many physiological processes. The cDNA of Zhikong Scallop Chlamys farreri selenium binding protein (zSeBP) was cloned by expressed sequence tag (EST) and RACE techniques. The high similarity of zSeBP deduced amino acid sequence with the SeBP in other organisms, such as bird, fish, frog, mosquito, fruit fly, mammalian, and even nematode and microorganism indicated that zSeBP should be a member of SeBP family. The temporal expression of zSeBP in the hemocytes was measured by semi-quantitative RT-PCR after scallops were stimulated by either oxidative stress or microbial challenge. The expression of zSeBP was up-regulated progressively after stimulation, and then dropped gradually to the original level. Meanwhile, malondialdehyde (MDA) measured by the colorimetric method in the microbial challenged scallops increased immediately after scallops was challenged by microbes, and was significantly higher than that in the control scallops. Results indicated that the microbial infection could incense the disorder of oxidation/reduction and may result in high MDA production. The negative correlation between the expression level of zSeBP and the MDA content suggested that zSeBP could play an important role in mediating the anti-oxidation mechanisms and immune response in marine invertebrates. (c) 2005 Published by Elsevier Ltd.

Metabolic characteristics of sea cucumber Apostichopus japonicus (Selenka) during aestivation

Metabolic characteristics of the sea cucumber Aposticholpus japonicus (Selenka) during aestivation were studied in the laboratory. The effects of water temperature on oxygen consumption rate (OCR) and ammonia-N excretion rate (AER) in A. japonicus were determined by the Winkler and Hypobromite methods, respectively. Mature (large, 148.5 +/- 15.4 g, medium 69.3 +/- 6.9 g) and immature (small, 21.2 +/- 4.7 g) individuals aestivated at water temperatures of 20 and 25 degrees C, respectively. The metabolic characteristics of mature individuals were different from immature individuals during this period. The OCR of mature sea cucumbers peaked at 20 degrees C, and then dropped significantly at higher temperatures, whereas the OCR of the immature animals continued to increase slightly, even beyond the aestivation temperature. The AER of mature individuals peaked at 20 T, while that of the immature animals peaked at 25 degrees C. The relationships between dry weight (DW) and absolute oxygen consumption (R) and absolute ammonia-N excretion (N) could be described by the regression equation R or N=aW(b). With the exception of 15 degrees C, the O/N ratios (calculated in atomic equivalents) of large size sea cucumbers was close to 20 across the temperatures used in this study, indicating that their energy Source was a combination of lipid and protein. Oil the other hand, apart from small individuals maintained at 10 degrees C, the O/N ratios of the medium and small sea Cucumbers were close to 10, indicating that protein was their major energy source. The O/N ratios in all size groups remained unchanged after aestivation was initiated. (c) 2005 Elsevier B.V. All rights reserved.

The manganese superoxide dismutase gene in bay scallop Argopecten irradians: Cloning, 3D modelling and mRNA expression

A novel manganese superoxide dismutase (MnSOD) was cloned from bay scallop Argopecten irradians by 3' and 5' rapid amplification of cDNA ends (RACE) PCR. The full-length cDNA of MnSOD was of 1207 bp with a 678 bp open reading frame encoding 226 amino acids. The deduced amino acid sequence contained a putative signal peptide of 26 amino acids. Sequence comparison showed that the MnSOD of A. irradians shared high identity with MnSOD in invertebrates and vertebrates, such as MnSOD from abalone Haliotis discus discus (ABG88843) and frog Xenopus laevis (AAQ63483). Furthermore, the 3D structure of bay scallop MnSOD was predicted by SWISS-MODEL Protein Modelling Server and compared with those of other MnSODs. The overall structure of bay scallop MnSOD was similar to those of zebrafish Danio rerio, fruit fly Drosophila melanogaster, Chinese shrimp Fenneropenaeus chinensis, human Homo sapiens, and had the highest similarity to scallop Mizuhopecten yessoensis and abalone H. discus discus. A quantitative real-time PCR (qRT-PCR) assay was developed to detect the mRNA expression of MnSOD in different tissues and the temporal expression in haemocytes following challenge with the bacterium Vibrio anguillarum. A higher-level of mRNA expression of MnSOD was detected in gill and mantle. The expression of MnSOD reached the highest level at 3 h post-injection with V. anguillarum and then slightly recovered from 6 to 48 h. The results indicated that bay scallop MnSOD was a constitutive and inducible protein and thus could play an important role in the immune responses against V anguillarum infection. (c) 2008 Elsevier Ltd. All rights reserved.

高原鼢鼠的挖掘行为及其与土壤硬度的关系(英文)

Burrowing behaviors of the plateau zokors ( Myospalax bailely) in relation to soil hardness were investigated by using radio2telemetry at Haibei Alpine Meadow Ecosystem Research Station ,Qinghai , China. The results showed that there were no differences of burrowing behaviors and the efficiencies of the excavating segment between male and female , except the digging duration of the male was longer than that of the female in the same soil. With increase of soil hardness , digging duration in incisors significantly increased , but dried soil mass dug out by the zokors in each bout reduced. Mean-while the field investigation also showed that soil hardness affected the distribution of the zokor.

Population dynamics and responses to management of plateau pikas Ochotona curzoniae

1. Plateau pikas Ochotona curzoniae are considered a pest species on the Tibetan Plateau because they compete with livestock for forage and their burrowing could contribute to soil erosion. The effectiveness of pest control programmes in Tibet has not been measured, and it is not known whether changes in livestock management have exacerbated problems with plateau pikas or compromised their control. This study measured the impact of control programmes and livestock management for forage conservation on populations of plateau pikas in alpine meadow in Naqu District, central Tibet, during 2004 and 2005.2. Current techniques for controlling plateau pikas in spring cause large reductions in abundance, but high density-dependent rates of increase result in no differences between treated and untreated populations by the following autumn. Rates of increase from spring to autumn are not influenced by standing plant biomass or concurrent grazing by yaks Bos grunniens and Tibetan sheep Ovis aries.3. In autumn there was significantly lower biomass outside fenced areas with year-round livestock grazing compared with inside fenced areas with equivalent or higher numbers of plateau pikas but predominantly winter grazing by livestock. Inside fenced areas, control of plateau pikas in spring produced no detectable effect on standing plant biomass at the end of the following summer compared with uncontrolled populations of plateau pikas.4. Regardless of their initial density, populations of plateau pikas declined rapidly over winter outside fenced areas where there was very low standing plant biomass in autumn. However, inside fenced areas with higher plant biomass in autumn, low-density populations of plateau pikas declined more slowly than high-density populations.5. Synthesis and applications. Current control programmes have limited effect because populations of plateau pikas can recover in one breeding season. There was no apparent increase in forage production in areas where plateau pikas were controlled. However, plateau pikas appear to benefit from changes in grazing management, with low-density populations declining less over winter inside fenced areas than elsewhere. It was not evident that control programmes are warranted or that they will improve the livelihoods of Tibetan herders.

The impact of plateau zokor Myospalax fontanierii burrows on alpine meadow vegetation on the Qinghai-Xizang (Tibetan) plateau

The impact of burrows constructed by plateau zokors Myospalax fontanierii (Milne-Edwards, 1867) on alpine meadow vegetation on the Qinghai-Xizang (Tibetan) plateau was investigated. Plant samples taken from quadrats directly over active zokor burrows, back-filled burrows, adjacent burrow controls, and random sites from a field, in which no burrows or mounds occurred were compared. The biomass of plants (below- and above-ground) directly over shallow active burrows was significantly lower than on control plots. This reduction in biomass was not significantly different than that between deep active burrows and control plots. There were no significant differences between above- and below-ground plant biomass on areas perpendicular to active burrows when compared to random sites. Back-filling soil in burrows could promote the growth of above-ground monocotyledonous plants. However, the burrowing activities of zokors had a negative effect on biomass of dicotyledonous plants.

真空机器人时间最优轨迹规划

在指定路径上的运行时间是衡量真空机器人性能的重要指标，使用时间最优轨迹规划方法能够缩短该运行时间.Frog-leg型结构的真空机器人是同时具有主动与从动关节的并联机构，进行轨迹规划之前必须进行运动学及动力学求解.在此基础上提出Frog-leg型结构的真空机器人时间最优轨迹规划方法，规划出在允许最大速度与加速度范围内的加速度、速度与位置曲线.利用Matlab软件进行了仿真研究.仿真实验结果证明，与梯形轨迹规划方法相比，时间最优轨迹规划方法能够在满足加速度力矩约束的条件下显著缩短真空机器人在指定路径上的运行时间。

地震波场模拟及叠前深度偏移的李群方法

The processes of seismic wave propagation in phase space and one way wave extrapolation in frequency-space domain, if without dissipation, are essentially transformation under the action of one parameter Lie groups. Consequently, the numerical calculation methods of the propagation ought to be Lie group transformation too, which is known as Lie group method. After a fruitful study on the fast methods in matrix inversion, some of the Lie group methods in seismic numerical modeling and depth migration are presented here. Firstly the Lie group description and method of seismic wave propagation in phase space is proposed, which is, in other words, symplectic group description and method for seismic wave propagation, since symplectic group is a Lie subgroup and symplectic method is a special Lie group method. Under the frame of Hamiltonian, the propagation of seismic wave is a symplectic group transformation with one parameter and consequently, the numerical calculation methods of the propagation ought to be symplectic method. After discrete the wave field in time and phase space, many explicit, implicit and leap-frog symplectic schemes are deduced for numerical modeling. Compared to symplectic schemes, Finite difference (FD) method is an approximate of symplectic method. Consequently, explicit, implicit and leap-frog symplectic schemes and FD method are applied in the same conditions to get a wave field in constant velocity model, a synthetic model and Marmousi model. The result illustrates the potential power of the symplectic methods. As an application, symplectic method is employed to give synthetic seismic record of Qinghai foothills model. Another application is the development of Ray+symplectic reverse-time migration method. To make a reasonable balance between the computational efficiency and accuracy, we combine the multi-valued wave field & Green function algorithm with symplectic reverse time migration and thus develop a new ray+wave equation prestack depth migration method. Marmousi model data and Qinghai foothills model data are processed here. The result shows that our method is a better alternative to ray migration for complex structure imaging. Similarly, the extrapolation of one way wave in frequency-space domain is a Lie group transformation with one parameter Z and consequently, the numerical calculation methods of the extrapolation ought to be Lie group methods. After discrete the wave field in depth and space, the Lie group transformation has the form of matrix exponential and each approximation of it gives a Lie group algorithm. Though Pade symmetrical series approximation of matrix exponential gives a extrapolation method which is traditionally regarded as implicit FD migration, it benefits the theoretic and applying study of seismic imaging for it represent the depth extrapolation and migration method in a entirely different way. While, the technique of coordinates of second kind for the approximation of the matrix exponential begins a new way to develop migration operator. The inversion of matrix plays a vital role in the numerical migration method given by Pade symmetrical series approximation. The matrix has a Toepelitz structure with a helical boundary condition and is easy to inverse with LU decomposition. A efficient LU decomposition method is spectral factorization. That is, after the minimum phase correlative function of each array of matrix had be given by a spectral factorization method, all of the functions are arranged in a position according to its former location to get a lower triangular matrix. The major merit of LU decomposition with spectral factorization (SF Decomposition) is its efficiency in dealing with a large number of matrixes. After the setup of a table of the spectral factorization results of each array of matrix, the SF decomposition can give the lower triangular matrix by reading the table. However, the relationship among arrays is ignored in this method, which brings errors in decomposition method. Especially for numerical calculation in complex model, the errors is fatal. Direct elimination method can give the exact LU decomposition But even it is simplified in our case, the large number of decomposition cost unendurable computer time. A hybrid method is proposed here, which combines spectral factorization with direct elimination. Its decomposition errors is 10 times little than that of spectral factorization, and its decomposition speed is quite faster than that of direct elimination, especially in dealing with a large number of matrix. With the hybrid method, the 3D implicit migration can be expected to apply on real seismic data. Finally, the impulse response of 3D implicit migration operator is presented.

Neural Representations for Sensory-Motor Control, III: Learning a Body-Centered Representation of 3-D Target Position

A neural model is described of how the brain may autonomously learn a body-centered representation of 3-D target position by combining information about retinal target position, eye position, and head position in real time. Such a body-centered spatial representation enables accurate movement commands to the limbs to be generated despite changes in the spatial relationships between the eyes, head, body, and limbs through time. The model learns a vector representation--otherwise known as a parcellated distributed representation--of target vergence with respect to the two eyes, and of the horizontal and vertical spherical angles of the target with respect to a cyclopean egocenter. Such a vergence-spherical representation has been reported in the caudal midbrain and medulla of the frog, as well as in psychophysical movement studies in humans. A head-centered vergence-spherical representation of foveated target position can be generated by two stages of opponent processing that combine corollary discharges of outflow movement signals to the two eyes. Sums and differences of opponent signals define angular and vergence coordinates, respectively. The head-centered representation interacts with a binocular visual representation of non-foveated target position to learn a visuomotor representation of both foveated and non-foveated target position that is capable of commanding yoked eye movementes. This head-centered vector representation also interacts with representations of neck movement commands to learn a body-centered estimate of target position that is capable of commanding coordinated arm movements. Learning occurs during head movements made while gaze remains fixed on a foveated target. An initial estimate is stored and a VOR-mediated gating signal prevents the stored estimate from being reset during a gaze-maintaining head movement. As the head moves, new estimates arc compared with the stored estimate to compute difference vectors which act as error signals that drive the learning process, as well as control the on-line merging of multimodal information.

Soft sediment ecology of Lough Hyne Marine Reserve - spatial and temporal patterns

Distribution of soft sediment benthic fauna and the environmental factors affecting them were studied, to investigate changes across spatial and temporal scales. Investigations took place at Lough Hyne Marine Reserve using a range of methods. Data on the sedimentation rates of organic and inorganic matter were collected at monthly intervals for one year at a number of sites around the Lough, by use of vertical midwater-column sediment traps. Sedimentation of these two fractions were not coupled; inorganic matter sedimentation depended on hydrodynamic and weather factors, while the organic matter sedimentation was more complex, being dependent on biological and chemical processes in the water column. The effects of regular hypoxic episodes on benthic fauna due to a natural seasonal thermocline were studied in the deep Western Trough, using camera-equipped remotely-operated vehicle to follow transects, on a three-monthly basis over one year. In late summer, the area below the thermocline of the Western Trough was devoid of visible fauna. Decapod crustaceans were the first taxon to make use of ameliorating oxygen conditions in autumn, by darting below the thermocline depth, most likely to scavenge. This was indicated by tracks that they left on the surface of the Trough floor. Some species, most noticeably Fries’ goby Lesueurigobius friesii, migrated below the thermocline depth when conditions were normoxic and established semi-permanent burrows. Their population encompassed all size classes, indicating that this habitat was not limited to juveniles of this territorial species. Recolonisation by macrofauna and burrowing megafauna was studied during normoxic conditions, from November 2009 to May 2010. Macrofauna displayed a typical post-disturbance pattern of recolonisation with one species, the polychaete Scalibregma inflatum, occurring at high abundance levels in March 2010. In May, this population had become significantly reduced and a more diverse community was established. The abundance of burrowing infauna comprising decapods crabs and Fries’ gobies, was estimated by identifying and counting their distinctive burrow structures. While above the summer thermocline depth, burrow abundance increased in a linear fashion, below the thermocline depth a slight reduction of burrow abundance occurred in May, when oxygen conditions deteriorated again. The majority of the burrows occurring in May were made by Fries’ gobies, which are thought to encounter low oxygen concentrations in their burrows. Reduction in burrow abundance of burrowing shrimps Calocaris macandreae and Callianassa subterranea (based on descriptions of burrow structures from the literature), from March to May, might be related to their reduced activity in hypoxia, leading to loss of structural burrow maintenance. Spatial and temporal changes to macrofaunal assemblage structures were studied seasonally for one year across 5 sites in the Lough and subject to multivariate statistical analysis. Assemblage structures were significantly correlated with organic matter levels in the sediment, the amounts of organic matter settling out of the water column one month before macrofaunal sampling took place as well as current speed and temperature. This study was the first to investigate patterns and processes in the Lough soft sediment ecology across all 3 basins on a temporal and spatial scale. An investigation into the oceanographic aspects of the development, behaviour and break-down of the summer thermocline of Lough Hyne was performed in collaboration with researchers from other Irish institutions.

Phosphorylation/dephosphorylation of the beta-adrenergic receptor regulates its functional coupling to adenylate cyclase and subcellular distribution.

Prolonged exposure of cells or tissues to drugs or hormones such as catecholamines leads to a state of refractoriness to further stimulation by that agent, known as homologous desensitization. In the case of the beta-adrenergic receptor coupled to adenylate cyclase, this process has been shown to be intimately associated with the sequestration of the receptors from the cell surface through a cAMP-independent process. Recently, we have shown that homologous desensitization in the frog erythrocyte model system is also associated with increased phosphorylation of the beta-adrenergic receptor. We now provide evidence that the phosphorylation state of the beta-adrenergic receptor regulates its functional coupling to adenylate cyclase, subcellular translocation, and recycling to the cell surface during the process of agonist-induced homologous desensitization. Moreover, we show that the receptor phosphorylation is reversed by a phosphatase specifically associated with the sequestered subcellular compartment. At 23 degrees C, the time courses of beta-adrenergic receptor phosphorylation, sequestration, and adenylate cyclase desensitization are identical, occurring without a lag, exhibiting a t1/2 of 30 min, and reaching a maximum at approximately 3 hr. Upon cell lysis, the sequestered beta-adrenergic receptors can be partially recovered in a light membrane vesicle fraction that is separable from the plasma membranes by differential centrifugation. The increased beta-adrenergic receptor phosphorylation is apparently reversed in the sequestered vesicle fraction as the sequestered receptors exhibit a phosphate/receptor stoichiometry that is similar to that observed under basal conditions. High levels of a beta-adrenergic receptor phosphatase activity appear to be associated with the sequestered vesicle membranes. The functional activity of the phosphorylated beta-adrenergic receptor was examined by reconstituting purified receptor with its biochemical effector the guanine nucleotide regulatory protein (Ns) in phospholipid vesicles and assessing the receptor-stimulated GTPase activity of Ns. Compared to controls, phosphorylated beta-adrenergic receptors, purified from desensitized cells, were less efficacious in activating the Ns GTPase activity. These results suggest that phosphorylation of the beta-adrenergic receptor leads to its functional uncoupling and physical translocation away from the cell surface into a sequestered membrane domain. In the sequestered compartment, the phosphorylation is reversed thus enabling the receptor to recycle back to the cell surface and recouple with adenylate cyclase.

A unified anatomy ontology of the vertebrate skeletal system.

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

Effects of Environmentally Relevant Concentrations of Poultry Litter Associated Contaminates on the Sexual Development of Xenopus laevis

Poultry litter contains high levels of natural sex hormones, nitrogen, phosphorous, and trace amounts of heavy metals. Poultry litter runoff from poultry and farming operations in the Delmarva region can have serious impacts on frog development in the Chesapeake Bay Watershed. In this study, we investigated potential effects of litter compounds on Xenopus laevis development when exposed to environmental levels (0.35 and 0.70 g/L) of litter solution. We found that despite rapid hormone degradation, poultry litter solution still affected X. laevis development. Hormones were also more persistent in the lower poultry litter concentration, leading to even greater effects. Slowed growth and increased female gonadal abnormalities were observed after exposure to 0.35 g/L but not to 0.70 g/L of litter solution, and increased male gonadal abnormalities were observed after treatment to both litter concentrations. The developmental impacts examined in this study may have greater environmental impacts on frog reproduction and survival.

The use of biological indicators of heavy metal contamination in estuaries. Occasional Publication of the Marine Biological Association 1

The use of the deposit-feeding molluscs Scrobicularia plana and Macoma balthica and the burrowing polychaete Nereis diversicolor as indicators of the biological availability of heavy metals in sediments has been evaluated. Concentrations of Ag, As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb, Sn and Zn have been measured in organisms and sediments from more than 30 estuaries in south west England and South Wales and indicate that the biological availability of most metals varies by order of magnitude between uncontaminated and contaminated sites. The results have been compared with those obtained with the use of other species of indicator organisms in estuaries.