Identification of Crassostrea ariakensis and related oysters by multiplex species-specific PCR

Genetic markers are needed for rapid and reliable identification of oysters. In this study, we developed multiplex genus- and species-specific PCR markers for the identification of oysters from China. We used the mitochondrial cytochrome oxidase I (COI) and nuclear 28S ribosomal RNA genes for marker development. DNA sequences from different species were obtained from GenBank or by direct sequencing. Sequences were aligned, and genus- and species-specific nucleotides were identified. Primers were designed for genus/species-specific amplification to generate fragments of different sizes. A multiplex set of genus- and species-specific primers from the 28S gene was able to separate C. ariakensis and C. hongkongensis from other species and assign oysters to four genera. A set of species-specific COI primers provided positive identification of all five Crassostrea species from China, C. ariakensis, C. hongkongensis, C. angulata, C. gigas, and C. sikamea in a single PCR. The multiplex PCR assays do not require fluorescence-labeling or post-PCR enzyme digestion, providing a simple, fast and reliable method for the identification of oysters from China.

Its length polymorphism in oysters and its use in species identification

In an effort to develop genetic markers for oyster identification, we studied length polymorphism in internal transcribed spacers (ITS) between major ribosomal RNA genes in 12 common species of Ostreidae: Crassostrea virginica, C. rhizophorae, C. gigas, C. angulata, C. sikamea, C. ariakensis, C. hongkongensis, Saccostrea echinata, S. glomerata, Ostrea angasi, O. edulis, and O. conchaphila. We designed two pairs of primers and optimized PCR conditions for simultaneous amplification of ITS 1 and ITS2 in a single PCR. Amplification was successful in all 12 species, and PCR products were visualized on high-resolution agarose gels. ITS2 was longer than ITS 1 in all Crassostrea and Saccostrea species, whereas they were about the same size in the three Ostrea species. No intraspecific variation in ITS length was detected. Among species, the length of ITS I and ITS2 was polymorphic and provided unique identification of 8 species or species pairs: C. ariakensis, C. hongkongensis, C. sikamea, O. conchaphila, C. virginica/C. rhizophorae, C. gigas/C. angulata, S. echinata/S. glonzerata, and O. angasi/O. edulis. The ITS assay provides simple, rapid and effective identification of C. ariakensis and several other oyster species. Because the primer sequences are conserved, the ITS assay may be useful in the identification of other bivalve species.

一种低功耗微弱信号放大电路的优化设计与研究

针对远距离声源发射的水声信号微弱、水声接收设备电源能量有限的特点,提出一种功耗小、对无源元件误差灵敏度低、高增益放大的微弱水声信号通用放大电路。系统采用场效应管共源单调谐放大器为前置放大级,由四级级联低功耗运放构成带通滤波放大电路,省去传统的R、C低通网络,实现了对微弱水声信号的高增益放大和海洋背景噪声的归一化处理。通过计算电路网络传递函数极点证明了电路系统的稳定性。海上使用表明系统具有精度高、适应性强、电路稳定性好、功耗小等优点。

并联Stewart机构位姿误差分析

从并联机构与串联机构的运动学等效 ,并联机构本身特征与并联机构实际工作空间出发 ,考虑各分支末端误差对最终运动平台末端误差的影响 ,提出了并联机构位姿误差放大因子分析法·依据位姿误差放大因子具有对误差定量分析的特点 ,该分析方法既可用于机构参数优化 ,又可用于结构精度设计· 最后 ,给出了一个实例说明本方法的有效性·

基于广义Lippmann-Schwinger方程的地震波场模拟算法与应用

In the last several decades, due to the fast development of computer, numerical simulation has been an indispensable tool in scientific research. Numerical simulation methods which based on partial difference operators such as Finite Difference Method (FDM) and Finite Element Method (FEM) have been widely used. However, in the realm of seismology and seismic prospecting, one usually meets with geological models which have piece-wise heterogeneous structures as well as volume heterogeneities between layers, the continuity of displacement and stress across the irregular layers and seismic wave scattering induced by the perturbation of the volume usually bring in error when using conventional methods based on difference operators. The method discussed in this paper is based on elastic theory and integral theory. Seismic wave equation in the frequency domain is transformed into a generalized Lippmann-Schwinger equation, in which the seismic wavefield contributed by the background is expressed by the boundary integral equation and the scattering by the volume heterogeneities is considered. Boundary element-volume integral method based on this equation has advantages of Boundary Element Method (BEM), such as reducing one dimension of the model, explicit use the displacement and stress continuity across irregular interfaces, high precision, satisfying the boundary at infinite, etc. Also, this method could accurately simulate the seismic scattering by the volume heterogeneities. In this paper, the concrete Lippmann-Schwinger equation is specifically given according to the real geological models. Also, the complete coefficients of the non-smooth point for the integral equation are introduced. Because Boundary Element-Volume integral equation method uses fundamental solutions which are singular when the source point and the field are very close，both in the two dimensional and the three dimensional case, the treatment of the singular kernel affects the precision of this method. The method based on integral transform and integration by parts could treat the points on the boundary and inside the domain. It could transform the singular integral into an analytical one both in two dimensional and in three dimensional cases and thus it could eliminate the singularity. In order to analyze the elastic seismic wave scattering due to regional irregular topographies, the analytical solution for problems of this type is discussed and the analytical solution of P waves by multiple canyons is given. For the boundary reflection, the method used here is infinite boundary element absorbing boundary developed by a pervious researcher. The comparison between the analytical solutions and concrete numerical examples validate the efficiency of this method. We thoroughly discussed the sampling frequency in elastic wave simulation and find that, for a general case, three elements per wavelength is sufficient, however, when the problem is too complex, more elements per wavelength are necessary. Also, the seismic response in the frequency domain of the canyons with different types of random heterogeneities is illustrated. We analyzed the model of the random media, the horizontal and vertical correlation length, the standard deviation, and the dimensionless frequency how to affect the seismic wave amplification on the ground, and thus provide a basis for the choice of the parameter of random media during numerical simulation.

太阳活动变化对中低纬电离层的影响

With the variations of solar activity, solar EUV and X-ray radiations change over different timescales (e.g., from solar cycle variation to solar flare burst). Since solar EUV and X-ray radiations are the primary energy sources for the ionosphere, theirs variations undoubtedly produce significant and complicated effects on the ionosphere. So the variations of solar activity significantly affect the ionosphere. It is essential for both ionospheric theory and applications to study solar activity effects on the ionosphere. The study about solar activity variations of the ionosphere is an important part of the ionospheric climatology. It can enhance the understanding for the basic processes in the ionosphere, ionospheric structure and its change, ionosphere/thermosphere coupling, and so on. As for applications, people need sufficient knowledges about solar activity variations of the ionosphere in order to improve ionospheric models so that more accurate forecast for the ionospheric environments can be made. Presently, the whole image about the modalities of ionospheric solar activity variations is still unknown, and related mechanisms still cannot be well understood. This paper is about the effects of the 11-year change in solar activity to the low- and mid-latitude ionosphere. We use multi-type ionospheric observations and model to investigate solar activity effects on the electron density and ionospheric spatial structure, and we focus on discussing some related mechanisms. The main works are as follows: Firstly, solar activity variations of ionospheric peak electron density (NmF2) around 1400 LT were investigated using ionosonde observations in the 120°E sector. The result shows that the variation trend of NmF2 with F107 depends on latitudes and seasons. There is obvious saturation trend in low latitudes in all seasons; while in middle latitudes, NmF2 increases linearly with F107 in winter but saturates with F107 at higher solar activity levels in the other seasons. We calculated the photochemical equilibrium electron density to discuss the effects induced by the changes of neutral atmosphere and dynamics processes on the solar activity variations of NmF2. We found that: (1) Seasonal variation of neutral atmosphere plays an important role in the seasonal difference of the solar activity variations of NmF2 in middle latitudes. (2) Less [O]/[N2] and higher neutral temperature are important for the saturation effect in summer, and the increase of vibrational excited N2 is also important for the saturation effect. (3) Dynamics processes can significantly weaken the increase of NmF2 when solar activity enhances, which is also a necessary factor for the saturation effect. Secondly, solar activity variations of nighttime NmF2 were investigated using ionosonde observations in the 120°E sector. The result shows that the variation trends of NmF2 with F107 in nighttime are different from that in daytime in some cases, and the nighttime variation trends depend on seasons. There is linear increase trend in equinox nighttime, and saturation trend in summer nighttime, while the increase rate of NmF2 with F107 increases when solar activity enhances in winter nighttime (we term it with “amplification trend”). We discussed the possible mechanisms which affect the solar activity variations of nighttime NmF2. The primary conclusions are as follows: (1) In the equatorial ionization anomaly (EIA) crest region, the plasma influx induced by the pre-reversal enhancement (PRE) results in the change of the variation trend between NmF2 and F107 from “saturation” to “linear” after sunset in equinoxes and winter; while the recombination process at the F2-peak is the primary factor that affects the variation trend of NmF2 with F107 in middle latitudes. (2) The recombination coefficient at the F2-peak height reaches its maximum at moderate solar activity level in winter nighttime, which induces NmF2 attenuates more quickly at moderate solar activity level. This is the main reason for the amplification trend. (3) The change of the recombination process at the F2-peak with solar activity depends on the increases of neutral parameters (temperature, density et al.) and the F2-peak height (hmF2). The seasonal differences in the changes of neutral atmosphere and hmF2 with solar activity are the primary reasons for the seasonal difference in the variation trend of nighttime NmF2 with F107. Finally, we investigated the solar activity dependence of the topside ionosphere in low latitudes using ROCSAT-1 satellite (at 600 km altitude) observations. The primary results and conclusions are as follows: (1) Latitudinal distribution of the plasma density is local time, seasonal, and solar activity dependent. In daytime, there is a plasma density peak at the dip equator. The peak is obviously enhanced at high solar activity level, and the strength of the peak strongly depends on seasons. While at sunset, two profound plasma density peaks (double-peak structure) are found in solar maximum equinox months. (2) Local time dependence of the latitudinal distribution is due to the local time variation of the equatorial dynamics processes. Double-peak structure is attributed to the fountain effect induced by strong PRE. Daytime peak enhances with solar activity since the plasma density increases with solar activity more strongly at the dip equator due to the equatorial vertical drift, and its seasonal dependence is mainly due to the seasonal variations of neutral density and the equatorial vertical drift. In the sunset sector, seasonal and solar activity dependences of the latitudinal distribution are related to the seasonal and solar activity variations of PRE. (3) The variation trend of the plasma density with solar activity shows local time, seasonal, and latitudinal differences. That is different from the changeless amplification trend at the DMSP altitude (840 km). Profound saturation effect is found in the dip equator region at equinox sunset. This saturation effect in the topside ionosphere is realated to the increase of PRE with solar activity. Solar activity variation trend of the topside plasma density was discussed quantitatively by Chapman-α function. The result shows that the effect induced by the change of the scale height is dominant at high altitudes; while the variation trend of ROCSAT-1 plasma density with solar activity is suggested to be related to the changes of the peak height, the scale height, and the peak electron density with solar activity.

A biotecnologia nos programas de melhoramento de forrageiras tropicais da Embrapa Gado de Corte.

Neste trabalho procurou-se apresentar e discutir, de forma ampla, o uso da biotecnologia e seu potencial para os programas de melhoramento de forrageiras tropicais realizados na Embrapa Gado de Corte. O uso da biotecnologia nesses programas é uma atividade recente, mas importantes resultados vêm sendo gerados a fim de auxiliar o processo de obtenção de novas cultivares forrageiras. A maioria dos trabalhos apresentados utiliza marcadores Random Amplification of Polymorphic DNA (RAPD) para aplicações em curto prazo: estudos de diversidade em acessos de bancos de germoplasma, identificação de híbridos e estimação da taxa de cruzamento. Aplicações em médio e longo prazos do uso de marcadores, como mapeamento genético e seleção auxiliada por marcadores moleculares (SAMM), ainda necessitam de maiores investimentos, tanto na busca de novos marcadores, quanto no desenvolvimento de populações adequadas para esses estudos. Em 2007, teve início uma nova linha de pesquisa nessa unidade, a prospecção de genes com características econômicas. Genes para a tolerância ao alumínio são o foco dessa pesquisa que pretende explorar a sintenia entre os genomas de gramíneas, visando ao desenvolvimento de cultivares de braquiária mais tolerantes ao alumínio. A Embrapa Gado de Corte vem investindo em pessoal e aquisição de equipamentos para avançar não só na produção de cultivares de forrageiras mais adaptadas às necessidades de um mercado cada vez mais exigente, como também no crescimento institucional do setor de biotecnologia.

Identification, Selection, and Enrichment of Cardiomyocyte Precursors

The large-scale production of cardiomyocytes is a key step in the development of cell therapy and tissue engineering to treat cardiovascular diseases, particularly those caused by ischemia. the main objective of this study was to establish a procedure for the efficient production of cardiomyocytes by reprogramming mesenchymal stem cells from adipose tissue. First, lentiviral vectors expressing neoR and GFP under the control of promoters expressed specifically during cardiomyogenesis were constructed to monitor cell reprogramming into precardiomyocytes and to select cells for amplification and characterization. Cellular reprogramming was performed using 5'-azacytidine followed by electroporation with plasmid pOKS2a, which expressed Oct4, Sox2, and Klf4. Under these conditions, GFP expression began only after transfection with pOKS2a, and less than 0.015% of cells were GFP(+). These GFP(+) cells were selected for G418 resistance to find molecular markers of cardiomyocytes by RT-PCR and immunocytochemistry. Both genetic and protein markers of cardiomyocytes were present in the selected cells, with some variations among them. Cell doubling time did not change after selection. Together, these results indicate that enrichment with vectors expressing GFP and neoR under cardiomyocyte-specific promoters can produce large numbers of cardiomyocyte precursors (CMPs), which can then be differentiated terminally for cell therapy and tissue engineering.

Variation of modal parameters of pile-supported structures in seismically liquefiable soils.

This paper presents experimental results that aimed to investigate the effects of soil liquefaction on the modal parameters (i.e. frequency and damping ratio) of pile-supported structures. The tests were carried out using the shaking table facility of the Bristol Laboratory for Advanced Dynamics Engineering (BLADE) at the University of Bristol (UK) whereby four pile-supported structures (two single piles and two pile groups) with and without superstructure mass were tested. The experimental investigation aimed to monitor the variation in natural frequency and damping of the four physical models at different degrees of excess pore water pressure generation and in full-liquefaction condition. The experimental results showed that the natural frequency of pile-supported structures may decrease considerably owing to the loss of lateral support offered by the soil to the pile. On the other hand, the damping ratio of structure may increase to values in excess of 20%. These findings have important design consequences: (a) for low-period structures, substantial reduction of spectral acceleration is expected; (b) during and after liquefaction, the response of the system may be dictated by the interactions of multiple loadings, that is, horizontal, axial and overturning moment, which were negligible prior to liquefaction; and (c) with the onset of liquefaction due to increased flexibility of pile-supported structure, larger spectral displacement may be expected, which in turn may enhance Pdelta effects and consequently amplification of overturning moment. Practical implications for pile design are discussed.

A general model of error-prone PCR

Pritchard, L., Corne, D., Kell, D.B., Rowland, J. & Winson, M. (2005) A general model of error-prone PCR. Journal of Theoretical Biology 234, 497-509.

Antroponimy w Quo Vadis Henryka Sienkiewicza i w koreańskich przekładach powieści. Ocalone czy stracone w tłumaczeniu?

Filologia Polska i Klasyczna: Instytut Filologii Polskiej; Zakład Gramatyki Współczesnego Języka Polskiego i Onomastyki

Laserterapia em Implantologia

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Medicina Dentária

Nonlinear Acoustics in Underwater and Biomedical Applications: Array Performance Degradation and Time Reversal Invariance

This dissertation describes a model for acoustic propagation in inhomogeneous flu- ids, and explores the focusing by arrays onto targets under various conditions. The work explores the use of arrays, in particular the time reversal array, for underwater and biomedical applications. Aspects of propagation and phasing which can lead to reduced focusing effectiveness are described. An acoustic wave equation was derived for the propagation of finite-amplitude waves in lossy time-varying inhomogeneous fluid media. The equation was solved numerically in both Cartesian and cylindrical geometries using the finite-difference time-domain (FDTD) method. It was found that time reversal arrays are sensitive to several debilitating factors. Focusing ability was determined to be adequate in the presence of temporal jitter in the time reversed signal only up to about one-sixth of a period. Thermoviscous absorption also had a debilitating effect on focal pressure for both linear and nonlinear propagation. It was also found that nonlinearity leads to degradation of focal pressure through amplification of the received signal at the array, and enhanced absorption in the shocked waveforms. This dissertation also examined the heating effects of focused ultrasound in a tissue-like medium. The application considered is therapeutic heating for hyperther- mia. The acoustic model and a thermal model for tissue were coupled to solve for transient and steady temperature profiles in tissue-like media. The Pennes bioheat equation was solved using the FDTD method to calculate the temperature fields in tissue-like media from focused acoustic sources. It was found that the temperature-dependence of the medium's background prop- erties can play an important role in the temperature predictions. Finite-amplitude effects contributed excess heat when source conditions were provided for nonlinear ef- fects to manifest themselves. The effect of medium heterogeneity was also found to be important in redistributing the acoustic and temperature fields, creating regions with hotter and colder temperatures than the mean by local scattering and lensing action. These temperature excursions from the mean were found to increase monotonically with increasing contrast in the medium's properties.

Adaptive Neural Networks for Control of Movement Trajectories Invariant under Speed and Force Rescaling

This article describes two neural network modules that form part of an emerging theory of how adaptive control of goal-directed sensory-motor skills is achieved by humans and other animals. The Vector-Integration-To-Endpoint (VITE) model suggests how synchronous multi-joint trajectories are generated and performed at variable speeds. The Factorization-of-LEngth-and-TEnsion (FLETE) model suggests how outflow movement commands from a VITE model may be performed at variable force levels without a loss of positional accuracy. The invariance of positional control under speed and force rescaling sheds new light upon a familiar strategy of motor skill development: Skill learning begins with performance at low speed and low limb compliance and proceeds to higher speeds and compliances. The VITE model helps to explain many neural and behavioral data about trajectory formation, including data about neural coding within the posterior parietal cortex, motor cortex, and globus pallidus, and behavioral properties such as Woodworth's Law, Fitts Law, peak acceleration as a function of movement amplitude and duration, isotonic arm movement properties before and after arm-deafferentation, central error correction properties of isometric contractions, motor priming without overt action, velocity amplification during target switching, velocity profile invariance across different movement distances, changes in velocity profile asymmetry across different movement durations, staggered onset times for controlling linear trajectories with synchronous offset times, changes in the ratio of maximum to average velocity during discrete versus serial movements, and shared properties of arm and speech articulator movements. The FLETE model provides new insights into how spina-muscular circuits process variable forces without a loss of positional control. These results explicate the size principle of motor neuron recruitment, descending co-contractive compliance signals, Renshaw cells, Ia interneurons, fast automatic reactive control by ascending feedback from muscle spindles, slow adaptive predictive control via cerebellar learning using muscle spindle error signals to train adaptive movement gains, fractured somatotopy in the opponent organization of cerebellar learning, adaptive compensation for variable moment-arms, and force feedback from Golgi tendon organs. More generally, the models provide a computational rationale for the use of nonspecific control signals in volitional control, or "acts of will", and of efference copies and opponent processing in both reactive and adaptive motor control tasks.

Genetic analysis of bacteriophages from clinical and environmental samples

Bacteriophages, viruses infecting bacteria, are uniformly present in any location where there are high numbers of bacteria, both in the external environment and the human body. Knowledge of their diversity is limited by the difficulty to culture the host species and by the lack of the universal marker gene present in all viruses. Metagenomics is a powerful tool that can be used to analyse viral communities in their natural environments. The aim of this study was to investigate diverse populations of uncultured viruses from clinical (a sputum of patient with cystic fibrosis, CF) and environmental samples (a sludge from a dairy food wastewater treatment plant) containing rich bacterial populations using genetic and metagenomic analyses. Metagenomic sequencing of viruses obtained from these samples revealed that the majority of the metagenomic reads (97-99%) were novel when compared to the NCBI protein database using BLAST. A large proportion of assembled contigs were assignable as novel phages or uncharacterised prophages, the next largest assignable group being single-stranded eukaryotic virus genomes. Sputum from a cystic fibrosis patient contained DNA typical of phages of bacteria that are traditionally involved in CF lung infections and other bacteria that are part of the normal oral flora. The only eukaryotic virus detected in the CF sputum was Torque Teno virus (TTV). A substantial number of assigned sequences from dairy wastewater could be affiliated with phages of bacteria that are typically found in the soil and aquatic environments, including wastewater. Eukaryotic viral sequences were dominated by plant pathogens from the Geminiviridae and Nanoviridae families, and animal pathogens from the Circoviridae family. Antibiotic resistance genes were detected in both metagenomes suggesting phages could be a source for transmissible antimicrobial resistance. Overall, diversity of viruses in the CF sputum was low, with 89 distinct viral genotypes predicted, and higher (409 genotypes) in the wastewater. Function-based screening of a metagenomic library constructed from DNA extracted from dairy food wastewater viruses revealed candidate promoter sequences that have ability to drive expression of GFP in a promoter-trap vector in Escherichia coli. The majority of the cloned DNA sequences selected by the assay were related to ssDNA circular eukaryotic viruses and phages which formed a minority of the metagenome assembly, and many lacked any significant homology to known database sequences. Natural diversity of bacteriophages in wastewater samples was also examined by PCR amplification of the major capsid protein sequences, conserved within T4-type bacteriophages from Myoviridae family. Phylogenetic analysis of capsid sequences revealed that dairy wastewater contained mainly diverse and uncharacterized phages, while some showed a high level of similarity with phages from geographically distant environments.