Molecular cloning, expression of a big defensin gene from bay scallop Argopecten irradians and the antimicrobial activity of its recombinant protein

Antimicrobial peptides are important components of the host innate immune responses by exerting broad-spectrum microbicidal activity against pathogenic microbes. The first mollusk big defensin (designated AiBD) cDNA was cloned from bay scallop Argopecten irradians by expressed sequence tag (EST) and rapid amplification of cDNA ends (RACE) techniques. The scallop AiBD consisted of 531 nucleotides with a canonical polyadenylation signal sequence AATAAA and a poly(A) tail, encoding a polypeptide of 122 amino acids. The high similarity of AiBD deduced amino acid sequence with big defensin from Tachypleus tridentatus and Branchiostoma belcheri tsingtaunese indicated that AiBD should be a member of big defensin family. The expression of AiBD in various tissues was measured by using Northern blotting analysis. mRNA transcripts of AiBD could be detected in haemocytes of unchallenged scallops. The temporal expression of AiBD in haemolymph after Vibrio anguilarum challenge was recorded by quantitative real time PCR. The relative expression level of AiBD in haemolymph was up-regulated evenly in the first 8 h, followed by a drastic increase, and increased 131.1-fold at 32 h post-injection. These results indicated that AiBD could be induced by bacterial challenge, and it should participate in the immune responses of A. irradians. Biological activity assay revealed that recombinant AiBD could inhibit the growth of both Gram-positive and Gram-negative bacteria, and also showed strong fungicidal activity towards the expression host. Recombinant expression of AiBD made it possible to further characterize its functions involved in immune responses, and also provided a potential therapeutic agent for disease control in aquaculture. (c) 2006 Elsevier Ltd. All rights reserved.

Predicting protein interaction interfaces from protein sequences: Case studies of subtilisin and phycocyanin

Identification of protein interaction interfaces is very important for understanding the molecular mechanisms underlying biological phenomena. Here, we present a novel method for predicting protein interaction interfaces from sequences by using PAM matrix (PIFPAM). Sequence alignments for interacting proteins were constructed and parsed into segments using sliding windows. By calculating distance matrix for each segment, the correlation coefficients between segments were estimated. The interaction interfaces were predicted by extracting highly correlated segment pairs from the correlation map. The predictions achieved an accuracy 0.41-0.71 for eight intraprotein interaction examples, and 0.07-0.60 for four interprotein interaction examples. Compared with three previously published methods, PIFPAM predicted more contacting site pairs for 11 out of the 12 example proteins, and predicted at least 34% more contacting site pairs for eight proteins of them. The factors affecting the predictions were also analyzed. Since PIFPAM uses only the alignments of the two interacting proteins as input, it is especially useful when no three-dimensional protein structure data are available.

Suitability of extractants for predicting available sulfur in natural grassland in the Inner Mongolia steppe of China

It was the objective of this study to compare the suitability of different extractants for predicting the availability of sulfur (S) in natural grassland in a sulfur response trial on three different soil types in the Inner Mongolia steppe of China. For soil analysis, seven different extractants have been employed. The inorganic SO4-S concentration was determined by ion chromatography. Additionally, in the Ca(H-2-PO4)(2) extract the total soluble S was determined employing turbidimetry. Weak salt solutions (0.15% CaCl2, Ca(H2PO4)(2), and KH2PO4) extracted similar amounts Of SO4-S. Extraction with 0.025 M KCl provided the lowest SO4-S values. Deionized water dissolved significantly more SO4-S in the control plots than most weak salt extractants. The concentration of soluble organic S decreased in the control plots after 100 days of plant growth, indicating that the organic S pool contributed significantly to the S nutrition of the forage crops. Significant relationships among the SO4-S in the soil determined in different extracts and crop yield, sulfur content in the forage, and total sulfur uptake were only found for the Ca(H2PO4)(2) extract. In general, the correlation coefficients proved to be unsatisfactory for field experimentation.

Development of a sensitive fluorescent derivatization reagent 1,2-benzo-3,4-dihydrocarbazole-9-ethyl chloroformate (BCEOC) and its application for determination of amino acids from seeds and bryophyte plants using high-performance liquid chromatography with fluorescence detection and identification with electrospray ionization mass spectrometry

A pre-column derivatization method for the sensitive determination of amino acids and peptides using the tagging reagent 1,2-benzo-3,4dihydrocarbazole-9-ethyl chloroformate (BCEOC) followed by high-performance liquid chromatography with fluorescence detection has been developed. Identification of derivatives was carried out by liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS/MS). The chromophore of 2-(9-carbazole)-ethyl chloroformate (CEOC) reagent was replaced by 1,2-benzo-3,4-dihydrocarbazole functional group, which resulted in a sensitive fluorescence derivatizing reagent BCEOC. BCEOC can easily and quickly label peptides and amino acids. Derivatives are stable enough to be efficiently analyzed by high-performance liquid chromatography. The derivatives showed an intense protonated molecular ion corresponding m/z (M + H)(+) under electrospray ionization (ESI) positive-ion mode with an exception being Tyr detected at negative mode. The collision-induced dissociation of protonated molecular ion formed a product at m/z 246.2 corresponding to the cleavage of C-O bond of BCEOC molecule. Studies on derivatization demonstrate excellent derivative yields over the pH 9.0-10.0. Maximal yields close to 100% are observed with a 3-4-fold molar reagent excess. Derivatives exhibit strong fluorescence and extracted detzvatization solution with n-hexane/ethyl acetate (10:1, v/v) allows for the direct injection with no significant interference from the major fluorescent reagent degradation by-products, such as 1,2-benzo-3,4-dihydrocarbazole-9-ethanol (BDC-OH) (a major by-product), mono- 1,2-benzo-3,4-dihydrocarbazole-9-ethyl carbonate (BCEOC-OH) and bis-(1,2-benzo-3,4-dihydrocarbazole-9-ethyl) carbonate (BCEOC)(2). In addition, the detection responses for BCEOC derivatives are compared to those obtained with previously synthesized 2-(9-carbazole)-ethyl chloroformate (CEOC) in our laboratory. The ratios AC(BCEOC)/AC(CEOC) = 2.05-6.51 for fluorescence responses are observed (here, AC is relative fluorescence response). Separation of the derivatized peptides and amino acids had been optimized on Hypersil BDS C-18 column. Detection limits were calculated from 1.0 pmol injection at a signal-to-noise ratio of 3, and were 6.3 (Lys)-177.6 (His) fmol. The mean interday accuracy ranged from 92 to 106% for fluorescence detection with mean %CV < 7.5. The mean interday precision for all standards was < 10% of the expected concentration. Excellent linear responses were observed with coefficients of > 0.9999. Good compositional data could be obtained from the analysis of derivatized protein hydrolysates containing as little as 50.5 ng of sample. Therefore, the facile BCEOC derivatization coupled with mass spectrometry allowed the development of a highly sensitive and specific method for the quantitative analysis of trace levels of amino acids and peptides from biological and natural environmental samples. (c) 2005 Elsevier B.V. All rights reserved.

碳酸盐岩缝洞型储层地球物理响应特征及预测方法研究

Proven by the petroleum exploration activities, the karsts-fissure reservoir in carbonate rocks is significant to find out the large scale oil & gas field. They are made up of the four reservoir types: karsts-cave, karsts-crack, crack-cave and fracture-pore-cave. Each reservoir space and each reservoir bed has different features of reservoir heterogeneity and small scale of pore-crack-cave. The fracture-cave reservoir in carbonate rocks is characteristic by multi-types and long oiliness well. The reservoir shape is controlled by the irregular pore-crack-cave. The development level of fracture and karst-cave is the key element of hydrocarbon enriching, high productivity and stable production. However, most of Carbonate formation are buried deeply and the signal-ration-noise of seismic reflection are very low. It is reason why the fracture-cave reservoir are difficult to be predicted effectively. In terms of surveyed and studied lots of the former research outcome, The author applied the methods of synthetical reservoir geophysical prediction from two ways including macrosopic and microcomic technics in terms of the reservoir-cap condition, geophysics and geology feature and difficulty of prediction in carbonate rocks. It is guiden by the new ideas of stratigraphy, sedimentology, sedimentography, reservoir geology and karst geology. The geophysics technology is key technics. In aspects of macroscopic studies, starting off the three efficiencies of controlling the reservoir distribution including sedimental facies, karst and fracture, by means of comprehensive utilization of geology, geophysics, boring well and well log, the study of reservoir features and karst inside story are developed in terms of data of individual well and multiple well. Through establishing the carbonate deposition model, karstic model and fracture model, the macro-distribution laws of carbonatite are carried out by the study of coherence analysis, seismic reflection feature analysis and palaeotectonics analysis. In aspects of microcosmic studies, starting off analysis in reservoir geophysical response feature of fracture and karst-cave model according to guidance of the macroscopic geological model in carbonate reservoir, the methods of the carbonate reservoir prediction are developed by comprehensively utilization of seismic multi-attribution intersection analysis, seismic inversion restricted by log, seismic discontinuity analysis, seimic spectrum attenuation gradient, moniliform reflection feature analysis and multiparameter karst reservoir appraisement.Through application of carbonate reservoir synthetical geophysics prediction, the author r successfully develops the beneficial reservoir distribution province in Ordovician of Katake block 1in middle Tarim basin. The fracture-cave reservoir distributions are delineated. The prospect direction and favorable aims are demonstrated. There are a set of carbonate reservoir prediction methods in middle Tarim basin. It is the favorable basic technique in predicting reservoir of the Ordovician carbonate in middle Tarim. Proven by exploration drilling, the favorable region of moniliform reflection fracture and pore-cave and cave-fracture in lower-middle Ordovician are coincidence with the region of hydrocarbon show. It’s indicated that the reservoir prediction methods described in the study of Ordovician carbonate formation are feasible practicably.

地震采集观测系统的共聚焦分析

Focal beam analysis is a method for assessment of acquisition geometries that is directly linked to pre-stack migration. About dealing with the complex subsurface structures, the conventional survey design methods which do not take into account the subsurface are no longer valid. Based on the Fourier finite-difference (FFD) large-step wave field extrapolation and Born-Kirchhoff (BK) small-step wavefield interpolation, the thesis presents a rapid resolution analysis of 3D seismic survey design by focal beams in complicated media. Subsequently, The SEG/EAEG salt model is used to illustrate the method. Based on the focal beam resolution definition, each kind of influence factor is discussed. The focal beam analysis usually is carried out in a single frequency, but the actual seismic waves always contain a frequency bandwidth. In this thesis, theoretical relationship between focal beam analysis and frequency is derived. Since the effects of focal beam analysis are linear with frequency simply, the multi-frequency focal beam analysis using interpolation is developed. At the same time, the resolution of different frequency bandwidth is interconvertible in accordance with Signal uncertainty principle. The resolution of all frequency bands can be calculated by using only a few focal beam analysis for a seismic survey. In the last section of this thesis, I propose a new approach to predicting acquisition footprint, based on the assumption of Common-Middle-Point stack without constructing a special velocity model. The approach is a simplistic analytical method in which the acquisition footprint pattern is a weighted, linear summation of limited-offset fold-of-stack plots. Because the value of acquisition can be got by quantificational and rapidly calculating, we can exactly do a comparative analysis among different plans of seismic survey by this method.

f-x-y域去除随机噪音方法研究

The seismic survey is the most effective prospecting geophysical method during exploration and development of oil/gas. The structure and the lithology of the geological body become increasingly complex now. So it must assure that the seismic section own upper resolution if we need accurately describe the targets. High signal/noise ratio is the precondition of high-resolution. For the sake of improving signal/noise ratio, we put forward four methods for eliminating random noise on the basis of detailed analysis of the technique for noise elimination using prediction filtering in f-x-y domain. The four methods are put forward for settling different problems, which are in the technique for noise elimination using prediction filtering in f-x-y domain. For weak noise and large filters, the response of the noise to the filter is little. For strong noise and short filters, the response of the noise to the filter is important. For the response of the noise, the predicting operators are inaccurate. The inaccurate operators result in incorrect results. So we put forward the method using prediction filtering by inversion in f-x-y domain. The method makes the assumption that the seismic signal comprises predictable proportion and unpredictable proportion. The transcendental information about predicting operator is introduced in the function. The method eliminates the response of the noise to filtering operator, and assures that the filtering operators are accurate. The filtering results are effectively improved by the method. When the dip of the stratum is very complex, we generally divide the data into rectangular patches in order to obtain the predicting operators using prediction filtering in f-x-y domain. These patches usually need to have significant overlap in order to get a good result. The overlap causes that the data is repeatedly used. It effectively increases the size of the data. The computational cost increases with the size of the data. The computational efficiency is depressed. The predicting operators, which are obtained by general prediction filtering in f-x-y domain, can not describe the change of the dip when the dip of the stratum is very complex. It causes that the filtering results are aliased. And each patch is an independent problem. In order to settle these problems, we put forward the method for eliminating noise using space varying prediction filtering in f-x-y domain. The predicting operators accordingly change with space varying in this method. Therefore it eliminates the false event in the result. The transcendental information about predicting operator is introduced into the function. To obtain the predicting operators of each patch is no longer independent problem, but related problem. Thus it avoids that the data is repeatedly used, and improves computational efficiency. The random noise that is eliminated by prediction filtering in f-x-y domain is Gaussian noise. The general method can't effectively eliminate non-Gaussian noise. The prediction filtering method using lp norm (especially p=l) can effectively eliminate non-Gaussian noise in f-x-y domain. The method is described in this paper. Considering the dip of stratum can be accurately obtained, we put forward the method for eliminating noise using prediction filtering under the restriction of the dip in f-x-y domain. The method can effectively increase computational efficiency and improve the result. Through calculating in the theoretic model and applying it to the field data, it is proved that the four methods in this paper can effectively solve these different problems in the general method. Their practicability is very better. And the effect is very obvious.

陆相砂泥岩层序的高精度检测方法研究及应用

Ordos Basin is a typical cratonic petroliferous basin with 40 oil-gas bearing bed sets. It is featured as stable multicycle sedimentation, gentle formation, and less structures. The reservoir beds in Upper Paleozoic and Mesozoicare are mainly low density, low permeability, strong lateral change, and strong vertical heterogeneous. The well-known Loess Plateau in the southern area and Maowusu Desert, Kubuqi Desert and Ordos Grasslands in the northern area cover the basin, so seismic data acquisition in this area is very difficult and the data often takes on inadequate precision, strong interference, low signal-noise ratio, and low resolution. Because of the complicated condition of the surface and the underground, it is very difficult to distinguish the thin beds and study the land facies high-resolution lithologic sequence stratigraphy according to routine seismic profile. Therefore, a method, which have clearly physical significance, based on advanced mathematical physics theory and algorithmic and can improve the precision of the detection on the thin sand-peat interbed configurations of land facies, is in demand to put forward.Generalized S Transform (GST) processing method provides a new method of phase space analysis for seismic data. Compared with wavelet transform, both of them have very good localization characteristics; however, directly related to the Fourier spectra, GST has clearer physical significance, moreover, GST adopts a technology to best approach seismic wavelets and transforms the seismic data into time-scale domain, and breaks through the limit of the fixed wavelet in S transform, so GST has extensive adaptability. Based on tracing the development of the ideas and theories from wavelet transform, S transform to GST, we studied how to improve the precision of the detection on the thin stratum by GST.Noise has strong influence on sequence detecting in GST, especially in the low signal-noise ratio data. We studied the distribution rule of colored noise in GST domain, and proposed a technology to distinguish the signal and noise in GST domain. We discussed two types of noises: white noise and red noise, in which noise satisfy statistical autoregression model. For these two model, the noise-signal detection technology based on GST all get good result. It proved that the GST domain noise-signal detection technology could be used to real seismic data, and could effectively avoid noise influence on seismic sequence detecting.On the seismic profile after GST processing, high amplitude energy intensive zone, schollen, strip and lentoid dead zone and disarray zone maybe represent specifically geologic meanings according to given geologic background. Using seismic sequence detection profile and combining other seismic interpretation technologies, we can elaborate depict the shape of palaeo-geomorphology, effectively estimate sand stretch, distinguish sedimentary facies, determine target area, and directly guide oil-gas exploration.In the lateral reservoir prediction in XF oilfield of Ordos Basin, it played very important role in the estimation of sand stretch that the study of palaeo-geomorphology of Triassic System and the partition of inner sequence of the stratum group. According to the high-resolution seismic profile after GST processing, we pointed out that the C8 Member of Yanchang Formation in DZ area and C8 Member in BM area are the same deposit. It provided the foundation for getting 430 million tons predicting reserves and unite building 3 million tons off-take potential.In tackling key problem study for SLG gas-field, according to the high-resolution seismic sequence profile, we determined that the deposit direction of H8 member is approximately N-S or NNE-SS W. Using the seismic sequence profile, combining with layer-level profile, we can interpret the shape of entrenched stream. The sunken lenticle indicates the high-energy stream channel, which has stronger hydropower. By this way we drew out three high-energy stream channels' outline, and determined the target areas for exploitation. Finding high-energy braided river by high-resolution sequence processing is the key technology in SLG area.In ZZ area, we studied the distribution of the main reservoir bed-S23, which is shallow delta thin sand bed, by GST processing. From the seismic sequence profile, we discovered that the schollen thick sand beds are only local distributed, and most of them are distributary channel sand and distributary bar deposit. Then we determined that the S23 sand deposit direction is NW-SE in west, N-S in central and NE-SW in east. The high detecting seismic sequence interpretation profiles have been tested by 14 wells, 2 wells mismatch and the coincidence rate is 85.7%. Based on the profiles we suggested 3 predicted wells, one well (Yu54) completed and the other two is still drilling. The completed on Is coincident with the forecastThe paper testified that GST is a effective technology to get high- resolution seismic sequence profile, compartmentalize deposit microfacies, confirm strike direction of sandstone and make sure of the distribution range of oil-gas bearing sandstone, and is the gordian technique for the exploration of lithologic gas-oil pool in complicated areas.

A new method of predicting of gas chromatographic retention indices for polychlorinated dibenzofurans (PCDFs)

A new method has been developed to describe the quantitative relationship between molecular structures of PCDFs and their gas chromatographic retention indices on a 30-m fused silica column coated with DB-5 stationary phase. The regression equation is derived with a multiple correlation coefficient greater than 0.9995. The highest residual is 20 index units. The standard deviation is less than 7 index units. Using this regression equation, the retention indices of PCDFs for which data is not available have also been predicted. (C) 2000 Elsevier Science Ltd. All rights reserved.

Separation of peptides by strong cation-exchange capillary electrochromatography

Separation of small peptides on ion-exchange capillary electrochromatography (IE-CEC) with strong cation-exchange packing (SCX) as stationary phase was investigated. It was observed that the number of theoretical plates for small peptides varied from 240 000 to 460 000/m, and the relative standard deviation for t(0) and the migration time of peptides were less than 0.57% and 0.27%, respectively for ten consecutive runs. Unusually high column efficiency has been explained by the capillary electrophoretic stacking and chromatofocusing phenomena during the injection and separation of positively charged peptides. The sample buffer concentration had a marked effect on the column efficiency and peak area of the retained peptides. The influences of the buffer concentration and pH value as well as the applied voltage on the separation were investigated. It has been shown that the electrostatic interaction between the positively charged peptides and the SCX stationary phase played a very important role in IE-CEC, which provided the different separation selectivity from those in the capillary electrophoresis and reversed-phase liquid chromatography. A fast separation of ten peptides in less than 3.5 min on IE-CEC by adoption of the highly applied voltage was demonstrated. (C) 2000 Elsevier Science B.V. All rights reserved.