利用半球图像法提取植被冠层结构特征参数

植被冠层结构深刻地影响着植物群落与环境的相互作用,对植被冠层结构的研究是深入理解植被生态系统格局、过程及其运作机制的重要基础。冠层结构特征参数的快速测量方法是植被冠层结构研究的前提,目前测量方法主要是基于实际测量的地面法,地面法一般费时费力,受人为因素影响较大,因此本文探索利用半球图像法获取植被冠层结构特征参数。通过对半球图像进行几何纠正并建立参数图层,与分类后的植被冠层图层进行运算提取植被冠层结构特征参数。将该方法应用于祁连山旺腰沟流域青海云杉冠层结构特征参数的提取,包括植被冠幅、冠层面积、冠层周长等,结果显示：半球图像法能够较好的提取植被冠层结构特征参数,该方法具有简单、客观、可重复等优点,也可作为植被冠层结构变化的监测方法。     

Optimisation of cultivation parameters in photobioreactors for microalgae cultivation using the A-stat technique

Light availability inside the reactor is often the bottleneck in microalgal cultivation and for this reason much attention is being given to light limited growth kinetics of microalgae, aiming at the increase of productivity in photobioreactors. Steady-state culture characteristics are commonly used for productivity optimisation and for cell physiology studies in continuous cultures, and are normally achieved using chemostat cultivations. In the present study, we investigated the applicability of a new and dynamic cultivation method called acceleration-stat (A-stat) to microalgae cultivations where light is the limiting substrate. In the A-stat, the dilution rate is increased at a constant rate. This acceleration rate should be a compromise between a short cultivation time, in order to make it a fast process, and the metabolic adaptation rate of the microorganism to changes in the environment. Simulations of the A-stat were done with different acceleration rates to have an indication of the best rate to use. An A-stat was performed in a pilot plant bubble column (65 l) with Dunaliella tertiolecta as a model organism, and results showed that a pseudo steady state was maintained throughout the experiment. From this work, it was concluded that the A-stat can be used as a fast and accurate tool to determine kinetic parameters and to optimise any specific type of photobioreactor.     

A novel method for determining the parameters of microbial kinetics

It is conventional to describe the relationship between the specific rate of microbial growth and the concentration of the inhibitory substrate in terms of the Andrews–Edwards equation. A novel method for establishing the constants of this equation is presented. The equation is transformed to a polynomial and the empirical data are approximated by a quadratic polynomial. The results obtained for the biodegradation of phenol in a mixed culture (activated sludge) are discussed.     

A method to optimize PEG-coating of red blood cells

Alloimmunization to donor blood group antigens remains a significant problem in transfusion medicine. A proposed method to overcome donor-recipient blood group incompatibility is to mask the blood group antigens by the covalent attachment of poly(ethylene glycol) (PEG) to the red blood cell (RBC) membrane. Despite much work in the development of PEG-coating of RBCs, there is a paucity of data on the optimization of the PEG-coating technique; it is the aim of this study to determine the optimum conditions for PEG coating using a cyanuric chloride reactive derivative of methoxy-PEG as a model polymer. Activated PEG of molecular mass 5 kDa was covalently attached to human RBCs under various reaction conditions. Inhibition of binding of a blood-type specific antiserum (anti-D) was employed to evaluate the effect of the PEG-coating, quantified by hemocytometry and flow-cytometry. RBC morphology was examined by light and scanning electron microscopy. Statistical analysis of experimental design together with microscopy results showed that the optimum PEGylation conditions are pH = 8.7, temperature = 14 degrees C, and reaction time = 30 min. An optimum concentration of reactive PEG could not be determined. At high polymer concentrations (>25 mg/mL) a predominance of type III echinocytes was observed, and as a result, a concentration of 15 mg/mL is the highest recommended concentration for a linear PEG of molecular mass 5 kDa.     

A novel two-stage cultivation method to optimize carbon concentration and carbon-to-nitrogen ratio for sporulation of biocontrol fungi

A two-stage solid cultivation method was used to determine the precise requirements of carbon concentration (1–16 g/L) and C: N ratio (0.625: 1 to 80: 1) for the sporulation of six biocontrol fungi. The C concentration and C: N ratio producing the highest conidia yield were 1 g/L and 5: 1 for Paecilomyces lilacinus IPC-P; 2 g/L and 10: 1 for P. lilacinus M-14; 16 g/L and 80: 1 for Metarhizium anisopliae SQZ-1-21; 4 g/L and 5: 1 for M. anisopliae RS-4-1 and Lecanicillium lecanii CA-1-G; and 2 g/L and 10: 1 for Trichoderma viride TV-1. Sporulation was more affected by C: N ratio than by C and N concentration per se. More spores per colony were produced by the two-stage method than by a conventional, single-stage cultivation method. These results should be useful for improving the mass production of these biocontrol agents.     

Calcium signaling as a novel method to optimize the biosynthetic response of chondrocytes to dynamic mechanical loading

Chondrocyte sensitization and desensitization to mechanical stimuli are complex phenomena that have not been fully described. In this study, we investigated the temporal response of chondrocytes to dynamic mechanical loading and whether changes in calcium signaling could be used a predictor of the biosynthetic response. Cell-seeded agarose gels pre-incubated with an intracellular \(\hbox {Ca}^{2+}\) dye (Fluo-4) were subjected to dynamic compressive loading under varying conditions (amplitude and duration). Induced changes in \(\hbox {Ca}^{2+}\) signaling were determined by confocal imaging and matrix biosynthesis by radioisotope incorporation. It was observed that chondrocytes required a minimum amount of stimulation in order to elicit an anabolic response and they quickly became insensitive to the imposed stimulus. The response appeared to be amplitude dependent and could be predicted by measuring resultant changes in \(\hbox {Ca}^{2+}\) signaling. A positive correlation between \(\hbox {Ca}^{2+}\) signaling and matrix synthesis was achieved when changes in \(\hbox {Ca}^{2+}\) signaling was expressed as a relative number of cells experiencing multiple transients. In addition, these changes in \(\hbox {Ca}^{2+}\) signaling were effective at determining optimal recovery period between successive applications of intermittent mechanical loading, in which full mechanosensitivity was achieved when \(\hbox {Ca}^{2+}\) signaling was allowed to return to baseline (control) levels. The use of \(\hbox {Ca}^{2+}\) signaling to predict the effectiveness of a particular mechanical stimulus as well as to determine optimal refractory periods appears to be advantageous over empirical-based approaches. Future work will investigate the process of \(\hbox {Ca}^{2+}\) ion sequestration into intracellular stores to elucidate potential desensitization mechanisms to dynamic mechanical loading.     

A novel method for protein secondary structure prediction using dual-layer SVM and profiles

A high-performance method was developed for protein secondary structure prediction based on the dual-layer support vector machine (SVM) and position-specific scoring matrices (PSSMs). SVM is a new machine learning technology that has been successfully applied in solving problems in the field of bioinformatics. The SVM's performance is usually better than that of traditional machine learning approaches. The performance was further improved by combining PSSM profiles with the SVM analysis. The PSSMs were generated from PSI-BLAST profiles, which contain important evolution information. The final prediction results were generated from the second SVM layer output. On the CB513 data set, the three-state overall per-residue accuracy, Q3, reached 75.2%, while segment overlap (SOV) accuracy increased to 80.0%. On the CB396 data set, the Q3 of our method reached 74.0% and the SOV reached 78.1%. A web server utilizing the method has been constructed and is available at http://www.bioinfo.tsinghua.edu.cn/pmsvm.     

A theoretical method to improve and optimize the design of bioartificial livers

Bioartificial livers (BALs) are a potentially effective countermeasure against liver failure, particularly in cases of acute or fulminant liver failure. It is hoped these devices can sustain a patient's liver function until recovery or transplant. However, no large‐scale clinical trial has yet proven that BALs are particularly effective and evidently design issues remain to be addressed. One aspect of BAL design that must be considered is the mass transfer of adequate oxygen to the hepatocytes within the device. We present here a mathematical modeling approach to oxygen mass transport in a BAL. A mathematical model based upon Krogh cylinders is outlined to describe a diffusion‐limited hollow fiber bioreactor. In addition, operating constraints are defined on the system—cells should not experience hypoxia and the cell population should be of adequate size. By combining modeling results with these operating constraints and presenting the results graphically, “operating region” charts can be constructed for the hollow fiber BAL (HF‐BAL). The effects of varying various operating parameters on the BAL are then established. It is found that smaller radii and short, thin walled fibers are generally advantageous while cell populations in excess of 10 billion could be supported in the BAL with a plasma flow rate of 200 mL/min. For fibers of intermediate length and lumen radius, the minimum number of fibers required to produce a viable design ranges approximately from 7,000–10,000. In theory, this may be enough to support patients with failing livers. Biotechnol. Bioeng. 2010;106: 980–988. © 2010 Wiley Periodicals, Inc.     

A novel method to identify topological domains using Hi-C data

Over the last decade the 3C-based (Chromosome Conformation Capture, 3C) approaches have been developed to describe the frequency of chromatin interaction. The invention of Hi-C allows us to obtain genome-wide chromatin interaction map. However, it is challenging to develop efficient and robust analytical tools to interpret the Hi-C data. Here we present a new method called Clustering based Hi-C Domain Finder (CHDF), which is based on the difference of interaction intensity inside/outside domains, to identify Hi-C domains. We also compared CHDF with existing methods including Direction Index (DI) and HiCseg. CHDF can define more chromatin domains validated by higher resolution local chromatin structure data (Chromosome Conformation Capture Carbon Copy (5C) data). Using Hi-C data of lower sequencing depth, chromatin structure identified by CHDF is closer to that discovered by data of higher sequencing depth. Furthermore, the implement of CHDF is faster than the other two. Using CHDF, we are potentially able to discover more hints and clues about chromatin structural elements at domain level.     

A method to optimize precision and scale in grassland monitoring

Abstract. Methods for monitoring and survey of plant species abundance which do not account for variation in scale are often insensitive and imprecise. In monitoring, repeated observations are usually made within a fixed unit. Counts of species' presence must be made in a range of subunit sizes to accommodate the range of scales at which different species occur. A method comprising a rectangular fixed unit containing an 8 × 4 grid of square subunits has been developed and tested. Each subunit comprises a series of nested cells of increasing size, within which species are recorded cumulatively. Using this method, the concept of optimum scale is introduced. The optimum scale for a species is that for which its frequency count is closest to the midpoint. Two characteristics, sensitivity (absolute change detected) and blindness (failure to detect change in a species) were calculated for 24 plots from lowland grazing marsh which had been partially flooded between the time of two surveys. Optimum scale had greater sensitivity and lower blindness than any single scale in the majority of plots. Combining sensitivity and blindness, optimum scale was always superior. For the whole sample, optimum scale was less likely to cause Type I or Type II errors. The method is recommended for monitoring grasslands and allied plant communities in large geographical areas.     

利用模拟退火算法优化Biome-BGC模型参数

生态过程模型建立在明确的机理之上,能够较好地模拟陆地生态系统的行为和特征,但模型众多的参数,成为模型具体应用的瓶颈。本文以Biome-BGC模型为例,采用模拟退火算法,对其生理、生态参数进行优化。在优化过程中,先对待优化参数进行了选择,然后采取逐步优化的方法进行优化。结果表明,使用优化后的参数,模型模拟结果与实际观测更为接近,参数优化能有效地降低模型模拟的不确定性。文中参数优化的过程和方法,可为生态模型的参数识别和优化提供一种实例和思路,有助于生态模型应用区域的扩展。     

A method to optimize selection on multiple identified quantitative trait loci

A mathematical approach was developed to model and optimize selection on multiple known quantitative trait loci (QTL) and polygenic estimated breeding values in order to maximize a weighted sum of responses to selection over multiple generations. The model allows for linkage between QTL with multiple alleles and arbitrary genetic effects, including dominance, epistasis, and gametic imprinting. Gametic phase disequilibrium between the QTL and between the QTL and polygenes is modeled but polygenic variance is assumed constant. Breeding programs with discrete generations, differential selection of males and females and random mating of selected parents are modeled. Polygenic EBV obtained from best linear unbiased prediction models can be accommodated. The problem was formulated as a multiple-stage optimal control problem and an iterative approach was developed for its solution. The method can be used to develop and evaluate optimal strategies for selection on multiple QTL for a wide range of situations and genetic models.     

A novel method to replicate the kinematics of the carpus using a six degree-of-freedom robot

Understanding the kinematics of the carpus is essential to the understanding and treatment of wrist pathologies. However, many of the previous techniques presented are limited by non-functional motion or the interpolation of points from static images at different postures. We present a method that has the capability of replicating the kinematics of the wrist during activities of daily living using a unique mechanical testing system. To quantify the kinematics of the carpal bones, we used bone pin-mounted markers and optical motion capture methods. In this paper, we present a hammering motion as an example of an activity of daily living. However, the method can be applied to a wide variety of movements. Our method showed good accuracy (1.0–2.6°) of in vivo movement reproduction in our ex vivo model. Most carpal motion during wrist flexion–extension occurs at the radiocarpal level while in ulnar deviation the motion is more equally shared between radiocarpal and midcarpal joints, and in radial deviation the motion happens mainly at the midcarpal joint. For all rotations, there was more rotation of the midcarpal row relative to the lunate than relative to the scaphoid or triquetrum. For the functional motion studied (hammering), there was more midcarpal motion in wrist extension compared to pure wrist extension while radioulnar deviation patterns were similar to those observed in pure wrist radioulnar deviation. Finally, it was found that for the amplitudes studied the amount of carpal rotations was proportional to global wrist rotations.     

A novel protein refolding method using a zeolite

We have succeeded in developing a simple and effective protein refolding method using the inorganic catalyst, beta-zeolite. The method involves the adsorption of proteins solubilized with 6M guanidine hydrochloride from inclusion body (IB) preparations onto the zeolite. The denaturant is then removed, and the proteins in the IBs are released from the zeolite with polyoxyethylene detergent and salt. All of the IBs tested (11 different species) were successfully refolded under these conditions. The refolded proteins are biochemically active, and NMR analysis of one of the proteins (replication protein A 8) supports the conclusion that correct refolding does occur. Based on these results, we discuss the refolding mechanism.     

A novel method for using accelerometer data to predict energy expenditure.

The purpose of this study was to develop a new two-regression model relating Actigraph activity counts to energy expenditure over a wide range of physical activities. Forty-eight participants [age 35 yr (11.4)] performed various activities chosen to represent sedentary, light, moderate, and vigorous intensities. Eighteen activities were split into three routines with each routine being performed by 20 individuals, for a total of 60 tests. Forty-five tests were randomly selected for the development of the new equation, and 15 tests were used to cross-validate the new equation and compare it against already existing equations. During each routine, the participant wore an Actigraph accelerometer on the hip, and oxygen consumption was simultaneously measured by a portable metabolic system. For each activity, the coefficient of variation (CV) for the counts per 10 s was calculated to determine whether the activity was walking/running or some other activity. If the CV was 10, a lifestyle/leisure time physical activity regression was used. In the cross-validation group, the mean estimates using the new algorithm (2-regression model with an inactivity threshold) were within 0.75 metabolic equivalents (METs) of measured METs for each of the activities performed (P >or= 0.05), which was a substantial improvement over the single-regression models. The new algorithm is more accurate for the prediction of energy expenditure than currently published regression equations using the Actigraph accelerometer.     

A general method to optimize the amount of enzyme in restriction and DNA modification reactions using the beta galactosidase blue-white plaques assay

We propose a simple and economical method for assaying the activity of restriction and other modifying enzymes. The method involves assaying the use of the blue and white colored phenotypes of bacterial colonies obtained by digesting the polylinker sequence of M13 bacteriophage vectors followed by transformation in appropriate strains on X-gal/IPTG plates. In conjunction with restriction enzymes and DNA ligases, the method can evaluate polymerase activity and can be applied to test 3'...5' exonuclease activities such as that of T4 DNA polymerase, without having to use expensive radioisotopes. We describe its application in the assessment of restriction enzymes, DNA ligase and DNA polymerase activities.     

A novel method of plasmid isolation using laundry detergent

Since the discovery of plasmid, various methods have been developed to isolate plasmid DNA. All the methods have one common and important target of isolating plasmid DNA of high quality and quantity in less time. These methods are not completely safe because of use of toxic chemicals compounds. The developed protocol for plasmid extraction is based on the alkaline lysis method of plasmid preparation (extraction atpH 8.0) with slight modifications. Cell lysis reagent sodium dodecyl sulfate is replaced by lipase enzyme present in laundry detergent. A good plasmid preparation can be made, which is well suited for subsequent molecular biology applications. By taking safety measures on count, contaminants like, RNA and protein can be completely avoided with maximized plasmid yield. The resultant plasmid quality and quantity can be well comparable to other prevalent methods.     

How to optimize the drop plate method for enumerating bacteria

The drop plate (DP) method can be used to determine the number of viable suspended bacteria in a known beaker volume. The drop plate method has some advantages over the spread plate (SP) method. Less time and effort are required to dispense the drops onto an agar plate than to spread an equivalent total sample volume into the agar. By distributing the sample in drops, colony counting can be done faster and perhaps more accurately. Even though it has been present in the laboratory for many years, the drop plate method has not been standardized. Some technicians use 10-fold dilutions, others use twofold. Some technicians plate a total volume of 0.1 ml, others plate 0.2 ml. The optimal combination of such factors would be useful to know when performing the drop plate method.This investigation was conducted to determine (i) the standard deviation of the bacterial density estimate, (ii) the cost of performing the drop plate procedure, (iii) the optimal drop plate design, and (iv) the advantages of the drop plate method in comparison to the standard spread plate method. The optimal design is the combination of factor settings that achieves the smallest standard deviation for a fixed cost. Computer simulation techniques and regression analysis were used to express the standard deviation as a function of the beaker volume, dilution factor, and volume plated. The standard deviation expression is also applicable to the spread plate method.