A method for the quantification ofFrankia by estimation of hyphal length

Summary The cellular mass ofFrankia, a filamentous actinomycete, was readily quantified by estimating hyphal length, using a modification of Tennant's method for the estimation of root length. Each sample ofFrankia was stained with Coomassie Brilliant blue G 250, dispersed well, and suspended in a 0.5% agar solution. One drop of the suspension was placed in a Petroff-Hausser counting chamber with 0.05 by 0.05mm grid squares. The number of intersections betweenFrankia hyphae and the grid lines in a standard area were counted under a microscope and converted to hyphal length. Using the formula: hyphal length (HL) in mm equals (11/14) times the number of intersections (n) times the grid dimension (0.05 mm). The validity of the line intersection method was tested by comparison with total protein estimates of replicate aliquots ofFrankia culture. Correlations between total protein and hyphal length estimates were strong (r² from 0.76 to 0.95; standard errors of 3 to 9% of estimated length). These results show that line intersection counts may be a satisfactory routine method for quantifyingFrankia in culture and may be especially suitable for detecting small amounts of livingFrankia in less time than with other methods.Dedicated to the memory of Professor John G. Torrey     

长白山阔叶红松林的零平面位移和粗糙度

根据长白山阔叶红松林气象观测塔上 16个月的风速、温度、湿度及气压的连续观测资料 ,根据中性层结条件下风速随高度的对数变化规律 ,利用廓线法中的牛顿迭代法计算了该森林的零平面位移d和粗糙度z0 ,结果表明 ,d和z0 均存在着较明显的季节变化 ,在生长季d较大 ,z0 较小 ,而非生长季恰好相反 ,标准化的零平面位移d/h和粗糙度z0 /h在生长季和非生长季平均分别为 0 86 7,0 76 4和 4 4 7× 10 -2 ,3 5 9× 10 -2 。与叶面积指数对比分析发现 ,d/h和z0 /h与叶面积指数分别存在正相关和负相关的关系。敏感性分析表明 ,牛顿迭代法求d和z0对风速的精度要求较高 ,需要精度高的仪器和长期的数据积累。     

Use of direct and iterative solvers for estimation of SNP effects in genome-wide selection

The aim of this study was to compare iterative and direct solvers for estimation of marker effects in genomic selection. One iterative and two direct methods were used: Gauss-Seidel with Residual Update, Cholesky Decomposition and Gentleman-Givens rotations. For resembling different scenarios with respect to number of markers and of genotyped animals, a simulated data set divided into 25 subsets was used. Number of markers ranged from 1,200 to 5,925 and number of animals ranged from 1,200 to 5,865. Methods were also applied to real data comprising 3081 individuals genotyped for 45181 SNPs. Results from simulated data showed that the iterative solver was substantially faster than direct methods for larger numbers of markers. Use of a direct solver may allow for computing (co)variances of SNP effects. When applied to real data, performance of the iterative method varied substantially, depending on the level of ill-conditioning of the coefficient matrix. From results with real data, Gentleman-Givens rotations would be the method of choice in this particular application as it provided an exact solution within a fairly reasonable time frame (less than two hours). It would indeed be the preferred method whenever computer resources allow its use.     

Application of the digital volume correlation technique for the measurement of displacement and strain fields in bone: A literature review

Digital volume correlation (DVC) provides experimental measurements of displacements and strains throughout the interior of porous materials such as trabecular bone. It can provide full-field continuum- and tissue-level measurements, desirable for validation of finite element models, by comparing image volumes from subsequent µCT scans of a sample in unloaded and loaded states.     

A rapid survey method for the estimation of density and cover in desert plant communities

Abstract. The Log-series survey method allows rapid estimates of density and cover and is applicable for studies of perennial vegetation in arid environments. An optical rangefinder is used to determine boundaries of large circular plots. Numbers of individuals of each species within a plot are assessed; this information is used to assign species to logarithmic density classes equivalent to the logarithm base 2 of actual abundances. Each species is then assigned to a logarithmic canopy cover class, equivalent to the logarithmbase 2 of average cover per individual. Log total cover per species per plot is obtained by the addition of logarithmic density and cover classes. Percent cover per species is rapidly computed by taking the antilog of the difference between log total cover per species and log total plot area.     

Introduction and verification of a novel method for measuring wood fiber length using a single cross section in Acacia mangium

A novel method for calculating the wood fiber length using a single cross section was devised and verified in Acacia mangium. This method is based on the ratio of cell tips to total cell number in a cross section related to the wood fiber. The fiber length was calculated using the single cross-section method and was compared with the measurements obtained using the conventional maceration method and the serial cross-section method. There was no significant difference among the three methods.     

A method for the estimation of bacterial biomass and community structure in mangrove-associated sediments

Many recent reports have proposed that certain monocarboxylic fatty acids found in sediments originate in the in situ bacterial population. In this study we have divided the acids derived from bacteria into nine subgroups, each characteristic of a distinct compositional group of bacteria. It is proposed that the abundance of selected marker acids from each bacterial subgroup (chemotype) can be used to estimate the biomass of that chemotype. Conversion factors from acid abundance to bacterial biomass have been estimated using literature data. Since this procedure results in nine biomass parameters, bacterial communities can be compared in terms of both total biomass and chemotype distribution, that is, biomass and community structure. The ability of this procedure to resolve community structure variations is illustrated with the interpretation of the fatty acid profiles of a spatially distributed set of mangrove-associated sediments.     

A simple and nondestructive method for estimation of worker population size in Myrmica ant nests

A method to estimate the number of workers in Myrmica ant nests on abandoned meadows was developed based on removal of workers. Ant workers have a tendency to climb up on wooden sticks put into their nests, therefore, assuming that the number of workers removed on sticks is related to the total number of workers within the nests, regression models for Myrmica rubra, M. ruginodis and M. scabrinodis may be built. We used a general regression model to perform a backward stepwise elimination of explanatory variables. These were the number of workers removed on sticks, temperature at the nest and site (a categorical variable). In case of each species the final model contained only the number of workers removed as a significant variable. The method is apparently non-destructive as we did not observe decreased survival of nests surveyed as compared to control nests. The method can be a very useful tool in population studies of ants as well as in biodiversity projects, where ants are used as bioinidcators. Received 10 February 2005; revised 4 August 2005; accepted 24 August 2005.     

A novel approach for estimating growth phases and parameters of bacterial population in batch culture

Using mathematical analysis, a new method has been developed for studying the growth kinetics of bacterial populations in batch culture. First, sampling data were smoothed with the spline interpolation method. Second, the instantaneous rates were derived by numerical differential techniques and finally, the derived data were fitted with the Gaussian function to obtain growth parameters. We named this the Spline-Numerical-Gaussian or SNG method. This method yielded more accurate estimates of the growth rates of bacterial populations and new parameters. It was possible to divide the growth curve into four different but continuous phases based on changes in the instantaneous rates. The four phases are the accelerating growth phase, the constant growth phase, the decelerating growth phase and the declining phase. Total DNA content was measured by flow cytometry and varied depending on the growth phase. The SNG system provides a very powerful tool for describing the kinetics of bacterial population growth. The SNG method avoids the unrealistic assumptions generally used in the traditional growth equations.     

A modified mini-prep method for economical and rapid extraction of genomic DNA in plants

Molecular markers for map-based cloning, marker-assisted selection in crop breeding, and genetic studies require DNA isolation from a large number of plants in a short span of time. Here we describe a modified DNA extraction method that is economical in terms of cost, time and labour. The method allows DNA extraction from as little as 0.2–0.3 g of leaves that are homogenized in zipper plastic bags, followed by DNA isolation in 1.5-mL Eppendorf tubes. By using the modified method, a DNA yield of 700–800 μg/300 mg leaf tissue was obtained from cotton and wheat samples. The quality of the DNA was quite suitable for PCR-based markers.     

A method for quantifying the anterior load–displacement behavior of the human knee in both the low and high stiffness regions

The anterior load–displacement behavior of the human knee with an intact ACL is characterized by a very low stiffness region initially and a high stiffness region that develops as anterior load is increased. Although this behavior has been well recognized for some time, a method for quantitatively describing the behavior in these two regions based on limits of motion at specific values of anterior/posterior force has not yet been developed. Thus, the purposes of this study were to describe and justify such a method for measuring the laxity and stiffness in both of these regions in the intact knee.

Unique to this study, low stiffness and high stiffness laxities were computed based on three limits of motion for seven cadaveric knees tested at flexion angles ranging from 0° to 90°. Defining the reference position of the tibia relative to the femur, one limit was the 0 N posterior limit which was determined using a specially designed load cycle to reduce uncertainty in establishing a reference position. Defining the upper bound of the load–displacement curve, a second limit was the 225 N anterior limit. A third intermediate limit was the 45 N anterior limit, which was the load that represented the transition from the low stiffness to the high stiffness region. Stiffnesses corresponding to each of the two regions were computed using regression analysis and also estimated based on the laxities. Comparison between the computed and estimated stiffnesses demonstrated that the stiffnesses in both the low and high stiffness regions can be estimated reasonably accurately based on the laxities. Therefore, the 0 N posterior limit and the two laxities are the three quantities needed to describe the load–displacement behavior of the normal knee.     

A method for the enumeration of myxomycetes in soils and its application to a wide range of soils

Abstract A standardised most-probable-number technique for estimating the number of myxomycete plasmodium-forming units (PFUs) in soils has been developed and tested experimentally. Application of the method to a local soil showed that the uppermost layers contained the most PFUs. Its application to 44 surface soils from various parts of the world detected myxomycetes in 36, of which 4 were desert soils. In general, highest numbers of PFUs (up to 9000·g⁻¹ soil) were recorded in grassland and agricultural soils. The nature of the PFUs has not been definitely resolved but they are probably myxamoebae, myxoflagellates and microcysts.     

A reversed-phase high-performance liquid chromatographic method for the determination of aloesin, aloeresin A and anthraquinone in Aloe ferox

A reversed-phase HPLC method for the quantification of aloesin, aloeresin a and anthraquinone (as barbaloin) in Aloe ferox Miller and aloe-related products has been developed and validated. The method utilized a C18 column with a water-methanol gradient and UV detection at 297 nm. The method validation included linearity, accuracy, precision, limit of detection, limit of quantitation, specificity and standard solution stability. The method showed good linearity (r > 0.99 for all components) and recovery (>85% for all components). The detection and quantitation limits for barbaloin were determined to be 0.02 and 0.1 ppm at signal-to-noise ratios of approximately 3:1 and 10:1, respectively.     

A proximity based general method for identification of ligand and receptor interactions in living cells

Autocrine based selections from intracellular combinatorial antibody and peptide libraries have proven to be a powerful method for selection of agonists and identification of new therapeutic targets. However, success requires a case-by-case construction of a robust selection system which is a process that can be time consuming and expensive. Here we report a general system that takes advantage of the chemical rate acceleration caused by approximation of a membrane tethered ligand and its receptor. The system uses an artificial signal transduction and is, thus, agnostic to the endogenous signal transduction of the receptor–ligand system. This method allows analysis of receptor–ligand interactions and selection of molecules from large libraries that interact with receptors when they are in their natural milieu.     

A dot-blot method for quantification of apurinic/apyrimidinic sites in DNA using an avidin plate and liposomes encapsulating a fluorescence dye

A dot-blot method for quantification of apurinic/apyrimidinic (AP) sites in genomic DNA (calf thymus DNA) is described using an avidin-modified glass slip and biotinylated liposomes containing sulforhodamine B as a fluorescence marker. Aldehyde reactive probe (ARP)-tagged DNA was found to be strongly adsorbed on an avidin slip, even if treated with ethanolamine and biotin, with an efficiency of 51% due to the positive surface charge of avidin, and unbound ARP was easily washed out of the surface with Milli-Q water. In the assay protocol, calf thymus DNA containing AP sites is reacted with ARP in solution and immobilized on an ethanolamine- and biotin-treated avidin slip (EAB-avidin slip), followed by incubation with streptavidin. The AP sites were finally quantified with biotinylated liposomes containing 1.5 mM sulforhodamine B as a fluorescence marker. The mean fluorescence intensity over the surface of the slip was an analytically relevant measure of the amount of AP sites in calf thymus DNA. By using the dot-blot assay, 1-5 AP sites per 10(4) nucleotides in 5 and 100 ng of DNA were quantified. The current dot-blot method has potential for quantification of AP sites in genomic DNA at a level of several nanograms.     

A sensitive method for quantification of aceticlastic methanogens and estimation of total methanogenic cells in natural environments based on an analysis of ether-linked glycerolipids

Abstract A highly sensitive method for the quantification of methanogens in anaerobic digestor sludges was developed, based on an analysis of ether-linked glycerolipids. Core lipids were prepared from total lipids by HF treatment and mild methanolysis, and these core lipids were quantified as the corresponding 9-anthroyl derivatives by high-performance liquid chromatography with fluorescence detection. The amounts, in terms of cell carbon content, of Methanosaeta and Methanosarcina were proportional to the amounts of α-hydroxyarchaeol and β-hydroxyarchaeol, respectively. Moreover, the total amount of core lipids was well correlated with the cell mass of aceticlastic and H₂/CO₂-consuming methanogens. The limit of detection for Methanosaeta concilii was 17 ng of cell carbon when the signal/noise ratio was 3. This method allowed us to quantitate aceticlastic methanogens with high accuracy and to make a rough estimate of total methanogenic cells without any interference by the multifarious impurities that are present in anaerobic sludges. These results suggest that the present method will be a useful tool for investigations of methanogenic ecosystems.     

A practical method of Ludox density gradient centrifugation combined with protargol staining for extracting and estimating ciliates in marine sediments

Methodological impediments have long been the main problem in estimating the ecological role of marine benthic ciliates. Percoll density centrifugation is currently the most efficient technique for extracting ciliates from fine-grained sediments, while the high cost and low density of Percoll limit its wide application. We developed a protocol of density gradient centrifugation using the cheap sol Ludox HS 40 in combination with the quantitative protargol stain (QPS) to enumerate and identify marine benthic ciliates. The combined Ludox-QPS method involves sample collection and salt reduction, extraction with Ludox centrifugation, and preparation with the QPS technique. The recovery efficiency of Ludox was first tested with azoic sandy and muddy sediments. A 94–100% recovery rate of ciliates was reached. The method was further tested with natural sandy, muddy-sand and muddy sediments. Excellent extraction efficiencies were consistently obtained: an average of 97.6% for ciliates in sand, and 96.9–97.8% for nematodes in the three types of sediments. The high efficiencies indicate that the method allows for simultaneous enumeration of micro- and meiobenthos. Advantages of the new method include: (i) reliable and cost-efficient operation; (ii) appropriate centrifugation for both micro- and meiobenthos; and (iii) applicability to large samples and routine ecological surveys.