Structure-based method for analyzing protein–protein interfaces

Hydrogen bond, hydrophobic and vdW interactions are the three major non-covalent interactions at protein–protein interfaces. We have developed a method that uses only these properties to describe interactions between proteins, which can qualitatively estimate the individual contribution of each interfacial residue to the binding and gives the results in a graphic display way. This method has been applied to analyze alanine mutation data at protein–protein interfaces. A dataset containing 13 protein–protein complexes with 250 alanine mutations of interfacial residues has been tested. For the 75 hot-spot residues (G1.5 kcal mol^-1), 66 can be predicted correctly with a success rate of 88%. In order to test the tolerance of this method to conformational changes upon binding, we utilize a set of 26 complexes with one or both of their components available in the unbound form. The difference of key residues exported by the program is 11% between the results using complexed proteins and those from unbound ones. As this method gives the characteristics of the binding partner for a particular protein, in-depth studies on protein–protein recognition can be carried out. Furthermore, this method can be used to compare the difference between protein–protein interactions and look for correlated mutation. Figure Key interaction grids at the interface between barnase and barstar. Key interaction grid for barnase and barstar are presented in one figure according to their coordinates. In order to distinguish the two proteins, different icons were assigned. Crosses represent key grids for barstar and dots represent key grids for barnase. The four residues in ball and stick are Asp40 in barstar and Arg83, Arg87, His102 in barnase.     

Preparative centrifugation — a new method for preparing pollen concentrates suitable for radiocarbon dating by AMS

Methods of preparative centrifugation eliminate many of the difficulties involved in preparing pollen concentrates from deposits rich in resistant organic material. Density centrifugation for the separation of pollen from a gyttja sample rich in resistant organic matter was tested. Combining centrifugations in two CsCl solutions, one of higher density and one of lower density than pollen, a pure pollen fraction was successfully prepared. Data on the isodensity and sedimentation rate of fossilized recent pollen from twelve tree taxa are also presented, and the potential for separating a single taxon from pollen assemblages is demonstrated.     

PCR–DGGE method for analyzing the bacterial community in a high temperature petroleum reservoir

Different PCR–denaturing gradient gel electrophoresis (DGGE) protocols were employed to investigate bacterial communities in a high temperature and water flooded petroleum reservoir in Dagang oil field, China. Bacterial universal primers sets frequently used in PCR–DGGE were evaluated. Three primers sets P1 (341F-GC and 534R), P2 (341F-GC and 907R) and P3 (1055F and 1406R-GC) showed different DGGE patterns. Good separation and quality of patterns were obtained in DGGE analysis with the set P3. A total of 12 DNA fragments were excised from the DGGE gels and their sequences were determined. Clustering analysis of the DGGE profiles showed that bacteria in this petroleum reservoir belonged to four clusters. These results indicate that the procedure of DGGE analysis with the primer P3 (1055F and 1406R-GC) is suitable for investigating microbial community in petroleum reservoirs.     

A batch correction method for liquid chromatography–mass spectrometry data that does not depend on quality control samples

The need for reproducible and comparable results is of increasing importance in non-targeted metabolomic studies, especially when differences between experimental groups are small. Liquid chromatography–mass spectrometry spectra are often acquired batch-wise so that necessary calibrations and cleaning of the instrument can take place. However this may introduce further sources of variation, such as differences in the conditions under which the acquisition of individual batches is performed. Quality control (QC) samples are frequently employed as a means of both judging and correcting this variation. Here we show that the use of QC samples can lead to problems. The non-linearity of the response can result in substantial differences between the recorded intensities of the QCs and experimental samples, making the required adjustment difficult to predict. Furthermore, changes in the response profile between one QC interspersion and the next cannot be accounted for and QC based correction can actually exacerbate the problems by introducing artificial differences. “Background correction” methods utilise all experimental samples to estimate the variation over time rather than relying on the QC samples alone. We compare non-QC correction methods with standard QC correction and demonstrate their success in reducing differences between replicate samples and their potential to highlight differences between experimental groups previously hidden by instrumental variation.     

Determination of thiamin diphosphate in whole blood samples by high-performance liquid chromatography—A method suitable for pediatric diagnostics

An improved and easy to use method for the determination of thiamin diphosphate (TDP) in 100 μl of whole blood was developed. The small sample volume makes it possible to assess the nutritional status of vitamin B₁ in infants and even in preterm infants. Sample preparation comprises the extraction of TDP from whole blood by hemolysis, protein precipitation with trichloroacetic acid, and subsequent centrifugation. Potassium ferricyanide is used for pre-column derivatization of TDP to its fluorescent thiochrome derivative. Chromatographic separation was carried out using a reversed-phase column and an isocratic elution which consisted of a phosphate buffer and acetonitrile. TDP was detected fluorimetrically and quantified by external standardization. Method validation showed a high precision, almost complete recovery, and a high sensitivity. The lower limit of detection and the lower limit of quantification were 0.2 ng/ml and 4 ng/ml, respectively. Linearity was demonstrated over the expected concentration range of 4–400 ng/ml. In conclusion, we present a convenient HPLC method for the determination of TDP which is precise, sensitive and suitable for pediatric diagnostics.     

A practical approximation of pollen dispersal–deposition for calculation of pollen productivity and quantification of vegetation

We compared simple mathematical pollen dispersal–deposition models with Gaussian plume models. The simple mathematical models proved equal or better approximations of real world pollen dispersal–deposition. We concluded that for most standard applications, such as estimating pollen productivity or quantitative vegetation reconstructions, simple mathematical models would perform satisfactory. Such easy-to-use models may lower the threshold to employ quantitative tools to palaeoecological questions.     

A screening method for DNA aptamers that bind to␣a␣specific, unidentified protein in tissue samples

Aptamers are oligonucleotide ligands with a high affinity to, and specificity for, various target molecules and they are expected to be powerful tools for proteomic analysis. To select aptamers that bind to a specific unidentified protein in tissues for protein analysis, a screening method was developed using chicken skeletal muscle as a model. Target proteins in the target mixture were separated by electrophoresis and transferred to a membrane, and a DNA library was added onto it. The aptamers that bound to the target protein were visualized by chemiluminescence and collected by cutting out the visualized band. The specific aptamers to the target protein were selected by only one round of selection using this screening, suggesting this screening method might be useful for selecting aptamers for proteome analysis.     

A simple method of using ø(ρz) curves for the x-ray microanalysis of frozen-hydrated bulk biological samples

As an alternative to the conventional ZAF correction for microprobe analysis, a combined absorption and atomic number correction can be obtained from ø(ρz) curves. This can be easily applied to the analysis of bulk frozen-hydrated biological samples using inorganic standards. It is shown that the method is accurate by analysis of a number of organic and inorganic compounds and gelatine models. Because the corrections vary little with changes in protein concentration over the normal cellular range, iterative ø(ρz) computations are not necessary and the correction procedure is therefore fast and simple.     

A unified GMDR method for detecting gene–gene interactions in family and unrelated samples with application to nicotine dependence

Gene–gene and gene–environment interactions govern a substantial portion of the variation in complex traits and diseases. In convention, a set of either unrelated or family samples are used in detection of such interactions; even when both kinds of data are available, the unrelated and the family samples are analyzed separately, potentially leading to loss in statistical power. In this report, to detect gene–gene interactions we propose a generalized multifactor dimensionality reduction method that unifies analyses of nuclear families and unrelated subjects within the same statistical framework. We used principal components as genetic background controls against population stratification, and when sibling data are included, within-family control were used to correct for potential spurious association at the tested loci. Through comprehensive simulations, we demonstrate that the proposed method can remarkably increase power by pooling unrelated and offspring’s samples together as compared with individual analysis strategies and the Fisher’s combining p value method while it retains a controlled type I error rate in the presence of population structure. In application to a real dataset, we detected one significant tetragenic interaction among CHRNA4, CHRNB2, BDNF, and NTRK2 associated with nicotine dependence in the Study of Addiction: Genetics and Environment sample, suggesting the biological role of these genes in nicotine dependence development.     

A GIS based method to calculate regionalized land use characterization factors for life cycle impact assessment using LANCA®

The International Journal of Life Cycle Assessment - Land is used and modified in its natural function for the cultivation of food and energy crops, for infrastructure and other production...     

A method for preparing 2- to 50-µm-thick fresh-frozen sections of large samples and undecalcified hard tissues

This article describes a method for preparing 2- to 50-micron-thick fresh-frozen sections from large samples and completely calcified tissue samples. In order to perform the more routine work involved, a tungsten carbide disposable blade was installed to a heavy-duty sledge cryomicrotome. An entire 10-day-old rat and bone and tooth samples from a 7-month-old rat were rapidly frozen. The frozen samples were attached to the cryomicrotome stage. The cutting surface of the samples was covered with a polyvinylidene chloride film coated with synthetic rubber cement and cut at -25 degrees C. The soft tissues and the hard tissues were satisfactorily preserved and all tissue cells were easily identifiable. Enzymatic activity in the fresh sections was much stronger than that in chemically fixed and/or decalcified sections. The sections permitted histological and histochemical studies without trouble. In addition, the sections can be used for multiple experiments such as immunohistochemistry, in situ hybridization, and electron microprobe X-ray micro-analysis. This method can be used with conventional cryomicrotome equipment.     

A new method to isolate lichen algae by using Percoll®gradient centrifugation

Abstract:A rapid method to isolate intact functional algae from the lichens Evernia prunastri and Ramalina farinacea has been developed. This method is based on the use of Percoll^®gradients after mechanical disruption of lichen thalli. Results obtained show that the algal preparations were virtually free of contamination by fungal hyphae. The purified algal cells were photosynthetically active and without symptoms of photoinhibition, which indicates their functional integrity. This method may be used for the isolation of intact algae from a broad range of lichen species.     

A novel hunting method for banded kōkopu

Banded kōkopu (Galaxias fasciatus) were observed attempting to catch insects off the bank of the pool in which they lived. This is previously unrecorded behaviour for this species. Details of this behaviour were recorded and described when individuals responded to the placement of insect larvae on the bank of the pool. This behaviour could explain the differences between stomach and drift net samples in previous diet studies.     

A simple method for monitoring protein–DNA interactions

A simple, efficient and cheap method is reported for monitoring interactions between single stranded desoxyribonucleic acids and proteins, using fluorescence spectroscopy and complexes of 5′-dye–DNA conjugates with bovine serum albumin as probes. In the presence of a single stranded DNA-binding protein the complexes with bovine serum albumin are disrupted, which results in a reduction of fluorescence intensity.     

A method for compression — Reconstruction of ECG signals

A new method of data compression — reconstruction for ECG signals is presented. The method gives the ability (a) to control the final accuracy of the reconstructed signal before the transmission (or storage) of samples and (b) to control the compression ratio (CR) in order to obtain an optimum use of the channel capacity. The main advantage of the method was found to be the very strong improvement of the local re-construction during the active periods. Indeed, we can obtain CR values between 3 and 10 with local root mean square error (r.m.s.e.) improvement, compared to the total r.m.s.e. value, by 85% during the active period.     

A 13C NMR spectrometric method for the determination of intramolecular δ13C values in fructose from plant sucrose samples

Recent developments in (13) C NMR spectrometry have allowed the determination of intramolecular (13) C/(12) C ratios with high precision. However, the analysis of carbohydrates requires their derivatization to constrain the anomeric carbon. Fructose has proved to be particularly problematic because of a byproduct occurring during derivatization and the complexity of the NMR spectrum of the derivative. Here, we describe a method to determine the intramolecular (13) C/(12) C ratios in fructose by (13) C NMR analysis of the acetyl-isopropylidene derivative. We have applied this method to measure the intramolecular (13) C/(12) C distribution in the fructosyl moiety of sucrose and have compared this with that in the glucosyl moiety. Three prominent features stand out. First, in sucrose from both C(3) and C(4) plants, the C-1 and C-2 positions of the glucosyl and fructosyl moieties are markedly different. Second, these positions in C(3) and C(4) plants show a similar profile. Third, the glucosyl and fructosyl moieties of sucrose from Crassulacean acid metabolism (CAM) metabolism have a different profile. These contrasting values can be interpreted as a result of the isotopic selectivity of enzymes that break or make covalent bonds in glucose metabolism, whereas the distinctive (13) C pattern in CAM sucrose probably indicates a substantial contribution of gluconeogenesis to glucose synthesis.     

A “GC-rich” method for mammalian gene expression: A dominant role of non-coding DNA GC content in regulation of mammalian gene expression

High mammalian gene expression was obtained for more than twenty different proteins in different cell types by just a few laboratory scale stable gene transfections for each protein. The stable expression vectors were constructed by inserting a naturally-occurring 1.006 kb or a synthetic 0.733 kb DNA fragment (including intron) of extremely GC-rich at the 5′ or/and 3′ flanking regions of these protein genes or their gene promoters. This experiment is the first experimental evidence showing that a non-coding extremely GC-rich DNA fragment is a super “chromatin opening element” and plays an important role in mammalian gene expression. This experiment has further indicated that chromatin-based regulation of mammalian gene expression is at least partially embedded in DNA primary structure, namely DNA GC-content.     

All’s well? Comparing on- and off-site pollen samples and exploring the potential of pollen from man-made contexts

Vegetation History and Archaeobotany - Pollen analysis has long been used as a tool to make an assessment of regional vegetation. On-site pollen samples are taken for the same purpose at some...