A novel method for estimating linkage maps

The goal of linkage mapping is to find the true order of loci from a chromosome. Since the number of possible orders is large even for a modest number of loci, the problem of finding the optimal solution is known as a NP-hard problem or traveling salesman problem (TSP). Although a number of algorithms are available, many either are low in the accuracy of recovering the true order of loci or require tremendous amounts of computational resources, thus making them difficult to use for reconstructing a large-scale map. We developed in this article a novel method called unidirectional growth (UG) to help solve this problem. The UG algorithm sequentially constructs the linkage map on the basis of novel results about additive distance. It not only is fast but also has a very high accuracy in recovering the true order of loci according to our simulation studies. Since the UG method requires n-1 cycles to estimate the ordering of n loci, it is particularly useful for estimating linkage maps consisting of hundreds or even thousands of linked codominant loci on a chromosome.     

A novel method for estimating the number of species within a region

Ecologists are often required to estimate the number of species in a region or designated area. A number of diversity indices are available for this purpose and are based on sampling the area using quadrats or other means, and estimating the total number of species from these samples. In this paper, a novel theory and method for estimating the number of species is developed. The theory involves the use of the Laplace method for approximating asymptotic integrals. The method is shown to be successful by testing random simulated datasets. In addition, several real survey datasets are tested, including forests that contain a large number (tens to hundreds) of tree species, and an aquatic system with a large number of fish species. The method is shown to give accurate results, and in almost all cases found to be superior to existing tools for estimating diversity.     

Three-phase partitioning as an efficient method for extraction/concentration of immunoreactive excreted-secreted proteins of Corynebacterium pseudotuberculosis

The three-phase partitioning (TPP) technique was used upstream to isolate/concentrate secreted proteins from Corynebacterium pseudotuberculosis cultured in a complex liquid medium. Several parameters of the TPP technique (15, 30, or 60% ammonium sulfate concentration; 4.0, 5.5, or 7.0 pH; and primary (n) or tertiary (t)-butanol solvent isomer) were varied to determine the optimal recovery of serologically and cellularly immunoreactive extracted proteins. A TPP extraction made with 30% ammonium sulfate and an initial pH of 4.0 gave the best humoral and cellular immunoreactivity of caseous lymphadenitis infected goats. In particular, two immunogenic secreted (16 and 125 kDa) proteins, which had not been found by other extraction methods, were identified.     

Red cell Na+,K+-ATPase: a method for estimating the extent of inhibition of an enzyme sample containing an unknown amount of bound cardiac glycoside.

Na⁺, K⁺-ATPase activities of the membranes obtained from intact red cells that are exposed to ouabain, digoxin, and digitoxin are inhibited. The extent of inhibition of each enzyme sample can be found by the following two assays: 1) Activity is measured by the addition of enzyme to a buffered solution containing 2 mM ATP, 3 mM Mg²⁺, 1 mM EDTA, 100 mM Na⁺, and 25 mM K⁺. Since little regeneration of the inhibited enzyme occurs under these conditions, the measured activity is that of the partially inhibited enzyme. 2) Enzyme is preincubated for ten minutes in the same solution from which Mg²⁺ and K⁺ are omitted, and then assayed by the addition of Mg⁺ and K⁺. Since the inhibited enzyme is completely regenerated during the preincubation period, the activity measured here serves as a control for that determined in the first assay.     

A method for estimating the concentration of spermatozoa in the rat cauda epididymidis

A method for estimating the concentration of spermatozoa in the rat cauda epididymidis is described. Treatment of a sperm suspension with 0.05% collagenase for 20-60 min or 0.025% trypsin for 1-2 min at 34-37 degrees C was found to result in consistently homogeneous sperm. Sperm concentration ranged from 152.5 to 230.0 X 10(7) spermatozoa/ml, with a mean of 187.7 (+/- 5.6 SEM) X 10(7) spermatozoa/ml.     

A novel method for detergent concentration determination

A fast and precise method for detergent concentration determination is presented. (Patent applications for the method described here have been submitted (EP05011904 and US60/702,261). Depending on the interest of the scientific community, the system will be commercialized. (For further information contact Hervé-W. Rémigy at the e-mail address below.) A small droplet of the detergent solution is deposited on a piece of Parafilm M and side views are recorded by two orthogonally arranged TV cameras. The droplet contours are then approximated by ellipses to determine the contact angles. Comparison of the observed contact angle values to calibrated standard curves of known detergent concentrations gives the concentration of the detergent assessed. A range of commonly used detergents was studied to demonstrate the reproducibility and precision of this simple method. As a first application, the detergent binding capacity of the Escherichia coli galactose/proton symporter (GalP) was assessed. Aggregation of GalP was observed when <260 +/- 5 dodecyl-beta,D-maltoside molecules were bound to one GalP molecule. These measurements document the efficacy of the drop-shape based detergent concentration determination described.     

TRICORE, a novel bead-based specimen concentration method for the culturing of Mycobacterium tuberculosis

Centrifugation is a necessary concentrating step for the detection of Mycobacterium tuberculosis in a liquid culture. However, centrifugation is biologically hazardous and presents an obstacle in the development of an automated culture system. A bead-based bacterial concentration method, TRICORE, was recently developed by Genetein Co., Ltd. We compared the efficacy of TRICORE and conventional centrifugation for concentrating M. tuberculosis in clinical sputum specimens by using liquid and solid culture systems. Among 90 pretreated clinical sputum specimens, 51 (57.3%) and 55 (61.8%) M. tuberculosis isolates were recovered by the MGIT culture system by using the centrifugation and TRICORE methods, respectively (chi-square test, p=0.5413). The detection time for the centrifugation method was 359.3±117.0 h, while that for the bead-based concentration method was 377.6±162.3 h (p=0.5637). However, the number of colonies recovered on solid media were significantly higher with the TRICORE method (p=0.003). In particular, among the smear-negative specimens, culture positivity of the TRICORE method was 39.6%, while that of the centrifugation method was 15.1%. The TRICORE bead-based concentration method was considered equivalent to centrifugation and enabled efficient collection of paucibacillary specimens in solution. Thus, the new noncentrifugation concentration method could yield more positive culture results.     

LY79771: a novel compound for weight control

Compound LY79771 given subcutaneously reduced weight or decreased weight gain of genetically obese rats and mice, gold thioglucose obese mice, and obese beagles. The compound had no effect on body weight of lean rats. Food consumption was not decreased. Obese rats showed a transient rise in body temperature after each administration of the drug. The change in body weight was due mainly to a decrease in body fat mass.     

A novel method for measurement of submembrane ATP concentration

There has been considerable debate as to whether adenosine triphosphate (ATP) is compartmentalized within cells and, in particular, whether the ATP concentration directly beneath the plasma membrane, experienced by membrane proteins, is the same as that of the bulk cytoplasm. This issue has been difficult to address because there is no indicator of cytosolic ATP, such as those available for Ca(2+), capable of resolving the submembrane ATP concentration ([ATP](sm)) in real time within a single cell. We show here that mutant ATP-sensitive K(+) channels can be used to measure [ATP](sm) by comparing the increase in current amplitude on patch excision with the ATP dose-response curve. In Xenopus oocytes, [ATP](sm) was 4.6 +/- 0.3 mm (n = 29) under resting conditions, slightly higher than that measured for the bulk cytoplasm (2.3 mm). In mammalian (COSm6) cells, [ATP](sm) was slightly lower and averaged 1.4 +/- 0.1 mm (n = 66). Metabolic poisoning (10 min of 3 mm azide) produced a significant fall in [ATP](sm) in both types of cells: to 1.2 +/- 0.1 mm (n = 24) in oocytes and 0.8 +/- 0.11 mm for COSm6 cells. We conclude that [ATP](sm) lies in the low millimolar range and that there is no gradient between bulk cytosolic and submembrane [ATP].     

iGLASS: an improvement to the GLASS method for estimating species trees from gene trees

Several methods have been designed to infer species trees from gene trees while taking into account gene tree/species tree discordance. Although some of these methods provide consistent species tree topology estimates under a standard model, most either do not estimate branch lengths or are computationally slow. An exception, the GLASS method of Mossel and Roch, is consistent for the species tree topology, estimates branch lengths, and is computationally fast. However, GLASS systematically overestimates divergence times, leading to biased estimates of species tree branch lengths. By assuming a multispecies coalescent model in which multiple lineages are sampled from each of two taxa at L independent loci, we derive the distribution of the waiting time until the first interspecific coalescence occurs between the two taxa, considering all loci and measuring from the divergence time. We then use the mean of this distribution to derive a correction to the GLASS estimator of pairwise divergence times. We show that our improved estimator, which we call iGLASS, consistently estimates the divergence time between a pair of taxa as the number of loci approaches infinity, and that it is an unbiased estimator of divergence times when one lineage is sampled per taxon. We also show that many commonly used clustering methods can be combined with the iGLASS estimator of pairwise divergence times to produce a consistent estimator of the species tree topology. Through simulations, we show that iGLASS can greatly reduce the bias and mean squared error in obtaining estimates of divergence times in a species tree.     

A method of measuring protein dry weight in solutions of unknown salt concentration and an application to lipoproteins

The dialysis bag dry weight method was developed for the measurement of dry weights of lipoproteins subfractionated on density gradients where total recovery of lipoprotein in the gradient was to be determined. Use of the conventional method for dry weight determination was precluded because of inconsistent concentration changes which would occur in the dialysis step due to differences in both the lipoprotein and salt concentration among gradient fractions. The method described consists of transfer of measured undialyzed samples into previously weighed bags followed by dialysis against water, lyophilization of the protein-bag combination and calculation of the protein dry weight as the difference between the bag weight and the total weight.Since the method described incorporates dialysis in the assay, it is capable of giving an accurate protein dry weight measure of a non-predialyzed sample, whereas the conventional dry weight method gives an accurate value only of a previously dialyzed sample. The increase in the standard deviation of the overall dialysis bag method was shown to be less than double that of the conventional method for a sample of known salt concentration and there is no distinguishable difference in the central values obtained by the two methods.The particular usefulness of this method for lipoprotein solutions was presented.     

A novel method for measuring intracellular pH and potassium concentration

The concentration of Na⁺and K⁺ and the pH in the cytoplasm of Lettré cells was measured by monitoring the net flux of H⁺, Na⁺, or K⁺ across the plasma membrane which had been rendered permeable to these ions by the action of Sendal virus. Ion flux was measured directly by analysis of cell composition, or indirectly by observing the change in membrane potential of cells treated with a specific ionophore. Cytoplasmic concentrations of cations were obtained by establishing the concentration of the cation in the medium at which addition of Sendai virus causes no change in cytoplasmic cation content. The value of Lettré-cell pH was confirmed by direct measurement employing 3tp nuclear magnetic resonance, and the values of Na⁺ and K⁺ concentration were confirmed by analysis of cell cation and water content. Lettré cells suspended at 32°C in Hepes-buffered saline at pH 7.3 maintain a cytosolic pH of 7.0 and contain 30 mM Na⁺ and 80 mM K⁺.