A method for delineating structurally homogeneous regions in protein sequences

A homogeneous region in a protein sequence is a set of contiguousresidues that share common features, concerning physsico-chemical,structural and mutational information. This paper presents amethod for identifying such homogeneous regions. From a profiledescribing a given type of biological information along thesequence, the algorithm allows the segmentation of the sequenceby optimizing a criterion characterized by two user-definedcontrol parameters: the ‘homogenizing degree’ ofthe regions and the ‘site neighbourhood’ size. Weapply the method to the envelope proteins of the human immunodeficiencyvirus HIV-1, for the identification of homogeneous regions ina hydrophobicity profile and the delineation of variable andconserved regions in a variability profile.     

A simple and rapid method for calculating identity-by-descent matrices using multiple markers

A fast, partly recursive deterministic method for calculating Identity-by-Descent (IBD) probabilities was developed with the objective of using IBD in Quantitative Trait Locus (QTL) mapping. The method combined a recursive method for a single marker locus with a method to estimate IBD between sibs using multiple markers. Simulated data was used to compare the deterministic method developed in the present paper with a stochastic method (LOKI) for precision in estimating IBD probabilities and performance in the task of QTL detection with the variance component approach. This comparison was made in a variety of situations by varying family size and degree of polymorphism among marker loci. The following were observed for the deterministic method relative to MCMC: (i) it was an order of magnitude faster; (ii) its estimates of IBD probabilities were found to agree closely, even though it does not extract information when haplotypes are not known with certainty; (iii) the shape of the profile for the QTL test statistic as a function of location was similar, although the magnitude of the test statistic was slightly smaller; and (iv) the estimates of QTL variance was similar. It was concluded that the method proposed provided a rapid means of calculating the IBD matrix with only a small loss in precision, making it an attractive alternative to the use of stochastic MCMC methods. Furthermore, developments in marker technology providing denser maps would enhance the relative advantage of this method.     

Distinct modes of blockade in cardiac ATP-sensitive K+ channels suggest multiple targets for inhibitory drug molecules

Elementary K⁺ currents were recorded at 19°C in inside-out patches from cultured neonatal rat cardiocytes to elucidate the block phenomenology in cardiac ATP-sensitive K⁺ channels when inhibitory drug molecules, such as the sulfonylurea glibenclamide, the phenylalkylamine verapamil or sulfonamide derivatives (HE 93 and sotalol), are interacting in an attempt to stress the hypothesis of multiple channel-associated drug targets.Similar to their adult relatives, neonatal cardiac K_(ATP) channels are characterized by very individual open state kinetics, even in cytoplasmically well-controlled, cell-free conditions; at –7 mV, _open(1) ranged from 0.7 to 4.9 msec in more than 200 patches and _open(2) from 10 to 64 msec—an argument for a heterogeneous channel population. Nevertheless, a common response to drugs was observed. Glibenclamide and the other inhibitory molecules caused long-lasting interruptions of channel activity, after cytoplasmic application, as if drug occupancy trapped cardiac K_(ATP) channels in a very stable, nonconducting configuration. The resultant NP ₀ depression was strongest with glibenclamide (apparent IC₅₀ 13 nmol/liter) and much weaker with verapamil (apparent IC₅₀ 9 mol/liter), HE 93 (apparent IC₅₀ 29 mol/liter) and sotalol (apparent IC₅₀ 43 mol/ liter) and may have resulted from the occupancy of a single site with drug-specific affinity or of two sites, the high affinity glibenclamide target and a distinct nonglibenclamide, low affinity target.Changes in open state kinetics, particularly in the transition between the O₁ state and the O₂ state, are other manifestations of drug occupancy of the channel. Any inhibitory drug molecule reduced the likelihood of attaining the O₂ state, consistent with a critical reduction of the forward rate constant governing the O₁-O₁ transition. But only HE 93 (10 mol/liter) associated (with an apparent association rate constant of 2.3 × 10⁶ mol^–1 sec^–1) to shorten significantly _open(2) to 60.6 ± 6% of the predrug value, not the expected result when the entrance in and the exit from the O₂ state would be drug-unspecifically nfluenced. Sotalol found yet another and definitely distinctly located binding site to interfere with K⁺ permeation; both enantiomers associated with a rate close to 5×10⁵ mol^–1 sec^–1 with the open pore thereby flicker-blocking cardiac K_(ATP) channels. Clearly, these channels accommodate more than one drug-binding domain.     

A device for simultaneously controlling multiple treatment levels of dissolved oxygen in laboratory experiments

Hypoxia is common in freshwater, estuarine, and shallow or enclosed marine systems. Research on the sub-lethal effects of hypoxia on feeding and growth includes both field and laboratory studies. Extended regulation of dissolved oxygen (DO) is difficult to precisely control in the laboratory. Here we describe a device that is capable of simultaneously monitoring and controlling DO at multiple treatment levels, in replicate experimental tanks, for indefinite periods of time. Each treatment level may be static or fluctuate on a diel cycle. The device consists of a series of independent aquarium systems, each of which is monitored and adjusted by a computer program. A data file and chart of DO levels in each treatment level is recorded. A computer program that repeatedly measures and adjusts DO controls the device. Because this apparatus is software-controlled, the user has the flexibility of altering treatment parameters at any time without interrupting experiments.     

Probing possible egress channels for multiple ligands in human CYP3A4: A molecular modeling study

Human cytochrome P450 (CYP) 3A4 extensively contributes to metabolize 50% of the marketed drugs. Recently, a CYP3A4 structure with two molecules of ketoconazole (2KT) was identified. However, channels for egresses of these inhibitors are unexplored. Thus, we applied molecular dynamics simulations followed by channel analyses. Two simulations of empty and 2KT-bound CYP3A4 results revealed the multiple ligand-induced conformational changes in channel forming regions, which appear to be important for the regulation of channels. In addition, we observed that the channel-3 entrance is closed due to the large structural deviation of the key residues from Phe-cluster. F215 and F220 are known as entrance blockers of channel-2 in metyrapone-bound CYP3A4. Currently, F220 blocks the channel-3 along with F213 and F241. Therefore, it suggested that channel-1 and 2 could potentially serve as egress routes for 2KT. It is also supported by the results from MOLAxis analyses, in which the frequency of channel occurrence and bottleneck radius during simulation favor channel-1 and 2. Several bottleneck residues of these channels may have critical roles in 2KT egresses, especially S119. Our modeling study for multiple ligand-channeling of CYP3A4 could be very helpful to gain new insights into channel selectivity of CYP3A4.     

用便携式光谱仪同步测定和计算光强和光质的新方法

外界光强和光质对植物的影响在植物生理生态研究领域中一直受到高度关注。而测定光强的光量子计不能测定光质; 测定光质的光谱仪不能直接测定光强, 两者均不能同步测定光强和光质。该文作者建立了一个基于光谱仪测定条件的能量与光量子的经验转换公式, 用4只不同波长的窄带发光二极管(LED)光源结合光量子计(LI-190SB)对便携式光谱仪(AvaSpec-ULS2048×64)所获得的光谱进行了快速标定, 实现了用便携式光谱仪同步直接测定光量子通量密度和光质的目的。在自然光照条件下, 采用转换公式计算出光量子通量密度(PPFD)与实测的PPFD之间误差在-2%-5%范围内, 证实了这种方法的可靠性。通过这个新方法, 可以极大地拓宽便携式光谱仪的适用范围: 1)实验室内或野外只需用便携式光谱仪即可对光源及植物生长的光强和光质环境进行同步精确测定和计算; 2)可以计算光谱仪测定范围内任意波长区段的光量子通量密度; 3)无需采用标准光源即可获得绝对辐射(光)通量值。因此, 这项技术在植物生理生态研究领域具有广阔的应用前景。     

A new method to measure and calculate light intensity and light quality simultaneously by using portable spectrometer

The influence of light intensity and light quality on plants is highly concerned in the field of plant physiology and ecology. However, the calibrated quantum meter for measurement of light intensity cannot measure light quality, and vice versa. Here we developed an empirical formula to convert light energy to photon flux density, based on the measurement conditions of spectrometer. Under the guide of the formula, a portable spectrometer (AvaSpec-ULS2048×64) was calibrated by using four narrowband light emitting diode (LEDs) in combination with a calibrated quantum meter (LI-190SB). After calibration of the spectrometer, we can calculate photosynthetic photon flux density (PPFD or PAR) and measure spectrum of radiation flux simultaneously. Under natural light conditions, the errors between measured and calculated PPFDs are in the range from -2% to 5%, indicating the reliability of the method. With this new approach, the application of portable spectrometer can be greatly broadened: 1) the light intensity and quality of light source and plant growth light environment can be obtained simultaneously, 2) PPFD can be obtained within any specified wavelength range, and 3) there is no need to use standard light source to obtain the absolute light/radiation flux of a spectrum measured by spectrometer. In conclusion, this method has potential applications for the study of plant physiology and ecology.     

A rapid procedure for visualising the inner cell mass and trophectoderm nuclei of mouse blastocysts in situ using polynucleotide-specific fluorochromes

A rapid procedure has been devised to count the numbers of outer trophectoderm (TE) and inner cell mass (ICM) cells of mouse blastocysts by differentially labelling their nuclei in situ with polynucleotide-specific fluorochromes. The TE nuclei were labelled with propidium iodide (PI) by permeabilising the cells using selective antibody-mediated complement lysis (Solter and Knowles, '75). The blastocysts were then fixed in ethanol and the ICM nuclei labelled with bisbenzimide. These two fluorochromes have widely different fluorescent spectra. Thus, by using fluorescence microscopy with appropriate filter combinations, the PI-labelled TE nuclei appeared pink or red; the bisbenzimide-labelled ICM nuclei, blue or unlabelled. The total numbers of blastocyst nuclei and the numbers of ICM nuclei counted by differential labelling were similar to the numbers detected after spreading the nuclei of intact blastocysts or immunosurgically isolated ICMs by air-drying (Tarkowski '66). Differential labelling of TE and ICM nuclei in situ has two important advantages--that the numbers of both these cell types can be determined for individual blastocysts and that spatial relationships are partially preserved so that regional interactions can be studied.     

An improved method for detecting and delineating genomic regions with altered gene expression in cancer

Genomic regions with altered gene expression are a characteristic feature of cancer cells. We present a novel method for identifying such regions in gene expression maps. This method is based on total variation minimization, a classical signal restoration technique. In systematic evaluations, we show that our method combines top-notch detection performance with an ability to delineate relevant regions without excessive over-segmentation, making it a significant advance over existing methods. Software (Rendersome) is provided.     

A simplified HPLC method for simultaneously quantifying ribonucleotides and deoxyribonucleotides in cell extracts or frozen tissues

Agents and conditions that induce alterations in deoxyribonucleotide pools can have important regulatory effects on the rate of DNA synthesis as well as cell cycle progression. A simplified procedure for the separation of both ribonucleoside triphos-phates (NTP) and deoxyribonucleoside triphosphates (dNTP) is presented which utilizes reversed phase high-performance liquid chromatography coupled with diode array detection. The simultaneous resolution of NTP and dNTP peaks within the same cell extract effectively eliminates the need for post-extraction steps such as periodate oxidation and/or boronate affinity chromatography previously used to degrade or isolate co-eluting NTP from dNTP. The resolution of two nucleotides, dGTP and ADP, was found empirically to vary with the efficiency of the C18 column. High efficiency columns (>90 000 plates/m) provided good separation; however, less efficient columns resulted in co-elution of dGTP and ADP. These co-eluting nucleotides can be accurately quantified, if necessary, using diode array technology and a mathematical expression which incorporates molar peak coefficients and peak areas obtained by monitoring at dual wavelengths. Tissue samples or single cell suspensions were extracted with trichloroacetic acid and the neutralized extract was injected directly into the column without prior lyophilization. The per cent recovery of standards was .99% and replicate extractions within or between samples were highly reproducible (sd<5%). The single step method described minimizes potential losses associated with post-extraction manipulation and provides the capability to examine alterations in nucleotide precursor–product metabolism under various physiological and pharmacological conditions.     

Set-size effects for spatial frequency change and discrimination in multiple targets

In visual search tasks with a near-threshold target amongst distracters, log detection thresholds rise in proportion to the log of the number of stimuli. Previous research has shown a very steep slope for this set-size effect where the target is a change in spatial frequency (SF) across an ISI, suggesting a low-level explanation for 'change blindness (Wright et al., 2000). Here, we analyse stimulus and task variables in order to determine the contributions of stimulus detection and attention processes. Stimuli consisted of two 150 ms frames each containing 1 to 4 Gabor targets, with an ISI of 250 ms. In a 2AFC detection task with uniform distracters, slopes of 0.23-0.52 were found, in line with visual search results. 2AFC SF discrimination tasks gave slopes of 0.68, 0.69 with homogeneous distracters and 0.76-0.96 with inhomogeneous distracters, consistent with averaging of stimuli within a frame. If the distracters were also made to change across ISI, averaging was impossible, and focal attention was required to solve the discrimination. This always gave set-size slopes > 1. It is concluded that, under conditions where a stimulus array can be analysed globally, change detection performance is limited by signal detection mechanisms, rather than limited capacity attention or memory mechanisms. However, where this is prevented, for example by changing more than one item, limitations due to attention or memory produce an even steeper set-size effect.     

The PASDORO method for simultaneously demonstrating DNA and lipids in the brain

Conclusions and summary The PASDORO method has the advantage of allowing DNA and globular lipid to be demonstrated in frozen sections of formalin-fixed tissue. Its disadvantage is that, in most tissues, basement membrane staining interferes with the selective demonstration of DNA. However, in the central nervous system it is advantageous to be, able to trace capillary basement membrane. In this way cells related to the capillary endothelium can be easily identified. The addition of staining with Oil Red O to the basic PASD technique permits lipid-laden microglia to be readily identified around necrotic and demyelinating lesions.     

A fast, efficient and sequence-independent method for flexible multiple segmental isotope labeling of RNA using ribozyme and RNase H cleavage

Structural information on RNA, emerging more and more as a major regulator in gene expression, dramatically lags behind compared with information on proteins. Although NMR spectroscopy has proven to be an excellent tool to solve RNA structures, it is hampered by the severe spectral resonances overlap found in RNA, limiting its use for large RNA molecules. Segmental isotope labeling of RNA or ligation of a chemically synthesized RNA containing modified nucleotides with an unmodified RNA fragment have proven to have high potential in overcoming current limitations in obtaining structural information on RNA. However, low yields, cumbersome preparations and sequence requirements have limited its broader application in structural biology. Here we present a fast and efficient approach to generate multiple segmentally labeled RNAs with virtually no sequence requirements with very high yields (up to 10-fold higher than previously reported). We expect this approach to open new avenues in structural biology of RNA.