TESTLoc: protein subcellular localization prediction from EST data

Background  

The eukaryotic cell has an intricate architecture with compartments and substructures dedicated to particular biological processes. Knowing the subcellular location of proteins not only indicates how bio-processes are organized in different cellular compartments, but also contributes to unravelling the function of individual proteins. Computational localization prediction is possible based on sequence information alone, and has been successfully applied to proteins from virtually all subcellular compartments and all domains of life. However, we realized that current prediction tools do not perform well on partial protein sequences such as those inferred from Expressed Sequence Tag (EST) data, limiting the exploitation of the large and taxonomically most comprehensive body of sequence information from eukaryotes.     

A microprocessor-regulated constant voltage, current, wattage, and temperature electrophoresis power supply

The analog control circuitry typically found in commercial electrophoresis power supplies was replaced by a digital microcomputer. Analog to digital converters were used to monitor the voltage applied to and current passed through an electrophoresis cell. Microcomputer programming was employed to compare converter input values with preselected operating parameters and then calculate a required output voltage. Timing sequences were generated through programming utilizing clocks located on the interface boards. A digital to analog converter was employed to apply a control voltage to a constant voltage power supply. This process was completed at least 20 times each second. BASIC programming subroutines were written to maintain constant voltage, current, power (wattage), and temperature. To these operating procedures, other techniques such as automated endpoint detection of isoelectric focusing and pulsed waveform outputs were easily added. This power supply containing a microcomputer system as the feedback element was shown to have a greater stability and versatility than conventional supplies.     

Wiener analysis of nonlinear systems using Poisson-Charlier crosscorrelation

Nonlinear systems with event-sequence input, such as are often encountered in neurophysiology, may be experimentally tested with all possible input sequences by stimulation with a Poisson process eventsequence. A complete predictive model of the system's response may be constructed from this data with the Wiener expansion based on the Poisson-Charlier polynomials. Here it is shown how this formulation leads to an efficient method for the evaluation of unknown systems by crosscorrelation, generalizing previous methods. The basic statistical properties of the procedure are demonstrated and the length of experiment required for accurate estimation of the model is computed. The procedure is translated into digital algorithms and the analogous procedures for white noise analysis are presented.     

A polychromator-based microspectrophotometer

A microspectrophotometer is a digital microscope used to measure absorption and fluorescence spectra. In this paper we describe a polychromator-based microspectrophotometer that performs in vivo absorption or emission measurements at the same time on different subcellular compartments such as photoreceptive and photosynthetic structures of algal cells. In this system, a flat field imaging concave grating polychromator is connected to the slit-shaped exit pupil of a light-guide probe mounted onto a microscope equipped with an epifluorescence module. The subcellular components, on which the spectra will be measured, are placed in the microscope field and finely adjusted. The outer bundle of the probe is used for centering the objects, while the central bundle of the probe, containing 19 light guides, is used for acquiring either transmitted or emitted light (i.e. fluorescence). The light transmitted or emitted by the subcellular components is collected by the probe mounted in the back focal plane of the ocular. The exit pupil of this probe, connected to a flat field imaging concave grating polychromator, produces a dispersion image that in turn is focused onto a digital slow scan cooled CCD camera. Absorption and emission spectra of algal subcellular compartments are presented.     

Generation of phospholipid vesicle-nanotube networks and transport of molecules therein

We describe micromanipulation and microinjection procedures for the fabrication of soft-matter networks consisting of lipid bilayer nanotubes and surface-immobilized vesicles. These biomimetic membrane systems feature unique structural flexibility and expandability and, unlike solid-state microfluidic and nanofluidic devices prepared by top-down fabrication, they allow network designs with dynamic control over individual containers and interconnecting conduits. The fabrication is founded on self-assembly of phospholipid molecules, followed by micromanipulation operations, such as membrane electroporation and microinjection, to effect shape transformations of the membrane and create a series of interconnected compartments. Size and geometry of the network can be chosen according to its desired function. Membrane composition is controlled mainly during the self-assembly step, whereas the interior contents of individual containers is defined through a sequence of microneedle injections. Networks cannot be fabricated with other currently available methods of giant unilamellar vesicle preparation (large unilamellar vesicle fusion or electroformation). Described in detail are also three transport modes, which are suitable for moving water-soluble or membrane-bound small molecules, polymers, DNA, proteins and nanoparticles within the networks. The fabrication protocol requires ～90 min, provided all necessary preparations are made in advance. The transport studies require an additional 60-120 min, depending on the transport regime.     

A sense of closeness: protein detection by proximity ligation

Highly specific and sensitive procedures will be required to evaluate proteomes. Proximity ligation is a recently introduced mechanism for protein analysis. In this technique, the convergence of sets of protein-binding reagents on individual target molecules juxtaposes attached nucleic acid sequences. Through a ligation reaction a DNA reporter sequence is created, which can be amplified. The procedure thus encodes detected proteins as specific nucleic acid sequences in what may be viewed as a reverse translation reaction.     

Nanomechanics of vascular endothelium

The mechanical characteristics of endothelial cells reveal four distinct compartments, namely glycocalyx, cell cortex, cytoplasm and nucleus. There is accumulating evidence that endothelial nanomechanics of these individual compartments control vascular physiology. Depending on protein composition, filament formation and interaction with cross-linker proteins, these four compartments determine endothelial stiffness. Structural organization and mechanical properties directly influence physiological processes such as endothelial barrier function, nitric oxide release and gene expression. This review will focus on endothelial nanomechanics and its impact on vascular function.     

Inferring evolutionary rates using serially sampled sequences from several populations

The estimation of evolutionary rates from serially sampled sequences has recently been the focus of several studies. In this paper, we extend these analyzes to allow the estimation of a joint rate of substitution, omega, from several evolving populations from which serial samples are drawn. In the case of viruses evolving in different hosts, therapy may halt replication and therefore the accumulation of substitutions in the population. In such cases, it may be that only a proportion, p, of subjects are nonresponders who have viral populations that continue to evolve. We develop two likelihood-based procedures to jointly estimate p and omega, and empirical Bayes' tests of whether an individual should be classified as a responder or nonresponder. An example data set comprising HIV-1 partial envelope sequences from six patients on highly active antiretroviral therapy is analyzed.     

The J-domain proteins of Arabidopsis thaliana: an unexpectedly large and diverse family of chaperones

A total of 89 J-domain proteins were identified in the genome of the model flowering plant Arabidopsis thaliana. The deduced amino acid sequences of the J-domain proteins were analyzed for an assortment of structural features and motifs. Based on the results of sequence comparisons and structure and function predictions, 51 distinct families were identified. The families ranged in size from 1 to 6 members. Subcellular localizations of the A thaliana J-domain proteins were predicted; species were found in both the soluble and membrane compartments of all cellular organelles. Based on digital Northern analysis, the J-domain proteins could be separated into groups of low, medium, and moderate expression levels. This genomics-based analysis of the A thaliana J-domain proteins establishes a framework for detailed studies of biological function and specificity. It additionally provides a comprehensive basis for evolutionary comparisons.     

Using digital pedometers to monitor travel of cows grazing arid rangeland

Cows grazing large (3000+ ha) arid rangeland paddocks were fitted with digital pedometers. Raw pedometer readings should be corrected for instrument and cow biases by calibrating the pedometers to individual cows, because both cows and pedometers exhibited substantial variability. If routine procedures are followed for recording pedometer readings and adjusting them with the calibration information, digital pedometers appear to be a promising tool to monitor travel of grazing cows. In the context of this study, age of cow and pregnancy status had no apparent effect on the distance these mature cows traveled. However, genotype, external parasites and movement of the herd to a new paddock did have an influence. Because mean daily travel of grazing cows appears to be influenced by management decisions, the impact of various management alternatives deserves further research. Bipedometered cows can contribute to such research, but this work shows that accurate comparisons of distances traveled require a substantial number of bipedometered cows.     

Inconsistency of phylogenetic estimates from concatenated data under coalescence

Although multiple gene sequences are becoming increasingly available for molecular phylogenetic inference, the analysis of such data has largely relied on inference methods designed for single genes. One of the common approaches to analyzing data from multiple genes is concatenation of the individual gene data to form a single supergene to which traditional phylogenetic inference procedures - e.g., maximum parsimony (MP) or maximum likelihood (ML) - are applied. Recent empirical studies have demonstrated that concatenation of sequences from multiple genes prior to phylogenetic analysis often results in inference of a single, well-supported phylogeny. Theoretical work, however, has shown that the coalescent can produce substantial variation in single-gene histories. Using simulation, we combine these ideas to examine the performance of the concatenation approach under conditions in which the coalescent produces a high level of discord among individual gene trees and show that it leads to statistically inconsistent estimation in this setting. Furthermore, use of the bootstrap to measure support for the inferred phylogeny can result in moderate to strong support for an incorrect tree under these conditions. These results highlight the importance of incorporating variation in gene histories into multilocus phylogenetics.     

Quantification of fluorescence in situ hybridization signals by image cytometry.

In this study we aimed at the development of a cytometric system for quantification of specific DNA sequences using fluorescence in situ hybridization (ISH) and digital imaging microscopy. The cytochemical and cytometric aspects of a quantitative ISH procedure were investigated, using human peripheral blood lymphocyte interphase nuclei and probes detecting high copy number target sequences as a model system. These chromosome-specific probes were labeled with biotin, digoxigenin, or fluorescein. The instrumentation requirements are evaluated. Quantification of the fluorescence ISH signals was performed using an epi-fluorescence microscope with a multi-wavelength illuminator, equipped with a cooled charge couple device (CCD) camera. The performance of the system was evaluated using fluorescing beads and a homogeneously fluorescing specimen. Specific image analysis programs were developed for the automated segmentation and analysis of the images provided by ISH. Non-uniform background fluorescence of the nuclei introduces problems in the image analysis segmentation procedures. Different procedures were tested. Up to 95% of the hybridization signals could be correctly segmented using digital filtering techniques (min-max filter) to estimate local background intensities. The choice of the objective lens used for the collection of images was found to be extremely important. High magnification objectives with high numerical aperture, which are frequently used for visualization of fluorescence, are not optimal, since they do not have a sufficient depth of field. The system described was used for quantification of ISH signals and allowed accurate measurement of fluorescence spot intensities, as well as of fluorescence ratios obtained with double-labeled probes.     

Human immunodeficiency virus type 1 genomic RNA sequences in the female genital tract and blood: compartmentalization and intrapatient recombination

Investigation of human immunodeficiency virus type 1 (HIV-1) in the genital tract of women is crucial to the development of vaccines and therapies. Previous analyses of HIV-1 in various anatomic sites have documented compartmentalization, with viral sequences from each location that were distinct yet phylogenetically related. Full-length RNA genomes derived from different compartments in the same individual, however, have not yet been studied. Furthermore, although there is evidence that intrapatient recombination may occur frequently, recombinants comprising viruses from different sites within one individual have rarely been documented. We compared full-length HIV-1 RNA sequences in the plasma and female genital tract, focusing on a woman with high HIV-1 RNA loads in each compartment who had been infected heterosexually and then transmitted HIV-1 by the same route. We cloned and sequenced 10 full-length HIV-1 RNA genomes from her genital tract and 10 from her plasma. We also compared viral genomes from the genital tract and plasma of four additional heterosexually infected women, sequencing 164 env and gag clones obtained from the two sites. Four of five women, including the one whose complete viral sequences were determined, displayed compartmentalized HIV-1 genomes. Analyses of full-length, compartmentalized sequences made it possible to document complex intrapatient HIV-1 recombinants that were composed of alternating viral sequences characteristic of each site. These findings demonstrate that the genital tract and blood harbor genetically distinct populations of replicating HIV-1 and provide evidence that recombination between strains from the two compartments contributes to rapid evolution of viral sequence variation in infected individuals.     

A comparison of the influence of global functional loads vs. local contact anatomy on articular cartilage thickness at the knee

Cartilage contact geometry, along with joint loading, can play an important role in determining local articular cartilage tissue stress. Thus individual variations in cartilage thickness can be associated with both individual variations in joint loading associated with activities of daily living as well as individual differences in the anatomy of the contacting surfaces of the joint. The purpose of this study was to isolate the relationship between cartilage thickness predicted by individual variations in contact surface geometry based on the radii of the femur and tibia vs. cartilage thickness predicted by individual variations in joint loading. Knee magnetic resonance (MR) images and the peak knee adduction moments during walking were obtained from 11 young healthy male subjects (age 30.5+/-5.1 years). The cartilage thicknesses and surface radii of the femoral and tibial cartilage were measured in the weight-bearing regions of the medial and lateral compartments of three-dimensional models from the MR images. The ratio of contact pressure between the medial and lateral compartments was calculated from the radii of tibiofemoral contact surface geometries. The results showed that the medial to lateral pressure ratios were not correlated with the medial to lateral cartilage thickness ratios. However, in general, pressure was higher in the lateral than medial compartments and cartilage was thicker in the lateral than medial compartments. The peak knee adduction moment showed a significant positive linear correlation with medial to lateral thickness ratio in both femur (R(2)=0.43,P<0.01) and tibia (R(2)=0.32,P<0.01). The results of this study suggest that the dynamics of walking is an important factor to describe individual differences in cartilage thickness for normal subjects.     

Search-based optimization

The problem of determining the minimum cost hypothetical ancestral sequences for a given cladogram is known to be NP-complete (Wang and Jiang, 1994). Traditionally, point estimations of hypothetical ancestral sequences have been used to gain heuristic, upper bounds on cladogram cost. These include procedures with such diverse approaches as non-additive optimization of multiple sequence alignment, direct optimization (Wheeler, 1996), and fixed-state character optimization (Wheeler, 1999). A method is proposed here which, by extending fixed-state character optimization, replaces the estimation process with a search. This form of optimization examines a diversity of potential state solutions for cost-efficient hypothetical ancestral sequences and can result in greatly more parsimonious cladograms. Additionally, such an approach can be applied to other NP-complete phylogenetic optimization problems such as genomic break-point analysis.     

Structured exploratory data analysis (SEDA) of finger ridge-count inheritance: I. Major gene index, midparental correlation, and offspring-between-parents function in 125 south Indian families

Fourteen dermatoglyphic traits measured on 125 Velanadu Brahmin families were analyzed for mode of inheritance using three Structured Exploratory Data Analysis (SEDA) statistics: the major gene index, the offspring between parents function, and the traditional midparental correlation coefficient. Since the traits are integer valued with restricted ranges of variation, we simulated various transmission models with discrete expression to better understand the nature of the SEDA statistics for such variables. In addition, permutation procedures were employed to aid the interpretation of the SEDA results. These analyses suggest that corresponding homologous fingers on the left and right hands exhibit similar transmission characteristics. The relationship of the parent and child total ridge-counts of the two hands separately, as well as their combined total, virtually simulate complete Galtonian blending inheritance. Results for the individual digital ridge-counts as well as the pattern-intensity-index variable also suggest a multifactorial mode of transmission or possibly one involving several genes.     

Simple Bulk Readout of Digital Nucleic Acid Quantification Assays

Digital assays are powerful methods that enable detection of rare cells and counting of individual nucleic acid molecules. However, digital assays are still not routinely applied, due to the cost and specific equipment associated with commercially available methods. Here we present a simplified method for readout of digital droplet assays using a conventional real-time PCR instrument to measure bulk fluorescence of droplet-based digital assays.We characterize the performance of the bulk readout assay using synthetic droplet mixtures and a droplet digital multiple displacement amplification (MDA) assay. Quantitative MDA particularly benefits from a digital reaction format, but our new method applies to any digital assay. For established digital assay protocols such as digital PCR, this method serves to speed up and simplify assay readout.Our bulk readout methodology brings the advantages of partitioned assays without the need for specialized readout instrumentation. The principal limitations of the bulk readout methodology are reduced dynamic range compared with droplet-counting platforms and the need for a standard sample, although the requirements for this standard are less demanding than for a conventional real-time experiment. Quantitative whole genome amplification (WGA) is used to test for contaminants in WGA reactions and is the most sensitive way to detect the presence of DNA fragments with unknown sequences, giving the method great promise in diverse application areas including pharmaceutical quality control and astrobiology.     

Immunogold quantification of amino acids and proteins in complex subcellular compartments

An increasing number of imaging techniques are in use to study the localization of molecules involved in cell-to-cell signaling. Here we describe the use of immunogold procedures to detect and quantify molecules on electron micrographs. To measure the areas of the subcellular compartments under investigation, the protocol uses an overlay screen with an array of regularly spaced points. On the basis of this, the densities of the gold-labeled molecules can be calculated. Despite the limited lateral resolution of the immunogold method as used by many investigators ( approximately 30 nm), it is possible to measure the content of molecules associated with tiny tissue compartments, e.g., synaptic vesicles and different types of membrane, such as plasma membranes and vesicle membranes. The quantification protocol can be carried out without using computer programs. The entire protocol can be completed in approximately 15 d.     

Studies on peroxisomes III. Further studies on the intraparticulate localization of peroxisomal components in the liver of the rat

The peroxisome-rich fraction prepared from rat liver homogenate was treated by various procedures and the behavior of the peroxisomal core on sucrose density gradient centrifugation was investigated.Peroxisomes were destroyed by various treatments, such as pH 9.0, VirTis blender, sonication and deoxycholate, resulting in the solubilization of catalase from the particles. Urate oxidase was not solubilized at all such treatments. Although D-amino acid oxidase was solubilized by treatments with deoxycholate and VirTis blender, this enzyme was found to be resistant to solubilization by treatment with pH 9.0 or sonication, in contrast to catalase.When the peroxisomal core was investigated, using urate oxidase activity as a marker, its density proved to be changed when submitted to various treatments. These results indicated that the peroxisomes consist of four compartments: a catalase-containing compartment (matrix), a urate oxidase containing compartment (core), a D-amino acid oxidase containing compartment and a low density compartment which is proposed for the first time in the present paper. Furthermore, it was also found that the last two compartments seem to be bound to the core, though the binding might be weak.     

A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome

We develop a probabilistic system for predicting the subcellular localization of proteins and estimating the relative population of the various compartments in yeast. Our system employs a Bayesian approach, updating a protein's probability of being in a compartment, based on a diverse range of 30 features. These range from specific motifs (e.g. signal sequences or the HDEL motif) to overall properties of a sequence (e.g. surface composition or isoelectric point) to whole-genome data (e.g. absolute mRNA expression levels or their fluctuations). The strength of our approach is the easy integration of many features, particularly the whole-genome expression data. We construct a training and testing set of approximately 1300 yeast proteins with an experimentally known localization from merging, filtering, and standardizing the annotation in the MIPS, Swiss-Prot and YPD databases, and we achieve 75 % accuracy on individual protein predictions using this dataset. Moreover, we are able to estimate the relative protein population of the various compartments without requiring a definite localization for every protein. This approach, which is based on an analogy to formalism in quantum mechanics, gives better accuracy in determining relative compartment populations than that obtained by simply tallying the localization predictions for individual proteins (on the yeast proteins with known localization, 92% versus 74%). Our training and testing also highlights which of the 30 features are informative and which are redundant (19 being particularly useful). After developing our system, we apply it to the 4700 yeast proteins with currently unknown localization and estimate the relative population of the various compartments in the entire yeast genome. An unbiased prior is essential to this extrapolated estimate; for this, we use the MIPS localization catalogue, and adapt recent results on the localization of yeast proteins obtained by Snyder and colleagues using a minitransposon system. Our final localizations for all approximately 6000 proteins in the yeast genome are available over the web at: http://bioinfo.mbb.yale. edu/genome/localize.