Robust inference of positive selection from recombining coding sequences

MOTIVATION: Accurate detection of positive Darwinian selection can provide important insights to researchers investigating the evolution of pathogens. However, many pathogens (particularly viruses) undergo frequent recombination and the phylogenetic methods commonly applied to detect positive selection have been shown to give misleading results when applied to recombining sequences. We propose a method that makes maximum likelihood inference of positive selection robust to the presence of recombination. This is achieved by allowing tree topologies and branch lengths to change across detected recombination breakpoints. Further improvements are obtained by allowing synonymous substitution rates to vary across sites. RESULTS: Using simulation we show that, even for extreme cases where recombination causes standard methods to reach false positive rates >90%, the proposed method decreases the false positive rate to acceptable levels while retaining high power. We applied the method to two HIV-1 datasets for which we have previously found that inference of positive selection is invalid owing to high rates of recombination. In one of these (env gene) we still detected positive selection using the proposed method, while in the other (gag gene) we found no significant evidence of positive selection. AVAILABILITY: A HyPhy batch language implementation of the proposed methods and the HIV-1 datasets analysed are available at http://www.cbio.uct.ac.za/pub_support/bioinf06. The HyPhy package is available at http://www.hyphy.org, and it is planned that the proposed methods will be included in the next distribution. RDP2 is available at http://darwin.uvigo.es/rdp/rdp.html     

A liquid synchronized-growth culture assay for the identification of true positive and negative yeast three-hybrid transformants

AIMS: To develop a simple and easy-to-use assay for detection of truely positive transformants from a yeast three-hybrid assay. METHODS AND RESULTS: The yeast three-hybrid system is a new powerful system for studying RNA-protein interactions in vivo. There are, however, many reports from investigators about the difficulty in distinguishing a positive from a negative result due to the hard-to-detect differences between truely positive transformants and the negative ones. A liquid synchronous-growth culture approach has been described for all positive and negative transformants and their growth densities have been compared to each other at fixed intervals of incubation times. We have designed a simple yet effective procedure to assay for positive and negative RNA-protein interactions based on liquid culture analysis of synchronously growing yeast cells. Results obtained from this new procedure clearly show differences in positive and negative transformants after a 24-h incubation of synchronously growing transformants in liquid culture. CONCLUSIONS: The procedure mentioned in this report shows clearly the differences between positive and negative results from a three-hybrid system. SIGNIFICANCE AND IMPACT OF THE STUDY: The method proposed here is a clear advantage over existing methods based on measuring growth on restrictive growth medium plates by the naked eye. This method will have substantial usage with investigators using the yeast three-hybrid studies for RNA-protein interactions.     

Alpha activity decreases during the perception of Necker cube reversals: an application of wavelet transform

Since the first observation of perceptual reversal by Necker, many theoretical approaches have been proposed. In a previous study, we showed that a positive wave appeared approximately 250 ms prior to the button press of the subjects, indicating perceptual reversal during the observation of the Necker cube figure. A basic difficulty in this type of study is the possible jitter in the latency of the button press due to the variability of the subjects' reaction time during a recording session. To overcome this difficulty, a pattern selection method based on the wavelet transform was proposed in the previous study. A dominant positive wavelet coefficient in the delta band was found to represent the perceptual-reversal-related positivity. In the present study, we aim to analyze the changes in the alpha frequency band during perceptual reversal by using the Necker cube. The RMS values of the alpha frequency band were measured for two time periods: ±3 SD around the mean peak latency of the perceptual-reversal-related positivity and a time window of the same length before the positive wave. We found significantly increased delta power and decreased alpha power during the perceptual-reversal-related positivity. Received: 29 March 1999 / Accepted in revised form: 15 October 1999     

快速LacZ检测法提高酵母双杂交试验的敏感度

目的：建立快速简单敏感准确的LacZ检测法。方法：将在SD/-Trp-Leu培养液中过培养的待检测酵母菌直接点样在滤纸上进行LacZ检测,筛选出LacZ阳性克隆。结果：将小鼠3T3文加转化含有WWP1的酵母菌,选出10个较大的SD/-Trp-Leu-His培养阳性的克隆,利用快速LacZ检测法检测这10个酵母克隆,结果在5h内不同程度地变蓝,呈阳性结果;而作为对照的传统检测方法在8h内的检测结果均显示为阴性。结论：采用快速LacZ检测法检测蛋白质之间的相互作用可以大大缩短筛选的时间,简化筛选的步骤,增加检测的敏感度和准确性。     

Preparation and Standardisation of Smoke-Water for Seed Germination and Plant Growth Stimulation

Smoke-water (SW) has a positive effect on seed germination in many plant species and its application in various fields of plant science has become popular. The method of preparing SW is relatively easy and inexpensive. However, many researchers working in the field of smoke biology are still unfamiliar with preparing SW and testing it for bioactivity. Thus, the aim of this study was to develop a low-cost efficient apparatus to produce SW using grasses, its standardisation and quantification of major active biomolecules. The prepared crude SW was diluted with distilled water (SW:DW) to 75:25, 50:50 and 25:75 (v/v) and these sub-dilutions were further diluted to 1:500; 1:1000; 1:1500; 1:2000; 1:2500; 1:3000 and 1:3500 (v/v). For the standardisation of SW, lettuce seeds (Lactuca sativa L. cv. Grand Rapids) were tested to determine the best working concentration. The ratio 1:2500 (v/v) from the sub-dilution 25:75 (v/v) of SW was the best for germination of lettuce seeds in the dark, achieving 91% germination against the water control that had only 7–10% germination. This is the first study which reports the levels of stimulatory (karrikinolide 1, KAR₁ and karrikinolide 2, KAR₂) and inhibitory (trimethylbutenolide, TMB) compounds present in SW using ultrahigh-performance liquid chromatography–electrospray positive ionisation tandem mass spectrometry (UHPLC-ESI(+)-MS/MS).

     

Single quadrupole mass spectrometry for pre-clinical pharmacokinetic analysis: quantitation of carvedilol in dog plasma

The pharmaceutical industry standard for bioanalysis is LC/MS/MS. There are, however, many instances where a single quadrupole detector could successfully be used to provide adequate sensitivity and selectivity for quantitation of drug substances in biological matrices. This paper presents one example of how a single quadrupole detector can be employed in a sensitive and selective analytical method for quantitation of carvedilol. A Synergi Hydro-RP (50 mm x 2 mm i.d.; 4 microm) column was used with acetonitile:water:formic acid mobile phase (32:68:0.01, v/v) at a flow rate of 200 microL/min into a single quadrupole mass spectrometer with an electrospray interface in the positive SIM mode. Using a 300 microL plasma aliquot and a liquid-liquid extraction procedure the limit of quantitation for the assay was 1 ng/mL. The assay utility was demonstrated in the analysis of carvedilol pharmacokinetic profiles in beagle dogs following oral carvedilol administration.     

Detection of oligonucleotide-ligand complexes by ESI-MS (DOLCE-MS) as a component of high throughput screening

With the advent of combinatorial chemistry and high throughput screening, a major bottleneck in the pharmaceutical industry has changed from quickly finding active compounds to limiting them to a manageable number for proper follow-up. With hundreds to thousands of active compounds identified by a multitude of biological screens, there need to be rapid and unambiguous methods for eliminating false positive, toxic, or otherwise difficult compounds from further scrutiny. We have used electrospray ionization mass spectrometry as a rapid screening method to identify compounds from viral screens that yield a positive assay response by interaction with DNA rather than inhibiting the target enzyme. Both the sample preparation and data acquisition have been automated, allowing the screening of all hits from relevant biological screens (up to 1,000/week). The assay was validated using several known DNA intercalators and minor groove binders. These "standards" and many but not all of our "active compounds" were shown to form noncovalent complexes with a variety of different DNA:DNA and DNA:RNA duplexes.     

Detection of molecular alterations in methamphetamine‐activated Fos‐expressing neurons from a single rat dorsal striatum using fluorescence‐activated cell sorting (FACS)

Methamphetamine and other drugs activate a small proportion of all neurons in the brain. We previously developed a fluorescence‐activated cell sorting (FACS)‐based method to characterize molecular alterations induced selectively in activated neurons that express the neural activity marker Fos. However, this method requires pooling samples from many rats. We now describe a modified FACS‐based method to characterize molecular alterations in Fos‐expressing dorsal striatal neurons from a single rat using a multiplex pre‐amplification strategy. Fos and NeuN (a neuronal marker) immunohistochemistry indicate that 5–6% of dorsal striatum neurons were activated 90 min after acute methamphetamine injections (5 mg/kg, i.p.) while less than 0.5% of neurons were activated by saline injections. We used FACS to separate NeuN‐labeled neurons into Fos‐positive and Fos‐negative neurons and assessed mRNA expression using RT‐qPCR from as little as five Fos‐positive neurons. Methamphetamine induced 3–20‐fold increases of immediate early genes arc, homer‐2, c‐fos, fosB, and its isoforms (ΔfosB and a novel isoform ΔfosB‐2) in Fos‐positive but not Fos‐negative neurons. Immediate early gene mRNA induction was 10‐fold lower or absent when assessed in unsorted samples from single dorsal striatum homogenates. Our modified method makes it feasible to study unique molecular alterations in neurons activated by drugs or drug‐associated cues in complex addiction models.

     

重组乙型肝炎疫苗(CHO细胞)鉴别试验的方法研究

目的：建立重组乙型肝炎疫苗(CHO细胞)鉴别试验的方法。方法：取重组乙型肝炎疫苗(CHO细胞)以1：10比例加入lmol/L盐酸调节pH值,采用ELISA双抗体夹心法检测,同时设以氢氧化铝、未处理的重组乙型肝炎疫苗、狂犬疫苗、出血热疫苗,以及试剂盒的阴、阳性作为对照。结果：狂犬疫苗、出血热疫苗及氢氧化铝对照为阴性,直接检测重组乙型肝炎疫苗(CHO细胞)呈弱阳性,加入盐酸调节pH值后原倍样品呈弱阳性,10倍稀释后呈强阳性。采用该方法检测5批疫苗均呈强阳性。组内平行试验,组间重复试验。结论：将重组乙型肝炎疫苗(CHO细胞)调节pH值后10倍稀释,用ELISA双抗体夹心法检测呈阳性,而且稳定可靠,该方法可用于该疫苗的鉴别试验。     

Vimentin and leukocyte common antigen-negative molding cells in pleural effusions of patients with small cell lung carcinoma

OBJECTIVE: To determine whether the presence of vimentin and leukocyte common antigen (LCA)-negative molding cells (VLNMC) could help in identifying rare small cell lung carcinoma (SCLC) cells. STUDY DESIGN: Thirty-four cell blocks of pleural effusions (PEs) from 26 patients with confirmed SCLC were stained immunohistochemically with vimentin and LCA antibodies and compared with hematoxylin and eosin-stained preparations. RESULTS: VLNMC were present in 22/22 PEs originally diagnosed as positive or atypical/suspicious for SCLC. Focal vimentin staining was seen in SCLC in 10/22 cases, and 1 case showed many vimentin-positive SCLC cells. One of 11 PEs originally interpreted as negative showed rare groups of VLNMC. This was supported by a subsequent PE obviously positive for SCLC. CONCLUSION: Immunoperoxidase stains for vimentin and LCA highlight SCLC in PEs as VLNMC; however, morphologic criteria must prevail in making the final diagnosis.     

A whole genome long-range haplotype (WGLRH) test for detecting imprints of positive selection in human populations

MOTIVATION: The identification of signatures of positive selection can provide important insights into recent evolutionary history in human populations. Current methods mostly rely on allele frequency determination or focus on one or a small number of candidate chromosomal regions per study. With the availability of large-scale genotype data, efficient approaches for an unbiased whole genome scan are becoming necessary. METHODS: We have developed a new method, the whole genome long-range haplotype test (WGLRH), which uses genome-wide distributions to test for recent positive selection. Adapted from the long-range haplotype (LRH) test, the WGLRH test uses patterns of linkage disequilibrium (LD) to identify regions with extremely low historic recombination. Common haplotypes with significantly longer than expected ranges of LD given their frequencies are identified as putative signatures of recent positive selection. In addition, we have also determined the ancestral alleles of SNPs by genotyping chimpanzee and gorilla DNA, and have identified SNPs where the non-ancestral alleles have risen to extremely high frequencies in human populations, termed 'flipped SNPs'. Combining the haplotype test and the flipped SNPs determination, the WGLRH test serves as an unbiased genome-wide screen for regions under putative selection, and is potentially applicable to the study of other human populations. RESULTS: Using WGLRH and high-density oligonucleotide arrays interrogating 116 204 SNPs, we rapidly identified putative regions of positive selection in three populations (Asian, Caucasian, African-American), and extended these observations to a fourth population, Yoruba, with data obtained from the International HapMap consortium. We mapped significant regions to annotated genes. While some regions overlap with genes previously suggested to be under positive selection, many of the genes have not been previously implicated in natural selection and offer intriguing possibilities for further study. AVAILABILITY: the programs for the WGLRH algorithm are freely available and can be downloaded at http://www.affymetrix.com/support/supplement/WGLRH_program.zip.     

Maximum Likelihood Estimation on Large Phylogenies and Analysis of Adaptive Evolution in Human Influenza Virus A

Algorithmic details to obtain maximum likelihood estimates of parameters on a large phylogeny are discussed. On a large tree, an efficient approach is to optimize branch lengths one at a time while updating parameters in the substitution model simultaneously. Codon substitution models that allow for variable nonsynonymous/synonymous rate ratios (ω=d _N/d _S) among sites are used to analyze a data set of human influenza virus type A hemagglutinin (HA) genes. The data set has 349 sequences. Methods for obtaining approximate estimates of branch lengths for codon models are explored, and the estimates are used to test for positive selection and to identify sites under selection. Compared with results obtained from the exact method estimating all parameters by maximum likelihood, the approximate methods produced reliable results. The analysis identified a number of sites in the viral gene under diversifying Darwinian selection and demonstrated the importance of including many sequences in the data in detecting positive selection at individual sites. Received: 25 April 2000 / Accepted: 24 July 2000     

An assessment of the uses of homologous interactions

MOTIVATION: Protein-protein interactions have proved to be a valuable starting point for understanding the inner workings of the cell. Computational methodologies have been built which both predict interactions and use interaction datasets in order to predict other protein features. Such methods require gold standard positive (GSP) and negative (GSN) interaction sets. Here we examine and demonstrate the usefulness of homologous interactions in predicting good quality positive and negative interaction datasets. RESULTS: We generate GSP interaction sets as subsets from experimental data using only interaction and sequence information. We can therefore produce sets for several species (many of which at present have no identified GSPs). Comprehensive error rate testing demonstrates the power of the method. We also show how the use of our datasets significantly improves the predictive power of algorithms for interaction prediction and function prediction. Furthermore, we generate GSN interaction sets for yeast and examine the use of homology along with other protein properties such as localization, expression and function. Using a novel method to assess the accuracy of a negative interaction set, we find that the best single selector for negative interactions is a lack of co-function. However, an integrated method using all the characteristics shows significant improvement over any current method for identifying GSN interactions. The nature of homologous interactions is also examined and we demonstrate that interologs are found more commonly within species than across species. CONCLUSION: GSP sets built using our homologous verification method are demonstrably better than standard sets in terms of predictive ability. We can build such GSP sets for several species. When generating GSNs we show a combination of protein features and lack of homologous interactions gives the highest quality interaction sets. AVAILABILITY: GSP and GSN datasets for all the studied species can be downloaded from http://www.stats.ox.ac.uk/~deane/HPIV.     

Detection of serum antibodies against Helicobacter pylori using a chromatographic immunoassay in outpatients

OBJECTIVES: The presence of the antibodies against Helicobacter pylori was tested in 163 subjects (children and adults) in the outpatient department, in the years 2005 and 2006. METHODS: Of the 163 investigated patients 108 (66.3%) were females and 55 (33.7%) were males. The antibodies against Helicobacter pylori were determined by "One Step Helicobacter pylori Test Device (Serum/Plasma)" (ACON Laboratories, Inc.), a rapid, high quality chromatographic immunoassay using human antibodies against IgG immobilized and particles covered with Helicobacter pylori antigen, in contact with the serum of the tested subjects. RESULTS: Of the 163 investigated subjects, 60 (36.8%) presented a positive test suggesting the passage through the infection with Helicobacter pylori. The positive tests were found in adults, 1 case was a boy of 12 years and 5 cases were teenagers between 16 and 18 years. The incidence of the antibodies increased with age. Only 40% of the patients with positive test had a clinical diagnosis of gastritis or gastro-duodenal ulcer, the remaining patients presenting symptoms of chronic hepatitis, cholecystitis or urticaria. CONCLUSIONS: Antibody assay is considered by many authors as a simple, noninvasive, rapid method, applicable in the diagnosis of Helicobacter pylori infection. Other authors asserted that the performance of these assays is less satisfactory and the results should be confirmed by other tests, such as ureea breath test. High levels of antibodies against Helicobacter spp. were encountered in liver and biliary chronic diseases, suggesting a possible role of these bacteria in the development of hepatitis or cholecystitis.     

A method to infer positive selection from marker dynamics in an asexual population

MOTIVATION: The observation of positive selection acting on a mutant indicates that the corresponding mutation has some form of functional relevance. Determining the fitness effects of mutations thus has relevance to many interesting biological questions. One means of identifying beneficial mutations in an asexual population is to observe changes in the frequency of marked subsets of the population. We here describe a method to estimate the establishment times and fitnesses of beneficial mutations from neutral marker frequency data. RESULTS: The method accurately reproduces complex marker frequency trajectories. In simulations for which positive selection is close to 5% per generation, we obtain correlations upwards of 0.91 between correct and inferred haplotype establishment times. Where mutation selection coefficients are exponentially distributed, the inferred distribution of haplotype fitnesses is close to being correct. Applied to data from a bacterial evolution experiment, our method reproduces an observed correlation between evolvability and initial fitness defect.     

Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments

PD-(D/E)XK nucleases, initially represented by only Type II restriction enzymes, now comprise a large and extremely diverse superfamily of proteins. They participate in many different nucleic acids transactions including DNA degradation, recombination, repair and RNA processing. Different PD-(D/E)XK families, although sharing a structurally conserved core, typically display little or no detectable sequence similarity except for the active site motifs. This makes the identification of new superfamily members using standard homology search techniques challenging. To tackle this problem, we developed a method for the detection of PD-(D/E)XK families based on the binary classification of profile-profile alignments using support vector machines (SVMs). Using a number of both superfamily-specific and general features, SVMs were trained to identify true positive alignments of PD-(D/E)XK representatives. With this method we identified several PFAM families of uncharacterized proteins as putative new members of the PD-(D/E)XK superfamily. In addition, we assigned several unclassified restriction enzymes to the PD-(D/E)XK type. Results show that the new method is able to make confident assignments even for alignments that have statistically insignificant scores. We also implemented the method as a freely accessible web server at http://www.ibt.lt/bioinformatics/software/pdexk/.     

Detection of tetrodotoxin by thin-layer chromatography/fast atom bombardment mass spectrometry

A new method for detection of tetrodotoxin (TTX) by thin-layer chromatography/fast atom bombardment (FAB) mass spectrometry was developed. TTX and/or related substances were separated by TLC on LHP-K high-performance precoated plates, with a solvent system of pyridine:ethyl acetate:acetic acid:water (15:5:3:4). The plates were subjected to positive FAB mass spectrometry, under scanning within a mass range from m/z 100 to 500. TTX was identified by selected ion-monitored chromatograms at m/z 320 (M + H)+ and 302 (M + H - H2O)+, along with full scan positive ion FAB mass spectrometry. The limit of detection for TTX was about 0.1 micrograms. TTX was also detected by cellulose acetate membrane electrophoresis/FAB mass spectrometry.     

Genome-wide co-expression based prediction of differential expressions

MOTIVATION: Microarrays have been widely used for medical studies to detect novel disease-related genes. They enable us to study differential gene expressions at a genomic level. They also provide us with informative genome-wide co-expressions. Although many statistical methods have been proposed for identifying differentially expressed genes, genome-wide co-expressions have not been well considered for this issue. Incorporating genome-wide co-expression information in the differential expression analysis may improve the detection of disease-related genes. RESULTS: In this study, we proposed a statistical method for predicting differential expressions through the local regression between differential expression and co-expression measures. The smoother span parameter was determined by optimizing the rank correlation between the observed and predicted differential expression measures. A mixture normal quantile-based method was used to transform data. We used the gene-specific permutation procedure to evaluate the significance of a prediction. Two published microarray data sets were analyzed for applications. For the data set collected for a prostate cancer study, the proposed method identified many genes with weak differential expressions. Several of these genes have been shown in literature to be associated with the disease. For the data set collected for a type 2 diabetes study, no significant genes could be identified by the traditional methods. However, the proposed method identified many genes with significantly low false discovery rates. AVAILABILITY: The R codes are freely available at http://home.gwu.edu/~ylai/research/CoDiff, where the gene lists ranked by our method are also provided as the Supplementary Material.     

Using dynamic programming to create isotopic distribution maps from mass spectra

MOTIVATION: This article presents a method to identify the isotopic distributions within a mass spectrum using a probabilistic classifier supplemented with dynamic programming. Such a system is needed for a variety of purposes, including generating robust and meaningful features from mass spectra to be used in classification. RESULTS: The primary result of this article is that the dynamic programming approach significantly improves sensitivity, without harming specificity, of a probabilistic classifier for identifying the isotopic distributions. When annotating isotopic distributions where an expert has performed the initial 'peak-picking' (removal of noise peaks), the dynamic programming approach gives a true positive rate of 96% and a false positive rate of 0.0%, whereas the classifier alone has a true positive rate of only 47% when the false positive rate is 0.0%. When annotating isotopic distributions in machine peak-picked spectra, which may contain many noise peaks, the dynamic programming approach gives a true positive rate of only 22.0%, but it still keeps a low false positive rate of 1.0% and still outperforms the classifier alone. It is important to note that all these rates are when we require exact matches with the distributions in annotated spectra; in our evaluation a distribution is considered 'entirely incorrect' if it is missing even one peak or contains even one extraneous peak. We compared to the THRASH and AID-MS systems using a looser requirement: correctly identifying the distribution that contains the mono-isotopic mass. Under this measure, our dynamic programming approach achieves a true positive rate of 82% and a false positive rate of 1%, which again outperforms the classifier alone. The dynamic programming approach ends up being more conservative than THRASH and AID-MS, yielding both fewer true and false peaks, but the F-score of the dynamic programming approach is significantly better than those of THRASH and AID-MS. All results were obtained with 10-fold cross-validation of 99 sections of mass spectra with a total of 214 hand-annotated isotopic distributions. AVAILABILITY: Programs are available via http://www.cs.wisc.edu/~mcilwain/IDM.     

测定Epstein-Barr病毒IgA/EA抗体的改进方法

用免疫酶法(IE)检查鼻咽癌(NPC)病人血清中IgA/EA抗体,阳性率为73％,几何平均滴度为25,将血清用马抗人IgG血清或葡萄球菌菌体A蛋白(SPA)处理后,以除去竞争性IgG类抗体后,阳性率可增高至92％,几何平均滴度提高到89,有15例NPC病人血清,经马抗人IgG血清处理前IgA/EA抗体为阴性,处理后均呈阳性反应。