Multilocus consensus genetic maps (MCGM): formulation, algorithms, and results

In process of creating genetic maps different labs/research groups obtain overlapping parts of the map. Merging these parts into one integrative map is based on looking for maximum shared marker orders among the maps. Really, not all shared markers of such maps have consensus order that obstructs building of the integrative maps. In this paper we propose a new approach to build verified multilocus consensus genetic maps in which shared markers always are integrated in stable consensus order. The approach is based on combined analysis of initial mapping data rather than manipulating with previously constructed maps. We show that more effective and reliable solutions may be obtained based on "synchronized ordering" facilitated by cycles of "re-sampling-->ordering-->removing unstable markers". The proposed formulation of consensus genetic mapping can be considered as a version of traveling salesperson problem (TSP) that we refer to as synchronized-TSP. From the viewpoint of optimization, synchronized-TSP belongs to discrete constrained optimization problems. Earlier we developed new powerful and fast guided evolution strategy algorithms for some types of discrete constrained optimization. These algorithms were used here as a basis for solving more challenging problems of consensual marker ordering.     

The kinetic and thermodynamic study of the removal of Cr(VI) ion from aqueous solution by human hair waste

The removal of Cr(VI) ions from aqueous solution by human hair waste is investigated by using UV–Vis spectrophotometer technique. The morphological analysis of the human hair was also investigated by the scanning electron microscopy, Fourier transforms infrared spectroscopy and X-ray photoelectron spectroscopy. The influence of various physicochemical effective parameters such as pH, ionic strength, adsorbent amount, contact time, initial concentration of metal ion on removal of Cr(VI) ions by human hair process was also studied. The optimum conditions for this adsorption process were obtained at pH = 2 and contact time of 150 min while the highest Cr(VI) uptake is recorded for 0.5 g of the adsorbent per 100 ml of solution. Three isotherms models including Langmuir, Freundlich and Temkin were applied to describe the equilibrium data. It was found that the experimental data were well described by Freundlich isothermal model. The maximum adsorption capacity was found to be 11.64 mg g^?1.The thermodynamic study data showed that the adsorption process of Cr(VI) on human hair is an endothermic, spontaneous and physisorption reaction. The kinetics of the adsorption process was studied using three kinetics models including Lagergren-first-order, pseudo-second-order and Elovich model. The obtained data are indicated that the adsorption processes of Cr(VI) over human hair could be described by the pseudo-second-order kinetic model.     

人发微量元素与性别关系的模式识别分类研究

通过对人发样品中22种元素含量的数据进行变量扩维及压缩筛选处理,选出了影响性别判断较显著的变量,用PLS法处理这些变量组成的数据,得到男性与女性分类清晰的二维判别图及预报模型,并根据所建立的预报模型及人发微量元素的含量判别人的性别,准确率为81%.     

Generalised 2D-correlation NMR analysis of a wine fermentation

A wine fermentation has been monitored on a daily basis by (1)H NMR spectroscopy. Following data pre-processing that includes synthesis of the spectra to ensure all peaks are of constant half-width, the series of spectra were examined using generalised two-dimensional correlation techniques. Synchronous and asynchronous data maps have been generated and employed to interpret the changes in the fermentation process as a function of time. The results illustrate the potential of high resolution NMR with multivariate data analysis as a tool for process monitoring and the manner in which two-dimensional correlation mapping can aid in data interpretation.     

Feature-Based Molecular Networks Identification of Bioactive Metabolites from Three Plants of the Polynesian Cosmetopoeia Targeting the Dermal Papilla Cells of the Hair Cycle

The term cosmetopoeia refers to the use of plants in folks’ cosmetics. The aerial parts of Bidens pilosa L., the leaves of Calophyllum inophyllum L. and the fruits of Fagraea berteroana A.Gray ex Benth are traditionally used in French Polynesia for hair and skin care. During the hair cycle, dermal papilla cells and their interaction with epithelial cells are essential to promote hair follicle elongation. The aim of our investigations was the identification of metabolites from these three plants and chemical families responsible for their hair growth activity. A bioactivity-based molecular network was produced by mapping the correlation between features obtained from LC-MS/MS data and dermal papilla cell proliferation, using the Pearson correlation coefficient. The analyses pointed out glycosylated flavonols and phenolic acids from B. pilosa and C. inophyllum, along with C-flavonoids, iridoids and secoiridoids from F. berteroana, as potential bioactive molecules involved in the proliferation of hair follicle dermal papilla cells. Our results highlight the metabolites of the plant species potentially involved in the induction of hair follicle growth and support the traditional uses of these plants in hair care.     

Atomic emission analysis of human hair for the presence of trace elements

A procedure is developed for the atomic emission analysis of human hair with the preliminary acid mineralization of samples and excitation of spectra in samples of dry residues of hair mineralizate on the end face of a carbon electrode in an alternating current arch. Spectra were recorded on an MFS-8 spectrograph modernized with a MAES photodiode array. Using the developed analytical procedure, samples of hair were analyzed for the presence of Al, B, Ca, Cu, Mg, Mn, Fe, P, Pb, and Zn. The average concentrations and concentration ranges of these elements were calculated for samples collected from 42 donors. The results obtained were compared with the published data for other geographical regions.     

Development of an experimental procedure to analyse the ‘soil health state’ by microcalorimetry

This work is a ‘historical’revision of the evolution of an experimental procedure developed by Prof.Lisardo Núñez and his research group TERBIPROMAT to study thesustainability and the soil health state.From the very beginning,in 1993, the microbial activity was the main bioindicator selected to analysethe ‘soil health state’. For this reason, a microcalorimetrictechnique was used lately to analyse the influence of different human activitiessuch as reforestations, agricultural exploitation or pollution on the microbialactivity in different soils. Microcalorimetry is the main scientific techniqueused in this research to follow the stimulation of the microbial activityby addition of glucose. The data obtained were complemented by a study ofphysical, chemical and biological parameters of soil and allowed to followthe microbial activity in soils of Galicia (Spain) along the year.The final results, still in revision, will be helpful in establishinga data basis for real maps of the ‘health state’ of differentsoils. Such maps could be used to design processes that help us to decidehow we should exploit soils ensuring their sustainability.     

Methodology for fiber-optic Raman mapping and FTIR imaging of metastases in mouse brains

The objectives of this study were to optimize the preparation of pristine brain tissue to obtain reference information, to optimize the conditions for introducing a fiber-optic probe to acquire Raman maps, and to transfer previous results obtained from human brain tumors to an animal model. Brain metastases of malignant melanomas were induced by injecting tumor cells into the carotid artery of mice. The procedure mimicked hematogenous tumor spread in one brain hemisphere while the other hemisphere remained tumor free. Three series of sections were prepared consecutively from whole mouse brains: dried, thin sections for FTIR imaging, hematoxylin and eosin-stained thin sections for histopathological assessment, and pristine, 2-mm thick sections for Raman mapping. FTIR images were recorded using a spectrometer with a multi-channel detector. Raman maps were collected serially using a spectrometer coupled to a fiber-optic probe. The FTIR images and the Raman maps were segmented by cluster analysis. The color-coded cluster memberships coincided well with the morphology of mouse brains in stained tissue sections. More details in less time were resolved in FTIR images with a nominal resolution of 25 microm than in Raman maps collected with a laser focus 60 microm in diameter. The spectral contributions of melanin in tumor cells were resonance enhanced in Raman spectra on excitation at 785 nm which enabled their sensitive detection in Raman maps. Possible reasons why metastatic cells of malignant melanomas were not identified in FTIR images are discussed.     

Characterisation of low abundance wool proteins through novel differential extraction techniques

Fibres from human hair and wool are characterised by two main types of proteins: intermediate filament proteins (IFPs) and keratin associated proteins (KAPs). The IFPs, comprising over 50% of the fibre, tend to dominate 2‐D electrophoretic maps, hindering identification of the less‐abundant KAPs. This has been compounded in wool fibres by the relatively limited amount of sequence information available, with approximately 35 distinct protein sequences from ten KAP families being available, in contrast to human hair, where the sequences from well over 80 proteins from 26 KAP families are known. Additional complications include the high degree of homology within these families, ranging from 70 to 95%, and the dominance of cysteine residues in a number of KAP families with their high propensity to form cross‐links. The lack of sequence information for wool KAPs has been partly overcome through the recent acquisition of new sequences. Fractionation of the proteins on the basis of their solubility with pH, urea and DTT concentration has resulted in protein extracts in which the IFP concentration has been considerably reduced. These improvements have enabled the identification of low‐abundance proteins in 2‐D electrophoretic maps and represent a significant advance in our knowledge of the wool proteome.     

Zinc-catalyzed oxidation of 5-S-cysteinyldopa to 2,2'-bi(2H-1,4-benzothiazine): tracking the biosynthetic pathway of trichochromes, the characteristic pigments of red hair

Trichochromes, the peculiar pigments of red human hair, featuring the Delta(2,2)(')-bi(2H-1,4-benzothiazine) skeleton, are known to arise from cysteinyldopas, mainly the 5-S-isomer (5). However, the mode of formation and the direct precursors have remained largely undefined. To fill this gap, we investigated the oxidation of 5 in air or with chemical and enzymatic agents under biomimetic conditions. In the presence of zinc ions, which occur in epidermal tissues at significant concentrations, the reaction course is diverted toward the formation of a labile 3-carboxy-2H-1,4-benzothiazine intermediate (11), which was identified by direct NMR analysis. Structural formulation was supported by characterization of the analogous compound 13 isolated from oxidation of the model 5-methyl-3-S-cysteinylcatechol (12) after methylation. In the further stages of the oxidation, diastereomeric 2,2'-bi(2H-1,4-benzothiazine) 15 and 14 were obtained from 5 and 12, respectively, the reaction proceeding at a higher rate and to a greater extent in the presence of acids. The dimers were shown to readily convert to each other in the presence of acids. In the case of the methylated dimers 14, a 2,2'-bi(4H-1,4-benzothiazine) intermediate (16) was isolated and characterized. In acidic media, trichochrome C (1a), the most abundant in red human hair, was smoothly formed from aerial oxidation of 15, and under similar conditions, trichochrome-related products (17 and 18) were obtained from 14 prior to or after methylation. The presence of 1a and precursors 5 and 15 was investigated by HPLC analysis of red hair samples following mild proteolytic digestion. On the basis of these data, a likely biosynthetic route to trichochrome pigments of red human hair is depicted.     

An inter-laboratory comparative study into sample preparation for both reproducible and repeatable forensic 2H isotope analysis of human hair by continuous flow isotope ratio mass spectrometry

Stable isotope analysis of organic materials for their hydrogen ((2)H), carbon ((13)C), nitrogen ((15)N) or oxygen ((18)O) isotopic composition using continuous flow isotope ratio mass spectrometry (CF-IRMS) is an increasingly used tool in forensic chemical analysis. (2)H isotopic analysis can present a huge challenge, especially when dealing with exhibits comprising exchangeable hydrogen such as human scalp hair. However, to yield forensic data that are fit for purpose, analysis of the (2)H isotopic composition of the same homogeneous human hair sample by any laboratory worldwide must yield the same isotopic composition within analytical uncertainty. This paper presents longitudinal (2)H isotope data for four human hair samples of different provenance, measured by three different laboratories whose sample preparation was based on a two-stage H exchange equilibration method. Although each laboratory employed varying means to comply with the generic features of the sample preparation protocol such as the (2)H isotopic composition of exchange waters or drying down of samples prior to analysis, within each laboratory the Principle of Identical Treatment (P.I.T.) was applied for each individual experiment. Despite the variation in materials and procedures employed by the three laboratories, repeatable and reproducible 'true' (2)H isotope values (δ(2)H(hair,true)) were determined by each laboratory for each of the four stock samples of human scalp hair. The between-laboratory differences for obtained δ(2)H(hair,true) values ranged from 0.1 to 2.5 ‰. With an overall 95% confidence interval of ±2.8 ‰, these differences were not significantly different, which suggests that the general method of two-stage exchange equilibration carried out at ambient temperature is suitable for accurately and reproducibly determining 'true' δ(2)H-values for hair and other proteins provided that certain key conditions are met.     

Elemental analysis of hair using PIXE-tomography and INAA

3D quantitative elemental maps of a section of a strand of hair were produced using a combination of PIXE-Tomography and simultaneous On/Off Axis STIM-Tomography at the University of Surrey Ion Beam Centre. The distributions of S, K, Cl, Ca, Fe and Zn were determined using the PIXE-T reconstruction package DISRA. The results were compared with conventional bulk PIXE analysis of tomographic data as determined using Dan32. The overall concentrations determined by PIXE were compared with elemental concentrations held in the University of Surrey Hair Database. All the entries currently in the database were produced using INAA. The merits and possible contributions of tomographic PIXE analysis to analysis of hair are discussed. The conclusions drawn from the PIXE-Tomography analysis can be used to argue for more stringent procedures for hair analysis at the University of Surrey.     

白卡奴鸽动脉粥样硬化模型微量元素谱的计算机多元分析

用ＩＣＰ－ＡＥＳ测定了白卡奴鸽动脉粥样硬化模型和对照组的器官和组织中１９种元素含量，通过因子分析，取得一系列因子得分图，结果表明，动脉粥样硬化和对照组样品点分布在不同区域，且可分辨。     

Fast and high precision algorithms for optimization in large-scale genomic problems

There are several very difficult problems related to genetic or genomic analysis that belong to the field of discrete optimization in a set of all possible orders. With n elements (points, markers, clones, sequences, etc.), the number of all possible orders is n!/2 and only one of these is considered to be the true order. A classical formulation of a similar mathematical problem is the well-known traveling salesperson problem model (TSP). Genetic analogues of this problem include: ordering in multilocus genetic mapping, evolutionary tree reconstruction, building physical maps (contig assembling for overlapping clones and radiation hybrid mapping), and others. A novel, fast and reliable hybrid algorithm based on evolution strategy and guided local search discrete optimization was developed for TSP formulation of the multilocus mapping problems. High performance and high precision of the employed algorithm named guided evolution strategy (GES) allows verification of the obtained multilocus orders based on different computing-intensive approaches (e.g., bootstrap or jackknife) for detection and removing unreliable marker loci, hence, stabilizing the resulting paths. The efficiency of the proposed algorithm is demonstrated on standard TSP problems and on simulated data of multilocus genetic maps up to 1000 points per linkage group.     

PHOTOINDUCED OXYGEN CONSUMPTION IN MELANIN SYSTEMS–II. ACTION SPECTRA and QUANTUM YIELDS FOR PHEOMELANINS

Abstract— Photoinduced oxygen consumption in systems containing synthetic and natural pheomelanins has been studied by ESR spectroscopy using a nitroxide spin probe to monitor oxygen concentration. Action spectra and quantum yields have been determined for melanin from 5-S-cysteinyldopa and for pheomelanins extracted from red human hair and red chicken feathers. For comparison, data also were obtained for eumelanins from black hair and black feathers. The action spectrum for oxygen consumption by cysteinyldopa melanin is closely related to that previously obtained for eumelanins except that it shows slightly less efficiency at intermediate wavelengths (ca. 300–400 nm). Action spectra for the natural pheomelanins resemble either that for cysteinyldopa melanin or that for eumelanin. In general pheomelanins are no more effective than eumelanins in promoting oxygen consumption, i.e. they are no more susceptible to net photooxidation.     

Use of principal component analysis and a spectral mapping technique for the evaluation of the antifungal activity of anthracene-based synthetic dyes

The antifungal activity of 14 anthracene-based synthetic dyes and 6 reference compounds was measured on 36 fungal strains and the data matrix was evaluated separately by principal component analysis (PCA) and using a spectral mapping technique (SPM). The dimensionality of the maps of principal component loadings and variables and the selectivity maps was reduced to two by non-linear mapping. Except for two compounds, the dyes showed marked antifungal activity. Calculations proved that both the strength and selectivity of the biological effect of anthracene-based dyes were highly dependent on the chemical structure of the dye and on the type of fungi. PCA and SPM revealed different aspects of the antifungal activity, therefore, their simultaneous application in future quantitative structure–activity relationship studies is highly recommended.     

Comparative study on the use of Ir, W and Zr-coated graphite tubes for the determination of chromium in slurries of human scalp hair by electrothermal atomic absorption spectrometry

The use of Ir, W and Zr-coated graphite tubes, as permanent chemical modifiers, was studied for the determination of chromium in human scalp hair by ETAAS using the slurry sampling technique. The use of Mg(NO₃)₂ and Pd, as aqueous chemical modifiers, was also investigated and compared to the use of the permanent chemical modifiers. Scalp hair samples were pulverized using a Zr vibrational ball mill, (mean particle diameter of 0.8 μm) and suspended in ultrapure water. The lowest limit of detection, 44.5 μg kg^–1,was achieved for the use of W-coated graphite tubes. The repeatability of the overall procedures (slurry preparation and ETAAS determination) were 15.7, 14.5 and 16.7% for W- and Zr-coated graphite tubes and Mg(NO₃)₂, respectively. The methods were applied to several reference materials, CRM 397 (human hair), DOLT-1 (dogfish liver) and DORM-1 (dogfish muscle), and the results obtained were in agreement to the certified values. Finally, the methods were applied to several human scalp hair samples from healthy adults.     

Three New Phthalide Glycosides from the Rhizomes of Cnidium officinale and Their Recovery Effect on Damaged Otic Hair Cells in Zebrafish

The extract from Cnidium officinale rhizomes was shown in a prior experiment to markedly recover otic hair cells in zebrafish damaged by neomycin. The current study was brought about to identify the principal metabolite. Column chromatography using octadecyl SiO₂ and SiO₂ was performed to isolate the major metabolites from the active fraction. The chemical structures were resolved on the basis of spectroscopic data, including NMR, IR, MS, and circular dichroism (CD) data. The isolated phthalide glycosides were assessed for their recovery effect on damaged otic hair cells in neomycin-treated zebrafish. Three new phthalide glycosides were isolated, and their chemical structures, including stereochemical characteristics, were determined. Two glycosides (0.1 μM) showed a recovery effect (p < 0.01) on otic hair cells in zebrafish affected by neomycin ototoxicity. Repeated column chromatography led to the isolation of three new phthalide glycosides, named ligusticosides C (1), D (2), and E (3). Ligusticoside C and ligusticoside E recovered damaged otic hair cells in zebrafish.     

HPLC with fluorescence detection of methamphetamine and amphetamine in segmentally analyzed human hair

A sensitive high-performance liquid chromatographic method with fluorescence detection for determining methamphetamine and its major metabolite, amphetamine, in abusers' hair segments was developed. Methamphetamine and amphetamine in hair samples collected from addicts were extracted into acidified methanol, derivatized with 4-(4,5-diphenyl-1H-imidazol-2-yl)benzoyl chloride, separated isocratically on an ODS column using TRIS-HCl buffer (0.1 mol dm-3, pH 7.0)-methanol (30 + 70 v/v) as the mobile phase and the derivatives were detected fluorimetrically at 440 nm (lambda ex 330 nm). Calibration curves obtained by using control human hair spiked with standard solutions were linear (r > or = 0.999) up to at least 676.1 ng mg-1 for amphetamine and 746.1 ng mg-1 for methamphetamine. The detection limits at a signal-to-noise ratio of 3 were 51.4 and 74.6 pg mg-1 hair for amphetamine and methamphetamine, respectively. Using control hair spiked with standard solutions, the intra- and inter-day relative standard deviations (n = 5) were < or = 8.6% for both the target compounds. The method was successfully applied to the segmental analyses of methamphetamine abusers' hair samples.     

Application of high-resolution EFTEM SI in an AEM

In this work we show how energy-filtered imaging can be used to obtain spectrum images of electron energy-loss spectrometric data. Focus is placed on improved energy resolution within these data sets. Using two multilayer samples (GaN/AlN and InP/InAs), we demonstrate the advantages of spectrum-imaging and its extended mapping capabilities. Plasmon-ratio maps are used to quickly create high-contrast material maps with high signal-to-noise ratio, ratio-contrast plots are used to gain optimum settings for the ratio maps, and plasmon-position maps are used to map small shifts of the energy position of bulk plasmon peaks. Figure Scheme of EELS SI and derived plasman-position map