Data mining in proteomic mass spectrometry

Data mining application to proteomic data from mass spectrometry has gained much interest in recent years. Advances made in proteomics and mass spectrometry have resulted in considerable amount of data that cannot be easily visualized or interpreted. Mass spectral proteomic datasets are typically high dimensional but with small sample size. Consequently, advanced artificial intelligence and machine learning algorithms are increasingly being used for knowledge discovery from such datasets. Their overall goal is to extract useful information that leads to the identification of protein biomarker candidates. Such biomarkers could potentially have diagnostic value as tools for early detection, diagnosis, and prognosis of many diseases. The purpose of this review is to focus on the current trends in mining mass spectral proteomic data. Special emphasis is placed on the critical steps involved in the analysis of surface-enhanced laser desorption/ionization mass spectrometry proteomic data. Examples are drawn from previously published studies and relevant data mining terminology and techniques are exlained.     

Expression, purification, and characterization of His-tagged Staphylococcus xylosus lipase wild-type and its mutant Asp 290 Ala

The gene encoding the extracellular lipase of Staphylococcus xylosus (SXL) was cloned using PCR technique. The sequence corresponding to the mature lipase was subcloned in the pET-14b expression vector, with a strong T7 promoter, to construct a recombinant lipase protein containing six histidine residues at the N-terminal. High level expression of the lipase by Escherichia coli BL21 (DE3) cells harbouring the lipase gene containing expression vector was observed upon induction with 0.4 mM IPTG at 37 degrees C. One-step purification of the recombinant lipase was achieved with Ni-NTA resin. The specific activity of the purified His-tagged SXL was 1500 or 850 U/mg using tributyrin or olive oil emulsion as substrate, respectively. It has been proposed that the region near the residue Asp290 could be involved in the selection of the substrate. Therefore, we also mutated the residue Asp 290 by Ala using site-directed mutagenesis. The mutant SXL-D290A was overexpressed in E. coli BL21 (DE3) and purified with the same nickel metal affinity column. The specific activity of the purified His-tagged SXL-D290A mutant was 1000 U/mg using either tributyrin or olive oil emulsion as substrate. A comparative study of the wild type (His(6)-SXL) and the mutant (His(6)-SXL-D290A) proteins was carried out. Our results confirmed that Asp290 is important for the chain length specificity and catalytic efficiency of the enzyme.     

The kinetics of germination in bacterial spores

The entire absorbance vs. time curve of a sample of germinating bacterial spores can be accurately described by a model which considers that the spores rate of entry into the phase initiation of germination is determined by transitions between three spore states. The first of these transitions is easily identified with the triggering event, while the existence of the intermediate state, and its identification with the triggered spore, can be established from theoretical as well as experimental considerations. The observed sample lag time is seen to arise from the position of the measured event in the single spore in the sequence of indices of germination. Consideration that the single spore may effect the measured change in a complex way over a finite interval of time leads to a mathematical formulation of our model which can describe the germination process whatever the endpoint chosen for its observation.     

Amplitude modulation of the nightly melatonin rise in the neonatal lamb and the subsequent timing of puberty

Spring-born female lambs require a decrease in day length for the normal timing of puberty the following autumn. If this decrease occurs early in postnatal life (i.e. 0-10 weeks), puberty is delayed. This study tested the hypothesis that failure of the neonatal lamb to respond to the critical long-day to short-day signal is due to inadequate nocturnal melatonin secretion. The approach was to artificially increase, to adult levels, the low nighttime rises of melatonin during the early postnatal period. Eight female lambs served as controls; they were raised on short days until 17 wk of age, and then exposed to 5 wk of long days, after which they were returned to short days. This alternating sequence of photoperiods during mid-development would be expected to induce normal puberty. Sixteen experimental females were exposed to the critical block of long days much earlier; they were placed in long days between 2 and 7 wk of age and in short days thereafter. Half (n = 8) received no further treatment. The other half (n = 8) were infused nightly with melatonin during the 8-h dark phase of the 5-wk, long-day photoperiod. This increased the amplitude of the natural nighttime melatonin rises 3- to 4-fold, well into the adult range.(ABSTRACT TRUNCATED AT 250 WORDS)     

Nucleic Acid Components and Their Analogues: New Synthesis of Bicyclic Thiopyrimidine Nucleosides

Abstract

A novel synthesis of condensed bicyclic thiopyrimidine glycosides utilising 1H-cyclopentapyrimidine-2(3H)-thiones and α-bromoglucose or α-bromogalactose tetraacetate as starting components is described.     

Musculoskeletal chest wall pain

The musculoskeletal structures of the thoracic wall and the neck are a relatively common source of chest pain. Pain arising from these structures is often mistaken for angina pectoris, pleurisy or other serious disorders. In this article the clinical features, pathogenesis and management of the various musculoskeletal chest wall disorders are discussed. The more common causes are costochondritis, traumatic muscle pain, trauma to the chest wall, “fibrositis” syndrome, referred pain, psychogenic regional pain syndrome, and arthritis involving articulations of the sternum, ribs and thoracic spine. Careful analysis of the history, physical findings and results of investigation is essential for precise diagnosis and effective treatment.     

Structure,composition and regeneration of riparian forest along an altitudinal gradient in northern Iran

In order to protect and understand the regeneration of riparian forests, it is important to understand the environmental conditions that lead to their vegetation differentiation. We evaluated the structure, composition, density and regeneration of woody species in forests along the river Safaroud in Ramsar forest in northern Iran in relation to elevation, soil properties and distance from the river. Using 60 transects located perpendicularly to river and 300 quadrats, we examined forests 0, 50, 100, 150 and 200 m from the stream along an elevation gradient spanning from 350 to 2,400 m a.s.l. We found that total density, regeneration, diameter and basal area of trees were significantly higher in the interior of the forest whereas shrub density was higher close to the river. The uneven-aged forest structure showed no significant differences among gradient from the river to the forest interior. Hydro-geomorphic processes, flooding, the elevation gradient, distance from the river and soil properties were the most important factors that influenced plant community distribution in relation to the river.     

Phylogenetic,toxigenic and virulence profiles of <Emphasis Type="Italic">Alternaria</Emphasis> species causing leaf blight of tomato in Egypt

Species of Alternaria are serious plant pathogens, causing major losses on a wide range of crops. Leaf blight symptoms were observed on tomato leaves, and samples were collected from various regions. Isolation was done from symptomatic tomato leaves, and 15 representatives were selected from a collection of 65 isolates of Alternaria species. The virulence of Alternaria isolates was investigated on detached leaves (DL) and whole plants of tomato cv. Super strain B. A phylogenetic analysis was performed based on three partial gene regions, the glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the RNA polymerase second largest subunit (RPB2) and the Alternaria major allergen gene (Alt a 1). The potentiality of Alternaria isolates to produce toxins was also investigated on the basis of thin-layer chromatography (TLC). Our investigations revealed that Alternaria isolates showed different levels of virulence either on tomato plants or DL. Based on the phylogeny of three genes, Alternaria isolates encompassed two species of small-spored morphospecies: A. alternata (14 isolates) and A. arborescens (single isolate). The produced toxins varied among Alternaria isolates with tenuazonic acid (TeA) being the most abundant mycotoxin produced by most isolates. This study highlighted on other Alternaria species in Egypt that might represent a serious concern for tomato producers as causal agents of leaf blight over other species, i.e. A. solani.     

High Concentration of Fluoride Can Be Increased Risk of Abortion

The presence of fluoride in drinking water can be either beneficial or harmful for human health, depending on its concentration. Most adverse effects of fluoride are observed at high concentrations (above 1.5 mg/L). This study was aimed to evaluate the effect of fluoride concentrations in drinking water on spontaneous abortion in two regions: one with low fluoride concentration and another with high fluoride concentration. The results showed that there is a relationship between the concentration of fluoride in drinking water and abortion, so that the risk of abortion increased at high concentrations of fluoride. However, further studies are needed to clarify this relationship due to the small area and population in this study.     

Lithostratigraphy and facies development of upper cretaceous carbonates in east central Sinai,Egypt

Summary The Upper Cretaceous exposures in east central Sinai are represented by carbonate-dominated successions interbedding few sandstone, chert, shale and marl horizons. The recognised rock units are correlated with their counterparts commonly used in the Gulf of Suez region and central Sinai including from base to top: the Raha Formation, Abu Qada Formation, Wata Formation, Matulla Formation and the Sudr Chalk. Twelve limestone microfacies are encountered and are categorised as mudstones (pelmicrite and ostracod micrite), wackestones (pelagic biomicrite and foraminiferal biomicrite), grainstones (foraminiferal biopelsparite and oosparite), boundstones (bindstone and framestone), floatstones (coated-grained biomicrudite, rudist biomicrudite and shelly biomicrudite) and rudstones (shelly biosparudite). The dolostone microfacies include fine-medium crystalline ostracod dolostones and shelly dolostones. These microfacies have been compared with the Standard Microfacies Types and their depositional environments are discussed. The encountered litho- and biofacies suggest that the Cenomanian shallow transgressive sea had covered east central Sinai as far south as the Dahab region. By the advent of the Turonian, open marine subtidal conditions prevailed. This was followed by transitional conditions with shoals and tidal bars in the Late Turonian pointing to a regressive phase more pronounced at the southern localities. The rocks of the Matulla Formation were deposited in an oscillating environment of shallow subtidal to intertidal conditions during Coniacian-Santonian. In the Late Santonian and during most of the Campanian-Maastrichtian, sedimentation was influenced by open marine conditions with low sedimentation rates; local shallow subtidal regressive events occurred.