Multiple approaches to data-mining of proteomic data based on statistical and pattern classification methods

The data-mining challenge presented is composed of two fundamental problems. Problem one is the separation of forty-one subjects into two classifications based on the data produced by the mass spectrometry of protein samples from each subject. Problem two is to find the specific differences between protein expression data of two sets of subjects. In each problem, one group of subjects has a disease, while the other group is nondiseased. Each problem was approached with the intent to introduce a new and potentially useful tool to analyze protein expression from mass spectrometry data. A variety of methodologies, both conventional and nonconventional were used in the analysis of these problems. The results presented show both overlap and discrepancies. What is important is the breadth of the techniques and the future direction this analysis will create.     

Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production

Background

Although interactions between microorganisms involved in biogas production are largely uncharted, it is commonly accepted that methanogenic Archaea are essential for the process. Methanogens thrive in various environments, but the most extensively studied communities come from biogas plants. In this study, we employed a metagenomic analysis of deeply sequenced methanogenic communities, which allowed for comparison of taxonomic and functional diversity as well as identification of microorganisms directly involved in various stages of methanogenesis pathways.

Results

A comprehensive metagenomic approach was used to compare seven environmental communities, originating from an agricultural biogas plant, cattle-associated samples, a lowland bog, sewage sludge from a wastewater treatment plant and sediments from an ancient gold mine. In addition to the native consortia, two laboratory communities cultivated on maize silage as the sole substrate were also analyzed. Results showed that all anaerobic communities harbored genes of all known methanogenesis pathways, but their abundance varied greatly between environments and that genes were encoded by different methanogens. Identification of microorganisms directly involved in different stages of methane production revealed that hydrogenotrophic methanogens, such as Methanoculleus, Methanobacterium, Methanobrevibacter, Methanocorpusculum or Methanoregula, predominated in most native communities, whereas acetoclastic Methanosaeta seemed to be the key methanogen in the wastewater treatment plant. Furthermore, in many environments, the methylotrophic pathway carried out by representatives of Methanomassiliicoccales, such as Candidatus Methanomethylophilus and Candidatus Methanoplasma, seemed to play an important role in methane production. In contrast, in stable laboratory reactors substrate versatile Methanosarcina predominated.

Conclusions

The metagenomic approach presented in this study allowed for deep exploration and comparison of nine environments in which methane production occurs. Different abundance of methanogenesis-related functions was observed and the functions were analyzed in the phylogenetic context in order to identify microbes directly involved in methane production. In addition, a comparison of two metagenomic analytical tools, MG-RAST and MetAnnotate, revealed that combination of both allows for a precise characterization of methanogenic communities.

     

Pseudomonas silesiensis sp. nov. strain A3T isolated from a biological pesticide sewage treatment plant and analysis of the complete genome sequence

Microorganisms classified in to the Pseudomonas genus are a ubiquitous bacteria inhabiting variety of environmental niches and have been isolated from soil, sediment, water and different parts of higher organisms (plants and animals). Members of this genus are known for their metabolic versatility and are able to utilize different chemical compounds as a source of carbon, nitrogen or phosphorus, which makes them an interesting microorganism for bioremediation or bio-transformation. Moreover, Pseudomonas sp. has been described as a microorganism that can easily adapt to new environmental conditions due to its resistance to the presence of high concentrations of heavy metals or chemical pollution. Here we present the isolation and analysis of Pseudomonas silesiensis sp. nov. strain A3^T isolated from peaty soil used in a biological wastewater treatment plant exploited by a pesticide packaging company. Phylogenetic MLSA analysis of 4 housekeeping genes (16S rRNA, gyrB, rpoD and rpoB), complete genome sequence comparison (ANIb, Tetranucleotide identity, digital DDH), FAME analysis, and other biochemical tests indicate the A3^T strain (type strain PCM 2856^T = DSM 103370^T) differs significantly from the closest relative species and therefore represents a new species within the Pseudomonas genus. Moreover, bioinformatic analysis of the complete sequenced genome showed that it consists of 6,823,539 bp with a 59.58 mol% G + C content and does not contain any additional plasmids. Genome annotation predicted the presence of 6066 genes, of which 5875 are coding proteins and 96 are RNA genes.     

High‐performance liquid chromatographic enantioseparation of N‐aryl‐thioureidoalkylphosphonates and thiourylenedi(alkylphosphonates) on polysaccharide‐based chiral stationary phases

The first successful enantioseparation of representative O,O‐diphenyl‐N‐arylthioureidoalkylphosphonates, (±)‐Ptc‐Val^P(OPh)₂ & (±)‐Ptc‐Leu^P(OPh)₂ and thiourylenedi(isobutyl phosphonate), Tcm[Val^P(OPh)₂]₂ on analytical and semipreparative scale was achieved by high‐performance liquid chromatography using polysaccharide‐based chiral stationary phases (CPs). Atc‐AA^P(OPh)₂ was obtained using modified tricomponent condensations of the corresponding aldehydes, N‐arylthiourea and triphenyl phosphite whereas Tcm[Val^P(OPh)₂]₂ by the condensations of aldehydes, thiourea, and triphenyl phosphite. The prepared, racemic (±)‐Atc‐AA^P(OPh)₂ [(±)‐Ptc‐Val^P(OPh)₂, (±)‐Ptc‐Leu^P(OPh)₂, (±)‐Ptc‐Pgly^P(OPh)₂ and (±)‐Ntc‐Pgly^P(OPh)₂] and racemic (±)‐Tcm[AA^P(OPh)₂]₂ [(±)‐Tcm[Nva^P(OPh)₂]₂ & (±)‐Tcm[Val^P(OPh)₂]₂] were adequately characterized and used for chromatographic separations on high‐performance liquid chromatography–chiral stationary phases. The best results were obtained for (±)‐Ptc‐Val^P(OPh)₂, (±)‐Ptc‐Leu^P(OPh)₂ and (±)‐Tcm[Val^P(OPh)₂]₂.     

Estimation of urinary cotinine cut-off points distinguishing non-smokers,passive and active smokers

Abstract

An objective assessment of exposure to tobacco smoke may be accomplished by means of examining particular biomarkers in body fluids. The most common biomarker of tobacco smoke exposure is urinary, or serum, cotinine. In order to distinguish non-smokers from passive smokers and passive smokers from active smokers, it is necessary to estimate cotinine cut-off points. The objective of this article was to apply statistical distribution of urinary cotinine concentration to estimate cut-off points distinguishing the three above-mentioned groups. The examined group consisted of 327 volunteers (187 women and 140 men) who were ethnically homogenous inhabitants of the same urban agglomeration (Sosnowiec, Poland). The values which enabled differentiation of the examined population into groups and subgroups were as follows: 50 µg l^?1 (differentiation of non-smokers from passive smokers), 170 µg l^?1 (to divide the group of passive smokers into two subgroups: minimally and highly exposed to environmental tobacco smoke), 550 µg l^?1 (differentiation of passive smokers from active smokers), and 2100 µg l^?1 (to divide group of active smokers into two subgroups: minimally and highly exposed to tobacco smoke). The results suggest that statistical distribution of urinary cotinine concentration is useful for estimating urinary cotinine cut-off points and for assessing the smoking status of persons exposed to tobacco smoke.     

PARASITISM VERSUS COMMENSALISM: THE CASE OF TABULATE ENDOBIONTS

Abstract:  Tube-like traces of organisms belonging to the ichnogenus Chaetosalpinx Sokolov have been considered in the literature as commensal endobiontic organisms of tabulate corals. Their position between the corallites (or sometimes within the septa), perforation of the host's skeleton and soft tissue, modification of its phenotype and a possible inhibition of its growth show that the relationship between these organisms and tabulate corals can best be interpreted as parasitism rather than commensalism, as previously suggested. Such an interpretation may be extended to the ichnogenera Helicosalpinx Oekentorp and Actinosalpinx Sokolov, which show identical placement within the host colony and similar features, such as the absence of their own wall.     

Amiloride-sensitive sodium absorption is different in vertebrates and invertebrates

Amiloride-sensitive Na+ absorption is a well-described feature of numerous transporting epithelia in vertebrates. Yet, very little is known about this important physiological process regarding invertebrates. In the present paper, we compare vertebrate Na+ absorption mediated by the amiloride-sensitive epithelial Na+ channel (ENaC) and its invertebrate counterpart. We used the dorsal skin of the annelid Hirudo medicinalis as a model for the Na+ absorption of invertebrate epithelia. In applying electrophysiological, molecular, and biochemical techniques we found striking functional and structural differences between vertebrate and invertebrate amiloride-sensitive Na+ absorption. Using modified Ussing chambers, we analyzed the influence of different known blockers and effectors of vertebrate ENaC on leech epithelial Na+ absorption. We demonstrate that the serine protease trypsin had no effect on the Na+ transport across leech integument, while it strongly activates vertebrate ENaC. While protons, and the divalent cations Ni2+ and Zn2+ stimulate vertebrate ENaC, amiloride-sensitive Na+ currents in leech integument were substantially reduced. For molecular studies, we constructed a cDNA library of Hirudo medicinalis and screened it with specific ENaC antibodies. We performed numerous PCR approaches using a vast number of different degenerated and specific ENaC primers to identify ENaC-like structures. Yet, both strategies did not reveal any ENaC-like sequence in leech integument. From these data we conclude that amiloride-sensitive Na+ absorption in leech skin is not mediated by an ENaC-like Na+ channel but by a still unknown invertebrate member of the ENaC/DEG family that we termed lENaTP (leech epithelial Na+ transporting protein).