Robust and stable feature selection by integrating ranking methods and wrapper technique in genetic data classification

High dimensional data increase the dimension of space and consequently the computational complexity and result in lower generalization. From these types of classification problems microarray data classification can be mentioned. Microarrays contain genetic and biological data which can be used to diagnose diseases including various types of cancers and tumors. Having intractable dimensions, dimension reduction process is necessary on these data. The main goal of this paper is to provide a method for dimension reduction and classification of genetic data sets. The proposed approach includes different stages. In the first stage, several feature ranking methods are fused for enhancing the robustness and stability of feature selection process. Wrapper method is combined with the proposed hybrid ranking method to embed the interaction between genes. Afterwards, the classification process is applied using support vector machine. Before feeding the data to the SVM classifier the problem of imbalance classes of data in the training phase should be overcame. The experimental results of the proposed approach on five microarray databases show that the robustness metric of the feature selection process is in the interval of [0.70, 0.88]. Also the classification accuracy is in the range of [91%, 96%].     

Internalization of Flax Rust Avirulence Proteins into Flax and Tobacco Cells Can Occur in the Absence of the Pathogen

Translocation of pathogen effector proteins into the host cell cytoplasm is a key determinant for the pathogenicity of many bacterial and oomycete plant pathogens. A number of secreted fungal avirulence (Avr) proteins are also inferred to be delivered into host cells, based on their intracellular recognition by host resistance proteins, including those of flax rust (Melampsora lini). Here, we show by immunolocalization that the flax rust AvrM protein is secreted from haustoria during infection and accumulates in the haustorial wall. Five days after inoculation, the AvrM protein was also detected within the cytoplasm of a proportion of plant cells containing haustoria, confirming its delivery into host cells during infection. Transient expression of secreted AvrL567 and AvrM proteins fused to cerulean fluorescent protein in tobacco (Nicotiana tabacum) and flax cells resulted in intracellular accumulation of the fusion proteins. The rust Avr protein signal peptides were functional in plants and efficiently directed fused cerulean into the secretory pathway. Thus, these secreted effectors are internalized into the plant cell cytosol in the absence of the pathogen, suggesting that they do not require a pathogen-encoded transport mechanism. Uptake of these proteins is dependent on signals in their N-terminal regions, but the primary sequence features of these uptake regions are not conserved between different rust effectors.     

Contribution to the cytotaxonomy of Oryzopsis (Poaceae)

Meiotic studies were performed in twelve populations of four Oryzopsis species (O. pubiflora, O. lateralis, O. holciformis var. longiglomis and O. barbellata) to obtain data on the ploidy level and cytological evolution of the genus. The chromosome number 2n=2x=24 was revealed in all the species and populations studied. The present and other studies show the occurrence of two basic chromosome numbers in the genus, i.e. x=11 and x=12. Although Oryzopsis species and populations studied are diploid and are expected to form only bivalents in metaphase of meiosis‐I, quadrivalents were observed in O. pubiflora and O. lateralis, possibly due to the occurrence of heterozygote translocations. B‐chromosomes of 0–2 were observed in all species and populations studied. This is the first report of the occurrence of B‐chromosomes in the genus Oryzopsis. Several meiocytes showed the presence of double chromosome number in O. lateralis, and multipolar cells were observed in populations of O. barbellata, O. lateralis and O. holciformis var. longiglomis. The occurrence of large pollen grains (possibly unreduced) was observed along with smaller (normal) pollen grains in these species. Significant differences observed in chiasma frequency and distribution among studied species may be of use in species delimitation. The Kakan population differed significantly from the other populations of O. lateralis in meiotic characteristics. If such cytological differences are accompanied by morphological variation (under investigation), we may consider this population as a new variety or subspecies.     

Optimizing a Proteomics Platform for Urine Biomarker Discovery

Biomarker discovery approaches in urine have been hindered by concerns for reproducibility and inadequate standardization of proteomics protocols. In this study, we describe an optimized quantitative proteomics strategy for urine biomarker discovery, which is applicable to fresh or long frozen samples. We used urine from healthy controls to standardize iTRAQ (isobaric tags for relative and absolute quantitation) for variation induced by protease inhibitors, starting protein and iTRAQ label quantities, protein extraction methods, and depletion of albumin and immunoglobulin G (IgG). We observed the following: (a) Absence of protease inhibitors did not affect the number or identity of the high confidence proteins. (b) Use of less than 20 μg of protein per sample led to a significant drop in the number of identified proteins. (c) Use of as little as a quarter unit of an iTRAQ label did not affect the number or identity of the identified proteins. (d) Protein extraction by methanol precipitation led to the highest protein yields and the most reproducible spectra. (e) Depletion of albumin and IgG did not increase the number of identified proteins or deepen the proteome coverage. Applying this optimized protocol to four pairs of long frozen urine samples from diabetic Pima Indians with or without nephropathy, we observed patterns suggesting segregation of cases and controls by iTRAQ spectra. We also identified several previously reported candidate biomarkers that showed trends toward differential expression, albeit not reaching statistical significance in this small sample set.With ongoing advances in mass spectrometry (MS) and proteomics technology, proteomics analysis is progressively occupying a central position in biomarker discovery platforms. Biofluids such as urine and blood are the preferred media for proteomics analysis because of their ease of collection and extensive history of use in clinical laboratory practice. Urine, in particular, is an information-rich fluid that can be collected non-invasively and in large quantities. Many urine proteins are produced or shed in the kidney and urogenital tract (1), making urine a promising proximal source of biomarkers for diseases affecting these structures.However, proteomics-based biomarker discovery in urine faces multiple challenges. Urine proteomics is complicated by low urine protein concentration, variations in pH, and high concentrations of salts and urea or other urine components that interfere with sample processing. The urine proteome can also change with individual variables such as hydration, diurnal change, diet, and physical activity as well as variation in sample collection, processing, and storage. In addition, urine proteomics shares the usual challenges of biomarker discovery in other biofluids such as throughput, cost, and the need for a reproducible and quantitative work flow.Isotopic or isobaric labeling methods to reduce variation, increase throughput, and enable quantitative analysis have been developed to address some of these challenges. One such method, isobaric tags for relative and absolute quantitation (iTRAQ)¹ (2), combines relative and absolute peptide quantification with multiplexing ability to enable an increased throughput as well as simultaneous comparison of up to eight samples within one experimental run. Variations induced by urine sample processing have been systematically evaluated for proteomics analyses using two-dimensional gel electrophoresis (3–6), differential gel electrophoresis (7), and liquid chromatography-coupled mass spectrometry (LC-MS) (5, 8, 9). However, no systematic analyses of urine sample collection and processing have been reported for iTRAQ.Before utilizing iTRAQ-based quantitative proteomics for urine biomarker discovery, we evaluated the impact of variation in several processing steps (addition of protease inhibitors, the starting protein quantities, quantity of the iTRAQ label, protein extraction methods, and depletion of abundant proteins) on iTRAQ protein identification and quantitation. Applying this optimized biomarker discovery protocol to small quantities of long frozen urine samples from the Pima longitudinal study of diabetic nephropathy, we observed patterns suggestive of segregation of cases and controls by iTRAQ spectra. We also observed trends toward differential expression in several proteins that had been identified as putative biomarkers in previous studies. However, given the small sample size, none of these proteins retained statistical significance after multiple testing correction.     

N-acetyltransferase polymorphism among northern Sudanese

Interindividual and interethnic differences in allele frequencies of N-acetyltransferase (NAT2) single nucleotide polymorphisms (SNPs) are responsible for phenotypic variability of adverse drug reactions and susceptibility to cancer. We genotyped the seven NAT2 common SNPs in 127 randomly selected unrelated northern Sudanese subjects using allele-specific and RFLP polymerase chain reaction (PCR) based methods. Molecular genotyping was enough to designate alleles for 41 individuals unambiguously, whereas 63 individuals' alleles were inferred from haplotypes previously described. In the remaining 23 individuals, however, the phase of the SNPs could not be decided because of multiple SNP heterozygotes. Using computational methods in the HAP and Phase programs, we confirmed the inferred alleles of the 62 individuals and predicted the remaining 23 ambiguous alleles. Twelve NAT2 alleles were identified. Four alleles coded for rapid acetylators (18%), and eight alleles coded for slow acetylators (82%). Two genotypes coded for rapid acetylation (3.9%), 10 for intermediate acetylation (27.6%), and 13 for slow acetylation (68.5%). The G191A African SNP and the G857A predominantly Asian SNP were each detected at a low frequency of 3.1%. The combination of molecular and computational analysis was useful in resolving ambiguous genotypes of NAT2 in multiple SNP heterozygotes. Among the northern Sudanese the SNPs associated with slow acetylation are more prevalent than in Caucasians and Asians. This and other African studies are suggestive of an African origin for NAT2-associated polymorphism.     

Evaluation of culture conditions for cellulase production by two Trichoderma reesei mutants under solid-state fermentation conditions

Response surface methodology (RSM) was used to evaluate the effects of fermentation parameters for cellulase production by Trichoderma reesei QM9414 and T. reesei MCG77 in solid-state fermentation using rice bran as substrate. Initial pH, moisture content and temperature were optimized using filter paper activity (FPA) as response. Statistical analysis of the results for T. reesei QM9414 showed that only moisture content had significant effect on cellulase activity and had a linear effect on enzyme activity (maximum enzyme activities were obtained at 70% moisture content). The results for T. reesei MCG77 showed that temperature and moisture content were the most significant parameters for cellulase activity. The optimum cellulase production was in the temperature range of 25-30 degrees C and moisture content between 55% and 70%. After the optimization, the FPA in T. reesei MCG77 was increased by 2.5 folds compared to that of T. reesei QM9414.     

Relationship between the Structure and Chaperone Activity of Human αA-Crystallin after Its Modification with Diabetes-Associated Oxidative Agents and Protective Role of Antioxidant Compounds

Biochemistry (Moscow) - The study was aimed to evaluate the impact of peroxynitrite (PON, oxidative stress agent in diabetes), methylglyoxal (MGO, diabetes-associated reactive carbonyl compound),...     

Recognition of functional genetic polymorphism using ESE motif definition: a conservative evolutionary approach to CYP2D6/CYP2C19 gene variants

Genetica - Although predicting the effects of variants near intron-exon boundaries is relatively straightforward, predicting the functional Exon Splicing Enhancers (ESEs) and the possible effects...     

Systematic analysis of HD-ZIP transcription factors in sesame genome and gene expression profiling of SiHD-ZIP class I entailing drought stress responses at early seedling stage

Molecular Biology Reports - Sesame is an ancient oilseed crop, known for its high oil content and quality. Its sensitivity to drought at early seedling stage is one of the limiting factors...     

The relation of omentin gene expression and glucose homeostasis of visceral and subcutaneous adipose tissues in non-diabetic adults

Molecular Biology Reports - Adipose tissue (AT) is a passive reservoir for energy storage and an active endocrine organ responsible for synthesizing bioactive molecules called...