Uneven distribution of potential triplex sequences in the human genome. In silico study using the R/Bioconductor package triplex.

Eukaryotic genomes are rich in sequences capable of forming non-B DNA structures. These structures are expected to play important roles in natural regulatory processes at levels above those of individual genes, such as whole genome dynamics or chromatin organization, as well as in processes leading to the loss of these functions, such as cancer development. Recently, a number of authors have mapped the occurrence of potential quadruplex sequences in the human genome and found them to be associated with promoters. In this paper, we set out to map the distribution and characteristics of potential triplex-forming sequences in human genome DNA sequences. Using the R/Bioconductor package {\it triplex}, we found these sequences to be excluded from exons, while present mostly in a small number of repetitive sequence classes, especially short sequence tandem repeats (microsatellites), Alu and combined elements, such as SVA. We also introduce a novel way of classifying potential triplex sequences, using a lexicographically minimal rotation of the most frequent k-mer to assign class membership automatically. Members of such classes typically have different propensities to form parallel and antiparallel intramolecular triplexes (H-DNA). We observed an interesting pattern, where the predicted third strands of antiparallel H-DNA were much less likely to contain a deletion against their duplex structural counterpart than were their parallel versions

Hammock:a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets

Motivation: Proteins often recognize their interaction partners on the basis of short linear motifs located in disordered regions on proteins’ surface. Experimental techniques that study such motifs use short peptides to mimic the structural properties of interacting proteins. Continued development of these methods allows for large-scale screening, resulting in vast amounts of peptide sequences, potentially containing information on multiple protein-protein interactions. Processing of such datasets is a complex but essential task for large-scale studies investigating protein-protein interactions. Results: The software tool presented in this article is able to rapidly identify multiple clusters of sequences carrying shared specificity motifs in massive datasets from various sources and generate multiple sequence alignments of identified clusters. The method was applied on a previously published smaller dataset containing distinct classes of ligands for SH3 domains, as well as on a new, an order of magnitude larger dataset containing epitopes for several monoclonal antibodies. The software successfully identified clusters of sequences mimicking epitopes of antibody targets, as well as secondary clusters revealing that the antibodies accept some deviations from original epitope sequences. Another test indicates that processing of even much larger datasets is computationally feasible. Availability and implementation: Hammock is published under GNU GPL v. 3 license and is freely available as a standalone program (from http://www.recamo.cz/en/software/hammock-cluster-peptides/) or as a tool for the Galaxy toolbox (from https://toolshed.g2.bx.psu.edu/view/hammock/hammock). The source code can be downloaded from https://github.com/hammock-dev/hammock/releases. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Patients With Common Variable Immunodeficiency (CVID) Show Higher Gut Bacterial Diversity and Levels of Low-Abundance Genes Than the Healthy Housemates

Common variable immunodeficiency (CVID) is a clinically and genetically heterogeneous disorder with inadequate antibody responses and low levels of immunoglobulins including IgA that is involved in the maintenance of the intestinal homeostasis. In this study, we analyzed the taxonomical and functional metagenome of the fecal microbiota and stool metabolome in a cohort of six CVID patients without gastroenterological symptomatology and their healthy housemates. The fecal microbiome of CVID patients contained higher numbers of bacterial species and altered abundance of thirty-four species. Hungatella hathewayi was frequent in CVID microbiome and absent in controls. Moreover, the CVID metagenome was enriched for low-abundance genes likely encoding nonessential functions, such as bacterial motility and metabolism of aromatic compounds. Metabolomics revealed dysregulation in several metabolic pathways, mostly associated with decreased levels of adenosine in CVID patients. Identified features have been consistently associated with CVID diagnosis across the patients with various immunological characteristics, length of treatment, and age. Taken together, this initial study revealed expansion of bacterial diversity in the host immunodeficient conditions and suggested several bacterial species and metabolites, which have potential to be diagnostic and/or prognostic CVID markers in the future

The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery

Our understanding of human gut microbiota in health and disease depends on accurate and reproducible microbial data acquisition. The critical step in this process is to apply an appropriate methodology to extract microbial DNA, since biases introduced during the DNA extraction process may result in inaccurate microbial representation. In this study, we attempted to find a DNA extraction protocol which could be effectively used to analyze both the bacterial and fungal community. We evaluated the effect of five DNA extraction methods (QIAamp DNA Stool Mini Kit, PureLinkTM Microbiome DNA Purification Kit, ZR Fecal DNA MiniPrepTM Kit, NucleoSpin® DNA Stool Kit, and IHMS protocol Q) on bacterial and fungal gut microbiome recovery using (i) a defined system of germ-free mice feces spiked with bacterial or fungal strains, and (ii) non-spiked human feces. In our experimental setup, we confirmed that the examined methods significantly differed in efficiency and quality, which affected the identified stool microbiome composition. In addition, our results indicated that fungal DNA extraction might be prone to be affected by reagent/kit contamination, and thus an appropriate blank control should be included in mycobiome research. Overall, standardized IHMS protocol Q, recommended by the International Human Microbiome Consortium, performed the best when considering all the parameters analyzed, and thus could be applied not only in bacterial, but also in fungal microbiome research

The Effect of the Site of Nitrogen Assimilation on Plant Growth

173 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 1999.In this dissertation, I have explored this question experimentally. My approach was to obtain plants with NO3- reduction mostly in the roots or mostly in the leaves, measure growth and biomass allocation parameters of those plants when grown on NO3-, and compare them to growth of wild-type (WT) plants and nitrate reductase deficient mutants. Two techniques were used to manipulate the site of NO 3- reduction: (i) grafting and (ii) genetic transformation. Grafted wildtype and nitrate reductase-deficient pea plants adapted to changes in the location of NO3- reduction. The results support the idea of rapid mixing of metabolite pools and provide evidence for shoot to root signalling of nitrogen status. Utilizing tissue-specific promoters, plants were created with altered levels of nitrate reductase in roots and shoots. The results showed that transformation of WT plants with nia2 tobacco gene resulted in greater alterations in NRA than the transformation of the corresponding double mutant. Changes in growth and co-suppression-like leaf chlorosis was the most frequent outcome, often causing a lowering or disappearance of NRA. A negative correlation between the ratio of root and shoot reduction of nitrate and the root shoot ratio of transformed plants was found. The possible reasons for differences between the two approaches are discussed.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD

The Effect of the Site of Nitrogen Assimilation on Plant Growth

173 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 1999.The allocation of biomass and nutrients to roots and shoots is an important process that affects the morphology of a growing plant and dictates its capacity for photosynthesis, nutrient uptake and other key physiological processes. Plants growing on NO3- differ in the proportion of NO3- reduced in their roots and leaves. The importance of a particular reduction site for the plant is not clear, however. Simulation models suggest that root reduction of NO3 - might increase biomass and nutrient allocation to the root, and possibly result in other growth changes. Understanding the effects of root or shoot NO3- reduction will provide a better understanding of the existing variability in the site of NO 3- reduction in different species and of its physiological and ecological significance.In this dissertation, I have explored this question experimentally. My approach was to obtain plants with NO3- reduction mostly in the roots or mostly in the leaves, measure growth and biomass allocation parameters of those plants when grown on NO3-, and compare them to growth of wild-type (WT) plants and nitrate reductase deficient mutants. Two techniques were used to manipulate the site of NO 3- reduction: (i) grafting and (ii) genetic transformation. Grafted wildtype and nitrate reductase-deficient pea plants adapted to changes in the location of NO3- reduction. The results support the idea of rapid mixing of metabolite pools and provide evidence for shoot to root signalling of nitrogen status. Utilizing tissue-specific promoters, plants were created with altered levels of nitrate reductase in roots and shoots. The results showed that transformation of WT plants with nia2 tobacco gene resulted in greater alterations in NRA than the transformation of the corresponding double mutant. Changes in growth and co-suppression-like leaf chlorosis was the most frequent outcome, often causing a lowering or disappearance of NRA. A negative correlation between the ratio of root and shoot reduction of nitrate and the root shoot ratio of transformed plants was found. The possible reasons for differences between the two approaches are discussed.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD

Data-mining protein structure by clustering, segmentation and evolutionary algorithms

Bio-inspired methods which include evolutionary algorithms are currently widely used to solve very difficult problems. Such problems include bioinformatics problems such as the synthesis of protein structures, identifying parts of DNA, etc. This chapter presents the basic description of evolutionary algorithms and outlining their potential application in bioinformatics.Z(MSM7088352101