Covering Pairs in Directed Acyclic Graphs

The Minimum Path Cover problem on directed acyclic graphs (DAGs) is a classical problem that provides a clear and simple mathematical formulation for several applications in different areas and that has an efficient algorithmic solution. In this paper, we study the computational complexity of two constrained variants of Minimum Path Cover motivated by the recent introduction of next-generation sequencing technologies in bioinformatics. The first problem (MinPCRP), given a DAG and a set of pairs of vertices, asks for a minimum cardinality set of paths "covering" all the vertices such that both vertices of each pair belong to the same path. For this problem, we show that, while it is NP-hard to compute if there exists a solution consisting of at most three paths, it is possible to decide in polynomial time whether a solution consisting of at most two paths exists. The second problem (MaxRPSP), given a DAG and a set of pairs of vertices, asks for a path containing the maximum number of the given pairs of vertices. We show its NP-hardness and also its W[1]-hardness when parametrized by the number of covered pairs. On the positive side, we give a fixed-parameter algorithm when the parameter is the maximum overlapping degree, a natural parameter in the bioinformatics applications of the problem

1012-101 Vascular Smooth Muscle-Directed Adenovlral Vectors

Gene transfer to the vascular wall utilizing locally-delivered recombinant adenoviral vectors has shown promise as a novel technique for therapeutic as well as experimental modulation of vascular wall gene expression. Infusion of such vectors using porous balloon catheters (PBC) has previously been demonstrated to result in transduction of extravascular cells at the delivery site, as well as substantial systemic transduction as a consequence of release of vector into the circulation. Introduction of a vascular-directed promoter into the adenoviral vector should thus contribute to targeting the expression of genes to the vascular wall, while reducing peri-vascular and systemic expression. In order to test the feasibility of utilizing the vascular smooth muscle α-actin (SMA) promoter to confer tissue specificity upon a recombinant adenoviral vector, we constructed an adenovirus (AvLacZ5) employing a 1.1 kilobase region of the murine SMA promoter to direct the expression of the nuclear-targeted beta-galactosidase (lacZ) gene and evaluated gene transduction by this vector, in comparison with a vector differing only by the presence of the RSV-LTR promoter. Several cell types were used as targets, including bovine aortic smooth muscle cells (BASMC). human pulmonary epithelial carcinoma cells (A549 cells), and transformed human embryonic kidney epithelial cells which are competent to replicate these adenoviral vectors (293 cells). The vector incorporating the SMA promoter demonstrated substantial selectivity for vascular smooth muscle gene expression, with typical transductions carried out in parallel under identical conditions manifesting 90–95% lacZ-expressing BASMC, 0.3% lacZ-positive A549 cells, and 4% positive 293 cells. Conversely, parallel transductions with the vector employing the RSV promoter typically resulted in 95–99% lac-expressing 293 cells at vector concentrations yielding only 5–10% positive BASMC. These data support cell lineage-specificity of AvLacZ5 at the level of promoter function rather than due to intrinsic cellular differences in capacity for adenovirally-mediated transduction. However, it is notable that a limited subpopulation of 293 cells clearly are able to direct sufficient transcription from the SMA promoter sequences chosen to yield detectable lacZ expression; the molecular basis for this heterogeneity of expression remains to be determined. Adenoviral vectors utilizing these promoter sequences may render vascular-restricted gene transfer feasible when used in conjunction with mechanical devices providing a component of spatial localization

SAMStat: monitoring biases in next generation sequencing data

Motivation: The sequence alignment/map format (SAM) is a commonly used format to store the alignments between millions of short reads and a reference genome. Often certain positions within the reads are inherently more likely to contain errors due to the protocols used to prepare the samples. Such biases can have adverse effects on both mapping rate and accuracy. To understand the relationship between potential protocol biases and poor mapping we wrote SAMstat, a simple C program plotting nucleotide overrepresentation and other statistics in mapped and unmapped reads in a concise html page. Collecting such statistics also makes it easy to highlight problems in the data processing and enables non-experts to track data quality over time

GM-CSF Regulates Alveolar Macrophage Differentiation and Innate Immunity in the Lung through PU.1

AbstractGM-CSF gene targeted (GM−/−) mice are susceptible to respiratory infections and develop alveolar proteinosis due to defects in innate immune function and surfactant catabolism in alveolar macrophages (AMs), respectively. Reduced cell adhesion, phagocytosis, pathogen killing, mannose- and Toll-like receptor expression, and LPS- or peptidoglycan-stimulated TNFα release were observed in AMs from GM−/− mice. The transcription factor PU.1 was markedly reduced in AMs of GM−/− mice in vivo and was restored by selective expression of GM-CSF in the lungs of SPC-GM/GM−/− transgenic mice. Retrovirus-mediated expression of PU.1 in AMs from GM−/− mice rescued host defense functions and surfactant catabolism by AMs. We conclude that PU.1 mediates GM-CSF-dependent effects on terminal differentiation of AMs regulating innate immune functions and surfactant catabolism by AMs

Thyroid hormone regulates distinct paths to maturation in pigment cell lineages

Thyroid hormone (TH) regulates diverse developmental events and can drive disparate cellular outcomes. In zebrafish, TH has opposite effects on neural crest derived pigment cells of the adult stripe pattern, limiting melanophore population expansion, yet increasing yellow/orange xanthophore numbers. To learn how TH elicits seemingly opposite responses in cells having a common embryological origin, we analyzed individual transcriptomes from thousands of neural crest-derived cells, reconstructed developmental trajectories, identified pigment cell-lineage specific responses to TH, and assessed roles for TH receptors. We show that TH promotes maturation of both cell types but in distinct ways. In melanophores, TH drives terminal differentiation, limiting final cell numbers. In xanthophores, TH promotes accumulation of orange carotenoids, making the cells visible. TH receptors act primarily to repress these programs when TH is limiting. Our findings show how a single endocrine factor integrates very different cellular activities during the generation of adult form

RNA editing signature during myeloid leukemia cell differentiation

Adenosine deaminases acting on RNA (ADARs) are key proteins for hematopoietic stem cell self-renewal and for survival of differentiating progenitor cells. However, their specific role in myeloid cell maturation has been poorly investigated. Here we show that ADAR1 is present at basal level in the primary myeloid leukemia cells obtained from patients at diagnosis as well as in myeloid U-937 and THP1 cell lines and its expression correlates with the editing levels. Upon phorbol-myristate acetate or Vitamin D3/granulocyte macrophage colony-stimulating factor (GM-CSF)-driven differentiation, both ADAR1 and ADAR2 enzymes are upregulated, with a concomitant global increase of A-to-I RNA editing. ADAR1 silencing caused an editing decrease at specific ADAR1 target genes, without, however, interfering with cell differentiation or with ADAR2 activity. Remarkably, ADAR2 is absent in the undifferentiated cell stage, due to its elimination through the ubiquitin–proteasome pathway, being strongly upregulated at the end of the differentiation process. Of note, peripheral blood monocytes display editing events at the selected targets similar to those found in differentiated cell lines. Taken together, the data indicate that ADAR enzymes play important and distinct roles in myeloid cells

Sorting apples from oranges in single-cell expression comparisons.

Two methods for comparing single-cell expression datasets help address the challenge of integrating data across conditions and experiments

ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data

RNA-Seq and microarray platforms have emerged as important tools for detecting changes in gene expression and RNA processing in biological samples. We present ExpressionPlot, a software package consisting of a default back end, which prepares raw sequencing or Affymetrix microarray data, and a web-based front end, which offers a biologically centered interface to browse, visualize, and compare different data sets. Download and installation instructions, a user's manual, discussion group, and a prototype are available at http://expressionplot.com/ webcite.ALS Therapy Allianc

Exploration of wheat and pathogen transcriptomes during tan spot infection

Objectives: The fungus Pyrenophora tritici-repentis is the causal agent of tan spot, a major disease of wheat (Triticum aestivum). Here, we used RNA sequencing to generate transcriptional datasets for both the host and pathogen during infection and during in vitro pathogen growth stages. Data description: To capture gene expression during wheat infection with the P. tritici-repentis isolate M4, RNA datasets were generated for wheat inoculated with P. tritici-repentis (infection) and a mock (control) at 3 and 4 days post-infection, when scorable leaf disease symptoms manifest. The P. tritici-repentis isolate M4 was also RNA sequenced to capture gene expression in vitro at two different growth stages: 7-day old vegetative mycelia and 9-day old sporulating mycelia, to coincide with a latent growth stage and early sporulation respectively. In total, 6 RNA datasets are available to aid in the validation of predicted genes of P. tritici-repentis and wheat. The datasets generated offer an insight into the transcriptomic profile of the host-pathogen interaction and can be used to investigate the expression of a subset of transcripts or targeted genes prior to designing cost-intensive RNA sequencing experiments, that would be best further explored with replication and a time series analysis

IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels

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