A Universal Point Set for 2-Outerplanar Graphs

A point set $S \subseteq \mathbb{R}^2$ is universal for a class $\cal G$ if every graph of ${\cal G}$ has a planar straight-line embedding on $S$. It is well-known that the integer grid is a quadratic-size universal point set for planar graphs, while the existence of a sub-quadratic universal point set for them is one of the most fascinating open problems in Graph Drawing. Motivated by the fact that outerplanarity is a key property for the existence of small universal point sets, we study 2-outerplanar graphs and provide for them a universal point set of size $O(n \log n)$.Comment: 23 pages, 11 figures, conference version at GD 201

Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB

BACKGROUND: Combination of biochemical and bioinformatic analyses led to the discovery of oxidative demethylation – a novel DNA repair mechanism catalyzed by the Escherichia coli AlkB protein and its two human homologs, hABH2 and hABH3. This discovery was based on the prediction made by Aravind and Koonin that AlkB is a member of the 2OG-Fe(2+ )oxygenase superfamily. RESULTS: In this article, we report identification and sequence analysis of five human members of the (2OG-Fe(2+)) oxygenase superfamily designated here as hABH4 through hABH8. These experimentally uncharacterized and poorly annotated genes were not associated with the AlkB family in any database, but are predicted here to be phylogenetically and functionally related to the AlkB family (and specifically to the lineage that groups together hABH2 and hABH3) rather than to any other oxygenase family. Our analysis reveals the history of ABH gene duplications in the evolution of vertebrate genomes. CONCLUSIONS: We hypothesize that hABH 4–8 could either be back-up enzymes for hABH1-3 or may code for novel DNA or RNA repair activities. For example, enzymes that can dealkylate N3-methylpurines or N7-methylpurines in DNA have not been described. Our analysis will guide experimental confirmation of these novel human putative DNA repair enzymes

Superpatterns and Universal Point Sets

An old open problem in graph drawing asks for the size of a universal point set, a set of points that can be used as vertices for straight-line drawings of all n-vertex planar graphs. We connect this problem to the theory of permutation patterns, where another open problem concerns the size of superpatterns, permutations that contain all patterns of a given size. We generalize superpatterns to classes of permutations determined by forbidden patterns, and we construct superpatterns of size n^2/4 + Theta(n) for the 213-avoiding permutations, half the size of known superpatterns for unconstrained permutations. We use our superpatterns to construct universal point sets of size n^2/4 - Theta(n), smaller than the previous bound by a 9/16 factor. We prove that every proper subclass of the 213-avoiding permutations has superpatterns of size O(n log^O(1) n), which we use to prove that the planar graphs of bounded pathwidth have near-linear universal point sets.Comment: GD 2013 special issue of JGA

Increased Responsiveness to Toll-Like Receptor 4 Stimulation in Peripheral Blood Mononuclear Cells from Patients with Recent Onset Rheumatoid Arthritis

Background. Cell signaling via Toll-like receptors (TLRs) leads to synovial inflammation in rheumatoid arthritis (RA). We aimed to assess effects of TLR2 and TLR4 stimulation on proinflammatory cytokine production by peripheral blood mononuclear cells (PBMCs) from patients with recent-onset RA, osteoarthrosis (OA), and healthy control (HC). Methods. PBMCs were stimulated with LPS, biglycan and cytokine mix. Cytokines were analyzed in supernatants with ELISA. Expression of toll-like receptors mRNA in leukocytes was analyzed using real-time qPCR. Results. PBMCs from RA patients spontaneously produced less IL-6 and TNFα than cells from OA and HC subjects. LPS increased cytokines' production in all groups. In RA patients increase was dramatic (30 to 48-fold and 17 to 31-fold, for respective cytokines) compared to moderate (2 to 8-fold) in other groups. LPS induced 15-HETE generation in PBMCs from RA (mean 251%) and OA patients (mean 43%), although only in OA group, the increase was significant. TLR2 and TLR4 gene expressions decreased in response to cytokine mix, while LPS enhanced TLR2 expression in HC and depressed TLR4 expression in OA patients. Conclusion. PBMCs from recent-onset RA patients are overresponsive to stimulation with bacterial lipopolysaccharide. TLR expression is differentially regulated in healthy and arthritic subjects

The RNA–Methyltransferase Misu (NSun2) Poises Epidermal Stem Cells to Differentiate

Homeostasis of most adult tissues is maintained by balancing stem cell self-renewal and differentiation, but whether post-transcriptional mechanisms can regulate this process is unknown. Here, we identify that an RNA methyltransferase (Misu/Nsun2) is required to balance stem cell self-renewal and differentiation in skin. In the epidermis, this methyltransferase is found in a defined sub-population of hair follicle stem cells poised to undergo lineage commitment, and its depletion results in enhanced quiescence and aberrant stem cell differentiation. Our results reveal that post-transcriptional RNA methylation can play a previously unappreciated role in controlling stem cell fate

Cities and Disturbed Areas as Man-made Shelters for Orchid Communities

Many species from the family Orchidaceae spread in anthropogenic habitats and numerous studies documenting this process are known. Unfortunately, such data are scattered throughout various papers and reports, sometimes fragmentary and hard to reach (the ‘grey literature’). Scientific elaboration on this topic still lacks a comprehensive review and summary of the scale of this phenomenon. Therefore, the main aim of this study was to gather, review and analyse such data, seeking the answer to the question whether the man-made habitats can be considered as refugee for orchids. The paper summarises data on the occurrence of orchid species in man-made habitats in Europe originating from published and unpublished sources. The particular emphasis was placed in urban habitats. For this purpose, the floristically data from 42 European cities were used. The conducted studies showed that the apohytism phenomenon in the family Orchidaceae was more widespread than had been previously reported. As a result, 70 species of orchids in the distinguished man-made habitats were found. The majority of the species grow on sand and clay pits. The most common species were Epipactis helleborine and Dactylorhiza majalis. The gathered data have confirmed that man-made habitats become refugee for many orchid species in the aftermath of the loss of their natural habitats. Thus, protection of sites transformed by man with orchid occurrence should be taken into consideration. These sites can become a source of very useful information for biogeographically and phylo-geographically analyses of many valuable and endangered species

Model Checking for Formal Verification of Space Systems

The goal of the presented activity is to integrate an existing model checking engine – SPIN1 – with the TASTE2 MBSE environment. For this purpose, the modelling languages used in TASTE – ASN.1, AADL and SDL need to be translated into PROMELA, a language for modelling and verification of concurrent systems. This paper describes the current achievements of the activity – proposal of a TASTE model checking workflow, formalization of requirement specification and established PROMELA translation patterns. Finally, the development of SDL models for validation of the tools and exploration of their utility in the design of space systems is discussed

De novo genome assembly of Solanum sitiens reveals structural variation associated with drought and salinity tolerance

Motivation: Solanum sitiens is a self-incompatible wild relative of tomato, characterised by salt and drought resistance traits, with the potential to contribute through breeding programmes to crop improvement in cultivated tomato. This species has a distinct morphology, classification and ecotype compared to other stress resistant wild tomato relatives such as S. pennellii and S. chilense. Therefore, the availability of a reference genome for S. sitiens will facilitate the genetic and molecular understanding of salt and drought resistance. Results: A high-quality de novo genome and transcriptome assembly for S. sitiens (Accession LA1974) has been developed. A hybrid assembly strategy was followed using Illumina short reads (~159X coverage) and PacBio long reads (~44X coverage), generating a total of ~262 Gbp of DNA sequence. A reference genome of 1,245 Mbp, arranged in 1,483 scaffolds with a N50 of 1.826 Mbp was generated. Genome completeness was estimated at 95% using the Benchmarking Universal Single-Copy Orthologs (BUSCO) and the K-mer Analysis Tool (KAT). In addition, ~63 Gbp of RNA-Seq were generated to support the prediction of 31,164 genes from the assembly, and to perform a de novo transcriptome. Lastly, we identified three large inversions compared to S. lycopersicum, containing several drought resistance related genes, such as beta-amylase 1 and YUCCA7. Availability: S. sitiens (LA1974) raw sequencing, transcriptome and genome assembly have been deposited at the NCBI’s Sequence Read Archive, under the BioProject number “PRJNA633104”