On Feedback Vertex Set: New Measure and New Structures

We present a new parameterized algorithm for the {feedback vertex set} problem ({\sc fvs}) on undirected graphs. We approach the problem by considering a variation of it, the {disjoint feedback vertex set} problem ({\sc disjoint-fvs}), which finds a feedback vertex set of size $k$ that has no overlap with a given feedback vertex set $F$ of the graph $G$. We develop an improved kernelization algorithm for {\sc disjoint-fvs} and show that {\sc disjoint-fvs} can be solved in polynomial time when all vertices in $G \setminus F$ have degrees upper bounded by three. We then propose a new branch-and-search process on {\sc disjoint-fvs}, and introduce a new branch-and-search measure. The process effectively reduces a given graph to a graph on which {\sc disjoint-fvs} becomes polynomial-time solvable, and the new measure more accurately evaluates the efficiency of the process. These algorithmic and combinatorial studies enable us to develop an $O^*(3.83^k)$-time parameterized algorithm for the general {\sc fvs} problem, improving all previous algorithms for the problem.Comment: Final version, to appear in Algorithmic

Depth, Highness and DNR Degrees

A sequence is Bennett deep [5] if every recursive approximation of the Kolmogorov complexity of its initial segments from above satisfies that the difference between the approximation and the actual value of the Kolmogorov complexity of the initial segments dominates every constant function. We study for different lower bounds r of this difference between approximation and actual value of the initial segment complexity, which properties the corresponding r(n)-deep sets have. We prove that for r(n) = εn, depth coincides with highness on the Turing degrees. For smaller choices of r, i.e., r is any recursive order function, we show that depth implies either highness or diagonally-non-recursiveness (DNR). In particular, for left-r.e. sets, order depth already implies highness. As a corollary, we obtain that weakly-useful sets are either high or DNR. We prove that not all deep sets are high by constructing a low order-deep set. Bennett's depth is defined using prefix-free Kolmogorov complexity. We show that if one replaces prefix-free by plain Kolmogorov complexity in Bennett's depth definition, one obtains a notion which no longer satisfies the slow growth law (which stipulates that no shallow set truth-table computes a deep set); however, under this notion, random sets are not deep (at the unbounded recursive order magnitude). We improve Bennett's result that recursive sets are shallow by proving all K-trivial sets are shallow; our result is close to optimal. For Bennett's depth, the magnitude of compression improvement has to be achieved almost everywhere on the set. Bennett observed that relaxing to infinitely often is meaningless because every recursive set is infinitely often deep. We propose an alternative infinitely often depth notion that doesn't suffer this limitation (called i.o. depth).We show that every hyperimmune degree contains a i.o. deep set of magnitude εn, and construct a π01- class where every member is an i.o. deep set of magnitude εn. We prove that every non-recursive, non-DNR hyperimmune-free set is i.o. deep of constant magnitude, and that every nonrecursive many-one degree contains such a set

TbPIF5 Is a Trypanosoma brucei Mitochondrial DNA Helicase Involved in Processing of Minicircle Okazaki Fragments

Trypanosoma brucei's mitochondrial genome, kinetoplast DNA (kDNA), is a giant network of catenated DNA rings. The network consists of a few thousand 1 kb minicircles and several dozen 23 kb maxicircles. Here we report that TbPIF5, one of T. brucei's six mitochondrial proteins related to Saccharomyces cerevisiae mitochondrial DNA helicase ScPIF1, is involved in minicircle lagging strand synthesis. Like its yeast homolog, TbPIF5 is a 5′ to 3′ DNA helicase. Together with other enzymes thought to be involved in Okazaki fragment processing, TbPIF5 localizes in vivo to the antipodal sites flanking the kDNA. Minicircles in wild type cells replicate unidirectionally as theta-structures and are unusual in that Okazaki fragments are not joined until after the progeny minicircles have segregated. We now report that overexpression of TbPIF5 causes premature removal of RNA primers and joining of Okazaki fragments on theta structures. Further elongation of the lagging strand is blocked, but the leading strand is completed and the minicircle progeny, one with a truncated H strand (ranging from 0.1 to 1 kb), are segregated. The minicircles with a truncated H strand electrophorese on an agarose gel as a smear. This replication defect is associated with kinetoplast shrinkage and eventual slowing of cell growth. We propose that TbPIF5 unwinds RNA primers after lagging strand synthesis, thus facilitating processing of Okazaki fragments

Rudimentary G-Quadruplex-Based Telomere Capping In Saccharomyces Cerevisiae

Telomere capping conceals chromosome ends from exonucleases and checkpoints, but the full range of capping mechanisms is not well defined. Telomeres have the potential to form G-quadruplex (G4) DNA, although evidence for telomere G4 DNA function in vivo is limited. In budding yeast, capping requires the Cdc13 protein and is lost at nonpermissive temperatures in cdc13-1 mutants. Here, we use several independent G4 DNA-stabilizing treatments to suppress cdc13-1 capping defects. These include overexpression of three different G4 DNA binding proteins, loss of the G4 DNA unwinding helicase Sgs1, or treatment with small molecule G4 DNA ligands. In vitro, we show that protein-bound G4 DNA at a 3\u27 overhang inhibits 5\u27-\u3e 3\u27 resection of a paired strand by exonuclease I. These findings demonstrate that, at least in the absence of full natural capping, G4 DNA can play a positive role at telomeres in vivo

JEFET SCHWILI ERZÄHLT. Hundertneunundsechzig jemenitische Volkserzählungen aufgeszeichnet in Israel 1957 - 1960. Herausgegeben von DOV NOY. Supplement - Serie zu Fabula , Reihe A, Band 4. Walter de Gruyter, Berlin 1963.

Precautionary conservation and cooperative global governance are needed to protect Antarctic blue carbon: the world’s largest increasing natural form of carbon storage with high sequestration potential. As patterns of ice‐loss around Antarctica become more uniform, there is an underlying increase in carbon capture‐to‐storage‐to‐sequestration on the seafloor. The amount of carbon captured per unit area is increasing and the area available to blue carbon is also increasing. Carbon sequestration could further increase under moderate (+1 °C) ocean warming, contrary to decreasing global blue carbon stocks elsewhere. For example, in warmer waters, mangroves and seagrasses are in decline and benthic organisms are close to their physiological limits, so a 1°C increase in water temperature could push them above their thermal tolerance (e.g. bleaching of coral reefs). In contrast, on the basis of past change and current research we expect that Antarctic blue carbon could increase by orders of magnitude.The Antarctic seafloor is biophysically unique and the site of carbon sequestration, the benthos, faces less anthropogenic disturbance than any other ocean continental shelf environment. This isolation imparts both vulnerability to change, and an avenue to conserve one of the world’s last biodiversity refuges. In economic terms, the value of Antarctic blue carbon is estimated at between £0.65 billion and £1.76 billion (~2.27 billion USD), for sequestered carbon in the benthos around the continental shelf. To balance biodiversity protection against society’s economic objectives, this paper builds on a proposal incentivising protection by building a ‘non‐market framework’ via the 2015 Paris Agreement to the United Nations Framework Convention on Climate Change. This could be connected and coordinated through the Antarctic Treaty System to promote and motivate member states to value Antarctic blue carbon and maintain scientific integrity and conservation for the positive societal values ingrained in the Antarctic Treaty System

Signatures of arithmetic simplicity in metabolic network architecture

Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their evolutionary history and complex wiring constitutes one of the most fascinating open questions in biology, intimately related to the enigma of life's origin itself. Is the evolution of metabolism subject to general principles, beyond the unpredictable accumulation of multiple historical accidents? Here we search for such principles by applying to an artificial chemical universe some of the methodologies developed for the study of genome scale models of cellular metabolism. In particular, we use metabolic flux constraint-based models to exhaustively search for artificial chemistry pathways that can optimally perform an array of elementary metabolic functions. Despite the simplicity of the model employed, we find that the ensuing pathways display a surprisingly rich set of properties, including the existence of autocatalytic cycles and hierarchical modules, the appearance of universally preferable metabolites and reactions, and a logarithmic trend of pathway length as a function of input/output molecule size. Some of these properties can be derived analytically, borrowing methods previously used in cryptography. In addition, by mapping biochemical networks onto a simplified carbon atom reaction backbone, we find that several of the properties predicted by the artificial chemistry model hold for real metabolic networks. These findings suggest that optimality principles and arithmetic simplicity might lie beneath some aspects of biochemical complexity

Mineral and volatile composition of agua-mel from Portugal

Agua-mel (honey-water) is a typical honey-based product produced by the Portuguese beekeepers, particularly in southern Portugal. Agua-mel was characterized by mineral content and volatiles contents. Mineral content evaluation was performed based on a random sampling of 14 samples from a total of 16 samples provided by local producers. Mineral content showed that potassium predominated in agua-mel samples (1270-4105 mg/kg). The concentration of aluminium in one sample was tenfold higher (5.8 mg/kg) than in the remaining samples (0.3-0.6 mg/kg). Agua-mel volatiles were isolated by hydrodistillation and analysed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) from a subset of eight samples. Cluster analysis showed two poorly correlated clusters (S (corr) < 0.3). Cluster I only sample was dominated by trans-beta-ocimene (19 %), gamma-terpinene (15 %) and 2-furfural (9 %). Cluster II that included the remaining seven samples showed two moderately correlated subclusters (S (corr) < 0.5). The six samples with high correlation from subcluster IIa were dominated by 2-furfural (18-41 %) and benzene acetaldehyde (12-39 %). n-Nonadecane (14 %), n-heneicosane and 2-furfural (both 13 %) were the main components of subcluster IIb sample. Although the presence of some volatile compounds can help in the correlation between agua-mel and honey botanical source, the final product varies largely according to the preparation process even for the same producer, in different years. Agua-mel detailed characterization may assist in bringing added value to this typical Portuguese honey-based product

Preventive interventions in families with parental depression: children’s psychosocial symptoms and prosocial behaviour

The aim is to document the effectiveness of a preventive family intervention (Family Talk Intervention, FTI) and a brief psychoeducational discussion with parents (Let’s Talk about the Children, LT) on children’s psychosocial symptoms and prosocial behaviour in families with parental mood disorder, when the interventions are practiced in psychiatric services for adults in the finnish national health service. Patients with mood disorder were invited to participate with their families. Consenting families were randomized to the two intervention groups. The initial sample comprised 119 families and their children aged 8–16. Of these, 109 completed the interventions and the baseline evaluation. Mothers and fathers filled out questionnaires including standardized rating scales for children’s symptoms and prosocial behaviour at baseline and at 4, 10 and 18 months post-intervention. The final sample consisted of parental reports on 149 children with 83 complete data sets. Both interventions were effective in decreasing children’s emotional symptoms, anxiety, and marginally hyperactivity and in improving children’s prosocial behaviour. The FTI was more effective than the LT on emotional symptoms particularly immediately after the intervention, while the effect of the LT emerged after a longer interval. The study supports the effectiveness of both interventions in families with depressed parents. The FTI is applicable in cultural settings other than the USA. Our findings provide support for including preventive child mental health measures as part of psychiatric services for mentally ill parents

Effects of Intracellular Calcium and Actin Cytoskeleton on TCR Mobility Measured by Fluorescence Recovery

Background: The activation of T lymphocytes by specific antigen is accompanied by the formation of a specialized signaling region termed the immunological synapse, characterized by the clustering and segregation of surface molecules and, in particular, by T cell receptor (TCR) clustering. Methodology/Principal Findings: To better understand TCR motion during cellular activation, we used confocal microscopy and photo-bleaching recovery techniques to investigate the lateral mobility of TCR on the surface of human T lymphocytes under various pharmacological treatments. Using drugs that cause an increase in intracellular calcium, we observed a decrease in TCR mobility that was dependent on a functional actin cytoskeleton. In parallel experiments measurement of filamentous actin by FACS analysis showed that raising intracellular calcium also causes increased polymerization of the actin cytoskeleton. These in vitro results were analyzed using a mathematical model that revealed effective binding parameters between TCR and the actin cytoskeleton. Conclusion/Significance: We propose, based on our results, that increase in intracellular calcium levels leads to actin polymerization and increases TCR/cytoskeleton interactions that reduce the overall mobility of the TCR. In a physiological setting, this may contribute to TCR re-positioning at the immunological synapse

Identification of a Bacterial-Like HslVU Protease in the Mitochondria of Trypanosoma brucei and Its Role in Mitochondrial DNA Replication

ATP-dependent protease complexes are present in all living organisms, including the 26S proteasome in eukaryotes, Archaea, and Actinomycetales, and the HslVU protease in eubacteria. The structure of HslVU protease resembles that of the 26S proteasome, and the simultaneous presence of both proteases in one organism was deemed unlikely. However, HslVU homologs have been identified recently in some primordial eukaryotes, though their potential function remains elusive. We characterized the HslVU homolog from Trypanosoma brucei, a eukaryotic protozoan parasite and the causative agent of human sleeping sickness. TbHslVU has ATP-dependent peptidase activity and, like its bacterial counterpart, has essential lysine and N-terminal threonines in the catalytic subunit. By epitope tagging, TbHslVU localizes to mitochondria and is associated with the mitochondrial genome, kinetoplast DNA (kDNA). RNAi of TbHslVU dramatically affects the kDNA by causing over-replication of the minicircle DNA. This leads to defects in kDNA segregation and, subsequently, to continuous network growth to an enormous size. Multiple discrete foci of nicked/gapped minicircles are formed on the periphery of kDNA disc, suggesting a failure in repairing the gaps in the minicircles for kDNA segregation. TbHslVU is a eubacterial protease identified in the mitochondria of a eukaryote. It has a novel function in regulating mitochondrial DNA replication that has never been observed in other organisms