A safe and complete algorithm for metagenomic assembly

Background

Reconstructing the genome of a species from short fragments is one of the oldest bioinformatics problems. Metagenomic assembly is a variant of the problem asking to reconstruct the circular genomes of all bacterial species present in a sequencing sample. This problem can be naturally formulated as finding a collection of circular walks of a directed graph G that together cover all nodes, or edges, of G.

Approach

We address this problem with the “safe and complete” framework of Tomescu and Medvedev (Research in computational Molecular biology—20th annual conference, RECOMB 9649:152–163, 2016). An algorithm is called safe if it returns only those walks (also called safe) that appear as subwalk in all metagenomic assembly solutions for G. A safe algorithm is called complete if it returns all safe walks of G.

Results

We give graph-theoretic characterizations of the safe walks of G, and a safe and complete algorithm finding all safe walks of G. In the node-covering case, our algorithm runs in time \(O(m^2 + n^3)\), and in the edge-covering case it runs in time \(O(m^2n)\); n and m denote the number of nodes and edges, respectively, of G. This algorithm constitutes the first theoretical tight upper bound on what can be safely assembled from metagenomic reads using this problem formulation.

     

Silver oxynitrate – an efficacious compound for the prevention and eradication of dual-species biofilms

Preventing and eradicating biofilms remains a challenge in clinical and industrial settings. Recently, the present authors demonstrated that silver oxynitrate (Ag₇NO₁₁) prevented and eradicated single-species planktonic and biofilm populations of numerous microbes at lower concentrations than other silver (Ag) compounds. Here, the antimicrobial and anti-biofilm efficacy of Ag₇NO₁₁ is elaborated by testing its in vitro activity against combinations of dual-species, planktonic and biofilm populations of Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa. As further evidence emerges that multispecies bacterial communities are more common in the environment than their single-species counterparts, this study reinforces the diverse applicability of the minimal biofilm eradication concentration (MBEC?) assay for testing antimicrobial compounds against biofilms. Furthermore, this study demonstrated that Ag₇NO₁₁ had enhanced antimicrobial and anti-biofilm activity compared to copper sulfate (CuSO₄) and silver nitrate (AgNO₃) against the tested bacterial species.     

Early Evaluation and Monitoring of Critical Patients with Acute Respiratory Distress Syndrome (ARDS) Using Specific Genetic Polymorphisms

A high percentage of critical patients are found to develop acute respiratory distress syndrome (ARDS). Several studies have reported high mortality rates in these cases which are most frequently associated with multiple organ dysfunctions syndrome. Lately, many efforts have been made to evaluate and monitor ARDS in critical patients. In this regard, the assessment of genetic polymorphisms responsible for developing ARDS present as a challenge and are considered future biomarkers. Early detection of the specific polymorphic gene responsible for ARDS in critically ill patients can prove to be a useful tool in the future, able to help decrease the mortality rates in these cases. Moreover, identifying the genetic polymorphism in these patients can help in the implementation of a personalized intensive therapy scheme for every type of patient, based on its genotype.     

Endogenous circadian rhythms in pigment composition induce changes in photochemical efficiency in plant canopies

There is increasing evidence that the circadian clock is a significant driver of photosynthesis that becomes apparent when environmental cues are experimentally held constant. We studied whether the composition of photosynthetic pigments is under circadian regulation, and whether pigment oscillations lead to rhythmic changes in photochemical efficiency. To address these questions, we maintained canopies of bean and cotton, after an entrainment phase, under constant (light or darkness) conditions for 30–48 h. Photosynthesis and quantum yield peaked at subjective noon, and non‐photochemical quenching peaked at night. These oscillations were not associated with parallel changes in carbohydrate content or xanthophyll cycle activity. We observed robust oscillations of Chl a/b during constant light in both species, and also under constant darkness in bean, peaking when it would have been night during the entrainment (subjective nights). These oscillations could be attributed to the synthesis and/or degradation of trimeric light‐harvesting complex II (reflected by the rhythmic changes in Chl a/b), with the antenna size minimal at night and maximal around subjective noon. Considering together the oscillations of pigments and photochemistry, the observed pattern of changes is counterintuitive if we assume that the plant strategy is to avoid photodamage, but consistent with a strategy where non‐stressed plants maximize photosynthesis.     

Thioureides of 2-(phenoxymethyl)benzoic acid 4-R substituted: A novel class of anti-parasitic compounds

Fifty members of a novel class of antimicrobial compounds, 2-(4-R-phenoxymethyl)benzoic acid thioureides, were synthesized and characterized with respect to their activities against three parasites of human relevance, namely the protozoa Giardia lamblia and Toxoplasma gondii, and the larval (metacestode) stage of the tapeworm Echinococcus multilocularis. To determine the selective toxicity of these compounds, the human colon cancer cell line Caco2 and primary cultures of human foreskin fibroblasts (HFF) were also investigated. The new thioureides were obtained in a three-step-reaction process and subsequently characterized by their physical constants (melting point, solubility). The chemical structures were elucidated by ¹H NMR, ¹³C NMR, IR spectral methods and elemental analysis. The analyses confirmed the final and intermediate compound structures and the synthesis. The compounds were then tested on the parasites in vitro. All thioureides, except two compounds with a nitro group, were totally ineffective against Giardia lamblia. 23 compounds inhibited the proliferation of T. gondii, three of them with an IC₅₀ of approximately 1 μM. The structural integrity of E. multilocularis metacestodes was affected by 22 compounds. In contrast, HFF were not susceptible to any of these thioureides, while Caco2 cells were affected by 17 compounds, two of them inhibiting proliferation with an IC₅₀ in the micromolar range. Thioureides may thus present a promising class of anti-infective agents.     

Patterns of contemporary hybridization inferred from paternity analysis in a four-oak-species forest

Background  

Few studies address the issue of hybridization in a more than two-species context. The species-rich Quercus complex is one of the systems which can offer such an opportunity. To investigate the contemporary pattern of hybridization we sampled and genotyped 320 offspring from a natural mixed forest comprising four species of the European white oak complex: Quercus robur, Q. petraea, Q. pubescens, and Q. frainetto.     

The NCI-N87 cell line as a gastric epithelial barrier model for drug permeability assay

The objective of this study was to evaluate the human NCI-N87 cell line as a model for gastric permeability drug studies under pH conditions of the stomach. The optimal conditions that led NCI-N87 cells to form a typical differentiated gastric epithelial barrier were a seeding density of 2.5 × 10⁵ cells/cm² on porous inserts and growth in serum-complemented RPMI-1640 medium until 18–27 days post-confluency. The resulting cell monolayers showed moderately high transepithelial electrical resistance (TEER) values of about 500 Ω cm², cells of polygonal morphology expressing E-cadherin and ZO-1 proteins at their contact surfaces, and production of mucus clusters. The monolayers withstood apical pH of 7.4 down to 3.0 with the basal pH fixed at 7.4. The apparent permeability coefficients (P_app) of model compounds were evaluated in the apical-to-basolateral and basolateral-to-apical directions under different pH gradients. The monolayers were impermeable to the integrity marker Lucifer Yellow (low P_app of 0.3–1.1 × 10⁻⁶ cm/s). The furosemide P_app (0.4–1.5 × 10⁻⁵ cm/s) were slightly dependent on pH but remained moderate. The caffeine P_app (4.2–5.0 × 10⁻⁵ cm/s) were higher and insensitive to pH changes. The NCI-N87 cell line provides a useful in vitro tool to assess gastric drug permeability and absorption under physiologic conditions prevailing in the human stomach.