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.

     

Native woody vegetation in central Argentina: Classification of Chaco and Espinal forests

Question

What are the composition and spatial patterns of native woody plant communities in the southern Great Chaco and Espinal?

Location

Córdoba Province, central Argentina, an area of ca. 161,000 km².

Methods

We collected 351 geo‐referenced relevés representative of the geographic, topographic and ecological variation of the Chaco and Espinal woody vegetation in central Argentina. The relevés were classified into vegetation types using the hierarchical ISOPAM method. Forest and shrubland types were described on the basis of diagnostic species occurrences and their distribution in relation to environmental factors. A map of the actual vegetation derived from remote‐sensed images (Landsat) and field data was used to describe the current distribution and abundance of the different vegetation types.

Results

The classification of the 351 plots × 837 species matrix revealed two major clusters comprising seven woody vegetation types corresponding to Chaco lowland and mountain forests and shrublands, Espinal forests and edaphic vegetation. The most important gradients in woody vegetation types are related to elevation, temperature and rainfall variables.

Conclusions

Subtropical seasonally dry woody plant communities from the southern extreme of the Great Chaco and Espinal forests were described for the first time based on complete floristic data. Our results show that lowland Chaco native forests, as well as replacement communities, are still present in its southern distribution range and are well distinguishable from other vegetation types such as the Espinal and mountain forests. Overall, extensive Espinal forests have almost disappeared while Chaco vegetation is highly fragmented and degraded.

     

Phenotypic and genotypic profile of clinical and animal multidrug‐resistant Salmonella enterica isolates from Mexico

Aims

The objective of this study was to obtain a phenotypic and genotypic profile of Salmonella enterica including multidrug‐resistant (MDR) isolates from food‐producing animals and clinical isolates, as well as their genetic relatedness in two different States of Mexico (Jalisco and State of Mexico).

Methods and Results

A total of 243 isolates were evaluated in terms of antimicrobial resistance (AMR) and related genes through a disk diffusion method and PCR respectively; we found 16 MDR isolates, all of them harbouring the bla_CMY gene but not qnr genes, these isolates represent less than 10% of the collection. The pulsed‐field gel electrophoresis revealed a higher genotypic similitude within isolates of State of Mexico than Jalisco.

Conclusions

A low percentage of Salmonella isolates were resistant to relevant antibiotics in human health, nevertheless, the AMR and involved genes were similar despite the different serovars and origin of the isolates.

Significance and Impact of the Study

This investigation provided an insight of the current status of AMR of Salmonella isolates in two States of Mexico and pinpoint the genes involved in AMR and their epidemiological relationship, the information could help to determine an adequate therapy in human and veterinary medicine.     

Carotenoids in roots indicated the level of stress induced by mannitol and sodium azide treatment during the early stages of maize germination

Chemical mutagens, such as sodium azide, have attracted the interest of plant breeders. Azide creates DNA point mutations and affects plant growth and development, disturbs metabolic activity and inhibits protein and DNA replication, whereas mannitol is used to simulate drought stresses in tissue culture. To identify biochemical markers for stress tolerance, maize seeds were germinated under mannitol and sodium azide induced stress in controlled conditions for 7 days. Then levels of chlorophyll, carotenoids, phenolics and aldehydes produced were subsequently determined. Germination percentage was not affected by either mannitol or sodium azide and was always above 85%. However, total fresh weight decreased by 50% with the application of 153.4 mM mannitol and 0.26 mM azide in combination. This treatment significantly reduced plantlet growth from 0.94 g in the control to 0.53 g in the treated materials. Root weight reduced by 68.1%, cotyledons by 14.3%, stems by 65.0% and leaves by 70.0% in treated samples. The level of carotenoids in roots was the clearest biochemical indicator of stress produced by the mannitol and sodium azide treatment. Carotenoids increased from 0.01 µg g^??1 fresh weight in the control to 9.03 µg g^??1 fresh weight in the treated materials. A large-scale seed treatment with mannitol and sodium azide was carried out. 2296 seeds were placed in magenta containers with 153.4 mM mannitol and 0.26 mM NaN₃. At 7 days of germination, the heaviest seedlings (450) (450/2296?=?20%) were transferred to soil environment. Forty-two plants (42/450?=?9.3%) were off-type phenotypes at 45 days. Genetic variants may have been obtained following the novel procedure described here which combines chronic treatment with sodium azide and selection pressure with mannitol to simulate drought conditions.     

The effect of electric fields on brain cephalin and lecithin films

Summary The effect of a direct-current electric field on cephalin and lecithin films was measured using infrared spectral techniques. The intensities of the spectral bands assigned to the vibrations of the phosphate and the fatty acid chain increased to a maximum as the applied potential was increased. These changes were observed only with brain cephalin and brain lecithin films and not with synthetic lipid films. These observations may be due to changes in the alignments of the phosphate and base dipoles in the lipid molecule as the applied field is changed. The electric field strengths at which the maximum intensities of the spectral bands are observed increase as the thickness decreases. Extrapolation to the thickness of the nerve membrane yields a value of the field strength that is much larger than is to be expected in the neuron. This suggests that only the phosphate group and the hydrocarbon chain change conformation during the passage of the nerve impulse.Presented in part at the First Meeting of the International Society for Neurochemistry, 1967, and the 156th Meeting of the American Chemical Society, 1968.     

Purification and characterization of patagonfibrase, a metalloproteinase showing alpha-fibrinogenolytic and hemorrhagic activities, from Philodryas patagoniensis snake venom

Venoms of Colubridae snakes are a rich source of novel compounds, which may have applications in medicine and biochemistry. In the present study, we describe the purification and characterization of a metalloproteinase (patagonfibrase), the first protein to be isolated from Philodryas patagoniensis (Colubridae) snake venom. Patagonfibrase is a single-chain protein, showing a molecular mass of 53,224 Da and an acidic isoelectric point (5.8). It hydrolyzed selectively the Aalpha-chain of fibrinogen and when incubated with fibrinogen or plasma, the thrombin clotting time was prolonged. Prominent hemorrhage developed in mouse skin after intradermal injection of patagonfibrase. When administered into mouse gastrocnemius muscle, it induced local hemorrhage and necrosis, and systemic bleeding in lungs. Patagonfibrase showed proteolytic activity toward azocasein, which was enhanced by Ca(2+) and inhibited by Zn(2+), cysteine, dithiothreitol and Na(2)EDTA. Patagonfibrase impaired platelet aggregation induced by collagen and ADP. Thus, patagonfibrase may play a key role in the pathogenesis of disturbances that occur in P. patagoniensis envenomation, and may be used as a biological tool to explore many facets of hemostasis.     

Synthesis of N-desmethyl derivatives of 17alpha-acetoxy-11beta-(4-N,N-dimethylaminophenyl)-19-norpregna-4,9-die ne-3,20-dione and mifepristone1: substrates for the synthesis of radioligands.

The syntheses of N-desmethyl derivatives of CDB-2914 and the mono-N-desmethyl derivative of Mifepristone are described. We also describe the use of the mono-desmethyl derivatives as substrates for the synthesis of N-tritomethyl derivatives of CDB-2914 and Mifepristone with high specific activity (ca. 80 Ci/mmol), which serve as radioligands for radioimmunoassay.     

Relation between climate and vegetation along a Mediterranean-Temperate boundary in central Italy

The relationship between climate and vegetation was investigated along a Mediterranean-Temperate boundary in central Italy. The study area is a transition zone between the Temperate (Eurosiberian) and Mediterranean regions and has an altitudinal range of almost 1750 m. Ordination and cluster analysis were used. The results did not show any sharp boundary but a climate-vegetation mosaic ranging from upper mountain thermotype and lower hyperhumid ombrotype with Fagus sylvatica L. woodlands at higher altitudes, to meso-Mediterranean thermotype and lower subhumid ombrotype with Mediterranean maquis and Quercus ilex L. woods on the coast. Six phytoclimatic groups are distinguished and described in terms of climatic parameters, vegetation types and morphological and chorological traits. These parameters indicate a change without sharp discontinuities between groups. The Mediterranean to Temperate transition in this Tyrrhenian sector is broad and includes most of the study area.