Distribution and function of prophage phiRv1 and phiRv2 among Mycobacterium tuberculosis complex

Mycobacterium tuberculosis complex (MTBC) is notorious for causing diseases, such as tuberculosis. Tuberculosis caused by M. tuberculosis remains a global public health concern. Two prophages, phiRv1 and phiRv2, can be found among most MTBC genomes. However, no precise functions have been assigned for the two prophages. In this paper, to find out the function of these two prophages, the distribution and function of phiRv1 and phiRv2 in MTBC genomes were analyzed from multiple omics data. We found that complex insertion, deletion, and reorganization appeared on the locus of two prophages in MTBC genomes; some genes of the two prophages can be translated and are functional from proteomic data; the expression of other prophage genes, such as Rv1577c, Rv2650c, Rv2652c, Rv2659c, and Rv2658c, can vary with environmental stresses and might enhance the fitness of MTBC. These data will facilitate our in-depth understanding of their function.     

A novel task scheduling approach based on dynamic queues and hybrid meta-heuristic algorithms for cloud computing environment

Task scheduling is one of the most challenging aspects to improve the overall performance of cloud computing and optimize cloud utilization and Quality of Service (QoS). This paper focuses on Task Scheduling optimization using a novel approach based on Dynamic dispatch Queues (TSDQ) and hybrid meta-heuristic algorithms. We propose two hybrid meta-heuristic algorithms, the first one using Fuzzy Logic with Particle Swarm Optimization algorithm (TSDQ-FLPSO), the second one using Simulated Annealing with Particle Swarm Optimization algorithm (TSDQ-SAPSO). Several experiments have been carried out based on an open source simulator (CloudSim) using synthetic and real data sets from real systems. The experimental results demonstrate the effectiveness of the proposed approach and the optimal results is provided using TSDQ-FLPSO compared to TSDQ-SAPSO and other existing scheduling algorithms especially in a high dimensional problem. The TSDQ-FLPSO algorithm shows a great advantage in terms of waiting time, queue length, makespan, cost, resource utilization, degree of imbalance, and load balancing.     

Explaining variability in the production of seed and allergenic pollen by invasive <Emphasis Type="Italic">Ambrosia artemisiifolia</Emphasis> across Europe

To better manage invasive populations, it is vital to understand the environmental drivers underlying spatial variation in demographic performance of invasive individuals and populations. The invasive common ragweed, Ambrosia artemisiifolia, has severe adverse effects on agriculture and human health, due to its vast production of seeds and allergenic pollen. Here, we identify the scale and nature of environmental factors driving individual performance of A. artemisiifolia, and assess their relative importance. We studied 39 populations across the European continent, covering different climatic and habitat conditions. We found that plant size is the most important determinant in variation of per-capita seed and pollen production. Using plant volume as a measure of individual performance, we found that the local environment (i.e. the site) is far more influential for plant volume (explaining 25% of all spatial variation) than geographic position (regional level; 8%) or the neighbouring vegetation (at the plot level; 4%). An overall model including environmental factors at all scales performed better (27%), including the weather (bigger plants in warm and wet conditions), soil type (smaller plants on soils with more sand), and highlighting the negative effects of altitude, neighbouring vegetation and bare soil. Pollen and seed densities varied more than 200-fold between sites, with highest estimates in Croatia, Romania and Hungary. Pollen densities were highest on arable fields, while highest seed densities were found along infrastructure, both significantly higher than on ruderal sites. We discuss implications of these findings for the spatial scale of management interventions against A. artemisiifolia.     

Simultaneous increase in cellular content and volumetric concentration of lipids in <Emphasis Type="Italic">Bracteacoccus bullatus</Emphasis> cultivated at reduced nitrogen and phosphorus concentrations

Manipulation of the nutrient concentration is an inexpensive and efficient method for increasing lipid and TAG accumulation in algal cells. However, high volumetric production requires finding a proper balance between the decrease of biomass production and the increase in the total lipid content. We isolated a strain of green microalga Bracteacoccus bullatus and increased its lipid content from 17 to 59% of biomass dry weight by manipulating of nitrogen and phosphorus content in the medium. The 10-fold reduction of the nitrogen and phosphorus concentration in the medium was the most efficient method of the lipid induction compared to nutrient deplete and high nutrient conditions. The oleic (48–64% mass of total fatty acids) and linoleic (14–24% mass of total fatty acids) acids dominated in the fatty acid profile, thus making this strain a suitable candidate for biodiesel production.     

Testing transposable elements as genetic drive mechanisms using Drosophila P element constructs as a model system

The use of transposable elements (TEs) as genetic drive mechanisms was explored using Drosophila melanogaster as a model system. Alternative strategies, employing autonomous and nonautonomous P element constructs were compared for their efficiency in driving the ry⁺ allele into populations homozygous for a ry^- allele at the genomic rosy locus. Transformed flies were introduced at 1%, 5%, and 10% starting frequencies to establish a series of populations that were monitored over the course of 40 generations, using both phenotypic and molecular assays. The transposon-borne ry⁺ marker allele spread rapidly in almost all populations when introduced at 5% and 10% seed frequencies, but 1% introductions frequently failed to become established. A similar initial rapid increase in frequency of the ry⁺ transposon occurred in several control populations lacking a source of transposase. Constructs carrying ry⁺ markers also increased to moderate frequencies in the absence of selection on the marker. The results of Southern and in situ hybridization studies indicated a strong inverse relationship between the degree of conservation of construct integrity and transposition frequency. These finding have relevance to possible future applications of transposons as genetic drive mechanisms. This revised version was published online in July 2006 with corrections to the Cover Date.     

Short Communication: Antibiotic resistance among faecal coliform bacteria isolated from wastewater before and after treatment by an experimental sand filter

During the functioning period of a sand filter, 254 and 234 faecal-coliform strains were isolated from raw wastewater and reclaimed effluent, respectively. When tested for their susceptibility to ampicillin, kanamycin, chloramphenicol, streptomycin and tetracycline, 53% of the strains from the raw sewage and 84% of those isolated from the effluent were resistant to at least one antibiotic. The high incidence of drug resistance in the effluent was connected with a high proportion of Klebsiella pneumoniae, Enterobacter cloacae and Citrobacter freundii.     

Whole-Genome Shotgun Optical Mapping of Rhodospirillum rubrum

Rhodospirillum rubrum is a phototrophic purple nonsulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems and as a source of hydrogen and biodegradable plastic production. To better understand this organism and to facilitate assembly of its sequence, three whole-genome restriction endonuclease maps (XbaI, NheI, and HindIII) of R. rubrum strain ATCC 11170 were created by optical mapping. Optical mapping is a system for creating whole-genome ordered restriction endonuclease maps from randomly sheared genomic DNA molecules extracted from cells. During the sequence finishing process, all three optical maps confirmed a putative error in sequence assembly, while the HindIII map acted as a scaffold for high-resolution alignment with sequence contigs spanning the whole genome. In addition to highlighting optical mapping's role in the assembly and confirmation of genome sequence, this work underscores the unique niche in resolution occupied by the optical mapping system. With a resolution ranging from 6.5 kb (previously published) to 45 kb (reported here), optical mapping advances a “molecular cytogenetics” approach to solving problems in genomic analysis.     

A Bioinformatician's Guide to Metagenomics

Summary: As random shotgun metagenomic projects proliferate and become the dominant source of publicly available sequence data, procedures for the best practices in their execution and analysis become increasingly important. Based on our experience at the Joint Genome Institute, we describe the chain of decisions accompanying a metagenomic project from the viewpoint of the bioinformatic analysis step by step. We guide the reader through a standard workflow for a metagenomic project beginning with presequencing considerations such as community composition and sequence data type that will greatly influence downstream analyses. We proceed with recommendations for sampling and data generation including sample and metadata collection, community profiling, construction of shotgun libraries, and sequencing strategies. We then discuss the application of generic sequence processing steps (read preprocessing, assembly, and gene prediction and annotation) to metagenomic data sets in contrast to genome projects. Different types of data analyses particular to metagenomes are then presented, including binning, dominant population analysis, and gene-centric analysis. Finally, data management issues are presented and discussed. We hope that this review will assist bioinformaticians and biologists in making better-informed decisions on their journey during a metagenomic project.