Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized

Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity

Background: Environmental mycobacteria (EM) include species commonly found in various terrestrial and aquatic environments, encompassing animal and human pathogens in addition to saprophytes. Approximately 150 EM species can be separated into fast and slow growers based on sequence and copy number differences of their 16S rRNA genes. Cultivation methods are not appropriate for diversity studies; few studies have investigated EM diversity in soil despite their importance as potential reservoirs of pathogens and their hypothesized role in masking or blocking M. bovis BCG vaccine. Methods: We report here the development, optimization and validation of molecular assays targeting the 16S rRNA gene to assess diversity and prevalence of fast and slow growing EM in representative soils from semi tropical and temperate areas. New primer sets were designed also to target uniquely slow growing mycobacteria and used with PCR-DGGE, tag-encoded Titanium amplicon pyrosequencing and quantitative PCR. Results: PCR-DGGE and pyrosequencing provided a consensus of EM diversity; for example, a high abundance of pyrosequencing reads and DGGE bands corresponded to M. moriokaense, M. colombiense and M. riyadhense. As expected pyrosequencing provided more comprehensive information; additional prevalent species included M. chlorophenolicum, M. neglectum, M. gordonae, M. aemonae. Prevalence of the total Mycobacterium genus in the soil samples ranged from 2.3×107 to 2.7×108 gene targets g−1; slow growers prevalence from 2.9×105 to 1.2×107 cells g−1. Conclusions: This combined molecular approach enabled an unprecedented qualitative and quantitative assessment of EM across soil samples. Good concordance was found between methods and the bioinformatics analysis was validated by random resampling. Sequences from most pathogenic groups associated with slow growth were identified in extenso in all soils tested with a specific assay, allowing to unmask them from the Mycobacterium whole genus, in which, as minority members, they would have remained undetected

Evolutionary tradeoffs in cellular composition across diverse bacteria

One of the most important classic and contemporary interests in biology is the connection between cellular composition and physiological function. Decades of research have allowed us to understand the detailed relationship between various cellular components and processes for individual species, and have uncovered common functionality across diverse species. However, there still remains the need for frameworks that can mechanistically predict the tradeoffs between cellular functions and elucidate and interpret average trends across species. Here we provide a comprehensive analysis of how cellular composition changes across the diversity of bacteria as connected with physiological function and metabolism, spanning five orders of magnitude in body size. We present an analysis of the trends with cell volume that covers shifts in genomic, protein, cellular envelope, RNA and ribosomal content. We show that trends in protein content are more complex than a simple proportionality with the overall genome size, and that the number of ribosomes is simply explained by cross-species shifts in biosynthesis requirements. Furthermore, we show that the largest and smallest bacteria are limited by physical space requirements. At the lower end of size, cell volume is dominated by DNA and protein content—the requirement for which predicts a lower limit on cell size that is in good agreement with the smallest observed bacteria. At the upper end of bacterial size, we have identified a point at which the number of ribosomes required for biosynthesis exceeds available cell volume. Between these limits we are able to discuss systematic and dramatic shifts in cellular composition. Much of our analysis is connected with the basic energetics of cells where we show that the scaling of metabolic rate is surprisingly superlinear with all cellular components

Design, fabrication and control of soft robots

Conventionally, engineers have employed rigid materials to fabricate precise, predictable robotic systems, which are easily modelled as rigid members connected at discrete joints. Natural systems, however, often match or exceed the performance of robotic systems with deformable bodies. Cephalopods, for example, achieve amazing feats of manipulation and locomotion without a skeleton; even vertebrates such as humans achieve dynamic gaits by storing elastic energy in their compliant bones and soft tissues. Inspired by nature, engineers have begun to explore the design and control of soft-bodied robots composed of compliant materials. This Review discusses recent developments in the emerging field of soft robotics.National Science Foundation (U.S.) (Grant IIS-1226883

Имитация распределенной обработки информации в вычислительных системах и локальных вычислительных сетях

Предложено использовать для анализа вариантов организации распределенной обработки информации в вычислительных системах и локальных вычислительных сетях вероятностный граф реализации вычислительного процесса с явными связями типа вероятностных сетевых графиков.Запропоновано використовувати для аналізу варіантів організації розподіленої обробки інформації в обчислювальних системах і в локальних обчислювальних мережах імовірнісний граф реалізації обчислювального процесу з явними зв’язками типу імовірнісних сіткових графіків.It іs оffered to use for analyzing variants of organization of distributed information processing in computing systems and local computing networks a probabilistic graph for realizing a computing process with evident relationships of the type probabilistic network diagrams

Prevention of ulcer disease in goldfish by means of vaccination

A vaccine comprising cells of Aeromonas bestiarum grown in tryptic soy broth and atypical A. salmonicida cells produced in iron-limited and iron-supplemented media protected goldfish Carassius auratus when administered by immersion (dosage ≈ 5 × 107 cells/mL for 60 s) followed after 28 d by an oral booster (dosage = 5 × 107 cells/g of feed), which was fed for 7 d so that each fish received about 1 g of vaccine-containing feed. After challenge by intramuscular injection of a virulent culture of atypical A. salmonicida, the relative percent survival (RPS) was more than 90%. The approach was more successful than using a commercial furunculosis vaccine with or without supplementation with A. bestiarum or atypical A. salmonicida cells. Moreover, a smooth derivative of the virulent rough culture of atypical A. salmonicida was less effective as a vaccine candidate, yielding an RPS of only 65%. Low antibody titers of 1:39–1:396 were found in the vaccinated fish. The vaccinated fish had a significantly higher proportion of dead head kidney macrophages (10.9 ± 3.5%; P = 0.0149) than did the controls (6.8 ± 3.1%). However, differences in the number of erythrocytes and leukocytes, the level of phagocytic and lysozyme activities, and the proportion of lymphocytes, monocytes, and polymorphonuclear cells were not statistically significant between the two groups

Geomicrobiology of the built environment

Microbial colonization and growth can have significant effects in the built environment, resulting in a range of effects from discolouration and staining to biodeterioration and decay. In some cases, formation of biofilms, crusts and patinas may confer bioprotection of the substrate. This perspective aims to discuss how geomicrobial transformations in the natural environment - particularly involving rocks, minerals, metals and organic matter - may be applied to understand similar processes occurring on fabricated human structures. However, the built environment may offer further strictures as well as benefits for microbial activity and these should be taken into consideration when considering analogy with natural processes, especially when linking observations of microbial biodiversity to the more obvious manifestations of microbial attack