Maintenance of the cellobiose utilization genes of Escherichia coli in a cryptic state

The genes for cellobiose utilization are normally cryptic in Escherichia coli. The cellobiose system was used as a model to understand the process by which silent genes are maintained in microbial populations. Previously reported was (1) the isolation of a mutant strain that expresses the cellobiose-utilization (Cel) genes and (2) that expression of those genes allows utilization of three beta- glucoside sugars: cellobiose, arbutin, and salicin. The Cel gene cluster has now been cloned from that mutant strain. In the course of locating the Cel genes within the cloned DNA segment, it was discovered that inactivation of the Cel-encoded hydrolase rendered the host strain sensitive to all three beta-glucosides as potent inhibitors. This sensitivity arises from the accumulation of the phosphorylated beta- glucosides. Because even the fully active genes conferred some degree of beta-glucoside sensitivity, the effects of cellobiose on a series of five Cel+ mutants of independent origin were investigated. Although each of those strains utilizes cellobiose as a sole carbon and energy source, cellobiose also acts as a potent inhibitor that reduces the growth rate on glycerol 2.5-16.5-fold. On the other hand, wild-type strains that cannot utilize cellobiose are not inhibited. The observation that the same compound can serve either as a nutrient or as an inhibitor suggests that, under most conditions in which cellobiose will be present together with other resources, there is a strong selective advantage to having the cryptic (Cel0) allele. In those environments in which cellobiose is the sole, or the best, resource, mutants that express the genes (Cel+) will have a strong selective advantage. It is suggested that temporal alternation between these two conditions is a major factor in the maintenance of these genes in E. coli populations. This alternation of environments and fitnesses was predicted by the model for cryptic-gene maintenance that was previously published.      

Model of a predatory stealth behaviour camouflaging motion

A computational model of a stealth strategy inspired by the apparent mating tactics of male hoverflies is presented. The stealth strategy (motion camouflage) paradoxically allows a predator to approach a moving prey in such a way that it appears to be a stationary object. In the model, the predators are controlled by neural sensorimotor systems that base their decisions on realistic levels of input information. They are shown to be able to employ motion camouflage to approach prey that move along both real hoverfly flight paths and artificially generated flight paths. The camouflaged approaches made demonstrate that the control systems have an ability to predict future prey movements. This is illustrated using two- and three-dimensional simulations.     

Fracture prevention in COPD patients; a clinical 5-step approach

Although osteoporosis and its related fractures are common in patients with COPD, patients at high risk of fracture are poorly identified, and consequently, undertreated. Since there are no fracture prevention guidelines available that focus on COPD patients, we developed a clinical approach to improve the identification and treatment of COPD patients at high risk of fracture. We organised a round-table discussion with 8 clinical experts in the field of COPD and fracture prevention in the Netherlands in December 2013. The clinical experts presented a review of the literature on COPD, osteoporosis and fracture prevention. Based on the Dutch fracture prevention guideline, they developed a 5-step clinical approach for fracture prevention in COPD. Thereby, they took into account both classical risk factors for fracture (low body mass index, older age, personal and family history of fracture, immobility, smoking, alcohol intake, use of glucocorticoids and increased fall risk) and COPD-specific risk factors for fracture (severe airflow obstruction, pulmonary exacerbations and oxygen therapy). Severe COPD (defined as postbronchodilator FEV₁ < 50% predicted) was added as COPD-specific risk factor to the list of classical risk factors for fracture. The 5-step clinical approach starts with case finding using clinical risk factors, followed by risk evaluation (dual energy X-ray absorptiometry and imaging of the spine), differential diagnosis, treatment and follow-up. This systematic clinical approach, which is evidence-based and easy-to-use in daily practice by pulmonologists, should contribute to optimise fracture prevention in COPD patients at high risk of fracture.     

Robust velocity computation from a biologically motivated model of motion perception

Current computational models of motion processing in the primate motion pathway do not cope well with image sequences in which a moving pattern is superimposed upon a static texture. The use of non-linear operations and the need for contrast normalization in motion models mean that the separation of the influences of moving and static patterns on the motion computation is not trivial. Therefore, the response to the superposition of static and moving patterns provides an important means of testing various computational strategies. Here we describe a computational model of motion processing in the visual cortex, one of the advantages of which is that it is highly resistant to interference from static patterns.     

FReD: the floral reflectance database--a web portal for analyses of flower colour

Background

Flower colour is of great importance in various fields relating to floral biology and pollinator behaviour. However, subjective human judgements of flower colour may be inaccurate and are irrelevant to the ecology and vision of the flower''s pollinators. For precise, detailed information about the colours of flowers, a full reflectance spectrum for the flower of interest should be used rather than relying on such human assessments.

Methodology/Principal Findings

The Floral Reflectance Database (FReD) has been developed to make an extensive collection of such data available to researchers. It is freely available at http://www.reflectance.co.uk. The database allows users to download spectral reflectance data for flower species collected from all over the world. These could, for example, be used in modelling interactions between pollinator vision and plant signals, or analyses of flower colours in various habitats. The database contains functions for calculating flower colour loci according to widely-used models of bee colour space, reflectance graphs of the spectra and an option to search for flowers with similar colours in bee colour space.

Conclusions/Significance

The Floral Reflectance Database is a valuable new tool for researchers interested in the colours of flowers and their association with pollinator colour vision, containing raw spectral reflectance data for a large number of flower species.     

From microbial gene essentiality to novel antimicrobial drug targets

Background

Bacterial respiratory tract infections, mainly caused by Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis are among the leading causes of global mortality and morbidity. Increased resistance of these pathogens to existing antibiotics necessitates the search for novel targets to develop potent antimicrobials.

Result

Here, we report a proof of concept study for the reliable identification of potential drug targets in these human respiratory pathogens by combining high-density transposon mutagenesis, high-throughput sequencing, and integrative genomics. Approximately 20% of all genes in these three species were essential for growth and viability, including 128 essential and conserved genes, part of 47 metabolic pathways. By comparing these essential genes to the human genome, and a database of genes from commensal human gut microbiota, we identified and excluded potential drug targets in respiratory tract pathogens that will have off-target effects in the host, or disrupt the natural host microbiota. We propose 249 potential drug targets, 67 of which are targets for 75 FDA-approved antimicrobials and 35 other researched small molecule inhibitors. Two out of four selected novel targets were experimentally validated, proofing the concept.

Conclusion

Here we have pioneered an attempt in systematically combining the power of high-density transposon mutagenesis, high-throughput sequencing, and integrative genomics to discover potential drug targets at genome-scale. By circumventing the time-consuming and expensive laboratory screens traditionally used to select potential drug targets, our approach provides an attractive alternative that could accelerate the much needed discovery of novel antimicrobials.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-958) contains supplementary material, which is available to authorized users.     

Humans deceived by predatory stealth strategy camouflaging motion

Motion camouflage is a stealth strategy that allows a predator to conceal its apparent motion as it approaches a moving prey. Although male hoverflies have been observed to move in a manner consistent with motion camouflage to track females, the successful application of the technique has not previously been demonstrated. This article describes the implementation and results of a psychophysical experiment suggesting that humans are susceptible to motion camouflage. The experiment masqueraded as a computer-game competition. The basis of the competition was a game designed to test the comparative success of different predatory-approach strategies. The experiment showed that predators were able to approach closer to their prey (the player of the game) before being detected when using motion camouflage than when using other approach strategies tested. For an autonomous predator, the calculation of a motion-camouflage approach is a non-trivial problem. It was, therefore, of particular interest that in the game the players were deceived by motion-camouflage predators controlled by artificial neural systems operating using realistic levels of input information. It is suggested that these results are especially of interest to biologists, visual psychophysicists, military engineers and computer-games designers.     

Biological computation of image motion from flows over boundaries.

A theory of early motion processing in the human and primate visual system is presented which is based on the idea that spatio-temporal retinal image data is represented in primary visual cortex by a truncated 3D Taylor expansion that we refer to as a jet vector. This representation allows all the concepts of differential geometry to be applied to the analysis of visual information processing. We show in particular how the generalised Stokes theorem can be used to move from the calculation of derivatives of image brightness at a point to the calculation of image brightness differences on the boundary of a volume in space-time and how this can be generalised to apply to integrals of products of derivatives. We also provide novel interpretations of the roles of direction selective, bi-directional and pan-directional cells and of type I and type II cells in V5/MT.     

Gene and domain duplication in the chordate Otx gene family: insights from amphioxus Otx

We report the genomic organization and deduced protein sequence of a cephalochordate member of the Otx homeobox gene family (AmphiOtx) and show its probable single-copy state in the genome. We also present molecular phylogenetic analysis indicating that there was single ancestral Otx gene in the first chordates which was duplicated in the vertebrate lineage after it had split from the lineage leading to the cephalochordates. Duplication of a C-terminal protein domain has occurred specifically in the vertebrate lineage, strengthening the case for a single Otx gene in an ancestral chordate whose gene structure has been retained in an extant cephalochordate. Comparative analysis of protein sequences and published gene expression patterns suggest that the ancestral chordate Otx gene had roles in patterning the anterior mesendoderm and central nervous system. These roles were elaborated following Otx gene duplication in vertebrates, accompanied by regulatory and structural divergence, particularly of Otx1 descendant genes.