Virtual profiling: a new way to analyse phenotypes

Simulation models can be used to perform virtual profiling in order to analyse eco‐physiological processes controlling plant phenotype. To illustrate this, an eco‐physiological model has been used to compare and contrast the status of a virtual fruit system under two situations of carbon supply. The model simulates fruit growth, accumulation of sugar, citric acid and water, transpiration, respiration and ethylene emission, and was successfully tested on peach (Prunus persica L. Batsch) for two leaf‐to‐fruit ratios (6 and 18 leaves per fruit). The development stage and the variation in leaf number had large effects of the fruit model variables dealing with growth, metabolism and fruit quality. A sensitivity analysis showed that changing a single parameter value, which could correspond to a genotypic change induced by a mutation, either strongly affects most of the processes, or affects a specific process or none. Correlation analysis showed that, in a complex system such as fruit, the intensity of many physiological processes and quality traits co‐varies. It also showed unexpected co‐variations resulting from emergent properties of the system. This virtual profiling approach opens a new route to explore the impact of mutations, or naturally occurring genetic variations, under differing environmental conditions.     

Asymmetric cell division: a new way to divide unequally

It has long been known that cells can divide unequally by shifting the mitotic spindle to one side. Two recent reports identify an alternative way to generate daughter cells of different sizes.     

Modulated excitability: a new way to obtain bursting neurons

Classical burster models are based on a fast system that either oscillates or is quiescent, depending on temporarily fixed values of slow variables. In a study of the lobster heart ganglion, we found a new type of burster for which the fast system is globally stable for all relevant fixed values of the slow variables. We describe how this burster works and speculate on its biological significance. Received: 14 July 1994 / Accepted in revised form: 25 October 1994     

Photosensitizers and antioxidants: a way to new drugs?

Photodynamic therapy (PDT) is a relatively new modality of treatment of diseases involving uncontrolled cell proliferation. It is based on the production of reactive species upon illumination of a photosensitizer in the presence of oxygen. Antioxidants are primarily reducing agents prone to scavenge reactive species in one way or another. Their presence in photodynamic reactions usually reduces the efficacy of PDT. Some antioxidants like ascorbic acid, alpha-tocopherol or butyl-4-hydroxyanisole, however, when added to cells at adequate concentrations may enhance the photodamaging activity of PDT. The presence of transition metals and precise timing of antioxidant administration may also be important factors in increasing the efficacy of PDT. Antioxidant carrier sensitizers have been designed, synthesised and tested for their antibacterial PDT activity. The promising results raise the question whether the introduction of antioxidant moieties into sensitizer molecules would lead to the synthesis of highly effective new drugs.     

Cell migration: fibroblasts find a new way to get ahead

Fibroblasts migrate on two-dimensional (2D) surfaces by forming lamellipodia-actin-rich extensions at the leading edge of the cell that have been well characterized. In this issue, Petrie et al. (2012. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201201124) show that in some 3D environments, including tissue explants, fibroblasts project different structures, termed lobopodia, at the leading edge. Lobopodia still assemble focal adhesions; however, similar to membrane blebs, they are driven by actomyosin contraction and do not accumulate active Rac, Cdc42, and phosphatidylinositol 3-kinases.     

Toponomics and neurotoponomics: a new way to medical systems biology

The fluorescence robot imaging technology multi-epitope-ligand-cartography/toponome imaging system has revolutionized the field of proteomics/functional genomics, because it enables the investigator to locate and decipher functional protein networks, the toponome, consisting of hundreds of different proteins in a single cell or tissue section. The technology has been proven to solve key problems in biology and therapy research. It has uncovered a new cellular transdifferentiation mechanism of vascular cells giving rise to myogenic cells in situ and in vivo; a finding that has led to efficient cell therapy models of muscle disorders, and discovered a new target protein in sporadic amyotrophic lateral sclerosis by hierarchical protein network analysis, a finding that has been confirmed by a mouse knockout model. A lead target protein in tumor cells that controls cell polarization as a mechanism that is fundamental for migration and metastasis formation has also been uncovered, and new functional territories in the CNS defined by high-dimensional synaptic protein clusters have been unveiled. The technology can be effectively interlocked with genomics and proteomics to optimize time-to-market and the overall attrition rate of new drugs. This review outlines major proofs of principle with an emphasis on neurotoponomics.     

SHIPing news: a new way to keep your weight down

Almost always, obesity is an obligate prerequisite for the development of type 2 diabetes mellitus. Loss of a well-known lipid phosphatase appears to prevent insulin-resistant diabetes in mice by removal of a positive regulator of adiposity.     

Sequence logos: a new way to display consensus sequences.

A graphical method is presented for displaying the patterns in a set of aligned sequences. The characters representing the sequence are stacked on top of each other for each position in the aligned sequences. The height of each letter is made proportional to its frequency, and the letters are sorted so the most common one is on top. The height of the entire stack is then adjusted to signify the information content of the sequences at that position. From these 'sequence logos', one can determine not only the consensus sequence but also the relative frequency of bases and the information content (measured in bits) at every position in a site or sequence. The logo displays both significant residues and subtle sequence patterns.     

Toponomics and neurotoponomics: a new way to medical systems biology

The fluorescence robot imaging technology multi-epitope-ligand-cartography/toponome imaging system has revolutionized the field of proteomics/functional genomics, because it enables the investigator to locate and decipher functional protein networks, the toponome, consisting of hundreds of different proteins in a single cell or tissue section. The technology has been proven to solve key problems in biology and therapy research. It has uncovered a new cellular transdifferentiation mechanism of vascular cells giving rise to myogenic cells in situ and in vivo; a finding that has led to efficient cell therapy models of muscle disorders, and discovered a new target protein in sporadic amyotrophic lateral sclerosis by hierarchical protein network analysis, a finding that has been confirmed by a mouse knockout model. A lead target protein in tumor cells that controls cell polarization as a mechanism that is fundamental for migration and metastasis formation has also been uncovered, and new functional territories in the CNS defined by high-dimensional synaptic protein clusters have been unveiled. The technology can be effectively interlocked with genomics and proteomics to optimize time-to-market and the overall attrition rate of new drugs. This review outlines major proofs of principle with an emphasis on neurotoponomics.     

Bacterial effector interplay: a new way to view effector function

Bacterial pathogens are dependent on virulence factors to efficiently colonize and propagate within their hosts. Many Gram-negative bacterial pathogens rely on specialized proteinaceous secretion systems that inject virulence factors, termed effectors, directly into host cells. These bacterial effector proteins perform various functions within host cells; however, regulation of their function within the host cell is highly enigmatic. It is becoming increasingly apparent that many of these effectors directly influence and regulate each other and their mechanisms within the host cell. We discuss the emerging theme of bacterial effector interplay impacting infection and the importance of investigating this topic.     

Acridone-tagged DNA as a new probe for DNA detection by fluorescence resonance energy transfer and for mismatch DNA recognition

Acridone is highly fluorescent and stable against photodegradation, oxidation, and heat. It is also a small molecule with no charge, making it a promising fluorescent agent for use in a DNA probe. Thus, we have prepared 5'-terminal acridone-labeled DNAs by post-modification, and have examined their photophysical properties and their use as donors for a fluorescence resonance energy transfer (FRET) system in combination with a 3'-terminal dabcyl-tagged DNA as an acceptor, which can detect the target DNA by emission-quenching caused by FRET. The FRET with an acridone and dabcyl pair has been found to complement that with fluorescence and dabcyl and other fluorescence-quencher pairs. Significant amounts of quenching of the acridone emissions by guanine in the DNA were observed when guanine was close to acridone, which can be applied as a quencher-free probe for the detection of special sequence of DNA. The DNA bearing acridone at the C5 position of inner thymidine could discriminate the opposite T-T base mismatch, although enhancement of discrimination ability is needed for the practical use of SNP typing.     

Focal plane array infrared imaging: a new way to analyse leaf tissue

* Here, a new approach to macromolecular imaging of leaf tissue using a multichannel focal plane array (FPA) infrared detector was compared with the proven method of infrared mapping with a synchrotron source, using transverse sections of leaves from a species of Eucalyptus. * A new histological method was developed, ideally suited to infrared spectroscopic analysis of leaf tissue. Spatial resolution and the signal-to-noise ratio of the FPA imaging and synchrotron mapping methods were compared. * An area of tissue 350 microm(2) required approx. 8 h to map using the synchrotron technique and approx. 2 min to image using the FPA. The two methods produced similar infrared images, which differentiated all tissue types in the leaves according to their macromolecular chemistry. * The synchrotron and FPA methods produced similar results, with the synchrotron method having superior signal-to-noise ratio and potentially better spatial resolution, whereas the FPA method had the advantage in terms of data acquisition time, expense and ease of use. FPA imaging offers a convenient, laboratory-based approach to microscopic chemical imaging of leaves.     

Targeted genotyping by sequencing: a new way to genome profile the cat

Targeted GBS is a recent approach for obtaining an effective characterization for hundreds to thousands of markers. The high throughput of next‐generation sequencing technologies, moreover, allows sample multiplexing. The aims of this study were to (i) define a panel of single nucleotide polymorphisms (SNPs) in the cat, (ii) use GBS for profiling 16 cats, and (iii) evaluate the performance with respect to the inference using standard approaches at different coverage thresholds, thereby providing useful information for designing similar experiments. Probes for sequencing 230 variants were designed based on the Felis_catus_8.0. 8.0 genome. The regions comprised anonymous and non‐anonymous SNPs. Sixteen cat samples were analysed, some of which had already been genotyped in a large group of loci and one having been whole‐genome sequenced in the 99_Lives Cat Genome Sequencing Project. The accuracy of the method was assessed by comparing the GBS results with the genotypes already available. Overall, GBS achieved good performance, with 92–96% correct assignments, depending on the coverage threshold used to define the set of trustable genotypes. Analyses confirmed that (i) the reliability of the inference of each genotype depends on the coverage at that locus and (ii) the fraction of target loci whose genotype can be inferred correctly is a function of the total coverage. GBS proves to be a valid alternative to other methods. Data suggested a depth of less than 11× is required for greater than 95% accuracy. However, sequencing depth must be adapted to the total size of the targets to ensure proper genotype inference.