Tissue repair and stem cell renewal in carcinogenesis

Cancer is increasingly being viewed as a stem cell disease, both in its propagation by a minority of cells with stem-cell-like properties and in its possible derivation from normal tissue stem cells. But stem cell activity is tightly controlled, raising the question of how normal regulation might be subverted in carcinogenesis. The long-known association between cancer and chronic tissue injury, and the more recently appreciated roles of Hedgehog and Wnt signalling pathways in tissue regeneration, stem cell renewal and cancer growth together suggest that carcinogenesis proceeds by misappropriating homeostatic mechanisms that govern tissue repair and stem cell self-renewal.     

Three modes of synaptic vesicular recycling revealed by single-vesicle imaging

Synapses recycle their spent vesicles in order to keep up with on-going neurotransmitter release. To investigate vesicle recycling in the small synapses of hippocampal neurons, we have used an optical recording method that permits us to resolve single-vesicle events. Here we show that an exocytic event can terminate with three modes of vesicle retrieval: a fast (400-860 ms) 'kiss-and-run' mode that has a selective fusion pore; a slow (8-21 s) 'compensatory' mode; and a 'stranded' mode of recycling, in which a vesicle is left on the cell surface until a nerve impulse triggers its retrieval. We have also observed that, in response to a nerve impulse, synapses with low release probability primarily use the kiss-and-run mode, whereas high release probability terminals predominantly use the compensatory mode of vesicle retrieval.     

Using Wittgenstein’s Family Resemblance Principle to Learn Exemplars

The introduction of the notion of family resemblance represented a major shift in Wittgenstein’s thoughts on the meaning of words, moving away from a belief that words were well defined, to a view that words denoted less well defined categories of meaning. This paper presents the use of the notion of family resemblance in the area of machine learning as an example of the benefits that can accrue from adopting the kind of paradigm shift taken by Wittgenstein. The paper presents a model capable of learning exemplars using the principle of family resemblance and adopting Bayesian networks for a representation of exemplars. An empirical evaluation is presented on three data sets and shows promising results that suggest that previous assumptions about the way we categories need reopening.

Association of the ADAM33 gene with asthma and bronchial hyperresponsiveness

Asthma is a common respiratory disorder characterized by recurrent episodes of coughing, wheezing and breathlessness. Although environmental factors such as allergen exposure are risk factors in the development of asthma, both twin and family studies point to a strong genetic component. To date, linkage studies have identified more than a dozen genomic regions linked to asthma. In this study, we performed a genome-wide scan on 460 Caucasian families and identified a locus on chromosome 20p13 that was linked to asthma (log(10) of the likelihood ratio (LOD), 2.94) and bronchial hyperresponsiveness (LOD, 3.93). A survey of 135 polymorphisms in 23 genes identified the ADAM33 gene as being significantly associated with asthma using case-control, transmission disequilibrium and haplotype analyses (P = 0.04 0.000003). ADAM proteins are membrane-anchored metalloproteases with diverse functions, which include the shedding of cell-surface proteins such as cytokines and cytokine receptors. The identification and characterization of ADAM33, a putative asthma susceptibility gene identified by positional cloning in an outbred population, should provide insights into the pathogenesis and natural history of this common disease.     

IgH class switching and translocations use a robust non-classical end-joining pathway

Immunoglobulin variable region exons are assembled in developing B cells by V(D)J recombination. Once mature, these cells undergo class-switch recombination (CSR) when activated by antigen. CSR changes the heavy chain constant region exons (Ch) expressed with a given variable region exon from Cmu to a downstream Ch (for example, Cgamma, Cepsilon or Calpha), thereby switching expression from IgM to IgG, IgE or IgA. Both V(D)J recombination and CSR involve the introduction of DNA double-strand breaks and their repair by means of end joining. For CSR, double-strand breaks are introduced into switch regions that flank Cmu and a downstream Ch, followed by fusion of the broken switch regions. In mammalian cells, the 'classical' non-homologous end joining (C-NHEJ) pathway repairs both general DNA double-strand breaks and programmed double-strand breaks generated by V(D)J recombination. C-NHEJ, as observed during V(D)J recombination, joins ends that lack homology to form 'direct' joins, and also joins ends with several base-pair homologies to form microhomology joins. CSR joins also display direct and microhomology joins, and CSR has been suggested to use C-NHEJ. Xrcc4 and DNA ligase IV (Lig4), which cooperatively catalyse the ligation step of C-NHEJ, are the most specific C-NHEJ factors; they are absolutely required for V(D)J recombination and have no known functions other than C-NHEJ. Here we assess whether C-NHEJ is also critical for CSR by assaying CSR in Xrcc4- or Lig4-deficient mouse B cells. C-NHEJ indeed catalyses CSR joins, because C-NHEJ-deficient B cells had decreased CSR and substantial levels of IgH locus (immunoglobulin heavy chain, encoded by Igh) chromosomal breaks. However, an alternative end-joining pathway, which is markedly biased towards microhomology joins, supports CSR at unexpectedly robust levels in C-NHEJ-deficient B cells. In the absence of C-NHEJ, this alternative end-joining pathway also frequently joins Igh locus breaks to other chromosomes to generate translocations.     

Investigation of coupled cobalt–silver nanoparticle system by plan view TEM

We present a transmission electron microscopy (TEM) investigation of a coupled cobalt and silver nanoparticle system. A plan view in situ lift-out method for preparing samples for TEM using the focused ion beam (FIB) microscope was used. This technique is used to prepare high quality TEM samples with site specificity in a short time and with a high success rate. We demonstrate the ability of the plan view sample preparation technique to provide information about an ordered system of nanoparticles which could not be observed using standard FIB cross sectioning of the sample. High resolution TEM and energy dispersive X-ray spectroscopy mapping of both cross sectional and plan view samples are presented, clearly showing the significant benefit of plan view TEM analysis for certain samples     

An Architecture of Computer Aided Process Planning System Integrated with Scheduling Using Decision Support System

Process planning and scheduling are two major plann in g and control activities that consume significant part of the lead-time, theref ore all attempts are being made to reduce lead-time by automating them. Compute r Aided Process Planning (CAPP) is a step in this direction. Most of the existin g CAPP systems do not consider scheduling while generating a process plan. Sched uling is done separately after the process plan has been generated and therefore , it is possible that a process plan so generated is e...