Classification-based comparison of pre-processing methods for interpretation of mass spectrometry generated clinical datasets

Background  

Mass spectrometry is increasingly being used to discover proteins or protein profiles associated with disease. Experimental design of mass-spectrometry studies has come under close scrutiny and the importance of strict protocols for sample collection is now understood. However, the question of how best to process the large quantities of data generated is still unanswered. Main challenges for the analysis are the choice of proper pre-processing and classification methods. While these two issues have been investigated in isolation, we propose to use the classification of patient samples as a clinically relevant benchmark for the evaluation of pre-processing methods.     

Belowground ABA boosts aboveground production of DIMBOA and primes induction of chlorogenic acid in maize

Plants are important mediators between above- and belowground herbivores. Consequently, interactions between root and shoot defenses can have far-reaching impacts on entire food webs. We recently reported that infestation of maize roots by larvae of the beetle Diabrotica virgifera virgifera induced shoot resistance against herbivores and pathogens. Root herbivory also enhanced aboveground DIMBOA and primed for enhanced induction of chlorogenic acid, two secondary metabolites that have been associated with plant stress resistance. Interestingly, the plant hormone abscisic acid (ABA) emerged as a putative long-distance signal in the regulation of these systemic defenses. In this addendum, we have investigated the role of root-derived ABA in aboveground regulation of DIMBOA and the phenolic compounds chlorogenic acid, caffeic and ferulic acid. Furthermore, we discuss the relevance of ABA in relation to defense against the leaf herbivore Spodoptera littoralis. Soil-drench treatment with ABA mimicked root herbivore-induced accumulation of DIMBOA in the leaves. Similarly, ABA mimicked aboveground priming of chlorogenic acid production, causing augmented induction of this compound after subsequent shoot attack by S. littoralis caterpillars. These findings confirm our notion that ABA acts as an important signal in the regulation of aboveground defenses during belowground herbivory. However, based on our previous finding that ABA alone is not sufficient to trigger aboveground resistance against S. littoralis caterpillars, our results also suggest that the ABA-inducible effects on DIMBOA and chlorogenic acid are not solely responsible for root herbivore-induced resistance against S. littoralis.Key words: induced resistance, Spodoptera littoralis, Zea mays, Diabrotica virgifera, DIMBOA, chlorogenic acid, absisic acid, priming     

mlstdbNet – distributed multi-locus sequence typing (MLST) databases

Background  

Multi-locus sequence typing (MLST) is a method of typing that facilitates the discrimination of microbial isolates by comparing the sequences of housekeeping gene fragments. The mlstdbNet software enables the implementation of distributed web-accessible MLST databases that can be linked widely over the Internet.     

A rat model to study the role of STn antigen in colon cancer

Expression of the mucin-associated sialyl-Tn (STn) antigen has been associated with a decreased survival in patients with colorectal, gastric, and ovarian cancer. To better understand the role of STn antigen in tumor biology, we developed STn(+) (called LP) and STn(-) (called LN) clonal cell lines from a parental metastatic rat colon carcinoma cell line (LMCR). Both derivative cell lines exhibited identical proliferation rates in vitro. LP cells strongly expressed STn antigen both in vitro and in vivo, and were poorly tumorigenic when given to syngeneic rats. LN cells did not express STn antigen in vitro, but as in vivo tumors these cells rapidly acquired STn expression, readily formed tumors, and were highly lethal. When rats were given an otherwise lethal inoculum of i.p. LN cells, pre-immunization with synthetic STn antigen conjugated to keyhole limpet hemocyanin (STn-KLH) resulted in a 60% survival rate. When LN cells were injected subcutaneously in the presence of STn-KLH-sensitized lymphocytes, tumor growth was decreased. Distribution of STn antigen in normal organs of host rats is quite similar to that of humans. This model mimics human disease and should facilitate studies of mucin-associated antigens in tumor biology and the development of immunotherapeutic agents based on mucin-related antigens.     

Mechanically Induced Calcium Movements in Astrocytes, Bovine Aortic Endothelial Cells and C6 Glioma Cells

Forces applied to resting primary astrocytes, bovine aortic endothelial cells and C6 glioma cells with collagen-coated magnetite particles produce a fast transient change of intracellular Ca²⁺. It peaks in the micromolar range as measured by Fura-2. This mechanical response adapts within seconds so that repeated stimulation causes smaller responses requiring >10 min for recovery. When cytoplasmic Ca²⁺ is high after treating with ATP, cyclopiazonic acid and thapsigargin, stimulation causes a transient decrease in Ca²⁺. In these three cell types, no influx of ions is required for Ca²⁺ elevation showing the response is not caused by activation of plasmalemmal mechanosensitive channels. Approximately half the cells tested showed similar behavior, while the other half, such as fibroblasts, required extracellular Ca²⁺. The Ca²⁺ response is not temperature sensitive suggesting the possible involvement of intracellular mechanosensitive channels. We tested a number of second messenger reagents and were only able to block the response in BAECs, but not C6 glioma cells, with Xestospongin C, a blocker of IP₃-activated channels. Despite the lack of a causal involvement of plasmalemmal mechanosensitive channels, mechanical stimulation immediately activates a persistent Mn²⁺ influx pathway. This Mn²⁺ pathway may be mechanosensitive channels, Ca²⁺-activated cation channels or depletion-activated Ca²⁺ channels. Received: 7 July 1999/Revised: 12 November 1999     

Casein Accumulation by Rat Mammary Epithelial Cells Grown within a Reconstituted Basement Membrane Is Modulated by Fatty Acids in a Hormone- and Time-Dependent Manner

The mammary gland is under complex regulation involving the participation of hormones, growth factors, and stromal components, including lipids. Our laboratory has developed a unique primary culture system that allows undifferentiated mammary epithelial cells from immature virgin rats to proliferate and differentiate to an extent equivalent to the lactating mammary gland. Using this model system we have examined the effects of the unsaturated fatty acids oleate and linoleate on mammary epithelial cell proliferation as well as both morphological and functional differentiation. Neither fatty acid showed any effect on cell proliferation whether added to cells in the presence of optimal serum-free medium or under suboptimal conditions of epidermal growth factor (EGF) and prolactin. Morphological differentiation also was not affected by fatty acid addition under either optimal or suboptimal conditions, although a decrease was observed when medium depleted in EGF and prolactin was compared to optimal medium. The notable finding in this study was that both oleate and linoleate modulated functional differentiation, as assessed by casein accumulation, in a time- and hormone-dependent manner. At early times in culture, casein levels were stimulated by both oleate and linoleate; this effect was most dramatic under suboptimal conditions of prolactin and EGF. In marked contrast, however, linoleate decreased casein levels by approximately 50% in optimal medium, at all concentrations tested, after at least 7 days in culture. This decrease was also observed in suboptimal medium, although the concentration of EGF and prolactin influenced the extent of the reduction. Although the mechanism is currently unknown, it is tempting to speculate that the cellular and biochemical events that result in linoleate-induced inhibition of functional differentiation may also be involved in the tumor-enhancing properties of this fatty acid.     

Site specific labelling of sugar residues in oligoribonucleotides: reactions of aliphatic isocyanates with 2' amino groups.

Considerable effort has been directed towards studying the structure and function of nucleic acids and several approaches rely on the attachment of reporter groups or reactive functional groups to nucleic acids. We report here the selective modification of 2-amino groups in oligoribonucleotides, through their reaction with aliphatic isocyanates, to give the corresponding 2'-urea derivatives in >95% yield. Furthermore, such modification with (2-isocyanato)ethyl 2-pyridyl disulfide enables subsequent coupling to other thiols (such as those contained in peptides and proteins) or to thiol-reactive electrophiles. A modified decamer was not significantly destabilized by the 2'-urea group, compared with a 2'-amino group, as demonstrated by a mere 1.3 degrees C drop in the melting temperature of the duplex.     

Isolation and Characterization of Basal Cells from Human Upper Respiratory Epithelium

Cellular pathways of normal and reparative differentiation of upper airway epithelium are not well understood. Of the three main cell types, basal and secretory cells are known to divide, while ciliated cells are considered terminally differentiated. Several investigations support the role of the basal cell as a progenitor cell type, but others suggest that the secretory cell can regenerate a complete mucocilliary epithelium. Thus, lineage relationships within renewing adult epithelia are still unclear. Understanding the pathways involved in upper airway epithelial cell differentiation is critical for studying injury and repair mechanisms and for developing clinical strategies for tracheal reconstruction. We undertook the current studies to determine the integrin profile of isolated human upper airway basal cells. Respiratory epithelial cells (REC) were isolated by elastase digestion, stained with FITC-labeledGriffonia simplicifoliaisolectin B₄(GSI-B₄), and sorted by flow cytometry. Approximately 80% of the lectin-positive cells were basal cells, as determined by morphology and cytokeratin staining. These cells expressed integrins α₁, α₂, α₃, α₅, α_vβ₅, β₁, β₃, and α₆β₄, by immunohistochemistry. This is the first report to identify the integrin profile of isolated human upper airway basal cells. These basal cells could be maintained on type I collagen for at least 7 days, where they became partially confluent and retained expression of cytokeratins 5 and 14. Availability of pure populations of basal cells should permit investigations of their role in both normal and maladaptive repair of adult upper airway epithelium.     

Wildlife detector dogs and camera traps: a comparison of techniques for detecting feral cats

A major challenge in controlling overabundant wildlife is monitoring their populations, particularly as they decline to very low density. Camera traps and wildlife detector dogs are increasingly being used for this purpose. We compared the cost-effectiveness of these two approaches for detecting feral cats (Felis catus) on two pastoral properties in Hawke's Bay, North Island, New Zealand. One property was subject to intensive pest removal, while the other had no recent history of pest control. Camera traps and wildlife detector dogs detected cats at similar rates at both sites. The operating costs of each method were also comparable. We identify a number of advantages and disadvantages of each technique, and suggest priorities for further research.