Inferring tree models for oncogenesis from comparative genome hybridization data.

Comparative genome hybridization (CGH) is a laboratory method to measure gains and losses of chromosomal regions in tumor cells. It is believed that DNA gains and losses in tumor cells do not occur entirely at random, but partly through some flow of causality. Models that relate tumor progression to the occurrence of DNA gains and losses could be very useful in hunting cancer genes and in cancer diagnosis. We lay some mathematical foundations for inferring a model of tumor progression from a CGH data set. We consider a class of tree models that are more general than a path model that has been developed for colorectal cancer. We derive a tree model inference algorithm based on the idea of a maximum-weight branching in a graph, and we show that under plausible assumptions our algorithm infers the correct tree. We have implemented our methods in software, and we illustrate with a CGH data set for renal cancer.     

Centrins, cell cycle regulation proteins in human malaria parasite Plasmodium falciparum

Molecules and cellular mechanisms that regulate the process of cell division in malaria parasites remain poorly understood. In this study we isolate and characterize the four Plasmodium falciparum centrins (PfCENs) and, by growth complementation studies, provide evidence for their involvement in cell division. Centrins are cytoskeleton proteins with key roles in cell division, including centrosome duplication, and possess four Ca(2+)-binding EF hand domains. By means of phylogenetic analysis, we were able to decipher the evolutionary history of centrins in eukaryotes with particular emphasis on the situation in apicomplexans and other alveolates. Plasmodium possesses orthologs of four distinct centrin paralogs traceable to the ancestral alveolate, including two that are unique to alveolates. By real time PCR and/or immunofluorescence, we determined the expression of PfCEN mRNA or protein in sporozoites, asexual blood forms, gametocytes, and in the oocysts developing inside mosquito mid-gut. Immunoelectron microscopy studies showed that centrin is expressed in close proximity with the nucleus of sporozoites and asexual schizonts. Furthermore, confocal and widefield microscopy using the double staining with alpha-tubulin and centrin antibodies strongly suggested that centrin is associated with the parasite centrosome. Following the episomal expression of the four PfCENs in a centrin knock-out Leishmania donovani parasite line that exhibited a severe growth defect, one of the PfCENs was able to partially restore Leishmania growth rate and overcome the defect in cytokinesis in such mutant cell line. To our knowledge, this study is the first characterization of a Plasmodium molecule that is involved in the process of cell division. These results provide the opportunity to further explore the role of centrins in cell division in malaria parasites and suggest novel targets to construct genetically modified, live attenuated malaria vaccines.     

NY-BR-1 protein expression in breast carcinoma: a mammary gland differentiation antigen as target for cancer immunotherapy

NY-BR-1 is a recently identified differentiation antigen of the mammary gland. To use NY-BR-1 for T-cell-based immunotherapy, analysis of its co-expression with HLA class I antigens is required. In the present tissue microarray study, primary breast cancers (n = 1,444), recurrences (n = 88), lymph node (n = 525) and distant metastases (n = 91) were studied for NY-BR-1 expression using a novel monoclonal antibody. NY-BR-1 expression was compared with prognosis, estrogen receptor, HER2-status, EGFR and HLA class I antigen expression. NY-BR-1 was more frequently expressed in grade 1 (82%) than in grade 2 (69%) and grade 3 (46%) carcinomas (P < 0.0001). Moreover, NY-BR-1 expression correlated directly with estrogen receptor expression (P < 0.0001) and inversely correlated with HER2-status and EGFR expression (P < 0.0001 for both). Considering high expression level of co-expression, 198/1,321 (15%) primary breast carcinomas and 4/65 (6%) distant metastases expressed NY-BR-1 and HLA class I, suggesting that active immunotherapy can be applied to about 10% of breast cancer patients. Survival analysis showed an association of NY-BR-1 expression with better patient outcome (P = 0.015). No difference between NY-BR-1 expression of primary tumors and metastases could be found, indicating that the presence of NY-BR-1 in metastases can be deduced from their corresponding primary. Forty-three paired biopsies taken from patients before and after chemotherapy suggest that NY-BR-1 expression is not influenced by preceding chemotherapy (kappa = 0.89, P < 0.0001). In summary, the co-expression of NY-BR-1 with HLA class I antigens and its expression in metastases without modification by chemotherapy suggest that NY-BR-1 targeted immunotherapy represents a viable strategy in addition to other targeted cancer drug therapies of breast cancer.     

The Role of Extracellular and Cytoplasmic Splice Domains of α7-Integrin in Cell Adhesion and Migration on Laminins

The major laminin-binding integrin of skeletal, smooth, and heart muscle is α7β1-integrin, which is structurally related to α6β1. It occurs in three cytoplasmic splice variants (α7A, -B, and -C) and two extracellular forms (X1 and X2) which are developmentally regulated and differentially expressed in skeletal muscle. Previously, we have shown that ectopic expression of the α7β-integrin splice variant in nonmotile HEK293 cells specifically induced cell locomotion on laminin-1 but not on fibronectin. To investigate the specificity and the mechanism of the α7-mediated cell motility, we expressed the three α7-chain cytoplasmic splice variants, as well as α6A- and α6B-integrin subunits in HEK293 cells. Here we show that all three α7 splice variants (containing the X2 domain), as well as α6A and α6B, promote cell attachment and stimulate cell motility on laminin-1 and its E8 fragment. Deletion of the cytoplasmic domain (excluding the GFFKR consensus sequence) from α7B resulted in a loss of the motility-enhancing effect. On laminin-2/4 (merosin), the predominant isoform in mature skeletal muscle, only α7-expressing cells showed enhanced motility, whereas cells transfected with α6A and α6B neither attached nor migrated on laminin-2. Adhesion of α7-expressing cells to both laminin-1 and laminin-2 was specifically inhibited by a new monoclonal antibody (6A11) specific for α7. Expression of the two extracellular splice variants α7X1 and α7X2 in HEK293 cells conferred different motilities on laminin isoforms: Whereas α7X2B promoted cell migration on both laminin-1 and laminin-2, α7X1B supported motility only on laminin-2 and not on laminin-1, although both X1 and X2 splice variants revealed similar adhesion rates to laminin-1 and -2. Fluorescence-activated cell sorter analysis revealed a dramatic reduction of surface expression of α6-integrin subunits after α7A or -B transfection; also, surface expression of α1-, α3-, and α5-integrins was significantly reduced. These results demonstrate selective responses of α6- and α7-integrins and of the α7 splice variants to laminin-1 and -2 and indicate differential roles in laminin-controlled cell adhesion and migration.     

Feeding a ROS-generator to Caenorhabditis elegans leads to increased expression of small heat shock protein HSP-16.2 and hormesis

Reactive oxygen species (ROS) are thought to be a driving force in the aging process. In transgenic Caenorhabditis elegans expressing green fluorescent protein (GFP) under control of the hsp-16.2 promoter (CL2070) 100 μM of the ROS-generator juglone induced GFP-expression. This was associated with translocation of DAF-16 to the nucleus as visualized in a transgenic strain expressing a DAF-16::GFP fusion protein (TJ356) and with increased cellular levels of reduced glutathione. RNA-interference for DAF-16 in CL2070 blocked the juglone-induced HSP-16.2 expression and the increase in glutathione levels. Higher concentrations of juglone did not further increase the adaptive responses but caused premature death, indicating hormetic adaptations unless the stressor exceeds the intrinsic protective capacity. The addition of the ROS-scavenger ascorbic acid finally blocked lifespan reductions and all of the adaptations to juglone stressing that ROS are indeed the molecular species that require protective response.     

An opportunistic promoter sharing regulatory sequences with either a muscle-specific or a ubiquitous promoter in the human aldolase A gene.

The human aldolase A gene is transcribed from three different promoters, pN, pM, and pH, all of which are clustered within a small 1.6-kbp DNA domain. pM, which is highly specific to adult skeletal muscle, lies in between pN and pH, which are ubiquitous but particularly active in heart and skeletal muscle. A ubiquitous enhancer, located just upstream of pH start sites, is necessary for the activity of both pH and pN in transient transfection assays. Using transgenic mice, we studied the sequence controlling the muscle-specific promoter pM and the relations between the three promoters and the ubiquitous enhancer. A 4.3-kbp fragment containing the three promoters and the ubiquitous enhancer showed an expression pattern consistent with that known in humans. In addition, while pH was active in both fast and slow skeletal muscles, pM was active only in fast muscle. pM activity was unaltered by the deletion of a 1.8-kbp region containing the ubiquitous enhancer and the pH promoter, whereas pN remained active only in fast skeletal muscle. These findings suggest that in fast skeletal muscle, a tissue-specific enhancer was acting on both pN and pM, whereas in other tissues, the ubiquitous enhancer was necessary for pN activity. Finally, a 2.6-kbp region containing the ubiquitous enhancer and only the pH promoter was sufficient to bring about high-level expression of pH in cardiac and skeletal muscle. Thus, while pH and pM function independently of each other, pN, remarkably, shares regulatory elements with each of them, depending on the tissue. Importantly, expression of the transgenes was independent of the integration site, as originally described for transgenes containing the beta-globin locus control region.     

Development of a multiplex PCR assay for fine-scale population genetic analysis of the Komodo monitor Varanus komodoensis based on 18 polymorphic microsatellite loci

Multiplex PCR assays for the coamplification of microsatellite loci allow rapid and cost-effective genetic analyses and the production of efficient screening protocols for international breeding programs. We constructed a partial genomic library enriched for di-nucleotide repeats and characterized 14 new microsatellite loci for the Komodo monitor (or Komodo dragon, Varanus komodoensis). Using these novel microsatellites and four previously described loci, we developed multiplex PCR assays that may be loaded on a genetic analyser in three separate panels. We tested the novel set of microsatellites for polymorphism using 69 individuals from three island populations and evaluated the resolving power of the entire panel of 18 loci by conducting (i) a preliminary assignment test to determine population(s) of origin and (ii) a parentage analysis for 43 captive Komodo monitors. This panel of polymorphic loci proved useful for both purposes and thus can be exploited for fine-scale population genetic analyses and as part of international captive breeding programs directed at maintaining genetically viable ex situ populations and reintroductions.     

Hollow fiber-based liquid phase microextraction (HF-LPME) for a highly sensitive HPLC determination of sulfonamides and their main metabolites

In this paper, three phase-hollow fiber-based liquid phase microextraction (HF-LPME) combined with a HPLC procedure using diode array (DAD) and fluorescence detection (FLD) has been developed for the determination of four widely used sulfonamides: sulfadiazine, sulfamerazine, sulfamethazine, sulfamethoxazole and their main metabolites, the corresponding N(4)-acetyl derivatives: N(4)-acetyl-sulfadiazine, N(4)-acetyl-sulfamerazine, N(4)-acetyl-sulfamethazine, N(4)-acetyl-sulfamethoxazole. A Q3/2 Accurel KM polypropylene hollow fiber supporting 1-octanol was used between a 2 M Na(2)SO(4) aqueous solution (pH 4) as a donor phase and aqueous solution (pH 12) as an acceptor phase. The procedure allows very low detection and quantitation limits of 0.3-33 ng L(-1) and 0.9-100 ng L(-1), respectively. The proposed method was applied to the determination of the analytes in environmental water samples (surface, tap and wastewater).     

Rapid assessment of oxygen transfer impact for Corynebacterium glutamicum

Oxygen supply is crucial in industrial application of microbial systems, such as Corynebacterium glutamicum, but oxygen transfer is often neglected in early strain characterizations, typically done under aerobic conditions. In this work, a new procedure for oxygen transfer screening is presented, assessing the impact of maximum oxygen transfer conditions (OTR_max) within microtiter plate-based cultivation for enhanced throughput. Oxygen-dependent growth and productivity were characterized for C. glutamicum ATCC13032 and C. glutamicum DM1933 (lysine producer). Biomass and lysine product yield are affected at OTR_max below 14 mmol L^?1 h^?1 in a standardized batch process, but not by further increase of OTR_max above this threshold value indicating a reasonable tradeoff between power input and oxygen transfer capacity OTR_max. The described oxygen transfer screening allows comparative determination of metabolic robustness against oxygen transfer limitation and serves identification of potential problems or opportunities later created during scale-up.