Mechanisms of intrinsic and acquired resistance to kinase‐targeted therapies

Cancer drugs that target pivotal signaling molecules required for malignant cell survival and growth have demonstrated striking antitumor activities in appropriately selected patient populations. Unfortunately, however, therapeutic responses are often of limited duration, typically 6–12 months, because of emergence of drug‐resistant subclones of tumor cells. In this review, we highlight several of the mechanisms of emergent resistance to several kinase‐targeted small molecule therapies used in melanoma, non‐small cell lung cancer (NSCLC) and other solid tumors as illustrative examples. We discuss the implications of these findings for the development of new treatment strategies to delay or prevent the onset of drug resistance.     

Cotton plants expressing a hemipteran-active Bacillus thuringiensis crystal protein impact the development and survival of Lygus hesperus (Hemiptera: Miridae) nymphs

The plant bugs Lygus hesperus Knight (Hemiptera: Miridae) and L. lineolaris (Palisot de Beauvois) have emerged as economic pests of cotton in the United States. These hemipteran species are refractory to the insect control traits found in genetically modified commercial varieties of cotton. In this article, we report the isolation and characterization of a 35 kDa crystal protein from Bacillus thuringiensis, designated TIC807, which causes reduced mass gain and mortality of L. hesperus and L. lineolaris nymphs when presented in an artificial diet feeding assay. Cotton plants expressing the TIC807 protein were observed to impact the survival and development of L. hesperus nymphs in a concentration-dependent manner. These results, demonstrating in planta activity of a Lygus insecticidal protein, represent an important milestone in the development of cotton varieties protected from Lygus feeding damage.     

Enhanced survival and function of neural stem cells-derived dopaminergic neurons under influence of olfactory ensheathing cells in parkinsonian rats

Transplantation of neural stem cell (NSC)-derived dopamine (DA) neurons is associated with low survival of cells, which could be due to limited striatal innervations and uneven distribution of graft because of its dense neuronal core, limited host–graft interaction, poor axonal outgrowth, lack of continuous neurotrophic factors supply, and an absence of cell adhesion molecules mediated appropriate developmental cues. Olfactory ensheathing cells (OEC) express a variety of growth factors and cell adhesion molecules and promote axonal regrowth and functional recovery in spinal cord injury in animal models and patients. In the present study, we explored the possibility to increase the survival, function, axonal outgrowth and striatal reinnervation of NSC by co-grafting with OEC in 6-OHDA lesioned parkinsonian rats. In the presence of OEC, significantly enhanced survival of NSC-derived DA neurons and axonal fiber outgrowth was evident in the striatum of NSC+OEC co-grafted rats at 24 weeks post-grafting as compared with NSC alone grafted rats. The increased survival of NSC and their striatal reinnervation was further manifested in the form of significant and substantial restitution of motor function and neurochemical recovery in the co-grafted group. Significant enhanced expression of p75NTR (from OEC) and tyrosine hydroxylase (TH) (from NSC) confirmed the co-localization and survival of both types of cells at the transplantation site in co-grafted rats. Co-grafting results co-related well with our in vitro studies, which suggest that OEC not only significantly increase survival, neurite outgrowth and DA release of NSC-derived DA neuron but also protect against 6-OHDA neurotoxicity in co-culture conditions. These results collectively suggest that OEC increase the survival and function of transplanted NSC in 6-OHDA lesioned parkinsonian rats.     

Swf1p, a member of the DHHC-CRD family of palmitoyltransferases, regulates the actin cytoskeleton and polarized secretion independently of its DHHC motif

Rho and Rab family GTPases play a key role in cytoskeletal organization and vesicular trafficking, but the exact mechanisms by which these GTPases regulate polarized cell growth are incompletely understood. A previous screen for genes that interact with CDC42, which encodes a Rho GTPase, found SWF1/PSL10. Here, we show Swf1p, a member of the DHHC-CRD family of palmitoyltransferases, localizes to actin cables and cortical actin patches in Saccharomyces cerevisiae. Deletion of SWF1 results in misorganization of the actin cytoskeleton and decreased stability of actin filaments in vivo. Cdc42p localization depends upon Swf1p primarily after bud emergence. Importantly, we revealed that the actin regulating activity of Swf1p is independent of its DHHC motif. A swf1 mutant, in which alanine substituted for the cysteine required for the palmitoylation activity of DHHC-CRD proteins, displayed wild-type actin organization and Cdc42p localization. Bgl2p-marked exocytosis was found wild type in this mutant, although invertase secretion was impaired. These data indicate Swf1p has at least two distinct functions, one of which regulates actin organization and Bgl2p-marked secretion. This report is the first to link the function of a DHHC-CRD protein to Cdc42p and the regulation of the actin cytoskeleton.     

Changes in the In Vivo Absorption and Fluorescence Excitation Spectra with Growth Irradiance in Three Species of Phytoplankton

The fluorescence excitation spectrum is sometimes used as aproxy for the action spectrum of photosynthesis in phytoplankton.The main assumption behind this approximation is that the shapesof absorption and fluorescence excitation spectra are similarexcept for the absorption by photoprotective pigments, whichdo not contribute to the fluorescence spectrum. In this study,we compare the shapes of the absorption and fluorescence spectrain three species of phytoplankton grown at differentirradiances:two diatoms (Thalassiosira weissflogii and Chaetoceros sp.)and a cyanophyte (Synechococcus sp.). The contribution to absorptionby photoprotective pigments was estimated for each experiment.Results showed that the differences between the shapes of absorptionand fluorescence spectra were similar to the estimated absorptionby photoprotective pigments only in the case ofT. weissflogii.In Synechococcus sp., and to a lesser degree in Chaetocerossp., the differences between the two types of spectra were largerthan the absorption by photoprotective pigments. In the caseof Synechococcus sp., the difference between these spectra wasapparently due mainly to the extreme imbalance of chlorophylla distribution between the two photosystems. Chaetoceros sp.seemed to be an intermediate case: a small part of the chlorophylla of the cell appeared to be exclusively associated with photosystemI and therefore did not contribute to fluorescence. Fluorescenceand absorption values were normalized to their values at 545nm, and the ratio of normalized absorption to normalized fluorescencewas computed for the blue (439 nm) and red (676 nm) peaks inthe spectra. The results showed that these peak ratios can beused to distinguish between the effects of photoprotective pigmentsand the arrangement of the photosynthetic apparatus on differencesbetweenfluorescence and absorption spectra.     

Recent advances in Rhizobium-legume symbiosis

The research findings in the field of Rhizobium-legume symbiosis reported worldwide during the years 2002 and 2003 (up to September) have been summarized. The information is presented under the various topics, viz., isolation and characterization of rhizobial strains, physiological aspects of nitrogen fixation, rhizosphere interactions and root surface signals, genomics and proteomics, plant genes involved in nodule formation, bioremediation and biocontrol, and review articles and conference reports. The postal and e-mail addresses of the concerned scientists have also been included.     

A functional annotation of subproteomes in human plasma

The data collected by Human Proteome Organization's Plasma Proteome Pilot project phase was analyzed by members of our working group. Accordingly, a functional annotation of the human plasma proteome was carried out. Here, we report the findings of our analyses. First, bioinformatic analyses were undertaken to determine the likely sources of plasma proteins and to develop a protein interaction network of proteins identified in this project. Second, annotation of these proteins was performed in the context of functional subproteomes involved in the coagulation pathway, the mononuclear phagocytic system, the inflammation pathway, the cardiovascular system, and the liver; as well as the subset of proteins associated with DNA binding activities. Our analyses contributed to the Plasma Proteome Database (http://www.plasmaproteomedatabase.org), an annotated database of plasma proteins identified by HPPP as well as from other published studies. In addition, we address several methodological considerations including the selective enrichment of post-translationally modified proteins by the use of multi-lectin chromatography as well as the use of peptidomic techniques to characterize the low molecular weight proteins in plasma. Furthermore, we have performed additional analyses of peptide identification data to annotate cleavage of signal peptides, sites of intra-membrane proteolysis and post-translational modifications. The HPPP-organized, multi-laboratory effort, as described herein, resulted in much synergy and was essential to the success of this project.     

From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways

Novel drug targets are required in order to design new defenses against antibiotic-resistant pathogens. Comparative genomics provides new opportunities for finding optimal targets among previously unexplored cellular functions, based on an understanding of related biological processes in bacterial pathogens and their hosts. We describe an integrated approach to identification and prioritization of broad-spectrum drug targets. Our strategy is based on genetic footprinting in Escherichia coli followed by metabolic context analysis of essential gene orthologs in various species. Genes required for viability of E. coli in rich medium were identified on a whole-genome scale using the genetic footprinting technique. Potential target pathways were deduced from these data and compared with a panel of representative bacterial pathogens by using metabolic reconstructions from genomic data. Conserved and indispensable functions revealed by this analysis potentially represent broad-spectrum antibacterial targets. Further target prioritization involves comparison of the corresponding pathways and individual functions between pathogens and the human host. The most promising targets are validated by direct knockouts in model pathogens. The efficacy of this approach is illustrated using examples from metabolism of adenylate cofactors NAD(P), coenzyme A, and flavin adenine dinucleotide. Several drug targets within these pathways, including three distantly related adenylyltransferases (orthologs of the E. coli genes nadD, coaD, and ribF), are discussed in detail.