Metabolite Imager: customized spatial analysis of metabolite distributions in mass spectrometry imaging

Mass spectrometry (MS) is currently the most utilized analytical instrument for evaluating the metabolite composition of a biological sample at both the qualitative and quantitative level. The exponential growth of raw data generated through increasingly versatile mass spectrometers requires sophisticated algorithms to process and visualize the raw data to address biological questions. The structural and quantitative diversity of a single species’ metabolome (e.g. all metabolite species) under different experimental conditions itself forms a very large and complex dataset to analyze. We have developed a free, Java-based metabolomics application “Metabolite Imager” (www.metaboliteimager.com) that enables customized analysis and visualization of the metabolite distributions in tissues acquired through MS-based imaging approaches. Metabolite Imager algorithms perform customized targeted searching of metabolites through user-defined and publicly-available databases enabling the analysis of spatial distributions of large metabolite numbers in tissue sections. Metabolite Imager’s automated, two-dimensional image generator has several customizable features for producing high-resolution images. Additional Metabolite Imager algorithms support identifying targeted and unknown detected metabolites in selected tissue regions using spatially-based enrichment analysis that could impact metabolic engineering strategies. Co-localization algorithms of metabolites and selected ions by m/z enable analysis of precursor-product relationships in situ that will be important for expanding the biological context of metabolic pathways.     

Nonhomogeneous spatial distributions of populations

Summary Spatial inhomogeneities such as nonconstant population densities usually will be attributed to random effects or to an inhomogeneous substrate. Such an explanation may be incorrect since from certain chemical reactions it is known that the interaction of species together with diffusion may generate nonhomogeneous spatial structures. However, the effect of boundary conditions has been so far neglected. In this paper nonlinear and linear interaction-diffusion models are investigated under various side-conditions by analytic methods and by computer simulations. A remarkable fact, as compared with earlier results in the field, is the example of an interaction-diffusion process which in the whole space has only the constant as a stable limit distribution, whereas the introduction of a side condition, e.g. a population reservoir or a barrier, leads to standing spatial population waves.     

A computational approach to discovering the functions of bacterial phytochromes by analysis of homolog distributions

Background  

Phytochromes are photoreceptors, discovered in plants, that control a wide variety of developmental processes. They have also been found in bacteria and fungi, but for many species their biological role remains obscure. This work concentrates on the phytochrome system of Agrobacterium tumefaciens, a non-photosynthetic soil bacterium with two phytochromes. To identify proteins that might share common functions with phytochromes, a co-distribution analysis was performed on the basis of protein sequences from 138 bacteria.     

Contributions of satellite remote sensing to analysis of spatial variability in zooplankton distributions

Zooplankton populations in Lake Tahoe and other large lakes often exhibit considerable variability due to changing predator assemblages and interactions between littoral and pelagial regions. Wind-induced advection of Emerald Bay populations of Bosmina longirostris into Lake Tahoe was hypothesized to be the mechanism for Bosmina's reappearance in the main body of that lake in late 1978 following an absence of more than three years (Threlkeld 1981).Landsat satellite imagery is examined here to determine if a significant spatial-temporal interaction in water quality in Emerald Bay and Lake Tahoe consistent with this hypothesis occurred during the period when Bosmina reappeared. Densitometer measurements of Landsat MSS band 4 and 5 images were compared by ANOVA; significant station-season interactions were detected, and enlarged Landsat film images revealed plumes, streaks and other surface features which may have been associated with the hypothesized mixing events in Lake Tahoe. A major limitation of this method is the need for pre-flyover water truth data for interpretation of detectable surface features.     

Cluster size distributions: signatures of self-organization in spatial ecologies

Three different lattice-based models for antagonistic ecological interactions, both nonlinear and stochastic, exhibit similar power-law scalings in the geometry of clusters. Specifically, cluster size distributions and perimeter-area curves follow power-law scalings. In the coexistence regime, these patterns are robust: their exponents, and therefore the associated Korcak exponent characterizing patchiness, depend only weakly on the parameters of the systems. These distributions, in particular the values of their exponents, are close to those reported in the literature for systems associated with self-organized criticality (SOC) such as forest-fire models; however, the typical assumptions of SOC need not apply. Our results demonstrate that power-law scalings in cluster size distributions are not restricted to systems for antagonistic interactions in which a clear separation of time-scales holds. The patterns are characteristic of processes of growth and inhibition in space, such as those in predator-prey and disturbance-recovery dynamics. Inversions of these patterns, that is, scalings with a positive slope as described for plankton distributions, would therefore require spatial forcing by environmental variability.     

Dimerization of VEGF receptors and implications for signal transduction: a computational study

Vascular endothelial growth factor (VEGF) is a potent cytokine involved in the induction of neovascularization. Secreted as a cysteine-linked dimer, it has two binding sites at opposite poles through which it may bind VEGF receptors (VEGFRs), receptor tyrosine kinases found on the surface of endothelial and other cells. The binding of a VEGF molecule to two VEGFR molecules induces transphosphorylation of the intracellular domains of the receptors, leading to signal transduction. The dominant mechanism of receptor dimerization is not clear: the receptors may be present in an inactive pre-dimerized form, VEGF binding first to one of the receptors, the second receptor then ideally located for dimerization; or VEGF may bind receptor monomers on the cell surface, which then diffuse and bind to available unligated receptor monomers to complete the activation. Both processes take place and one or other may dominate on different cell types. We demonstrate the impact of dimerization mechanism on the binding of VEGF to the cell surface and on the formation of active signaling receptor complexes. We describe two methods to determine which process dominates, based on binding and phosphorylation assays. The presence of two VEGF receptor populations, VEGFR1 and VEGFR2, can result in receptor heterodimer formation. Our simulations predict that heterodimers will comprise 10-50% of the active, signaling VEGF receptor complexes, and that heterodimers will form at the expense of homodimers of VEGFR1 when VEGFR2 populations are larger. These results have significant implications for VEGF signal transduction and interpretation of experimental studies. These results may be applicable to other ligand-receptor pairs, in particular PDGF.     

The spatial distributions of randomly coiling polynucleotides

Statistical mechanical averages of vectors and tensors characterizing the allowed configurations of randomly coiling polynucleotides have been calculated for chains of 2⁰–2¹⁰ repeating units. Specifically, the persistence vector p = 〈 r 〉 has been obtained as a function of chain length. Configurational averages of the Cartesian tensors formed from the displacement vector ρ = r – p have been computed up to and including the tensor of seventh rank. From these tensors the three-dimensional spatial distributions of end-to-end vectors have been constructed to provide comprehensive pictures of the directional tendencies of the randomly coiling polynucleotide. The elements of the third and fourth moment tensors, however, give sufficient information to represent accurately the qualitative features of the spatial distributions. For long chains, more than 2⁶ (64) repeating units, the spatial distributions assume spherically symmetric shapes that can be adequately characterized by one-dimensional radial distribution functions. These radial distribution functions agree well with the radial distributions calculated from Monte Carlo samples containing more than 5000 chains. The constraints of fixed bond lengths, fixed bond angles, and hindered internal rotations severely distort the spatial distributions of short polynucleotide chains to mushroom-shaped volumes. These skewed distributions provide information useful to the analysis of small, single-stranded loops, bulges, and circles. The formation of these structures requires the termini of the polynucleotides to lie within specifically delineated volumes with respect to coordinate systems affixed to the first bonds of the chains. The extent to which these loop closure volumes overlap the three-dimensional spatial distributions provides estimates of loop formation that are much more reliable than earlier studies based upon the radial distribution function.     

Formation of RNA spatial structures

The review considers different experimental and theoretical approaches to the investigation of RNA folding and identification of nucleotides that critically affect the folding of molecules, such as tRNA, and several classes of ribozymes. For instance, it has been shown that nucleotides of the D- and T-loop regions are the last to be involved in the tRNA structure, or, rather, they are not included in the tRNA folding nucleus. A specially developed SHAPE method was used to show that the long-recognized hierarchical folding model does not hold true for tRNA folding. In the second part of the review, algorithms and programs used for the prediction of RNA secondary structures, as well as for modeling RNA folding, are considered.     

VEGF promotes tumorigenesis and angiogenesis of human glioblastoma stem cells

There is increasing evidence for the presence of cancer stem cells (CSCs) in malignant brain tumors, and these CSCs may play a pivotal role in tumor initiation, growth, and recurrence. Vascular endothelial growth factor (VEGF) promotes the proliferation of vascular endothelial cells (VECs) and the neurogenesis of neural stem cells. Using CSCs derived from human glioblastomas and a retrovirus expressing VEGF, we examined the effects of VEGF on the properties of CSCs in vitro and in vivo. Although VEGF did not affect the property of CSCs in vitro, the injection of mouse brains with VEGF-expressing CSCs led to the massive expansion of vascular-rich GBM, tumor-associated hemorrhage, and high morbidity, suggesting that VEGF promoted tumorigenesis via angiogenesis. These results revealed that VEGF induced the proliferation of VEC in the vascular-rich tumor environment, the so-called stem cell niche.     

Mechanisms of coronary angiogenesis in response to stretch: role of VEGF and TGF-beta

To test the hypotheses that cyclic stretch of 1) cardiac myocytes produces factors that trigger angiogenic events in coronary microvascular endothelial cells (CMEC) and 2) CMEC enhances the expression of growth factors, cardiac myocytes and CMEC were subjected to cyclic stretch in a Flexercell Strain Unit. Vascular endothelial growth factor (VEGF) but not basic fibroblast growth factor mRNA and protein levels increased approximately twofold in myocytes after 1 h of stretch. CMEC DNA synthesis increased approximately twofold when conditioned medium from stretched myocytes or VEGF protein was added, and addition of VEGF neutralizing antibody blocked the increase. CMEC migration and tube formation increased with the addition of conditioned media but were markedly attenuated by VEGF neutralizing antibody. Myocyte transforming growth factor-beta [corrected] (TGF-beta) increased 2.5-fold after 1 h of stretch, and the addition of TGF-beta neutralizing antibodies inhibited the stretch-induced upregulation of VEGF. Stretch of CMEC increased VEGF mRNA in these cells (determined by Northern blot and RT-PCR) and increased the levels of VEGF protein (determined by ELISA analysis) in the conditioned media. Therefore, cyclic stretch of cardiac myocytes and CMEC appears to be an important primary stimulus for coronary angiogenesis through both paracrine and autocrine VEGF pathways. These data indicate that 1) CMEC DNA synthesis, migration, and tube formation are increased in response to VEGF secreted from stretched cardiac myocytes; 2) VEGF in CMEC subjected to stretch is upregulated and secreted; and 3) TGF-beta signaling may regulate VEGF expression in cardiac myocytes.     

Signal transduction by VEGF receptors in regulation of angiogenesis and lymphangiogenesis

The VEGF/VPF (vascular endothelial growth factor/vascular permeability factor) ligands and receptors are crucial regulators of vasculogenesis, angiogenesis, lymphangiogenesis and vascular permeability in vertebrates. VEGF-A, the prototype VEGF ligand, binds and activates two tyrosine kinase receptors: VEGFR1 (Flt-1) and VEGFR2 (KDR/Flk-1). VEGFR1, which occurs in transmembrane and soluble forms, negatively regulates vasculogenesis and angiogenesis during early embryogenesis, but it also acts as a positive regulator of angiogenesis and inflammatory responses, playing a role in several human diseases such as rheumatoid arthritis and cancer. The soluble VEGFR1 is overexpressed in placenta in preeclampsia patients. VEGFR2 has critical functions in physiological and pathological angiogenesis through distinct signal transduction pathways regulating proliferation and migration of endothelial cells. VEGFR3, a receptor for the lymphatic growth factors VEGF-C and VEGF-D, but not for VEGF-A, regulates vascular and lymphatic endothelial cell function during embryogenesis. Loss-of-function variants of VEGFR3 have been identified in lymphedema. Formation of tumor lymphatics may be stimulated by tumor-produced VEGF-C, allowing increased spread of tumor metastases through the lymphatics. Mapping the signaling system of these important receptors may provide the knowledge necessary to suppress specific signaling pathways in major human diseases.     

Structure and function of VEGF/VEGF-receptor system involved in angiogenesis

Angiogenesis is an essential biological process not only in embryogenesis but also in the progression of a variety of major diseases such as cancer, diabetes and inflammation. Vascular endothelial growth factor (VEGF) family and its receptor system has been shown to be the fundamental regulator in the cell signaling of angiogenesis. Other systems, Angiopoietin-Tie and EphrinB2-Eph4B etc. are also involved in and cooperate with VEGF system to establish the dynamic blood vessel structures. VEGF receptor belongs to PDGF receptor super-gene family, and carries seven Ig-domains in the extracellular region and a tyrosine kinase domain in the intracellular region. Three members of VEGF receptor family, Flt-1, KDR/Flk-1 and Flt-4, have unique characteristics in terms of the signal transduction, and regulate angiogenesis, lymphangiongenesis and vascular permeability. Further studies on VEGF-VEGF receptor system may significantly facilitate our understanding on the physiological as well as pathological vascular systems in the body and the development of new strategies to control and suppress the major diseases in humans.     

Peptides encoded by exon 6 of VEGF inhibit endothelial cell biological responses and angiogenesis induced by VEGF

VEGF induces pathological angiogenesis and is an important target for the development of novel antiangiogenic molecules. In this study, we tested synthetic peptides based on the sequence of VEGF(189) for their ability to inhibit VEGF receptor binding and biological responses. We identified 12-amino acid peptides derived from exon 6 that inhibited VEGF binding to HUVECs, VEGF-stimulated ERK activation, and prostacyclin production. These peptides inhibited VEGF-induced mitogenesis, migration, and VEGF-dependent survival of endothelial cells, but caused no increase in apoptosis in the absence of VEGF. Exon 6-encoded peptides also caused a marked inhibition of VEGF-induced angiogenesis in vitro. Studies of effects of peptides on cross-linking of VEGF to its receptors and on binding of VEGF to porcine aortic endothelial cells expressing either KDR or neuropilin-1 showed that exon 6-encoded peptides effectively blocked the interaction of VEGF with both receptors. Exon 6-derived peptides caused release of bFGF from endothelial cells but inhibited bFGF-dependent ERK activation, cell proliferation and angiogenesis. Our findings indicate that VEGF exon 6-encoded peptides inhibit VEGF-induced angiogenesis, at least in part through inhibition of VEGF binding to KDR. In addition, exon 6-encoded peptides are also effective inhibitors of bFGF-mediated angiogenesis.     

ApoB-containing lipoproteins regulate angiogenesis by modulating expression of VEGF receptor 1

Despite the clear major contribution of hyperlipidemia to the prevalence of cardiovascular disease in the developed world, the direct effects of lipoproteins on endothelial cells have remained obscure and are under debate. Here we report a previously uncharacterized mechanism of vessel growth modulation by lipoprotein availability. Using a genetic screen for vascular defects in zebrafish, we initially identified a mutation, stalactite (stl), in the gene encoding microsomal triglyceride transfer protein (mtp), which is involved in the biosynthesis of apolipoprotein B (ApoB)-containing lipoproteins. By manipulating lipoprotein concentrations in zebrafish, we found that ApoB negatively regulates angiogenesis and that it is the ApoB protein particle, rather than lipid moieties within ApoB-containing lipoproteins, that is primarily responsible for this effect. Mechanistically, we identified downregulation of vascular endothelial growth factor receptor 1 (VEGFR1), which acts as a decoy receptor for VEGF, as a key mediator of the endothelial response to lipoproteins, and we observed VEGFR1 downregulation in hyperlipidemic mice. These findings may open new avenues for the treatment of lipoprotein-related vascular disorders.