Author Correction: A cell-free platform for the prenylation of natural products and application to cannabinoid production.

In the original version of this Article, the genotype of the M30 mutant presented in Fig. 3b was given incorrectly as Y288V/A232S, and the M31 mutant was given incorrectly as M1/A232S. The correct genotype of the M30 mutant is Y288A/A232S and for M31 it is Y288V/A232S. In addition, to keep consistency in genotype formatting, the genotype of the M27 mutant should be Y288V/G286S. The errors have been corrected in both the PDF and HTML versions of the Article.

A cell-free platform for the prenylation of natural products and application to cannabinoid production.

Prenylation of natural compounds adds structural diversity, alters biological activity, and enhances therapeutic potential. Because prenylated compounds often have a low natural abundance, alternative production methods are needed. Metabolic engineering enables natural product biosynthesis from inexpensive biomass, but is limited by the complexity of secondary metabolite pathways, intermediate and product toxicities, and substrate accessibility. Alternatively, enzyme catalyzed prenyl transfer provides excellent regio- and stereo-specificity, but requires expensive isoprenyl pyrophosphate substrates. Here we develop a flexible cell-free enzymatic prenylating system that generates isoprenyl pyrophosphate substrates from glucose to prenylate an array of natural products. The system provides an efficient route to cannabinoid precursors cannabigerolic acid (CBGA) and cannabigerovarinic acid (CBGVA) at >1 g/L, and a single enzymatic step converts the precursors into cannabidiolic acid (CBDA) and cannabidivarinic acid (CBDVA). Cell-free methods may provide a powerful alternative to metabolic engineering for chemicals that are hard to produce in living organisms.

Calli Essential Oils Synergize with Lawsone against Multidrug Resistant Pathogens.

The fast development of multi-drug resistant (MDR) organisms increasingly threatens global health and well-being. Plant natural products have been known for centuries as alternative medicines that can possess pharmacological characteristics, including antimicrobial activities. The antimicrobial activities of essential oil (Calli oil) extracted from the Calligonum comosum plant by hydro-steam distillation was tested either alone or when combined with lawsone, a henna plant naphthoquinone, against MDR microbes. Lawsone showed significant antimicrobial activities against MDR pathogens in the range of 200-300 µg/mL. Furthermore, Calli oil showed significant antimicrobial activities against MDR bacteria in the range of 180-200 µg/mL, Candida at 220-240 µg/mL and spore-forming Rhizopus fungus at 250 µg/mL. Calli oil's inhibition effect on Rhizopus, the major cause of the lethal infection mucormycosis, stands for 72 h, followed by an extended irreversible white sporulation effect. The combination of Calli oil with lawsone enhanced the antimicrobial activities of each individual alone by at least three-fold, while incorporation of both natural products in a liposome reduced their toxicity by four- to eight-fold, while maintaining the augmented efficacy of the combination treatment. We map the antimicrobial activity of Calli oil to its major component, a benzaldehyde derivative. The findings from this study demonstrate that formulations containing essential oils have the potential in the future to overcome antimicrobial resistance.

Read-through compound 13 restores dystrophin expression and improves muscle function in the mdx mouse model for Duchenne muscular dystrophy.

Molecules that induce ribosomal read-through of nonsense mutations in mRNA and allow production of a full-length functional protein hold great therapeutic potential for the treatment of many genetic disorders. Two such read-through compounds, RTC13 and RTC14, were recently identified by a luciferase-independent high-throughput screening assay and were shown to have potential therapeutic functions in the treatment of nonsense mutations in the ATM and the dystrophin genes. We have now tested the ability of RTC13 and RTC14 to restore dystrophin expression into skeletal muscles of the mdx mouse model for Duchenne muscular dystrophy (DMD). Direct intramuscular injection of compound RTC14 did not result in significant read-through activity in vivo and demonstrated the levels of dystrophin protein similar to those detected using gentamicin. In contrast, significant higher amounts of dystrophin were detected after intramuscular injection of RTC13. When administered systemically, RTC13 was shown to partially restore dystrophin protein in different muscle groups, including diaphragm and heart, and improved muscle function. An increase in muscle strength was detected in all treated animals and was accompanied by a significant decrease in creatine kinase levels. These studies establish the therapeutic potential of RTC13 in vivo and advance this newly identified compound into preclinical application for DMD.

Anti-fibrotic activity and enhanced interleukin-6 production by hepatic stellate cells in response to imatinib mesylate.

OBJECTIVE: To examine imatinib mesylate's effects on stellate cell responses in vivo and in vitro. The hepatic stellate cell (HSC) is a key target of anti-fibrotic therapies. Imatinib mesylate is a small molecule receptor tyrosine kinase inhibitor indicated for treatment of chronic myelogenous leukaemia and GI stromal tumours. DESIGN: Because imatinib inhibits ß-PDGFR signalling, which stimulates HSC proliferation, we assessed its activity in culture and in vivo, and examined downstream targets in a human stellate cell line (LX-2) using cDNA microarray. METHODS AND RESULTS: Imatinib inhibited proliferation of LX-2 cells (0.5-10 mM) but not primary human stellate cells, with no effect on viability, associated with attenuated ß-PDGFR phosphorylation. Mitochondrial activity and superoxide anion production were decreased in response to imatinib. cDNA microarray uncovered up-regulation of 29 genes in response to imatinib, including interleukin-6 (IL-6) mRNA, which was correlated with progressive IL-6 secretion. Imatinib also decreased gene expression of collagen α(1) (I), alpha smooth muscle actin, ß-PDGFR, transforming growth factor ß receptor type 1, matrix metalloproteinase 2 and tissue inhibitor of metalloproteinase 2. In vivo, imatinib administered to rats beginning 4 weeks after starting thioacetamide (TAA) led to reduced collagen content, with significant reductions in portal pressure and down-regulation of fibrogenic genes in whole liver. Importantly, hepatic IL-6 mRNA levels were significantly increased in TAA-treated animals receiving imatinib. CONCLUSIONS: These findings reinforce the anti-fibrotic activity of imatinib and uncover an unexpected link between inhibition of HSC activation by imatinib and enhanced secretion of IL-6, a regenerative cytokine.

Genetic background of patients from a university medical center in Manhattan: implications for personalized medicine.

BACKGROUND: The rapid progress currently being made in genomic science has created interest in potential clinical applications; however, formal translational research has been limited thus far. Studies of population genetics have demonstrated substantial variation in allele frequencies and haplotype structure at loci of medical relevance and the genetic background of patient cohorts may often be complex. METHODS AND FINDINGS: To describe the heterogeneity in an unselected clinical sample we used the Affymetrix 6.0 gene array chip to genotype self-identified European Americans (N = 326), African Americans (N = 324) and Hispanics (N = 327) from the medical practice of Mount Sinai Medical Center in Manhattan, NY. Additional data from US minority groups and Brazil were used for external comparison. Substantial variation in ancestral origin was observed for both African Americans and Hispanics; data from the latter group overlapped with both Mexican Americans and Brazilians in the external data sets. A pooled analysis of the African Americans and Hispanics from NY demonstrated a broad continuum of ancestral origin making classification by race/ethnicity uninformative. Selected loci harboring variants associated with medical traits and drug response confirmed substantial within- and between-group heterogeneity. CONCLUSION: As a consequence of these complementary levels of heterogeneity group labels offered no guidance at the individual level. These findings demonstrate the complexity involved in clinical translation of the results from genome-wide association studies and suggest that in the genomic era conventional racial/ethnic labels are of little value.

Influence of prothymosin-alpha on HIV-1 target cells.

The important role of CD8(+) T cells in controlling HIV-1 infection through the innate as well as the adaptive immune system is well established. In addition to the major histocompatibility complex (MHC)-dependent cytotoxic activity of CD8(+) T cells, they produce soluble factors that suppress HIV-1 replication in an MHC-independent manner. Several of those factors have been identified, including beta-chemokines, Rantes, MIP-1alpha, MIP-1beta, and MDC. We previously identified that prothymosin alpha (ProTalpha) in the conditioned medium of HVS transformed CD8(+) T cells was a potent inhibitor of HIV-1 replication following proviral integration. In this report we further characterize the anti-HIV-1 activity of ProTalpha by demonstrating its target-cell specificity, distinction from additional inhibitors of HIV-1 transcription in CD8(+) T cell supernatants, as well as the differential regulation of host cell antiviral genes that could impact HIV-1 replication. These genes include a number of transcription factors as well IFN-alpha-inducible genes including PKR, IRF1, and Rantes, in the absence of induction of IFN-alpha. These data suggest that the anti-HIV-1 activity of ProTalpha is mediated through the modulation of a number of genes that have been reported to suppress HIV-1 replication including the dysregulation of transcription factors and the induction of PKR and Rantes mRNA.

A molecular signature to discriminate dysplastic nodules from early hepatocellular carcinoma in HCV cirrhosis.

BACKGROUND & AIMS: Small liver nodules approximately 2 cm are difficult to characterize by radiologic or pathologic examination. Our aim was to identify a molecular signature to diagnose early hepatocellular carcinoma (HCC). METHODS: The transcriptional profiles of 55 candidate genes were assessed by quantitative real-time reverse-transcription polymerase chain reaction (RT-PCR) in 17 dysplastic nodules (diameter, 10 mm) and 20 early HCC (diameter, 18 mm) from HCV cirrhotic patients undergoing resection/transplantation and 10 nontumoral cirrhotic tissues and 10 normal liver tissues. Candidate genes were confirmed by quantitative RT-PCR in 20 advanced HCCs and by immunohistochemistry in 75 samples and validated in an independent set of 29 samples (dysplastic nodules [10] and small HCC [19; diameter, 20 mm]). RESULTS: Twelve genes were significantly, differentially expressed in early HCCs compared with dysplastic nodules (>2-fold change; area under the receiver operating characteristic curve > or =0.8): this included TERT, GPC3, gankyrin, survivin, TOP2A, LYVE1, E-cadherin, IGFBP3, PDGFRA, TGFA, cyclin D1, and HGF. Logistic regression analysis identified a 3-gene set including GPC3 (18-fold increase in HCC, P = .01), LYVE1 (12-fold decrease in HCC, P = .0001), and survivin (2.2-fold increase in HCC, P = .02), which had a discriminative accuracy of 94%. The validity of the gene signature was confirmed in a prospective testing set. GPC3 immunostaining was positive in all HCCs and negative in dysplastic nodules (22/22 vs 0/14, respectively, P < .001). Nuclear staining for survivin was positive in 12 of 13 advanced HCC cases and in 1 of 9 early tumors. CONCLUSIONS: Molecular data based on gene transcriptional profiles of a 3-gene set allow a reliable diagnosis of early HCC. Immunostaining of GPC3 confirms the diagnosis of HCC.

The ABRF MARG microarray survey 2005: taking the pulse of the microarray field.

Over the past several years, microarray technology has evolved into a critical component of any discovery-based program. Since 1999, the Association of Biomolecular Resource Facilities (ABRF) Microarray Research Group (MARG) has conducted biennial surveys designed to generate a profile of microarray service laboratories and, more importantly, an overview of technology development and implementation. Survey questions addressed instrumentation, protocols, staffing, funding, and work flow in a microarray facility. Presented herein are the results of the MARG 2005 survey; where possible, trends in the field are discussed and compared to data collected from previous surveys.

Magnetism, electron paramagnetic resonance, electrochemistry, and mass spectrometry of the pentacopper(II)-substituted tungstosilicate [Cu5(OH)4(H2O)2(A-alpha-SiW9O33)2]10-, a model five-spin frustrated cluster.

The dimeric, pentacopper(II)-substituted tungstosilicate [Cu(5)(OH)(4)(H(2)O)(2)(A-alpha-SiW(9)O(33))(2)](10)(-) (1) has been characterized by single-crystal X-ray diffraction, elemental analysis, IR, electrochemistry, magnetic measurements, electron paramagnetic resonance (EPR), and mass spectrometry (MS). Magnetization and high-field EPR measurements reveal that the pentameric copper core {Cu(5)(OH)(4)(H(2)O)(2)}(6+) of 1 exhibits strong antiferromagnetic interactions (J(a) = -51 +/- 6 cm(-)(1), J(b) = -104 +/- 1 cm(-)(1), and J(c) = -55 +/- 3 cm(-)(1)) resulting in a spin S(T) = (1)/(2) ground state. EPR data show that the unpaired electron spin density is localized on the spin-frustrated apical Cu(2+) ion with g(zz) = 2.4073 +/- 0.0005, g(yy) = 2.0672 +/- 0.0005, g(xx) = 2.0240 +/- 0.0005, and A(zz) = -340 +/- 20 MHz (-0.0113 cm(-)(1)). 1 can therefore be considered as a model system for a five-spin, electronically coupled, spin-frustrated system. Polyanion 1, which is stable over a wide pH domain (pH 1-7), was characterized by cyclic voltammetry (CV) in a pH 5 medium. Its CV was constituted by an initial two-step reduction of the Cu(2+) centers to Cu(0) through Cu(+), followed at more negative potential by the redox processes of the W centers. Controlled potential coulometry of 1 allows for the reduction of the five Cu(2+) centers, as seen by consumption of 10.05 +/- 0.05 electrons per molecule. Polyanion 1 triggers efficiently the electrocatalytic reduction of nitrate and nitrite, and it also catalyzes the reduction of N(2)O. To our knowledge, this is the first example of N(2)O catalytic reduction by a polyoxoanion. Fourier transform ion cyclotron resonance MS was used to unambiguously assign the molecular weight of the solution-phase species 1 and the oxidation states of the Cu atoms in the central {Cu(5)(OH)(4)(H(2)O)(2)}(6+) core. Infrared (IR) multiphoton dissociation MS/MS of 1 showed evidence of a condensation process similar to bronze formation at low irradiation intensity. Higher IR intensity resulted in the formation of stable fragments consistent with those previously observed in the solution chemistry of polyoxoanions.

Characterization of Ti(6)O(4)(O(2)C(4)H(5))(8)(OCH(2)CH(3))(8) by electrospray time of flight mass spectrometry.

A titanium oxide molecular cluster prepared by hydrolysis of titanium tetraethoxide in the presence of methacrylic acid, can be characterized by electrospray time of flight mass spectrometry (ESMS-TOF). The chemistry of such systems is not well known and ESMS is a powerful technique for studying the reactions of clusters in solution. The fingerprint of the cluster fragmentation suggests formation of Ti(x)O(y) core fragments that represent commonly observed structural constructs in bulk titanium oxide metallates. The fragmentation steps provide insight into the hydrolytic conversion of this molecular sol gel intermediate into bulk TiO(2). While MS has been applied to the study of metal alkoxide hydrolysis mechanisms, mass spectra of isolated individual titanium oxide clusters have not previously been reported.

Expression profile of genes associated with antimetastatic gene: nm23-mediated metastasis inhibition in breast carcinoma cells.

Metastases of various malignancies have been shown to be inversely related to the abundance of nm23 protein expression. However, the downstream pathways involved in nm23-mediated suppression of metastasis have not been elucidated. In the present investigation, we used cDNA microarrays to identify novel genes and functional pathways in nm23-mediated spontaneous breast metastasis. Microarray experiments were performed in a pair of cell lines, namely, C-100 (only vector transfected; highly metastatic) and H1-177 (nm23 transfected; low metastatic), derived from human mammary carcinoma cell line MDA-MB-435. The cDNA microarray analysis using GeneSpring software revealed significant as well as consistent alterations in the expression (up- and downregulation) of 2158 genes in a total of 18889 genes between high and low metastatic cells. Some of these genes were grouped into 6 functional categories, namely, invasion and metastasis, apoptosis and senescence, signal transduction molecules and transcription factors, cell cycle and repair, adhesion, and angiogenesis to extrapolate an association between these genes and different functional pathways involved in nm23-regulated metastasis. The results suggest that nm23 gene plays a major role in metastasis and its mechanism of action of metastasis suppression may involve downregulation of genes associated with cell adhesion, motility (integrins alpha2, -8, -9, -L and -V, collagen type VIII alpha1, fibronectin 1, catenin, TGF-beta2, FGF7, MMP14 and 16, ErbB2) and possibly certain tumor/metastasis suppressors (2 members of SWI/SNF-related matrix-associated proteins 2 and 5 and PTEN).

ZnS nanomaterial characterization by MALDI-TOF mass spectrometry.

We present a methodology for mass and size dispersity analysis by MALDI-TOF mass spectrometry of lyothermally grown 2.5-3.7 nm ZnS nanocrystals having a Zn blende crystal structure. These results correlate with information obtained by TEM and absorption spectroscopy. The use of MS methods to probe size and size dispersity provides a convenient method to rapidly analyze II-VI materials at the nanoscale. We believe these results represent the first mass spectrometric analysis of size and size dispersities on II-VI nanocrystals.

Enzymatic manipulation of DNA-nanomaterial constructs.

The demonstration and control of biofunction between inorganic nanomaterials and biological scaffolding is crucial to the development of the field of biomaterials. Although unique hierarchical structures can be generated, the impact of nanosized materials on the biological activity of DNA-protein interactions is relatively unknown. Using highly selective proteins that induce sequence-specific conformational perturbations within DNA, we demonstrate the absolute maintenance of biofunction for biomaterials composed of duplex DNA appended with 1.4-nm Au particles. Enzyme activity and DNA binding affinities (K(d)) are unaltered by the nanoparticle-DNA conjugates. Our results provide a foundation for interfacing more complex and diverse protein-DNA-systems.