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Find video protocols related to scientific articles indexed in Pubmed.
ARMC5 mutations are common in familial bilateral macronodular adrenal hyperplasia.
J. Clin. Endocrinol. Metab.
PUBLISHED: 06-06-2014
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Bilateral macronodular adrenal hyperplasia (BMAH) is a rare form of adrenal Cushing's syndrome. Familial cases have been reported, but at the time we conducted this study, the genetic basis of BMAH was unknown. Recently, germline variants of armadillo repeat containing 5 (ARMC5) in patients with isolated BMAH and somatic, second-hit mutations in tumor nodules, were identified.
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Introducing a combinatorial DNA-toolbox platform constituting defined protein-based biohybrid-materials.
Biomaterials
PUBLISHED: 05-13-2014
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The access to defined protein-based material systems is a major challenge in bionanotechnology and regenerative medicine. Exact control over sequence composition and modification is an important requirement for the intentional design of structure and function. Herein structural- and matrix proteins provide a great potential, but their large repetitive sequences pose a major challenge in their assembly. Here we introduce an integrative "one-vector-toolbox-platform" (OVTP) approach which is fast, efficient and reliable. The OVTP allows for the assembly, multimerization, intentional arrangement and direct translation of defined molecular DNA-tecton libraries, in combination with the selective functionalization of the yielded protein-tecton libraries. The diversity of the generated tectons ranges from elastine-, resilin, silk- to epitope sequence elements. OVTP comprises the expandability of modular biohybrid-materials via the assembly of defined multi-block domain genes and genetically encoded unnatural amino acids (UAA) for site-selective chemical modification. Thus, allowing for the modular combination of the protein-tecton library components and their functional expansion with chemical libraries via UAA functional groups with bioorthogonal reactivity. OVTP enables access to multitudes of defined protein-based biohybrid-materials for self-assembled superstructures such as nanoreactors and nanobiomaterials, e.g. for approaches in biotechnology and individualized regenerative medicine.
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Designer amphiphilic proteins as building blocks for the intracellular formation of organelle-like compartments.
Nat Mater
PUBLISHED: 03-31-2014
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Nanoscale biological materials formed by the assembly of defined block-domain proteins control the formation of cellular compartments such as organelles. Here, we introduce an approach to intentionally 'program' the de novo synthesis and self-assembly of genetically encoded amphiphilic proteins to form cellular compartments, or organelles, in Escherichia coli. These proteins serve as building blocks for the formation of artificial compartments in vivo in a similar way to lipid-based organelles. We investigated the formation of these organelles using epifluorescence microscopy, total internal reflection fluorescence microscopy and transmission electron microscopy. The in vivo modification of these protein-based de novo organelles, by means of site-specific incorporation of unnatural amino acids, allows the introduction of artificial chemical functionalities. Co-localization of membrane proteins results in the formation of functionalized artificial organelles combining artificial and natural cellular function. Adding these protein structures to the cellular machinery may have consequences in nanobiotechnology, synthetic biology and materials science, including the constitution of artificial cells and bio-based metamaterials.
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Nutlin-3a efficacy in sarcoma predicted by transcriptomic and epigenetic profiling.
Cancer Res.
PUBLISHED: 12-13-2013
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Nutlin-3a is a small molecule antagonist of p53/MDM2 that is being explored as a treatment for sarcoma. In this study, we examined the molecular mechanisms underlying the sensitivity of sarcomas to Nutlin-3a. In an ex vivo tissue explant system, we found that TP53 pathway alterations (TP53 status, MDM2/MDM4 genomic amplification/mRNA overexpression, MDM2 SNP309, and TP53 SNP72) didnt confer apoptotic or cytostatic responses in sarcoma tissue biopsies (n=24). Unexpectedly, MDM2 status didnt predict Nutlin-3a sensitivity. RNA sequencing revealed that the global transcriptomic profiles of these sarcomas provided a more robust prediction of apoptotic responses to Nutlin-3a. Expression profiling revealed a subset of TP53 target genes which were transactivated specifically in sarcomas that were highly sensitive to Nutlin-3a. Of these target genes, the GADD45A promoter region was shown to be hypermethylated in 82% of wild-type TP53 sarcomas that didnt respond to Nutlin-3a, thereby providing mechanistic insight into the innate ability of sarcomas to resist apoptotic death following Nutlin-3a treatment. Collectively, our findings argue that the existing benchmark biomarker for MDM2 antagonist efficacy (MDM2 amplification) should not be used to predict outcome, but rather global gene expression profiles and epigenetic status of sarcomas dictate their sensitivity to p53/MDM2 antagonists.
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A comparative analysis of algorithms for somatic SNV detection in cancer.
Bioinformatics
PUBLISHED: 07-09-2013
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With the advent of relatively affordable high-throughput technologies, DNA sequencing of cancers is now common practice in cancer research projects and will be increasingly used in clinical practice to inform diagnosis and treatment. Somatic (cancer-only) single nucleotide variants (SNVs) are the simplest class of mutation, yet their identification in DNA sequencing data is confounded by germline polymorphisms, tumour heterogeneity and sequencing and analysis errors. Four recently published algorithms for the detection of somatic SNV sites in matched cancer-normal sequencing datasets are VarScan, SomaticSniper, JointSNVMix and Strelka. In this analysis, we apply these four SNV calling algorithms to cancer-normal Illumina exome sequencing of a chronic myeloid leukaemia (CML) patient. The candidate SNV sites returned by each algorithm are filtered to remove likely false positives, then characterized and compared to investigate the strengths and weaknesses of each SNV calling algorithm.
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Sequencing error correction without a reference genome.
BMC Bioinformatics
PUBLISHED: 05-03-2013
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Next (second) generation sequencing is an increasingly important tool for many areas of molecular biology, however, care must be taken when interpreting its output. Even a low error rate can cause a large number of errors due to the high number of nucleotides being sequenced. Identifying sequencing errors from true biological variants is a challenging task. For organisms without a reference genome this difficulty is even more challenging.
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Comparison of pretreatment methods for rye straw in the second generation biorefinery: effect on cellulose, hemicellulose and lignin recovery.
Bioresour. Technol.
PUBLISHED: 03-11-2013
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The increasing interest in lignocellulose-based biorefineries boosts the further development of the needed pretreatment methods for preprocessing biomass. There are a large number of different processes that are being investigated; however research is made mostly based on different types of biomass with the same pretreatment or several modifications of the same process for a given type of biomass. In this work a comparison of promising chemical pretreatments using the same biomass was performed. Organosolv (OS), Steam (SE) and Liquid-Hot-Water (LHW) processes were used for the pretreatment of rye straw and the treated solids further enzymatically hydrolyzed. Best results for carbohydrate and lignin yield were found for the OS pretreatment followed close by the LHW and SE with similar results. All of the processes showed satisfactory performance for the pretreatment of lignocellulosic biomass for application in the second generation biorefinery.
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GTV differentially impacts locoregional control of non-small cell lung cancer (NSCLC) after different fractionation schedules: subgroup analysis of the prospective randomized CHARTWEL trial.
Radiother Oncol
PUBLISHED: 01-17-2013
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To evaluate the impact of fractionation schedule on the size of the gross tumour volume (GTV) effect on tumour control after radiotherapy of NSCLC.
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Photon propagation in a discrete fiber network: an interplay of coherence and losses.
Phys. Rev. Lett.
PUBLISHED: 08-09-2011
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We study light propagation in a photonic system that shows stepwise evolution in a discretized environment. It resembles a discrete-time version of photonic waveguide arrays or quantum walks. By introducing controlled photon losses to our experimental setup, we observe unexpected effects like subexponential energy decay and formation of complex fractal patterns. This demonstrates that the interplay of linear losses, discreteness and energy gradients leads to genuinely new coherent phenomena in classical and quantum optical experiments. Moreover, the influence of decoherence is investigated.
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Discovery of barley miRNAs through deep sequencing of short reads.
BMC Genomics
PUBLISHED: 02-25-2011
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MicroRNAs are important components of the regulatory network of biological systems and thousands have been discovered in both animals and plants. Systematic investigations performed in species with sequenced genomes such as Arabidopsis, rice, poplar and Brachypodium have provided insights into the evolutionary relationships of this class of small RNAs among plants. However, miRNAs from barley, one of the most important cereal crops, remain unknown.
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Early FDG PET at 10 or 20 Gy under chemoradiotherapy is prognostic for locoregional control and overall survival in patients with head and neck cancer.
Eur. J. Nucl. Med. Mol. Imaging
PUBLISHED: 02-02-2011
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Our study aimed to explore the optimal timing as well as the most appropriate prognostic parameter of (18)F-fluorodeoxyglucose positron emission tomography (FDG PET) during chemoradiotherapy (CRT) for an early prediction of outcome for patients with head and neck squamous cell carcinoma (HNSCC).
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The tegument protein UL71 of human cytomegalovirus is involved in late envelopment and affects multivesicular bodies.
J. Virol.
PUBLISHED: 02-02-2011
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Morphogenesis of human cytomegalovirus (HCMV) is still only partially understood. We have characterized the role of HCMV tegument protein pUL71 in viral replication and morphogenesis. By using a rabbit antibody raised against the C terminus of pUL71, we could detect the protein in infected cells, as well as in virions showing a molecular mass of approximately 48 kDa. The expression of pUL71, detected as early as 48 h postinfection, was not blocked by the antiviral drug foscarnet, indicating an early expression. The role of pUL71 during virus replication was investigated by construction and analysis of a UL71 stop mutant (TBstop71). The mutant could be reconstituted on noncomplementing cells proving that pUL71 is nonessential for virus replication in human fibroblasts. However, the inhibition of pUL71 expression resulted in a severe growth defect, as reflected by an up to 16-fold reduced extracellular virus yield after a high-multiplicity infection and a small-plaque phenotype. Ultrastructural analysis of cells infected with TBstop71 virus revealed an increased number of nonenveloped nucleocapsids in the cytoplasm, many of them at different stages of envelopment, indicating that final envelopment of nucleocapsids in the cytoplasm was affected. In addition, enlarged multivesicular bodies (MVBs) were found in close proximity to the viral assembly compartment, suggesting that pUL71 affects MVBs during virus infection. The observation of numerous TBstop71 virus particles attached to MVB membranes and budding processes into MVBs indicated that these membranes can be used for final envelopment of HCMV.
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Cell-specific vacuolar calcium storage mediated by CAX1 regulates apoplastic calcium concentration, gas exchange, and plant productivity in Arabidopsis.
Plant Cell
PUBLISHED: 01-21-2011
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The physiological role and mechanism of nutrient storage within vacuoles of specific cell types is poorly understood. Transcript profiles from Arabidopsis thaliana leaf cells differing in calcium concentration ([Ca], epidermis <10 mM versus mesophyll >60 mM) were compared using a microarray screen and single-cell quantitative PCR. Three tonoplast-localized Ca(2+) transporters, CAX1 (Ca(2+)/H(+)-antiporter), ACA4, and ACA11 (Ca(2+)-ATPases), were identified as preferentially expressed in Ca-rich mesophyll. Analysis of respective loss-of-function mutants demonstrated that only a mutant that lacked expression of both CAX1 and CAX3, a gene ectopically expressed in leaves upon knockout of CAX1, had reduced mesophyll [Ca]. Reduced capacity for mesophyll Ca accumulation resulted in reduced cell wall extensibility, stomatal aperture, transpiration, CO(2) assimilation, and leaf growth rate; increased transcript abundance of other Ca(2+) transporter genes; altered expression of cell wall-modifying proteins, including members of the pectinmethylesterase, expansin, cellulose synthase, and polygalacturonase families; and higher pectin concentrations and thicker cell walls. We demonstrate that these phenotypes result from altered apoplastic free [Ca(2+)], which is threefold greater in cax1/cax3 than in wild-type plants. We establish CAX1 as a key regulator of apoplastic [Ca(2+)] through compartmentation into mesophyll vacuoles, a mechanism essential for optimal plant function and productivity.
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HCMV-encoded chemokine receptor US28 mediates proliferative signaling through the IL-6-STAT3 axis.
Sci Signal
PUBLISHED: 08-05-2010
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US28 is a viral G protein (heterotrimeric guanosine triphosphate-binding protein)-coupled receptor encoded by the human cytomegalovirus (HCMV). In addition to binding and internalizing chemokines, US28 constitutively activates signaling pathways linked to cell proliferation. Here, we show increased concentrations of vascular endothelial growth factor and interleukin-6 (IL-6) in supernatants of US28-expressing NIH 3T3 cells. Increased IL-6 was associated with increased activation of the signal transducer and activator of transcription 3 (STAT3) through upstream activation of the Janus-activated kinase JAK1. We used conditioned growth medium, IL-6-neutralizing antibodies, an inhibitor of the IL-6 receptor, and short hairpin RNA targeting IL-6 to show that US28 activates the IL-6-JAK1-STAT3 signaling axis through activation of the transcription factor nuclear factor kappaB and the consequent production of IL-6. Treatment of cells with a specific inhibitor of STAT3 inhibited US28-dependent [(3)H]thymidine incorporation and foci formation, suggesting a key role for STAT3 in the US28-mediated proliferative phenotype. US28 also elicited STAT3 activation and IL-6 secretion in HCMV-infected cells. Analyses of tumor specimens from glioblastoma patients demonstrated colocalization of US28 and phosphorylated STAT3 in the vascular niche of these tumors. Moreover, increased phospho-STAT3 abundance correlated with poor patient outcome. We propose that US28 induces proliferation in HCMV-infected tumors by establishing a positive feedback loop through activation of the IL-6-STAT3 signaling axis.
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Serial FDG-PET on patients with head and neck cancer: implications for radiation therapy.
Int. J. Radiat. Biol.
PUBLISHED: 09-04-2009
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To assess possible consequences for radiotherapy (RT) planning, e.g., reduction of treatment volume by a decreased tumour volume in Fluor-18-fluoro-deoxy-glucose-Positron emission tomography (FDG-PET) based on a close-meshed evaluation of FDG uptake in primary head and neck cancer (HNC) during RT.
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The extreme radiosensitivity of the squamous cell carcinoma SKX is due to a defect in double-strand break repair.
Radiother Oncol
PUBLISHED: 05-21-2009
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Squamous cell carcinomas (SCCs) are characterized by moderate radiosensitivity. We have established the human head & neck SCC cell line SKX, which shows an exceptionally high radiosensitivity. It was the aim of this study to understand the underlying mechanisms.
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Pharmacological and biochemical characterization of human cytomegalovirus-encoded G protein-coupled receptors.
Meth. Enzymol.
PUBLISHED: 05-19-2009
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Human cytomegalovirus (HCMV) is a widely spread herpesvirus that can have serious consequences in immunocompromised hosts. Interestingly, HCMV genome encodes for four viral G protein-coupled receptors (vGPCRs), namely, US27, US28, UL33, and UL78. Thus far, US28 and UL33 have been shown to activate signaling pathways in a ligand-independent manner. US28 is the best characterized vGPCR and has been shown to be potentially involved in the development of HCMV-related diseases. As such, detailed investigation of these viral GPCR is of importance in order to understand molecular events occurring during viral pathogenesis and the potential identification of novel therapeutic targets. Herewith, we describe several approaches to study these HCMV-encoded vGPCRs. Using molecular biology, tags can be introduced in the vGPCRs, which may facilitate the study of their protein expression with various techniques, such as microscopy, Western blotting, enzyme-linked immunosorbent assay (ELISA), and flow cytometry. Furthermore, radioligand binding studies can be performed to screen for ligands for vGPCRs, but also to study kinetics of internalization. We also describe several signal transduction assays that can evaluate the signaling activity of these vGPCRs. In addition, we discuss different proliferation assays and an in vivo xenograft model that were used to identify the oncogenic potential of US28. The study of these vGPCRs in their viral context can be examined using recombinant HCMV strains generated by bacterial artificial chromosome mutagenesis. Finally, we show how these mutants can be used in several pharmacological and biochemical assays.
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The human cytomegalovirus-encoded chemokine receptor US28 promotes angiogenesis and tumor formation via cyclooxygenase-2.
Cancer Res.
PUBLISHED: 03-24-2009
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The human cytomegalovirus (HCMV), potentially associated with the development of malignancies, encodes the constitutively active chemokine receptor US28. Previously, we have shown that US28 expression induces an oncogenic phenotype both in vitro and in vivo. Microarray analysis revealed differential expression of genes involved in oncogenic signaling in US28-expressing NIH-3T3 cells. In particular, the expression of cyclooxygenase-2 (COX-2), a key mediator of inflammatory diseases and major determinant in several forms of cancer, was highly up-regulated. US28 induced increases in COX-2 expression via activation of nuclear factor-kappaB, driving the production of vascular endothelial growth factor. Also, in HCMV-infected cells, US28 contributed to the viral induction of COX-2. Finally, the involvement of COX-2 in US28-mediated tumor formation was evaluated using the COX-2 selective inhibitor Celecoxib. Targeting COX-2 in vivo with Celecoxib led to a marked delay in the onset of tumor formation in nude mice injected with US28-transfected NIH-3T3 cells and a reduction of subsequent growth by repressing the US28-induced angiogenic activity. Hence, the development of HCMV-related proliferative diseases may partially be ascribed to the ability of US28 to activate COX-2.
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Antiviral treatment of cytomegalovirus infection and resistant strains.
Expert Opin Pharmacother
PUBLISHED: 02-25-2009
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This review discusses the management of resistant cytomegalovirus and prevention strategies for fatal therapy failures. Five drugs, ganciclovir/valganciclovir, cidofovir, foscarnet and fomivirsen, have been approved so far for the treatment of human cytomegalovirus (HCMV) diseases. Except for fomivirsen, all of the approved drugs share the same target molecule, the viral DNA polymerase. The emergence of drug-resistant HCMV has also been reported for all of them. For optimal care of patients, the clinical virologist has to provide the most meaningful assays for monitoring of therapy and early detection of emerging drug-resistant HCMV. Additionally, a quantitative drug monitoring would be helpful. New antiviral agents are urgently needed with less adverse effects, good oral bioavailability and possibly novel targets or mechanisms of action to avoid cross-resistance and to improve the ability to suppress the selection of resistant virus strains by combination therapy. Compounds like maribavir, leflunomide and artesunate, which exhibit anti-HCMV activity in vitro and in patients need to be evaluated in clinical studies. Besides these, new therapy approaches like immunotherapy or new diagnostic techniques like pyrosequencing have to be considered in the future.
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Comparative transcriptomics in the Triticeae.
BMC Genomics
PUBLISHED: 02-18-2009
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Barley and particularly wheat are two grass species of immense agricultural importance. In spite of polyploidization events within the latter, studies have shown that genotypically and phenotypically these species are very closely related and, indeed, fertile hybrids can be created by interbreeding. The advent of two genome-scale Affymetrix GeneChips now allows studies of the comparison of their transcriptomes.
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Constitutive ?-catenin signaling by the viral chemokine receptor US28.
PLoS ONE
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Chronic activation of Wnt/?-catenin signaling is found in a variety of human malignancies including melanoma, colorectal and hepatocellular carcinomas. Interestingly, expression of the HCMV-encoded chemokine receptor US28 in intestinal epithelial cells promotes intestinal neoplasia in transgenic mice, which is associated with increased nuclear accumulation of ?-catenin. In this study we show that this viral receptor constitutively activates ?-catenin and enhances ?-catenin-dependent transcription. Our data illustrate that this viral receptor does not activate ?-catenin via the classical Wnt/Frizzled signaling pathway. Analysis of US28 mediated signaling indicates the involvement of the Rho-Rho kinase (ROCK) pathway in the activation of ?-catenin. Moreover, cells infected with HCMV show significant increases in ?-catenin stabilization and signaling, which is mediated to a large extent by expression of US28. The modulation of the ?-catenin signal transduction pathway by a viral chemokine receptor provides alternative regulation of this pathway, with potential relevance for the development of colon cancer and virus-associated diseases.
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Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat.
BMC Genomics
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Bread wheat is one of the worlds most important food crops and considerable efforts have been made to develop genomic resources for this species. This includes an on-going project by the International Wheat Genome Sequencing Consortium to assemble its large and complex genome, which is hexaploid and contains three closely related homoeologous copies for each chromosome. This multi-national effort avoids the complications polyploidy entails for correct assembly of the genome by sequencing flow-sorted chromosome arms one at a time. Here we report on an alternate approach, a direct homoeolog-specific assembly of the expressed portion of the genome, the transcriptome.
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Clusters of genes encoding fructan biosynthesizing enzymes in wheat and barley.
Plant Mol. Biol.
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Fructans are soluble carbohydrates with health benefits and possible roles in plant adaptation. Fructan biosynthetic genes were isolated using comparative genomics and physical mapping followed by BAC sequencing in barley. Genes encoding sucrose:sucrose 1-fructosyltransferase (1-SST), fructan:fructan 1-fructosyltransferase (1-FFT) and sucrose:fructan 6-fructosyltransferase (6-SFT) were clustered together with multiple copies of vacuolar invertase genes and a transposable element on two barley BAC. Intron-exon structures of the genes were similar. Phylogenetic analysis of the fructosyltransferases and invertases in the Poaceae showed that the fructan biosynthetic genes may have evolved from vacuolar invertases. Quantitative real-time PCR was performed using leaf RNA extracted from three wheat cultivars grown under different conditions. The 1-SST, 1-FFT and 6-SFT genes had correlated expression patterns in our wheat experiment and in existing barley transcriptome database. Single nucleotide polymorphism (SNP) markers were developed and successfully mapped to a major QTL region affecting wheat grain fructan accumulation in two independent wheat populations. The alleles controlling high- and low- fructan in parental lines were also found to be associated in fructan production in a diverse set of 128 wheat lines. To the authors knowledge, this is the first report on the mapping and sequencing of a fructan biosynthetic gene cluster and in particular, the isolation of a novel 1-FFT gene from barley.
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A 2D quantum walk simulation of two-particle dynamics.
Science
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Multidimensional quantum walks can exhibit highly nontrivial topological structure, providing a powerful tool for simulating quantum information and transport systems. We present a flexible implementation of a two-dimensional (2D) optical quantum walk on a lattice, demonstrating a scalable quantum walk on a nontrivial graph structure. We realized a coherent quantum walk over 12 steps and 169 positions by using an optical fiber network. With our broad spectrum of quantum coins, we were able to simulate the creation of entanglement in bipartite systems with conditioned interactions. Introducing dynamic control allowed for the investigation of effects such as strong nonlinearities or two-particle scattering. Our results illustrate the potential of quantum walks as a route for simulating and understanding complex quantum systems.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.