Purpose: Histone deacetylase inhibitors can alter gene expression and mediate diverse antitumor activities. Herein, we report the safety and activity of the histone deacetylase inhibitor panobinostat (LBH589) in cutaneous T-cell lymphoma (CTCL) and identify genes commonly regulated by panobinostat. Experimental Design: Panobinostat was administered orally to patients with CTCL on Monday, Wednesday, and Friday of each week on a 28-day cycle. A dose of 30 mg was considered excessively toxic, and subsequent patients were treated at the expanded maximum tolerated dose of 20 mg. Biopsies from six patients taken 0, 4, 8, and 24 h after administration were subjected to microarray gene expression profiling and real-time quantitative PCR of selected genes. Results: Patients attained a complete response (n = 2), attained a partial response (n = 4), achieved stable disease with ongoing improvement (n = 1), and progressed on treatment (n = 2). Microarray data showed distinct gene expression response profiles over time following panobinostat treatment, with the majority of genes being repressed. Twenty-three genes were commonly regulated by panobinostat in all patients tested. Conclusions: Panobinostat is well tolerated and induces clinical responses in CTCL patients. Microarray analyses of tumor samples indicate that panobinostat induces rapid changes in gene expression, and surprisingly more genes are repressed than are activated. A unique set of genes that can mediate biological responses such as apoptosis, immune regulation, and angiogenesis were commonly regulated in response to panobinostat. These genes are potential molecular biomarkers for panobinostat activity and are strong candidates for the future assessment of their functional role(s) in mediating the antitumor responses of panobinostat.

BackgroundRadish (Raphanus sativus L.), is an important root vegetable crop worldwide. Glucosinolates in the fleshy taproot significantly affect the flavor and nutritional quality of radish. However, little is known about the molecular mechanisms underlying glucosinolate metabolism in radish taproots. The limited availability of radish genomic information has greatly hindered functional genomic analysis and molecular breeding in radish.ResultsIn this study, a high-throughput, large-scale RNA sequencing technology was employed to characterize the de novo transcriptome of radish roots at different stages of development. Approximately 66.11 million paired-end reads representing 73,084 unigenes with a N50 length of 1,095 bp, and a total length of 55.73 Mb were obtained. Comparison with the publicly available protein database indicates that a total of 67,305 (about 92.09% of the assembled unigenes) unigenes exhibit similarity (e –value ≤ 1.0e-5) to known proteins. The functional annotation and classification including Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the main activated genes in radish taproots are predominately involved in basic physiological and metabolic processes, biosynthesis of secondary metabolite pathways, signal transduction mechanisms and other cellular components and molecular function related terms. The majority of the genes encoding enzymes involved in glucosinolate (GS) metabolism and regulation pathways were identified in the unigene dataset by targeted searches of their annotations. A number of candidate radish genes in the glucosinolate metabolism related pathways were also discovered, from which, eight genes were validated by T-A cloning and sequencing while four were validated by quantitative RT-PCR expression profiling.ConclusionsThe ensuing transcriptome dataset provides a comprehensive sequence resource for molecular genetics research in radish. It will serve as an important public information platform to further understanding of the molecular mechanisms involved in biosynthesis and metabolism of the related nutritional and flavor components during taproot formation in radish.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-836) contains supplementary material, which is available to authorized users.

We quantitatively evaluated the effectiveness of a repeat administration of a recombinant adenoviral vector expressing bacterial Escherichia coli lacZ into the same arterial site of a relatively large animal, the dog. The replication-defective adenoviral vector was introduced percutaneously into balloon-injured femoral arteries through a double-balloon catheter. After a single dose of adenoviral vector, up to 90% of surface (73 +/- 16%, n = 7) and smooth muscle cells in multiple layers of the media showed transgene expression as evaluated by 5-bromo-4-chloro-3-indoyl beta-D-galactopyranoside histostaining without extralocal expression, as assessed by polymerase chain reaction. High-level expression (measured as beta-galactosidase activity) peaked 7 days after transfer and was transient, although it was retained for a month. Second does of the same adenovirus to the same arterial site were given 1, 2, 5, or 8 weeks after the first administration. At 1 week the second dose significantly enhanced lacZ expression. At 2, 5, or 8 weeks the second dose reinduced lacZ expression at 25% to 30% of the full expression. lacZ expression was also detected in preimmuned dogs, although the expression levels correlated inversely to the titer of neutralizing antibodies in their serum. These results demonstrate that arterial gene expression can be enhanced by a second administration of the same adenovirus after a short interval and that a repeat dose after a long interval partially but significantly reinduces gene expression despite the presence of an immune response. These data may provide an additional scientific foundation for the use of adenovirus-mediated arterial gene transfer in future clinical practice.

ORCID IDs: 0000-0002-1560-7935 (J.Y.W.); 0000-0002-3129-5206 (X.S.Z.).Timing of flowering is not only an interesting topic in developmental biology, but it also plays a significant role in agriculture for its effects on the maturation time of seed. The hexaploid wheat (Triticum aestivum) is one of the most important crop species whose flowering time, i.e. heading time, greatly influences yield. However, it remains unclear whether and how microRNAs regulate heading time in it. In our current study, we identified the tae-miR408 in wheat and its targets in vivo, including Triticum aestivum TIMING OF CAB EXPRESSION-A1 (TaTOC-A1), TaTOC-B1, and TaTOC-D1. The tae-miR408 levels were reciprocal to those of TaTOC1s under long-day and short-day conditions. Wheat plants with a knockdown of TaTOC1s via RNA interference and overexpression of tae-miR408 showed early-heading phenotype. Furthermore, TaTOC1s expression was down-regulated by the tae-miR408 in the hexaploid wheat. In addition, other important agronomic traits in wheat, such as plant height and flag leaf angle, were regulated by both tae-miR408 and TaTOC1s. Thus, our results suggested that the tae-miR408 functions in the wheat heading time by mediating TaTOC1s expression, and the study provides important new information on the mechanism underlying heading time regulation in wheat.

Our findings demonstrate that a catheter-mediated direct injection with an adenovirus can induce gene expression in the ventricle more efficiently without additional myocardial damage and inflammation compared with injection with a plasmid. A repeat dose of the same adenovirus elicited gene expression at an attenuated but significant level. This method may potentially have clinical applications: in modifying myocardial phenotype and/or improving general circulation under certain circumstances.

Advanced drilling technology has been widely and successfully applied to construct multilateral wells in reservoirs. This paper presents several field applications of the modeling of complex well architectures. A generalized semi-analytical segmented model, accounting for multilateral well systems in commingled layered reservoirs was used in several field applications. Cases include evaluating the flow efficiency of different configurations of wells with multiple laterals, analyzing an interference test between three horizontal wells in Al Rayyan oil field offshore Qatar, and analyzing a well test in a commingled multilateral well in a multilayer reservoir in the Dos Cuadras field offshore California. The model can predict the production performance under either constant-rate or constant-pressure conditions of a well system with any number of arbitrarily oriented laterals of any length and nonuniform formation damage. The reservoir layers, with different porosities, anisotropic permeabilities and drainage areas, are non-communicating except through the wellbore. The solution is valid for large reservoirs and when no-flow or constant-pressure boundaries affect the pressure behavior. Results of applying this method in the field cases showed that the model enabled us to predict multilateral well performance, to obtain information about reservoir connectivity, and to estimate well and reservoir properties in a multilayer system. Uncertainty, due to the large number of unknown parameters in such a complex system, represents the main challenge in using this method. It is recommended to use other means (e.g. production logging and PNC log) together with pressure transient data to reduce the uncertainty. Whenever possible, each lateral should be tested individually to provide more reliable estimates of reservoir and well properties. The presented model and the lessons learned from the field applications provide engineers a tool to use transient data collected from multilateral wells in multilayer systems for reservoir characterization and performance forecast. Background Information Methods are becoming commonplace for drilling horizontal wells, slanted wells and one or more curved wells from a common central hole in producing formations. These wells will have productivities exceeding that of a single vertical well or a single horizontal well. The performance of these wells depends greatly on appropriate reservoir selection, substantial predrilling formation evaluation and optimized completion and stimulation practices. Several studies addressed pressure transient behavior of slanted, horizontal and multilateral wells. Examples include work on spatial transformation for deviated well in anisotropic reservoir (Besson 1990), multiple horizontal wells (Economides et al. 1996, Retnanto and Economides 1996, and Yildiz 2000), and segmentation technique (Gommanard and Horne 1996). There are also studies of transient solution in layered reservoirs (Kuchuk and Wilkinson 1988, Spath, et al. 1990, and Kuchuk 1991, etc.), and field applications of multilateral well in multilayer formation (Vo and Madden 1995 and Youcef, et al. 2008, etc.) A comprehensive single- and multilateral wellbore pressure response prediction model allows arbitrary positioning of the well laterals in layered anisotropic formations. Such a flexible and generalized model can be used to study several plausible scenarios, especially the economic advantages of drilling multiple laterals from the same wellbore in a layered reservoir.

Abstract.The resonant behavior of a porous medium composed of periodic channel structures was studied. The natural frequencies of the dry pore system were obtained by theoretical analysis. The resonant frequencies of the saturated porous medium were calculated by numerical simulation, which considered the two-phase coupling effects of fluid and solid. The numerical results showed that most of the resonant frequencies of the saturated porous medium match .with the natural frequencies of the corresponding dry porous medium but that some of the resonant frequencies are different from those of the solid matrix depending on the porosity of the pore system. Both the theoretical study and the numerical study suggest that the resonant frequencies of a porous medium are functions of the porosity or the fracture density.

Background Mitogen-activated protein kinase (MAPK) cascade is a conserved and universal signal transduction module in organisms. Although it has been well characterized in many plants, no systematic analysis has been conducted in barley. Results Here, we identified 20 MAPKs, 6 MAPKKs and 156 MAPKKKs in barley through a genome-wide search against the updated reference genome. Then, phylogenetic relationship, gene structure and conserved protein motifs organization of them were systematically analyzed and results supported the predictions. Gene duplication analysis revealed that segmental and tandem duplication events contributed to the expansion of barley MAPK cascade genes and the duplicated gene pairs were found to undergone strong purifying selection. Expression profiles of them were further investigated in different organs and under diverse abiotic stresses using the available 173 RNA-seq datasets, and then the tissue-specific and stress-responsive candidates were found. Finally, co-expression regulatory network of MAPK cascade genes was constructed by WGCNA tool, resulting in a complicated network composed of a total of 72 branches containing 46 HvMAPK cascade genes and 46 miRNAs. Conclusion This study provides the targets for further functional study and also contribute to better understand the MAPK cascade regulatory network in barley and beyond.