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Duarte, CA, United States

The Beckman Research Institute is a research facility located at the City of Hope National Medical Center in Duarte, CA, United States. It is dedicated to studying normal and abnormal biological processes which may be related to cancer. The institute was dedicated in 1952, and endowed by the Arnold and Mabel Beckman Foundation in 1983 when it was given its current name. It was the first of five Beckman institutes in the United States. It also hosts the Irell & Manella Graduate School of Biological science whose founding dean was Arthur Riggs. The BRI's current director is Richard Jove, Ph.D. Wikipedia.

MicroRNAs (miRNAs) are emerging molecules in the pathogenesis of human diseases. Identification of miRNAs related to renal fibrosis provides clues to find new signaling pathways to fill the gaps between signaling molecules. Li et al. report another new pathway mediated by miR-433 that is induced by transforming growth factor-β1 in mouse models of renal fibrosis. The signaling also makes a positive-feedback circuit loop, which could be translated into new therapeutic targets.© 2013 International Society of Nephrology.

Micro RNAs (miRNAs) are 21-23 nucleotide long RNAs that associate with the Argonaute family of proteins and direct interactions of these and RNA-induced silencing complex (RISC) components to the 30-UTRs of mRNAs that harbour partially complementary sequences. The paradigm for miRNA function has been that they inhibit gene expression by translational inhibition and subsequent mRNA degradation. However, a series of recent studies have revealed that subsets of miRNAs are also localized in the nucleus, suggesting that they perform different functions in this cellular compartment. In this issue of The EMBO Journal, Hansen et al (2011) describe that nuclear localized miRNAs target non-coding RNAs (ncRNAs) revealing an intriguing and novel mechanism for gene regulation. © 2011 European Molecular Biology Organization | All Rights Reserved.

Zaia J.A.,Beckman Research Institute
Hematology / the Education Program of the American Society of Hematology. American Society of Hematology. Education Program | Year: 2013

With the advent of effective antiretroviral therapy, the treatment of patients with HIV-related malignancies, especially lymphoma, has greatly improved, yielding results comparable to those seen in patients with lymphoma unrelated to HIV. The platform of transplantation of hematopoietic stem cells has facilitated studies of genetically modified stem cells engineered to express antiretroviral genes to resist infection by the HIV virus, testing the concept that engraftment of these cells will lead to HIV resistance and elimination of the reservoir of virus in the body. Results in patients with HIV and lymphoma have now led to studies that will test these principles in HIV patients without concomitant malignancy. In addition, in a patient with HIV and acute myeloid leukemia, the success of an allogeneic transplantation from an unrelated donor carrying a mutation in the CCR5 genes has demonstrated that, in principle, such an approach could also lead to cure of patients with HIV. Case studies in HIV patients with leukemia undergoing allogeneic transplantation also suggest that there may be a therapeutic effect on the HIV reservoir that could alter the natural history of HIV in the allogeneic setting.

Boldin M.P.,Beckman Research Institute | Baltimore D.,California Institute of Technology
Immunological Reviews | Year: 2012

Since its discovery 25years ago, nuclear factor-κB (NF-κB) has emerged as a transcription factor that controls diverse biological functions, ranging from inflammation to learning and memory. Activation of NF-κB initiates an elaborate genetic program. Some of the NF-κB-driven genes do not encode proteins but rather are precursors to microRNAs. These microRNAs play important roles in the regulation of the inflammatory process, some being inhibitory and others activating. Here, we discuss both the regulation of their expression and the function of some of these non-coding RNA genes. We also include a personal discussion of how NF-κB was first discovered. © 2012 John Wiley & Sons A/S.

Deng X.,Beckman Research Institute
BMC Bioinformatics | Year: 2011

Background: The popularity of massively parallel exome and transcriptome sequencing projects demands new data mining tools with a comprehensive set of features to support a wide range of analysis tasks.Results: SeqGene, a new data mining tool, supports mutation detection and annotation, dbSNP and 1000 Genome data integration, RNA-Seq expression quantification, mutation and coverage visualization, allele specific expression (ASE), differentially expressed genes (DEGs) identification, copy number variation (CNV) analysis, and gene expression quantitative trait loci (eQTLs) detection. We also developed novel methods for testing the association between SNP and expression and identifying genotype-controlled DEGs. We showed that the results generated from SeqGene compares favourably to other existing methods in our case studies.Conclusion: SeqGene is designed as a general-purpose software package. It supports both paired-end reads and single reads generated on most sequencing platforms; it runs on all major types of computers; it supports arbitrary genome assemblies for arbitrary organisms; and it scales well to support both large and small scale sequencing projects. The software homepage is http://seqgene.sourceforge.net. © 2011 Deng; licensee BioMed Central Ltd.

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