Showing papers by "Natasha V. Raikhel published in 2005"
TL;DR: Deregulation of apoptosis, the main form of PCD in animals, is associated with diseases such as Parkinson's disease and Huntington's disease.
Abstract: Programmed cell death (PCD) is the genetically controlled suicide of cells. The tight regulation of this program is essential to ensure that it is only activated in the required cells at the proper moment. Deregulation of apoptosis, the main form of PCD in animals, is associated with diseases such
144 citations
TL;DR: A library of 10,000 diverse chemicals for compounds that affected the gravitropism of Arabidopsis seedlings positively or negatively and four of the 34 compounds were found to cause aberrant endomembrane morphologies.
Abstract: Chemical genomics is a powerful approach to dissect processes that may be intractable using conventional genetics because of gene lethality or redundancy. Recently, a link has been established between endomembrane trafficking and gravitropism. To understand this link, we screened a library of 10,000 diverse chemicals for compounds that affected the gravitropism of Arabidopsis seedlings positively or negatively. Sixty-nine of 219 compounds from the primary screen were retested, and 34 of these were confirmed to inhibit or enhance gravitropism. Four of the 34 compounds were found to cause aberrant endomembrane morphologies. The chemicals affected gravitropism and vacuole morphology in concert in a tissue-specific manner, underscoring the link between endomembranes and gravitropism. One of the chemicals (5403629) was structurally similar to the synthetic auxin 2,4-dichlorophenoxy acetate, whereas the other three chemicals were unique in their structures. An in vivo functional assay using the reporter β-glucuronidase under the auxin-inducible DR5 promoter confirmed that the unique compounds were not auxins. Interestingly, one of the unique chemicals (5850247) appeared to decrease the responsiveness to auxin in roots, whereas another (5271050) was similar to pyocyanin, a bacterial metabolite that has been suggested to target the endomembranes of yeast. These reagents will be valuable for dissecting endomembrane trafficking and gravitropism and for cognate target identification.
104 citations
TL;DR: Chemical genomics is a promising new technology for studying gene functions in the context of living organisms or cell systems by allowing fine-tunable in vivo modulations of protein functions and cellular processes.
Abstract: Chemical genomics is a promising new technology for studying gene functions in the context of living organisms or cell systems It complements existing molecular and genetics tools (eg mutagenesis, RNAi) by allowing fine-tunable in vivo modulations of protein functions and cellular processes ([
60 citations
TL;DR: The genome-wide protein sequences from Arabidopsis and rice spp.
Abstract: The genome-wide protein sequences from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) spp. japonica were clustered into families using sequence similarity and domain-based clustering. The two fundamentally different methods resulted in separate cluster sets with complementary properties to compensate the limitations for accurate family analysis. Functional names for the identified families were assigned with an efficient computational approach that uses the description of the most common molecular function gene ontology node within each cluster. Subsequently, multiple alignments and phylogenetic trees were calculated for the assembled families. All clustering results and their underlying sequences were organized in the Web-accessible Genome Cluster Database (http://bioinfo.ucr.edu/projects/GCD) with rich interactive and user-friendly sequence family mining tools to facilitate the analysis of any given family of interest for the plant science community. An automated clustering pipeline ensures current information for future updates in the annotations of the two genomes and clustering improvements. The analysis allowed the first systematic identification of family and singlet proteins present in both organisms as well as those restricted to one of them. In addition, the established Web resources for mining these data provide a road map for future studies of the composition and structure of protein families between the two species.
40 citations
TL;DR: The scope of the authors' knowledge regarding plant genetic mechanisms and gene functions is rapidly evolving and expanding, primarily due to the availability of genetic and genomic methods for investigating model species, such as Arabidopsis.
Abstract: The scope of our knowledge regarding plant genetic mechanisms and gene functions is rapidly evolving and expanding. This is primarily due to the availability of genetic and genomic methods for investigating model species, such as Arabidopsis ( Arabidopsis thaliana ). To fuel future advances, current
31 citations
TL;DR: Emerging proteomics techniques coupled with other systems biology approaches now provide researchers with a plethora of methods for elucidating the final location of these proteins on a large scale, as well as the ability to dissect protein-sorting pathways in plants.
Abstract: The functions of approximately one-third of the proteins encoded by the Arabidopsis thaliana genome are completely unknown. Moreover, many annotations of the remainder of the genome supply tentative functions, at best. Knowing the ultimate localization of these proteins, as well as the pathways used for getting there, may provide clues as to their functions. The putative localization of most proteins currently relies on in silico-based bioinformatics approaches, which, unfortunately, often result in erroneous predictions. Emerging proteomics techniques coupled with other systems biology approaches now provide researchers with a plethora of methods for elucidating the final location of these proteins on a large scale, as well as the ability to dissect protein-sorting pathways in plants.
15 citations
TL;DR: For example, the authors states that science is the highest personification of the nation because that nation will remain the first which carries the furthest the works of thought and intelligence, and that knowledge belongs to humanity and is the torch which illuminates the world.
Abstract: “Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world. Science is the highest personification of the nation because that nation will remain the first which carries the furthest the works of thought and intelligence.”
Louis Pasteur
It is
1 citations
TL;DR: The NIH intends the manuscript repository to provide an alternative means through which NIH grantees can partially fulfill progress reporting requirements and be part of a central resource through which the public may view research funded by U.S. taxpayers.
Abstract: Beginning May 2, 2005, the National Institutes of Health (NIH) requests that authors whose research was supported in whole or in part by NIH deposit their peer-reviewed, accepted manuscripts in PubMed Central, NIH's central repository. The NIH intends the manuscript repository to (1) provide an alternative means through which NIH grantees can partially fulfill progress reporting requirements and (2) be part of a central resource through which the public may view research funded by U.S. taxpayers. The full NIH policy can be viewed at http://grants1.nih.gov/grants/guide/notice-files/NOT-OD-05-022.html.
1 citations