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  • 1
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    The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-07-26
    Description: A key event in the domestication and breeding of the oil palm Elaeis guineensis was loss of the thick coconut-like shell surrounding the kernel. Modern E. guineensis has three fruit forms, dura (thick-shelled), pisifera (shell-less) and tenera (thin-shelled), a hybrid between dura and pisifera. The pisifera palm is usually female-sterile. The tenera palm yields far more oil than dura, and is the basis for commercial palm oil production in all of southeast Asia. Here we describe the mapping and identification of the SHELL gene responsible for the different fruit forms. Using homozygosity mapping by sequencing, we found two independent mutations in the DNA-binding domain of a homologue of the MADS-box gene SEEDSTICK (STK, also known as AGAMOUS-LIKE 11), which controls ovule identity and seed development in Arabidopsis. The SHELL gene is responsible for the tenera phenotype in both cultivated and wild palms from sub-Saharan Africa, and our findings provide a genetic explanation for the single gene hybrid vigour (or heterosis) attributed to SHELL, via heterodimerization. This gene mutation explains the single most important economic trait in oil palm, and has implications for the competing interests of global edible oil production, biofuels and rainforest conservation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4209285/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4209285/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Singh, Rajinder -- Low, Eng-Ti Leslie -- Ooi, Leslie Cheng-Li -- Ong-Abdullah, Meilina -- Ting, Ngoot-Chin -- Nagappan, Jayanthi -- Nookiah, Rajanaidu -- Amiruddin, Mohd Din -- Rosli, Rozana -- Manaf, Mohamad Arif Abdul -- Chan, Kuang-Lim -- Halim, Mohd Amin -- Azizi, Norazah -- Lakey, Nathan -- Smith, Steven W -- Budiman, Muhammad A -- Hogan, Michael -- Bacher, Blaire -- Van Brunt, Andrew -- Wang, Chunyan -- Ordway, Jared M -- Sambanthamurthi, Ravigadevi -- Martienssen, Robert A -- R01 GM067014/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2013 Aug 15;500(7462):340-4. doi: 10.1038/nature12356. Epub 2013 Jul 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia. raviga@mpob.gov.my〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23883930" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis Proteins/genetics ; Arecaceae/*genetics/*metabolism ; Chromosome Mapping ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Genes, Plant/*genetics ; Genetic Variation ; Homozygote ; MADS Domain Proteins/genetics ; Molecular Sequence Data ; Mutation ; *Plant Oils ; Sequence Alignment
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-07-26
    Description: Oil palm is the most productive oil-bearing crop. Although it is planted on only 5% of the total world vegetable oil acreage, palm oil accounts for 33% of vegetable oil and 45% of edible oil worldwide, but increased cultivation competes with dwindling rainforest reserves. We report the 1.8-gigabase (Gb) genome sequence of the African oil palm Elaeis guineensis, the predominant source of worldwide oil production. A total of 1.535 Gb of assembled sequence and transcriptome data from 30 tissue types were used to predict at least 34,802 genes, including oil biosynthesis genes and homologues of WRINKLED1 (WRI1), and other transcriptional regulators, which are highly expressed in the kernel. We also report the draft sequence of the South American oil palm Elaeis oleifera, which has the same number of chromosomes (2n = 32) and produces fertile interspecific hybrids with E. guineensis but seems to have diverged in the New World. Segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. The oil palm sequence enables the discovery of genes for important traits as well as somaclonal epigenetic alterations that restrict the use of clones in commercial plantings, and should therefore help to achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929164/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929164/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Singh, Rajinder -- Ong-Abdullah, Meilina -- Low, Eng-Ti Leslie -- Manaf, Mohamad Arif Abdul -- Rosli, Rozana -- Nookiah, Rajanaidu -- Ooi, Leslie Cheng-Li -- Ooi, Siew-Eng -- Chan, Kuang-Lim -- Halim, Mohd Amin -- Azizi, Norazah -- Nagappan, Jayanthi -- Bacher, Blaire -- Lakey, Nathan -- Smith, Steven W -- He, Dong -- Hogan, Michael -- Budiman, Muhammad A -- Lee, Ernest K -- DeSalle, Rob -- Kudrna, David -- Goicoechea, Jose Luis -- Wing, Rod A -- Wilson, Richard K -- Fulton, Robert S -- Ordway, Jared M -- Martienssen, Robert A -- Sambanthamurthi, Ravigadevi -- Howard Hughes Medical Institute/ -- England -- Nature. 2013 Aug 15;500(7462):335-9. doi: 10.1038/nature12309. Epub 2013 Jul 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia. raviga@mpob.gov.my〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23883927" target="_blank"〉PubMed〈/a〉
    Keywords: Arecaceae/*classification/*genetics ; Carbohydrate Metabolism/genetics ; Chromosomes, Plant/genetics ; Genome, Plant/*genetics ; Lipid Metabolism/genetics ; Models, Genetic ; Molecular Sequence Data ; *Phylogeny
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    198AuNP-EGCg for prostate cancer therapy [Applied Biological Sciences] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-08-01
    Description: Systemic delivery of therapeutic agents to solid tumors is hindered by vascular and interstitial barriers. We hypothesized that prostate tumor specific epigallocatechin-gallate (EGCg) functionalized radioactive gold nanoparticles, when delivered intratumorally (IT), would circumvent transport barriers, resulting in targeted delivery of therapeutic payloads. The results described herein support our hypothesis. We report the development of inherently therapeutic gold nanoparticles derived from the Au-198 isotope; the range of the 198Au β-particle (approximately 11 mm in tissue or approximately 1100 cell diameters) is sufficiently long to provide cross-fire effects of a radiation dose delivered to cells within the prostate gland and short enough to minimize the radiation dose to critical tissues near the periphery of the capsule. The formulation of biocompatible 198AuNPs utilizes the redox chemistry of prostate tumor specific phytochemical EGCg as it converts gold salt into gold nanoparticles and also selectively binds with excellent affinity to Laminin67R receptors, which are over expressed in prostate tumor cells. Pharmacokinetic studies in PC-3 xenograft SCID mice showed approximately 72% retention of 198AuNP-EGCg in tumors 24 h after intratumoral administration. Therapeutic studies showed 80% reduction of tumor volumes after 28 d demonstrating significant inhibition of tumor growth compared to controls. This innovative nanotechnological approach serves as a basis for designing biocompatible target specific antineoplastic agents. This novel intratumorally injectable 198AuNP-EGCg nanotherapeutic agent may provide significant advances in oncology for use as an effective treatment for prostate and other solid tumors.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    A review of recent developments in climate change science. Part I: Understanding of future change in the large-scale climate system (2011)
    Sage
    Details
    Publication Date: 2011-06-09
    Description: This article reviews some of the major lines of recent scientific progress relevant to the choice of global climate policy targets, focusing on changes in understanding since publication of the Intergovernmental Panel on Climate Change Fourth Assessment Report (IPCC AR4). Developments are highlighted in the following major climate system components: ice sheets; sea ice; the Atlantic Meridional Overturning Circulation; tropical forests; and accelerated carbon release from permafrost and ocean hydrates. The most significant developments in each component are identified by synthesizing input from multiple experts from each field. Overall, while large uncertainties remain in all fields, some substantial progress in understanding is revealed.
    Print ISSN: 0309-1333
    Electronic ISSN: 1477-0296
    Topics: Geography
    Published by Sage
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  • 5
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    Concatenation and Concordance in the Reconstruction of Mouse Lemur Phylogeny: An Empirical Demonstration of the Effect of Allele Sampling in Phylogenetics (2012)
    Oxford University Press
    Details
    Publication Date: 2012-05-16
    Description: The systematics and speciation literature is rich with discussion relating to the potential for gene tree/species tree discordance. Numerous mechanisms have been proposed to generate discordance, including differential selection, long-branch attraction, gene duplication, genetic introgression, and/or incomplete lineage sorting. For speciose clades in which divergence has occurred recently and rapidly, recovering the true species tree can be particularly problematic due to incomplete lineage sorting. Unfortunately, the availability of multilocus or "phylogenomic" data sets does not simply solve the problem, particularly when the data are analyzed with standard concatenation techniques. In our study, we conduct a phylogenetic study for a nearly complete species sample of the dwarf and mouse lemur clade, Cheirogaleidae. Mouse lemurs (genus, Microcebus ) have been intensively studied over the past decade for reasons relating to their high level of cryptic species diversity, and although there has been emerging consensus regarding the evolutionary diversity contained within the genus, there is no agreement as to the inter-specific relationships within the group. We attempt to resolve cheirogaleid phylogeny, focusing especially on the mouse lemurs, by employing a large multilocus data set. We compare the results of Bayesian concordance methods with those of standard gene concatenation, finding that though concatenation yields the strongest results as measured by statistical support, these results are found to be highly misleading. By employing an approach where individual alleles are treated as operational taxonomic units, we show that phylogenetic results are substantially influenced by the selection of alleles in the concatenation process.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Does the worsening galactic cosmic radiation environment observed by CRaTER preclude future manned deep-space exploration? (2014)
    Wiley
    Details
    Publication Date: 2014-10-05
    Description: The Sun and its solar wind are currently exhibiting extremely low densities and magnetic field strengths, representing states that have never been observed during the space age. The highly abnormal solar activity between cycles 23 and 24 has caused the longest solar minimum in over 80 years and continues into the unusually small solar maximum of cycle 24. As a result of the remarkably weak solar activity, we have also observed the highest fluxes of galactic cosmic rays in the space age, and relatively small solar energetic particle events. We use observations from the Cosmic Ray Telescope for the Effects of Radiation (CRaTER) on the Lunar Reconnaissance Orbiter (LRO) to examine the implications of these highly unusual solar conditions for human space exploration. We show that while these conditions are not a show-stopper for long duration missions (e.g., to the Moon, an asteroid, or Mars), galactic cosmic ray radiation remains a significant and worsening factor that limits mission durations. While solar energetic particle events in cycle 24 present some hazard, the accumulated doses for astronauts behind 10 g/cm 2 shielding are well below current dose limits. Galactic cosmic radiation presents a more significant challenge: the time to 3% Risk of Exposure Induced Death (REID) in interplanetary space was less than 400 days for a 30 year old male and less than 300 days for a 30 year old female in the last cycle 23–24 minimum. The time to 3% REID is estimated to be ~20% lower in the coming cycle 24–25 minimum. If the heliospheric magnetic field continues to weaken over time, as is likely, then allowable mission durations will decrease correspondingly. Thus, we estimate exposures in extreme solar minimum conditions and the corresponding effects on allowable durations.
    Print ISSN: 1539-4964
    Electronic ISSN: 1542-7390
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 7
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    Direct measurements of the seasonality of emission factors from savanna fires in northern Australia (2012)
    Wiley
    Details
    Publication Date: 2012-10-26
    Description: Current good practice guidelines for national greenhouse gas inventories requires that seasonal variation in emission factors from savanna fires be considered when compiling national accounts. African studies concluded that the emission factor for methane decreases during the dry season principally due to curing of the fuels. However, available data from Australian tropical savannas shows no effect of seasonality on emission factors, consistent with observations that the fine fuels appear to cure fully soon after the start of the fire season. To test whether the seasonality in greenhouse gas emission factors reported for Africa also occurs in Australia, methane and nitrous oxide emission factors were measured in early and in late dry season fires in Western Arnhem Land, a region typical of much of the northern Australia savanna zone. We found no significant seasonality in methane emission factors, but there was substantial variation in emission factors associated with inter-fire differences in vegetation and fuel. This variation could be explained almost completely by combustion efficiency. Nitrous oxide emission factors were not related to combustion efficiency but showed some variation across vegetation and fuel size class. Both methane and nitrous oxide emission factors were consistent with previous work in northern Australia and with some published values from Africa. The absence of a significant seasonal trend in emission factors indicates that savanna fire emissions in northern Australia can be managed by strategic prescribed burning.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 8
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    2'-Deoxyriboguanylurea, the primary breakdown product of 5-aza-2'-deoxyribocytidine, is a mutagen, an epimutagen, an inhibitor of DNA methyltransferases and an inducer of 5-azacytidine-type fragile sites (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-24
    Description: 5-Aza-2'-deoxycytidine (5azaC-dR) has been employed as an inhibitor of DNA methylation, a chemotherapeutic agent, a clastogen, a mutagen, an inducer of fragile sites and a carcinogen. However, its effects are difficult to quantify because it rapidly breaks down in aqueous solution to the stable compound 2'-deoxyriboguanylurea (GuaUre-dR). Here, we used a phosphoramidite that permits the introduction of GuaUre-dR at defined positions in synthetic oligodeoxynucleotides to demonstrate that it is a potent inhibitor of human DNA methyltransferase 1 (hDNMT1) and the bacterial DNA methyltransferase (M. Eco RII) and that it is a mutagen that can form productive base pairs with either Guanine or Cytosine. Pure GuaUre-dR was found to be an effective demethylating agent and was able to induce 5azaC-dR type fragile sites FRA1J and FRA9E in human cells. Moreover, we report that demethylation associated with C:G -〉 G:C transversion and C:G -〉 T:A transition mutations was observed in human cells exposed to pure GuaUre-dR. The data suggest that most of the effects attributed to 5azaC-dR are exhibited by its stable primary breakdown product.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Modeling and Characterization of Damage Processes in Metallic Materials (2011)
    In:  CASI
    Details
    Publication Date: 2019-07-13
    Description: This paper describes a broad effort that is aimed at understanding the fundamental mechanisms of crack growth and using that understanding as a basis for designing materials and enabling predictions of fracture in materials and structures that have small characteristic dimensions. This area of research, herein referred to as Damage Science, emphasizes the length scale regimes of the nanoscale and the microscale for which analysis and characterization tools are being developed to predict the formation, propagation, and interaction of fundamental damage mechanisms. Examination of nanoscale processes requires atomistic and discrete dislocation plasticity simulations, while microscale processes can be examined using strain gradient plasticity, crystal plasticity and microstructure modeling methods. Concurrent and sequential multiscale modeling methods are being developed to analytically bridge between these length scales. Experimental methods for characterization and quantification of near-crack tip damage are also being developed. This paper focuses on several new methodologies in these areas and their application to understanding damage processes in polycrystalline metals. On-going and potential applications are also discussed.
    Keywords: Metals and Metallic Materials
    Type: NF1676L-11179 , 52nd AIAA/ASME/ASCE/AHS/ASC Structures, Structural Dynamics, and Materials Conference; Apr 04, 2011 - Apr 07, 2011; Denver, CO; United States
    Format: application/pdf
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