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  • Open Access English
    Authors: 
    Ling, Maurice H. T.; Rabara, Roel C.; Tripathi, Prateek; Rushton, Paul J.; Ge, Xijin;
    Publisher: Hindawi Publishing Corporation
    Project: NIH | Large-scale expression an... (1R01GM083226-01A1)

    Microarrays are a large-scale expression profiling method which has been used to study the transcriptome of plants under various environmental conditions. However, manual inspection of microarray data is difficult at the genome level because of the large number of genes (normally at least 30 000) and the many different processes that occur within any given plant. MapMan software, which was initially developed to visualize microarray data for Arabidopsis, has been adapted to other plant species by mapping other species onto MapMan ontology. This paper provides a detailed procedure and the relevant computing codes to generate a MapMan ontology mapping file for tobacco (Nicotiana tabacum L.) using potato and Arabidopsis as intermediates. The mapping file can be used directly with our custom-made NimbleGen oligoarray, which contains gene sequences from both the tobacco gene space sequence and the tobacco gene index 4 (NTGI4) collection of ESTs. The generated dataset will be informative for scientists working on tobacco as their model plant by providing a MapMan ontology mapping file to tobacco, homology between tobacco coding sequences and that of potato and Arabidopsis, as well as adapting our procedure and codes for other plant species where the complete genome is not yet available.

  • Open Access English
    Authors: 
    Shah, A. M.; Morrill, C.; Gille, E. P.; Gross, W. S.; Anderson, D. M.; Bauer, B. A.; Buckner, R.; Hartman, M.;
    Publisher: Hindawi Publishing Corporation

    This synthesis of thirty-six sites (sixty cores with over 27 000 measurements) located around the world facilitates scientific research on the climate of the last 21 000 years ago obtained from oxygen isotope ( or delta-O-18) measurements. Oxygen isotopes in speleothem calcite record the influence of ambient temperature and the isotopic composition of the source water, the latter providing evidence of hydrologic variability and change. Compared to paleoclimate proxies from sedimentary archives, the age uncertainty is unusually small, around +/−100 years for the last 21 000-year interval. Using data contributed to the World Data Center (WDC) for Paleoclimatology, we have created consistently formatted data files for individual sites as well as composite dataset of annual to millennial resolution. These individual files also contain the chronology information about the sites. The data are useful in understanding hydrologic variability at local and regional scales, such as the Asian summer monsoon and the Intertropical Convergence Zone (as discussed in the underlying source publications), and should also be useful in understanding large-scale aspects of hydrologic change since the Last Glacial Maximum (LGM).

  • Open Access English
    Authors: 
    Cannon, Ethalinda K. S.; Cannon, Steven B.;
    Publisher: Hindawi Publishing Corporation
    Project: NSF | Sequencing the Gene Space... (0321460)

    CViT (chromosome visualization tool) is a Perl utility for quickly generating images of features on a whole genome at once. It reads GFF3-formated data representing chromosomes (linkage groups or pseudomolecules) and sets of features on those chromosomes. It can display features on any chromosomal unit system, including genetic (centimorgan), cytological (centiMcClintock), and DNA unit (base-pair) coordinates. CViT has been used to track sequencing progress (status of genome sequencing, location and number of gaps), to visualize BLAST hits on a whole genome view, to associate maps with one another, to locate regions of repeat densities to display syntenic regions, and to visualize centromeres and knobs on chromosomes.

  • Open Access English
    Authors: 
    Namusoke, Fatuma; Rasti, Niloofar; Kironde, Fred; Wahlgren, Mats; Mirembe, Florence;
    Publisher: SAGE-Hindawi Access to Research
  • Open Access English
    Authors: 
    Ballas, Samir K.; Kesen, Muge R.; Goldberg, Morton F.; Lutty, Gerard A.; Dampier, Carlton; Osunkwo, Ifeyinwa; Wang, Winfred C.; Hoppe, Carolyn; Hagar, Ward; Darbari, Deepika S.; +1 more
    Publisher: Hindawi Publishing Corporation
  • Open Access English
    Authors: 
    Chan, P. K.; Zhao, X.-P.; Heidinger, A. K.;
    Publisher: Hindawi Publishing Corporation

    Aerosol optical thickness (AOT) was retrieved using the Advanced Very High Resolution Radiometer (AVHRR) PATMOS-x Level-2b gridded radiances and the two-channel algorithm of the National Climatic Data Center (NCDC). The primary retrieval product is AOT at 0.63 μm channel. AOT is also retrieved at 0.83 μm or 1.61 μm channel for consistent check. The retrieval was made during day time, under clear sky and snow-free conditions, and over the global oceans. The spatial resolution is 0.1×0.1 degree grid and the temporal resolution is both daily and monthly. The resultant AVHRR AOT climate data record (CDR) spans from August 1981 to December 2009 and provides the longest aerosol CDR currently available from operational satellites. This dataset is useful in studying aerosol climate forcing, monitoring long-term aerosol trends, and evaluating global air pollution and aerosol transport models over the global ocean.

  • Open Access English
    Authors: 
    Zhang, Haojian; Li, Shaoguang;
    Publisher: Hindawi Publishing Corporation
    Project: NIH | Survival Mechanisms of Ca... (1R01CA122142-01A2), NIH | Src Kinases in Ph+ Lympho... (1R01CA114199-01)

    Chronic myeloid leukemia (CML) is a myeloproliferative disease derived from an abnormal hematopoietic stem cell (HSC) and is consistently associated with the formation of Philadelphia (Ph) chromosome. Tyrosine kinase inhibitors (TKIs) are highly effective in treating chronic phase CML but do not eliminate leukemia stem cells (LSCs), which are believed to be related to disease relapse. Therefore, one major challenge in the current CML research is to understand the biology of LSCs and to identify the molecular difference between LSCs and its normal stem cell counterparts. Comparing the gene expression profiles between LSCs and normal HSCs by DNA microarray assay is a systematic and unbiased approach to address this issue. In this paper, we present a DNA microarray dataset for CML LSCs and normal HSCs to show that the microarray assay will benefit the current and future studies of the biology of CML stem cells.

  • Open Access English
    Authors: 
    Myster, Randall W.;
    Publisher: Hindawi Publishing Corporation
    Project: NSF | LTER: Long-Term Ecologica... (0218039), NSF | LTER: The Luquillo Experi... (9411973)

    I report here on an ongoing permanent plot study in areas recovering from agriculture in Ecuador. These plots were set up in 1995 at Maquipucuna Reserve where the forest is tropical lower montane. The study consists of replicate fields in three past crop types (Sugarcane, Banana, and Pasture) for a total of six fields. Each field was first divided into 25 continuous 2 m × 5 m subplots which together form a 10 m × 25 m plot with the longest side bordering the adjacent forest. Then starting in 1996, and continuing annually every year since, each subplot has been sampled for percent cover of all plants and diameter at breast height (dbh) for all trees whose dbh is greater than or equal to 1 cm. I have used that data in these published studies: (1) species composition and life form, richness, and basal area trends, (2) computation of all positive and negative pairwise species associations, (3) relationships between richness and productivity over time, (4) dominance-diversity curves, and (5) definition and quantification of old field plant communities. Finally with the help of the LTER program in Puerto Rico, this sampling continues, with 2012 marking the sixteenth year of continuous annual sampling.

  • Open Access English
    Authors: 
    How, Jian Ann; Lim, Joshua Z. R.; Goh, Desmond J. W.; Ng, Wei Chuan; Oon, Jack S. H.; Lee, Kun Cheng; Lee, Chin How; Ling, Maurice H. T.;
    Publisher: Hindawi Publishing Corporation

    Escherichia coli (E. coli) is a nonhalophilic microbe and used to indicate faecal contamination. Salt (sodium chloride, NaCl) is a common food additive and is used in preservatives to encounter microbial growth. The effect of how E. coli interacts with the salt present in the human diet is unclear. Thus, it is important to investigate this relationship. In order to adapt and survive the changes in the environment, E. coli may undergo halophilization. In this study, we observed the genetic changes and growth kinetics of E. coli ATCC 8739 under 3%–11% NaCl over 80 passages. Our results suggest that E. coli adapted to 1% increase in NaCl every month with a successful adaptation to 11% NaCl. Gram staining and PCR/RFLP showed that the cultures are Gram negative and the DNA profiles of all 4 replicates to be similar, suggesting that the cultures had not been contaminated.

  • Open Access English
    Authors: 
    Champion, Cody J.; Kukutla, Phanidhar; Glennon, Elizabeth K. K.; Wang, Bo; Luckhart, Shirley; Xu, Jiannong;
    Publisher: Hindawi
    Project: NSF | Graduate Research Fellows... (1144468), NIH | Bacterial colonization an... (5SC1AI112786-02), NIH | Systems biology approach ... (5R01AI080799-04), NIH | Mosquito larval immunity ... (5SC2GM092789-03), NIH | Insulin, IGF and Insulin ... (5R01AI073745-04)

    The mosquito midgut is a physiological organ essential for nutrient acquisition as well as an interface that encounters various mosquito-borne pathogens. Metabolomic characterization would reveal biochemical fingerprints that are generated by various cellular processes. The metabolite profiles of the mosquito midgut will provide an overview of the biochemical events in both physiological states and the dynamic responses to pathogen infections. In this study, the midgut metabolic profiles of Anopheles gambiae mosquitoes following feeding with sugar, human blood, mouse blood, and Plasmodium falciparum-infected human blood were examined. A mass spectrometry system coupled to liquid and gas chromatography produced a time series of metabolites in the midgut at discrete conditions (sugar feeding, 24 h and 48 h post-normal blood and P. falciparum-infected blood feeding). Triplicates were included to ensure system validity. A total of 512 individual compounds were identified; 511 were assigned to 8 superpathways and 75 subpathways. The dataset can be used for further inquiry into the metabolic dynamics of sugar and blood digestion and of malaria parasite infection. The dataset is accessible at the repository Dryad.

search
Include:
14 Research products, page 1 of 2
  • Open Access English
    Authors: 
    Ling, Maurice H. T.; Rabara, Roel C.; Tripathi, Prateek; Rushton, Paul J.; Ge, Xijin;
    Publisher: Hindawi Publishing Corporation
    Project: NIH | Large-scale expression an... (1R01GM083226-01A1)

    Microarrays are a large-scale expression profiling method which has been used to study the transcriptome of plants under various environmental conditions. However, manual inspection of microarray data is difficult at the genome level because of the large number of genes (normally at least 30 000) and the many different processes that occur within any given plant. MapMan software, which was initially developed to visualize microarray data for Arabidopsis, has been adapted to other plant species by mapping other species onto MapMan ontology. This paper provides a detailed procedure and the relevant computing codes to generate a MapMan ontology mapping file for tobacco (Nicotiana tabacum L.) using potato and Arabidopsis as intermediates. The mapping file can be used directly with our custom-made NimbleGen oligoarray, which contains gene sequences from both the tobacco gene space sequence and the tobacco gene index 4 (NTGI4) collection of ESTs. The generated dataset will be informative for scientists working on tobacco as their model plant by providing a MapMan ontology mapping file to tobacco, homology between tobacco coding sequences and that of potato and Arabidopsis, as well as adapting our procedure and codes for other plant species where the complete genome is not yet available.

  • Open Access English
    Authors: 
    Shah, A. M.; Morrill, C.; Gille, E. P.; Gross, W. S.; Anderson, D. M.; Bauer, B. A.; Buckner, R.; Hartman, M.;
    Publisher: Hindawi Publishing Corporation

    This synthesis of thirty-six sites (sixty cores with over 27 000 measurements) located around the world facilitates scientific research on the climate of the last 21 000 years ago obtained from oxygen isotope ( or delta-O-18) measurements. Oxygen isotopes in speleothem calcite record the influence of ambient temperature and the isotopic composition of the source water, the latter providing evidence of hydrologic variability and change. Compared to paleoclimate proxies from sedimentary archives, the age uncertainty is unusually small, around +/−100 years for the last 21 000-year interval. Using data contributed to the World Data Center (WDC) for Paleoclimatology, we have created consistently formatted data files for individual sites as well as composite dataset of annual to millennial resolution. These individual files also contain the chronology information about the sites. The data are useful in understanding hydrologic variability at local and regional scales, such as the Asian summer monsoon and the Intertropical Convergence Zone (as discussed in the underlying source publications), and should also be useful in understanding large-scale aspects of hydrologic change since the Last Glacial Maximum (LGM).

  • Open Access English
    Authors: 
    Cannon, Ethalinda K. S.; Cannon, Steven B.;
    Publisher: Hindawi Publishing Corporation
    Project: NSF | Sequencing the Gene Space... (0321460)

    CViT (chromosome visualization tool) is a Perl utility for quickly generating images of features on a whole genome at once. It reads GFF3-formated data representing chromosomes (linkage groups or pseudomolecules) and sets of features on those chromosomes. It can display features on any chromosomal unit system, including genetic (centimorgan), cytological (centiMcClintock), and DNA unit (base-pair) coordinates. CViT has been used to track sequencing progress (status of genome sequencing, location and number of gaps), to visualize BLAST hits on a whole genome view, to associate maps with one another, to locate regions of repeat densities to display syntenic regions, and to visualize centromeres and knobs on chromosomes.

  • Open Access English
    Authors: 
    Namusoke, Fatuma; Rasti, Niloofar; Kironde, Fred; Wahlgren, Mats; Mirembe, Florence;
    Publisher: SAGE-Hindawi Access to Research
  • Open Access English
    Authors: 
    Ballas, Samir K.; Kesen, Muge R.; Goldberg, Morton F.; Lutty, Gerard A.; Dampier, Carlton; Osunkwo, Ifeyinwa; Wang, Winfred C.; Hoppe, Carolyn; Hagar, Ward; Darbari, Deepika S.; +1 more
    Publisher: Hindawi Publishing Corporation
  • Open Access English
    Authors: 
    Chan, P. K.; Zhao, X.-P.; Heidinger, A. K.;
    Publisher: Hindawi Publishing Corporation

    Aerosol optical thickness (AOT) was retrieved using the Advanced Very High Resolution Radiometer (AVHRR) PATMOS-x Level-2b gridded radiances and the two-channel algorithm of the National Climatic Data Center (NCDC). The primary retrieval product is AOT at 0.63 μm channel. AOT is also retrieved at 0.83 μm or 1.61 μm channel for consistent check. The retrieval was made during day time, under clear sky and snow-free conditions, and over the global oceans. The spatial resolution is 0.1×0.1 degree grid and the temporal resolution is both daily and monthly. The resultant AVHRR AOT climate data record (CDR) spans from August 1981 to December 2009 and provides the longest aerosol CDR currently available from operational satellites. This dataset is useful in studying aerosol climate forcing, monitoring long-term aerosol trends, and evaluating global air pollution and aerosol transport models over the global ocean.

  • Open Access English
    Authors: 
    Zhang, Haojian; Li, Shaoguang;
    Publisher: Hindawi Publishing Corporation
    Project: NIH | Survival Mechanisms of Ca... (1R01CA122142-01A2), NIH | Src Kinases in Ph+ Lympho... (1R01CA114199-01)

    Chronic myeloid leukemia (CML) is a myeloproliferative disease derived from an abnormal hematopoietic stem cell (HSC) and is consistently associated with the formation of Philadelphia (Ph) chromosome. Tyrosine kinase inhibitors (TKIs) are highly effective in treating chronic phase CML but do not eliminate leukemia stem cells (LSCs), which are believed to be related to disease relapse. Therefore, one major challenge in the current CML research is to understand the biology of LSCs and to identify the molecular difference between LSCs and its normal stem cell counterparts. Comparing the gene expression profiles between LSCs and normal HSCs by DNA microarray assay is a systematic and unbiased approach to address this issue. In this paper, we present a DNA microarray dataset for CML LSCs and normal HSCs to show that the microarray assay will benefit the current and future studies of the biology of CML stem cells.

  • Open Access English
    Authors: 
    Myster, Randall W.;
    Publisher: Hindawi Publishing Corporation
    Project: NSF | LTER: Long-Term Ecologica... (0218039), NSF | LTER: The Luquillo Experi... (9411973)

    I report here on an ongoing permanent plot study in areas recovering from agriculture in Ecuador. These plots were set up in 1995 at Maquipucuna Reserve where the forest is tropical lower montane. The study consists of replicate fields in three past crop types (Sugarcane, Banana, and Pasture) for a total of six fields. Each field was first divided into 25 continuous 2 m × 5 m subplots which together form a 10 m × 25 m plot with the longest side bordering the adjacent forest. Then starting in 1996, and continuing annually every year since, each subplot has been sampled for percent cover of all plants and diameter at breast height (dbh) for all trees whose dbh is greater than or equal to 1 cm. I have used that data in these published studies: (1) species composition and life form, richness, and basal area trends, (2) computation of all positive and negative pairwise species associations, (3) relationships between richness and productivity over time, (4) dominance-diversity curves, and (5) definition and quantification of old field plant communities. Finally with the help of the LTER program in Puerto Rico, this sampling continues, with 2012 marking the sixteenth year of continuous annual sampling.

  • Open Access English
    Authors: 
    How, Jian Ann; Lim, Joshua Z. R.; Goh, Desmond J. W.; Ng, Wei Chuan; Oon, Jack S. H.; Lee, Kun Cheng; Lee, Chin How; Ling, Maurice H. T.;
    Publisher: Hindawi Publishing Corporation

    Escherichia coli (E. coli) is a nonhalophilic microbe and used to indicate faecal contamination. Salt (sodium chloride, NaCl) is a common food additive and is used in preservatives to encounter microbial growth. The effect of how E. coli interacts with the salt present in the human diet is unclear. Thus, it is important to investigate this relationship. In order to adapt and survive the changes in the environment, E. coli may undergo halophilization. In this study, we observed the genetic changes and growth kinetics of E. coli ATCC 8739 under 3%–11% NaCl over 80 passages. Our results suggest that E. coli adapted to 1% increase in NaCl every month with a successful adaptation to 11% NaCl. Gram staining and PCR/RFLP showed that the cultures are Gram negative and the DNA profiles of all 4 replicates to be similar, suggesting that the cultures had not been contaminated.

  • Open Access English
    Authors: 
    Champion, Cody J.; Kukutla, Phanidhar; Glennon, Elizabeth K. K.; Wang, Bo; Luckhart, Shirley; Xu, Jiannong;
    Publisher: Hindawi
    Project: NSF | Graduate Research Fellows... (1144468), NIH | Bacterial colonization an... (5SC1AI112786-02), NIH | Systems biology approach ... (5R01AI080799-04), NIH | Mosquito larval immunity ... (5SC2GM092789-03), NIH | Insulin, IGF and Insulin ... (5R01AI073745-04)

    The mosquito midgut is a physiological organ essential for nutrient acquisition as well as an interface that encounters various mosquito-borne pathogens. Metabolomic characterization would reveal biochemical fingerprints that are generated by various cellular processes. The metabolite profiles of the mosquito midgut will provide an overview of the biochemical events in both physiological states and the dynamic responses to pathogen infections. In this study, the midgut metabolic profiles of Anopheles gambiae mosquitoes following feeding with sugar, human blood, mouse blood, and Plasmodium falciparum-infected human blood were examined. A mass spectrometry system coupled to liquid and gas chromatography produced a time series of metabolites in the midgut at discrete conditions (sugar feeding, 24 h and 48 h post-normal blood and P. falciparum-infected blood feeding). Triplicates were included to ensure system validity. A total of 512 individual compounds were identified; 511 were assigned to 8 superpathways and 75 subpathways. The dataset can be used for further inquiry into the metabolic dynamics of sugar and blood digestion and of malaria parasite infection. The dataset is accessible at the repository Dryad.

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