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41.
Background
Unravelling the path from genotype to phenotype, as it is influenced by an organism's environment, is one of the central goals in biology. Gene expression profiling by means of microarrays has become very prominent in this endeavour, although resources exist only for relatively few model systems. As genomics has matured into a comparative research program, expression profiling now also provides a powerful tool for non-traditional model systems to elucidate the molecular basis of complex traits. 相似文献42.
S. G. Taylor D. G. Shilling K. H. Quesenberry 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1989,78(2):265-270
Summary In vitro, selection is a viable method of selecting herbicide-tolerant crops. This research was to evaluate in vitro selection techniques for enhancing 2,4-D [(2,4-dichlorophenoxy) acetic acid] tolerance in red clover (Trifolium pratense L.). In vivo and in vitro responses to 2,4-D of eight diverse red clover populations were correlated (r=0.77), justifying in vitro selection for 2,4-D tolerance. Suspension cultures of a red clover genotype capable of regeneration were plated onto agar-based nutrient media supplemented with 0.18 mM 2,4-D for selection experiments. After two cycles of selection, 16 2,4-D tolerant callus lines were identified based on visual growth assessment. These lines were evaluated for 2,4-D tolerance (based on 2,4-D content), using a 2,4-D bioassay procedure which consisted of placing selected callus tissue pieces on top of oat (Avena sativa L.) coleoptile or internode sections. The relative amount of 2,4-D in the callus tissue was estimated by the amount of oat section elongation after 24 h. Two of the more tolerant callus lines had 61% and 83% less 2,4-D in their tissues than the susceptible control tissue. These studies indicated that in vitro selection can enhance the levels of 2,4-D tolerance in red clover callus tissue.Florida Agricultural Experiment Station Journal Series No. 8943 相似文献
43.
44.
Marcilio CP de Souto Ivan G Costa Daniel SA de Araujo Teresa B Ludermir Alexander Schliep 《BMC bioinformatics》2008,9(1):497
Background
The use of clustering methods for the discovery of cancer subtypes has drawn a great deal of attention in the scientific community. While bioinformaticians have proposed new clustering methods that take advantage of characteristics of the gene expression data, the medical community has a preference for using "classic" clustering methods. There have been no studies thus far performing a large-scale evaluation of different clustering methods in this context. 相似文献45.
46.
Colvin GA Lambert JF Dooner MS Cerny J Quesenberry PJ 《Journal of cellular physiology》2007,211(2):386-391
Stem cell homing has been studied in syngeneic models and appears to be rapid (<1 h) and dependent on cellular adhesion and migration factors. We utilized a full H2-mismatched transplantation model to determine the basics of allogeneic homing. C57BL/6J Lin-Sca-1+ cells were labeled with CFSE and injected in non-myeloablated BALB/c mice. Fluorescent cell detection was via high-speed FACS analysis. Alternatively, B6.SJL whole bone marrow cells were injected in lethally irradiated BALB/c mice (10 Gy). One, 3, 6, and 24 h after transplant, marrow was harvested and cells were either plated for high proliferative potential colony-forming cell (HPP-CFC) assay or secondarily injected into myeloablated (8 Gy) C57BL/6J mice using 10% competing C57BL/6J marrow. Chimerism was evaluated at 8 weeks. CFSE+ cells were detected in the bone marrow 1, 3, and 6 h after injection. The numbers were moderately lower when compared to syngeneic homing possibly due to strain effect. Conversely, utilizing a surrogate or secondary assay, we observed a decline of secondary engraftment of harvested cells over time, but not of HPP-CFC. Combining experiments and normalizing the 1-h time point to 100% (to allow comparison), we observed a mean relative engraftment of 87 +/- 29%, 72 +/- 21%, 84 +/- 35% of the 1 h level at 3, 6, and 24 h respectively. HPP-CFC assay showed no significant variation as a homing surrogate over 1-6 h. These data indicate a rapid homing into allogeneic recipients with a plateau at 1 h. The decline of secondary engraftability over time may indicate a phenotype alteration of homed cells. 相似文献
47.
Letícia Muraro Wildner Maria Luiza Bazzo Susie Coutinho Liedke Christiane Louren?o Nogueira Gabriela Segat Simone Gon?alves Senna Aline Daiane Schlindwein Jaquelline Germano de Oliveira Darcita B Rovaris Claudio A Bonjardim Erna G Kroon Paulo CP Ferreira 《Memórias do Instituto Oswaldo Cruz》2014,109(3):356-361
The identification of mycobacteria is essential because tuberculosis (TB) and
mycobacteriosis are clinically indistinguishable and require different therapeutic
regimens. The traditional phenotypic method is time consuming and may last up to 60
days. Indeed, rapid, affordable, specific and easy-to-perform identification methods
are needed. We have previously described a polymerase chain reaction-based method
called a mycobacteria mobility shift assay (MMSA) that was designed for
Mycobacterium tuberculosis complex (MTC) and nontuberculous mycobacteria
(NTM) species identification. The aim of this study was to assess the MMSA for the
identification of MTC and NTM clinical isolates and to compare its performance with
that of the PRA-hsp65 method. A total of 204 clinical isolates (102
NTM and 102 MTC) were identified by the MMSA and PRA-hsp65. For
isolates for which these methods gave discordant results, definitive species
identification was obtained by sequencing fragments of the 16S rRNA and
hsp65 genes. Both methods correctly identified all MTC isolates. Among
the NTM isolates, the MMSA alone assigned 94 (92.2%) to a complex or species, whereas
the PRA-hsp65 method assigned 100% to a species. A 91.5% agreement
was observed for the 94 NTM isolates identified by both methods. The MMSA provided
correct identification for 96.8% of the NTM isolates compared with 94.7% for
PRA-hsp65. The MMSA is a suitable auxiliary method for routine
use for the rapid identification of mycobacteria. 相似文献
48.
Liu L Papa EF Dooner MS Machan JT Johnson KW Goldberg LR Quesenberry PJ Colvin GA 《PloS one》2012,7(2):e31300
Long-term hematopoietic stem cells (LT-HSC) and short-term hematopoietic stem cells (ST-HSC) have been characterized as having markedly different in vivo repopulation, but similar in vitro growth in liquid culture. These differences could be due to differences in marrow homing. We evaluated this by comparing results when purified ST-HSC and LT-HSC were administered to irradiated mice by three different routes: intravenous, intraperitoneal, and directly into the femur. Purified stem cells derived from B6.SJL mice were competed with marrow cells from C57BL/6J mice into lethally irradiated C57BL/6J mice. Serial transplants into secondary recipients were also carried out. We found no advantage for ST-HSC engraftment when the cells were administered intraperitoneally or directly into femur. However, to our surprise, we found that the purified ST-HSC were not short-term in nature but rather gave long-term multilineage engraftment out to 387 days, albeit at a lower level than the LT-HSC. The ST-HSC also gave secondary engraftment. These observations challenge current models of the stem cell hierarchy and suggest that stem cells are in a continuum of change. 相似文献
49.
Waters KM Liu T Quesenberry RD Willse AR Bandyopadhyay S Kathmann LE Weber TJ Smith RD Wiley HS Thrall BD 《PloS one》2012,7(3):e34515
To understand how integration of multiple data types can help decipher cellular responses at the systems level, we analyzed the mitogenic response of human mammary epithelial cells to epidermal growth factor (EGF) using whole genome microarrays, mass spectrometry-based proteomics and large-scale western blots with over 1000 antibodies. A time course analysis revealed significant differences in the expression of 3172 genes and 596 proteins, including protein phosphorylation changes measured by western blot. Integration of these disparate data types showed that each contributed qualitatively different components to the observed cell response to EGF and that varying degrees of concordance in gene expression and protein abundance measurements could be linked to specific biological processes. Networks inferred from individual data types were relatively limited, whereas networks derived from the integrated data recapitulated the known major cellular responses to EGF and exhibited more highly connected signaling nodes than networks derived from any individual dataset. While cell cycle regulatory pathways were altered as anticipated, we found the most robust response to mitogenic concentrations of EGF was induction of matrix metalloprotease cascades, highlighting the importance of the EGFR system as a regulator of the extracellular environment. These results demonstrate the value of integrating multiple levels of biological information to more accurately reconstruct networks of cellular response. 相似文献
50.
M Li JM Aliotta JM Asara L Tucker P Quesenberry M Lally B Ramratnam 《Proteomics》2012,12(13):2203-2211
HIV-1 infection causes profound effects both inside and outside of cells through multiple mechanisms, including those mediated by exosomes. Using the technique of stable isotope labeling by amino acids in cell culture, we compared protein expression patterns in the exosomal compartment of HIV-1-infected and -uninfected lymphocytic H9 cells. Of 770 proteins identified in two independent sets of exosomal samples, 14 proteins were found to be differentially expressed in the exosomal fraction of HIV-1-infected cells versus -uninfected controls. Gene Ontology survey and DAVID analysis revealed that identified proteins were enriched for functional categories such as binding. Of these 14 proteins, three immunomodulatory molecules were reproducibly identified in both replicates and included ADP-ribosyl cyclase 1 (CD38), L-lactate dehydrogenase B chain (LDHB), and Annexin A5 (ANXA5). In addition to previously reported HIV-1 associations with CD38 and LDHB, new interactions were identified and validated for ANXA5, CD38, and LDHB, which were found to bind to HIV-1 p24 and Tat. In summary, our studies reveal that exosomes released from HIV-1-infected cells are composed of a unique and quantitatively different protein signature and harbor regulatory molecules that impact the processes of cellular apoptosis (ANXA5 and LDHB) and proliferation (CD38). 相似文献