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1.  Effects of gender on gene expression in the blood of ischemic stroke patients 
This study examined the effects of gender on RNA expression after ischemic stroke (IS). RNA obtained from blood of IS patients (n=51; 153 samples at ⩽3, 5, and 24 hours) and from matched controls (n=52) were processed on Affymetrix microarrays. Analyses of covariance for stroke versus control samples were performed separately for both genders and the regulated genes for females compared with males. In all, 242, 227, and 338 male-specific genes were regulated at ⩽3, 5, and 24 hours after IS, respectively, of which 59 were regulated at all time points. Overall, 774, 3,437, and 571 female-specific stroke genes were regulated at ⩽3, 5, and 24 hours, respectively, of which 152 were regulated at all time points. Male-specific stroke genes were associated with integrin, integrin-liked kinase, actin, tight junction, Wnt/β-catenin, RhoA, fibroblast growth factors (FGF), granzyme, and tumor necrosis factor receptor (TNFR)2 signaling. Female-specific stroke genes were associated with p53, high-mobility group box-1, hypoxia inducible factor (HIF)1α, interleukin (IL)1, IL6, IL12, IL18, acute-phase response, T-helper, macrophage, and estrogen signaling. Cell death signaling was overrepresented in both genders, although the molecules and pathways differed. Gender affects gene expression in the blood of IS patients, which likely implies gender differences in immune, inflammatory, and cell death responses to stroke.
PMCID: PMC3345909  PMID: 22167233
blood; gender; gene expression; ischemic stroke; microarrays
2.  Y Chromosome gene expression in the blood of male ischemic stroke patients compared to male controls 
Gender medicine  2012;9(2):68-75.e3.
Background and Purpose
Gender is suggested to be an important determinant of ischemic stroke risk factors, etiology and outcome. However, the basis for this remains unclear. The Y chromosome is unique in males. Genes expressed in men on the Y chromosome that are associated with stroke may be important genetic contributors to the unique features of males with ischemic stroke, which would be helpful for explaining sex differences observed between men and women.
Blood samples were obtained from 40 males at ≤ 3, 5 and 24 hours following ischemic stroke and from 41 male controls (July 2003- April 2007). RNA was isolated from blood and processed on Affymetrix Human U133 Plus 2.0 Arrays. Y chromosome genes differentially expressed between male stroke and male control subjects were identified using an analysis of covariance (ANCOVA) adjusted for age and batch. A p<0.05 and fold change (FC) > ∣1.2∣ were considered significant.
Seven genes on the Y chromosome were differentially expressed in males with ischemic strokes compared to controls. Five of these genes (VAMP7, CSF2RA, SPRY3, DHRSX, PLCXD1,) are located on pseudoautosomal regions (PARs) of the human Y chromosome. The other two genes (EIF1AY and DDX3Y) are located on the non-recombining region of the human Y chromosome (NRY). The identified genes were associated with immunology, RNA metabolism, vesicle fusion and angiogenesis.
Specific genes on the Y chromosome are differentially expressed in blood following ischemic stroke. These genes provide insight into potential molecular contributors to sex differences in ischemic stroke.
PMCID: PMC3454519  PMID: 22365286
gene expression; ischemic stroke; gender; blood; Y chromosome
3.  Accessing long-lived nuclear singlet states between chemically equivalent spins without breaking symmetry 
Nature physics  2012;8(11):831-837.
Long-lived nuclear spin states could greatly enhance the applicability of hyperpolarized nuclear magnetic resonance. Using singlet states between inequivalent spin pairs has been shown to extend the signal lifetime by more than an order of magnitude compared to the spin lattice relaxation time (T1), but they have to be prevented from evolving into other states. In the most interesting case the singlet is between chemically equivalent spins, as it can then be inherently an eigenstate. However this presents major challenges in the conversion from bulk magnetization to singlet. In the only case demonstrated so far, a reversible chemical reaction to break symmetry was required. Here we present a pulse sequence technique that interconverts between singlet spin order and bulk magnetization without breaking the symmetry of the spin system. This technique is independent of field strength and is applicable to a broad range of molecules.
PMCID: PMC3596050  PMID: 23505397
4.  Reciprocal Metabolic Perturbations in the Adipose Tissue and Liver of GPIHBP1-deficient Mice 
Gpihbp1-deficient mice (Gpihbp1−/−) lack the ability to transport lipoprotein lipase to the capillary lumen, resulting in mislocalization of LPL within tissues, defective lipolysis of triglyceride-rich lipoproteins, and chylomicronemia. We asked whether GPIHBP1 deficiency and mislocalization of catalytically active LPL would alter the composition of triglycerides in adipose tissue or perturb the expression of lipid biosynthetic genes. We also asked whether perturbations in adipose tissue composition and gene expression, if they occur, would be accompanied by reciprocal metabolic changes in the liver.
Methods and Results
The chylomicronemia in Gpihbp1−/− mice was associated with reduced levels of essential fatty acids in adipose tissue triglycerides and increased expression of lipid biosynthetic genes. The liver exhibited the opposite changes—increased levels of essential fatty acids in triglycerides and reduced expression of lipid biosynthetic genes.
Defective lipolysis in Gpihbp1−/− mice causes reciprocal metabolic perturbations in adipose tissue and liver. In adipose tissue, the essential fatty acid content of triglycerides is reduced and lipid biosynthetic gene expression is increased, while the opposite changes occur in the liver.
PMCID: PMC3281771  PMID: 22173228
lipoprotein lipase; hypertriglyceridemia; lipolysis; essential fatty acids; lipid biosynthetic genes
5.  The relationship between tissue oxygenation and redox status using magnetic resonance imaging 
International Journal of Oncology  2012;41(6):2103-2108.
The recent development of a bi-modality magnetic resonance imaging/electron paramagnetic resonance imaging (MRI/EPRI) platform has enabled longitudinal monitoring of both tumor oxygenation and redox status in murine cancer models. The current study used this imaging platform to test the hypothesis that a more reducing tumor microenvironment accompanies the development of tumor hypoxia. To test this, the redox status of the tumor was measured using Tempol as a redox-sensitive MRI contrast agent, and tumor hypoxia was measured with Oxo63, which is an oxygen-sensitive EPRI spin probe. Images were acquired every 1–2 days in mice bearing SCCVII tumors. The median pO2 decreased from 14 mmHg at 7 days after tumor implantation to 7 mmHg at 15 days after implantation. Additionally, the hypoxic fraction, defined as the percentage of the tumor that exhibited a pO2<10 mmHg, increased with tumor size (from 10% at 500 mm3 to 60% at 3,500 mm3). The rate of Tempol reduction increased as a function of tumor volume (0.4 min−1 at 500 mm3 to 1.7 min−1 at 3,500 mm3), suggesting that the tumor microenvironment became more reduced as the tumor grew. The results show that rapid Tempol reduction correlates with decreased tumor oxygenation, and that the Tempol decay rate constant may be a surrogate marker for tumor hypoxia.
PMCID: PMC3583655  PMID: 23007796
redox status; hypoxia; electron paramagnetic resonance imaging; magnetic resonance imaging; nitroxide; non-invasive imaging; Tempol
6.  A Novel Nitroxide is an Effective Brain Redox Imaging Contrast Agent and in vivo Radioprotector 
Free radical biology & medicine  2011;51(3):780-790.
Individuals are exposed to ionizing radiation during medical procedures and nuclear disasters, and this exposure can be carcinogenic, toxic, and sometimes fatal. Drugs that protect individuals from the adverse effects of radiation may therefore be valuable countermeasures against the health risks of exposure. In the current study, the LD50/30 (the dose resulting in 50% of exposed mice surviving 30 days after exposure) was determined in control C3H mice and mice treated with the nitroxide radioprotectors Tempol, 3-CP, 16c, 22c, and 23c. The pharmacokinetics of 22c and 23c were measured with magnetic resonance imaging (MRI) in the brain, blood, submandibular salivary gland, liver, muscle, tongue, and myocardium. It was found 23c was the most effective radioprotector of the five studied: 23c increased the LD50/30 in mice from 7.9 ± 0.15 Gy (treated with saline) to 11.47 ± 0.13 Gy (an increase of 45%). Additionally, MRI-based pharmacokinetic studies revealed that 23c is an effective redox imaging agent in the mouse brain, and that 23c may allow functional imaging of the myocardium. The data in this report suggest that 23c is currently the most potent known nitroxide radioprotector, and that it may also be useful as a contrast agent for functional imaging.
PMCID: PMC3131550  PMID: 21664459
Radioprotection; Redox Imaging; Blood-Brain-Barrier Permeable Contrast Agents; Nitroxides; Magnetic Resonance Imaging
7.  Syntheses and Cytotoxic Properties of the Curcumin Analogs 2,6-Bis(benzylidene)-4-phenylcyclohexanones 
Archiv Der Pharmazie  2008;341(7):440-445.
Fifteen curcumin analogs were synthesized and tested for in-vitro cytotoxicity towards B16 and L1210 murine cancer cell lines using an MTT assay. Significant activity was discovered for two analogs: 8 (B16 IC50 = 1.6 μM; L1210 IC50 = 0.35 μM) and 9 (B16 IC50 = 0.51 μM; L1210 IC50 = 1.2 μM). Several other analogs exhibited notable cytotoxicity. The data from quantitative structure-activity relationships suggest that large electron-withdrawing substituents placed in the meta-position of the arylidene aryl rings enhance potencies. Compounds 8 and 9 were found using a cell-based assay to have virtually no effects on microtubules at concentrations up to 40 μM. These results suggest that tubulin inhibition is not the principal mechanism by which the curcumin analogs act.
PMCID: PMC3341358  PMID: 18574852 CAMSID: cams2194
B16; Curcumin analogs; L1210; Microtubules; Structure-activity relationships
8.  Leukocytes Are Recruited through the Bronchial Circulation to the Lung in a Spontaneously Hypertensive Rat Model of COPD 
PLoS ONE  2012;7(3):e33304.
Chronic obstructive pulmonary disease (COPD) kills approximately 2.8 million people each year, and more than 80% of COPD cases can be attributed to smoking. Leukocytes recruited to the lung contribute to COPD pathology by releasing reactive oxygen metabolites and proteolytic enzymes. In this work, we investigated where leukocytes enter the lung in the early stages of COPD in order to better understand their effect as a contributor to the development of COPD. We simultaneously evaluated the parenchyma and airways for neutrophil accumulation, as well as increases in the adhesion molecules and chemokines that cause leukocyte recruitment in the early stages of tobacco smoke induced lung disease. We found neutrophil accumulation and increased expression of adhesion molecules and chemokines in the bronchial blood vessels that correlated with the accumulation of leukocytes recovered from the lung. The expression of adhesion molecules and chemokines in other vascular beds did not correlate with leukocytes recovered in bronchoalveolar lavage fluid (BALF). These data strongly suggest leukocytes are recruited in large measure through the bronchial circulation in response to tobacco smoke. Our findings have important implications for understanding the etiology of COPD and suggest that pharmaceuticals designed to reduce leukocyte recruitment through the bronchial circulation may be a potential therapy to treat COPD.
PMCID: PMC3310053  PMID: 22457750
9.  Magnetic resonance imaging of organic contrast agents in mice: capturing the whole-body redox landscape 
Free radical biology & medicine  2010;50(3):459-468.
Nitroxides are a class of stable free radicals that have several biomedical applications including radioprotection and non-invasive assessment of tissue redox status. For both of these applications, it is necessary to understand the in vivo biodistribution and reduction of nitroxides. In this study, magnetic resonance imaging was used to compare tissue accumulation (concentration) and reduction of two commonly studied nitroxides: the piperidine nitroxide Tempol and the pyrrolidine nitroxide 3-CP. It was found that 3-CP is reduced three to eleven times slower (depending on the tissue) than Tempol in vivo, and that maximum tissue concentration varies substantially between tissues (0.6 mM – 7.2 mM.) For a given tissue, the maximum concentration usually did not vary between the two nitroxides. Furthermore, using electron paramagnetic resonance (EPR) spectroscopy, it was shown that the nitroxide reduction rate depends only weakly on cellular pO2 in the oxygen range expected in vivo. These observations, taken with the marked variation in nitroxide reduction rates observed between tissues, suggest that tissue pO2 is not a major determinant of the nitroxide reduction rate in vivo. For the purpose of redox imaging, 3-CP was shown to be an optimal choice based on the achievable concentrations and bioreduction observed in vivo.
PMCID: PMC3031128  PMID: 21130158
Magnetic resonance imaging (MRI); nitroxides; redox; radioprotection; electron paramagnetic resonance spectroscopy
10.  Simulation study for analysis of binary responses in the presence of extreme case problems 
Estimates of variance components for binary responses in presence of extreme case problems tend to be biased due to an under-identified likelihood. The bias persists even when a normal prior is used for the fixed effects.
A simulation study was carried out to investigate methods for the analysis of binary responses with extreme case problems. A linear mixed model that included a fixed effect and random effects of sire and residual on the liability scale was used to generate binary data. Five simulation scenarios were conducted based on varying percentages of extreme case problems, with true values of heritability equal to 0.07 and 0.17. Five replicates of each dataset were generated and analyzed with a generalized prior (g-prior) of varying weight.
Point estimates of sire variance using a normal prior were severely biased when the percentage of extreme case problems was greater than 30%. Depending on the percentage of extreme case problems, the sire variance was overestimated when a normal prior was used by 36 to 102% and 25 to 105% for a heritability of 0.17 and 0.07, respectively. When a g-prior was used, the bias was reduced and even eliminated, depending on the percentage of extreme case problems and the weight assigned to the g-prior. The lowest Pearson correlations between true and estimated fixed effects were obtained when a normal prior was used. When a 15% g-prior was used instead of a normal prior with a heritability equal to 0.17, Pearson correlations between true and fixed effects increased by 11, 20, 23, 27, and 60% for 5, 10, 20, 30 and 75% of extreme case problems, respectively. Conversely, Pearson correlations between true and estimated fixed effects were similar, within datasets of varying percentages of extreme case problems, when a 5, 10, or 15% g-prior was included. Therefore this indicates that a model with a g-prior provides a more adequate estimation of fixed effects.
The results suggest that when analyzing binary data with extreme case problems, bias in the estimation of variance components could be eliminated, or at least significantly reduced by using a g-prior.
PMCID: PMC3287251  PMID: 22128882
11.  Agpat6—a Novel Lipid Biosynthetic Gene Required for Triacylglycerol Production in Mammary Epithelium 
Journal of lipid research  2006;47(4):734-744.
In analyzing the sequence tags for mutant mouse embryonic stem (ES) cell lines in BayGenomics (a mouse gene-trapping resource), we identified a novel gene, Agpat6, with sequence similarities to previously characterized glycerolipid acyltransferases. Agpat6’s closest family member is another novel gene that we have provisionally designated Agpat8. Both Agpat6 and Agpat8 are conserved from plants, nematodes, and flies to mammals. AGPAT6, which is predicted to contain multiple membrane-spanning helices, is found exclusively within the endoplasmic reticulum in mammalian cells. To gain insights into the in vivo importance of Agpat6, we used the Agpat6 ES cell line from BayGenomics to create Agpat6-deficient (Agpat6−/−) mice. Agpat6−/− mice lacked full-length Agpat6 transcripts, as judged by northern blots. One of the most striking phenotypes of Agpat6−/− mice was a defect in lactation. Pups nursed by Agpat6−/− mothers die perinatally. Normally, Agpat6 is expressed at high levels in the mammary epithelium of breast tissue, but not in the surrounding adipose tissue. Histological studies revealed that the aveoli and ducts of Agpat6−/− lactating mammary glands were underdeveloped, and there was a dramatic decrease in size and number of lipid droplets within mammary epithelial cells and ducts. Also, the milk from Agpat6−/− mice was markedly depleted in diacylglycerols and triacylglycerols. Thus, we identified a novel glycerolipid acyltransferase of the endoplasmic reticulum, AGPAT6, which is crucial for the production of milk fat by the mammary gland.
PMCID: PMC3196597  PMID: 16449762
LPAAT; acyltransferase; transacylase; milk fat
12.  Early detection of malaria foci for targeted interventions in endemic southern Zambia 
Malaria Journal  2011;10:260.
Zambia has achieved significant reductions in the burden of malaria through a strategy of "scaling-up" effective interventions. Progress toward ultimate malaria elimination will require sustained prevention coverage and further interruption of transmission through active strategies to identify and treat asymptomatic malaria reservoirs. A surveillance system in Zambia's Southern Province has begun to implement such an approach. An early detection system could be an additional tool to identify foci of elevated incidence for targeted intervention.
Based on surveillance data collected weekly from 13 rural health centres (RHCs) divided into three transmission zones, early warning thresholds were created following a technique successfully implemented in Thailand. Alert levels were graphed for all 52 weeks of a year using the mean and 95% confidence interval upper limit of a Poisson distribution of the weekly diagnosed malaria cases for every available week of historic data (beginning in Aug, 2008) at each of the sites within a zone. Annually adjusted population estimates for the RHC catchment areas served as person-time of weekly exposure. The zonal threshold levels were validated against the incidence data from each of the 13 respective RHCs.
Graphed threshold levels for the three zones generally conformed to observed seasonal incidence patterns. Comparing thresholds with historic weekly incidence values, the overall percentage of aberrant weeks ranged from 1.7% in Mbabala to 36.1% in Kamwanu. For most RHCs, the percentage of weeks above threshold was greater during the high transmission season and during the 2009 year compared to 2010. 39% of weeks breaching alert levels were part of a series of three or more consecutive aberrant weeks.
The inconsistent sensitivity of the zonal threshold levels impugns the reliability of the alert system. With more years of surveillance data available, individual thresholds for each RHC could be calculated and compared to the technique outlined here. Until then, "aberrant" weeks during low transmission seasons, and during high transmission seasons at sites where the threshold level is less sensitive, could feasibly be followed up for household screening. Communities with disproportionate numbers of aberrant weeks could be reviewed for defaults in the scaling-up intervention coverage.
PMCID: PMC3182978  PMID: 21910855
13.  Accurate Detection of Low Levels of Fluorescence Emission in Autofluorescent Background: Francisella-Infected Macrophage Cells 
Cellular autofluorescence, though ubiquitous when imaging cells and tissues, is often assumed to be small in comparison to the signal of interest. Uniform estimates of autofluorescence intensity obtained from separate control specimens are commonly employed to correct for autofluorescence. While these may be sufficient for high signal-to-background applications, improvements in detector and probe technologies and introduction of spectral imaging microscopes have increased the sensitivity of fluorescence imaging methods, exposing the possibility of effectively probing the low signal-to-background regime. With spectral imaging, reliable monitoring of signals near or even below the noise levels of the microscope is possible if compensation for autofluorescence and background signals can be performed accurately. We demonstrate the importance of accurate autofluorescence modeling and the utility of spectral imaging and multivariate analysis methods using a case study focusing on fluorescence confocal spectral imaging of host-pathogen interactions. In this application fluorescent proteins are produced when Francisella novicida invade host macrophage cells. The resulting analyte signal is spectrally overlapped and typically weaker than the cellular autofluorescence. In addition to discussing the advantages of spectral imaging for following pathogen invasion, we present the spectral properties and cellular origin of macrophage autofluorescence.
PMCID: PMC2944771  PMID: 20569528
spectral imaging; fluorescence imaging; Francisella; autofluorescence; spectral crosstalk; multivariate curve resolution; macrophage; fluorescent proteins
14.  Design, Synthesis and Biological Evaluations of 2,5-Diaryl-2,3-dihydro-1,3,4-oxadiazoline Analogs of Combretastatin-A4 
Journal of medicinal chemistry  2010;53(1):325-334.
Twenty-four novel 2,5-diaryl-1,3,4-oxadiazoline analogs of combretastatin A-4 (CA-4, 1) were designed, synthesized and evaluated for biological activities. The compounds represent two structural classes; the Type I class has three methoxy groups on the A ring and the Type II class has a single methoxy group on the A ring. Biological evaluations demonstrate that multiple structural features control the biological potency. Four of the compounds, 2-(3’-bromophenyl)-5-(3”,4”,5”-trimethoxyphenyl)-2-acetyl-2,3-dihydro-1,3,4-oxadiazoline (9l), 2-(2’,5’-dimethoxyphenyl)-5-(3”-methoxyphenyl)-2-acetyl-2,3-dihydro-1,3,4-oxadiazoline (10h), 2-(3’,4’,5’-trimethoxyphenyl)-5-(3”-methoxyphenyl)-2-acetyl-2,3-dihydro-1,3,4-oxadiazoline (10i) and 2-(3’,5’-dimethoxyphenyl)-5-(3”-methoxyphenyl)-2-acetyl-2,3-dihydro-1,3,4-oxadiazoline (10j), have potent antiproliferative activities against multiple cancer cell lines. Mechanistic studies indicate that they retain the microtubule disrupting effects of compound 1 including microtubule loss, the formation of aberrant mitotic spindles, and mitotic arrest. Compound 10i inhibits purified tubulin polymerization and circumvents drug resistance mediated by P-glycoprotein and βIII tubulin expression. The oxadiazoline analog 10i is a promising lead candidate worthy of further investigation.
PMCID: PMC2810428  PMID: 19894742
15.  Brief focal cerebral ischemia that simulates transient ischemic attacks in humans regulates gene expression in rat peripheral blood 
Blood gene expression profiles of very brief (5 and 10 mins) focal ischemia that simulates transient ischemic attacks in humans were compared with ischemic stroke (120 mins focal ischemia), sham, and naïve controls. The number of significantly regulated genes after 5 and 10 mins of cerebral ischemia was 39 and 160, respectively (fold change ⩾∣1.5∣ and P<0.05). There were 103 genes common to brief focal ischemia and ischemic stroke. Ingenuity pathway analysis showed that genes regulated in the 5 mins group were mainly involved in small molecule biochemistry. Genes regulated in the 10 mins group were involved in cell death, development, growth, and proliferation. Such genes were also regulated in the ischemic stroke group. Genes common to ischemia were involved in the inflammatory response, immune response, and cell death—indicating that these pathways are a feature of focal ischemia, regardless of the duration. These results provide evidence that brief focal ischemia differentially regulates gene expression in the peripheral blood in a manner that could distinguish brief focal ischemia from ischemic stroke and controls in rats. We postulate that this will also occur in humans.
PMCID: PMC2949112  PMID: 19738631
blood; focal cerebral ischemia; gene expression; rat; stroke; transient ischemic attack
16.  (5S)-4-(2,2-Dimethyl­prop­yl)-5-isopropyl-1,3,4-oxadiazinan-2-one 
The title compound, C11H22N2O2, has one chiral center and packs in the monoclinic space group P21. The asymmetric unit has five crystallographically independent mol­ecules, four of which engage in inter­molecular N—H⋯O hydrogen bonding.
PMCID: PMC3011777  PMID: 21589605
17.  Small, mobile FcεRI aggregates are signaling competent 
Immunity  2009;31(3):469-479.
Crosslinking of IgE-bound FcεRI triggers mast cell degranulation. Previous FRAP and phosphorescent anisotropy studies suggested that FcεRI must immobilize to signal. Here, single quantum dot (QD) tracking and hyperspectral microscopy methods are used to redefine relationships between receptor mobility and signaling. QD-IgE-FcεRI aggregates of at least three receptors remain highly mobile over extended times at low concentrations of antigen that induce Syk kinase activation and near-maximal secretion. Multivalent antigen, presented as DNP-QD, also remains mobile at low doses that support secretion. FcεRI immobilization is marked at intermediate and high antigen concentrations, correlating with increases in cluster size and rates of receptor internalization. The kinase inhibitor PP2 blocks secretion without affecting immobilization or internalization. We propose that immobility is a feature of highly crosslinked immunoreceptor aggregates, is a trigger for receptor internalization, and is not required for tyrosine kinase activation leading to secretion.
PMCID: PMC2828771  PMID: 19747859
18.  Agpat6 deficiency causes subdermal lipodystrophy and resistance to obesityS 
Journal of lipid research  2006;47(4):745-754.
Triglyceride synthesis in most mammalian tissues involves the sequential addition of fatty acids to a glycerol backbone, with unique enzymes required to catalyze each acylation step. Acylation at the sn-2 position requires 1-acylglycerol-3-phosphate O-acyltransferase (AGPAT) activity. To date, seven Agpat genes have been identified based on activity and/or sequence similarity, but their physiological functions have not been well established. We have generated a mouse model deficient in AGPAT6, which is normally expressed at high levels in brown adipose tissue (BAT), white adipose tissue (WAT), and liver. Agpat6-deficient mice exhibit a 25% reduction in body weight and resistance to both diet-induced and genetically induced obesity. The reduced body weight is associated with increased energy expenditure, reduced triglyceride accumulation in BAT and WAT, reduced white adipocyte size, and lack of adipose tissue in the subdermal region. In addition, the fatty acid composition of triacylglycerol, diacylglycerol, and phospholipid is altered, with proportionally greater polyunsaturated fatty acids at the expense of monounsaturated fatty acids. Thus, Agpat6 plays a unique role in determining triglyceride content and composition in adipose tissue and liver that cannot be compensated by other members of the Agpat family.
PMCID: PMC2901549  PMID: 16436371
acyltransferase; gene-trap; adipose tissue; energy expenditure; 1-acylglycerol-3-phosphate O-acyltransferase
19.  Genome response to tissue plasminogen activator in experimental ischemic stroke 
BMC Genomics  2010;11:254.
Tissue plasminogen activator (tPA) is known to have functions beyond fibrinolysis in acute ischemic stroke, such as blood brain barrier disruption. To further delineate tPA functions in the blood, we examined the gene expression profiles induced by tPA in a rat model of ischemic stroke.
tPA differentially expressed 929 genes in the blood of rats (p ≤ 0.05, fold change ≥ |1.2|). Genes identified had functions related to modulation of immune cells. tPA gene expression was found to be dependent on the reperfusion status of cerebral vasculature. The majority of genes regulated by tPA were different from genes regulated by ischemic stroke.
tPA modulates gene expression in the blood of rats involving immune cells in a manner that is dependent on the status of vascular reperfusion. These non-fibrinolytic activities of tPA in the blood serve to better understand tPA-related complications.
PMCID: PMC2875237  PMID: 20406488
20.  Localization of Canine Brachycephaly Using an Across Breed Mapping Approach 
PLoS ONE  2010;5(3):e9632.
The domestic dog, Canis familiaris, exhibits profound phenotypic diversity and is an ideal model organism for the genetic dissection of simple and complex traits. However, some of the most interesting phenotypes are fixed in particular breeds and are therefore less tractable to genetic analysis using classical segregation-based mapping approaches. We implemented an across breed mapping approach using a moderately dense SNP array, a low number of animals and breeds carefully selected for the phenotypes of interest to identify genetic variants responsible for breed-defining characteristics. Using a modest number of affected (10–30) and control (20–60) samples from multiple breeds, the correct chromosomal assignment was identified in a proof of concept experiment using three previously defined loci; hyperuricosuria, white spotting and chondrodysplasia. Genome-wide association was performed in a similar manner for one of the most striking morphological traits in dogs: brachycephalic head type. Although candidate gene approaches based on comparable phenotypes in mice and humans have been utilized for this trait, the causative gene has remained elusive using this method. Samples from nine affected breeds and thirteen control breeds identified strong genome-wide associations for brachycephalic head type on Cfa 1. Two independent datasets identified the same genomic region. Levels of relative heterozygosity in the associated region indicate that it has been subjected to a selective sweep, consistent with it being a breed defining morphological characteristic. Genotyping additional dogs in the region confirmed the association. To date, the genetic structure of dog breeds has primarily been exploited for genome wide association for segregating traits. These results demonstrate that non-segregating traits under strong selection are equally tractable to genetic analysis using small sample numbers.
PMCID: PMC2835769  PMID: 20224736
21.  Effects of sample handling and storage on quantitative lipid analysis in human serum 
Metabolomics  2009;5(4):507-516.
There is sparse information about specific storage and handling protocols that minimize analytical error and variability in samples evaluated by targeted metabolomics. Variance components that affect quantitative lipid analysis in a set of human serum samples were determined. The effects of freeze-thaw, extraction state, storage temperature, and freeze-thaw prior to density-based lipoprotein fractionation were quantified. The quantification of high abundance metabolites, representing the biologically relevant lipid species in humans, was highly repeatable (with coefficients of variation as low as 0.01 and 0.02) and largely unaffected by 1–3 freeze-thaw cycles (with 0–8% of metabolites affected in each lipid class). Extraction state had effects on total lipid class amounts, including decreased diacylglycerol and increased phosphatidylethanolamine in thawed compared with frozen samples. The effects of storage temperature over 1 week were minimal, with 0–4% of metabolites affected by storage at 4°C, −20°C, or −80°C in most lipid classes, and 19% of metabolites in diacylglycerol affected by storage at −20°C. Freezing prior to lipoprotein fractionation by density ultracentrifugation decreased HDL free cholesterol by 37% and VLDL free fatty acid by 36%, and increased LDL cholesterol ester by 35% compared with fresh samples. These findings suggest that density-based fractionation should preferably be undertaken in fresh serum samples because up to 37% variability in HDL and LDL cholesterol could result from a single freeze-thaw cycle. Conversely, quantitative lipid analysis within unfractionated serum is minimally affected even with repeated freeze-thaw cycles.
PMCID: PMC2794342  PMID: 20046864
Metabolomics; Lipoprotein separation; Freeze-thaw; Targeted metabolomic lipid analysis; Effects of sample handling on analytical accuracy
22.  Src Kinase Inhibition Decreases Thrombin Induced Injury and Cell Cycle Re-Entry in Striatal Neurons 
Neurobiology of disease  2008;30(2):201-211.
Since Src kinase inhibitors decrease brain injury produced by intracerebral hemorrhage (ICH) and thrombin is activated following ICH, this study determined whether Src kinase inhibitors decrease thrombin induced brain injury. Thrombin injections into adult rat striatum produced focal infarction and motor deficits. The Src kinase inhibitor PP2 decreased thrombin-induced Src activation, infarction in striatum and motor deficits in vivo. Thrombin applied to cultured post-mitotic striatal neurons caused: injury to axons and dendrites; many TUNEL positive neuronal nuclei; and re-entry into the cell cycle as manifested by cyclin D1 expression, induction of several other cell cycle genes and cyclin-dependent kinase 4 activation. PP2 dose-dependently attenuated thrombin-induced injury to the cultured neurons; and attenuated thrombin-induced neuronal cell cycle re-entry. These results are consistent with the hypotheses that Src kinase inhibitors decrease injury produced by ICH by decreasing thrombin activation of Src kinases and, at least in part, by decreasing Src induced cell cycle re-entry.
PMCID: PMC2413433  PMID: 18343677
thrombin; mitogenic signaling; cell cycle; neuronal apoptosis; intracerebral hemorrhage; striatum
23.  High Throughput Genetic Analysis of Congenital Myasthenic Syndromes Using Resequencing Microarrays 
PLoS ONE  2007;2(9):e918.
The use of resequencing microarrays for screening multiple, candidate disease loci is a promising alternative to conventional capillary sequencing. We describe the performance of a custom resequencing microarray for mutational analysis of Congenital Myasthenic Syndromes (CMSs), a group of disorders in which the normal process of neuromuscular transmission is impaired.
Methodology/Principal Findings
Our microarray was designed to assay the exons and flanking intronic regions of 8 genes linked to CMSs. A total of 31 microarrays were hybridized with genomic DNA from either individuals with known CMS mutations or from healthy controls. We estimated an overall microarray call rate of 93.61%, and we found the percentage agreement between the microarray and capillary sequencing techniques to be 99.95%. In addition, our microarray exhibited 100% specificity and 99.99% reproducibility. Finally, the microarray detected 22 out of the 23 known missense mutations, but it failed to detect all 7 known insertion and deletion (indels) mutations, indicating an overall sensitivity of 73.33% and a sensitivity with respect to missense mutations of 95.65%.
Overall, our microarray prototype exhibited strong performance and proved highly efficient for screening genes associated with CMSs. Until indels can be efficiently assayed with this technology, however, we recommend using resequencing microarrays for screening CMS mutations after common indels have been first assayed by capillary sequencing.
PMCID: PMC1975473  PMID: 17878953
24.  Heterogeneity of mammary lesions represent molecular differences 
BMC Cancer  2006;6:275.
Human breast cancer is a heterogeneous disease, histopathologically, molecularly and phenotypically. The molecular basis of this heterogeneity is not well understood. We have used a mouse model of DCIS that consists of unique lines of mammary intraepithelial neoplasia (MIN) outgrowths, the premalignant lesion in the mouse that progress to invasive carcinoma, to understand the molecular changes that are characteristic to certain phenotypes. Each MIN-O line has distinguishable morphologies, metastatic potentials and estrogen dependencies.
We utilized oligonucleotide expression arrays and high resolution array comparative genomic hybridization (aCGH) to investigate whole genome expression patterns and whole genome aberrations in both the MIN-O and tumor from four different MIN-O lines that each have different phenotypes. From the whole genome analysis at 35 kb resolution, we found that chromosome 1, 2, 10, and 11 were frequently associated with whole chromosome gains in the MIN-Os. In particular, two MIN-O lines had the majority of the chromosome gains. Although we did not find any whole chromosome loss, we identified 3 recurring chromosome losses (2F1-2, 3E4, 17E2) and two chromosome copy number gains on chromosome 11. These interstitial deletions and duplications were verified with a custom made array designed to interrogate the specific regions at approximately 550 bp resolution.
We demonstrated that expression and genomic changes are present in the early premalignant lesions and that these molecular profiles can be correlated to phenotype (metastasis and estrogen responsiveness). We also identified expression changes associated with genomic instability. Progression to invasive carcinoma was associated with few additional changes in gene expression and genomic organization. Therefore, in the MIN-O mice, early premalignant lesions have the major molecular and genetic changes required and these changes have important phenotypic significance. In contrast, the changes that occur in the transition to invasive carcinoma are subtle, with few consistent changes and no association with phenotype.
We propose that the early lesions carry the important genetic changes that reflect the major phenotypic information, while additional genetic changes that accumulate in the invasive carcinoma are less associated with the overall phenotype.
PMCID: PMC1762020  PMID: 17147824

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