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Mechanism of U-insertion RNA Editing in Trypanosome Mitochondria: The Bimodal TUTase Activity of the Core Complex

Ringpis, Gene-Errol; Aphasizheva, Inna; Wang, Xiaorong; Huang, Lan; Lathrop, Richard H.; Hatfield, G. Wesley; Aphasizhev, Ruslan
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
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Expression of the trypanosomal mitochondrial genome requires the insertion and deletion of uridylyl residues at specific sites in pre-mRNAs. RET2 terminal uridylyl transferase (TUTase) is an integral component of the RNA editing core complex (RECC) and is responsible for the guide RNA-dependent U-insertion reaction. By analyzing RNAi-based knock-in Trypanosoma brucei cell lines, purified editing complex and individual protein, we have investigated RET2’s association with the RECC. In addition, the U-insertion activity exhibited by RET2 as RECC subunit was compared with characteristics of the monomeric protein. We show that RET2 interaction with RECC is accomplished via a protein-protein contact between its middle domain and a structural subunit MP81. The recombinant RET2 catalyzes a faithful editing on gapped (pre-cleaved) double-stranded RNA substrates and this reaction requires an internal monophosphate group at the 5′-end of the mRNA 3′-cleavage fragment. However, RET2 processivity is limited to insertion of three Us. Incorporation into the RECC voids the internal phosphate requirement and allows filling of longer gaps similar to those observed in vivo. Remarkably, monomeric and RECC-embedded enzymes display a similar bimodal activity: the distributive insertion of a single uracil is followed with a processive extension limited by the number of guiding nucleotides. Based on the RNA substrate specificity of RET2 and purine-rich nature of U-insertion sites...

Bimodal Analysis Reveals a General Scaling Law Governing Nondirected and Chemotactic Cell Motility

Gruver, J. Scott; Potdar, Alka A.; Jeon, Junhwan; Sai, Jiqing; Anderson, Bridget; Webb, Donna; Richmond, Ann; Quaranta, Vito; Cummings, Peter T.; Chung, Chang Y.
Fonte: The Biophysical Society Publicador: The Biophysical Society
Tipo: Artigo de Revista Científica
Publicado em 21/07/2010 EN
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Cell motility is a fundamental process with relevance to embryonic development, immune response, and metastasis. Cells move either spontaneously, in a nondirected fashion, or in response to chemotactic signals, in a directed fashion. Even though they are often studied separately, both forms of motility share many complex processes at the molecular and subcellular scale, e.g., orchestrated cytoskeletal rearrangements and polarization. In addition, at the cellular level both types of motility include persistent runs interspersed with reorientation pauses. Because there is a great range of variability in motility among different cell types, a key challenge in the field is to integrate these multiscale processes into a coherent framework. We analyzed the motility of Dictyostelium cells with bimodal analysis, a method that compares time spent in persistent versus reorientation mode. Unexpectedly, we found that reorientation time is coupled with persistent time in an inverse correlation and, surprisingly, the inverse correlation holds for both nondirected and chemotactic motility, so that the full range of Dictyostelium motility can be described by a single scaling relationship. Additionally, we found an identical scaling relationship for three human cell lines...

Lanthanide (III) complexes of PCTA-(tris-amide) derivatives as potential bimodal MRI and optical imaging agents

Rojas-Quijano, Federico A.; Benyó, Enikő Tircsóné; Tircsó, Gyula; Kálmán, Ferenc K.; Baranyai, Zsolt; Aime, Silvio; Sherry, A. Dean; Kovács, Zoltán
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 07/12/2009 EN
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Lanthanide complexes of two tris-(amide) derivatives of PCTA were synthesized and characterized. The relaxometric and luminescence properties of their lanthanide complexes were investigated as bimodal magnetic resonance (MR) and optical imaging agents. Luminescence studies show that one of the TbIII complexes dimerizes in solution at low millimolar concentrations while the other may have a higher than expected coordination number in solution. The corresponding GdIII complexes display unusually high T1 relaxivities and enhanced kinetic inertness compared to GdPCTA. These features suggest that these new chelates may be suitable for in vivo applications. The fast water exchange rates observed for these complexes make them unsuitable as paramagnetic chemical exchange saturation transfer (PARACEST) agents.

Bimodal, Reciprocal Regulation of Fibroblast Growth Factor Receptor 1 Promoter Activity by BTEB1/KLF9 during Myogenesis

Mitchell, Darrion L.; DiMario, Joseph X.
Fonte: The American Society for Cell Biology Publicador: The American Society for Cell Biology
Tipo: Artigo de Revista Científica
Publicado em 01/08/2010 EN
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Expression of FGFR1 controls both myoblast proliferation and differentiation. The Krüppel-like transcription factor BTEB1 demonstrates bimodal, reciprocal activity by activating the FGFR1 promoter in proliferating myoblasts and repressing the same promoter via the same DNA-binding site in differentiated myotubes.

Changing epidemiology of trauma deaths leads to a bimodal distribution

Gunst, Mark; Ghaemmaghami, Vafa; Gruszecki, Amy; Urban, Jill; Frankel, Heidi; Shafi, Shahid
Fonte: Baylor Health Care System Publicador: Baylor Health Care System
Tipo: Artigo de Revista Científica
Publicado em /10/2010 EN
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Injury mortality was classically described with a trimodal distribution, with immediate deaths at the scene, early deaths due to hemorrhage, and late deaths from organ failure. We hypothesized that the development of trauma systems has improved prehospital care, early resuscitation, and critical care and altered this pattern. This population-based study of all trauma deaths in an urban county with a mature trauma system reviewed data for 678 patients (median age, 33 years; 81% male; 43% gunshot, 20% motor vehicle crashes). Deaths were classified as immediate (scene), early (in hospital, ≤4 hours from injury), or late (>4 hours after injury). Multinomial regression was used to identify independent predictors of immediate and early versus late deaths, adjusted for age, gender, race, intention, mechanism, toxicology, and cause of death. Results showed 416 (61%) immediate, 199 (29%) early, and 63 (10%) late deaths. Compared with the classical description, the percentage of immediate deaths remained unchanged, and early deaths occurred much earlier (median 52 vs 120 minutes). However, unlike the classic trimodal distribution, the late peak was greatly diminished. Intentional injuries, alcohol intoxication, asphyxia, and injuries to the head and chest were independent predictors of immediate death. Alcohol intoxication and injuries to the chest were predictors of early death...

A Bimodal Distribution of Two Distinct Categories of Intrinsically Disordered Structures with Separate Functions in FG Nucleoporins*

Yamada, Justin; Phillips, Joshua L.; Patel, Samir; Goldfien, Gabriel; Calestagne-Morelli, Alison; Huang, Hans; Reza, Ryan; Acheson, Justin; Krishnan, Viswanathan V.; Newsam, Shawn; Gopinathan, Ajay; Lau, Edmond Y.; Colvin, Michael E.; Uversky, Vladimir N.
Fonte: The American Society for Biochemistry and Molecular Biology Publicador: The American Society for Biochemistry and Molecular Biology
Tipo: Artigo de Revista Científica
EN
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Nuclear pore complexes (NPCs) gate the only conduits for nucleocytoplasmic transport in eukaryotes. Their gate is formed by nucleoporins containing large intrinsically disordered domains with multiple phenylalanine-glycine repeats (FG domains). In combination, these are hypothesized to form a structurally and chemically homogeneous network of random coils at the NPC center, which sorts macromolecules by size and hydrophobicity. Instead, we found that FG domains are structurally and chemically heterogeneous. They adopt distinct categories of intrinsically disordered structures in non-random distributions. Some adopt globular, collapsed coil configurations and are characterized by a low charge content. Others are highly charged and adopt more dynamic, extended coil conformations. Interestingly, several FG nucleoporins feature both types of structures in a bimodal distribution along their polypeptide chain. This distribution functionally correlates with the attractive or repulsive character of their interactions with collapsed coil FG domains displaying cohesion toward one another and extended coil FG domains displaying repulsion. Topologically, these bipartite FG domains may resemble sticky molten globules connected to the tip of relaxed or extended coils. Within the NPC...

Bimodal viral vectors and in vivo imaging reveal the fate of human neural stem cells in experimental glioma model

Shah, Khalid; Hingtgen, Shawn; Kasmieh, Randa; Figueiredo, Jose Luiz; Garcia, Elisa; Martinez-Serrano, Alberto; Breakefield, Xandra; Weissleder, Ralph
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 23/04/2008 EN
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Transplantation of genetically engineered cells into the central nervous system (CNS) offers immense potential for the treatment of several neurological disorders. Monitoring expression levels of transgenes and following changes in cell function and distribution over time is critical in assessing therapeutic efficacy of such cells in vivo. We have engineered lentiviral vectors bearing fusions between different combinations of fluorescent and bioluminescent marker proteins and employed bioluminescence imaging and intravital-scanning microscopy in real-time to study the fate of human neural stem cells (hNSC) at a cellular resolution in glioma bearing brains in vivo. Using Renilla luciferase (Rluc)-DsRed2 or GFP-(Rluc) expressing malignant human glioma model, transduced hNSC were shown to migrate extensively towards gliomas, with hNSC populating gliomas at 10 days after transplantation. Furthermore, transduced hNSC survived longer in mice with gliomas than in normal brain, but did not modulate glioma progression in vivo. These studies demonstrate the utility of bimodal viral vectors and real-time imaging in evaluating fate of NSC in diseased models and thus provide a platform for accelerating cell-based therapies for CNS disorders.

Apigenin-induced apoptosis of leukemia cells is mediated by a bimodal and differentially regulated residue-specific phosphorylation of heat-shock protein–27

Gonzalez-Mejia, M E; Voss, O H; Murnan, E J; Doseff, A I
Fonte: Nature Publishing Group Publicador: Nature Publishing Group
Tipo: Artigo de Revista Científica
EN
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Apigenin, a natural plant flavonoid with antiproliferative activity, is emerging as a promising compound for cancer prevention and therapy, but its mechanism of action remains unclear. High expression of the small heat-shock protein-27 (Hsp27) in leukemia contributes to the resistance of these cells to cancer treatments. Changes in Hsp27 phosphorylation have been associated with heat and metabolic stress, but its role in flavonoid anticancer activity has not been investigated. In this study, we examined the effect of apigenin in the regulation of Hsp27 on leukemia. We showed that apigenin does not affect Hsp27 expression but induces a bimodal phosphorylation on Ser78 and Ser82. The phosphorylation at early times was regulated by p38. At later times, Hsp27 phosphorylation was dependent on p38 activity and for some residues on PKCδ. Silencing of p38 expression reduced apigenin-induced phosphorylation on Ser15, Ser78, and Ser82, whereas silencing of PKCδ expression reduced the phosphorylation on Ser15 and Ser82 without affecting Ser78. In addition, we found that apigenin-induced PKCδ activity is mediated by p38. We also showed that the phosphorylation of Hsp27 significantly increased the susceptibility of leukemia cells to apigenin-induced apoptosis. Together...

Conventions for sign and speech transcription of child bimodal bilingual corpora in ELAN

Chen Pichler, Deborah; Hochgesang, Julie A.; Lillo-Martin, Diane; de Quadros, Ronice Müller
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em //2010 EN
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This article extends current methodologies for the linguistic analysis of sign language acquisition to cases of bimodal bilingual acquisition. Using ELAN, we are transcribing longitudinal spontaneous production data from hearing children of Deaf parents who are learning either American Sign Language (ASL) and American English (AE), or Brazilian Sign Language (Libras, also referred to as Língua de Sinais Brasileira/LSB in some texts) and Brazilian Portuguese (BP). Our goal is to construct corpora that can be mined for a wide range of investigations on various topics in acquisition. Thus, it is important that we maintain consistency in transcription for both signed and spoken languages. This article documents our transcription conventions, including the principles behind our approach. Using this document, other researchers can chose to follow similar conventions or develop new ones using our suggestions as a starting point.

Ligand-binding domain subregions contributing to bimodal agonism in cyclic nucleotide–gated channels

Wong, Wai-Fung; Chan, Kerry S.C.; Michaleski, Matthew S.; Haesler, Adam; Young, Edgar C.
Fonte: The Rockefeller University Press Publicador: The Rockefeller University Press
Tipo: Artigo de Revista Científica
Publicado em /06/2011 EN
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Cyclic nucleotide–gated (CNG) channels bind cGMP or cAMP in a cytoplasmic ligand–binding domain (BD), and this binding typically increases channel open probability (Po) without inducing desensitization. However, the catfish CNGA2 (fCNGA2) subtype exhibits bimodal agonism, whereby steady-state Po increases with initial cGMP-binding events (“pro” action) up to a maximum of 0.4, but decreases with subsequent cGMP-binding events (“con” action) occurring at concentrations >3 mM. We sought to clarify if low pro-action efficacy was either necessary or sufficient for con action to operate. To find BD residues responsible for con action or low pro-action efficacy or both, we constructed chimeric CNG channels: subregions of the fCNGA2 BD were substituted with corresponding sequence from the rat CNGA4 BD, which does not support con action. Constructs were expressed in frog oocytes and tested by patch clamp of cell-free membranes. For nearly all BD elements, we found at least one construct where replacing that element preserved robust con action, with a ratio of steady-state conductances, g(10 mM cGMP)/g(3 mM cGMP) < 0.75. When all of the BD sequence C terminal of strand β6 was replaced, g(10 mM cGMP)/g(3 mM cGMP) was increased to 0.95 ± 0.05 (n = 7). However...

Annexin A5-Functionalized Bimodal Nanoparticles for MRI and Fluorescence Imaging of Atherosclerotic Plaques

van Tilborg, Geralda A. F.; Vucic, Esad; Strijkers, Gustav J.; Cormode, David P.; Mani, Venkatesh; Skajaa, Torjus; Reutelingsperger, Chris P. M.; Fayad, Zahi A.; Mulder, Willem J. M.; Nicolay, Klaas
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 20/10/2010 EN
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Apoptosis and macrophage burden are believed to correlate with atherosclerotic plaque vulnerability and are therefore considered important diagnostic and therapeutic targets for atherosclerosis. These cell types are characterized by the exposure of phosphatidylserine (PS) at their surface. In the present study, we developed and applied a small micellar fluorescent annexin A5-functionalized nanoparticle for noninvasive magnetic resonance imaging (MRI) of PS exposing cells in atherosclerotic lesions. Annexin A5-mediated target-specificity was confirmed with ellipsometry and in vitro binding to apoptotic Jurkat cells. In vivo T1-weighted MRI of the abdominal aorta in atherosclerotic ApoE−/− mice revealed enhanced uptake of the annexin A5-micelles as compared to control-micelles, which was corroborated with ex vivo near-infrared fluorescence images of excised whole aortas. Confocal laser scanning microscopy (CLSM) demonstrated that the targeted agent was associated with macrophages and apoptotic cells, whereas the nonspecific control agent showed no clear uptake by such cells. In conclusion, the annexin A5-conjugated bimodal micelles displayed potential for noninvasive assessment of cell types that are considered to significantly contribute to plaque instability and therefore may be of great value in the assessment of atherosclerotic lesion phenotype.

Dynamic processes at stress promoters regulate the bimodal expression of HOG response genes

Pelet, Serge; Peter, Matthias
Fonte: Landes Bioscience Publicador: Landes Bioscience
Tipo: Artigo de Revista Científica
Publicado em 01/11/2011 EN
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Osmotic stress triggers the activation of the HOG (high osmolarity glycerol) pathway in Saccharomyces cerevisiae. This signaling cascade culminates in the activation of the MAPK (mitogen-activated protein kinase) Hog1. Quantitative single cell measurements revealed a discrepancy between kinase- and transcriptional activities of Hog1. While kinase activity increases proportionally to stress stimulus, gene expression is inhibited under low stress conditions. Interestingly, a slow stochastic gene activation process is responsible for setting a tunable threshold for gene expression under basal or low stress conditions, which generates a bimodal expression pattern at intermediate stress levels.

Theoretical study of the frequency shift in bimodal FM-AFM by fractional calculus

Herruzo, Elena T; Garcia, Ricardo
Fonte: Beilstein-Institut Publicador: Beilstein-Institut
Tipo: Artigo de Revista Científica
Publicado em 07/03/2012 EN
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Bimodal atomic force microscopy is a force-microscopy method that requires the simultaneous excitation of two eigenmodes of the cantilever. This method enables the simultaneous recording of several material properties and, at the same time, it also increases the sensitivity of the microscope. Here we apply fractional calculus to express the frequency shift of the second eigenmode in terms of the fractional derivative of the interaction force. We show that this approximation is valid for situations in which the amplitude of the first mode is larger than the length of scale of the force, corresponding to the most common experimental case. We also show that this approximation is valid for very different types of tip–surface forces such as the Lennard-Jones and Derjaguin–Muller–Toporov forces.

Development of Iron Doped Silicon Nanoparticles as Bimodal Imaging Agents

Singh, Mani P.; Atkins, Tonya M.; Muthuswamy, Elayaraja; Kamali, Saeed; Tu, Chuqiao; Louie, Angelique Y.; Kauzlarich, Susan M.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
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We demonstrate the synthesis of water-soluble allylamine terminated Fe doped Si (SixFe) nanoparticles as bimodal agents for optical and magnetic imaging. The preparation involves the synthesis of a single source iron containing precursor, Na4Si4 with x% Fe (x = 1, 5, 10), and its subsequent reaction with NH4Br to produce hydrogen terminated SixFe nanoparticles. The hydrogen-capped nanoparticles are further terminated with allylamine via thermal hydrosilylation. Transmission electron microscopy (TEM) indicates that the average particle diameter is ~3.0±1.0 nm. The Si5Fe nanoparticles show strong photoluminescence quantum yield in water (~ 10 %) with significant T2 contrast (r2/r1value of 4.31). Electron paramagnetic resonance (EPR) and Mössbauer spectroscopies indicate that iron in the nanoparticles is in the +3 oxidation state. Analysis of cytotoxicity using the resazurin assay on HepG2 liver cells indicates that the particles have minimal toxicity.

Discrete Bimodal Probes for Thrombus Imaging

Uppal, Ritika; Ciesienski, Kate L.; Chonde, Daniel B.; Loving, Galen S.; Caravan, Peter
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
EN
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Here we report a generalizable solid/solution phase strategy for the synthesis of discrete bimodal fibrin-targeted imaging probes. A fibrin-specific peptide was conjugated with two distinct imaging reporters at the C- and N-terminus. In vitro studies demonstrated retention of fibrin affinity and specificity. Imaging studies showed that these probes could detect fibrin over a wide range of probe concentrations by optical, magnetic resonance, and positron emission tomography imaging.

Bimodal collagen fibril diameter distributions direct age-related variations in tendon resilience and resistance to rupture

Goh, K. L.; Holmes, D. F.; Lu, Y.; Purslow, P. P.; Kadler, K. E.; Bechet, D.; Wess, T. J.
Fonte: American Physiological Society Publicador: American Physiological Society
Tipo: Artigo de Revista Científica
EN
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Scaling relationships have been formulated to investigate the influence of collagen fibril diameter (D) on age-related variations in the strain energy density of tendon. Transmission electron microscopy was used to quantify D in tail tendon from 1.7- to 35.3-mo-old (C57BL/6) male mice. Frequency histograms of D for all age groups were modeled as two normally distributed subpopulations with smaller (DD1) and larger (DD2) mean Ds, respectively. Both DD1 and DD2 increase from 1.6 to 4.0 mo but decrease thereafter. From tensile tests to rupture, two strain energy densities were calculated: 1) uE [from initial loading until the yield stress (σY)], which contributes primarily to tendon resilience, and 2) uF [from σY through the maximum stress (σU) until rupture], which relates primarily to resistance of the tendons to rupture. As measured by the normalized strain energy densities uE/σY and uF/σU, both the resilience and resistance to rupture increase with increasing age and peak at 23.0 and 4.0 mo, respectively, before decreasing thereafter. Multiple regression analysis reveals that increases in uE/σY (resilience energy) are associated with decreases in DD1 and increases in DD2, whereas uF/σU (rupture energy) is associated with increases in DD1 alone. These findings support a model where age-related variations in tendon resilience and resistance to rupture can be directed by subtle changes in the bimodal distribution of Ds.

Synthesis and characterization of intrinsically radiolabeled quantum dots for bimodal detection

Sun, Minghao; Hoffman, David; Sundaresan, Gobalakrishnan; Yang, Likun; Lamichhane, Narottam; Zweit, Jamal
Fonte: e-Century Publishing Corporation Publicador: e-Century Publishing Corporation
Tipo: Artigo de Revista Científica
Publicado em 28/03/2012 EN
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A novel approach was developed to synthesize radioactive quantum dots (r-QDs) thereby enabling both optical and radionuclide signals to be detected from the same intrinsic bimodal probe. This proof-of-concept is exemplified by the incorporation of the radionuclide 109Cadmium into the core/shell of the nanoparticle. Green and near infrared (NIR) emission intrinsic r-QDs were synthesized and characterized. Zwitterionic and Poly-polyethlene glycol (PEGylated) ligands were synthesized and used to coat r-QDs. Zwitterionic NIR r-QDs (quantum yield = 11%) and PEGylated NIR r-QDs (quantum yield = 14%) with an average size of 13.8 nm and 16.8 nm were obtained respectively. The biodistribution of NIR zwitterionic and PEGylated r-QDs in nude mice was investigated and zwitterionic r-QDs showed longer blood circulation (t1/2 = 21.4±1.1 hrs) than their PEGylated counterparts (t1/2 = 6.4±0.5 min). Both zwitterionic and PEGylated r-QDs exhibited progressive accumulation in the liver and spleen, but the magnitude of the accumulation (%ID/g) was about 3-6 fold higher with the PEGylated r-QDs at all the time points. The results demonstrated the feasibility of r-QDs synthesis in quantitative yield and retention of fluorescence following incorporation of radioactivity into the core/shell of the nanoparticle. The gamma signal from the same fluorescent elemental material enabled quantitative and robust pharmacokinetic measurements and how these changed depended on the type of coating ligands used. This strategy for intrinsically radio-labeling the QDs is currently being implemented in our laboratory for the incorporation of other radiometals.

In vivo validation of a bimodal technique combining time-resolved fluorescence spectroscopy and ultrasonic backscatter microscopy for diagnosis of oral carcinoma

Sun, Yang; Xie, Hongtao; Liu, Jing; Lam, Matthew; Chaudhari, Abhijit J.; Zhou, Feifei; Bec, Julien; Yankelevich, Diego R.; Dobbie, Allison; Tinling, Steven L.; Gandour-Edwards, Regina F.; Monsky, Wayne L.; Gregory Farwell, D.; Marcu, Laura
Fonte: Society of Photo-Optical Instrumentation Engineers Publicador: Society of Photo-Optical Instrumentation Engineers
Tipo: Artigo de Revista Científica
EN
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Tissue diagnostic features generated by a bimodal technique integrating scanning time-resolved fluorescence spectroscopy (TRFS) and ultrasonic backscatter microscopy (UBM) are investigated in an in vivo hamster oral carcinoma model. Tissue fluorescence is excited by a pulsed nitrogen laser and spectrally and temporally resolved using a set of filters/dichroic mirrors and a fast digitizer, respectively. A 41-MHz focused transducer (37-μm axial, 65-μm lateral resolution) is used for UBM scanning. Representative lesions of the different stages of carcinogenesis show that fluorescence characteristics complement ultrasonic features, and both correlate with histological findings. These results demonstrate that TRFS-UBM provide a wealth of co-registered, complementary data concerning tissue composition and structure as it relates to disease status. The direct co-registration of the TRFS data (sensitive to surface molecular changes) with the UBM data (sensitive to cross-sectional structural changes and depth of tumor invasion) is expected to play an important role in pre-operative diagnosis and intra-operative determination of tumor margins.

Bimodal Distribution of Risk for Childhood Obesity in Urban Baja California, Mexico

Wojcicki, Janet M.; Jimenez-Cruz, Arturo; Bacardi-Gascon, Montserrat; Schwartz, Norah; Heyman, Melvin B.
Fonte: Springer US Publicador: Springer US
Tipo: Artigo de Revista Científica
EN
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In Mexico, higher socioeconomic status (SES) has been found to be associated with increased risk for obesity in children. Within developed urban areas, however, there may be increased risk among lower SES children. Students in grades 4–6 from five public schools in Tijuana and Tecate, Mexico, were interviewed and weight, height and waist circumference (WC) measurements were taken. Interviews consisted of questions on food frequency, food insecurity, acculturation, physical activity and lifestyle practices. Multivariate logistic models were used to assess risk factors for obesity (having a body mass index [BMI] ≥95th percentile) and abdominal obesity (a WC >90th percentile) using Stata 11.0. Five hundred and ninety students were enrolled; 43.7% were overweight or obese, and 24.3% were obese and 20.2% had abdominal obesity. Independent risk factors for obesity included watching TV in English (odds ratio [OR] 1.60, 95% confidence interval [CI] 1.06–2.41) and perceived child food insecurity (OR 1.57, 95% CI 1.05–2.36). Decreased risk for obesity was associated with female sex (OR 0.64, 95% CI 0.43–0.96), as was regular multivitamin use (OR 0.63, 95% CI 0.42–0.94). Risk obesity was also decreased with increased taco consumption (≥1×/week; OR 0.64...

Bimodal expression level polymorphisms in Arabidopsis thaliana

Nagano, Atsushi J.; Tsuchimatsu, Takashi; Okuyama, Yudai; Hara-Nishimura, Ikuko
Fonte: Landes Bioscience Publicador: Landes Bioscience
Tipo: Artigo de Revista Científica
Publicado em 01/07/2012 EN
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Differences in gene expression are termed expression level polymorphisms (ELPs). Here, we propose a new ELP class, bimodal ELPs (bELPs), as a criterion to screen for genes that are responsible for natural phenotypic variation and/or that are targeted by balancing selection. bELP genes are characterized by two expression level modes. Genomic scans based on nucleotide sequences are not ideal for identifying genes targeted for selection. A critical concern is that several genes can be present in the selection-targeted regions identified by such scans. This situation indicates the importance of integrating genomic sequence data and other information, such as gene expression data. Comparative transcriptomics is useful for determining evolutionarily and ecologically important polymorphisms. In a genome-wide expression screen of 34 accessions, we identified 344 Arabidopsis thaliana genes exhibiting bELPs. Population genetic analysis revealed that bELP genes had high nucleotide diversities and long linkage disequilibriums. The highest nucleotide diversity (11-fold greater than the genomic mean) was found in the At1g23780 gene, which encodes a putative F-box protein. We observed a clear association between the expression mode and sequence type of the At1g23780 gene. Our results suggest that bELPs will be useful for the screening and functional analysis of genes responsible for phenotypic polymorphisms. Such a “multi-omics” approach has the potential to facilitate the scanning of genes relevant to balanced polymorphisms not only in A. thaliana...