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Recommended isolated-line profile for representing high-resolution spectroscopic transitions (IUPAC Technical Report)
Jonathan Tennyson,Peter F. Bernath,Alain Campargue,Attila G. Csaszar,Ludovic Daumont,Robert R. Gamache,Joseph T. Hodges,Daniel Lisak,Olga V. Naumenko,Laurence S. Rothman,Ha Tran,Nikolai F. Zobov,Jeanna Buldyreva,Chris D. Boone,Maria Domenica De Vizia,Livio Gianfrani,Jean-Michel Hartmann,Robert McPheat,Jonathan Murray,Ngoc Hoa Ngo,Oleg L. Polyansky,Damien Weidmann
Physics , 2014, DOI: 10.1515/pac-2014-0208
Abstract: The report of an IUPAC Task Group, formed in 2011 on "Intensities and line shapes in high-resolution spectra of water isotopologues from experiment and theory" (Project No. 2011-022-2-100), on line profiles of isolated high-resolution rotational-vibrational transitions perturbed by neutral gas-phase molecules is presented. The well-documented inadequacies of the Voigt profile (VP), used almost universally by databases and radiative-transfer codes, to represent pressure effects and Doppler broadening in isolated vibrational-rotational and pure rotational transitions of the water molecule have resulted in the development of a variety of alternative line-profile models. These models capture more of the physics of the influence of pressure on line shapes but, in general, at the price of greater complexity. The Task Group recommends that the partially Correlated quadratic-Speed-Dependent Hard-Collision profile should be adopted as the appropriate model for high-resolution spectroscopy. For simplicity this should be called the Hartmann--Tran profile (HTP). The HTP is sophisticated enough to capture the various collisional contributions to the isolated line shape, can be computed in a straightforward and rapid manner, and reduces to simpler profiles, including the Voigt profile, under certain simplifying assumptions.
Effects of Physical Parameters on Bacterial Cell Adsorption onto Pre-Imprinted Sol-Gel Films  [PDF]
Jeanna Starosvetsky, Tally Cohen, Uta Cheruti, Dragoljub Dragoljub, Robert Armon
Journal of Biomaterials and Nanobiotechnology (JBNB) , 2012, DOI: 10.4236/jbnb.2012.324051
Abstract: Organically modified silica (ORMOSILS) thin films produced by sol-gel method were imprinted with two bacterial strains as whole cells in order to develop an easy, fast and specific probe to detect and specifically identify these micro-organisms when present in water samples. An important feature of the imprinting process was the molecular finger-prints left by these microorganisms alongside morphology, into imprinted film cavities. The films also showed high selectivity toward the imprinted template and were able to discriminate between two very close bacterial species (E. coli and S. typhimurium). In addition, several central physical parameters of the experimental water solution were examined (i.e., pH, ionic strength and the organic load exemplified by NaCl and TOC concentration, respectively). The method sensitivity to different bacterial concentrations was studied by confocal microscopy (CLSM) and quartz crystal microbalance (QCM) tools. Results showed that increased bacterial concentrations favor rapid adsorption onto imprinted sol-gel films with high affinity, while low pH, increased organic load and high ionic concentrations (i.e., seawater) interfere with bacteria re-adsorption, reducing detection capability. Under average drinking water chemical composition the method proved to be highly efficient.
Whole Cell Imprinting in Sol-Gel Thin Films for Bacterial Recognition in Liquids: Macromolecular Fingerprinting
Tally Cohen,Jeanna Starosvetsky,Uta Cheruti,Robert Armon
International Journal of Molecular Sciences , 2010, DOI: 10.3390/ijms11041236
Abstract: Thin films of organically modified silica (ORMOSILS) produced by a sol-gel method were imprinted with whole cells of a variety of microorganisms in order to develop an easy and specific probe to concentrate and specifically identify these microorganisms in liquids (e.g., water). Microorganisms with various morphology and outer surface components were imprinted into thin sol-gel films. Adsorption of target microorganism onto imprinted films was facilitated by these macromolecular fingerprints as revealed by various microscopical examinations (SEM, AFM, HSEM and CLSM). The imprinted films showed high selectivity toward each of test microorganisms with high adsorption affinity making them excellent candidates for rapid detection of microorganisms from liquids.
When environmental changes do not cause geographic separation of fauna: differential responses of Baikalian invertebrates
Varvara Fazalova, Bruno Nevado, Tatiana Peretolchina, Jeanna Petunina, Dmitry Sherbakov
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-320
Abstract: Species with stronger habitat preferences (gastropods B. turriformis, B. carinata and B. carinatocostata) exhibit rather stable population sizes through their evolutionary history, and their phylogeographic pattern indicates moderate habitat fragmentation. Conversely, species without strong habitat preference (gastropod M. herderiana and amphipod G. fasciatus) exhibit haplotype networks with a very abundant and widespread central haplotype and a big number of singleton haplotypes, while their reconstructed demographic histories show a population expansion starting about 25-50 thousand years ago, a period marked by climate warming and increase in diatom abundance as inferred from bottom-lake sedimentary cores.In agreement with previous studies, we found that species reacted differently to the same environmental changes. Our results highlight the important role of dispersal ability and degree of ecological specialization in defining a species' response to environmental changes.Many studies have demonstrated the strong influence of climate fluctuations on the patterns of genetic diversity of species. Continental glaciations resulted in geographic isolation of terrestrial species by affecting habitat availability [1,2]. After the climate warming, some species experienced demographic expansions and occupied newly created habitats [3-5]. Additionally, climate cooling was linked with low level of oceans and lakes [6]. When the water level decreased, marine species could experience range contractions and this again resulted in change of their phylogeographic patterns [7,8]. On the other hand, low ocean level affects the connectivity of islands and the distribution of species inhabiting them [9]. However, analysis of the demographic histories of species from northeastern Pacific showed that half of them were not affected by climatic changes in the Pleistocene [10]. This suggests that, even if the majority of studies consider geographic isolation as a driving force of changes
The Universe of Meanings
V. V. Nalimov,Jeanna Drogalina-Nalimov,K. Zuyev
International Journal of Transpersonal Studies , 2000,
The Influence of pH on the Specific Adhesion of P Piliated Escherichia coli
Jeanna E. Klinth, Micka?l Castelain, Bernt Eric Uhlin, Ove Axner
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0038548
Abstract: Adhesion to host tissues is an initiating step in a majority of bacterial infections. In the case of Gram-negative bacteria this adhesion is often mediated by a specific interaction between an adhesin, positioned at the distal end of bacterial pili, and its receptor on the surface of the host tissue. Furthermore, the rod of the pilus, and particularly its biomechanical properties, is believed to be crucial for the ability of bacteria to withstand external forces caused by, for example, (in the case of urinary tract infections) urinary rinsing flows by redistributing the force to several pili. In this work, the adhesion properties of P-piliated E. coli and their dependence of pH have been investigated in a broad pH range by both the surface plasmon resonance technique and force measuring optical tweezers. We demonstrate that P piliated bacteria have an adhesion ability throughout the entire physiologically relevant pH range (pH 4.5 – 8). We also show that pH has a higher impact on the binding rate than on the binding stability or the biomechanical properties of pili; the binding rate was found to have a maximum around pH 5 while the binding stability was found to have a broader distribution over pH and be significant over the entire physiologically relevant pH range. Force measurements on a single organelle level show that the biomechanical properties of P pili are not significantly affected by pH.
The biomechanical properties of F1C pili
Micka?l Castelain,Sarah Ehlers,Jeanna Klinth,Stina Lindberg,Magnus Andersson,Bernt Eric Uhlin,Ove Axner
Physics , 2014,
Abstract: Uropathogenic Escherichia coli (UPEC) express various kinds of organelles, so-called pili or fimbriae, that mediate adhesion to host tissue in the urinary tract through specific receptor-adhesin interactions. The biomechanical properties of these pili have been considered important for the ability of bacteria to withstand shear forces from rinsing urine flows. Force measuring optical tweezers have been used to characterize individual organelles of F1C type expressed by UPEC bacteria with respect to such properties. Qualitatively, the force-vs.-elongation response was found to be similar to that of other types of helix-like pili expressed by UPEC, i.e. type 1, P, and S, with force-induced elongation in three regions of which one represents the important uncoiling mechanism of the helix-like quaternary structure. Quantitatively, the steady-state uncoiling force was assessed to 26.4(1.4) pN, which is similar to those of other pili (which range from 21 pN for SI to 30 pN for type 1). The corner velocity for dynamic response (1400 nm/s) was found to be larger than those of the other pili (400 -700 nm/s for S and P pili, and 6 nm/s for type 1). The kinetics were found to be faster, with a thermal opening rate of 17 Hz, a few times higher than S and P pili, and three orders of magnitude times higher than type 1. These data suggest that F1C pili are, like P and S pili, evolutionary-selected to primarily withstand the conditions expressed in the upper urinary tract.
Increased Expression of the Very Low-Density Lipoprotein Receptor Mediates Lipid Accumulation in Clear-Cell Renal Cell Carcinoma
Jeanna Perman Sundelin, Marcus St?hlman, Annika Lundqvist, Max Levin, Paolo Parini, Martin E. Johansson, Jan Borén
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0048694
Abstract: Clear-cell renal cell carcinoma (RCC) is, in most cases, caused by loss of function of the tumor suppressor gene von Hippel–Lindau, resulting in constitutive activation of hypoxia-inducible factor (HIF)-1α and expression of hypoxia-induced genes in normoxic conditions. Clear-cell RCC cells are characterized histologically by accumulation of cholesterol, mainly in its ester form. The origin of the increased cholesterol remains unclear, but it is likely explained by an HIF-1α-driven imbalance between cholesterol uptake and excretion. Here, we showed that expression of the very low-density lipoprotein receptor (VLDL-R) was significantly increased in clear-cell RCC human biopsies compared with normal kidney tissue. Partial knockdown of HIF-1α in clear-cell RCC cells significantly reduced the VLDL-R expression, and knockdown of either HIF-1α or VLDL-R reduced the increased lipid accumulation observed in these cells. We also showed increased uptake of fluorescently labeled lipoproteins in clear-cell RCC cells, which was significantly reduced by knockdown of HIF-1α or VLDL-R. Taken together, our results support the concept that the pathological increase of HIF-1α in clear-cell RCC cells upregulates VLDL-R, which mediates increased uptake and accumulation of lipids. These results explain the morphological characteristics of clear-cell RCC, and open up novel possibilities for detection and treatment of clear-cell RCC.
Prospective Transcriptomic Pathway Analysis of Human Lymphatic Vascular Insufficiency: Identification and Validation of a Circulating Biomarker Panel
Shin Lin, Jeanna Kim, Mi-Joung Lee, Leslie Roche, Nancy L. Yang, Philip S. Tsao, Stanley G. Rockson
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0052021
Abstract: Background In our previous transcriptional profiling of a murine model, we have identified a remarkably small number of specific pathways with altered expression in lymphedema. In this investigation, we utilized microarray-based transcriptomics of human skin for an unbiased a priori prospective candidate identification, with subsequent validation of these candidates through direct serum assay. The resulting multi-analyte biomarker panel sensitively should sensitively discriminate human lymphedema subjects from normal individuals. Methods and Findings We enrolled 63 lymphedema subjects and 27 normals in our attempt to discover protein analytes that can distinguish diseased individuals from controls. To minimize technical and biologically irrelevant variation, we first identified potential candidates by performing transcriptional microarray analysis on paired diseased and normal skin specimens sampled from the same individuals. We focused our attention on genes with corresponding protein products that are secreted and took these candidates forward to a protein multiplex assay applied to diseased and normal subjects. We developed a logistic regression-based model on an eventual group of six proteins and validated our system on a separate cohort of study subjects. The area under the receiver operating characteristic curve was calculated to be 0.87 (95% CI : 0.75 to 0.97). Conclusions We have developed an accurate bioassay utilizing proteins representing four central pathogenetic modalities of the disease: lymphangiogenesis, inflammation, fibrosis, and lipid metabolism, suggesting that these proteins are directly related to the pathogenesis of the tissue pathology in lymphatic vascular insufficiency. Further studies are warranted to determine whether this newly-identified biomarker panel will possess utility as an instrument for in vitro diagnosis of early and latent disease; the ultimate applicability to risk stratification, quantitation of disease burden, and response to therapy can easily be envisioned.
Traumatic Brain Injury-Induced Dysregulation of the Circadian Clock
Deborah R. Boone, Stacy L. Sell, Maria-Adelaide Micci, Jeanna M. Crookshanks, Margaret Parsley, Tatsuo Uchida, Donald S. Prough, Douglas S. DeWitt, Helen L. Hellmich
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0046204
Abstract: Circadian rhythm disturbances are frequently reported in patients recovering from traumatic brain injury (TBI). Since circadian clock output is mediated by some of the same molecular signaling cascades that regulate memory formation (cAMP/MAPK/CREB), cognitive problems reported by TBI survivors may be related to injury-induced dysregulation of the circadian clock. In laboratory animals, aberrant circadian rhythms in the hippocampus have been linked to cognitive and memory dysfunction. Here, we addressed the hypothesis that circadian rhythm disruption after TBI is mediated by changes in expression of clock genes in the suprachiasmatic nuclei (SCN) and hippocampus. After fluid-percussion TBI or sham surgery, male Sprague-Dawley rats were euthanized at 4 h intervals, over a 48 h period for tissue collection. Expression of circadian clock genes was measured using quantitative real-time PCR in the SCN and hippocampus obtained by laser capture and manual microdissection respectively. Immunofluorescence and Western blot analysis were used to correlate TBI-induced changes in circadian gene expression with changes in protein expression. In separate groups of rats, locomotor activity was monitored for 48 h. TBI altered circadian gene expression patterns in both the SCN and the hippocampus. Dysregulated expression of key circadian clock genes, such as Bmal1 and Cry1, was detected, suggesting perturbation of transcriptional-translational feedback loops that are central to circadian timing. In fact, disruption of circadian locomotor activity rhythms in injured animals occurred concurrently. These results provide an explanation for how TBI causes disruption of circadian rhythms as well as a rationale for the consideration of drugs with chronobiotic properties as part of a treatment strategy for TBI.
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