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Now showing items 1 - 16 of 36


    Disclosed herein are systems, methods, systems and devices for measurement and visualization of chemical dynamics in living cells or tissues for diagnostic pathology. Devices can be open- or closed-channel microfluidic membrane devices for long-term IR spectroscopy of live adherent cells and ultimately for rapidly identifying time-dependent spectral features indicative of chemical abnormality in individual cells.
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  • Human age and skin physiology shape diversity and abundance of Archaea on skin

    Moissl-Eichinger, Christine   Probst, Alexander J.   Birarda, Giovanni   Auerbach, Anna   Koskinen, Kaisa   Wolf, Peter   Holman, Hoi-Ying N.  

    The human skin microbiome acts as an important barrier protecting our body from pathogens and other environmental influences. Recent investigations have provided evidence that Archaea are a constant but highly variable component of the human skin microbiome, yet factors that determine their abundance changes are unknown. Here, we tested the hypothesis that the abundance of archaea on human skin is influenced by human age and skin physiology by quantitative PCR of 51 different skin samples taken from human subjects of various age. Our results reveal that archaea are more abundant in human subjects either older than 60 years or younger than 12 years as compared to middle-aged human subjects. These results, together with results obtained from spectroscopy analysis, allowed us gain first insights into a potential link of lower sebum levels and lipid content and thus reduced skin moisture with an increase in archaeal signatures. Amplicon sequencing of selected samples revealed the prevalence of specific eury-and mainly thaumarchaeal taxa, represented by a core archaeome of the human skin.
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  • Synchrotron IR Spectromicroscopy: Chemistry of Living Cells

    Holman, Hoi-Ying N.   Bechtel, Hans A.   Hao, Zhao   Martin, Michael C.  

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  • Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria

    Dubinsky, Eric A.   DeSantis, Todd Z.   Andersen, Gary L.   Piceno, Yvette M.   Singh, Navjeet   Jansson, Janet K.   Probst, Alexander   Borglin, Sharon E.   Fortney, Julian L.   Stringfellow, William T.   Bill, Markus   Conrad, Mark E.   Tom, Lauren M.   Chavarria, Krystle L.   Alusi, Thana R.   Lamendella, Regina   Joyner, Dominique C.   Spier, Chelsea   Baelum, Jacob   Auer, Manfred   Zemla, Marcin L.   Chakraborty, Romy   Sonnenthal, Eric L.   D'haeseleer, Patrik   Holman, Hoi-Ying N.   Osman, Shariff   Lu, Zhenmei   Van Nostrand, Joy D.   Deng, Ye   Zhou, Jizhong   Mason, Olivia U.  

    The biological effects and expected fate of the vast amount of oil in the Gulf of Mexico from the Deepwater Horizon blowout are unknown owing to the depth and magnitude of this event. Here, we report that the dispersed hydrocarbon plume stimulated deep-sea indigenous gamma-Proteobacteria that are closely related to known petroleum degraders. Hydrocarbon-degrading genes coincided with the concentration of various oil contaminants. Changes in hydrocarbon composition with distance from the source and incubation experiments with environmental isolates demonstrated faster-than-expected hydrocarbon biodegradation rates at 5 degrees C. Based on these results, the potential exists for intrinsic bioremediation of the oil plume in the deep-water column without substantial oxygen drawdown.
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  • Decomposition of Cr(V)-diols to Cr(III) Complexes by Arthrobacter oxydans

    Tsibakhashvili, Nelly Y.   Kalabegishvili, Tamaz L.   Rcheulishvili, Alexander N.   Murusidze, Ivane G.   Rcheulishvili, Olia A.   Kerkenjia, Salome M.   Holman, Hoi-Ying N.  

    We demonstrated previously that Cr(VI) is readily reduced to oxoCr(V)-diols at the surface of Arthrobacter oxydans-a Gram-positive aerobic bacteria isolated from Columbia basalt rocks originated from a highly contaminated site in the USA. Here, we report an electron spin resonance (ESR) study of Cr(III) hydroxide formation from Cr(V)-diols by this bacterial strain as cells were exposed to 35, 200, and 400 mg/L of Cr(VI) under aerobic conditions as a batch culture and as lyophilized cells. The time-dependent ESR measurements show that the half-time of Cr(III) formation is almost equal to that of Cr(V) decomposition, which is in the range of 3-6 days for all cases. This rate is at least 300 times slower than that of Cr(V) formation. Additionally, atomic absorption spectrometry was also employed to examine the time course of total chromium in bacterial cells. This is the first time the kinetics of Cr(III) complexes formation in bacteria is evaluated.
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  • Mid-infrared reflectivity of experimental atheromas

    Holman, Hoi-Ying N.   Bjornstad, Kathy A.   Martin, Michael C.   Mckinney, Wayne R.   Blakely, Eleanor A.   Blankenberg, Francis G.  

    We report that the pathologic components present within the atheromatous plaques of ApoE knockout mice can reflect significant amounts of mid-infrared (mid-IR) light. Furthermore, the reflected light spectra contained the unique signatures of a variety of biologic features including those found in unstable or "vulnerable" plaque. This discovery may represent a unique opportunity to develop a new intravascular diagnostic modality that can detect and characterize sites of atherosclerosis. (c) 2008 Society of Photo-Optical Instrumentation Engineers.
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  • Ultrafast Self-Assembly of Microscale Particles by Open-Channel Flow RID C-1717-2011

    Choi, Sun   Park, Inkyu   Hao, Zhao   Holman, Hoi-ying N.   Pisano, Albert P.   Zohdi, Tarek I.  

    We developed an ultrafast microfluidic approach to self-assemble microparticles in three dimensions by taking advantage of simple photolithography and capillary action of microparticle-dispersed suspensions. The theoretical principles of high-speed assembly have been explained, and the experimental verifications of the assembly of various sizes of silica microspheres and silica gel microspheres within thin and long open microchannels by using this approach have been demonstrated. We anticipate that the presented technique will be widely used in the semiconductor and Bio-MEMS (microelectromechanical systems) fields because it offers a fast way to control 3D microscale particle assemblies and also has superb compatibility with photolithography, which can lead to an easy integration of particle assembly with existing CMOS (complementary metal oxide-semiconductor) and M EMS fabrication processes.
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  • Infrared Spectromicroscopy: Probing Live Cellular Responses to Environmental Changes

    Holman, Hoi-Ying N.   Hao, Zhao   Martin, Michael C.   Bechtel, Hans A.  

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  • Quantitative studies of long-term stable, top-down fabricated silicon nanowire pH sensors

    Choi, Sun   Park, Inkyu   Hao, Zhao   Holman, Hoi-Ying N.   Pisano, Albert P.  

    We report a simple and effective method to develop long-term stable, top-down fabricated silicon nanowire (SiNW) pH sensors along with systematic studies on the performance of the sensors. In this work, we fabricated the SiNW pH sensors based on top-down fabrication processes. In order to improve the stability of the sensor performance, the sensors were coated with a passivation layer (PECVD-based silicon nitride) for effective electrical insulation and ion-blocking. The stability, pH sensitivity, and repeatability of the sensor response are critically analyzed with regard to the physics of sensing interface between sample liquid and the sensor surface. Also, trade-off between the stability and pH sensitivity of the sensor response is discussed.
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  • Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

    Probst, Alexander J.   Holman, Hoi-Ying N.   DeSantis, Todd Z.   Andersen, Gary L.   Birarda, Giovanni   Bechtel, Hans A.   Piceno, Yvette M.   Sonnleitner, Maria   Venkateswaran, Kasthuri  

    Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth's energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging. The ISME Journal (2013) 7, 635-651; doi:10.1038/ismej.2012.133; published online 22 November 2012
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  • Estimation of the Cellular Antioxidant Response to Chromium Action Using ESR Method

    Kartvelishvili, Tamar   Abuladze, Marina   Asatiani, Nino   Akhvlediani, Joseph   Kiziria, Eugene   Asanishvili, Lali   Lejava, Lia   Holman, Hoi-Ying N.   Sapojnikova, Nelly  

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  • Catalysis of PAH Biodegradation by Humic Acid Shown in Synchrotron Infrared Studies

    Holman, Hoi-Ying N.   Nieman, Karl   Sorensen, Darwin L.   Miller, Charles D.   Martin, Michael C.   Borch, Thomas   McKinney, Wayne R.   Sims, Ronald C.  

    The role of humic acid (HA) in the biodegradation of toxic polycyclic aromatic hydrocarbons (PAHs) has been the subject of controversy, particularly in unsaturated environments, By utilizing an infrared spectromicroscope and a very bright, nondestructive synchrotron photon source, we monitored in situ and, over time, the influence of HA on the progression of degradation of pyrene (a model PAH) by a bacterial colony on a magnetite surface. Our results indicate that HA dramatically shortens the onset time for PAH biodegradation from 168 to 2 h. In the absence of HA, it takes the bacteria about 168 h to produce sufficient glycolipids to solubilize pyrene and make it bioavailable for biodegradation. These results will have large implications for the bioremediation of contaminated soils.
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  • Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria

    Probst, Alexander J.   Elling, Felix J.   Castelle, Cindy J.   Zhu, Qingzeng   Elvert, Marcus   Birarda, Giovanni   Holman, Hoi-Ying N.   Lane, Katherine R.   Ladd, Bethany   Ryan, M. Cathryn   Woyke, Tanja   Hinrichs, Kai-Uwe   Banfield, Jillian F.  

    Sediment-hosted CO2-rich aquifers deep below the Colorado Plateau (USA) contain a remarkable diversity of uncultivated microorganisms, including Candidate Phyla Radiation (CPR) bacteria that are putative symbionts unable to synthesize membrane lipids. The origin of organic carbon in these ecosystems is unknown and the source of CPR membrane lipids remains elusive. We collected cells from deep groundwater brought to the surface by eruptions of Crystal Geyser, sequenced the community, and analyzed the whole community lipidome over time. Characteristic stable carbon isotopic compositions of microbial lipids suggest that bacterial and archaeal CO2 fixation ongoing in the deep subsurface provides organic carbon for the complex communities that reside there. Coupled lipidomic-metagenomic analysis indicates that CPR bacteria lack complete lipid biosynthesis pathways but still possess regular lipid membranes. These lipids may therefore originate from other community members, which also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes. Our findings provide new insights into the carbon cycle in the deep subsurface and suggest the redistribution of lipids into putative symbionts within this community.
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  • Real-Time Chemical Imaging of Bacterial Activity in Biofilms Using Open-Channel Microfluidics and Synchrotron FTIR Spectromicroscopy

    Holman, Hoi-Ying N.   Miles, Robin   Hao, Zhao   Wozei, Eleanor   Anderson, L. Meadow   Yang, Haw  

    Real-time chemical imaging of bacterial activities can facilitate a comprehensive understanding of the dynamics of biofilm structures and functions. Synchrotron-radiation-based Fourier transform infrared (SR-MR) spectromicroscopy can yield high spatial resolution and label-free vibrational signatures of chemical bonds in biomolecules, but the abundance of water in biofilms has hindered SR-FTIR's sensitivity in investigating bacterial activity. We developed a simple open-channel microfluidic system that can circumvent the water-absorption barrier for chemical imaging of the developmental dynamics of bacterial biofilms with a spatial resolution of several micrometers. This system maintains a 10 mu m thick laminar-flow-through biofilm system that minimizes both the imaging volume in liquid and the signal interference from geometry-induced fringing, Here we demonstrate the ability of the open-channel microfluidic platform to maintain the functionality of living cells while enabling high-quality SR-FTIR measurements. We include several applications that show how microbes in biofilms adapt to their immediate environments. The ability to directly monitor and map bacterial changes in biofilms can yield significant insight into a wide range of microbial systems, especially when coupled to more sophisticated microfluidic platforms.
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  • Synchrotron infrared spectromicroscopy as a novel bioanalytical microprobe for individual living cells: cytotoxicity considerations

    Holman, Hoi-Ying N.   Bjornstad, Kathleen A.   McNamara, Morgan P.   Martin, Michael C.   McKinney, Wayne R.   Blakely, Eleanor A.  

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  • Evaluation of Gastrointestinal Solubilization of Petroleum Hydrocarbon Residues in Soil Using an In Vitro Physiologically Based Model

    Holman, Hoi-Ying N.   Goth-Goldstein, Regine   Aston, David   Yun, Mao   Kengsoontra, Jenny  

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