42 research outputs found
Isolation of bacterial extrachromosomal DNA from human dental plaque associated with periodontal disease,using transposonaided capture (TRACA)
The human oral cavity is host to a complex microbial community estimated to comprise > 700 bacterial species, of which at least half are thought to be not yet cultivable in vitro. To investigate the plasmids present in this community, we used a transposon-aided capture system, which allowed the isolation of plasmids from human oral supra- and subgingival plaque samples. Thirty-two novel plasmids and a circular molecule that could be an integrase-generated circular intermediate were isolated
The higher level of organization of the oxidative phosphorylation system: mitochondrial supercomplexes
The organization of the oxidative phosphorylation (OXPHOS) system within the inner mitochondrial membrane appears to be far more complicated than previously thought. In particular, the individual protein complexes of the OXPHOS system (complexes I to V) were found to specifically interact forming defined supramolecular structures. Blue-native polyacrylamide gel electrophoresis and single particle electron microscopy proved to be especially valuable in studying the so-called ârespiratory supercomplexesâ? Based on these procedures, increasing evidence was presented supporting a âsolid stateâ organization of the OXPHOS system. Here, we summarize results on the formation, organisation and function of the various types of mitochondrial OXPHOS supercomplexes
Star Formation in Ram Pressure Stripped Tails
We investigate the impact of star formation and feedback on ram pressure
stripping using high-resolution adaptive mesh simulations, building on a
previous series of papers that systematically investigated stripping using a
realistic model for the interstellar medium, but without star formation. We
find that star formation does not significantly affect the rate at which
stripping occurs, and only has a slight impact on the density and temperature
distribution of the stripped gas, indicating that our previous (gas-only)
results are unaffected. For our chosen (moderate) ram pressure strength,
stripping acts to truncate star formation in the disk over a few hundred
million years, and does not lead to a burst of star formation. Star formation
in the bulge is slightly enhanced, but the resulting change in the
bulge-to-disk ratio is insignificant. We find that stars do form in the tail,
primarily from gas that is ablated from the disk and the cools and condenses in
the turbulent wake. The star formation rate in the tail is low, and any
contribution to the intracluster light is likely to be very small. We argue
that star formation in the tail depends primarily on the pressure in the
intracluster medium, rather than the ram pressure strength. Finally, we compare
to observations of star formation in stripped tails, finding that many of the
discrepancies between our simulation and observed wakes can be accounted for by
different intracluster medium pressures.Comment: 18 pages, 14 figures, accepted to MNRA
Oxidative stress in children late after Kawasaki disease: relationship with carotid atherosclerosis and stiffness
Background: Persistent arterial dysfunction in patients with a history of Kawasaki disease (KD) and an integral role of oxidative stress in the development of cardiovascular disease are increasingly recognized. We sought to test the hypothesis that oxidative stress is increased in KD patients and related to carotid atherosclerotic changes and stiffness. Methods: We compared the serum levels of oxidative stress biomarkers, carotid intima-media thickness (IMT), and carotid stiffness index among KD patients with coronary aneurysms (n = 32), those without coronary complications (n = 19), and controls (n = 32). Results: Compared with controls, patients with coronary aneurysms had significantly higher serum levels of malonaldehyde (2.62 ± 0.12 ÎŒM vs 2.22 ± 0.07 ÎŒM, p = 0.014) and hydroperoxides (26.50 ± 1.13 ÎŒM vs 22.50 ± 0.62 ÎŒM, p = 0.008). A linear trend of the magnitude of oxidative stress in relation to inflammatory damage was observed for malonaldehyde (p = 0.018) and hydroperoxides (p = 0.014) levels. Serum malonaldehyde and hydroperoxide levels correlated positively with carotid IMT (p < 0.001 and p = 0.034, respectively) and stiffness index (p = 0.001 and p = 0.021, respectively). Multiple linear regression analysis identified serum malonaldehyde level as a significant determinant of carotid IMT (ÎČ = 0.31, p = 0.006) and stiffness (ÎČ = 0.27, p = 0.008). Conclusion: Our findings suggestoxidative stress is increased in KD patients with coronary aneurysms and is associated with carotid intima-media thickening and stiffening. © 2008 Cheung et al; licensee BioMed Central Ltd.published_or_final_versio
NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods
Glycosylation is a topic of intense current interest in the
development of biopharmaceuticals because it is related
to drug safety and efficacy. This work describes results of
an interlaboratory study on the glycosylation of the Primary
Sample (PS) of NISTmAb, a monoclonal antibody
reference material. Seventy-six laboratories from industry,
university, research, government, and hospital sectors
in Europe, North America, Asia, and Australia submit-
Avenue, Silver Spring, Maryland 20993; 22Glycoscience Research Laboratory, Genos, Borongajska cesta 83h, 10 000 Zagreb, Croatia;
23Faculty of Pharmacy and Biochemistry, University of Zagreb, A. KovacË icÂŽ a 1, 10 000 Zagreb, Croatia; 24Department of Chemistry, Georgia
State University, 100 Piedmont Avenue, Atlanta, Georgia 30303; 25glyXera GmbH, Brenneckestrasse 20 * ZENIT / 39120 Magdeburg, Germany;
26Health Products and Foods Branch, Health Canada, AL 2201E, 251 Sir Frederick Banting Driveway, Ottawa, Ontario, K1A 0K9 Canada;
27Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama Higashi-Hiroshima 739â8530 Japan; 28ImmunoGen,
830 Winter Street, Waltham, Massachusetts 02451; 29Department of Medical Physiology, Jagiellonian University Medical College,
ul. Michalowskiego 12, 31â126 Krakow, Poland; 30Department of Pathology, Johns Hopkins University, 400 N. Broadway Street Baltimore,
Maryland 21287; 31Mass Spec Core Facility, KBI Biopharma, 1101 Hamlin Road Durham, North Carolina 27704; 32Division of Mass
Spectrometry, Korea Basic Science Institute, 162 YeonGuDanji-Ro, Ochang-eup, Cheongwon-gu, Cheongju Chungbuk, 363â883 Korea
(South); 33Advanced Therapy Products Research Division, Korea National Institute of Food and Drug Safety, 187 Osongsaengmyeong 2-ro
Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, 363â700, Korea (South); 34Center for Proteomics and Metabolomics, Leiden
University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands; 35Ludger Limited, Culham Science Centre, Abingdon,
Oxfordshire, OX14 3EB, United Kingdom; 36Biomolecular Discovery and Design Research Centre and ARC Centre of Excellence for Nanoscale
BioPhotonics (CNBP), Macquarie University, North Ryde, Australia; 37Proteomics, Central European Institute for Technology, Masaryk
University, Kamenice 5, A26, 625 00 BRNO, Czech Republic; 38Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse
1, 39106 Magdeburg, Germany; 39Department of Biomolecular Sciences, Max Planck Institute of Colloids and Interfaces, 14424
Potsdam, Germany; 40AstraZeneca, Granta Park, Cambridgeshire, CB21 6GH United Kingdom; 41Merck, 2015 Galloping Hill Rd, Kenilworth,
New Jersey 07033; 42Analytical R&D, MilliporeSigma, 2909 Laclede Ave. St. Louis, Missouri 63103; 43MS Bioworks, LLC, 3950 Varsity Drive
Ann Arbor, Michigan 48108; 44MSD, Molenstraat 110, 5342 CC Oss, The Netherlands; 45Exploratory Research Center on Life and Living
Systems (ExCELLS), National Institutes of Natural Sciences, 5â1 Higashiyama, Myodaiji, Okazaki 444â8787 Japan; 46Graduate School of
Pharmaceutical Sciences, Nagoya City University, 3â1 Tanabe-dori, Mizuhoku, Nagoya 467â8603 Japan; 47Medical & Biological Laboratories
Co., Ltd, 2-22-8 Chikusa, Chikusa-ku, Nagoya 464â0858 Japan; 48National Institute for Biological Standards and Control, Blanche Lane, South
Mimms, Potters Bar, Hertfordshire EN6 3QG United Kingdom; 49Division of Biological Chemistry & Biologicals, National Institute of Health
Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158â8501 Japan; 50New England Biolabs, Inc., 240 County Road, Ipswich, Massachusetts
01938; 51New York University, 100 Washington Square East New York City, New York 10003; 52Target Discovery Institute, Nuffield Department
of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom; 53GlycoScience Group, The National Institute for
Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland; 54Department of Chemistry, North
Carolina State University, 2620 Yarborough Drive Raleigh, North Carolina 27695; 55Pantheon, 201 College Road East Princeton, New Jersey
08540; 56Pfizer Inc., 1 Burtt Road Andover, Massachusetts 01810; 57Proteodynamics, ZI La Varenne 20â22 rue Henri et Gilberte Goudier 63200
RIOM, France; 58ProZyme, Inc., 3832 Bay Center Place Hayward, California 94545; 59Koichi Tanaka Mass Spectrometry Research Laboratory,
Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho Nakagyo-ku, Kyoto, 604 8511 Japan; 60Childrenâs GMP LLC, St. Jude Childrenâs
Research Hospital, 262 Danny Thomas Place Memphis, Tennessee 38105; 61Sumitomo Bakelite Co., Ltd., 1â5 Muromati 1-Chome, Nishiku,
Kobe, 651â2241 Japan; 62Synthon Biopharmaceuticals, Microweg 22 P.O. Box 7071, 6503 GN Nijmegen, The Netherlands; 63Takeda
Pharmaceuticals International Co., 40 Landsdowne Street Cambridge, Massachusetts 02139; 64Department of Chemistry and Biochemistry,
Texas Tech University, 2500 Broadway, Lubbock, Texas 79409; 65Thermo Fisher Scientific, 1214 Oakmead Parkway Sunnyvale, California
94085; 66United States Pharmacopeia India Pvt. Ltd. IKP Knowledge Park, Genome Valley, Shamirpet, Turkapally Village, Medchal District,
Hyderabad 500 101 Telangana, India; 67Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta T6G 2G2 Canada; 68Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2 Canada; 69Department of Chemistry, University of California, One Shields Ave,
Davis, California 95616; 70HorvaÂŽ th Csaba Memorial Laboratory for Bioseparation Sciences, Research Center for Molecular Medicine, Doctoral
School of Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Egyetem ter 1, Hungary; 71Translational Glycomics
Research Group, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprem, Egyetem ut 10, Hungary;
72Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way Newark, Delaware 19711; 73Proteomics Core Facility, University
of Gothenburg, Medicinaregatan 1G SE 41390 Gothenburg, Sweden; 74Department of Medical Biochemistry and Cell Biology, University of
Gothenburg, Institute of Biomedicine, Sahlgrenska Academy, Medicinaregatan 9A, Box 440, 405 30, Gothenburg, Sweden; 75Department of
Clinical Chemistry and Transfusion Medicine, Sahlgrenska Academy at the University of Gothenburg, Bruna Straket 16, 41345 Gothenburg,
Sweden; 76Department of Chemistry, University of Hamburg, Martin Luther King Pl. 6 20146 Hamburg, Germany; 77Department of Chemistry,
University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba, Canada R3T 2N2; 78Laboratory of Mass Spectrometry of Interactions and
Systems, University of Strasbourg, UMR Unistra-CNRS 7140, France; 79Natural and Medical Sciences Institute, University of Tuš bingen,
Markwiesenstrae 55, 72770 Reutlingen, Germany; 80Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; 81Division of Bioanalytical Chemistry, Amsterdam Institute for
Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, de Boelelaan 1085, 1081 HV Amsterdam, The Netherlands; 82Department
of Chemistry, Waters Corporation, 34 Maple Street Milford, Massachusetts 01757; 83Zoetis, 333 Portage St. Kalamazoo, Michigan 49007
Authorâs ChoiceâFinal version open access under the terms of the Creative Commons CC-BY license.
Received July 24, 2019, and in revised form, August 26, 2019
Published, MCP Papers in Press, October 7, 2019, DOI 10.1074/mcp.RA119.001677
ER: NISTmAb Glycosylation Interlaboratory Study
12 Molecular & Cellular Proteomics 19.1
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ted a total of 103 reports on glycan distributions. The
principal objective of this study was to report and compare
results for the full range of analytical methods presently
used in the glycosylation analysis of mAbs. Therefore,
participation was unrestricted, with laboratories
choosing their own measurement techniques. Protein glycosylation
was determined in various ways, including at
the level of intact mAb, protein fragments, glycopeptides,
or released glycans, using a wide variety of methods for
derivatization, separation, identification, and quantification.
Consequently, the diversity of results was enormous,
with the number of glycan compositions identified by
each laboratory ranging from 4 to 48. In total, one hundred
sixteen glycan compositions were reported, of which 57
compositions could be assigned consensus abundance
values. These consensus medians provide communityderived
values for NISTmAb PS. Agreement with the consensus
medians did not depend on the specific method or
laboratory type. The study provides a view of the current
state-of-the-art for biologic glycosylation measurement
and suggests a clear need for harmonization of glycosylation
analysis methods. Molecular & Cellular Proteomics
19: 11â30, 2020. DOI: 10.1074/mcp.RA119.001677.L
Sex and strategy use matters for pattern separation, adult neurogenesis and immediate early gene expression in the hippocampus
Adult neurogenesis in the dentate gyrus (DG) plays a crucial role for pattern separation and there are sex differences in the regulation of neurogenesis. Although sex differences, favoring males, in spatial navigation have been reported, it is not known whether there are sex differences in pattern separation. The current study was designed to determine whether there are sex differences in the ability for separating similar or distinct patterns, learning strategy choice, adult neurogenesis and immediate early gene (IEG) expression in the DG in response to pattern separation training. Male and female Sprague-Dawley rats received a single injection of the DNA synthesis marker, bromodeoxyuridine (BrdU) and were tested for the ability of separating spatial patterns in a spatial pattern separation version of delayed nonmatching to place task using the 8-arm radial arm maze. Twenty eight days following BrdU injection, rats received a probe trial to determine whether they were idiothetic or spatial strategy users. We found that male spatial strategy users outperformed female spatial strategy users only when separating similar, but not distinct, patterns. Furthermore male spatial strategy users had greater neurogenesis in response to pattern separation training than all other groups. Interestingly neurogenesis was positively correlated with performance on similar pattern trials during pattern separation in female spatial strategy users but negatively correlated with performance in male idiothetic strategy users. These results suggest that the survival of new neurons may play an important positive role for pattern separation of similar patterns in females. Furthermore, we found sex and strategy differences in IEG expression in the CA1 and CA3 regions in response to pattern separation. These findings emphasize the importance of studying biological sex on hippocampal function and neural plasticity.Arts, Faculty ofOther UBCPsychology, Department ofReviewedFacult
Optimal energy for cell radiosensitivity enhancement by gold nanoparticles using synchrotron-based monoenergetic photon beams
Automated Area Calculation of Histopathologic Features Using SIVQ
Recently, with the advent of the 7th edition of the AJCC Cancer Staging manual, at least one set of criteria (e.g. breast) were modified to now require the measurement of maximal depth of stromal invasion. With the current manual interpretive morphological approaches typically employed by surgical pathologists to assess tumor extent, the specialty now potentially has stumbled upon a crossroads of practice, where the diagnostic criteria have exceeded the capabilities of our commonly available tools. While whole slide imaging (WSI) technology holds the potential to offer many improvements in clinical workflow over conventional slide microscopy including unambiguous utility for facilitating quantitative diagnostic tasks with one important example being the determination of both linear dimension and surface area. However, the availability of histology data in digital form is of little utility if time-consuming and cumbersome manual workflow steps are necessarily imposed upon the pathologist in order to generate such measurements, especially as encountered with the complex and ill-defined shapes inherent to infiltrative tumors. In this communication, we demonstrate the utility of the recently described SIVQ algorithm to serve as the basis of a highly accurate, precise and semi-automated tool for direct surface area measurement of tumor infiltration from WSI data sets. By anticipating the current trend in cancer staging that emphasizes increasingly precise feature characterization, as witnessed by the recent publication of AJCC's 7th edition of the Cancer Staging Manual, this tool holds promise to will be of value to pathologists for clinical utility