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61.
Ursula Pieper Narayanan Eswar Ashley C. Stuart Valentin A. Ilyin Andrej Sali 《Nucleic acids research》2002,30(1):255-259
MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAST, IMPALA and MODELLER. MODBASE uses the MySQL relational database management system for flexible and efficient querying, and the MODVIEW Netscape plugin for viewing and manipulating multiple sequences and structures. It is updated regularly to reflect the growth of the protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different datasets. The largest dataset contains models for domains in 304 517 out of 539 171 unique protein sequences in the complete TrEMBL database (23 March 2001); only models based on significant alignments (PSI-BLAST E-value < 10–4) and models assessed to have the correct fold are included. Other datasets include models for target selection and structure-based annotation by the New York Structural Genomics Research Consortium, models for prediction of genes in the Drosophila melanogaster genome, models for structure determination of several ribosomal particles and models calculated by the MODWEB comparative modeling web server. 相似文献
62.
63.
M. E. W. Hemels E. S. Hoendermis J. P. van Melle P. G. Pieper 《Netherlands heart journal》2011,19(3):107-111
In patients with unexplained hypertension, especially in combination with a cardiac murmur, the presence of an aortic coarctation should always be ruled out given the high morbidity and mortality. However, particularly patients with an isolated coarctation often remain asymptomatic for years and the defect may be unnoticed even until the fifth or sixth decade of life. In the present article, we describe two patients with late detected coarctation to illustrate the clinical consequences, diagnostic clues for earlier detection and current therapeutic options to achieve optimal treatment. The key sign of an aortic coarctation, a difference in arterial blood pressure measured between the upper and lower extremities, should always be examined, followed by echocardiography. We conclude that even in case of a late detected severe coarctation, surgical or percutaneous repair has proven to be feasible and substantially effective, improving quality of life and lowering the risk of further hypertension-associated problems. 相似文献
64.
Min-Kyoo Shin Edwin Vázquez-Rosa Yeojung Koh Matasha Dhar Kalyani Chaubey Coral J. Cintrón-Pérez Sarah Barker Emiko Miller Kathryn Franke Maria F. Noterman Divya Seth Rachael S. Allen Cara T. Motz Sriganesh Ramachandra Rao Lara A. Skelton Machelle T. Pardue Steven J. Fliesler Chao Wang Andrew A. Pieper 《Cell》2021,184(10):2715-2732.e23
65.
66.
Three aquatic ecosystems in South Africa, the Hartbeespoort, Klipvoor and Bospoort Dams, are classified as hyper-eutrophic, because of high nutrient loads and chemical pollution. Water and two fish species, Clarias gariepinus and Cyprinus carpio, were collected from these dams to assess the impact of eutrophication and chemical pollutants on their health status. Water and muscle samples were analysed for organic and inorganic chemicals. Condition factor was determined and a necropsy performed to note any macroscopic abnormalities. A histology-based fish health assessment was done on the liver, kidney, gills and gonads. A number of fish from the three dams exhibited livers with fatty change and focal discoloration, skin lesions and parasites within the visceral cavity. The prevalence and severity of histopathology in the liver resulted in higher liver index values than the index values for kidneys and gills. Aluminium, silicon and chromium were detected in the water and muscle tissue. The DDT metabolite p,p’-DDE was present in both species, as well as in fish from the reference site, Marico-Bosveld Dam. Only C. gariepinus from Hartbeespoort Dam had p,p’-DDD levels higher than 5 µg g?1 per edible portion. Water from hyper-eutrophic dams adversely affects the health of freshwater fish. 相似文献
67.
M. Megharaj R.-M. Wittich R. Blasco D. H. Pieper K. N. Timmis 《Applied microbiology and biotechnology》1997,48(1):109-114
The dibenzo-p-dioxin(DD)- and dibenzofuran(DF)-degrading bacterium, Sphingomonas sp. strain RW1, was tagged by insertion of a mini-Tn5 lacZ transposon in order to follow its fate in complex laboratory soil systems. The tagged strain was tested for its ability to
survive in soil and degrade DF and DD applied at a concentration of 1 mg/g. Bacteria pre-adapted to soil conditions were found
to survive better in DF- and DD-amended soil and degrade the substrate more efficiently than bacteria that had not been subjected
to pre-adaptation. The concentration of soil-applied DF and DD, individually and in combination, decreased to less than 2%
of the original concentrations within 3 weeks of addition of the RW1 derivative, accompanied by a short, but significant exponential
increase in RW1 viable cells. During the same period the native bacterial population in soil was stable while viable fungi
declined.
Received: 12 November 1996 / Received revision: 21 February 1997 / Accepted: 22 February 1997 相似文献
68.
Milica D olovi GM Jankovi RB olovi Vesna M Martinovi-emeriki 《Cancer immunology, immunotherapy : CII》1998,15(4):286-288
A case of primary nonsecretory plasmacytoma of the spleen is reported. On laparotomy and splenectomy a 920 g spleen was removed,
measuring 16×14×6 cm. The cut surface of the entire spleen showed that the tumour occupied most of the splenic tissue. A bone
marrow aspirate and trephine, skeletal survey showed no signs of myeloma. Biopsy of the liver and regional lymph nodes was
normal. Immunocytochemistry of the splenic tumour showed positivity for pan-B and plasma cell markers. After splenectomy the
patient was treated with chemotherapy according to protocol VBCMP (M2). 相似文献
69.
Automation of PRM‐dependent D3‐Leu tracer enrichment in HDL to study the metabolism of apoA‐I,LCAT and other apolipoproteins 下载免费PDF全文
Lang Ho Lee Allison B. Andraski Brett Pieper Hideyuki Higashi Frank M. Sacks Masanori Aikawa Sasha A. Singh 《Proteomics》2017,17(1-2)
We developed an automated quantification workflow for PRM‐enabled detection of D3‐Leu labeled apoA‐I in high‐density lipoprotein (HDL) isolated from humans. Subjects received a bolus injection of D3‐Leu and blood was drawn at eight time points over three days. HDL was isolated and separated into six size fractions for subsequent proteolysis and PRM analysis for the detection of D3‐Leu signal from ~0.03 to 0.6% enrichment. We implemented an intensity‐based quantification approach that takes advantage of high‐resolution/accurate mass PRM scans to identify the D3‐Leu 2HM3 ion from non‐specific peaks. Our workflow includes five modules for extracting the targeted PRM peak intensities (XPIs): Peak centroiding, noise removal, fragment ion matching using Δm/z windows, nine intensity quantification options, and validation and visualization outputs. We optimized the XPI workflow using in vitro synthesized and clinical samples of D0/D3‐Leu labeled apoA‐I. Three subjects’ apoA‐I enrichment curves in six HDL size fractions, and LCAT, apoA‐II and apoE from two size fractions were generated within a few hours. Our PRM strategy and automated quantification workflow will expedite the turnaround of HDL apoA‐I metabolism data in clinical studies that aim to understand and treat the mechanisms behind dyslipidemia. 相似文献
70.
Nadja Kabelitz Jirina Machackova Gwenaël Imfeld Maria Brennerova Dietmar H. Pieper Hermann J. Heipieper Howard Junca 《Applied microbiology and biotechnology》2009,82(3):565-577
In order to obtain insights in complexity shifts taking place in natural microbial communities under strong selective pressure,
soils from a former air force base in the Czech Republic, highly contaminated with jet fuel and at different stages of a bioremediation
air sparging treatment, were analyzed. By tracking phospholipid fatty acids and 16S rRNA genes, a detailed monitoring of the
changes in quantities and composition of the microbial communities developed at different stages of the bioventing treatment
progress was performed. Depending on the length of the air sparging treatment that led to a significant reduction in the contamination
level, we observed a clear shift in the soil microbial community being dominated by Pseudomonads under the harsh conditions
of high aromatic contamination to a status of low aromatic concentrations, increased biomass content, and a complex composition
with diverse bacterial taxonomical branches.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
The online version of an erratum to this article can be found at http://dx.doi.org/.
An erratum to this article can be found at 相似文献