CellMiner: a relational database and query tool for the NCI-60 cancer cell lines

<p>Abstract</p> <p>Background</p> <p>Advances in the high-throughput omic technologies have made it possible to profile cells in a large number of ways at the DNA, RNA, protein, chromosomal, functional, and pharmacological levels. A persistent problem is that some classes of molecular data are labeled with gene identifiers, others with transcript or protein identifiers, and still others with chromosomal locations. What has lagged behind is the ability to integrate the resulting data to uncover complex relationships and patterns. Those issues are reflected in full form by molecular profile data on the panel of 60 diverse human cancer cell lines (the NCI-60) used since 1990 by the U.S. National Cancer Institute to screen compounds for anticancer activity. To our knowledge, CellMiner is the first online database resource for integration of the diverse molecular types of NCI-60 and related meta data.</p> <p>Description</p> <p>CellMiner enables scientists to perform advanced querying of molecular information on NCI-60 (and additional types) through a single web interface. CellMiner is a freely available tool that organizes and stores raw and normalized data that represent multiple types of molecular characterizations at the DNA, RNA, protein, and pharmacological levels. Annotations for each project, along with associated metadata on the samples and datasets, are stored in a MySQL database and linked to the molecular profile data. Data can be queried and downloaded along with comprehensive information on experimental and analytic methods for each data set. A Data Intersection tool allows selection of a list of genes (proteins) in common between two or more data sets and outputs the data for those genes (proteins) in the respective sets. In addition to its role as an integrative resource for the NCI-60, the CellMiner package also serves as a shell for incorporation of molecular profile data on other cell or tissue sample types.</p> <p>Conclusion</p> <p>CellMiner is a relational database tool for storing, querying, integrating, and downloading molecular profile data on the NCI-60 and other cancer cell types. More broadly, it provides a template to use in providing such functionality for other molecular profile data generated by academic institutions, public projects, or the private sector. CellMiner is available online at <url>http://discover.nci.nih.gov/cellminer/</url>.</p

Consensus guidelines for the use and interpretation of angiogenesis assays

The formation of new blood vessels, or angiogenesis, is a complex process that plays important roles in growth and development, tissue and organ regeneration, as well as numerous pathological conditions. Angiogenesis undergoes multiple discrete steps that can be individually evaluated and quantified by a large number of bioassays. These independent assessments hold advantages but also have limitations. This article describes in vivo, ex vivo, and in vitro bioassays that are available for the evaluation of angiogenesis and highlights critical aspects that are relevant for their execution and proper interpretation. As such, this collaborative work is the first edition of consensus guidelines on angiogenesis bioassays to serve for current and future reference

Simulation of a Novel Renewable Energy Based Hybrid Power System

ABSTRACT: A combination of different energy generation systems based on renewable energies or mixed is known as Hybrid power system .Hybrid systems capture the best features of each energy resource and can provide &quot;grid-quality&quot;. Renewable energy sources are suitable option to supply electricity in fragmented areas or at certain distances from the grid. By choosing renewable energy the reduction of greenhouse gases and other pollutants can stabilize their CO2 emissions. This project describes dynamic modelling and simulation of a renewable energy based on hybrid power system. Modelling and simulations are carried out using Matlab/Simulink to verify the effectiveness of the proposed system. The results show that the proposed hybrid power system can tolerate the rapid changes in natural conditions and suppress the effects of these fluctuations on the voltage within acceptable range

Fluorescence and NMR studies of human seminal plasma prostatic inhibin: association of lifetimes with sterically constrained tryptophans

Human seminal plasma prostatic inhibin (HSPI) is one of the first seminal plasma proteins, which has been isolated, purified, and characterized. HSPI contains two tryptophans at positions 32 and 92 along its 94 amino acid primary sequence. Among the three fluorescence quenchers acrylamide (neutral), potassium iodide (anionic), and cesium chloride (cationic), potassium iodide is found to quench the tryptophan fluorescence more compared to the other two. The fluorescence decay of HSPI is biexponential with lifetimes 5.86 and 2.44 ns. The Stern-Volmer quenching curves in the case of fluorescence intensity and average lifetime are identical, indicating that the quenching mechanism is purely dynamic. The decay associated spectra of the two lifetimes show that the two tryptophans are solvent-exposed. The fluorescence quenching data is in favor of associating the two lifetimes to separate tryptophans. The fluorescence anisotropy decay of HSPI is single exponential with a correlation time of 9.2 ns, which is due to the rotation of entire protein. Absence of any fast component in the anisotropy decay indicates that the two tryptophans are in motionally restricted, rigid environments. In NMR studies, the cross-peak patterns observed in 2D-COSY and 2D-NOESY spectra of HSPI gave unambiguous evidence that each of the two tryptophans is sterically constrained and exists in a single rotamer population

Fluorescence and NMR Studies of Human Seminal Plasma Prostatic Inhibin: Association of Lifetimes with Sterically Constrained Tryptophans

Human seminal plasma prostatic inhibin (HSPI) is one of the first seminal plasma proteins, which has been isolated, purified, and characterized. HSPI contains two tryptophans at positions 32 and 92 along its 94 amino acid primary sequence. Among the three fluorescence quenchers acrylamide (neutral), potassium iodide (anionic), and cesium chloride (cationic), potassium iodide is found to quench the tryptophan fluorescence more compared to the other two. The fluorescence decay of HSPI is biexponential with lifetimes 5.86 and 2.44 ns. The Stern-Volmer quenching curves in the case of fluorescence intensity and average lifetime are identical, indicating that the quenching mechanism is purely dynamic. The decay associated spectra of the two lifetimes show that the two tryptophans are solvent-exposed. The fluorescence quenching data is in favor of associating the two lifetimes to separate tryptophans. The fluorescence anisotropy decay of HSPI is single exponential with a correlation time of 9.2 ns, which is due to the rotation of entire protein. Absence of any fast component in the anisotropy decay indicates that the two tryptophans are in motionally restricted, rigid environments. In NMR studies, the cross-peak patterns observed in 2D-COSY and 2D-NOESY spectra of HSPI gave unambiguous evidence that each of the two tryptophans is sterically constrained and exists in a single rotamer population. Human seminal plasma contains a variety of proteins secreted by seminal vesicles and the prostate. Human seminal plasma prostatic inhibin (HSPI) is one of first seminal plasma proteins that has been isolated, purified, and characterized. 1 It has 94 amino acids and has a molecular weight of 10.4 kDa. HSPI has been the subject of interest for more than a decade. Its biological activity ranges from preventing pregnancy to curing prostate cancer. Inhibin prevents pregnancy in mammals by modulating the level of circulating follicle stimulating hormones (FSH). 2 It suppresses prolactin, a hormone that promotes lactation. 3 Therefore, neutralizing inhibin through active immunization leads to increase in milk production. Seidah et al. have reported the primary sequence of HSPI. Materials and Methods Sample Preparation. HSPI has been isolated from the semen samples of healthy men obtained at infertility clinics and purified following the well-established procedure described elsewhere. Other chemicals used in this study were acrylamide (Sisco Research Laboratories Co., India), KI (potassium iodide, Qualigens Fine Chemicals Co., India), CsCl (cesium chloride, Spectrochem Pvt. Ltd., India), sodium thiosulfate (Na 2 S 2 O 3 , Qualigens Fine Chemicals Co., India), sodium acetate (Qualigens Fine Chemicals Co.), tryptophan (Sigma Chemical Co., United States), and NATA (N-acetyl tryptophanamide, Sigm

Assessment of Post-harvest Losses of Major Vegetables in Rangareddy District of Telangana

Objective: Keeping in view the non-availability of systematic studies on post-harvest loss in Telangana, the current study was undertaken to assess the extent of post-harvest losses in major vegetables viz., tomato and brinjal and to identify the factors affecting post-harvest losses at farm level. Methods: Tabular analysis was used to calculate the post-harvest losses, the data was summarized using statistical tools such as average and percentage and multiple linear regression analysis was carried out to examine the factors affecting post-harvest losses at farm level. The present study was conducted in Rangareddy district which is the leading vegetable growing district in Telangana with a sample of 30 farmers,6 wholesalers and 6 retailers for each crop. Findings: The overall post-harvest loss in tomato and brinjal was 28.51 and 23.27 kg per quintal respectively and maximum losses was occurring at farm level for both crops. Functional analysis revealed that the factors such as age, education, extent of crop production and labour dummy (where family contribution is &gt;50% in total labour demand ‘1’, else ‘0’) was significant in both crops studied. Timely plant protection measures in case of brinjal also significantly reduced the post-harvest losses. On an average, the per quintal monetary loss was relatively more for brinjal (Rs.239.6/q) than tomato (Rs.236.6/q). The total monetary loss at state level was Rs.251.6 crores for the study crops. Conclusion: It is evident from the results that losses are occurring in the value chain due to poor infrastructure and lack of post-harvest management techniques. Proper training on pest management and policies ensuring labour availability during peak harvesting period can aid in reducing the losses

Ceric (IV) ammonium nitrate: a novel reagent for the synthesis of homoallyl alcohols

A rapid and highly efficient method has been developed for the allylation of aldehydes with allyltributylstannane using a catalytic amount of ceric ammonium nitrate in acetonitrile under mild and neutral conditions to afford the corresponding homoallyl alcohols in excellent yields with high chemoselectivity. Allylation of ketones has also been achieved with tetraallytin under similar reaction conditions

Systematic review of agents for the management of gastrointestinal mucositis in cancer patients

<p>The aim of this study was to review the available literature and define clinical practice guidelines for the use of agents for the prevention and treatment of gastrointestinal mucositis.</p><p>A systematic review was conducted by the Mucositis Study Group of the Multinational Association of Supportive Care in Cancer/International Society of Oral Oncology (MASCC/ISOO). The body of evidence for each intervention, in each cancer treatment setting, was assigned an evidence level. Based on the evidence level, one of the following three guideline determinations was possible: recommendation, suggestion, and no guideline possible.</p><p>A total of 251 clinical studies across 29 interventions were examined. Panel members were able to make one new evidence-based negative recommendation; two new evidence-based suggestions, and one evidence-based change from previous guidelines. Firstly, the panel recommends against the use of misoprostol suppositories for the prevention of acute radiation-induced proctitis. Secondly, the panel suggests probiotic treatment containing Lactobacillus spp., may be beneficial for prevention of chemotherapy and radiotherapy-induced diarrhea in patients with malignancies of the pelvic region. Thirdly, the panel suggests the use of hyperbaric oxygen as an effective means in treating radiation-induced proctitis. Finally, new evidence has emerged which is in conflict with our previous guideline surrounding the use of systemic glutamine, meaning that the panel is unable to form a guideline. No guideline was possible for any other agent, due to inadequate and/or conflicting evidence.</p><p>This updated review of the literature has allowed new recommendations and suggestions for clinical practice to be reached. This highlights the importance of regular updates.</p>