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Meeting Review: Bioinformatics and Medicine – From Molecules to Humans, Virtual and Real
Roslin Russell
Comparative and Functional Genomics , 2002, DOI: 10.1002/cfg.178
Abstract: The Industrialization Workshop Series aims to promote and discuss integration, automation, simulation, quality, availability and standards in the high-throughput life sciences. The main issues addressed being the transformation of bioinformatics and bioinformaticsbased drug design into a robust discipline in industry, the government, research institutes and academia. The latest workshop emphasized the influence of the post-genomic era on medicine and healthcare with reference to advanced biological systems modeling and simulation, protein structure research, protein-protein interactions, metabolism and physiology. Speakers included Michael Ashburner, Kenneth Buetow, Francois Cambien, Cyrus Chothia, Jean Garnier, Francois Iris, Matthias Mann, Maya Natarajan, Peter Murray-Rust, Richard Mushlin, Barry Robson, David Rubin, Kosta Steliou, John Todd, Janet Thornton, Pim van der Eijk, Michael Vieth and Richard Ward.
SimArray: a user-friendly and user-configurable microarray design tool
Richard P Auburn, Roslin R Russell, Bettina Fischer, Lisa A Meadows, Santiago Sevillano Matilla, Steven Russell
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-102
Abstract: We have developed a user-friendly tool, SimArray, which generates a randomised spot layout, computes a maximum meta-grid area, and estimates the print time, in response to user-specified design decisions. Selected parameters include: the number of probes to be printed; the microtitre plate format; the printing pin configuration, and the achievable spot density. SimArray is compatible with all current robotic spotters that employ 96-, 384- or 1536-well microtitre plates, and can be configured to reflect most production environments. Print time and maximum meta-grid area estimates facilitate evaluation of each array design for its suitability. Randomisation of the spot layout facilitates correction of systematic biases by normalisation.SimArray is intended to help both established researchers and those new to the microarray field to develop microarray designs with randomised spot layouts that are compatible with their specific production environment. SimArray is an open-source program and is available from http://www.flychip.org.uk/SimArray/ webcite.The full utility of the spotted microarray format is clearly reflected in the range of its applications. Transcriptome arrays, containing cDNA, gDNA, or oligonucleotide probes, are used to measure differential gene expression [1-5]. Whole-genome arrays, typically composed of tiled gDNA or oligonucleotides [6], have been used to identify in vivo sites of protein-DNA interactions [7,8] or allelic variation [9,10]. Whilst these applications dominate, other formats, for example antibody arrays, facilitate analysis of protein and small-molecule analytes [11,12]. Thus, spotted microarrays enable high-throughput, cost-effective, and large-scale analysis of molecular interactions.Robotic spotters deposit probes as an ordered array by repetition of a simple multi-step procedure [13-15]. First, the print tool is positioned over the first batch of probes to be printed, arranged in 96-, 384- or 1536-well microtitre plates. Second, the
Saliva samples are a viable alternative to blood samples as a source of DNA for high throughput genotyping
Jean E Abraham, Mel J Maranian, Inmaculada Spiteri, Roslin Russell, Susan Ingle, Craig Luccarini, Helena M Earl, Paul DP Pharoah, Alison M Dunning, Carlos Caldas
BMC Medical Genomics , 2012, DOI: 10.1186/1755-8794-5-19
Abstract: Patients were recruited from the Pharmacogenetics of Breast Cancer Chemotherapy (PGSNPS) study. Paired blood and saliva samples were collected from 79 study participants. The Oragene DNA Self-Collection kit (DNAgenotek?) was used to collect and extract DNA from saliva. DNA from EDTA blood samples (median volume 8 ml) was extracted by Gen-Probe, Livingstone, UK. DNA yields, standard measures of DNA quality, genotype call rates and genotype concordance between paired, duplicated samples were assessed.Total DNA yields were lower from saliva (mean 24 μg, range 0.2–52 μg) than from blood (mean 210 μg, range 58–577 μg) and a 2-fold difference remained after adjusting for the volume of biological material collected. Protein contamination and DNA fragmentation measures were greater in saliva DNA. 78/79 saliva samples yielded sufficient DNA for use on Illumina Beadchip arrays and using Taqman assays. Four samples were randomly selected for genotyping in duplicate on the Illumina Beadchip arrays. All samples were genotyped using Taqman assays. DNA quality, as assessed by genotype call rates and genotype concordance between matched pairs of DNA was high (>97%) for each measure in both blood and saliva-derived DNA.We conclude that DNA from saliva and blood samples is comparable when genotyping using either Taqman assays or genome-wide chip arrays. Saliva sampling has the potential to increase participant recruitment within clinical trials, as well as reducing the resources and organisation required for multicentre sample collection.
Terpenoids as potential chemopreventive and therapeutic agents in liver cancer
Roslin J Thoppil,Anupam Bishayee
World Journal of Hepatology , 2011, DOI: 10.4254/wjh.v3.i9.228
Abstract: Despite significant advances in medicine, liver cancer, predominantly hepatocellular carcinoma remains a major cause of death in the United States as well as the rest of the world. As limited treatment options are currently available to patients with liver cancer, novel preventive control and effective therapeutic approaches are considered to be reasonable and decisive measures to combat this disease. Several naturally occurring dietary and non-dietary phytochemicals have shown enormous potential in the prevention and treatment of several cancers, especially those of the gastrointestinal tract. Terpenoids, the largest group of phytochemicals, traditionally used for medicinal purposes in India and China, are currently being explored as anticancer agents in clinical trials. Terpenoids (also called “isoprenoids”) are secondary metabolites occurring in most organisms, particularly plants. More than 40 000 individual terpenoids are known to exist in nature with new compounds being discovered every year. A large number of terpenoids exhibit cytotoxicity against a variety of tumor cells and cancer preventive as well as anticancer efficacy in preclinical animal models. This review critically examines the potential role of naturally occurring terpenoids, from diverse origins, in the chemoprevention and treatment of liver tumors. Both in vitro and in vivo effects of these agents and related cellular and molecular mechanisms are highlighted. Potential challenges and future directions involved in the advancement of these promising natural compounds in the chemoprevention and therapy of human liver cancer are also discussed.
Isolation and characterization of an antimicrobial compound from the traditional medicinal plant Pittosporum tetraspermum Wight & Arn.
International Journal of Medicinal and Aromatic Plants , 2012,
Abstract: Pittosporum tetraspermum Wight & Arn. belongs to the family Pittosporaceae of the order Polygalineae. It is used for treating chronic bronchitis and as an antidote for snake poisoning. The root bark is a remedy for rheumatic swelling. The bioactive principle present in the leaves of Pittosporum tetraspermum was isolated and characterized in the present study. Repeated extraction of powdered leaves of Pittosporum tetraspermum with petroleum ether resulted in defatted leaves, which was further extracted with methanol to yield crude methanol extract. The n-butanol fraction of methanol extract was passed through celite and obtained a mixture of crude saponins. The crude saponin mixture upon separation through silica gel column chromatography yielded 9 fractions. The structure of the bioactive fraction IX was determined by analyzing the peaks in IR, 1H NMR, 13C NMR, and ESI Mass Spectra. Fraction IX showed the highest zone of inhibition against fungal growth (13.3 mm in diameter) and it was higher than the zone of inhibition of the reference drug Nystatin. The IR spectrum of the bioactive fraction IX showed a broad signal at 3413 cm-1 due to the symmetrical stretching of –OH group in the molecule. The bioactive component responsible for the biological activity of Pittosporum tetraspermum is identified as trihydroxyoleanolic acid glycoside, whose aglycone part is characterized as trihydroxyoleanolic acid and the glycone part as sugars glucose and glucuronic acid.
S.Emalda Roslin,C.Gomathy
International Journal of Ad Hoc, Sensor & Ubiquitous Computing , 2011,
Abstract: Recent years showed a wide range of applications in Wireless Sensor Networks (WSN). For a WSN,Topology Control is crucial to obtain an energy efficient network without affecting the connectivity andother properties. In this paper the sequence of strategies carried out to obtain a better scheme for atopology control in terms of energy is discussed. An quantitative study is also done on the impact of N-tiersin the performance of the various proposed algorithms. Comparison on one tier , two tier and three tierarchitecture using the proposed methodology is also made. The results showed the effectiveness of thedifferent approaches proposed. The future works discussed also gives a wider vision on the probabilities ofthe various schemas for the forthcoming years.
The Equation of the Universe (According to the Theory of Relation)  [PDF]
Russell Bagdoo
Journal of Modern Physics (JMP) , 2019, DOI: 10.4236/jmp.2019.103022
Abstract: A new equation is found in which the concept of matter-space-time is mathematically connected; gravitation and electromagnetism are also bound by space-time. A mechanism is described showing how velocity, time, distance, matter, and energy are correlated. We are led to ascertain that gravity and electricity are two distinct manifestations of a single underlying process: electro-gravitation. The force of gravitation arises of electromagnetism—inherently much stronger—divided by the cosmological space-time. The radius of space-time belongs to the family of electromagnetic waves: the wavelength is the radius (1026 m) of the universe and the period (1017 s) is its cosmological age. For the first time, the cosmological time, considered as a real physical object, is integrated into a “cosmological equation” which makes coherent what we know regarding the time (its origin, its flow …), the matter, and space. It sets up a mathematical model allowing us to interpret dark energy (or cosmological constant) as being both “negative” and “tired” energy. After an introduction with a brief history of unifications and the presentation of two roughly equal ratios arising out from Dirac’s large-number hypotheses which relate to the ratio of electric force to gravitational force and the ratio of the age of the universe to the atomic time unit associated with atomic processes, we present in §2 this new equation of quantum cosmology which operates the reconciliation between the macrocosm and the microcosm. In §3 and §4, we discuss the irreversible cosmological time resulting from the equation, as well as the role of the mass (heavy) relative to the gravitational constant G. In §5 we discuss the links that the equation establishes between gravitation (structure of condensation) and electromagnetism (structure of expansion), between relativity and quantum theory. We apply the formula to Planck’s time. We speak of the new essential variable? ?\"\", and briefly of a new principle, the principle of compensation. In §6 we discuss the negative energy solutions banned by physics, and we deplore that half of the universe escapes us. We present the electro-gravitation in §7, from the equation which represents a super hydrogen atom. In § 8 we show that the global mass (gravitational) is variable: it increases during the expansion while the mass of the elementary
Scenario for the Origin of Matter (According to the Theory of Relation)  [PDF]
Russell Bagdoo
Journal of Modern Physics (JMP) , 2019, DOI: 10.4236/jmp.2019.102013
Abstract: Where did matter in the universe come from? Where does the mass of matter come from? Particle physicists have used the knowledge acquired in matter and space to imagine a standard scenario to provide satisfactory answers to these major questions. The dominant thought to explain the absence of antimatter in nature is that we had an initially symmetrical universe made of matter and antimatter and that a dissymmetry would have sufficed for more matter having constituted our world than antimatter. This dissymmetry would arise from an anomaly in the number of neutrinos resulting from nuclear reactions which suggest the existence of a new type of titanic neutrino who would exceed the possibilities of the standard model and would justify the absence of antimatter in the macrocosm. We believe that another scenario could better explain why we observe only matter. It involves the validation of the negative energy solution of the Dirac equation, itself derived from the Einstein energy equation. The theory of Relation describes a negative energy ocean with the creation of real particle/antiparticle pairs. The origin of the masses of the particles would come from this ocean. A physical mechanism would allow their separation in the opposite direction and, therefore, the matter would be enriched at the expense of the ocean. The matter would be favored without resorting to negation or annihilation of negative energy, without the need for a CP (the behavioral difference between particle and antiparticle) violation that would be responsible for matter/antimatter asymmetry in the universe. And without the savior contribution of an undetectable obese neutrino: his search appears to us more a desperate act towards an “ultra-massive catastrophe” than a real effort to try to discover what really happened.
A Review of Facility Layout Selection Models in Manufacturing Organizations
Eida Nadirah Roslin,Siti Zawiah Md Dawal,Shamsuddin Ahmed
Lecture Notes in Engineering and Computer Science , 2010,
Data Integration in Genetics and Genomics: Methods and Challenges
Jemila S. Hamid,Pingzhao Hu,Nicole M. Roslin,Vicki Ling
Human Genomics and Proteomics , 2009, DOI: 10.4061/2009/869093
Abstract: Due to rapid technological advances, various types of genomic and proteomic data with different sizes, formats, and structures have become available. Among them are gene expression, single nucleotide polymorphism, copy number variation, and protein-protein/gene-gene interactions. Each of these distinct data types provides a different, partly independent and complementary, view of the whole genome. However, understanding functions of genes, proteins, and other aspects of the genome requires more information than provided by each of the datasets. Integrating data from different sources is, therefore, an important part of current research in genomics and proteomics. Data integration also plays important roles in combining clinical, environmental, and demographic data with high-throughput genomic data. Nevertheless, the concept of data integration is not well defined in the literature and it may mean different things to different researchers. In this paper, we first propose a conceptual framework for integrating genetic, genomic, and proteomic data. The framework captures fundamental aspects of data integration and is developed taking the key steps in genetic, genomic, and proteomic data fusion. Secondly, we provide a review of some of the most commonly used current methods and approaches for combining genomic data with focus on the statistical aspects.
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