Physical Sciences and Mathematics Commons^™

A Hidden Markov Model Capable Of Predicting And Discriminating Β-Barrel Outer Membrane Proteins, Pantelis G. Bagos, Theodore D. Liakopoulos, Ioannis C. Spyropoulos, Stavros J. Hamodrakas

Pantelis Bagos

BACKGROUND: Integral membrane proteins constitute about 20-30% of all proteins in the fully sequenced genomes. They come in two structural classes, the alpha-helical and the beta-barrel membrane proteins, demonstrating different physicochemical characteristics, structure and localization. While transmembrane segment prediction for the alpha-helical integral membrane proteins appears to be an easy task nowadays, the same is much more difficult for the beta-barrel membrane proteins. We developed a method, based on a Hidden Markov Model, capable of predicting the transmembrane beta-strands of the outer membrane proteins of gram-negative bacteria, and discriminating those from water-soluble proteins in large datasets. The model is trained …

Developing A Research And Restoration Plan For Arctic-Yukon-Kuskokwim (Western Alaska) Salmon, Craig L. Fleener

Craig L Fleener

No abstract provided.

Quality Control And Peak Finding For Proteomics Data Collected From Nipple Aspirate Fluid Using Surface Enhanced Laser Desorption And Ionization., Jeffrey S. Morris, Kevin R. Coombes, Herbert A. Fritsche, Charlotte Clarke, Jeng-Neng Chen, Keith A. Baggerly, Lian-Chun Xiao, Mien-Chie Hung, Henry M. Kuerer

Jeffrey S. Morris

Background: Recently, researchers have been using mass spectroscopy to study cancer. For use of proteomics spectra in a clinical setting, stringent quality-control procedures will be needed.

Methods: We pooled samples of nipple aspirate fluid from healthy breasts and breasts with cancer to prepare a control sample. Aliquots of the control sample were used on two spots on each of three IMAC ProteinChip® arrays (Ciphergen Biosystems, Inc.) on 4 successive days to generate 24 SELDI spectra. In 36 subsequent experiments, the control sample was applied to two spots of each ProteinChip array, and the resulting spectra were analyzed to determine how …

A Comprehensive Approach To The Analysis Of Maldi-Tof Proteomics Spectra From Serum Samples., Keith A. Baggerly, Jeffrey S. Morris, Jing Wang, David Gold, Lian-Chun Xiao, Kevin R. Coombes

Jeffrey S. Morris

For our analysis of the data from the First Annual Proteomics Data Mining Conference, we attempted to discriminate between 24 disease spectra (group A) and 17 normal spectra (group B). First, we processed the raw spectra by (i) correcting for additive sinusoidal noise (periodic on the time scale) affecting most spectra, (ii) correcting for the overall baseline level, (iii) normalizing, (iv) recombining fractions, and (v) using variable- width windows for data reduction. Also, we identified a set of polymeric peaks (at multiples of 180.6 Da) that is present in several normal spectra (B1–B8). After data processing, we found the intensities …

Quelques Conseils À Nos Nouveau Diplomés, Fathi Habashi

Fathi Habashi

An advice, the old wise man Polonius offered to the young Hamlet was “Neither a borrower, nor a lender be”, may be no longer pertinent. Some more relevant advices are offered to new graduates of the twentieth century. Available in English, French, and Spanish

Bayesian Shrinkage Estimation Of The Relative Abundance Of Mrna Transcripts Using Sage, Jeffrey S. Morris, Keith A. Baggerly, Kevin R. Coombes

Jeffrey S. Morris

Serial analysis of gene expression (SAGE) is a technology for quantifying gene expression in biological tissue that yields count data that can be modeled by a multinomial distribution with two characteristics: skewness in the relative frequencies and small sample size relative to the dimension. As a result of these characteristics, a given SAGE sample may fail to capture a large number of expressed mRNA species present in the tissue. Empirical estimators of mRNA species’ relative abundance effectively ignore these missing species, and as a result tend to overestimate the abundance of the scarce observed species comprising a vast majority of …

The Press For Help Project Concept, Program And Working Paper Of Emmanuel Mario B Santos And His Marc Guerrero Communications Inc., Emmanuel Mario B. Santos Aka Marc Guerrero

Emmanuel Mario B Santos aka Marc Guerrero

FORETHOUGHT. DECLARATION OF IDEAOLOGY AND PRINCIPLES. VISION. MISSION. VALUES. GOALS. BASIC HELP project. EDUCATIONAL HELP project. MEDICAL HELP project. LEGAL HELP project. EMERGENCY HELP project. LIVELIHOOD HELP project. SPIRITUAL and CULTURAL HELP project. ENVIRONMENTAL HELP project. REENGINEERING HELP project. INTERNATIONAL HELP project. QUADRO CREDO Matthew 5.1-12, the Jerusalem Bible. The Universal Filipino Beatitudes. SALIN SA FILIPINO. DESIDERATA. AFTERTHOUGHT.

From Alchemy To Atomic Bombs. Book Review By George Kauffman, Fathi Habashi

Fathi Habashi

Review of the book "From Alchemy to Atomic Bombs" by Fathi Habashi published by Métallurgie Extractive Québec. The review is written by Professor George Kauffman at California State University, Fresno.

Pmr6, A Pectate Lyase–Like Gene Required For Powdery Mildew Susceptibility In Arabidopsis, John P. Vogel, Ted K. Raab, Celine Schiff, Shauna C. Somerville

Ted K. Raab

The plant genes required for the growth and reproduction of plant pathogens are largely unknown. In an effort to identify these genes, we isolated Arabidopsis mutants that do not support the normal growth of the powdery mildew pathogen Erysiphe cichoracearum. Here, we report on the cloning and characterization of one of these genes, PMR6. PMR6 encodes a pectate lyase-like protein with a novel C-terminal domain. Consistent with its predicted gene function, mutations in PMR6 alter the composition of the plant cell wall, as shown by Fourier transform infrared spectroscopy. pmr6-mediated resistance requires neither salicylic acid nor the ability to perceive …

Visualizing Rhizosphere Chemistry Of Legumes With Mid-Infrared Synchrotron Radiation, Ted K. Raab, Michael C. Martin

Ted K. Raab

A bright synchrotron light source operated by the Lawrence Berkeley National Laboratory served as an external source for infrared (IR) microscopy of plant root microcosms. Mid-IR light from synchrotrons is 2-3 orders of magnitude brighter than conventional sources, providing contrast based on the chemical information in the reflected signal at a spatial resolution near the diffraction-limit of 3-10 microns. In an experiment using plant root microcosms fitted with zinc selenide IR-transmissive windows (50 mm x 20 mm x 1 mm), we describe chemical differences and similarities within the root zone of mung bean (Vigna radiata L.), grown with or without …

N-Methyl-D-Aspartate Channel And Consciousness: From Signal Coincidence Detection To Quantum Computing, Armando F. Rocha, Alfredo Pereira Jr

Armando F Rocha

Research on Blindsight, Neglect/Extinction and Phantom limb syndromes, as well as electrical measurements of mammalian brain activity, have suggested the dependence of vivid perception on both incoming sensory information at primary sensory cortex and reentrant information from associative cortex. Coherence between incoming and reentrant signals seems to be a necessary condition for (conscious) perception. General reticular activating system and local electrical synchronization are some of the tools used by the brain to establish coarse coherence at the sensory cortex, upon which biochemical processes are coordinated. Besides electrical synchrony and chemical modulation at the synapse, a central mechanism supporting such a …

Terminology Work: Tools And Processes That Make A Difference, Uwe Muegge

Uwe Muegge

Technical texts, i.e., technical literature proper (data sheets, user documentation, scientific publications, etc.), as well as the whole range of medical and legal texts, have one feature in common: Their authors make generous use of: a) words not in common usage, e.g., dongle (a computer hardware device that prevents unauthorized use of protected software); and/or b) words that are in common usage but have a slightly, or even totally, different meaning in the special language, e.g., bug (in the general sense, this means a small insect, but in the computer software field, this is a small defect in the code …

Toward An Ecosystem Approach To Remediation In The Great Basin, Ted K. Raab

Ted K. Raab

We consider the web of interactions among geologic materials, soils, plants, and animals to ask, "If mining or other extractive energy technologies occur in desert regions, what do we need to know to return the land to productivity?" The Great Basin represents a formidable challenge in this regard, as winters in these cold deserts and seasonal lack of moisture during parts of the year severely constrain the growing season for vegetation. Due to the nature of current or proposed mining activities in this region, we have chosen to concentrate on two potential pollutants: the trace element selenium (Se) and nitrate …

Soil Amino Acid Utilization Among Species Of The Cyperaceae: Plant And Soil Processes, Ted K. Raab, David A. Lipson, Steven K. Scmidt, Russ K. Monson

Ted K. Raab

Amino acids are released during the decomposition of soil organic matter and have been shown to be utilized as a nitrogen source by some non-mycorrhizal species in the family Cyperaceae (the sedge family). Twelve out of 13 Cyperaceae species examined in the current study were capable of absorbing soil amino acids in the non-mycorrhizal state. With two exceptions (two species in the genus Kobresia), species from subalpine or alpine habitats exhibited lower rates of total nitrogen uptake compared to species from more temperate habitats, which is possibly explained by lower growth rates in the alpine and subalpine species and a …

Intracellular Coexpression Of Epidermal Growth Factor Receptor, Her-2/Neu, And P21ras In Human Breast Cancers: Evidence For The Existence Of Distinctive Patterns Of Genetic Evolution That Are Common To Tumors From Different Patients, Stanley E. Shackney, Agnese A. Pollice, Charles A. Smith, Laura E. Janocko, Lillian Sweeney, Kathryn A. Brown, Sarita G. Singh, Lingping Gu, Robert Yakulis, Joseph F. Lucke

Joseph Lucke

Multiparameter flow cytometry studies were performed on cells from the primary tumors of 94 patients with breast cancer. Correlated cellular measurements of cell DNA content, Her-2/neu, epidermal growth factor receptor (EGFR), and p21ras levels were performed on each of 5,000 to 100,000 cells from each tumor. When criteria for positivity were matched with those in common use for immunohistochemical studies, 28 of 94 (30\%) breast cancers were classified as positive for Her-2/neu overexpression. When similar criteria were applied to the EGFR measurements, 23 of 94 (24\%) cases were classified as positive for EGFR overexpression. Similarly, 23 of 94 (24\%) cases …

The Brain As A Symbol-Processing Machine., Armando F. Rocha

Armando F Rocha

The knowledge accumulated about the biochemistry of the synapsis in the last decades completely changes the notion of brain processing founded exclusively over an electrical mechanism, toward that supported by a complex chemical message exchange occurring both locally, at the synaptic site, as well as at other localities, depending on the solubility of the involved chemical substances in the extracellular compartment. These biochemical transactions support a rich symbolic processing of the information both encoded by the genes and provided by actual data collected from the surrounding environment, by means of either special molecular or cellular receptor systems. In this processing, …

Degradation Studies Of The Non-Lethal Bird Repellent, Methyl Anthranilate, Eugeny Aronov, Larry Clark

Larry Clark

Methyl anthranilate (MA), a food grade flavor and fragrance additive, has been reported to be an effective non-lethal bird repellent in a variety of situations. Despite the experimental success of MA, field studies have yielded widely differing levels of efficacy. Diminished efficacy in some field trials prob­ ably results from the failure of specific formulations to retain or protect the active ingredient under natural conditions. Therefore, a clearer understanding of the physical and chemical factors affecting the stability of MA is needed. We undertook a series of laboratory studies on hydrolysis, photolysis and microbial degradation of MA, the results of …

Assessing Sequential Oncogene Amplification In Human Breast Cancer, Laura E. Janocko, Joseph F. Lucke, David W. Groft, Kathryn A. Brown, Charles A. Smith, Agnese A. Pollice, Sarita G. Singh, Robert Yakulis, Robert J. Hartsock, Stanley E. Shackney

Joseph Lucke

Studies of amplification and/or overexpression of c-myc, HER-2/neu, and H-ras in breast cancer have shown that each is associated with a poor prognosis. The purpose of this study was to explore the possibility that there is a preferred sequence of amplification of these oncogenes in breast cancer. The frequencies of amplification and patterns of co-amplification of c-myc, HER-2/neu, and H-ras were studied in a group of 84 breast cancers. The data suggested a preferred sequence of amplification that consisted of c-myc amplification-HER-2/neu amplification-H-ras amplification. This model was supported by loglinear analysis. In addition, the levels of amplification of JC-A, a …

A Memorable Meeting, February 1994, Fathi Habashi

Fathi Habashi

Decision taken at the Steering Committee Meeting of the International Mineral Processing Congress in San Francisco February 1994 to name the IMPC Award.

Expression Of Prelamin A Confers Sensitivity Of Dna Biosynthesis To Lovastatin On F9 Teratocarcinoma Cells, Michael Sinensky, T. Mclain, K. Fantle

Michael Sinensky

No abstract provided.

The Processing Pathway Of Prelamin A, Michael Sinensky, K. Fantle, M. Trujillo, T. Mclain, A. Kupfer, M. Dalton

Michael Sinensky

The conversion of mammalian prelamin A to mature lamin A proceeds through the removal of 18 amino acids from the carboxyl terminus. The initial step in this processing is the isoprenylation of a CAAX box cysteine. This proteolytic event is distinctive for prelamin A among the known prenylated mammalian proteins. Since the carboxyl terminus of prelamin A is removed during maturation, it is not obvious that this protein would undergo the two reactions subsequent to prenylation observed in other CAAX box proteins-the endoproteolytic removal of the carboxyl-terminal 3 amino acids and the subsequent methylation of the now carboxyl-terminal cysteine. To …

The Hazardous Waste Land, Jerry L. Anderson

Jerry L. Anderson

This article was one of the first comprehensive critiques of the Superfund remediation and liability system. The article addresses systemic problems with the CERCLA mechanism that result in inequity and slow the pace of cleanups.

Isoprenylation Is Required For The Processing Of The Lamin A Precursor, Michael Sinensky, L. A. Beck, T. J. Hosick

Michael Sinensky

The nuclear lamina proteins, prelamin A, lamin B, and a 70-kD lamina-associated protein, are posttranslationally modified by a metabolite derived from mevalonate. This modification can be inhibited by treatment with (3-R,S)-3-fluoromevalonate, demonstrating that it is isoprenoid in nature. We have examined the association between isoprenoid metabolism and processing of the lamin A precursor in human and hamster cells. Inhibition of 3-hydroxy-3-methylglutaryl coenzyme A reductase by mevinolin (lovastatin) specifically depletes endogenous isoprenoid pools and inhibits the conversion of prelamin A to lamin A. Prelamin A processing is also blocked by mevalonate starvation of Mev-1, a CHO cell line auxotrophic for mevalonate. …

Incorporation Of A Product Of Mevalonic Acid Metabolism Into Proteins Of Chinese Hamster Ovary Nuclei, Michael Sinensky, L. A. Beck, T. Hosick

Michael Sinensky

We have examined the nuclear localization of isoprenylated proteins in CHO-K1 cells labeled with [14C]mevalonate. Nuclear proteins of 68, 70, and 74 kD, posttranslationally modified by an isoprenoid, are also components of a nuclear matrix-intermediate filament preparation from CHO cells. Furthermore, the 68-, 70-, and 74-kD isoprenylated polypeptides are immunoprecipitated from cell extracts with two different anti-lamin antisera. Based on exact two-dimensional comigration with lamin B, both from rat liver lamin and CHO nuclear matrix-intermediate filament preparations, and its immunoprecipitation with anti-lamin antisera, we conclude that the 68-kD isoprenylated protein found in nuclei from [14C]mevalonate-labeled CHO cells is lamin B. …

Adaptative Alteration In Phospholipid Composition Of Plasma Membranes From A Somatic Cell Mutant Defective In The Regulation Of Cholesterol Biosynthesis, Michael Sinensky

Michael Sinensky

A somatic cell mutant (CR1) of a Chinese hamster ovary cell (CHO-K1) which has previously been shown to be defective in the regulation of cholesterol biosynthesis accumulates more cholesterol than the parental cell line in plasma membranes. Although such an increase in membrane cholesterol should lead to an increase in the order parameter of these membranes, as measured with an electron spin resonance spin probe, the order parameters of mutant and wild-type plasma membranes are identical--apparently because of an adaptive alteration in membrane phospholipid composition. The phospholipid compositions of mutant and wild-type cell plasma membranes are compared and the mutant …

Hidrometalurjide Yeni, Fathi Habashi

Fathi Habashi

Turkish translation of F. Habashi, “Recent Advances in Hydrometallurgy,” Proceedings International Mineral Processing Congress, Warsaw, 1979, edited by J. Laskowski, published by Elsevier, pp. 902–935

Progress In Extractive Metallurgy, Volume 1. Review By G.N. Dobrokhotov, Fathi Habashi

Fathi Habashi

Review of the first volume of Progress in Extractive Metallurgy edited by Fathi Habashi and published by Gordon & Breach in New York in 1975. The review was written by Professor Dobrokhotov at the Leningrad Mining Institute.