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Relevant bibliographies by topics / Biochemistry and Molecular Biology (Theses)

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Academic literature on the topic 'Biochemistry and Molecular Biology (Theses)'

Author: Grafiati

Published: 4 June 2021

Last updated: 6 February 2022

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Journal articles on the topic "Biochemistry and Molecular Biology (Theses)"

1

Ngai, Courtney, and Hannah Sevian. "Probing the Relevance of Chemical Identity Thinking in Biochemical Contexts." CBE—Life Sciences Education 17, no. 4 (December 2018): ar58. http://dx.doi.org/10.1187/cbe.17-12-0271.

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The solving of problems in biochemistry often uses concepts from multiple disciplines such as chemistry and biology. Chemical identity (CI) is a foundational concept in the field of chemistry, and the knowledge, thinking, and practices associated with CI are used to answer the following questions: “What is this substance?” and “How is it different from other substances?” In this study, we examined the relevance of CI in biochemical contexts and first explored the ways in which practicing biochemists consider CI relevant in their work. These responses informed the development of creative exercises (CEs) given to second-semester biochemistry students. Analysis of the student responses to these CEs revealed that students incorporated precursors to CI thinking in more than half of their responses, which were categorized by seven previously identified themes of CI relevant to the presented biochemical contexts. The prevalence of these precursors in student responses to the CEs, coupled with the examples provided by practicing biochemists of contexts in which CI is relevant, indicate that CI thinking is relevant for both students training to be biochemists and practicing biochemists.

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Reynolds, Julie A., and Robert J. Thompson. "Want to Improve Undergraduate Thesis Writing? Engage Students and Their Faculty Readers in Scientific Peer Review." CBE—Life Sciences Education 10, no. 2 (June 2011): 209–15. http://dx.doi.org/10.1187/cbe.10-10-0127.

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One of the best opportunities that undergraduates have to learn to write like a scientist is to write a thesis after participating in faculty-mentored undergraduate research. But developing writing skills doesn't happen automatically, and there are significant challenges associated with offering writing courses and with individualized mentoring. We present a hybrid model in which students have the structural support of a course plus the personalized benefits of working one-on-one with faculty. To optimize these one-on-one interactions, the course uses BioTAP, the Biology Thesis Assessment Protocol, to structure engagement in scientific peer review. By assessing theses written by students who took this course and comparable students who did not, we found that our approach not only improved student writing but also helped faculty members across the department—not only those teaching the course—to work more effectively and efficiently with student writers. Students who enrolled in this course were more likely to earn highest honors than students who only worked one-on-one with faculty. Further, students in the course scored significantly better on all higher-order writing and critical-thinking skills assessed.

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Cabezas Fernández del Campo, José Antonio, and Mariano Esteban Rodríguez. "RELATIONSHIP OF THE VIROLOGIST PROFESSOR ADOLFO GARCÍA SASTRE WITH THE UNIVERSITY OF SALAMANCA AND THE ROYAL NATIONAL ACADEMY OF PHARMACY." Anales de la Real Academia Nacional de Farmacia, no. 87(01) (2021): 09–14. http://dx.doi.org/10.53519/analesranf.2021.87.01.001.

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We give some biographical details of the virologist Professor Adolfo Garcia Sastre, as a Graduate student (1981-1986) in the Biology School of University of Salamanca and during his PhD Thesis (1986-1990) in the Department of Biochemistry and Molecular Biology (Chairman Prof J.A. Cabezas), under the supervision of Prof. Enrique Villlar and obtaining the highest academic marks. The research lines that he established in collaboration with his Thesis director, with Prof. J.A Cabezas and others, as well as his results during his stay at the Pasteur Institute in Paris, are also highlighted. His findings in this period were published in prestigious Virology and Biochemistry journals and presented at national and international meetings. Thereafter, when he moved to Mount Sinai in New York, he met Prof Mariano Esteban, then working at Downstate Medical Center in New York, SUNY, and both, in collaboration with the group of Prof. Ruth Nussenzweig and Fidel Zavala at New York University, set up seminal immunological studies that are the basis for combined vaccination approaches, prime/boost and activation of CD8+ T cells, now widely used in preclinical and clinical studies. The scientific research contributions of Prof. García Sastre are growing at an exponential rate, opening new horizons in understanding the molecular biology of emerging viruses, their pathology, virus-host cell interactions and strategies of virus control.

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Bishop, J. Michael. "Molecular themes in oncogenesis." Cell 64, no. 2 (January 1991): 235–48. http://dx.doi.org/10.1016/0092-8674(91)90636-d.

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Bayliss, Richard, Andrew Fry, Tamanna Haq, and Sharon Yeoh. "On the molecular mechanisms of mitotic kinase activation." Open Biology 2, no. 11 (November 2012): 120136. http://dx.doi.org/10.1098/rsob.120136.

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During mitosis, human cells exhibit a peak of protein phosphorylation that alters the behaviour of a significant proportion of proteins, driving a dramatic transformation in the cell's shape, intracellular structures and biochemistry. These mitotic phosphorylation events are catalysed by several families of protein kinases, including Auroras, Cdks, Plks, Neks, Bubs, Haspin and Mps1/TTK. The catalytic activities of these kinases are activated by phosphorylation and through protein–protein interactions. In this review, we summarize the current state of knowledge of the structural basis of mitotic kinase activation mechanisms. This review aims to provide a clear and comprehensive primer on these mechanisms to a broad community of researchers, bringing together the common themes, and highlighting specific differences. Along the way, we have uncovered some features of these proteins that have previously gone unreported, and identified unexplored questions for future work. The dysregulation of mitotic kinases is associated with proliferative disorders such as cancer, and structural biology will continue to play a critical role in the development of chemical probes used to interrogate disease biology and applied to the treatment of patients.

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Kinikoğlu, Oğuzcan, Yağmur Ö. Güven, and Bekir B. Kilboz. "Publication and Citation Analysis of Medical Doctors’ Residency Master’s Theses Involving Animal Experiments on Rats in Turkey." Alternatives to Laboratory Animals 48, no. 1 (January 2020): 23–28. http://dx.doi.org/10.1177/0261192920907226.

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The number of non-human animals used in research has increased in line with advances in medical technology, although it has previously been shown that these experiments demonstrate poor human utility. This study aimed to determine the effectiveness of animal studies on rats that were performed as part of medical doctors’ residency master’s theses prepared in Turkey between January 2006 and December 2015. The number of thesis-derived published papers from each year, as well as the subsequent citation rate of these papers, was determined. Results from 34% of the 656 analysed studies (226/656) were published as papers in PubMed-indexed journals. These 226 studies got 1803 subsequent citations in total. Citation counts were statistically significantly different in 2009 and 2010, as compared to 2011, 2013, 2014 and 2015. Previous studies showed that the usual main objective for carrying out animal studies in Turkey was the preparation of a thesis or the furthering of an academic career (i.e. personal self-interest). In the current study, the publication rate and the number of subsequent citations of these thesis-derived papers were both low, and thus, the contribution of these animal studies to scientific progress is doubtful. It is recommended that institutional research ethics committees should be much more highly selective in approving the use of animals for the purposes of student thesis preparation.

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Weaver, K. F., V. Morales, M. Nelson, P. F. Weaver, A. Toledo, and K. Godde. "The Benefits of Peer Review and a Multisemester Capstone Writing Series on Inquiry and Analysis Skills in an Undergraduate Thesis." CBE—Life Sciences Education 15, no. 4 (December 2016): ar51. http://dx.doi.org/10.1187/cbe.16-01-0072.

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This study examines the relationship between the introduction of a four-course writing-intensive capstone series and improvement in inquiry and analysis skills of biology senior undergraduates. To measure the impact of the multicourse write-to-learn and peer-review pedagogy on student performance, we used a modified Valid Assessment of Learning in Undergraduate Education rubric for Inquiry and Analysis and Written Communication to score senior research theses from 2006 to 2008 (pretreatment) and 2009 to 2013 (intervention). A Fisher-Freeman-Halton test and a two-sample Student’s t test were used to evaluate individual rubric dimensions and composite rubric scores, respectively, and a randomized complete block design analysis of variance was carried out on composite scores to examine the impact of the intervention across ethnicity, legacy (e.g., first-generation status), and research laboratory. The results show an increase in student performance in rubric scoring categories most closely associated with science literacy and critical-thinking skills, in addition to gains in students’ writing abilities.

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Louie, A. H. "Relational biology and Church's thesis." Biosystems 197 (November 2020): 104179. http://dx.doi.org/10.1016/j.biosystems.2020.104179.

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Zeth, Kornelius, and Marcus Thein. "Porins in prokaryotes and eukaryotes: common themes and variations." Biochemical Journal 431, no. 1 (September 14, 2010): 13–22. http://dx.doi.org/10.1042/bj20100371.

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Gram-negative bacteria and mitochondria are both covered by two distinct biological membranes. These membrane systems have been maintained during the course of evolution from an early evolutionary precursor. Both outer membranes accommodate channels of the porin family, which are designed for the uptake and exchange of metabolites, including ions and small molecules, such as nucleosides or sugars. In bacteria, the structure of the outer membrane porin protein family of β-barrels is generally characterized by an even number of β-strands; usually 14, 16 or 18 strands are observed forming the bacterial porin barrel wall. In contrast, the recent structures of the mitochondrial porin, also known as VDAC (voltage-dependent anion channel), show an uneven number of 19 β-strands, but a similar molecular architecture. Despite the lack of a clear evolutionary link between these protein families, their common principles and differences in assembly, architecture and function are summarized in the present review.

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Sweeting, B., M. Qasim Khan, A. Chakrabartty, and E. F. Pai. "Structural factors underlying the species barrier and susceptibility to infection in prion diseaseThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process." Biochemistry and Cell Biology 88, no. 2 (April 2010): 195–202. http://dx.doi.org/10.1139/o09-172.

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The term prion disease describes a group of fatal neurodegenerative diseases that are believed to be caused by the pathogenic misfolding of a host cell protein, PrP. Susceptibility to prion disease differs between species and incubation periods before symptom onset can change dramatically when infectious prion strains are transmitted between species. This effect is referred to as the species or transmission barrier. Prion strains represent different structures of PrPScand the conformational selection model proposes that the source of theses barriers is the preferential incorporation of PrP from a given species into only a subset of PrPScstructures of another species. The basis of this preferential incorporation is predicted to reside in subtle structural differences in PrP from varying species. The overall fold of PrP is highly conserved among species, but small differences in the amino acid sequence give rise to structural variability. In particular, the loop between the second β-strand and the second α-helix has shown structural variability between species, with loop mobility correlating with resistance to prion disease. Single amino acid polymorphisms in PrP within a species can also affect prion susceptibility, but do not appear to drastically alter the biophysical properties of the native form. These polymorphisms affect the propensity of self-association, in recombinant PrP, to form β-sheet enriched, oligomeric, and amyloid-like forms. These results indicate that the major factor in determining susceptibility to prion disease is the ability of PrP to adopt these misfolded forms by promoting conformational change and self association.

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Dissertations / Theses on the topic "Biochemistry and Molecular Biology (Theses)"

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Schabort, Willem Petrus Du Toit. "Integration of kinetic models with data from 13C-metabolic flux experiments." Thesis, Link to the online version, 2007. http://hdl.handle.net/10019/707.

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Wu, Biing-Ru. "RAPID IDENTIFICATION OF ASPERGILLUS SPP. USING A PCR BASED MELTING CURVE METHOD AND CHARACTERIZATION OF A NOVEL CHITINASE IN INSECT RESISTANT MAIZE LINES." MSSTATE, 2009. http://sun.library.msstate.edu/ETD-db/theses/available/etd-11032009-141528/.

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Identification of fungal isolates is critical in studying Aspergillus flavus ecology and for developing methods to reduce aflatoxin contamination. In our efforts to track biocontrol applications of the atoxigenic A. flavus K49 (NRRL 30797), we have developed a rapid and accurate classification system for A. flavus based on PCR product melting temperatures (Tm). Using 18 primers and a total of 59 Aspergilli strains, including all 49 representatives of the Georgian peanut Vegetative Compatibility Groups (VCGs), a decision tree Tm flowchart was generated. The decision tree can classify all 59 strains using only 9 of the SSR primers and an average of 3.4 primers for each definitive classification. To confirm the effectiveness of the decision tree for strain identification, unknown samples isolated from experimental fields inoculated with various A. flavus strains in Stoneville, MS were analyzed. Ninety-six percent of the samples could be placed into a VCG using Tm(s) coupled with the decision tree. This dynamic system is an excellent tool for researchers studying biodiversity of A. flavus.

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Barnes, Daniel Joseph. "DETERMINATION OF RICIN CONTENT IN CASTOR (Ricinus communis L.) TISSUES AND COMPARISON OF DETOXIFICATION METHODS." MSSTATE, 2008. http://sun.library.msstate.edu/ETD-db/theses/available/etd-11042008-143054/.

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Experiments were conducted to test for ricin content in tissue samples from four castor cultivars, developing castor seed, germinating castor seedlings, and chemically and heat treated seed meal. Ricin content of each sample was examined via Western blotting with ricin A-chain specific antibodies. Results indicate that ricin is present solely within castor endosperm and is not present any other tissues. Samples from developing seed and germinating seedlings indicate ricin production begins around day 28 post pollination, and ricin is absent from the seedling 6 days after the onset of radicle emergence. This would seem to indicate that the purpose of ricin is to protect the seed and not the entire plant. Ricin content of seed meal treated separately with heat and chemicals was tested. It was found that hot-pressing of the seed was sufficient to denature ricin in the seed meal.

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Ho, Meng-Hsuan. "CHARACTERIZATION AND FUNCTIONAL ANALYSIS OF A COTTON RING-TYPE UBIQUITIN LIGASE (E3) GENE." MSSTATE, 2009. http://sun.library.msstate.edu/ETD-db/theses/available/etd-11032009-165510/.

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A cotton fiber cDNA, GhRING1, and its corresponding gene have been cloned and characterized. The GhRING1 gene encodes a RING-type ubiquitin ligase (E3) containing 337 amino acids (aa). The GhRING1 protein contains a RING finger motif with conserved cysteine and histine residues at the C-terminus and is classified as a C3H2C3-type RING protein. Blast searches show that GhRING1 has the highest homology to At3g19950 from Arabidopsis. Real time RT-PCR analysis indicates that the GhRING1 gene is highly expressed in cotton fiber in a developmental manner. The transcript level of the GhRING1 gene reaches a maximum in elongating fibers at 15 DPA. In vitro auto-ubiquitination assays using wheat germ extract and a reconstitution system demonstrate that GhRING1 has the ubiquitin E3 ligase activity. A fiber specific lipid transfer protein 4 (FSltp4) is identified as the target substrate of GhRING1 by using a bacterial two-hybrid system. The binding of GhRING1 and FSltp4 is confirmed by using an in vitro pull down assay and a yeast two-hybrid system. The histochemical GUS assay was performed to analyze tissue specificity of the GhRING1 and At3g19950 promoters in transgenic Arabidopsis plants. The GUS assay shows that the promoter of At3g19950 is highly activated in leaves, roots, trichomes and also in anthers and stigma of flowers. In contrast, the GUS expression directed by the promoter of GhRING1 is only located at stipules and anthers and stigma of flowers. The GhRING1 is the first ubiquitin E3 gene isolated and studied from cotton. Based on the expression pattern of GhRING1, FSltp4, and GhUBC E2s and the identification of a fiber-specific target protein, FSltp4, we propose that protein ubiquitination occurs in fiber and the ubiquitin-proteasome pathway regulates fiber development.

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Kapadia, Mayank S. "Identification of Collagen IV Associated Proteins in Drsophila Using Genetics and Mass Spectrometry." TopSCHOLAR®, 2016. http://digitalcommons.wku.edu/theses/1631.

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Metastatic cancer cells invade and spread to other locations by disrupting the basement membrane (BM). The membrane plays a major role during the normal development of an organism as well. In order to understand the invasion mechanism it is important to know about the interactions occurring between the proteins of the BM during normal development. This study concentrates on isolating and identifying the major factors associated with collagen IV, a major component of BM, during the third instar larval development of Drosophila. Western blot and mass spectrometry analysis revealed that collagen IV associates with various growth factors, signaling molecules, and proteins that may play a role during the development of Drosophila. Co-localization and knockdown studies performed on a single protein found through mass spectrometry suggested a possible role of this protein in the development of Drosophila. Further analysis of this proteins’ function will provide new insights into its developmental role and its potential role in collagen IV transport.

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Couch, Melanie. "Monitoring and Quantifying Tetracycline Resistance Genes in a Swine Waste Anaerobic Digester over a 100-Day Period." TopSCHOLAR®, 2018. https://digitalcommons.wku.edu/theses/2449.

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Unregulated use of growth promoting antibiotics like Tetracyclines in agricultural feeds is becoming an increasing problem in antibiotic resistance. Undigested antibiotics leads to significant concentrations in livestock waste. These concentrations provide continuous selection pressure for the development of antibiotic resistance genes in the environment. Antibiotic resistance related deaths are projected to surpass cancer related deaths by 2050 making antibiotic resistance a pressing public health issue. The purpose of this study is to determine the abundance and persistence of tetracycline (tet) resistance genes in swine waste over a period of 100 days in an anaerobic digester system. Tet(A), tet(B), tet(G), tet(M), tet(O), tet(Q), and tet(W) were quantified by quantitative polymerase chain reaction after DNA extraction. Primers that target ribosomal protection proteins and efflux proteins were used. Antibiotic resistance genes decreased from day one but were found to be present throughout the study.

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Modi, Tulsi. "Understanding the Molecular Level Interactions of Cancer Inhibitor Imatinib with Human Fibroblast Growth Factor-1." TopSCHOLAR®, 2015. http://digitalcommons.wku.edu/theses/1492.

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Fibroblast growth factors (FGFs) lack signal sequences, and are exported through endoplasmic reticulum (ER)-Golgi-independent non-classical routes. FGFs work as modulators of various cellular activities like mitosis, differentiation, survival etc. Among the FGF family, which comprises of 23 different heparin proteins, human FGF-1 (hFGF-1), a potent angiogenic factors are one of the targets in cancer inhibition, as they are involved in blood vessel formation in tissues. There has been intensive research directed at the development of drugs that could effectively inhibit angiogenesis. In this context, the purpose of this study is to fully understand the molecular principles essential to determine probability of inhibition of hFGF-1 signaling transduction by imatinib. Imatinib, a 2-phenyl amino pyrimidine derivative is a tyrosine kinase inhibitor with antineoplastic activity. Imatinib binds to the intracellular pocket located within tyrosine kinases and inhibit the downstream cell proliferation events, but the exact molecular mechanism is still elusive. In this study, expression of hFGF-1 in recombinant E. coli was carried out, and the expressed protein was purified using heparin affinity column chromatography. The structural interactions governing imatinib-hFGF-1 interaction was studied by monitoring its stability, conformation and binding affinity by equilibrium unfolding using steady state fluorescence and proteolytic digestion assay. These data show that imatinib binds to hFGF-1 and enhances its thermal stability and solvent accessibility. In addition, biacore analysis was carried out to determine the binding affinity of imatinib to hFGF-1.

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Mrwebi, Mandisi. "Testing Monod : growth rate as a function of glucose concentration in Saccharomyces cerevisiae." Thesis, Stellenbosch : University of Stellenbosch, 2004. http://hdl.handle.net/10019.1/16398.

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Thesis (MSc)--University of Stellenbosch, 2004.
ENGLISH ABSTRACT: The complexity of microbial systems has presented serious obstacles to the quantification of fermentation processes. Using computer modelling techniques progress has been made in monitoring, controlling and optimising microbial systems using material balancing techniques and empirical process models. The Monod equation is among the most commonly used models and is based on empirical findings with no mechanistic basis. Monod presents a simple model to describe the growth of a cell in a defined nutrient environment. The Monod equation is mathematically analogous to the formula that was proposed by Michaelis and Menten to describe enzyme kinetics. Both equations describe a hyperbolic function with a half-saturation constant (K_s in the monod equation and K_m in the Michaelis Menten equation) but the meaning of the two saturation constants K_s and K_m is different. In number of studies K_s and K_m are used as if they are equivalent. In contrast to Michaelis-Menten kinetics, which describes a process catalysed by a single enzyme, Monod kinetics describes an overall process involving thousands of enzymes. The Monod equation describes the specific growth rate of a microbial cell as the function of a limiting substrate concentration. The aim of this study was to test this principle, for Saccharomyces cerevisiae VIN13 under glucose limited aerobic chemostat conditions. The VIN13 was observed to follow the Monod description and when compared with other growth kinetic models gave one of the best fits to the data. A functional relationship between the half-saturation constant, K_s, and Michaelis Menten constant, K_m, was there after derived. This was achieved by using metabolic control analysis (MCA) to explain when K_m of the transporter becomes equal to the K_s. Using the deductions obtained from MCA a core kinetic model was then formulated to demonstrate that the K_s can either be smaller, equal or higher than the K_m of the transporter, depending on the flux control distribution in the model.
AFRIKAANSE OPSOMMING: Die kwantifisering van fermentasieprosesse word ernstig belemmer deur die kompleksiteit van mikrobiale sisteme. Deur gebruik te maak van rekenaar-ondersteunde modelleringstechnieke vir die opstelling van massa balans vergelykings en empiriese prosesmodelle is vordering gemaak in die waarneming, beheer en optimalisering van mikrobiale sisteme. Die Monod vergelyking is een van die mees gebruikte groeimodelle en is gebaseer op empiriese bevindings - die model het nie ‘n meganistiese grondslag nie. Die Monod vergelyking is wiskundig ekwivalent aan die vergelyking wat opgestel is deur Michaelis en Menten vir die beskrywing van ensiemkinetika. Beide vergelykings beskryf ‘n hyperboliese kurwe met ‘n konstante wat die halfversadigingswaarde aangee vir substraat (Ks in die Monod vergelyking en Km in die Michaelis-Menten vergelyking), maar die betekenis van die twee versadigingskonstantes is verskillend. In ‘n aantal studies word die Ks en Km waardes gebruik asof hulle gelyk is aan mekaar. In teenstelling met die Michaelis- Menten kinetika wat ‘n enkel ensiem-gekataliseerde reaksie beskryf, beskryf die Monod vergelyking ‘n proses wat duisende ensieme behels. Die Monod vergelyking beskryf die spesifieke groeitempo van ‘n bakteriële sel as ‘n funksie van die beperkende substraatkonsentrasie. Die doel van hierdie studie was om hierdie beginsel te toets vir Saccharomyces cerevisiae VIN13 wat onder glukose beperkte, aerobiese kondisies in ‘n chemostat gekweek word. Die VIN13 groei kon goed beskryf word met die Monod model, wat in vergelyking met ander groeimodelle een van die beste passings vir die meetpunte het gegee. Vervolgens is ‘n funksionele verwantskap afgelei tussen Ks en Km; deur gebruik te maak van metabole kontrole analise (MCA) kon verduidelik word wanneer die Ks gelyk is aan die Km van die transporter vir die beperkende substraat. Deur gebruik te maak van die MCA analise is ‘n eenvoudige kinetiese model opgestel om aan te toon dat die Ks kleiner, gelyk aan of groter kan wees as die Km van die transporter, afhanklik van die fluksie-kontrole verdeling in die model.

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Kim, Juhwa. "Multiplexed Detection of Double-Stranded Pathogenic DNA with Engineered Zinc Finger Proteins." TopSCHOLAR®, 2016. http://digitalcommons.wku.edu/theses/1616.

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The development of a new technology for the detection of doublestranded (ds) DNA enables multiple biomedical applications including identifying multiple pathogens simultaneously. We previously employed colorimetric SEquence-Enabled Reassembly with TEM-1 β-lacatamase (SEER-LAC) to detect specific bacterial DNA sequence. SEER-Lac consists of the two inactive β-lactamase fragments which of each attached to a zinc finger protein (ZFP) would reassemble into an active full-length enzyme upon ZFPs binding to its target DNA. Here, we engineered two pairs of ZFPs which of each recognizes shiga toxin in E. coli O157 and staphylococcal enterotoxin B in Staphylococus Aureus, respectively. Biotin was simply conjugated to the detection probe ZFP, which allows for generating chemiluminescent signal in streptavidin-HRP (Horseradish peroxidase) assay upon ZFPs binding to their target DNA. Our assay generates DNA-dependent signal and allows for a detection limit of 0.5 nM without DNA amplification or DNA labeling. Our system can be developed into a simple multiplexed detection diagnostic for multiplexed detection of dsDNA.

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Marpuri, ReddySalilaja. "Evaluation of Annotation Performances between Automated and Curated Databases of E.COLI Using the Correlation Coefficient." TopSCHOLAR®, 2009. http://digitalcommons.wku.edu/theses/94.

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This project compared the performance of the correlation coefficient to show similarities in annotations between a predictive automated bacterial annotation database and the curated EcoCyc database. EcoCyc is a conservative multidimensional annotation system that is exclusively based on experimentally validated findings by over 15,000 publications. The automated annotation system, used in the comparison was BASys. It is often used as a first pass annotation tool that tries to add as many annotations as possible by drawing upon over 30 information sources. Gene ontology served as one basis of comparison between these databases because of the limited common terms in the ontology annotations. Translation libraries were used to extend the number of BASys terms that could be compared to the gene ontology terms in EcoCyc. Additional, non-ontology terms and metadata in BASys were compared to EcoCyc terms after parsing them into root words. The different term sources were quantitatively compared by using the correlation coefficient as the evaluation metric. The direct gene ontology comparison gave the lowest correlation coefficient. The addition of gene ontology terms to BASys by using translation tables of metadata greatly increased the correlation coefficient, which was comparable to the parsed word comparison. The combination of enhanced gene ontology and parsed word methods gave the highest correlation coefficient of 0.16. The controlled vocabulary system of gene ontology was not sufficient to compare two annotated databases. The addition of gene ontology terms from translation libraries greatly increased the performance of these comparisons. In general, as the number of comparison terms increased the correlation coefficient increased. Future comparisons should include the enhanced gene ontology dataset in order to monitor the organization pertaining to formal nomenclature and the datasets generated from Word parsing can be used to monitor the degree of additional terms might be incorporated with translation libraries.

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Books on the topic "Biochemistry and Molecular Biology (Theses)"

1

Kaplan, Stanley H. Biochemistry: Molecular biology. [New York, N.Y.]: S.H. Kaplan Educational Center, 1993.

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Sandra, Kim, Glucksman Marc J, and Marks Dawn B, eds. Biochemistry and molecular biology. 4th ed. Baltimore: Lippincott Williams & Wilkins, 2007.

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Swanson, Todd A. Biochemistry and molecular biology. 4th ed. Philadelphia: Lippincott Williams & Wilkins, 2007.

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C, Elliott Daphne, ed. Biochemistry and molecular biology. 3rd ed. Oxford: Oxford University Press, 2005.

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C, Elliott Daphne, ed. Biochemistry and molecular biology. Oxford: Oxford University Press, 1997.

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Elliott, William H. Biochemistry and molecular biology. 2nd ed. Oxford: Oxford University Press, 2001.

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Brambl, Robert, and George A. Marzluf, eds. Biochemistry and Molecular Biology. Berlin, Heidelberg: Springer Berlin Heidelberg, 2004. http://dx.doi.org/10.1007/978-3-662-06064-3.

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Brambl, Robert, and George A. Marzluf, eds. Biochemistry and Molecular Biology. Berlin, Heidelberg: Springer Berlin Heidelberg, 1996. http://dx.doi.org/10.1007/978-3-662-10367-8.

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Hoffmeister, Dirk, ed. Biochemistry and Molecular Biology. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-27790-5.

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Swanson, Todd A. Biochemistry and molecular biology. Edited by Kim Sandra I, Glucksman Marc J, and Lieberman Michael 1950-. 5th ed. Philadelphia: Wolters Kluwer Health/Lippincott Williams & Wilkins, 2010.

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Book chapters on the topic "Biochemistry and Molecular Biology (Theses)"

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Stenesh, J. "Introduction to Molecular Biology." In Biochemistry, 407–24. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4757-9427-4_16.

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Kotyk, Arnošt. "Biochemistry and Molecular Biology." In Quantities, Symbols, Units, and Abbreviations in the Life Sciences, 39–61. Totowa, NJ: Humana Press, 1999. http://dx.doi.org/10.1007/978-1-59259-206-7_8.

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Bok, Jin Woo, and Nancy P. Keller. "2 Insight into Fungal Secondary Metabolism from Ten Years of LaeA Research." In Biochemistry and Molecular Biology, 21–29. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-27790-5_2.

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Park, Hee-Soo, and Jae-Hyuk Yu. "1 Molecular Biology of Asexual Sporulation in Filamentous Fungi." In Biochemistry and Molecular Biology, 3–19. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-27790-5_1.

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Rubio-Texeira, Marta, Griet Van Zeebroeck, and Johan M. Thevelein. "10 Trehalose Metabolism: Enzymatic Pathways and Physiological Functions." In Biochemistry and Molecular Biology, 191–277. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-27790-5_10.

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Todd, Richard B. "11 Regulation of Fungal Nitrogen Metabolism." In Biochemistry and Molecular Biology, 281–303. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-27790-5_11.

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Paietta, John V. "12 Regulation of Sulfur Metabolism in Filamentous Fungi." In Biochemistry and Molecular Biology, 305–19. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-27790-5_12.

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Kelly, Joan M. "13 The Regulation of Carbon Metabolism in Filamentous Fungi." In Biochemistry and Molecular Biology, 321–40. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-27790-5_13.

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Brock, Matthias, and Elena Geib. "14 Special Aspects of Fungal Catabolic and Anabolic Pathways." In Biochemistry and Molecular Biology, 341–60. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-27790-5_14.

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Voigt, Kerstin, Thomas Wolf, Katrin Ochsenreiter, Gábor Nagy, Kerstin Kaerger, Ekaterina Shelest, and Tamás Papp. "15 Genetic and Metabolic Aspects of Primary and Secondary Metabolism of the Zygomycetes." In Biochemistry and Molecular Biology, 361–85. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-27790-5_15.

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Conference papers on the topic "Biochemistry and Molecular Biology (Theses)"

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LeDuc, Philip. "Linking Molecular to Cellular Biomechanics With Nano- and Micro-Technology." In ASME 2003 International Mechanical Engineering Congress and Exposition. ASMEDC, 2003. http://dx.doi.org/10.1115/imece2003-43987.

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The link between mechanics and biochemistry has been implicated in a myriad of scientific and medical problem, from orthopedics and cardiovascular medicine, to cell motility and division, to signal transduction and gene expression. Most of these studies have been focused on organ-level issues, yet cellular and molecular level research has become essential over the last decade in this field thanks to the revolutionary developments in genetics, molecular biology, fabrication processes, and biotechnology. Developing the link between molecular and cellular biomechanics through subcellular studies can help uncover the complex interactions requisite for understanding higher order macroscopic behavior. Here, we will explore the link between molecular and cellular research through novel systems of nano- and micro-technology. In this, I will discuss novel technologies that we have developed and are utilizing, which include magnetic needles, three-dimension cell stretching systems, and microfluidics to examine the link between mechanics and biochemistry (including structural regulation through the cytoskeleton). By combining these novel approaches between engineering and biology, this multidisciplinary research can make a tremendous impact on the studies of human health and diseases through advances in fields such as proteomics, tissue engineering, and medical diagnostics.

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Wechsler, Marissa E., Courtney M. Creecy, Christine F. O’Neill, and Rena Bizios. "Effects of Electrical Stimulation on Select Functions of Bone Cells." In ASME 2012 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/sbc2012-80367.

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The present in vitro study was motivated by scientific literature reports that show enhanced healing of bone fractures in experimental animals in response to electrical stimulation. The underlying cellular- and molecular level mechanisms responsible for new bone formation, however, were not studied at that time. Since then, advances in cell biology, biochemistry and biomedical engineering provided knowledge, models, and instrumentation to investigate these unanswered questions.

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Schleuning, W. D. "THE BIOCHEMISTRY AND CELL BIOLOGY OF SINGLE CHAIN UROKINASE TYPE PLASMINOGEN ACTIVATOR." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642956.

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Urokinase was discovered in the late nineteenth century, as an enzymatic principle in urine, that initiates the dissolution of blood clots. The basis of this phenomenon was recognized more than fifty years ago as the activation of plasminogen, the precursor of a tryptic protease, then known as profibrinolysin. Despite this long history, detailed data on the biochemistry of plasminogen activation have only become available recently. Urokinase (now designated urokinase-type plasminogen activator : u-PA) is synthesized and secreted as a single chain polypeptide (Mr-: 53,000) by many cell types. Single chain u-PA (scu-PA) is with equal justification called prourokinase (pro-u-PA), notwithstanding its low catalytic activity for synthetic peptide substrates and plasminogen, as most proenzymes of proteases display a certain degree of activity. The structure of pro-u-PA has been elucidated by protein and cDNA sequencing. It consists of three domains, exhibiting characteristic homology to other proteins: a serine protease domain, homologous to trypsin, chymotrypsin and elastase; a kringle domain, likewise found in prothrombin, plasminogen, tissue-type plasminogen activator (t-PA) and Factor XII; and an epidermal growth factor (EGF)-like domain, found in many other proteins, including certain clotting factors. Pro-u-PA is activated by the cleavage of its LYS158-Ile159 h1 bY either plasmin or kallikrein. This cleavage leads to a high increase of Kcat values with respect to both plasminogen and synthetic peptide substrates, but apparently to a reduction of its affinity to plasminogen. Thrartoin inactivates pro-u-PA irreversibly by the cleavage of the Arg156-Phe157 bond. U-PA but not pro-u-PA rapidly forms ccnplexes with plasminogen activator inhibitors (PAI)-l and PAI-2: second order rate constants Kass are respectively > 107 and 0.9xl06 (M-11sec-1). Unknown enzymes process pro-u-PA and u-PA to low molecular weight (LMW) pro-u-PA and LMW u-PA (Mr: 33,000) by cutting off a fragment consisting of the kr ingle and the EGF—like region. Pro—u—PA mediated plasminogen activation is fibrin dependent in vivo, and to a certain degree in vitro. Hie biochemical basis of this fibrin specificity is at present uncertain, although there are reports indicating that it may require polyvalent cations. Through its EGF-like region HMW pro-u-PA and HMW u-PA are capable of binding to specific membrane protein receptors which are found on many cells. Thus, u-PA activity may be restricted to the cell surface. According to a recent report, binding of u—PA to the receptor may also mediate signal transduction in auto- or paracrine growth control. In cells permissive for the respective pathways, pro-u-PA gene transcription is stimulated by mechanisms of signal transduction, that include the cAMP, the tyrosine specific kinase and the protein kinase C dependent pathways. Glucocorticoid hormones downregulate pro-u-PA gene transcription in cells where the gene is canstitutively expressed. Although different cells vary greatly in their response to agents that stimulate urokinase biosynthesis, growth factors and other mitogens are in many cases effective inducers. Significantly elevated levels of u-PA are also found in many malignant tissues. These findings and many others suggest that plasminogen activation by u-PA provides localized extracellular matrix degradation which is required for invasive growth, cell migration and other forms of tissue remodelling. Fibrin represents in this view only a variant of an extracellular matrix, which is provided through the clotting system in the case of an emergency.

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Raykin, Julia, Alexander Rachev, Michael Zaucha, and Rudolph L. Gleason. "A Combined Theoretical-Experimental Paradigm for Studying Mechanical Conditioning of Tissue Engineered Arteries." In ASME 2008 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2008. http://dx.doi.org/10.1115/sbc2008-192746.

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There is a great unmet clinical need to develop small diameter tissue engineered blood vessels (TEBV) with low thrombogenicity and immune response, suitable mechanical properties, and a capacity to remodel to their environment [2, 3]. Development of a clinically useful small diameter TEBV will surely rely on techniques from a wide variety of disciplines, ranging from molecular and cell biology and biochemistry to material science and biomechanics. With regard to the latter, biomechanical stimuli, such as cyclic strain, have been shown to stimulate remodeling of collagen gel-derived TEBVs to greatly improve their mechanical behavior [5]. In native blood vessels, remodeling mechanisms appear to be aimed towards maintaining the local, 3-D mechanical environment (i.e., the local stresses or strains). It is becoming increasingly obvious that tissue engineered constructs also adapt to altered mechanical loading, and specific combinations of multidirectional loads appear to have a synergistic effect on the remodeling. Tissue engineered heart valve constructs exposed to cyclic flexure and shear stress, for example, exhibit a five-fold increase in production of extracellular matrix (ECM) constituents compared to constructs exposed to cyclic flexure or shear stress alone [1]. A critical gap remains, however, in understanding the role of both unidirectional and multidirectional loading on TEBV remodeling. Towards this end, we have developed theoretical and experimental frameworks to study remodeling of collagen and fibrin gel-derived TEBVs.

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GenTan, Xie, Lin Na, Bi ZhiLi, Shan Jie, and LI HongMei. "Application of Molecular Chemistry in Biochemistry and Chemistry and Biology Application of Traditional in Medicine." In 2021 10th International Conference on Applied Science, Engineering and Technology (ICASET 2021). Paris, France: Atlantis Press, 2021. http://dx.doi.org/10.2991/aer.k.210817.013.

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"Chronological Distribution of Emerging Referenced Disciplines in Biochemistry & Molecular Biology over the Last 100 Years." In iConference 2014 Proceedings: Breaking Down Walls. Culture - Context - Computing. iSchools, 2014. http://dx.doi.org/10.9776/14291.

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Young, Paul W. "Student-produced video of role-plays on topics in cell biology and biochemistry: A novel undergraduate group work exercise." In Learning Connections 2019: Spaces, People, Practice. University College Cork||National Forum for the Enhancement of Teaching and Learning in Higher Education, 2019. http://dx.doi.org/10.33178/lc2019.15.

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Group work or cooperative learning is a form of active learning that has potential benefits that extend beyond just being an alternative or improved way of learning course material. For example, Shimazoe and Aldrich (2010) identified six proposed benefits of active learning to students, namely (1) promoting deep learning, (2) helping students earn higher grades, (3) teaching social skills & civic values, (4) teaching higher order thinking skills, (5) promoting personal growth and (6) developing positive attitudes toward autonomous learning. There is evidence for the effectiveness of role-plays both in achieving learning outcomes (Azman, Musa, & Mydin, 2018; Craciun, 2010; Latif, Mumtaz, Mumtaz, & Hussain, 2018; McSharry & Jones, 2000; Yang, Kim, & Noh, 2010), but also in developing desirable graduate attributes such as teamwork, communication and problem solving skills [4]. The importance of such skills is widely touted by employers of science graduates, sometimes more so than discipline-specific knowledge, arguing in favour of the incorporation of role-plays and other forms of cooperative learning into undergraduate science curricula. Role-playing is probably not as widely used in the physical and life sciences as it is in other academic disciplines. In science the most obvious role-play scenarios in which students play the roles of people might be in examining historical figures at the centre of famous scientific discoveries or debates (Odegaard, 2003). In addition, role-plays fit well at the interface between science and other discipline when exploring ethical, legal or commercial implications of scientific discoveries(Chuck, 2011). However, to apply role-play to core topics in science or mathematics the roles that must be played are not those of people but rather of things like particles, forces, elements, atoms, numbers, laws, equations, molecules, cells, organs and so on. The learning scenarios for science-based roleplays in which the characters represented are not people are less obvious, probably explaining why the use of role-plays in science education is less common. Nevertheless, focusing on the life sciences, role-plays in which the characters are organelles in a cell or enzymes involved in fundamental cellular processes like DNA replication, RNA transcription and protein translation have been described for example (Cherif, Siuda, Dianne M. Jedlicka, & Movahedzadeh, 2016; Takemura & Kurabayashi, 2014). The communication of discipline-specific templates and successful models for the application of role-playing in science education is likely to encourage their wider adoption. Here I describe a videoed group role-play assignment that has been developed over a ten-year period of reflective teaching practice. I suggest that this model of videoed group role-plays is a useful cooperative learning format that will allow learners to apply their varied creativity and talents to exploring and explaining diverse scientific topics while simultaneously developing their teamwork skills.

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Chakraborty, Suman, and Tamal Das. "Frictional Characteristics of Liquid Flows in Narrow Confinements." In ASME 2009 7th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2009. http://dx.doi.org/10.1115/icnmm2009-82126.

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Probing the interfacial friction in narrow confinements is becoming increasingly important in various applications encompassing fluid dynamics over micrometer and nanometer length scales, including applications pertinent to molecular biology, biochemistry, and energy conversion. The present article aims to present a broad overview on the progresses made towards understanding the fundamental mechanisms dictating such interfacial phenomenon, from empirical, semi-empirical to more rigorous physical and mathematical considerations. Futuristic outlook on the related research activities are also outlined, both from fundamental considerations as well as from application viewpoints.

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Kaksis, Aris, Agnese Brangule, and Mihails Halitovs. "AN APPROACH TO TEACHING MEDICAL CHEMISTRY THAT HIGHLIGHTS INTERDISCIPLINARY NATURE OF SCIENCE." In 1st International Baltic Symposium on Science and Technology Education. Scientia Socialis Ltd., 2015. http://dx.doi.org/10.33225/balticste/2015.54.

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Thermodynamics is a branch of physics that deals with questions concerning energies and work of a system. It is one of the key topics for understanding processes in the universe as well as any separate system like a gas mixture or a single cell in a biological system. Thermodynamics is included in the university curriculum for engineering, chemistry and physics students as well as medical student curriculum. This paper outlines the problems faced by first year medical students learning thermodynamics at Riga Stradinš University. We describe a medically relevant context based approach to teaching that demonstrates the interdisciplinary nature of medical chemistry, molecular biology and biochemistry. Our method provides a model in which disciplinary barriers are diminished and increased effectiveness of teaching is achieved. Key words: interdisciplinary teaching, medical chemistry, thermodynamics, teaching and learning thermodynamics.

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