Relevant bibliographies by topics / HIV-1 Sequence Analysis

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  2. Dissertations / Theses
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  4. Conference papers

Academic literature on the topic 'HIV-1 Sequence Analysis'

Author: Grafiati
Published: 4 June 2021
Last updated: 3 February 2022

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Journal articles on the topic "HIV-1 Sequence Analysis"

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GUO, HONG-GUANG, JEAN-CLAUDE CHERMANN, DAVID WATERS, et al. "Sequence analysis of original HIV-1." Nature 349, no. 6312 (1991): 745–46. http://dx.doi.org/10.1038/349745a0.

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Goujon, C. P., V. M. Schneider, C. Jacomet, and J. C. Nicolas. "HIV-1 genotypic resistance: automated sequence analysis and interpretation." Bioinformatics 14, no. 10 (1998): 886–87. http://dx.doi.org/10.1093/bioinformatics/14.10.886.

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Sinha, Sahil, GaneshChandra Saho, SindhuPrabha Rana, et al. "NEXT GENERATION SEQUENCE ANALYSIS OF SEQUENCES FROM SRA FILE OF HIV-1 ENVELOPE PROTEIN." International Journal of Advanced Research 6, no. 9 (2018): 1118–30. http://dx.doi.org/10.21474/ijar01/7621.

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Raharjo, Irvan, and Afiono Agung Prasetyo. "A COMPLETE HIV-1 Env CODING SEQUENCES FROM HIV ISOLATED IN CENTRAL JAVA, INDONESIA." KnE Life Sciences 2, no. 1 (2015): 27. http://dx.doi.org/10.18502/kls.v2i1.112.

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Background:The HIV envelope glycoprotein (env) plays a central role in viral transmission to target cells.The genetic diversity of env gene contributes a great mechanism on how HIV-1 could survive.Aims:To determine the genotype and genetic relationship of our isolate compared to the other HIV-1 isolates, especially from Indonesia based on the env gene. Also, for further use, the molecular properties of our gene had been analyzed. Methods: A complete coding sequence of HIV-1 env gene was cloned from 09IDSKA-6 (HIV isolated in Central Java, Indonesia), inserted into an Escherichia coli expressio
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Wang, Yan, Reda Rawi, Daniel Hoffmann, Binlian Sun, and Rongge Yang. "Inference of global HIV-1 sequence patterns and preliminary feature analysis." Virologica Sinica 28, no. 4 (2013): 228–38. http://dx.doi.org/10.1007/s12250-013-3348-z.

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Aulicino, Paula C., Julieta Kopka, Carlos Rocco, Andrea Mangano, and Luisa Sen. "Sequence Analysis of a South American HIV Type 1 BC Recombinant." AIDS Research and Human Retroviruses 21, no. 10 (2005): 894–96. http://dx.doi.org/10.1089/aid.2005.21.894.

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WANG, Fu-xiang, Hui ZHOU, Hong LING, et al. "Subtype and sequence analysis of HIV-1 strains in Heilongjiang Province." Chinese Medical Journal 120, no. 22 (2007): 2006–10. http://dx.doi.org/10.1097/00029330-200711020-00013.

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Lee, Chun-Nan, Wei-Kung Wang, Wen-Sheng Fan, et al. "Determination of Human Immunodeficiency Virus Type 1 Subtypes in Taiwan by vpu Gene Analysis." Journal of Clinical Microbiology 38, no. 7 (2000): 2468–74. http://dx.doi.org/10.1128/jcm.38.7.2468-2474.2000.

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The genetic diversity of human immunodeficiency virus (HIV) type 1 (HIV-1) has been characterized mainly by analysis of theenv and gag genes. Information on thevpu genes in the HIV sequence database is very limited. In the present study, the nucleotide sequences of the vpugenes were analyzed, and the genetic subtypes determined by analysis of the vpu gene were compared with those previously determined by analysis of the gag and env genes. Thevpu genes were amplified by nested PCR of proviral DNA extracted from 363 HIV-1-infected individuals and were sequenced directly by use of the PCR product
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Ryland, Elizabeth G., Yanhua Tang, Celia D. Christie, and Margaret E. Feeney. "Sequence Evolution of HIV-1 following Mother-to-Child Transmission." Journal of Virology 84, no. 23 (2010): 12437–44. http://dx.doi.org/10.1128/jvi.01617-10.

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ABSTRACT The genetic heterogeneity of HIV-1 poses a major obstacle to vaccine development. Although most horizontally acquired HIV-1 infections are initiated by a single homogeneous virus, marked genetic diversification and evolution occur following transmission. The relative contribution of the antiviral immune response to intrahost viral evolution remains controversial, in part because the sequence of the transmitted virus and the array of T-cell epitopes targeted by both donor and recipient are seldom known. We directly compared predominant viral sequences derived from 52 mother-child trans
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Churchill, Melissa J., David I. Rhodes, Jennifer C. Learmont, et al. "Longitudinal Analysis of Human Immunodeficiency Virus Type 1 nef/Long Terminal Repeat Sequences in a Cohort of Long-Term Survivors Infected from a Single Source." Journal of Virology 80, no. 2 (2006): 1047–52. http://dx.doi.org/10.1128/jvi.80.2.1047-1052.2006.

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ABSTRACT We studied the evolution of human immunodeficiency virus type 1 (HIV-1) in a cohort of long-term survivors infected with an attenuated strain of HIV-1 acquired from a single source. Although the cohort members experienced differing clinical courses, we demonstrate similar evolution of HIV-1 nef/long-terminal repeat (LTR) sequences, characterized by progressive sequence deletions tending toward a minimal nef/LTR structure that retains only sequence elements required for viral replication. The in vivo pathogenicity of attenuated HIV-1 is therefore dictated by viral and/or host factors o
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Dissertations / Theses on the topic "HIV-1 Sequence Analysis"

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Shrestha, Ram Krishna. "Management and analysis of HIV -1 ultra-deep sequence data." University of the Western Cape, 2014. http://hdl.handle.net/11394/8466.

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Philosophiae Doctor - PhD<br>The continued success of antiretroviral programmes in the treatment of HIV is dependent on access to a cost-effective HIV drug resistance test (HIV-DRT). HIVDRT involves sequencing a fragment of the HIV genome and characterising the presence/absence of mutations that confer resistance to one or more drugs. HIV-DRT using conventional DNA sequencing is prohibitively expensive (~US$150 per patient) for routine use in resource-limited settings such as many African countries. While the advent of ultra deep pyrosequencing (UDPS) approaches have considerably reduced (3-5
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Russell, Rodney S. "Novel RNA and protein sequences involved in dimerization and packaging of HIV-1 genomic RNA." Thesis, McGill University, 2004. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=85092.

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During HIV-1 assembly, the Gag structural protein specifically encapsidates two copies of viral genomic RNA in the form of a dimer. An RNA stem-loop structure (SL1) in the 5' untranslated region, known as the dimerization initiation site (DIS), is important for dimerization and packaging of HIV-1 genomic RNA; however, the mechanisms involved are not fully understood. The major goal of this PhD study was to further understand HIV-1 RNA dimerization, and to study the role of the Gag protein in the dimerization and packaging processes. Despite the known involvement of the DIS in RNA dimeri
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Ait, Khaled. "Sequence analysis of human immunodeficiency virus type 1 : a cross-sectional and longitudinal study." Thesis, University College London (University of London), 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.244731.

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Truong, Hong-Ha Manh. "Molecular epidemiology of HIV-1 transmission : a case study of source partners of individuals with acute retroviral syndrome /." Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/9282.

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Anderson, Jon Paul. "Molecular diversity and evolution of human immunodeficiency virus type 1 /." Thesis, Connect to this title online; UW restricted, 1999. http://hdl.handle.net/1773/8049.

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Oliveira, Rafael Martins de. "Análise do perfil transcricional de células dendríticas derivadas de monócitos utilizadas na vacina terapêutica anti-HIV-1." Universidade de São Paulo, 2010. http://www.teses.usp.br/teses/disponiveis/5/5144/tde-22062010-133922/.

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Aplicando tecnologia de microarray, objetivamos traçar o perfil do programa de maturação das Mo-DC pulsadas com HIV autólogo inativado por AT-2, a fim de identificar marcadores específicos de ativação funcional e sugerir um perfil de expressão de genes úteis na identificação de respostas ao modelo in vitro das Mo-vacina DC. Essas informações podem ajudar a estabelecer assinaturas moleculares das funções celulares mais relevante para a melhoria das vacinas terapêuticas. O perfil transcricional foi analisado com base das vias celulares moduladas das Mo-DCs no estado imaturo, transitório e maduro
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Ngandu, Nobubelo Kwanele. "Evolutionary analyses of HIV-1 protein-coding sequences : adaptation to host cytotoxic immune responses and purifying selection at synonymous sites." Doctoral thesis, University of Cape Town, 2009. http://hdl.handle.net/11427/3072.

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Includes abstract.<br>Includes bibliographical references (p. 136-165).<br>This thesis exposes previously ignored evolutionary characteristics of the synonymous sites of virus nucleotide sequences and contributes new findings to the understanding of the evolution of HIV-1 in relation to the human immune response.
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Fan, Wen-Sheng, and 范文昇. "Sequence Analysis and Protein Expression of p17 Gene of The HIV-1 in Taiwan." Thesis, 1999. http://ndltd.ncl.edu.tw/handle/11863136037229402996.

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碩士<br>國立臺灣大學<br>醫事技術學研究所<br>87<br>It has been almost two decades since the first discovery of human immunodeficiency virus type 1 (HIV-1). However, the efficient way to control the HIV-1 infection infection is still lacking. Control of the HIV-1 dissemination is thought to be the most important work in public health. Detection of HIV-1 infection is one of the control measure. The development of highly efficient and accurate diagnostic tests for detection of HIV-1 infction is very important. Because of the genetic diver-sity of HIV-1, it would be necessary and important to develop a local diagn
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Book chapters on the topic "HIV-1 Sequence Analysis"

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Wlodawer, Alexander, Maria Miller, Amy L. Swain, and Mariusz Jaskólski. "Structures of Three Inhibitor Complexes of HIV-1 Protease." In Methods in Protein Sequence Analysis. Birkhäuser Basel, 1991. http://dx.doi.org/10.1007/978-3-0348-5678-2_21.

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Brack-Werner, Ruth, Thomas Görblich, Thomas Werner, et al. "Sequence Analysis of Neuroinvasive and Blood-Derived HIV-1 nef Genes." In Technical Advances in AIDS Research in the Human Nervous System. Springer US, 1995. http://dx.doi.org/10.1007/978-1-4615-1949-2_15.

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Chiodi, Francesca, Mariantonietta Di Stefano, and Farideh Sabri. "Contribution of V3 and Reverse Transcriptase Sequence Analysis to Understanding the Concept of HIV-1 Neurotropism." In Technical Advances in AIDS Research in the Human Nervous System. Springer US, 1995. http://dx.doi.org/10.1007/978-1-4615-1949-2_14.

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Kuiken, Carla L., and Thomas Leitner. "HIV-1 Subtyping." In Computational and Evolutionary Analysis of HIV Molecular Sequences. Springer US, 2002. http://dx.doi.org/10.1007/0-306-46900-6_3.

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Loeb, D. D., C. A. Hutchison, L. Everitt, W. G. Farmerie, and R. Swanstrom. "Mutational Analysis of the HIV-1 Protease: Importance for Function of Sequences within and Flanking the Protease Domain." In Proteases of Retroviruses, edited by Vladimír Kostka. De Gruyter, 1989. http://dx.doi.org/10.1515/9783110862782-014.

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Cliff, A. D., M. R. Smallman-Raynor, P. Haggett, D. F. Stroup, and S. B. Thacker. "Temporal Trends in Disease Emergence and Re-emergence: World Regions, 1850–2006." In Infectious Diseases: A Geographical Analysis. Oxford University Press, 2009. http://dx.doi.org/10.1093/oso/9780199244737.003.0019.

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In Chapters 4–8, we have examined a series of processes that, often working in combination, have served to precipitate the emergence and re-emergence of infectious and parasitic disease agents in the human population. In this chapter, we conclude our survey with an analysis of temporal trends in disease emergence and re-emergence since 1850. The discussion is informed by long-term shifts in the underlying causes of mortality encapsulated in Omran’s model of epidemiological transition (Section 1.4.1), paying particular attention to the manner in which sample infectious and parasitic diseases have waxed and waned at a variety of geographical scales from the global to the local over the last ∼150 years. Our choice of examples strikes a balance between coverage of geographical regions and epidemiological environments, and coverage of important diseases that we have not so far examined in detail. Our consideration is structured by geographical scale: (1) At the global level, we discuss three major human diseases that have undergone phases of rapid global expansion since 1850—plague, cholera, and HIV/AIDS (Section 9.2). (2) At the regional level, we examine twentieth-century trends in general infectious disease mortality in the advanced economies of Europe, North America, and the South Pacific, 1901–75, before looking at time sequences for sample emerging (Ebola–Marburg) and cyclically re-emerging (meningococcal) diseases in sub-Saharan Africa (Section 9.3). (3) At the national level, we use Hall’s (1993) data to establish the main trends in morbidity due to infectious diseases in Australia, 1917–91 (Section 9.4). (4) At the local level, we extend our examination of long-term disease trends in London, described for the pre-1850 period in Section 2.4, into the late twentieth century (Section 9.5). The chapter is concluded in Section 9.6. In this section, we examine long-term trends in three major human infectious diseases that have undergone phases of global expansion in the last 150 years: plague (Section 9.2.1); cholera (Section 9.2.2); and HIV/AIDS (Section 9.2.3).
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Insko, Jeffrey. "Diedrich Knickerbocker, Regular Bred Historian." In History, Abolition, and the Ever-Present Now in Antebellum American Writing. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198825647.003.0002.

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Chapter 1 analyzes the self-consciousness—and uncanny postmodernity—of Washington Irving in the various works attributed to his historian alter ego Diedrich Knickerbocker, particularly A History of New York and “Rip Van Winkle.” I argue that Irving’s Knickerbocker writings inaugurated an under-recognized tradition of antebellum writing devoted less to the creation of a coherent national past than to theorizing “history” itself. Irving’s A History of New York (1809) forms a kind of practical illustration of the dismantling of history writing in our own time. Irving’s metahistorical discourse, I claim, cannot be adequately accounted for by conventional historicist contextualization, by confining his works to a particular moment in time, much less one that has been superseded by or that is irretrievably distant and distinct from the critical present. Working in tandem with A History of New York’s disquisition on the mutability of historical knowledge is the experience of history “Rip Van Winkle” offers to its readers. A story of temporal dislocation, “Rip Van Winkle” exploits and critiques Rip’s—and the reader’s—desire to settle upon an orienting present and locate that present within a chronological sequence (before, during, and after the war).
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Wei, James. "Estimation by Associations and Trends." In Product Engineering. Oxford University Press, 2007. http://dx.doi.org/10.1093/oso/9780195159172.003.0011.

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Product engineers are often challenged to estimate: 1. the properties of new or obscure classes of material that have not been extensively studied before, or have never been made before; 2. the property changes on a material due to physical and chemical modifications; 3. the properties under a variety of ambient conditions, such as temperatures, pressures, electromagnetic fields, and prolonged environmental exposures and weathering. When theoretical understanding is insufficient and quantitative correlations are not available, we can often make useful qualitative estimations by using fragmentary empirical structure–property relations. The principal tools are observations of associations and trends, which are often the only methods available in biological, health, safety, and environmental properties. Association is based on analogy, or the probabilistic assumption that “similar substances have similar properties.” Does x◦, the material in question, resemble a known substance x1 or a class of substances {x1, x2, . . ., xi , . . .} that have known properties and structure? If we can find such a match, then we can use it to make qualitative property estimates for x◦.We know that metals are nearly always solids at room temperature, but mercury is an exception. Trend is based on the study of the variation of properties among the substances {x1, x2, . . ., xi, . . .} and how they depend on structure variations, which amounts to qualitative and empirical structure–property relations. For example, we know that a larger molecule tends to have higher melting and boiling points, but chlorobenzene has lower melting point than benzene. Thomas Midgley used qualitative trend analysis to help him to discover the chlorofluorocarbons as refrigerants. He did not have a well-organized database, nor did he have an established method of analysis and prediction, and his method was ad hoc and empirical. What he did know was that sulfur dioxide and ammonia were in use as refrigerants. He looked at the periodic table of nonmetallic elements and observed the trend that small compounds of these elements tend to become less flammable when we move from the left to the right of the table, which is certainly true in the sequence CH4, NH3, H2O, and HF.
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Turing, Alan, and Emil Post. "On Computable Numbers: Corrections and Critiques." In The Essential Turing. Oxford University Press, 2004. http://dx.doi.org/10.1093/oso/9780198250791.003.0006.

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As is not uncommon in work of such complexity, there are a number of mistakes in ‘On Computable Numbers’. Turing corrected some of these in his short note 2.1, published in the Proceedings of the London Mathematical Society a few months after the original paper had appeared. The mathematician Emil L. Post’s critique of ‘On Computable Numbers’ was published in 1947 and formed part of Post’s paper ‘Recursive Unsolvability of a Problem of Thue’. Post is one of the major figures in the development of mathematical logic in the twentieth century, although his work did not gainwide recognition until after his death. (Born in 1897, Post died in the same year as Turing.) By 1936 Post had arrived independently at an analysis of computability substantially similar to Turing’s. Post’s ‘problem solver’ operated in a ‘symbol space’ consisting of ‘a two way infinite sequence of spaces or boxes’. A box admitted ‘of but two possible conditions, i.e., being empty or unmarked, and having a single mark in it, say a vertical stroke’. The problem solver worked in accordance with ‘a fixed unalterable set of directions’ and could perform the following ‘primitive acts’: determine whether the box at present occupied is marked or not; erase any mark in the box that is at present occupied; mark the box that is at present occupied if it is unmarked; move to the box to the right of the present position; move to the box to the left of the present position. Later, Post considerably extended certain of the ideas in Turing’s ‘Systems of Logic Based on Ordinals’, developing the important field now called degree theory. In his draft letter to Church, Turing responded to Post’s remarks concerning ‘Turing convention-machines’. It is doubtful whether Turing ever sent the letter. The approximate time of writing can be inferred from Turing’s opening remarks: Kleene’s review appeared in the issue of the Journal of Symbolic Logic dated September 1947 (12: 90–1) and Turing’s ‘Practical Forms of Type Theory’ appeared in the same journal in June 1948.
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Conference papers on the topic "HIV-1 Sequence Analysis"

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Philips, M., A. G. Juul, S. Thorsen, J. Selmer, and L. Thim. "PURIFICATION AND CHARACTERIZATION OF REACTIVE AND NON-REACTIVE PLASMINOGEN ACTIVATOR INHIBITOR-1 (PAI-1) FROM HUMAN PLACENTA." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642806.

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Reactive and non-reactive forms of PAI-1 have been identified in various biological materials. The structural differences between these forms remain to be determined.A monoclonal antibody specific for a non-reactive PAI-1 and a monoclonal antibody reacting with both the reactive and nonreactive form of the inhibitor were obtained by immunization with a tissue-type plasminogen activator (t-PA)-PAI-1 complex (Philips et al., Thromb Haemostas 1986; 55:213-7). These antibodies were used for the isolation of reactive and non-reactive PAI-1 by solid-phase immunoadsorption from extracts of human plac
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Brändström, A., and M. Rånby. "t-PA PROTEIN DETERMINATION: IMPROVED ACCURACY THROUGH COMPOSITION CONSIOUS AMINO ACID ANALYSIS (CCAAA)." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644408.

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Protein determination by composition consious amino acid analysis (CCAAA) is generally applicable to polypeptides with known amino acid composition.Traditionally, in protein determination by AAA the mass of protein substance in a preparation is quantitated by simple summation of the mass of all amino acid residues found, although some amino acids e.g. Trp, Ser, Thr, Cys are unsatisfactorily determined. In this study we have explored the, possibility of improving protein determination by AAA in cases where the amino acid composition of the preparation is precisely known from sequence data. In C
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