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Microbial systematics and phylogeny should form the foundation and guiding light for a comprehensive understanding of different
aspects of microbiology. However, there are many critical issues in microbial systematics that are currently not resolved.
Some of these include: how to define and delimit a prokaryotic species; development of rationale criteria for the assignment
of higher taxonomic ranks; understanding what unique properties distinguish species from different groups; and understanding
the branching order and interrelationship among higher prokaryotic clades. The sequencing of genomes from large numbers of
cultured as well as uncultured microbes covering prokaryotic diversity provides unique means to achieve these important objectives.
Prokaryotic genomes are found to be very diverse and dynamic and horizontal gene transfers (HGTs) are indicated to have played
important role in species/genome evolution. Although HGT adds a layer of complexity in terms of understanding the genomes
and species evolution, it is contended that vast majority of genes and genetic characteristics that are distinctive characteristics
of higher prokaryotic taxa are vertically inherited and based on them a solid foundation for microbial systematics can be
developed. We describe two kinds of molecular markers consisting of conserved indels in protein sequences and whole proteins
that are specific for different groups that are proving particularly valuable in defining different prokaryotic groups in
clear molecular terms and in understanding their interrelationships. The genetic and biochemical studies on these taxa-specific
molecular markers also open the way to discover novel biochemical and physiological characteristics that are unique properties
of these groups. 相似文献
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Yuxian Zhu 《中国科学:生命科学英文版》2016,59(2):109-111
正As one of the important industrial crops and also an excellent model organism for studying cell elongation,cell wall biosynthesis as well as polyploidy evolution,cotton has always been in the limelight of the world(Shi et al.,2006;Qin and Zhu,2011).With the publication of the allotetraploid Gossypium hirsutum and Gossypium barbadense genomes this year(Li et al.,2015;Zhang et al.,2015;Liu et al.,2015),all three important cotton genomes,including the two ancestor diploid Gossypium raimondii(DD)(Wang et al.,2012;Paterson et al.,2012)and Gossypium arboreum(AA)(Li et al.,2014)have been successfully sequenced by scientists from China and from the United States of America.Since functional studies of Arabidopsis thaliana and 相似文献
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Savio de Siqueira Ferreira Milton Yutaka Nishiyama Jr Andrew H Paterson Glaucia Mendes Souza 《Genome biology》2013,14(6):210
The Saccharinae, especially sugarcane, Miscanthus and sorghum, present remarkable characteristics for bioenergy production. Biotechnology of these plants will be important for a sustainable feedstock supply. Herein, we review knowledge useful for their improvement and synergies gained by their parallel study. 相似文献
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丝状真菌不仅是传统发酵工业中抗生素、酶制剂和有机酸的主要生产者,而且也是代谢工程育种中异源蛋白表达的重要细胞工厂。丝状真菌的遗传修饰和代谢工程研究是现代工业生物技术领域最具活力的研究方向之一。特别是与细菌和酵母相比,丝状真菌在细胞生长、营养需求、环境适应性、翻译后修饰、蛋白分泌能力和生物安全性等方面具有显著的优势。文章综述了丝状真菌作为异源蛋白表达系统在基因组学技术研究和代谢工程研究方面的最新进展。作者在分析丝状真菌基因组结构、特点的基础上,阐述了比较基因组学、蛋白质组学、转录组学和代谢组学等对丝状真菌的代谢途径重构、新型蛋白挖掘和代谢工程育种中的作用和意义。另一方面,作者分析了丝状真菌在表达外源蛋白时遇到的瓶颈问题,总结了丝状真菌代谢工程育种中的常用策略包括异源基因的融合表达、反义核酸技术、蛋白分泌途径改造、密码子优化和蛋白酶缺陷宿主的选育等技术和手段。最后,对该领域的发展趋势进行了展望。 相似文献
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Currently, relatively little is known regarding the protein production of mammalian embryos. Unlike the genome, the proteome itself is dynamic reflecting both internal and external environmental stimuli. Until now the lack of sensitivity has remained a stumbling block for the global introduction of proteomics into the field of mammalian embryology. However, new developments in mass spectrometry have been revolutionary, utilizing protein profiling and peptide sequencing to elucidate underlying biological processes. The sensitivity of these platforms have allowed for the development of new protocols that are capable of profiling the proteome of individual mammalian oocytes and embryos. This information is fundamental to unravelling the complexity of embryo physiology including the dialogue between the developing embryo and its maternal environment. Such proteomic approaches are also assisting in the optimization of ART techniques, including oocyte cryopreservation and in vitro maturation. Embryo selection for transfer is another area of ART that should benefit in this era of proteomics. Currently, mammalian embryos are selected for transfer based on morphological grading systems. Although of great value, analysis of morphology alone cannot determine the embryo's physiological state or chromosomal complement. Subsequently, there is a need to identify in culture those embryos with the highest implantation potential. Proteomic analysis of the embryonic secretome (proteins produced by the embryo and secreted into the surrounding medium) followed by the identification of specific proteins critical for implantation, may lead to the development of a non-invasive viability assay to assist in the selection of embryos for transfer. 相似文献
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Edelman A 《Médecine sciences : M/S》2005,21(8-9):675-678
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Blood components (BCs) are highly complex mixtures of plasma proteins and cells. At present, BC and blood derivatives (BDs) quality control is mainly focused on standardized quantitative assessment, providing relatively limited information about products. Unfortunately, during the production, inactivation, and storage processes there is the risk of changes in their integrity, especially at the protein level, which could cause negative effects on transfusion. It is therefore a major challenge to identify significant alterations of these products, and, in this context, proteomics can play a potentially relevant role in transfusion medicine (TM) to assess the protein composition of blood-derived therapeutics, particularly for identifying modified proteins. It can provide comprehensive information about changes occurring during processing and storage of BCs and BDs and can be applied to assess or improve them, therefore potentially enabling a global assessment of processing, inactivation and storage methods, as well as of possible contaminants and neoantigens that may influence the immunogenic capacity of blood-derived therapeutics. Thus, proteomics could become a relevant part of quality-control process to verify the identity, purity, safety, and potency of various blood therapeutics. A more detailed understanding of the proteins found in blood and blood products, and the identification of their interactions, may also yield important information for the design of new small molecule therapeutics and also for future improvements in TM.
Proteomics, together with genomics in the near future, will presumably have an impact on disease diagnosis and prognosis as well as on further advances in the production, pathogen inactivation and storage processes of blood-based therapeutics. 相似文献
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《Expert review of proteomics》2013,10(1):97-110
Structural proteomics aims to understand the structural basis of protein interactions and functions. A prerequisite for this is the availability of 3D protein structures that mediate the biochemical interactions. The explosion in the number of available gene sequences set the stage for the next step in genome-scale projects – to obtain 3D structures for each protein. To achieve this ambitious goal, the slow and costly structure determination experiments are supplemented with theoretical approaches. The current state and recent advances in structure modeling approaches are reviewed here, with special emphasis on comparative protein structure modeling techniques. 相似文献
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Fiser A 《Expert review of proteomics》2004,1(1):97-110
Structural proteomics aims to understand the structural basis of protein interactions and functions. A prerequisite for this is the availability of 3D protein structures that mediate the biochemical interactions. The explosion in the number of available gene sequences set the stage for the next step in genome-scale projects -- to obtain 3D structures for each protein. To achieve this ambitious goal, the slow and costly structure determination experiments are supplemented with theoretical approaches. The current state and recent advances in structure modeling approaches are reviewed here, with special emphasis on comparative protein structure modeling techniques. 相似文献
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Sali A 《Structure (London, England : 1993)》2003,11(9):1043-1047
Recently, some 50 biologists and officials from government funding agencies met at the NIH campus in Bethesda, MD to explore the interdisciplinary science and organization of the emerging field of structural proteomics. Structural proteomics aims to discover most macromolecular complexes and characterize their three-dimensional structures and functional mechanisms in space and time. The goal seems daunting, but the consensus was that the prize would be commensurate with the effort invested, given the importance of molecular machines and functional networks in biology and medicine. Identification of assemblies and transient complexes combined with their structural and functional characterization will allow us to understand, control, design, and change the functioning of larger biological systems as well as to contribute to drug target discovery, lead discovery, and lead optimization for treatment of human disease. 相似文献
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Al-Tarawneh SK Border MB Dibble CF Bencharit S 《Omics : a journal of integrative biology》2011,15(6):353-361
Recent advancements in mass spectrometric proteomics provide a promising result in utilizing saliva to explore biomarkers for diagnostic purposes. However, the issues of specificity or redundancy of disease-associated salivary biomarkers have not been described. This systematic review was therefore aimed to define and summarize disease-related salivary biomarkers identified by mass spectrometry proteomics. Peer-reviewed articles published through July 2009 within three databases were reviewed. Out of 243 articles, 21 studies were selected in this systematic review with conditions including Sj?gren's syndrome, squamous cell carcinoma, dental caries, diabetes, breast cancer, periodontitis, gastric cancer, systemic sclerosis, oral lichen planus, bleeding oral cavity, and graft-versus-host disease. The sample size ranged from 3-41 in both diseased and control subjects, with no consensus on sample collection protocol. One hundred eighty biomarkers were identified in total; 87 upregulated, 63 downregulated, and 30 varying based on disease. Except for Sj?gren's syndrome, the majority of studies with the same disease produce inconsistent biomarkers. Larger sample size and standardization of sample collection/treatment protocol may improve future studies. 相似文献
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Belhocine TZ Tait JF Vanderheyden JL Li C Blankenberg FG 《Journal of proteome research》2004,3(3):345-349
In the past decade, genomics and proteomics have begun to develop many new targets for potential diagnostic and therapeutic agents. Among the life sciences, nuclear medicine is also deeply involved in the field of clinical investigation. Experience with radiolabeled annexin V highlights the many steps required to translate a good basic-science concept into the clinical setting. This model also emphasizes the value of synergy between basic and medical specialties in developing and optimizing a clinically useful product initially derived from basic investigation. 相似文献
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