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1.
《Expert review of proteomics》2013,10(3):259-267
Constitutive activity of kinases is known to be crucial for a tumor to maintain its malignant phenotype, a phenomenon which is often referred to as oncogene addiction. The in-depth analysis of aberrant signaling pathways by the analysis of protein phosphorylation has become feasible through recent advances in proteomics technology. In this article we will review developments in the field of phosphoproteomics and its application in cancer research. The most widely used technologies for the generic enrichment of phosphopeptides are discussed as well as targeted approaches for the analysis of a specific subset of phosphopeptides. Validation experiments of phosphorylation sites using targeted mass spectrometry are also explained. Finally, we will highlight applications of phosphoproteomic technology in cancer research using cell lines and tissue. 相似文献
2.
Background
Realizing constructive applications of synthetic biology requires continued development of enabling technologies as well as policies and practices to ensure these technologies remain accessible for research. Broadly defined, enabling technologies for synthetic biology include any reagent or method that, alone or in combination with associated technologies, provides the means to generate any new research tool or application. Because applications of synthetic biology likely will embody multiple patented inventions, it will be important to create structures for managing intellectual property rights that best promote continued innovation. Monitoring the enabling technologies of synthetic biology will facilitate the systematic investigation of property rights coupled to these technologies and help shape policies and practices that impact the use, regulation, patenting, and licensing of these technologies.Results
We conducted a survey among a self-identifying community of practitioners engaged in synthetic biology research to obtain their opinions and experiences with technologies that support the engineering of biological systems. Technologies widely used and considered enabling by survey participants included public and private registries of biological parts, standard methods for physical assembly of DNA constructs, genomic databases, software tools for search, alignment, analysis, and editing of DNA sequences, and commercial services for DNA synthesis and sequencing. Standards and methods supporting measurement, functional composition, and data exchange were less widely used though still considered enabling by a subset of survey participants.Conclusions
The set of enabling technologies compiled from this survey provide insight into the many and varied technologies that support innovation in synthetic biology. Many of these technologies are widely accessible for use, either by virtue of being in the public domain or through legal tools such as non-exclusive licensing. Access to some patent protected technologies is less clear and use of these technologies may be subject to restrictions imposed by material transfer agreements or other contract terms. We expect the technologies considered enabling for synthetic biology to change as the field advances. By monitoring the enabling technologies of synthetic biology and addressing the policies and practices that impact their development and use, our hope is that the field will be better able to realize its full potential.4.
Genome Editing—Principles and Applications for Functional Genomics Research and Crop Improvement 总被引:1,自引:0,他引:1
Genome editing technologies are powerful tools for studying gene function and for crop improvement. The technologies rely on engineered endonucleases to generate double stranded breaks (DSBs) at target loci. The DSBs are repaired through the error-prone non-homologous end joining (NHEJ) and homology-directed repair (HDR) pathways in cells, resulting in mutations and sequence replacement, respectively. In the widely used CRISPR/Cas9 system, the endonuclease Cas9 is targeted by a CRISPR small RNA to DNA sequence of interest. In this review, we describe the four available types of genome editing tools, ZFN, TALEN, CRISPR/Cas9 and CRISPR/Cpf1, and show their applications in functional genomics research and precision molecular breeding of crops. 相似文献
5.
The label-free detection of microbial cells attached to a surface is an active field of research. The field is driven by the need to understand and control the growth of biofilms in a number of applications, including basic research in natural environments, industrial facilities, and clinical devices, to name a few. Despite significant progress in the ability to monitor the growth of biofilms and related living cells, the sensitivity and selectivity of such sensors are still a challenge. We believe that among the many different technologies available for monitoring biofilm growth, optical techniques are the most promising, as they afford direct imaging and offer high sensitivity and specificity. Furthermore, as each technique offers different insights into the biofilm growth mechanism, our analysis allows us to provide an overview of the biological processes at play. In addition, we use a set of key parameters to compare state-of-the-art techniques in the field, including a critical assessment of each method, to identify the most promising types of sensors. We highlight the challenges that need to be overcome to improve the characteristics of current biofilm sensor technologies and indicate where further developments are required. In addition, we provide guidelines for selecting a suitable sensor for detecting microbial cells on a surface. 相似文献
6.
Soloviev M Finch P 《Journal of chromatography. B, Analytical technologies in the biomedical and life sciences》2005,815(1-2):11-24
Characterisation of the complement of expressed proteins from a single genome is a central focus of the evolving field of proteomics. Traditional proteomics technologies were developed in the 20th century and are based on two-dimensional electrophoresis or multidimensional liquid chromatography. These facilitated functional genomics analysis, but they currently represent a significant bottleneck to progress in this area. We are now witnessing the development of novel alternative technologies for use in expression proteomics research. This review aims to familiarise the reader with the principles underlying the peptidomics approaches to proteomics research and provide examples of their applications. 相似文献
7.
Aptamers are single stranded oligonucleotides, comparable to monoclonal antibodies (mAbs) in selectivity and affinity and have significant strategic properties in design, development and applications more than mAbs. Ease of design and development, simple chemical modification and the attachment of functional groups, easily handling and more adaptability with analytical methods, small size and adaptation with nanostructures are the valuable characteristics of aptamers in comparison to large protein based ligands. Among a broad range of targets that their specific aptamers developed, proteins and peptides have significant position according to the number of related studies performed so far. Since proteins control many of important physiological and pathological incidents in the living organisms, particularly human beings and because of the benefits of aptamers in clinical and analytical applications, aptamer related technologies in the field of proteins and peptides are under progress, exclusively. Currently, there is only one FDA approved therapeutic aptamer in the pharmaceutical market, which is specific to vascular endothelial growth factor and is prescribed for age related macular degenerative disease. Additionally, there are several aptamers in the different phases of clinical trials. Almost all of these aptamers are specific to clinically important peptide or protein targets. In addition, the application of protein specific aptamers in the design and development of targeted drug delivery systems and diagnostic biosensors is another intersting field of aptamer technology. In this review, significant efforts related to development and applications of aptamer technologies in proteins and peptides sciences were considered to emphasis on the importance of aptamers in medicinal and clinical applications. 相似文献
8.
场效应晶体管生物传感器因其灵敏度高、分析速度快、无标记、体积小、操作简单等特点而受到了很多关注,广泛应用于DNA、蛋白质、细胞、离子等生物识别物的检测。近年来,更有纳米材料和微电子技术在传感器设计中提高传感器的传感性能,场效应晶体管生物传感器朝着高灵敏、微型化、快速化以及多功能化的方向以令人惊叹的速度发展。研究场效应晶体管生物传感器工作原理,阐述近年来场效应晶体管生物传感器在生物医学检测领域中最新的研究进展与应用,探讨场效应晶体管生物传感器克服各种缺陷的应对策略,为该传感器在未来生物医学检测中的开发提供参考。 相似文献
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Summary. In the postgenomic era new technologies are emerging for global analysis of protein function. The introduction of active site-directed
chemical probes for enzymatic activity profiling in complex mixtures, known as activity-based proteomics has greatly accelerated
functional annotation of proteins. Here we review probe design for different enzyme classes including serine hydrolases, cysteine
proteases, tyrosine phosphatases, glycosidases, and others. These probes are usually detected by their fluorescent, radioactive
or affinity tags and their protein targets are analyzed using established proteomics techniques. Recent developments, such
as the design of probes for in vivo analysis of proteomes, as well as microarray technologies for higher throughput screenings
of protein specificity and the application of activity-based probes for drug screening are highlighted. We focus on biological
applications of activity-based probes for target and inhibitor discovery and discuss challenges for future development of
this field. 相似文献
12.
Iftikhar Ali Fiona Cawkwell Edward Dwyer Brian Barrett Stuart Green 《Journal of Plant Ecology》2016,9(6):649
Aims Grasslands are the world's most extensive terrestrial ecosystem, and are a major feed source for livestock. Meeting increasing demand for meat and other dairy products in a sustainable manner is a big challenge. At a field scale, Global Positioning System and ground-based sensor technologies provide promising tools for grassland and herd management with high precision. With the growth in availability of spaceborne remote sensing data, it is therefore important to revisit the relevant methods and applications that can exploit this imagery. In this article, we have reviewed the (i) current status of grassland monitoring/observation methods and applications based on satellite remote sensing data, (ii) the technological and methodological developments to retrieve different grassland biophysical parameters and management characteristics (i.e. degradation, grazing intensity) and (iii) identified the key remaining challenges and some new upcoming trends for future development.Important findings The retrieval of grassland biophysical parameters have evolved in recent years from classical regression analysis to more complex, efficient and robust modeling approaches, driven by satellite data, and are likely to continue to be the most robust method for deriving grassland information, however these require more high quality calibration and validation data. We found that the hypertemporal satellite data are widely used for time series generation, and particularly to overcome cloud contamination issues, but the current low spatial resolution of these instruments precludes their use for field-scale application in many countries. This trend may change with the current rise in launch of satellite constellations, such as RapidEye, Sentinel-2 and even the microsatellites such as those operated by Skybox Imaging. Microwave imagery has not been widely used for grassland applications, and a better understanding of the backscatter behaviour from different phenological stages is needed for more reliable products in cloudy regions. The development of hyperspectral satellite instrumentation and analytical methods will help for more detailed discrimination of habitat types, and the development of tools for greater end-user operation. 相似文献
13.
Butler JM 《BioTechniques》2007,43(4):ii-iv
Short tandem repeat (STR) typing methods are widely used today for human identity testing applications including forensic DNA analysis. Following multiplex PCR amplification, DNA samples containing the length-variant STR alleles are typically separated by capillary electrophoresis and genotyped by comparison to an allelic ladder supplied with a commercial kit. This article offers a brief perspective on the technologies and issues involved in STR typing. 相似文献
14.
Troost TA Wijsman JW Saraiva S Freitas V 《Philosophical transactions of the Royal Society of London. Series B, Biological sciences》2010,365(1557):3567-3577
Dynamic energy budget models for growth of individual cockles (Cerastoderma edule) and mussels (Mytilus edulis) are adjusted and calibrated to the Oosterschelde by formulating and parametrizing their functional responses using an extensive set of field observations. The resulting model predictions fit the observations satisfactorily. Results indicate that food quality and the importance of detritus as a food source are site-specific as well as species-specific. Despite these differences in their calibrated parameter values, both species show a very similar functional response. Compared with other systems, however, the functional responses of mussels in the present study are clearly higher than those of mussels in other systems. This may be explained by the absence of intra-specific competition in the measurement set-up that was used, and therefore supports the idea that the generally small functional response of M. edulis is caused by intra-specific competition. 相似文献
15.
The emerging field of biomarkers has applications in the diagnosis, staging, prognosis and monitoring of disease progression, as well as in the monitoring of clinical responses to a therapeutic intervention and the development and delivery of personalized treatments to reduce attrition in clinical trials. Moreover, biomarkers have a positive impact on health economics. The word "biomarker" has been used extensively across therapeutic areas and many disciplines, and its nature takes into consideration clinical, physiological, biochemical, developmental, morphological and molecular measures. In drug trials, biomarkers have been proposed for use in efficacy determination and patient population stratification, in deducing pharmacokinetic-pharmacodynamic relationships and in safety monitoring. The interfacing and integration of different technologies for data collection and analysis are pivotal to biomarker identification, characterization, validation and application. "Integrative functional informatics" represents a novel direction in such technology integration. 相似文献
16.
The development of electrospray ionization coupled to mass spectrometry has enabled the analysis of very large intact protein complexes, even when they are held together by weak non-covalent interactions. Together with equally spectacular advances in mass spectrometric instrumentation, a new field has emerged, termed native protein mass spectrometry, which focuses on the structural and functional analysis of the dynamics and interactions occurring in protein complexes. In the past two years, several important progressive steps in technologies have been reported that have led to exciting applications ranging from the detailed study of equilibria between different quaternary structures as influenced by environmental changes or binding of substrates or cofactors, to the analysis of intact nano-machineries, such as whole virus particles, proteasomes and ribosomes. 相似文献
17.
Engineering monoclonal antibodies, now widely used in the clinic, has made it possible to develop a new generation of antibodies with optimized functional properties. These antibodies should allow a significant improvement of the treatment of diseases where only few drugs are available, if any. However, the cost of treatments with monoclonal antibodies requires further improvements in production and purification technologies, and raises the question of generic antibodies. The present review summarizes some of the technological past and present challenges in the field. 相似文献
18.
Phage display with antibody libraries has been widely used with versatile applications. However, phage display with cDNA libraries
is rare and inefficient. Because of uncontrollable reading frames and stop codons in cDNA repertoires, high percentage of
phage clones identified from conventional cDNA libraries are non-open reading frames (non-ORFs) encoding unnatural short peptides
with minimal implications in protein networks. Consequently, phage display has not been used as a technology of functional
proteomics to elucidate protein–protein interactions like yeast two-hybrid system and mass spectrometry-based technologies.
Several strategies, including C-terminal display and ORF cDNA libraries, have been explored to circumvent the technical problem.
The accumulative endeavors eventually led to the efficient elucidation of a large number of tubby- and phosphatidylserine-binding
proteins in recent studies by ORF phage display with minimal reading frame issue. ORF phage display inherits all the versatile
applications of antibody phage display, but enables efficient identification of real endogenous proteins with efficiency,
sensitivity, and accuracy comparable to other technologies of functional proteomics. Its ELISA-like procedure can be conveniently
adapted by individual laboratories or fully automated for high-throughput screening. Thus, ORF phage display is an efficient,
sensitive, versatile, and convenient technology of functional proteomics for elucidation of global and pathway-specific protein–protein
interactions, disease mechanisms, or therapeutic targets. 相似文献
19.
Mixture enhances productivity in a two-species forest: evidence from a modeling approach 总被引:1,自引:0,他引:1
The effect of mixture on productivity has been widely studied for applications related to agriculture but results in forestry
are scarce due to the difficulty of conducting experiments. Using a modeling approach, we analyzed the effect of mixture on
the productivity of forest stands composed of sessile oak and Scots pine. To determine whether mixture had a positive effect
on productivity and if there was an optimum mixing proportion, we used an aggregation technique involving a mean-field approximation
to analyze a distance-dependent individual-based model. We conducted a local sensitivity analysis to identify the factors
that influenced the results the most. Our model made it possible to predict the species proportion where productivity peaks.
This indicates that transgressive over-yielding can occur in these stands and suggests that the two species are complementary.
For the studied growth period, mixture does have a positive effect on the productivity of oak-pine stands. Depending on the
plot, the optimum species proportion ranges from 38 to 74% of oak and the gain in productivity compared to the current mixture
is 2.2% on average. The optimum mixing proportion mainly depends on parameters concerning intra-specific oak competition and
yet, intra-specific competition higher than inter-specific competition was not sufficient to ensure over-yielding in these
stands. Our work also shows how results obtained for individual tree growth may provide information on the productivity of
the whole stand. This approach could help us to better understand the link between productivity, stand characteristics, and
species growth parameters in mixed forests. 相似文献
20.
高通量测序技术的发展促进了组学技术在环境微生物研究中的广泛应用,而宏基因组学是目前最为关键和成熟的组学方法。生物信息学在微生物宏基因组学研究中具有至关重要的作用。它贯穿于宏基因组学的数据收集和存储、数据处理和分析等各个阶段,既是宏基因组学推广的最大瓶颈,也是目前宏基因组学研究发展的关键所在。本文主要介绍和归纳了目前在高通量宏基因组测序中常用的生物信息学分析平台及其重要的信息分析工具。未来几年之内,测序成本的下降和测序深度的增加将进一步增大宏基因组学研究在数据存储、数据处理和数据挖掘层面的难度,因此相应生物信息学技术与方法的研究和发展也势在必行。近期内我们应该首先加强基础性分析和存储平台的建设以方便普通环境微生物研究者使用,同时针对目前生物信息分析的瓶颈步骤和关键任务重点突破,逐步发展。 相似文献