Abstract：
:The continuing expansion of protein and genome sequence databases is an opportunity to identify novel enzymes with biotechnological applications. Whether applied to enzymology, chemical biology, systems biology, and microbiology, database mining must be 'user-friendly' so that experimentalists can devise focused strategies to discover the in vitro activities and in vivo functions of uncharacterized enzymes. We developed a suite of genomic enzymology tools (https://efi.igb.illinois.edu/) to (1) generate sequence similarity networks (SSNs) for exploration of sequence-function space in protein families (EFI-EST) and (2) provide genome context for members of protein families (EFI-GNT). Integrated analysis of this complementary information allows to generate testable hypotheses about new functions. After a brief overview of EFI-EST and EFI-GNT, we describe applications that illustrate their use.
journal_name
Curr Opin Biotechnoljournal_title
Current opinion in biotechnologyauthors
Zallot R,Oberg N,Gerlt JAdoi
10.1016/j.copbio.2020.12.004subject
Has Abstractpub_date
2021-01-05 00:00:00pages
77-90eissn
0958-1669issn
1879-0429pii
S0958-1669(20)30190-7journal_volume
69pub_type
杂志文章,评审abstract：:Clinical testing of therapies for sepsis that target tumor necrosis factor and interleukin-1 is currently in progress. It is now clear from early clinical results that patients display a heterogeneous response to anti-cytokine therapies that may be related to the stage or severity of disease. Experimental results show...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/0958-1669(93)90055-2
更新日期：1993-12-01 00:00:00
abstract：:The world continues to increase its energy use, brought about by an expanding population and a desire for a greater standard of living. This energy use coupled with the realization of the impact of carbon dioxide on the climate, has led us to reanalyze the potential of plant-based biofuels. Of the potential sources of...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2011.10.013
更新日期：2012-06-01 00:00:00
abstract：:New biological inspired methods were recently developed to recover precious metals from waste streams and to concomitantly produce palladium nanoparticles on bacteria, that is, bio-Pd. This technology offers a variety of opportunities, as the process can considered to be green, tunable, affordable and scalable. The na...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2012.01.007
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abstract：:The recent adoption of whole plasmid genome sequencing as a routine analytical technique has provided the basis for cataloging the historical events through which plasmids are assembled from the available families of modular plasmid components. Horizontal gene transfer mediated by plasmids plays an important role in t...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
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abstract：:Microorganisms play important roles in the environmental fate of toxic metals and radionuclides with a multiplicity of mechanisms effecting transformations between soluble and insoluble forms. These mechanisms are integral components of natural biogeochemical cycles and are of potential for both in situ and ex situ bi...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/s0958-1669(00)00095-1
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abstract：:Diols are chemicals with two hydroxyl groups which have a wide range of appealing applications as chemicals and fuels. In particular, four diol compounds, namely 1,3-propanediol (1,3-PDO), 1,2-propanediol (1,2-PDO), 2,3-butanediol (2,3-BDO) and 1,4-butanediol (1,4-BDO) can be biotechnologically produced by direct micr...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2011.05.005
更新日期：2011-12-01 00:00:00
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journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2018.08.011
更新日期：2019-02-01 00:00:00
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journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2014.11.022
更新日期：2015-08-01 00:00:00
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journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2017.02.009
更新日期：2017-08-01 00:00:00
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journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2012.10.004
更新日期：2013-06-01 00:00:00
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journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2018.06.003
更新日期：2019-02-01 00:00:00
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journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2011.06.012
更新日期：2011-12-01 00:00:00
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journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2004.08.010
更新日期：2004-10-01 00:00:00
abstract：:Steady increases in the average sulfur content of petroleum and stricter environmental regulations concerning the sulfur content have promoted studies of bioprocessing to upgrade fossil fuels. Bioprocesses can potentially provide a solution to the need for improved and expanded fuel upgrading worldwide, because biopro...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2006.04.005
更新日期：2006-06-01 00:00:00
abstract：:Metabolic engineering is embraced as a method to sustainably enhance production of valuable phytochemicals with beneficial properties. However, successful production of these compounds in plants is not always predictable even when the pathways are fully known, frequently due to the lack of comprehensive understanding ...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2020.12.014
更新日期：2021-01-08 00:00:00
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journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2003.10.014
更新日期：2003-12-01 00:00:00
abstract：:Among different technologies of hydrogen production, bio-hydrogen production exhibits perhaps the greatest potential to replace fossil fuels. Based on recent research on dark fermentative hydrogen production, this article reviews the following aspects towards scaled-up application of this technology: bioreactor develo...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2011.04.022
更新日期：2011-06-01 00:00:00
abstract：:Summary of the in vitro data support a beneficial effect of cranberry or its proanthocyanin constituents by blocking adhesion to and biofilm formation on target tissues of pathogens. In vivo data partially support these beneficial effects. Consumption of various cranberry products benefited young and elderly females i...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2011.10.009
更新日期：2012-04-01 00:00:00
abstract：:Novel biotechnological approaches such as Metabolic Engineering (ME) and New Plant Breeding Techniques (NPBTs) are currently being developed to produce biological compounds for food and non-food products. NPBTs span a range of methods for in vivo production in crops, some of which are classified as GMOs while others a...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2018.08.012
更新日期：2019-04-01 00:00:00
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journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/s0958-1669(98)80086-4
更新日期：1998-02-01 00:00:00
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journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2018.12.005
更新日期：2019-04-01 00:00:00
abstract：:Plants have a remarkable capacity for the production of a wide range of metabolites. Much has been reported and reviewed on the diversity of these metabolites and how it is achieved, for example through the evolution of enzyme families. In comparison, relatively little is known on the extraordinary metabolic productiv...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2017.08.003
更新日期：2018-02-01 00:00:00
abstract：:Natural products have demonstrated value across numerous application areas, with antibiotics a notable historical example. Native cellular hosts provide an initial option in efforts to harness natural product production. However, various complexities associated with native hosts, including fastidious growth traits and...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2020.06.014
更新日期：2020-12-01 00:00:00
abstract：:The structure of microbial communities is key to their functionality. However, this structure is likely to be influenced by adaptive genetic change in members of the community, which can occur over a matter of days. Changes in community structure can in turn influence the evolutionary trajectories of species within th...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2013.02.022
更新日期：2013-08-01 00:00:00
abstract：:Most secretory proteins are synthesized as precursors with an amino-terminal signal peptide. Genetic identification of proteins essential for signal peptide dependent translocation to the Escherichia coli periplasm has led to the biochemical dissection of the secretion pathway. Additional mechanisms exist in Gram-nega...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/0958-1669(91)90031-y
更新日期：1991-10-01 00:00:00
abstract：:Broad application of microbial fuel cells will require substantial increases in current density. A better understanding of the microbiology of these systems may help. Recent studies have greatly expanded the range of microorganisms known to function either as electrode-reducing microorganisms at the anode or as electr...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2008.10.005
更新日期：2008-12-01 00:00:00
abstract：:Signal transduction is the process of converting one kind of signal or stimulus into another, with the goal of processing external or internal signals into diverse functions. In recent years, progress has been made in identifying signaling pathways, investigating cross-talk and feedbacks in signaling modules, analyzin...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2011.10.004
更新日期：2012-06-01 00:00:00
abstract：:The nature of DNA, the sequence of the human genome and our increased understanding of the genetic basis of many inherited and acquired disorders have made the possibility of curing diseases a reality. The modulation of a host's genome is now the ultimate goal in the treatment of genetic diseases. Historically, gene t...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/s0958-1669(02)00370-1
更新日期：2002-10-01 00:00:00
abstract：:Chinese hamster ovary (CHO) cell-based bioproduction of recombinant proteins can now routinely achieve >5 g/L titers in fed-batches. This progress is partly due to the rapid adaptability of CHO cells to various genetic manipulations and changing process conditions. An inherently plastic genome allows for this adaptabi...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2019.01.011
更新日期：2019-12-01 00:00:00
abstract：:Plant-based foods offer a wide range of nutrients that are essential for human and animal health. Among these nutrients, iron stands out as one of the most important micronutrients. Increasing the iron content in many staple and non-staple plant foods continues to be a goal of many scientists around the world. However...
journal_title：Current opinion in biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.copbio.2016.10.001
更新日期：2017-04-01 00:00:00
