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161.
Hisashi Mizutani Hideaki Sugawara Ashley M. Buckle Takeshi Sangawa Ken-ichi Miyazono Jun Ohtsuka Koji Nagata Tomoki Shojima Shohei Nosaki Yuqun Xu Delong Wang Xiao Hu Masaru Tanokura Kei Yura 《BMC structural biology》2017,17(1):4
Background
More than 7000 papers related to “protein refolding” have been published to date, with approximately 300 reports each year during the last decade. Whilst some of these papers provide experimental protocols for protein refolding, a survey in the structural life science communities showed a necessity for a comprehensive database for refolding techniques. We therefore have developed a new resource – “REFOLDdb” that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest.Results
We based our resource on the existing REFOLD database, which has not been updated since 2009. We redesigned the data format to be more concise, allowing consistent representations among data entries compared with the original REFOLD database. The remodeled data architecture enhances the search efficiency and improves the sustainability of the database. After an exhaustive literature search we added experimental refolding protocols from reports published 2009 to early 2017. In addition to this new data, we fully converted and integrated existing REFOLD data into our new resource. REFOLDdb contains 1877 entries as of March 17th, 2017, and is freely available at http://p4d-info.nig.ac.jp/refolddb/.Conclusion
REFOLDdb is a unique database for the life sciences research community, providing annotated information for designing new refolding protocols and customizing existing methodologies. We envisage that this resource will find wide utility across broad disciplines that rely on the production of pure, active, recombinant proteins. Furthermore, the database also provides a useful overview of the recent trends and statistics in refolding technology development.162.
The Effect of Sterilization Methods on the Physical Properties of Silk Sericin Scaffolds 总被引:1,自引:0,他引:1
Protein-based biomaterials respond differently to sterilization methods. Since protein is a complex structure, heat, or irradiation
may result in the loss of its physical or biological properties. Recent investigations have shown that sericin, a degumming
silk protein, can be successfully formed into a 3-D scaffolds after mixing with other polymers which can be applied in skin
tissue engineering. The objective of this study was to investigate the effectiveness of ethanol, ethylene oxide (EtO) and
gamma irradiation on the sterilization of sericin scaffolds. The influence of these sterilization methods on the physical
properties such as pore size, scaffold dimensions, swelling and mechanical properties, as well as the amount of sericin released
from sericin/polyvinyl alcohol/glycerin scaffolds, were also investigated. Ethanol treatment was ineffective for sericin scaffold
sterilization whereas gamma irradiation was the most effective technique for scaffold sterilization. Moreover, ethanol also
caused significant changes in pore size resulting from shrinkage of the scaffold. Gamma-irradiated samples exhibited the highest
swelling property, but they also lost the greatest amount of weight after immersion for 24 h compared with scaffolds obtained
from other sterilization methods. The results of the maximum stress test and Young’s modulus showed that gamma-irradiated
and ethanol-treated scaffolds are more flexible than the EtO-treated and untreated scaffolds. The amount of sericin released,
which was related to its collagen promoting effect, was highest from the gamma-irradiated scaffold. The results of this study
indicate that gamma irradiation should have the greatest potential for sterilizing sericin scaffolds for skin tissue engineering. 相似文献
163.
164.
Eftimie R Dushoff J Bridle BW Bramson JL Earn DJ 《Bulletin of mathematical biology》2011,73(12):2932-2961
Recent advances in virology, gene therapy, and molecular and cell biology have provided insight into the mechanisms through
which viruses can boost the anti-tumor immune response, or can infect and directly kill tumor cells. A recent experimental
report (Bridle et al. in Molec. Ther. 18(8):1430–1439, 2010) showed that a sequential treatment approach that involves two viruses that carry the same tumor antigen leads to an improved
anti-tumor response compared to the effect of each virus alone. In this article, we derive a mathematical model to investigate
the anti-tumor effect of two viruses, and their interactions with the immune cells. We discuss the conditions necessary for
permanent tumor elimination and, in this context, we stress the importance of investigating the long-term effect of non-linear
interactions. In particular, we discuss multi-stability and multi-instability, two complex phenomena that can cause abrupt
transitions between different states in biological and physical systems. In the context of cancer immunotherapies, the transitions
between a tumor-free and a tumor-present state have so far been associated with the multi-stability phenomenon. Here, we show
that multi-instability can also cause the system to switch from one state to the other. In addition, we show that the multi-stability
is driven by the immune response, while the multi-instability is driven by the presence of the virus. 相似文献
165.
ATP-binding cassette (ABC) transporters serve as importers and exporters for a wide variety of solutes in both prokaryotes
and eukaryotes, and are implicated in microbial drug resistance and a number of significant human genetic disorders. Initial
crystal structures of the soluble nucleotide binding domains (NBDs) of ABC transporters, while a significant step towards
understanding the coupling of ATP binding and hydrolysis to transport, presented researchers with important questions surrounding
the role of the signature sequence residues, the composition of the nucleotide binding sites, and the mode of NBD dimerization
during the transport reaction cycle. Recent studies have begun to address these concerns. This mini-review summarizes the
biochemical and structural characterizations of two archaebacterial NBDs from Methanocaldococcus jannaschii, MJ0796 and MJ1267, and offers current perspectives on the functional mechanism of ABC transporters. 相似文献
166.
Previous work has shown that bacterial isolates from the sheep rumen are capable of detoxifying 2,4,6-trinitrotoluene (TNT)
into polar constituents. In this study, the dietary effects of TNT on the sheep rumen microbial community were evaluated using
molecular microbiology ecology tools. Rumen samples were collected from sheep fed with and without TNT added to their diet,
genomic DNA was extracted, and the 16S rRNA-V3 gene marker was used to quantify changes in the microbial population in the
rumen. Control and treatment samples yielded 533 sequences. Phylogenetic analyses were performed to determine the microbial
changes between the two conditions. Results indicated the predominant bacterial populations present in the rumen were comprised
of the phyla Firmicutes and Bacteroidetes, irrespective of presence/absence of TNT in the diet. Significant differences (P < 0.001) were found between the community structure of the bacteria under TNT (−) and TNT (+) diets. Examination of the TNT
(+) diet showed an increase in the clones belonging to family Ruminococcaceae, which have previously been shown to degrade
TNT in pure culture experiments. 相似文献
167.
We introduce a novel computational approach to predict effective genome size (EGS; a measure that includes multiple plasmid copies, inserted sequences, and associated phages and viruses) from short sequencing reads of environmental genomics (or metagenomics) projects. We observe considerable EGS differences between environments and link this with ecologic complexity as well as species composition (for instance, the presence of eukaryotes). For example, we estimate EGS in a complex, organism-dense farm soil sample at about 6.3 megabases (Mb) whereas that of the bacteria therein is only 4.7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects. 相似文献
168.
Inventory and monitoring of wine microbial consortia 总被引:2,自引:0,他引:2
The evolution of the wine microbial ecosystem is generally restricted to Saccharomyces cerevisiae and Oenococcus oeni, which are the two main agents in the transformation of grape must into wine by acting during alcoholic and malolactic fermentation,
respectively. But others species like the yeast Brettanomyces bruxellensis and certain ropy strains of Pediococcus parvulus can spoil the wine. The aim of this study was to address the composition of the system more precisely, identifying other
components. The advantages of the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach to
wine microbial ecology studies are illustrated by bacteria and yeast species identification and their monitoring at each stage
of wine production. After direct DNA extraction, PCR-DGGE was used to make the most exhaustive possible inventory of bacteria
and yeast species found in a wine environment. Phylogenetic neighbor-joining trees were built to illustrate microbial diversity.
PCR-DGGE was also combined with population enumeration in selective media to monitor microbial changes at all stages of production.
Moreover, enrichment media helped to detect the appearance of spoilage species. The genetic diversity of the wine microbial
community and its dynamics during winemaking were also described. Most importantly, our study provides a better understanding
of the complexity and diversity of the wine microbial consortium at all stages of the winemaking process: on grape berries,
in must during fermentation, and in wine during aging. On grapes, 52 different yeast species and 40 bacteria could be identified.
The diversity was dramatically reduced during winemaking then during aging. Yeast and lactic acid bacteria were also isolated
from very old vintages. B. bruxellensis and O. oeni were the most frequent. 相似文献
169.
170.
Kawakami N Lee JM Mon H Kubo Y Banno Y Kawaguchi Y Maenaka K Park EY Koga K Kusakabe T 《Molecular biotechnology》2008,40(2):180-185
The recombinant protein expression by Bombyx mori nucleopolyhedrovirus (BmNPV) infecting silkworm larvae or pupae may endow us with a potent system for the production of large
eukaryotic proteins. However, the screening of silkworm strains ideally suited to this method has scarcely been conducted.
In the present study, we injected recombinant BmNPV containing a reporter gene, luciferase or DsRed, into hemocoel of fifth
instar larvae of selected 12 silkworm strains. Among them, the strain d17 is found to be the highest in reporter expression
from the intrinsic polyhedrin promoter of Autographa californica NPV or the silkworm actin A3 promoter. These results suggest that the d17 strain is highly permissive for BmNPV replication
and is the most likely candidate of a “factory” for large-scale expression using the BmNPV bacmid system. 相似文献