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The conversion of lactose — the main constituent of whey — to methane and carbon dioxide was studied using different defined constructed cultures, imploying strains of Methanosarcina barkeri, Methanobacterium bryantii, Escherichia coli, Acetobacterium woodii, Lactobacillus casei, and Lactobacillus plantarum. The following combinations of strains (food chains) were studied with respect to efficiency and yield of lactose conversion (methane yield in parentheses): E. coli and M. barkeri (4.5–7.6%), E. coli and M. bryantii (13.3%),E. coli, M. barkeri and M. bryantii (54%), L. casei, A. woodii and M. barkeri (93.3%). These conversions were carried out in pH controlled batch fermentations. A very efficient coculture was a combination of L. plantarum with A. woodii and M. barkeri: in chemostat cultures lactose was converted to methane and carbon dioxide with a yield of about 90%, at dilution rates of 0.27 d-1to 0.37 d-1. 相似文献
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Ruiyu Xie Logan J. Everett Hee-Woong Lim Nisha A. Patel Jonathan Schug Evert Kroon Olivia G. Kelly Allen Wang Kevin A. D’Amour Allan J. Robins Kyoung-Jae Won Klaus H. Kaestner Maike Sander 《Cell Stem Cell》2013,12(2):224-237
Highlights? Pancreatic lineage progression is governed by PcG-dependent chromatin remodeling ? A temporal chromatin signature predicts regulators of pancreatic development ? Endocrine cells differentiated from hESCs in vivo are similar to native human islets ? In vitro-produced malfunctioning endocrine cells exhibit aberrant chromatin structure 相似文献
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All-atom folding of the three-helix HIV accessory protein with an adaptive parallel tempering method
All-atom protein structure prediction from the amino acid sequence alone remains an important goal of biophysical chemistry. Recent progress in force field development and validation suggests that the PFF01 free-energy force field correctly predicts the native conformation of various helical proteins as the global optimum of its free-energy surface. Reproducible protein structure prediction requires the availability of efficient optimization methods to locate the global minima of such complex potentials. Here we investigate an adapted version of the parallel tempering method as an efficient parallel stochastic optimization method for protein structure prediction. Using this approach we report the reproducible all-atom folding of the three-helix 40 amino acid HIV accessory protein from random conformations to within 2.4 A backbone RMS deviation from the experimental structure with modest computational resources. 相似文献
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PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data
Bahl A Brunk B Crabtree J Fraunholz MJ Gajria B Grant GR Ginsburg H Gupta D Kissinger JC Labo P Li L Mailman MD Milgram AJ Pearson DS Roos DS Schug J Stoeckert CJ Whetzel P 《Nucleic acids research》2003,31(1):212-215
PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates the recently completed P. falciparum genome sequence and annotation, as well as draft sequence and annotation emerging from other Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for intra- and inter-species comparisons. Sequence information is integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects and proteomics studies. The relational schema used to build PlasmoDB, GUS (Genomics Unified Schema) employs a highly structured format to accommodate the diverse data types generated by sequence and expression projects. A variety of tools allow researchers to formulate complex, biologically-based, queries of the database. A stand-alone version of the database is also available on CD-ROM (P. falciparum GenePlot), facilitating access to the data in situations where internet access is difficult (e.g. by malaria researchers working in the field). The goal of PlasmoDB is to facilitate utilization of the vast quantities of genomic-scale data produced by the global malaria research community. The software used to develop PlasmoDB has been used to create a second Apicomplexan parasite genome database, ToxoDB (http://ToxoDB.org). 相似文献
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We isolated 96 dinucleotide repeats with five or more tandemly repeated units from a subgenomic Drosophila subobscura library. The mean repeat unit length of microsatellite clones in D. subobscura is 15, higher than that observed in other Drosophila species. Population variation was assayed in 32-40 chromosomes from Barcelona, Spain, using 18 randomly chosen microsatellite loci. Positive correlation between measures of variation and perfect repeat length measures (mean size, most common, and longest allele) is consistent with a higher mutation rate in loci with longer repeat units. Levels of microsatellite variation measured as variance in repeat number and heterozygosity in D. subobscura were similar to those of Drosophila pseudoobscura and higher than those of Drosophila melanogaster and Drosophila simulans. Our data suggest that higher levels of microsatellite variation, and possibly density, in D. subobscura compared with D. melanogaster are due to both a higher average effective population and a higher intrinsic slippage rate in the former species. 相似文献
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Georgia Anyatonwu M. Tariq Khan Zachary T. Schug Paula C. A. da Fonseca Edward P. Morris Suresh K. Joseph 《The Journal of biological chemistry》2010,285(32):25085-25093
We have used limited trypsin digestion and reactivity with PEG-maleimides (MPEG) to study Ca2+-induced conformational changes of IP3Rs in their native membrane environment. We found that Ca2+ decreased the formation of the 95-kDa C-terminal tryptic fragment when detected by an Ab directed at a C-terminal epitope (CT-1) but not with an Ab recognizing a protected intraluminal epitope. This suggests that Ca2+ induces a conformational change in the IP3R that allows trypsin to cleave the C-terminal epitope. Half-maximal effects of Ca2+ were observed at ∼0.5 μm and was sensitive to inhibition by IP3. Ca2+ also stimulated the reaction of MPEG-5 with an endogenous thiol in the 95-kDa fragment. This effect was eliminated when six closely spaced cysteine residues proximal to the transmembrane domains were mutated (C2000S, C2008S, C2010S, C2043S, C2047S, and C2053S) or when the N-terminal suppressor domain (amino acids 1–225) was deleted. A cysteine substitution mutant introduced at the C-terminal residue (A2749C) was freely accessible to MPEG-5 or MPEG-20 in the absence of Ca2+. However, cysteine substitution mutants in the interior of the tail were poorly reactive with MPEG-5, although reactivity was enhanced by Ca2+. We conclude the following: a) that large conformational changes induced by Ca2+ can be detected in IP3Rs in situ; b) these changes may be driven by Ca2+ binding to the N-terminal suppressor domain and expose a group of closely spaced endogenous thiols in the channel domain; and c) that the C-terminal cytosol-exposed tail of the IP3R may be relatively inaccessible to regulatory proteins unless Ca2+ is present. 相似文献
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An evolutionary strategy for all-atom folding of the 60-amino-acid bacterial ribosomal protein l20 下载免费PDF全文
We have investigated an evolutionary algorithm for de novo all-atom folding of the bacterial ribosomal protein L20. We report results of two simulations that converge to near-native conformations of this 60-amino-acid, four-helix protein. We observe a steady increase of "native content" in both simulated ensembles and a large number of near-native conformations in their final populations. We argue that these structures represent a significant fraction of the low-energy metastable conformations, which characterize the folding funnel of this protein. These data validate our all-atom free-energy force field PFF01 for tertiary structure prediction of a previously inaccessible structural family of proteins. We also compare folding simulations of the evolutionary algorithm with the basin-hopping technique for the Trp-cage protein. We find that the evolutionary algorithm generates a dynamic memory in the simulated population, which leads to faster overall convergence. 相似文献