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1.
Phillip A Patten Russell J Howard Willem PC Stemmer 《Current opinion in biotechnology》1997,8(6):724-733
DNA shuffling is a practical process for directed molecular evolution which uses recombination to dramatically accelerate the rate at which one can evolve genes. Single and multigene traits that require many mutations for improved phenotypes can be evolved rapidly. DNA shuffling technology has been significantly enhanced in the past year, extending its range of applications to small molecule pharmaceuticals, pharmaceutical proteins, gene therapy vehicles and transgenes, vaccines and evolved viruses for vaccines, and laboratory animal models. 相似文献
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Leonard Schmiester Yannik Schlte Frank T. Bergmann Tacio Camba Erika Dudkin Janine Egert Fabian Frhlich Lara Fuhrmann Adrian L. Hauber Svenja Kemmer Polina Lakrisenko Carolin Loos Simon Merkt Wolfgang Müller Dilan Pathirana Elba Raimúndez Lukas Refisch Marcus Rosenblatt Paul L. Stapor Philipp Stdter Dantong Wang Franz-Georg Wieland Julio R. Banga Jens Timmer Alejandro F. Villaverde Sven Sahle Clemens Kreutz Jan Hasenauer Daniel Weindl 《PLoS computational biology》2021,17(1)
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been—so far—no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PEtab, a format which facilitates the specification of parameter estimation problems using Systems Biology Markup Language (SBML) models and a set of tab-separated value files describing the observation model and experimental data as well as parameters to be estimated. We already implemented PEtab support into eight well-established model simulation and parameter estimation toolboxes with hundreds of users in total. We provide a Python library for validation and modification of a PEtab problem and currently 20 example parameter estimation problems based on recent studies. 相似文献
3.
Eva Veronesi Frank Antony Simon Gubbins Nick Golding Alison Blackwell Peter PC. Mertens Joe Brownlie Karin E. Darpel Philip S. Mellor Simon Carpenter 《PloS one》2013,8(8)
Background
Culicoides biting midges (Diptera: Ceratopogonidae) are the biological vectors of globally significant arboviruses of livestock including bluetongue virus (BTV), African horse sickness virus (AHSV) and the recently emerging Schmallenberg virus (SBV). From 2006–2009 outbreaks of BTV in northern Europe inflicted major disruption and economic losses to farmers and several attempts were made to implicate Palaearctic Culicoides species as vectors. Results from these studies were difficult to interpret as they used semi-quantitative RT-PCR (sqPCR) assays as the major diagnostic tool, a technique that had not been validated for use in this role. In this study we validate the use of these assays by carrying out time-series detection of BTV RNA in two colony species of Culicoides and compare the results with the more traditional isolation of infectious BTV on cell culture.Methodology/Principal Findings
A BTV serotype 1 strain mixed with horse blood was fed to several hundred individuals of Culicoides sonorensis (Wirth & Jones) and C. nubeculosus (Mg.) using a membrane-based assay and replete individuals were then incubated at 25°C. At daily intervals 25 Culicoides of each species were removed from incubation, homogenised and BTV quantified in each individual using sqPCR (Cq values) and virus isolation on a KC-C. sonorensis embryonic cell line, followed by antigen enzyme-linked immunosorbent assay (ELISA). In addition, comparisons were also drawn between the results obtained with whole C. sonorensis and with individually dissected individuals to determine the level of BTV dissemination.Conclusions/Significance
Cq values generated from time-series infection experiments in both C. sonorensis and C. nubeculosus confirmed previous studies that relied upon the isolation and detection of infectious BTV. Implications on the testing of field-collected Culicoides as potential virus vectors by PCR assays and the use of such assays as front-line tools for use in diagnostic laboratories in this role are discussed. 相似文献4.
Phylogenetic relationships were determined for 76 partial P-element
sequences from 14 species of the melanogaster species group within the
Drosophila subgenus Sophophora. These results are examined in the context
of the phylogeny of the species from which the sequences were isolated.
Sequences from the P-element family fall into distinct subfamilies, or
clades, which are often characteristic for particular species subgroups.
When examined locally among closely related species, the evolution of P
elements is characterized by vertical transmission, whereby the P-element
phylogeny traces the species phylogeny. On a broader scale, however, the
P-element phylogeny is not congruent with the species phylogeny. One
feature of P-element evolution in the melanogaster group is the presence of
more than one P-element subfamily, differing by as much as 36%, in the
genomes of some species. Thus, P elements from several individual species
are not monophyletic, and a likely explanation for the incongruence between
P-element and species phylogenies is provided by the comparison of
paralogous sequences. In certain instances, horizontal transfer seems to be
a valid alternative explanation for lack of congruence between species and
P-element phylogenies. The canonical P-element subfamily, which represents
the active, autonomous transposable element, is restricted to D.
melanogaster. Thus, its origin clearly lies outside of the melanogaster
species group, consistent with the earlier conclusion of recent horizontal
transfer.
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Carl PC Chen Chih-Chin Hsu Wen-Lin Yeh Hsiu-Chu Lin Sen-Yung Hsieh Shih-Cherng Lin Tai-Tzung Chen Max JL Chen Simon FT Tang 《Proteome science》2011,9(1):1-10
Background
Prenatal screening for Down Syndrome (DS) would benefit from an increased number of biomarkers to improve sensitivity and specificity. Improving sensitivity and specificity would decrease the need for potentially risky invasive diagnostic procedures.Results
We have performed an in depth two-dimensional difference gel electrophoresis (2D DIGE) study to identify potential biomarkers. We have used maternal plasma samples obtained from first and second trimesters from mothers carrying DS affected fetuses compared with mothers carrying normal fetuses. Plasma samples were albumin/IgG depleted and expanded pH ranges of pH 4.5 - 5.5, pH 5.3 - 6.5 and pH 6 - 9 were used for two-dimensional gel electrophoresis (2DE). We found no differentially expressed proteins in the first trimester between the two groups. Significant up-regulation of ceruloplasmin, inter-alpha-trypsin inhibitor heavy chain H4, complement proteins C1s subcomponent, C4-A, C5, and C9 and kininogen 1 were detected in the second trimester in maternal plasma samples where a DS affected fetus was being carried. However, ceruloplasmin could not be confirmed as being consistently up-regulated in DS affected pregnancies by Western blotting.Conclusions
Despite the in depth 2DE approach used in this study the results underline the deficiencies of gel-based proteomics for detection of plasma biomarkers. Gel-free approaches may be more productive to increase the number of plasma biomarkers for DS for non-invasive prenatal screening and diagnosis. 相似文献8.
Maggio CD Jennings SR Robichaux JL Stapor PC Hyman JM 《Bulletin of mathematical biology》2012,74(1):143-158
We extend and analyze the Wang and Politi modified Hai–Murphy model of smooth muscle cell contractions to capture uterine
muscle cell response to variations in intracellular calcium concentrations. This model is used to estimate values of unknown
parameters in uterine smooth muscle cell cross-bridging. Uterine motility is responsible for carrying out important processes
throughout all phases of the nonpregnant female reproductive cycle, including sperm transport, menstruation, and embryo implantation.
The modified Hai–Murphy partial differential equation model accounts for the displacement of myosin cross-bridge heads relative
to their binding sites. This model was originally developed for the study of airway contractions; we now extended it for use
in modeling nonisometric uterine contractions. Our extended model incorporates cross-bridge position and contractile velocity
into the original model, resulting in more accurate modeling of the initial stages of contraction and modeling nonisometric
contractions. Numerical simulations show that the contraction rate in our extended model is faster than the original Hai–Murphy
model. These simulations provide quantitative estimates for the increased level of responsiveness of our extended model to
intracellular calcium concentrations. The extended model and new parameter estimates for the cross-bridging can be coupled
with uterine flow models to advance our understanding of embryonic motility and intrauterine flow. 相似文献
9.
Plant Molecular Biology - 相似文献
10.
Martijn F Schenk Jan HG Cordewener Antoine HP America Wendy PC van't Westende Marinus JM Smulders Luud JWJ Gilissen 《BMC plant biology》2009,9(1):24