Abstract：
:Microarray analysis has become a popular and routine method in functional genomics. It is typical for such experiments to involve a small number of replicates, which causes unreliable estimates of the sample variance. Microarrays have fostered the development of new statistical methods to analyze data resulting from experiments with small sample sizes. In this study, we tackle the problem of evaluating the performance of statistical tests for generating ranked gene lists from two-channel direct comparisons. We propose an evaluation method based on a oligonucleotide microarray with a large number of replicate spots yielding a maximum of 400 replicates per gene. We apply Spearman's rank correlation coefficient to ranked gene-lists generated by eight widely used microarray specific test statistics, which are applied to small random samples. We could show that variance stabilizing methods such as Cyber-T, SAM, and LIMMA can be beneficial for very small sample sizes and that SAM and the t-test provide stronger control of the type I error rate than the other methods. Specifically, we report that for four replicates all methods reach a high to very high correlation with our reference standard.
journal_name
J Biotechnoljournal_title
Journal of biotechnologyauthors
Dondrup M,Hüser AT,Mertens D,Goesmann Adoi
10.1016/j.jbiotec.2009.01.009subject
Has Abstractpub_date
2009-03-10 00:00:00pages
18-26issue
1-2eissn
0168-1656issn
1873-4863pii
S0168-1656(09)00009-1journal_volume
140pub_type
杂志文章abstract：:The Pichia anomala gene PPHY, which codes for a cell-bound phytase, was isolated from genomic DNA by PCR, using oligonucleotide sequences derived from the N-terminal region of the purified phytase protein (Pphyp) and a degenerate primer derived from conserved sequences of yeast and fungal phytases as primers. The gene...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2010.06.017
更新日期：2010-08-20 00:00:00
abstract：:The thermostable glucose dehydrogenase (GDH) from Burkholderia cepacia sp. SM4 is composed of a catalytic subunit (alpha), an electron transfer subunit (beta), and a small gamma subunit of unknown function. We cloned a 1428-nucleotide gene encoding the beta subunit located immediately downstream of the alpha subunit. ...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2005.10.017
更新日期：2006-05-17 00:00:00
abstract：:Xylose-fermenting Saccharomyces strains are needed for commercialization of ethanol production from lignocellulosic biomass. Engineered Saccharomyces cerevisiae strains expressing XYL1, XYL2 and XYL3 from Pichia stipitis, however, utilize xylose in an oxidative manner, which results in significantly lower ethanol yiel...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2010.09.962
更新日期：2010-11-01 00:00:00
abstract：:For proteome research, antibodies against a growing number of antigens must be generated and characterized. The high throughput generation of antibody fragments, using in vitro selection, requires bacterial expression of antibody fragments. This created a need to establish an expression method to improve the parallel ...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2012.07.011
更新日期：2013-01-20 00:00:00
abstract：:Yarrowia lipolytica can accumulate large amounts of storage lipids and has considerable potential for the production of polyunsaturated fatty acids and other lipids for biofuels. When the nitrogen source is exhausted in the medium, the key intermediate, citrate, is converted to acetyl-CoA by ATP:citrate lyase (ACL) fo...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2014.10.004
更新日期：2014-12-20 00:00:00
abstract：:Pyrosequencing technology is a rather novel DNA sequencing method based on the sequencing-by-synthesis principle. This bioluminometric, real-time DNA sequencing technique employs a cascade of four enzymatic reactions producing sequence peak signals. The method has been proven highly suitable for single nucleotide poly...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2006.01.025
更新日期：2006-07-25 00:00:00
abstract：:In this paper we report the development of a recombinant strain of the yeast Pichia pastoris, which secretes an anti-carcinoembryonic antigen single chain Fv (scFv) antibody fragment to the culture supernatant as a biologically active protein, at levels of 1.2 g l(-1). The yeast scFv was purified by IMAC, with a final...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/s0168-1656(99)00183-2
更新日期：2000-01-21 00:00:00
abstract：:One of the major constraints to performing large-scale transfections of cultured mammalian cells for the transient expression of recombinant proteins is the production of large quantities of purified plasmid DNA. In this report partially purified plasmid DNA was prepared by a method that combines alkaline lysis of E. ...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/s0168-1656(03)00032-4
更新日期：2003-05-08 00:00:00
abstract：:A common approach for analyzing large-scale molecular data is to cluster objects sharing similar characteristics. This assumes that genes with highly similar expression profiles are likely participating in a common molecular process. Biological systems are extremely complex and challenging to understand, with proteins...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2020.12.002
更新日期：2021-01-20 00:00:00
abstract：:A microcarrier culture system was established for a large-scale production of functional human endothelial cells. It has been difficult to cultivate human endothelial cells in large quantities for the reasons that specific growth factor and extracellular matrix are required for the survival and proliferation of the ce...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2012.02.022
更新日期：2012-08-31 00:00:00
abstract：:Batch bioreactor cultivations using Saccharomyces cerevisiae at high (190-305 gl(-1) glucose) or low (21-25 gl(-1) glucose) gravity conditions were monitored on-line using multi-wavelength fluorescence (MWF) and standard monitoring sensors. Partial least squares models were calibrated for the prediction of cell dry we...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2009.08.018
更新日期：2009-10-26 00:00:00
abstract：:The elemental composition of microorganisms varies widely with respect to the N, S, P and ash content as well as many trace elements depending on microorganism and growth conditions. As a consequence, the mass of 1 C-mol of biomass can differ considerably from one microorganism to another. Experimental results show th...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/0168-1656(95)00135-0
更新日期：1995-12-01 00:00:00
abstract：:To achieve effective bioprocess monitoring, sensing systems are required which are suitable for an on-line determination of substrates, inhibitors, nutrients or products. Such devices may utilise biochemical principles, i.e. the specific interaction of biochemical receptors with their surroundings. They can be constru...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/0168-1656(93)90072-u
更新日期：1993-12-01 00:00:00
abstract：:The pharmaceutical production of recombinant proteins, such as monoclonal antibodies, is rather complex and requires proper development work. Accordingly, it is essential to develop appropriate scale-down models, which can mimic the corresponding production scale. In this work, we investigated the impact of the biorea...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2018.04.015
更新日期：2018-08-10 00:00:00
abstract：:The kinetics of microbial growth and the biodegradation of methanol and toluene in (a) biofilters (BFs), and (b) biotrickling filters (BTFs), packed with inert materials, has been studied and analyzed. The specific growth rate, mu, for the treatment of methanol was 0.037h(-1) for a wide range of operating conditions. ...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2008.08.001
更新日期：2008-11-25 00:00:00
abstract：:The global occurrence of prostate cancer with a range of patient outcome has prompted various investigators to explore novel molecular biomarkers that can precisely detect and track this type of cancer severity. Several studies suggest that micro-RNAs have emerged to act as a new largely unexplored class of biomarkers...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2017.07.029
更新日期：2017-10-10 00:00:00
abstract：:The inflammation of chronic wounds generally causes delaying their healing process. The present work aims to formulate a wound dressing polyelectrolyte membrane based on chitosan (Ch) and sodium hyaluronate (HA) loaded with glutathione (GSH). The membrane types (Ch/HA and Ch/HA/GSH) were examined by Fourier transform ...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2020.02.002
更新日期：2020-02-20 00:00:00
abstract：:The isolation of ars sequence from the yeast Yarrowia lipolytica has recently been reported (Fournier et al., 1991). Vectors containing ars18 have been used to increase homologous and heterologous protein production. Examples presented are the Yarrowia lipolytica alkaline extracellular protease (AEP), the porcine alph...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/0168-1656(91)90063-2
更新日期：1991-07-01 00:00:00
abstract：:The volatile fatty acid propionate inhibits anaerobic digestion during organic waste treatments. To examine potential microbial interactions that accelerate propionate oxidation, anaerobic digestion systems seeded with various types of anaerobic sludge were analyzed. Seed samples were collected from 10 different full-...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2015.09.040
更新日期：2015-11-20 00:00:00
abstract：:Myxobacteria are well established as proficient producers of natural products with numerous biological activities. Although some knowledge has been gained regarding the biosynthesis of secondary metabolites in this class of bacteria, almost nothing is known about the underlying regulatory mechanisms. In order to ident...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2005.08.014
更新日期：2006-02-24 00:00:00
abstract：:A pair of genes designated parA and parB are encoded by many low copy number plasmids and bacterial chromosomes. They work with one or more cis-acting sites termed centromere-like sequences to ensure better than random predivisional partitioning of the DNA molecule that encodes them. The centromere-like sequences nucl...
journal_title：Journal of biotechnology
pub_type： 杂志文章,评审
doi：10.1016/s0168-1656(01)00293-0
更新日期：2001-09-13 00:00:00
abstract：:In the two-step fermentative production of vitamin C, its precursor 2-keto-L-gulonic acid (2-KLG) was synthesized by Ketogulonicigenium vulgare through co-culture with Bacillus megaterium. The reconstruction of the amino acid metabolic pathway through completed genome sequence annotation demonstrated that K. vulgare w...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2011.08.007
更新日期：2011-12-10 00:00:00
abstract：:In earlier study from our group, cholera toxin B subunit had been expressed in tomato for developing a plant-based vaccine against cholera. In the present investigation, gene for accessory colonization factor (acf) subunit A, earlier reported to be essential for efficient colonization in the intestine, has been expres...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2008.03.002
更新日期：2008-05-20 00:00:00
abstract：:The utilisation of urban organic waste as feedstock for polyhydroxyalkanoates (PHA) production is growing since it allows to solve the main concerns about their disposal and simultaneously to recover added-value products. A pilot scale platform has been designed for this purpose. The VFA-rich fermentation liquid comin...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2020.07.022
更新日期：2020-11-10 00:00:00
abstract：:The energy which simple-stomached livestock can derive from dietary plant material is limited by the lack of plant polysaccharide degrading enzymes in their gastro-intestinal (GI) tract and the inefficient microbial fermentation of such material in their hind-gut. In poultry the non-starch polysaccharides found in cer...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/s0168-1656(99)00098-x
更新日期：1999-06-11 00:00:00
abstract：:Glycosylation is a prominent biological mechanism for structural and functional diversity of natural products. Uridine diphosphate-dependent glycosyltransferases with aglycon promiscuity are generally recognised as effective biocatalysts for glycodiversification of natural products for practical applications. In this ...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2017.03.009
更新日期：2017-04-20 00:00:00
abstract：:Enzyme engineering by molecular modelling and site-directed mutagenesis can be remarkably efficient. Directed enzyme evolution appears as a more general strategy for the isolation of catalysts as it can be applied to most chemical reactions in aqueous solutions. Selections, as opposed to screening, allow the simultane...
journal_title：Journal of biotechnology
pub_type： 杂志文章,评审
doi：10.1016/j.jbiotec.2004.03.032
更新日期：2004-09-30 00:00:00
abstract：:Rebuilding enzymes with high activities, stability and reusability has been constantly pursued for application of enzymaticcatalysis in wide field. Rebuilding enzymes by chemical approaches, including immobilization and chemicalmodification, represents a simple but effective route. Here, a class of highly stable and a...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2018.12.014
更新日期：2019-02-10 00:00:00
abstract：:Preussia sp. BSL10, family Sporormiaceae, was actively producing phytohormone (indole-3-acetic acid) and extra-cellular enzymes (phosphatases and glucosidases). The fungus was also promoting the growth of arid-land tree-Boswellia sacra. Looking at such prospects of this fungus, we sequenced its draft genome for the fi...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/j.jbiotec.2016.03.025
更新日期：2016-05-10 00:00:00
abstract：:Proteolytically cleaved human 22 kDa growth hormone (22K hGH) between the amino acid residues 134 and 150 by plasmin or other proteases in vitro has been reported to be most active in growth promoting activity. In this study a deleted mutant hGH lacking amino acid residues from 135 to 146 and having more sensitivity t...
journal_title：Journal of biotechnology
pub_type： 杂志文章
doi：10.1016/s0168-1656(99)00234-5
更新日期：2000-02-28 00:00:00
