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At least 469 records · Page 26Linked to original sources
PubMedDate not supplied

Cellular and metabolic engineering. An overview.

Metabolic engineering is defined as the purposeful modification of intermediary metabolism using recombinant DNA techniques. Cellular engineering, a more inclusive term, is defined as the purposeful modification of cell properties using the same techniques. Examples of cellular and metabolic engineering are divided into five categories: 1. Improved production of chemicals already produced by the host organism; 2. Extended substrate range for growth and product formation; 3. Addition of new catabolic activities for degradation of toxic chemicals; 4. Production of chemicals new to the host organism; and 5. Modification of cell properties. Over 100 examples of cellular and metabolic engineering are summarized. Several molecular biological, analytical chemistry, and mathematical and computational tools of relevance to cellular and metabolic engineering are reviewed. The importance of host selection and gene selection is emphasized. Finally, some future directions and emerging areas are presented.

Bacteria↗
PubMed2026

The opioid receptor-ligand network in human cancers: pan-cancer multi-omics profiling and translational implications.

BACKGROUND: Opioid receptor-ligand signalling has been implicated in tumour biology and perioperative outcomes; however, its pan-cancer molecular landscape and clinical relevance remain incompletely defined. METHODS: We performed a pan-cancer multi-omics analysis of eight predefined opioid receptor-ligand genes across 33 tumour types from The Cancer Genome Atlas. Analyses included gene expression analysis using the linear models for microarray data (limma) package, genomic alterations, DNA methylation, regulatory network inference, pathway activity estimation using gene set variation analysis, and survival modelling. Multivariable Cox regression models were adjusted for age, sex, and tumour stage. RESULTS: Opioid receptor-ligand genes exhibited heterogeneous and generally low-to-moderate expression across tumour types. Genomic and epigenetic alterations were tumour-specific and variably associated with gene expression. Selected genes showed associations with overall survival in a tumour-dependent manner; however, these associations were attenuated after adjustment for clinical covariates and were accompanied by wide confidence intervals in some cohorts. Pathway analyses suggested associations with broader biological programmes, including epithelial-mesenchymal transition and immune-related pathways. Regulatory analyses identified candidate transcription factors and miRNAs, although these findings are exploratory. CONCLUSIONS: This pan-cancer analysis provides a systematic overview of opioid receptor-ligand gene features across human cancers. The observed associations are context-dependent and should be interpreted as hypothesis-generating. Further mechanistic and prospective studies are required to determine the clinical relevance of opioid signalling in cancer and perioperative settings.

Humans↗
PubMed2004

A first generation physical map of the medaka genome in BACs essential for positional cloning and clone-by-clone based genomic sequencing.

In order to realize the full potential of the medaka as a model system for developmental biology and genetics, characterized genomic resources need to be established, culminating in the sequence of the medaka genome. To facilitate the map-based cloning of genes underlying induced mutations and to provide templates for clone-based genomic sequencing, we have created a first-generation physical map of the medaka genome in bacterial artificial chromosome (BAC) clones. In particular, we exploited the synteny to the closely related genome of the pufferfish, Takifugu rubripes, by marker content mapping. As a first step, we clustered 103,144 public medaka EST sequences to obtain a set of 21,121 non-redundant sequence entities. Avoiding oversampling of gene-dense regions, 11,254 of EST clusters were successfully matched against the draft sequence of the fugu genome, and 2363 genes were selected for the BAC map project. We designed 35mer oligonucleotide probes from the selected genes and hybridized them against 64,500 BAC clones of strains Cab and Hd-rR, representing 14-fold coverage of the medaka genome. Our data set is further supplemented with 437 results generated from PCR-amplified inserts of medaka cDNA clones and BAC end-fragment markers. Our current, edited, first generation medaka BAC map consists of 902 map segments that cover about 74% of the medaka genome. The map contains 2721 markers. Of these, 2534 are from expressed sequences, equivalent to a non-redundant set of 2328 loci. The 934 markers (724 different) are anchored to the medaka genetic map. Thus, genetic map assignments provide immediate access to underlying clones and contigs, simplifying molecular access to candidate gene regions and their characterization.

Animals↗
PubMed2006

The value of gene-based selection of tag SNPs in genome-wide association studies.

Genome-wide association scans are rapidly becoming reality, but there is no present consensus regarding genotyping strategies to optimise the discovery of true genetic risk factors. For a given investment in genotyping, should tag SNPs be selected in a gene-centric manner, or instead, should coverage be optimised based on linkage disequilibrium alone? We explored this question using empirical data from the HapMap-ENCODE project, and we found that tags designed specifically to capture common variation in exonic and evolutionarily conserved regions provide good coverage for 15-30% of the total common variation (depending on the population sample studied), and yield genotype savings compared with an anonymous tagging approach that captures all common variation. However, the same number of tags based on linkage disequilibrium alone captures substantially more (30-46%) of the total common variation. Therefore, the best strategy depends crucially on the unknown degree to which functional variation resides in recognisable exons and evolutionarily conserved sequence. A hypothetical but reasonable scenario might be one in which trait-causing variation is equally distributed between exons plus conserved sequence, and the rest of the genome. In this scenario, our analysis suggests that a tagging approach that captures variation in exons and conserved sequence provides only modestly better coverage of putatively causal variation than does anonymous tagging. In HapMap CEU samples (with northern and western European ancestry), we observed roughly equivalent coverage for equal investment for both tagging strategies.

Databases, Nucleic Acid↗
PubMed2004

Identifying periodically expressed transcripts in microarray time series data.

MOTIVATION: Microarray experiments are now routinely used to collect large-scale time series data, for example to monitor gene expression during the cell cycle. Statistical analysis of this data poses many challenges, one being that it is hard to identify correctly the subset of genes with a clear periodic signature. This has lead to a controversial argument with regard to the suitability of both available methods and current microarray data. METHODS: We introduce two simple but efficient statistical methods for signal detection and gene selection in gene expression time series data. First, we suggest the average periodogram as an exploratory device for graphical assessment of the presence of periodic transcripts in the data. Second, we describe an exact statistical test to identify periodically expressed genes that allows one to distinguish periodic from purely random processes. This identification method is based on the so-called g-statistic and uses the false discovery rate approach to multiple testing. RESULTS: Using simulated data it is shown that the suggested method is capable of identifying cell-cycle-activated genes in a gene expression data set even if the number of the cyclic genes is very small and regardless the presence of a dominant non-periodic component in the data. Subsequently, we re-examine 12 large microarray time series data sets (in part controversially discussed) from yeast, human fibroblast, human HeLa and bacterial cells. Based on the statistical analysis it is found that a majority of these data sets contained little or no statistical significant evidence for genes with periodic variation linked to cell cycle regulation. On the other hand, for the remaining data the method extends the catalog of previously known cell-cycle-specific transcripts by identifying additional periodic genes not found by other methods. The problem of distinguishing periodicity due to generic cell cycle activity and to artifacts from synchronization is also discussed. AVAILABILITY: The approach has been implemented in the R package GeneTS available from http://www.stat.uni-muenchen.de/~strimmer/software.html under the terms of the GNU General Public License.

Algorithms↗
PubMed2004

Classification of gene microarrays by penalized logistic regression.

Classification of patient samples is an important aspect of cancer diagnosis and treatment. The support vector machine (SVM) has been successfully applied to microarray cancer diagnosis problems. However, one weakness of the SVM is that given a tumor sample, it only predicts a cancer class label but does not provide any estimate of the underlying probability. We propose penalized logistic regression (PLR) as an alternative to the SVM for the microarray cancer diagnosis problem. We show that when using the same set of genes, PLR and the SVM perform similarly in cancer classification, but PLR has the advantage of additionally providing an estimate of the underlying probability. Often a primary goal in microarray cancer diagnosis is to identify the genes responsible for the classification, rather than class prediction. We consider two gene selection methods in this paper, univariate ranking (UR) and recursive feature elimination (RFE). Empirical results indicate that PLR combined with RFE tends to select fewer genes than other methods and also performs well in both cross-validation and test samples. A fast algorithm for solving PLR is also described.

Algorithms↗
PubMed1988

Transposon tagging using Ty elements in yeast.

We have used the ability to induce high levels of Ty transposition to develop a method for transposon mutagenesis in Saccharomyces cerevisiae. To facilitate genetic and molecular analysis, we have constructed GAL1-promoted TyH3 or Ty917 elements that contain unique cloning sites, and marked these elements with selectable genes. These genes include the yeast HIS3 gene, and the plasmid PiAN7 containing the Tn903 NEO gene. The marked Ty elements retain their ability to transpose, to mutate the LYS2, LYS5, or STE2 genes, and to activate the promoterless his3 delta 4 target gene. Ty elements containing selectable genes are also useful in strain construction, in chromosomal mapping, and in gene cloning strategies.

Cloning, Molecular↗
PubMed2001

Tetracycline resistance genes in isolates of Pasteurella multocida, Mannheimia haemolytica, Mannheimia glucosida and Mannheimia varigena from bovine and swine respiratory disease: intergeneric spread of the tet(H) plasmid pMHT1.

Tetracycline-resistant isolates of Pasteurella multocida and Mannheimia spp. from respiratory diseases in cattle and swine were investigated for the classes of tet gene and their chromosomal or plasmid location. The 34 isolates comprised eight P. multocida, 23 Mannheimia haemolytica, two Mannheimia varigena and a single Mannheimia glucosida isolate. Identification of the tet genes was achieved by PCR analysis and hybridization with specific probes. Transformation and hybridization experiments served to confirm the plasmid location of tet genes. Selected tet genes and their adjacent regions were sequenced. The tet genes tet(B), tet(G) and tet(H) were detected. The gene tet(H) was present in 26 isolates. The 4.4 kb tet(H)-carrying plasmid pMHT1 was detected in six isolates representing all four species. In the remaining 28 isolates, copies of tet(B), tet(G) and tet(H) were identified as chromosomal. No correlation between the tet gene type and the MIC of tetracycline, or between the number of tet gene copies and the MIC of tetracycline was observed. Tetracycline resistance in P. multocida and Mannheimia spp. is mediated by at least three different tet genes. A new type of tet(H)- carrying plasmid, pMHT1, was identified. The detection of pMHT1 in M. glucosida and M. varigena is the first report of resistance plasmids in isolates of these two species. For the first time, tet(G) genes were detected in members of the family Pasteurellaceae.

Animals↗
PubMed2000

Identification of Staphylococcus aureus genes expressed during growth in milk: a useful model for selection of genes important in bovine mastitis?

Staphylococcus aureus is a major cause of bovine mastitis. Since gene expression of many bacteria is known to be regulated by the environment, milk may play an important role in the regulation of the early steps in the pathogenesis of bovine mastitis by S. aureus. To get insight into the response of S. aureus to the milk environment, a Tn917-lacZ mutant library was generated and screened for genes specifically expressed during growth in milk. Twenty-eight mutants were identified and analysed. Four groups of genes were found, involved in cell-wall synthesis, nucleotide synthesis, transcriptional regulation and carbohydrate metabolism. A fifth group contained genes with hypothetical or unknown functions. Many of the genes identified belonged to biosynthetic pathways of S. aureus and other bacterial species which have also been shown to play a role in vivo as determined in murine infection models. Therefore, growth on milk may be an attractive model for the identification of genes preferentially expressed during bovine mastitis.

Animals↗
PubMed2006

Biological responses of ligament fibroblasts and gene expression profiling on micropatterned silicone substrates subjected to mechanical stimuli.

In this study, ligament fibroblasts were cultivated on micropatterned silicone substrates and subjected to cyclic stretching to simulate the in vivo biomechanical environment during ligament healing. Without stretching, ligament fibroblasts were aligned parallel to the microgrooves on the silicone substrate surface. However, we previously reported that uniaxial cyclic stretching induces alignment perpendicular to the stretching axis. With stretching on a microgrooved surface, cell proliferation and collagen production were greatly enhanced. The exact functions of the micropatterned surface and mechanical stimuli are unknown. Therefore, in gene expression microarray experiments, genes whose expression is inhibited by subculture from passage 0 (P0) to passage 8 (P8) and enhanced by micropatterning and stretching were sought out. The following six genes were selected: MGP, GADD45A, UNC5B, TGFB1, COL4A1, and COL4A2. The selected genes play fundamental roles in cell proliferation, differentiation, apoptosis, and structural maintenance. On the basis of the obtained gene expression profiles, we identified candidate genes that might be involved in responses to a micropatterned surface and mechanical stretching.

Anterior Cruciate Ligament↗
PubMed2005

Gene expression profile in rat small intestinal allografts after cold preservation/reperfusion.

AIM: To determine the changes of gene expression profile in small intestinal allografts in rats after cold preservation/reperfusion, and to identify the genes relevant to cold preservation/reperfusion injury. METHODS: Heterotopic segmental small bowel transplantation was performed in six rats with a sham operation and they were used as controls. Total RNA was extracted from the allografts (experimental group) and normal intestines (control group) 1 h after cold preservation/reperfusion, and then purified to mRNA, which was then reversely transcribed to cDNA, and labeled with fluorescent Cy5-dUTP and Cy3-dUTP to prepare hybridization probes. The mixed probes were hybridized to the cDNA microarray. After high-stringent washing, the fluorescent signals on cDNA microarray chip were scanned and analyzed. RESULTS: Among the 4 096 target genes, 82 differentially expressed genes were identified between the two groups. There were 18 novel genes, 33 expression sequence tags, and 31 previously reported genes. The selected genes may be divided into four classes: genes modulating cellular adhesion, genes regulating cellular energy, glucose and protein metabolism, early response genes and other genes. CONCLUSION: A total of 82 genes that may be relevant to cold preservation/reperfusion injury in small intestinal allografts are identified. Abnormal adhesion between polymorphonuclears and endothelia and failure in energy, glucose and protein metabolism of the grafts may contribute to preservation/reperfusion injury. The functions of the novel genes identified in our study need to be clarified further.

Animals↗
PubMed2002

Singular value decomposition regression models for classification of tumors from microarray experiments.

An important problem in the analysis of microarray data is correlating the high-dimensional measurements with clinical phenotypes. In this paper, we develop predictive models for associating gene expression data from microarray experiments with such outcomes. They are based on the singular value decomposition. We propose new algorithms for performing gene selection and gene clustering based on these predictive models. The estimation procedure using the regression models occurs in two stages. First, the gene expression measurements are transformed using the singular value decomposition. The regression parameters in the model linking the principal components with the clinical responses are then estimated using maximum likelihood. We demonstrate the application of the methodology to data from a breast cancer study.

Breast Neoplasms↗
PubMed1996

Response of two heat shock genes to selection for knockdown heat resistance in Drosophila melanogaster.

To identify genes involved in stress resistance and heat hardening, replicate lines of Drosophila melanogaster were selected for increased resistance to knockdown by a 39 degrees heat stress. Two selective regimes were used, one with and one without prior hardening. Mean knockdown times were increased from approximately 5 min to > 20 min after 18 generations. Initial realized heritabilities were as high as 10% for lines selected without hardening, and crosses between lines indicated simple additive gene effects for the selected phenotypes. To survey allelic variation and correlated selection responses in two candidate stress genes, hsr-omega and hsp68, we applied denaturing gradient gel electrophoresis to amplified DNA sequences from small regions of these genes. After eight generations of selection, allele frequencies at both loci showed correlated responses for selection following hardening, but not without hardening. The hardening process itself was associated with a hsp68 frequency change in the opposite direction to that associated with selection that followed hardening. These stress loci are closely linked on chromosome III, and the hardening selection established a disequilibrium, suggesting an epistatic effect on resistance. The data indicate that molecular variation in both hsr-omega and.hsp68 contribute to natural heritable variation for hardened heat resistance.

Alcohol Dehydrogenase↗
PubMedDate not supplied

Stable transformation of insect cells to coexpress a rapidly selectable marker gene and an inhibitor of apoptosis.

We have constructed several plasmid expression vectors to express foreign genes in stably transformed insect cells. Unlike baculovirus-based expression vectors by which genes of interest are expressed transiently before lysis of the virus-infected cells, genes can be expressed continuously over many passages in a stable cell line. Furthermore, the function of a gene or genes expressed in a stable cell line from an insect-specific promoter that is constitutively expressed can be studied in the absence of virus infection and viral gene expression. In this study, we have expressed a novel, selectable marker gene, puromycin acetyltransferase, under the control of the Drosophila melanogaster hsp 70 promoter or under the control of the AcMNPV ie-1 promoter which is active in Spodoptera frugiperda cells in the absence of virus infection. In addition, we have constructed expression vectors which coexpress two genes from separate promoters, the pac gene which confers resistance to puromycin and a baculovirus gene which inhibits apoptosis, derived from Orygia pseudotsugata nuclear polyhedrosis virus. Both genes were expressed in stable populations of S. frugiperda cells in the absence of continuous drug selection.

Acetyltransferases↗
PubMed2003

New selective amplifier genes containing c-Mpl for hematopoietic cell expansion.

We previously developed "selective amplifier genes (SAGs)" which confer a growth advantage to transduced cells. The SAG is a chimeric gene encoding the G-CSF receptor (GCR) and the estrogen or tamoxifen (Tm) receptor and is able to expand transduced hematopoietic cells by treatment with estrogen or Tm. In the current study, we examined the in vitro efficacy of modified SAGs containing the thrombopoietin (TPO) receptor (c-Mpl) gene instead of GCR as a more potent signal generator. In addition, we constructed various mutant Mpl-type SAGs to abolish the responsiveness to endogenous TPO while retaining Tm-dependency. When Ba/F3 cells were retrovirally transduced with the Mpl-type SAGs, the cells showed Tm- and TPO-dependent growth even without IL-3. The Mpl-type SAGs induced more potent proliferation of Ba/F3 and cynomolgus CD34(+) cells than the GCR-type SAG. One mutant Mpl-type SAG (Delta GCRMplTmR) successfully lost the responsiveness to TPO without affecting the Tm-dependence.

Animals↗
PubMed1975

How many genes are selected in populations of Dacus oleae.

Three natural populations of Dacus oleae have been sampled for six electrophoretically detected polymorphic genes. The distribution of the allele frequencies in the different populations were analyzed by the method suggested by Lewontin and Krakauer (1973) (the various in space one) in order to test for selective neutrality. This method, however, which in our case showed that one or more genes are or have been subjected to selection, does not permit estimation of the number of selected loci. An improvement of this method is proposed that perimts a minimum estimation of the selected genes. About a third of them seem to be selected in our material. In our case however, where a cytological analysis is not possible, genes are not differentiated from possible inversions including these genes.

Alcohol Oxidoreductases↗
PubMed1978

Tyrosyl-base-phenylalanyl intercalation in gene 5 protein-DNA complexes: proton nuclear magnetic resonance of selectively deuterated gene 5 protein.

The interactions of oligodeoxynucleotides with the aromatic residues of gene 5 protein in complexes with d(pA)8 and d(pT)8 have been determined by 1H NMR of the protein in which the five tyrosyl residues have been selectively deuterated either in the 2,6 or the 3,5 positions. Only the 3,5 protons of the three surface tyrosyls (26, 41, and 56) interact with the bases. The remainder of the aromatic protons undergoing base-dependent upfield ring-current shifts on complex formation are phenylalanyl protons, assigned to Phe(13) on the basis of model building. 19F NMR of the complexes of the m-fluorotyrosyl-labeled protein with d(pT)4 and d(pA)8 confirms the presence of ring-current perturbations of nuclei at the 3,5-tyrosyl positions of the three surface tyrosyls. Differential expression of the 19F(1H) nuclear Overhauser effect confirms the presence of two buried and three surface tyrosyl residues. A new model of the DNA binding groove is presented involving Tyr(26)-base-Phe(13) intercalation.

Coliphages↗
PubMedDate not supplied

Development and use of gene transfer for treatment of cardiovascular disease.

Gene therapy holds promise for the treatment of cardiovascular diseases for which effective pharmacological therapies are insufficient or unavailable. Recent studies have suggested that modification of current gene delivery systems combined with the use of efficacious therapeutic genes may ultimately be successful for clinical vascular gene therapy. Although certain applications such as vein-graft failure may be best suited for short-term transient overexpression of therapeutic genes, other disorders including human essential hypertension and atherosclerosis require sustained overexpression of genes. Hence, design and use of vector systems for delivery of genes to the required site in vivo requires careful consideration. Both viral and nonviral gene therapy vectors show low efficiency for gene transfer into vascular cells and demonstrate a lack of selectivity, as vectors have natural tropism for other cells and tissues. Recent work has focused on the design, development, and utility of vascular cell-selective gene therapy vectors for use in distinct and diverse vascular gene therapy scenarios. Using phage display technology we have isolated small peptide ligands that mediate selective binding to either vascular endothelial cells or vascular smooth muscle cells. When engineered into either adenoviral (Ad) or adeno-associated viral (AAV) vectors, candidate peptides enabled the virus to selectively bind to the desired cell type thus generating novel vascular cell-selective gene transfer. As preclinical studies have highlighted both the potential for vascular gene therapy as well as defining the potential pitfalls, the development of disease-selective gene therapeutics will increase safety and efficiency of gene therapy for future clinical use.

Cardiovascular Diseases↗