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PubMed2004

[MC1R--the key gene in mammalian melanin synthesis].

The study of the molecular regulation mechanism of melanin synthesis during animal development has become a new focus recently . The synthesis and production of melanin during animal development are regulated by many genes. This paper summarized the molecular function mechanism of melanocortin-1-receptor (MC1R) gene and the relationship between the consequences of polymorphic variation of the gene and melanin traits, in addition to summarized the identification and mutation of MC1R gene in birds. Furthermore, the melanin synthesis mechanism in birds is also discussed here.

Adrenocorticotropic Hormone↗
PubMed1994

[Features of linkage analysis of a "key" gene of a disease].

Peculiarities of linkage analysis are considered for the case of disease inheritance deviation from a simple Mendelian pattern, including incomplete and different for two sexes penetrance of genotypes and possible presence of phenocopies. With regard for the peculiarities and within the frames of the likelihood ratio method, a software package was developed and tested on IBM PC-compatible computers. The package allows one to obtain the highest lod score for small pedigrees and the corresponding estimates of recombination frequency in men and women.

Female↗
PubMed2005

Gene-expression profiles for five key glycosylation genes for galactose-fed CHO cells expressing recombinant IL-4/13 cytokine trap.

Recombinant protein glycosylation profiles have been shown to affect the in-vivo half-life, and therefore the efficacy and economics, for many therapeutics. While much research has been conducted correlating the effects of various stimuli on recombinant protein glycosylation characteristics, relatively little work has examined glycosylation-related gene-expression profiles. In this study, the effects of galactose feeding on the gene-expression profiles for five key glycosylation-related genes were determined for Chinese hamster ovary cells producing a recombinant IL-4/13 cytokine trap fusion. The genes investigated were sialidase, a putative alpha2,3-sialyltransferase, CMP-sialic acid transporter, beta1,4-galactosyltransferase, and UDP-galactosyltransferase. Additionally, the sialic acid content (sialylation) of the recombinant protein was examined. The peak sialic acid content of the IL-4/13 cytokine trap fusion protein was observed to be similar for the control and galactose-fed cultures. The gene-expression profiles for four of the glycosylation genes were observed to be sensitive to the glucose concentration and not significantly different for the control and galactose-fed cultures prior to glucose depletion. However, the sialidase gene-expression profiles were different for the control and galactose-fed cultures. The sialidase gene-expression profile increased significantly for the galactose-fed cultures prior to glucose depletion, whereas for the control cultures, the sialidase gene-expression profiles did not increase until the late stationary phase. The intracellular sialidase enzyme activity decreased exponentially with time for the control cultures; however, for the galactose-fed cultures, the intracellular sialidase enzyme activity decreased initially and then remained relatively high compared to the control cultures. These results indicate that the galactose feeding may increase the potential for desialylation, which offsets any improvements in the sialylation rate due to increased substrate levels. Thus, galactose feeding is an unnecessary expense for the production of the IL-4/13 cytokine trap fusion protein in a batch process.

Animals↗
PubMed2004

Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes.

BACKGROUND: Evolutionarily conserved sequences within or adjoining orthologous genes often serve as critical cis-regulatory regions. Recent studies have identified long, non-coding genomic regions that are perfectly conserved between human and mouse, termed ultra-conserved regions (UCRs). Here, we focus on UCRs that cluster around genes involved in early vertebrate development; genes conserved over 450 million years of vertebrate evolution. RESULTS: Based on a high resolution detection procedure, our UCR set enables novel insights into vertebrate genome organization and regulation of developmentally important genes. We find that the genomic positions of deeply conserved UCRs are strongly associated with the locations of genes encoding key regulators of development, with particularly strong positional correlation to transcription factor-encoding genes. Of particular importance is the observation that most UCRs are clustered into arrays that span hundreds of kilobases around their presumptive target genes. Such a hallmark signature is present around several uncharacterized human genes predicted to encode developmentally important DNA-binding proteins. CONCLUSION: The genomic organization of UCRs, combined with previous findings, suggests that UCRs act as essential long-range modulators of gene expression. The exceptional sequence conservation and clustered structure suggests that UCR-mediated molecular events involve greater complexity than traditional DNA binding by transcription factors. The high-resolution UCR collection presented here provides a wealth of target sequences for future experimental studies to determine the nature of the biochemical mechanisms involved in the preservation of arrays of nearly identical non-coding sequences over the course of vertebrate evolution.

Animals↗
PubMed2026

Predicting diagnostic gene biomarkers associated with immune infiltration in patients with diabetes.

Diabetes is a global public health problem with various complications, which can lead to disability and mortality. This study identified potential diagnostic markers for diabetes and explored the immunometabolic mechanisms in the pathological process. The gene expression of 17 diabetes cases and 16 normal controls were obtained from the Gene Expression Omnibus (GEO) database. The "limma" package was employed for screening differentially expressed genes (DEGs). Gene functions and enriched pathways of DEGs were analyzed via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Candidate key genes were screened using the least absolute shrinkage and selection operator (LASSO) regression model and support vector machine recursive feature elimination (SVM-RFE) analysis. The diagnostic effectiveness of identified markers was further verified via the receiver operating characteristic (ROC) curve. The compositional patterns of immune cell infiltration and signaling pathway enrichment associated with key genes were explored via single sample Gene Set Enrichment Analysis (ssGSEA) and GSEA analysis, respectively. Possible miRNAs interacting with key genes were predicted via miRcode database. B2M, FTL, SH3BGRL3, and SOD2 were recognized as diagnostic markers for diabetes based on LASSO regression and the support vector machine recursive feature elimination (SVM-RFE) feature selection algorithm. Analysis of immune cell infiltration demonstrated that the four key genes were related to B cells, neutrophils, macrophages, and CD8+ T cells. The diagnostic value of B2M, FTL, and SOD2 for diabetes was higher than that of SH3BGRL3 according to the ROC curve. Validation experiments indicated that the mRNA expression of B2M and FTL was increased in liver tissues of diabetic mice. B2M and FTL can act as diagnostic markers for diabetes and contribute to new understandings of the disease's molecular mechanisms.

Humans↗
PubMed2026

Metagenomic Insights into Microbial Assembly and Key Metabolic Genes Driving Flavor Formation in Spontaneously Fermented Zhejiang Rosy Vinegar.

The spontaneous fermentation of Zhejiang rosy vinegar (ZRV) is driven by environmental microbiota, but the processes underlying its flavor formation remain poorly understood. Using metagenomic sequencing, we investigated microbial community assembly, environmental drivers, and metabolic networks during industrial-scale ZRV fermentation. Acetic acid dominated the final organic acids. Community assembly shifted toward deterministic selection with rising acidity, with a slight rebound of stochastic processes in the late stage (R2 values of 0.442 and 0.346 for bacteria and fungi, respectively). Mantel tests confirmed that environmental factors significantly regulated microbial assembly. Co-occurrence networks grew more complex, with positive interactions accounting for 85.24% (bacteria) and 90.10% (fungi) in the late stage. Key genes (ldh, gapA, pgk) from Acetobacter pasteurianus and Lactobacillus acetotolerans dominated late-stage fermentation, while genes (adhP, SDH) from Aspergillus oryzae and Saccharomyces cerevisiae supported early- and mid-stage fermentation. These findings elucidate microbiota-driven metabolic pathways in ZRV, supporting the fermentation window optimization and industrial vinegar quality standardization.

Acetic Acid↗
PubMed1999

The transcription factors Elf-1 and GATA-1 bind to cell-specific enhancer elements of human high-affinity IgE receptor alpha-chain gene.

Key regulatory regions necessary for the expression of the gene encoding FcepsilonRI alpha-chain, a component of the high-affinity IgE receptor primarily responsible for IgE-dependent allergic response, were investigated. Two regions, -74/-69 and -55/-47, which contained binding motifs for proteins belonging to the Ets family and the GATA family, respectively, were shown to be necessary for the activation of the alpha-chain promoter. Both the regulatory elements enhanced the promoter activity only in alpha-chain-producing cells PT18 and RBL-2H3 (mast cell lines), indicating that the elements required specific trans-acting proteins present in the alpha-chain-producing cells. EMSA using nuclear extracts and in vitro-translated proteins revealed that Elf-1 and GATA-1 bound to the enhancer elements. This is the first report describing the regulation in the expression of the FcepsilonRI alpha-chain.

Animals↗
PubMed2005

Feed restriction induces pyruvate carboxylase but not phosphoenolpyruvate carboxykinase in dairy cows.

The ability of dairy cattle to adapt to changes in nutrient intake requires appropriately responsive expression of several key genes in liver. Holstein cows were used in 2 experiments to determine the effect of short-term feed restriction on expression of mRNA for gluconeogenic and ureagenic enzymes in liver. In experiment 1, cows were fed a total mixed diet for ad libitum intake for a 5-d period followed by 5 d of 50% of their previous 5-d ad libitum intake followed by 10 d of ad libitum feeding. Liver biopsies and blood samples were obtained on d 5, 10, and 20 of the experiment, the last day of each feeding period. Pyruvate carboxylase (PC) mRNA increased with feed restriction, but phosphoenolpyruvate carboxykinase (PEPCK) was unchanged. Expression of carbamoyl phosphate synthetase (CPS-I), argininosuccinate synthetase, and ornithine transcarbamylase mRNA were not altered by feed restriction; however, CPS-I mRNA expression tended to increase during realimentation. In experiment 2, cows were fed for ad libitum intake for 5 d and then fed 50% of previous intake for 5 d. Liver biopsy samples collected on d 5 and 10 were used for PC mRNA, PEPCK mRNA, and in vitro measure of gluconeogenesis from radiolabelled propionate and lactate. The data indicate expression of genes for key metabolic processes in liver of lactating cows is responsive to feeding level. Expression of PC mRNA is part of the adaptive response to feed intake restriction and is matched by increased capacity for gluconeogenesis from lactate.

Animals↗
PubMed2006

Genomic characterization of POS5, the Saccharomyces cerevisiae mitochondrial NADH kinase.

Disruption of the Saccharomyces cerevisiae mitochondrial NADH kinase POS5 increases the mitochondrial mutation rate 50-fold. Whereas most multicellular eukaryotic genomes have one NADH kinase gene, the yeast genome contains three distinct genes encoding NAD/H kinase activity. To determine if all three genes are essential for viability we constructed combinations of gene knockouts. We show that only the pos5Deltautr1Delta combination is synthetically lethal, demonstrating an essential overlapping function, and showing that NAD/H kinase activity is essential for eukaryotic viability. The single human NAD/H kinase gene can rescue the lethality of the double knockout in yeast, demonstrating that the single human gene can fill the various functions provided by the three yeast genes. The human NAD/H kinase gene harbors very common sequence variants, but all of these equally complement the synthetic lethality in yeast, illustrating that each of these are functionally wild-type. To understand the molecular mechanism of the mitochondrial genome instability of pos5 mutation we performed gene expression analysis on the pos5Delta. The pos5Delta resulted in an increase in expression of most of the iron transport genes including key genes involved in iron-sulfur cluster assembly. Decreased expression occurred in many genes involved in the electron transport chain. We show that the pos5Delta expression pattern is similar to the frataxin homolog knockout (yfh1Delta), the yeast model for Friedreich's ataxia. These combined data show that the POS5 NAD/H kinase is an important protein required for a variety of essential cellular pathways and that deficient iron-sulfur cluster assembly may play a critical role in the mitochondrial mutator phenotype observed in the pos5Delta.

Fungal Proteins↗
PubMed2005

Heme deficiency suppresses the expression of key neuronal genes and causes neuronal cell death.

Defective heme synthesis may cause acute porphyrias, which are associated with a wide array of neurological disturbances involving both the central and peripheral nervous systems. Thus, the understanding of the roles of heme in neuronal cell function may provide insights into the molecular events underlying the pathogenesis of neuropathies associated with defective heme synthesis. In this report, we use rat pheochromocytoma (PC12) clonal cells as a model system for studying the role of heme in neuronal cell survival. We examined the effects of inhibition of heme synthesis on signaling pathways and gene expression in nerve growth factor (NGF)-induced PC12 cells. We found that succinyl acetone-induced heme deficiency selectively caused apoptosis in NGF-induced PC12 cells. Further, we found that in succinyl acetone-treated, NGF-induced cells, the pro-survival Ras-ERK1/2 signaling pathway was inactivated and the pro-apoptotic JNK signaling pathway was activated. In these cells, the activation of caspase and the cleavage of nuclear poly (ADP-ribose) polymerase (PARP) were also evident. Importantly, microarray gene expression analysis showed that more than 20 key neuronal genes that were induced by NGF were suppressed by succinyl acetone. These genes include those encoding survival motor neuron protein, synaptic vesicle protein SVOP, and neural cell adhesion molecule NCAM. These results indicate that heme is important for neuronal cell signaling and the proper functioning of neuronal cells.

Animals↗
PubMed2004

Gene expression profiling shows that macrophages derived from mouse embryonic stem cells is an improved in vitro model for studies of vascular disease.

Macrophages (Mphi) play an important role in the initiation and progress of the atherogenic process. They contribute to the growth of atherosclerotic plaque by affecting lipoprotein metabolism, matrix homeostasis, lipoprotein modification and cholesterol accumulation. Access to in vitro Mphi models is therefore important for understanding the mechanisms involved in the transition of the relatively simple fatty streak to more complex type of lesions. The aim of the present work was to compare the expression profile of macrophages differentiated from the hematopoietic lineage to peritoneal mouse macrophages and two commonly used mouse macrophage cell lines (J774.A1 and RAW264.7). Our results showed that the embryonic stem cell-derived macrophages (ES Mphi) had a more similar expression profile to peritoneal macrophages than the two mouse macrophage cell lines. The ES Mphi had unchanged expression of the majority of cholesterol efflux mediators when compared to mouse peritoneal macrophages, whereas the cell lines showed altered expression of several of these genes. A key gene in this process is apolipoprotein E, which is expressed in ES Mphi but not in macrophage cell lines. In conclusion, ES Mphi are likely to provide a better in vitro model than mouse Mphi cell lines to study macrophage involvement in atherosclerosis.

Animals↗
PubMed1992

Dominant hemimelia and En-1 on mouse chromosome 1 are not allelic.

Previous studies have shown that En-1, a homeobox-containing gene, maps close to or at the Dh locus in the mouse. Since homeobox-containing genes are key genes in the control of development the close proximity of En-1 to the developmentally significant gene Dh raised the possibility that the Dh mutation represented a mutant allele of En-1. A genetic analysis involving En-1, Dh, and other chromosome 1 markers (Emv-17, ln and Pep-3) shows that although Dh and En-1 are closely linked they are separable by recombination (4/563). The likely gene order and recombination frequencies of these loci are: ln (5.2 +/- 0.9) Emv-17 (1.1 +/- 0.4) Dh (0.7 +/- 0.4) En-1 (3.0 +/- 0.7) Pep-3. This shows that Dh is not a mutant allele of En-1.

Animals↗
PubMed2004

Variability in the degree of expression of phosphorylated IkappaBalpha in chronic lymphocytic leukemia cases with nodal involvement.

PURPOSE: Based on previous preliminary observations, we hypothesize that the molecular and clinical variability of chronic lymphocytic leukemia (CLL) reflects differences in the degree of nuclear factor (NF)-kappaB activation, as determined by the expression of phosphorylated IkappaBalpha (p-IkappaBalpha). EXPERIMENTAL DESIGN: The expression profile (mRNA and protein expression) was analyzed with the Centro Nacional de Investigaciones Oncologicas Oncochip, a cDNA microarray containing 6386 cancer-related genes, and a tissue microarray (TMA). The results were correlated with the IgV(H) mutational status, ZAP-70 expression, cytogenetic alterations, and clinical outcome. RESULTS: We found correlations between the presence of p-IkappaBalpha, a surrogate marker of NF-kappaB activation, and changes in the expression profile (mRNA and protein expression) and clinical outcome in a series of CLL cases with lymph node involvement. Activation of NF-kappaB, as determined by the expression of p-IkappaBalpha, was associated with the expression of a set of genes comprising key genes involved in the control of B-cell receptor signaling, signal transduction, and apoptosis, including SYK, LYN, BCL2, CCR7, BTK, PIK3CD, and others. Cases with increased expression of p-IkappaBalpha showed longer overall survival than cases with lower expression. A Cox regression model was derived to estimate some parameters of prognostic interest: IgV(H) mutational status, ZAP-70, and p-IkappaBalpha expression. The multivariate analysis disclosed p-IkappaBalpha and ZAP-70 expression as independent prognostic factors of survival. CONCLUSIONS: A variable degree of activation of NF-kappaB, as determined by the expression of p-IkappaBalpha, is an identifiable event in CLL, and is correlated with changes in the expression profile and overall survival.

Adult↗
PubMed1997

Adrenomedullin gene expression and its different regulation in human adrenocortical and medullary tumors.

Adrenomedullin (ADM) is a polypeptide originally discovered in a human pheochromocytoma and is also present in normal adrenal medulla. It has been proposed that ADM could be involved in the regulation of adrenal steroidogenesis via paracrine mechanisms. Our aim was to find out if ADM gene is expressed in adrenocortical tumors and how ADM gene expression is regulated in adrenal cells. ADM mRNA was detectable by Northern blotting in most normal and hyperplastic adrenals, adenomas and carcinomas. The average concentration of ADM mRNA in the hormonally active adrenocortical adenomas was about 80% and 7% of that in normal adrenal glands and separated adrenal medulla respectively. In adrenocortical carcinomas, the ADM mRNA concentration was very variable, but on average it was about six times greater than that in normal adrenal glands. In pheochromocytomas, ADM mRNA expression was about ten times greater than that in normal adrenals and three times greater than in separated adrenal medulla. In primary cultures of normal adrenal cells, a protein kinase C inhibitor, staurosporine, reduced ADM mRNA accumulation in a dose- and time-dependent fashion (P < 0.01), whereas it simultaneously increased the expression of human cholesterol side-chain cleavage enzyme (P450 scc) gene (a key gene in steroidogenesis). In cultured Cushing's adenoma cells, adrenocorticotropin, dibutyryl cAMP ((Bu)2cAMP) and staurosporine inhibited the accumulation of ADM mRNA by 40, 50 and 70% respectively (P < 0.05), whereas the protein kinase C activator, 12-O-tetradecanoyl phorbol 13-acetate (TPA), increased it by 50% (P < 0.05). In primary cultures of pheochromocytoma cells, treatment with (Bu)2cAMP for 1 and 3 days increased ADM mRNA accumulation two- to threefold (P < 0.05). Our results show that ADM mRNA is present not only in adrenal medulla and pheochromocytomas, but also in adrenocortical neoplasms. Both protein kinase A- and C-dependent mechanisms regulate ADM mRNA expression in adrenocortical and pheochromocytoma cells supporting the suggested role for ADM as an autocrine or paracrine (or both) regulator of adrenal function.

8-Bromo Cyclic Adenosine Monophosphate↗
PubMedDate not supplied

Tooth agenesis: in search of mutations behind failed dental development.

Tooth agenesis are the most common craniofacial malformations. Its prevalence in permanent dentition reaches 20% and its expressivity ranges from only one tooth, usually a third molar, to the whole dentition. Genetic linkage and molecular biology studies have allowed, in the last decade, the identification of mutations responsible for some patterns of syndromic and nonsyndromic tooth agenesis. The mutated genes are key genes for the development of dentition, like the ones that encode the transcription factors MSX1, PAX9 and PITX2, the signalling protein EDA and its receptor EDAR. Current research would lead to the development of new classifications of tooth agenesis that took into account both the phenotypes and the genetic background. This would allow an early diagnosis of the condition, before the development of the somatic defect, that could eventually be repaired with gene therapy or tissue and organ engineering.

Anodontia↗
PubMed2005

[Advances in the Study on Marker Genes in transgenic Plants.].

Plant transgenic engineering is becoming more and more important in the world. The safety of selectable marker genes in the transgenic plants has been noticed widely. The new advances of selectable markers in transgenic plants were reviewed in this paper in three aspects. The first is the establishment of transformation systems allowing resistant marker genes to be eliminated from the transgenic plants, including co-transformation, site-specific recombination and transposition, as well as other methods. In these ways, the transgenes can be inserted into transgenic plants more than once. The second is the utilization and development of bio-safe positively selective marker genes, mainly referred to the carbohydrates metabolism genes, the stress- resistant enzymatic genes and the green fluorescent protein(GFP) gene. At the same time, the mercuric reductase genes, the key genes for chloroplast synthesis and other genes should also be quickly developed as markers. The third is the establishment of marker-free and skelecton-free transformation vector systems, which are efficient and simple. The prospects in application of these novel methods, marker free and safe selectable markers are also viewed in the article.

Genetic Markers↗