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At least 991 records · Page 55Linked to original sources
PubMed2007

Effect of cytoplast on the development of inter-subspecies nuclear transfer reconstructed goat embryo.

The aim of this study was to investigate effect of cytoplast on the development competence of reconstructed embryos derived from inter-subspecies somatic cell nucleus transfer (SCNT). First, the development potency of reconstructed embryos produced by transferring Boer goat fibroblast cell nucleus of different ages into enucleated Sannen goat ova was evaluated in order to determine which age of nuclear donor is favorable for the reconstructed embryos development. Secondly, the another component of reconstructed embryos, "cytoplast," was evaluated by comparing the effect of ovum cytoplast derived from Sannen male symbol x Boer female symbol descendant on the reconstructed embryos development to that of Sannen goat ovum cytoplast. The results revealed that the development rate of the reconstructed embryos derived from 2 months old Boer goat somatic cells was the highest, their gestation rate was up to 50%, and one viable male offspring was obtained. The cytoplast derived from the crossbreeding goats improves the development competence of reconstructed embryos, which birth rate was 5.5%. The genetic identification of offspring by using PCR-SSCP analysis confirmed that these cloned kids were derived from the donor. The results above reveal that the cytoplast of Sannen goat ovum could induce the dedifferentiation of somatic cell nuclei derived from Boer goat, but the reprogramming process of these reconstructed embryos seems incomplete, probably due to some incorrect processes happened after implantation. Relatedness components of nucleus donor in cytoplast of the crossbreeding goat may be helpful to induce the dedifferentiation of somatic cell nuclei completely and improve the development competence of the reconstructed embryos.

Animals↗
PubMed2002

Aberrant methylation patterns at the two-cell stage as an indicator of early developmental failure.

The fertilized mouse egg actively demethylates the paternal genome within a few hours after fertilization, whereas the maternal genome is only passively demethylated by a replication-dependent mechanism after the two-cell stage. This evolutionarily conserved assymetry in the early diploid mammalian embryo may have a role in methylation reprogramming of the two very different sets of sperm and egg chromatin for somatic development and formation of totipotent cells. Immunofluorescence staining with an antibody against 5-methylcytosine (MeC) showed that the incidence of abnormal methylation patterns differs between mouse two-cell embryos from superovulated females, nonsuperovulated matings, and in vitro fertilization (IVF). It also depends on embryo culture conditions and genetic background. In general, there was a good correlation with the number of embryos (from the same experiment) which did not develop in vitro up to the blastocyst stage. Thus, aberrant genome-wide DNA methylation in early embryos may be an important mechanism contributing to the high incidence of developmental failure in mammals. Similar to the situation in abnormally methylated embryos from nuclear transfer, it may cause a high incidence of pregnancy loss and abnormal phenotypes.

Acetaldehyde↗
PubMed2026

De novo transcriptome meta-analysis reveals candidate genes involved in life-stage transitions for RNAi-mediated management of the citrus root weevil (Diaprepes abbreviatus).

BACKGROUND: The citrus root weevil, Diaprepes abbreviatus, is a destructive agricultural pest for which molecular control options remain limited due to historically sparse genomic resources. Leveraging a comprehensive de novo transcriptome, we investigated developmental gene regulation across larval, pupal, and adult stages and identified essential targets for RNA interference (RNAi)-based intervention. RESULTS: Stage-resolved transcriptomic analyses revealed extensive transcriptional reprogramming associated with metabolism, detoxification, cuticle biosynthesis, endocrine signaling, and sensory perception. Among these, chitin synthase (DaCHS) emerged as a critical developmental gene, exhibiting pronounced up-regulation during late larval and pupal stages corresponding to intensive cuticle synthesis. Phylogenetic and structural analyses demonstrated that DaCHS is highly conserved among insects and retains canonical catalytic domains and transmembrane topology. Alpha Fold-based structural modeling and molecular docking confirmed stable interaction of DaCHS with its substrate, N-acetylglucosamine, supporting functional conservation of enzymatic activity. Oral delivery of DaCHS double-stranded RNA induced robust transcript suppression, leading to significant mortality and severe developmental defects, including larval and pupal abnormalities, and adults with disrupted wing and abdominal morphogenesis. CONCLUSION: These findings establish DaCHS as an indispensable gene for D. abbreviates development and validate transcriptome-guided RNAi as a powerful framework for target discovery. This work provides a strong molecular foundation for developing RNAi-based strategies that can be integrated into sustainable management programs for citrus root weevil control. © 2026 Society of Chemical Industry.

Animals↗
PubMed2025

BMDx2: A Tool for Integrating Toxicogenomics-Based Dose-Dependency Analysis and AOP-Based Mechanistic Insights.

Despite the advent of mechanistic toxicology using omics data to link molecular perturbations with systemic outcomes, regulatory toxicology still lacks the application of mechanism-anchored metrics from such data. This is partially because traditional gene-centric analysis often falls short of linking molecular changes to adverse outcomes. To address this gap, BMDx2, an open-source tool that transforms multi-dose toxicogenomics datasets into quantitative, mechanistic evidence for human chemical safety assessment is developed. BMDx2 couples benchmark-dose modeling with Adverse Outcome Pathway (AOP) enrichment to derive transcriptomic-based points of departure, enabling potency ranking, chemical prioritization, and mechanistically anchored explanations of the effect of chemical exposures. BMDx2 can process a broad range of data, including DNA microarray and RNA sequencing studies. Here, case studies are used to illustrate the versatility of BMDx2 in characterizing the mechanism of action of chemicals. An initial case study on carbon nanotubes exposure applies integrative analysis of transcriptomics and genome-wide DNA methylation data, uncovering cellular reprogramming processes underlying fibrosis. A second case study on bleomycin exposure demonstrate how transcriptomic data alone can be mapped to fibrosis-related AOPs in a standardized, regulatory appropriate manner. Together, these examples show how BMDx2 supports the regulatory application of toxicogenomics and accelerates mechanism-based chemical safety evaluation.

Toxicogenetics↗
PubMed2003

Genome-wide monitoring of wine yeast gene expression during alcoholic fermentation.

The transcriptome of a wine yeast was monitored throughout an alcoholic fermentation under conditions mimicking an enological environment. Major changes in gene expression occurred during fermentation, affecting more than 2000 genes, as the yeast adapted to changing nutritional, environmental and physiological conditions. The genes of many pathways are regulated in a highly coordinated manner, and genes involved in the key metabolic pathways of fermentation are strongly expressed. We showed that, during fermentation of a synthetic medium mimicking a natural must in which growth arrest was caused by nitrogen exhaustion, entry into the stationary phase triggered major transcriptional reprogramming. Many TOR target genes involved in nitrogen utilization or other functions are induced at this stage, suggesting that this signalling pathway plays a critical role in changes in gene expression in response to nitrogen depletion. Entry into stationary phase is a key physiological event and is followed by a general stress response. The superimposition of multiple stresses, including starvation and ethanol stress, gives rise to a unique stress response, involving hundreds of genes encoding proteins involved in various cellular processes, many of unknown function.

Ethanol↗
PubMed2004

Ady2p is essential for the acetate permease activity in the yeast Saccharomyces cerevisiae.

To identify new genes involved in acetate uptake in Saccharomyces cerevisiae, an analysis of the gene expression profiles of cells shifted from glucose to acetic acid was performed. The gene expression reprogramming of yeast adapting to a poor non-fermentable carbon source was observed, including dramatic metabolic changes, global activation of translation machinery, mitochondria biogenesis and the induction of known or putative transporters. Among them, the gene ADY2/YCR010c was identified as a new key element for acetate transport, being homologous to the Yarrowia lipolytica GPR1 gene, which has a role in acetic acid sensitivity. Disruption of ADY2 in S. cerevisiae abolished the active transport of acetate. Microarray analyses of ady2Delta strains showed that this gene is not a critical regulator of acetate response and that its role is directly connected to acetate transport. Ady2p is predicted to be a membrane protein and is a valuable acetate transporter candidate.

Acetic Acid↗
PubMed2006

Evolution of the genetic code in yeasts.

During the last 30 years, a number of genetic code alterations have been uncovered in bacteria and in the mitochondria and cytoplasm of various eukaryotes, invalidating the hypothesis that the genetic code is universal and frozen. In the mitochondria of most yeasts, the UGA stop codon is decoded as tryptophan and the four leucine codons of the CUN family (N = any nucleotide) are decoded as threonine. Recently, a unique genetic code change involving the decoding of the leucine CUG codon as serine was discovered in the cytoplasm of Candida and Debaryomyces species, indicating that the genetic code of yeasts may be under specific evolutionary pressures whose molecular nature is not yet fully understood. This genetic code alteration is mediated by a novel serine-tRNA that acquired a leucine 5'-CAG-3' anticodon (ser-tRNACAG) through insertion of an adenosine in the intron of its gene. This event, which occurred 272 +/- 25 million years ago, reprogrammed the identity of approximately 30 000 CUG codons existent in the ancestor of these yeasts and had a profound impact on the evolution of the genus Candida and of other species. Here, we review the most recent results and concepts arising from the study of this genetic code change and highlight how its study is changing our views of the evolution of the genetic code.

Base Sequence↗
PubMed1998

Improving the recovery of lysine in automated protein sequencing.

Automated protein sequencing is an important tool in protein characterization. Most instruments use tetrahydrofuran (THF) as the HPLC eluent for separation of the derivatized amino acids residues. THF is highly perishable when exposed to air, generating peroxides which can degrade amino acids, mainly lysine, leading to uncertainty in chromatogram interpretations. Modifications of the existing HPLC equipment were introduced to create a permanent inert atmosphere inside the bottle of THF solution. This was carried out by changing the argon plumbing and some electrical connections and by reprogramming the software of the protein sequencer. The positive results of this procedure were demonstrated by comparing the decreasing lysine peak area during 28 days before and after the modifications. In the modified instrument, lysine recovery was much better as a function of the age of the THF eluent. Since these modifications improved the instrument performance, they have been adopted for routine use in our laboratory.

Amino Acid Sequence↗
PubMed1994

Mitogenic signals control translation of the early growth response gene-1 in myogenic cells.

Muscle is a major site of expression of the early growth response gene-1 (Egr-1). To investigate its role in muscle proliferation and/or differentiation we studied the effect of a variety of growth factors on cultured mouse muscle Sol8 cells. Three groups of responses could be distinguished: 1. AII, endothelin, phenylephrine, and PMA induced Egr-1 mRNA accumulation, but the message remained untranslated. These factors induced neither differentiation nor proliferation. 2. Insulin induced differentiation. It stimulated Egr-1 mRNA accumulation, but no translation into the Egr-1 protein was seen. 3. bFGF, PDGF BB, and FCS strongly induced DNA- and protein synthesis (i.e. proliferation) and Egr-1 mRNA accumulation. Only under these conditions was the message translated into protein. We conclude: 1. AII, endothelin, phenylephrine, and PMA elicit a nuclear response in Sol8 muscle cells which may lead to reprogramming of genes unrelated to differentiation or proliferation. 2. Differentiation induces a translational block of the Egr-1 mRNA which is only relieved by mitotic stimuli. 3. These results strongly suggest a pivotal role of Egr-1 in muscle proliferation and define translational control as a new mechanism of Egr-1 regulation.

Angiotensin II↗
PubMed1994

Krüppel expression during postembryonic development of Drosophila.

The Drosophila gap gene Krüppel (Kr) codes for a Zn2+ finger transcription factor important in embryo patterning, segment identity, and specification of various cell types. Based on Northern blot analysis, Kr function has been thought to be restricted to embryogenesis. I report here that Kr is also expressed during larval development, primarily in the fat body. Using both a P-element enhancer-trap line and a portion of the Kr promoter fused to lacZ, I find the activation of Kr in the fat body does not begin until the early-third-instar stage. Earlier in larval development, Kr is detected in the nerve cells associated with the gut. Kr's role as a transcription factor during early embryogenesis is well established. After gastrulation Kr protein is detected in a variety of cell types and is probably involved in cell specification. Kr is not detected in fat cells during embryogenesis nor during the first- and second-instar stages. The delayed expression of Kr in the fat cells occurs at a time in which the larva is undergoing a reprogramming in preparation for metamorphosis. It is possible that Kr serves as a transcriptional regulator in the fat body in this last larval instar. During this last larval stage, several fat-body-specific genes are transcriptionally activated in response to increasing levels of ecdysone. The possible role of Kr in the expression of these ecdysone-regulated genes is discussed.

Animals↗
PubMed1994

Alterations in protein synthesis following transplantation of mouse 8-cell stage nuclei to enucleated 1-cell embryos.

Enucleated mouse 1-cell embryos arrest development at the 2-cell stage following transplantation of cleavage stage nuclei. Earlier studies employing one-dimensional protein gel electrophoresis failed to reveal obvious differences in gene expression in the manipulated embryos that might account for this block. We report here the results of a quantitative, two-dimensional gel electrophoretic analysis that reveals at least 50 alterations in protein synthesis in the 8-->1-cell nuclear transplant embryos. Approximately half of these alterations involve proteins that normally decrease in synthesis between the 2-cell and 8-cell stages and half involve proteins that are synthesized constitutively between these two stages. These results are the first to reveal significant biochemical alterations that accompany the morphological and cytological differences previously described and indicate that the 8-cell stage nucleus is unable to completely recapitulate the normal progression of changes in protein synthesis pattern that occur during the 2-cell stage. Our results indicate that developmental arrest may result from a combination of (1) failure to re-activate genes that normally become repressed between the 2-cell and 8-cell stages and (2) failure to up-regulate genes that become repressed during reprogramming of the 8-cell nucleus by the 1-cell cytoplasm. The failure to up-regulate the synthesis of proteins expressed at both the 2-cell and the 8-cell stages may indicate that, for some genes, a transcriptionally inactive state, possibly related to a particular chromatin configuration, may serve a protective function by restricting access of factors that can permanently reduce the ability of a gene to be expressed. This may partially account for the need to delay the widespread activation of zygotic gene transcription until the 2-cell stage, when much of the nuclear remodeling that occurs postfertilization is complete.

Animals↗
PubMed1995

Ecdysteroid regulation and DNA binding properties of Drosophila nuclear hormone receptor superfamily members.

Pulses of the steroid hormone 20-hydroxyecdysone (20E) trigger the larval-to-adult metamorphosis of Drosophila by reprogramming gene expression throughout the organism. 20E directly induces a small set of early regulatory genes that repress their own expression and induce a large set of late secondary-response genes. We show here that two members of the Drosophila nuclear hormone receptor superfamily, DHR3 and DHR39, are rapidly induced by 20E, in parallel with the early regulatory genes. Both genes also require protein synthesis at high 20E concentrations for their maximal induction by the hormone. Developmental Northern blot analysis reveals that DHR39 is induced in mid third instar larvae and expressed throughout most of third instar larval and prepupal development, while DHR3 is briefly expressed in late third instar larvae and early prepupae. The 20E-induction and temporal patterns of DHR3 and DHR39 transcription strongly suggest that these genes function together with the early regulatory genes to coordinate the complex gene networks that direct the early stages of Drosophila metamorphosis. In an initial effort to understand how these two orphan receptors might function during development, we examined their DNA binding properties and compared them with the known Drosophila nuclear receptor superfamily members that are involved in the ecdysteroid response: EcR, Usp, E75A, E78A, and beta FTZ-F1. Upon testing all pairwise combinations of these seven proteins on a panel of seven oligonucleotides, only EcR and Usp bound DNA as a heterodimer, indicating that this interaction is highly specific. With the exception of E78A, which did not bind any sequence tested, each of the remaining proteins is able to bind to a single consensus AGGTCA half-site; however, each displayed different specificities depending on the flanking nucleotide sequence. These observations suggest that the 20E-regulated orphan receptors function as monomers to control the expression of their target genes.

Animals↗
PubMed1995

Repression of gene expression at the beginning of mouse development.

The transition from maternal to zygotic gene expression in the mouse occurs in the 2-cell embryo. Previous studies in which DNA was injected into 2-cell embryos revealed that transcription promoters and origins of DNA replication are strongly repressed in cleavage stage embryos unless linked to an embryo-responsive enhancer. Repression also occurs when DNA is injected into the paternal pronucleus of a 1-cell embryo and the injected embryo subsequently undergoes mitosis, except that repression is no longer relieved by enhancers. Here we extend this observation to maternal pronuclei in 1-cell embryos and show that this repression could not be relieved either by linking the promoter to an embryo-responsive enhancer or by inducing hyperacetylation of chromatin inorder to increase its accessibility to transcription factors. However, repression could be relieved by transplanting the injected pronucleus to a 2-cell embryo, even when the recipient cell subsequently underwent mitosis. Both the extent of promoter repression and the ability of enhancers to stimulate promoter activity increased as development proceeded from the early 2-cell stage to the 4-cell stage. Once repression was established in late 2-cell embryos, transplanting an injected 2-cell embryo nucleus back to an early 1-cell embryo failed to restore activity to the injected promoter, even when it was linked to an enhancer. These and other data demonstrate that cytoplasmic factors appear during formation of a 2-cell embryo that can repress promoter activity and activate enhancer activity. These factors are absent from the paternal pronucleus and cytoplasm of early (S-phase arrested) 1-cell embryos. Moreover, the cytoplasm of early 1-cell embryos appears to lack the ability to reprogram expression of genes once they have progressed to the late 2-cell stage in mouse development.

Animals↗
PubMed1998

Juvenile hormone prevents ecdysteroid-induced expression of broad complex RNAs in the epidermis of the tobacco hornworm, Manduca sexta.

A cDNA homolog of the Drosophila melanogaster Broad Complex (BRC) gene was isolated from the tobacco hornworm, Manduca sexta, which shows a predicted 88% amino acid identity with Drosophila BRC in the N-terminal BTB domain. Three zinc finger domains encoding homologs of the Drosophila Z2, Z3, and Z4 domains (93, 100, and 85% identity, respectively) were obtained by RT-PCR. In Manduca dorsal abdominal epidermis, BRC RNAs were not observed during the larval molt. Three BRC transcripts-6.0, 7.0, and 9.0 kb-first appeared at the end of the feeding stage of the fifth (final) instar when the epidermis is exposed to ecdysteroids in the absence of juvenile hormone (JH) and becomes committed to pupal differentiation. These RNAs were induced in day 2 fifth larval epidermis in vitro by 20-hydroxyecdysone (20E) in the absence of JH with dose-response and time courses similar to the induction of pupal commitment. This induction by 20E in vitro was prevented by the presence of JH I at levels seen in vivo during the larval molt. In the wing discs, the BRC RNAs appeared shortly after ecdysis to the fifth instar and coincided with the onset of metamorphic competence of these discs. Application of a JH analogue pyriproxifen during the fourth instar molt delayed and reduced the levels of BRC mRNAs seen in the wing discs in the early fifth instar, but did not completely prevent their appearance in this tissue that first differentiates at metamorphosis. The expression of the BRC transcription factors thus appears to be one of the first molecular indications of the genetic reprogramming of the epidermis necessary for insect metamorphosis. How JH prevents BRC expression in this epidermis may provide the key to understanding how this hormone controls metamorphosis.

Amino Acid Sequence↗
PubMed1999

A widespread and early requirement for a novel Notch function during Drosophila embryogenesis.

The Notch pathway plays a key role in the formation of many tissues and cell types in Metazoans. We recently showed that Notch acts in two pathways to determine muscle precursor fates. The first is the "standard" Notch pathway, in which Delta activates the Notch receptor, which then translocates into the nucleus in conjunction with Su(H) to reprogram transcription patterns and bring about changes in cell fates. The second pathway is poorly defined, but known to be independent of the ligands and downstream effectors of the standard pathway. The standard pathway is required in many different developmental contexts and we wondered if there was also a general requirement for the novel pathway. Here we show that the novel Notch pathway is required for the development of each of five examined cell types. These results indicate that the novel pathway is a widespread and fundamental component of Notch function. We further show that both Notch pathways operate in the differentiation of the same cell types. In such cases, the novel pathway acts first and appears to set up or limit the size of equivalence groups. The standard pathway then acts within the equivalence groups to limit individual cell fates.

Animals↗
PubMed1999

Dimerization of the docking/adaptor protein HEF1 via a carboxy-terminal helix-loop-helix domain.

HEF1, p130(Cas), and Efs define a family of multidomain docking proteins which plays a central coordinating role for tyrosine-kinase-based signaling related to cell adhesion. HEF1 function has been specifically implicated in signaling pathways important for cell adhesion and differentiation in lymphoid and epithelial cells. While the SH3 domains and SH2-binding site domains (substrate domains) of HEF1 family proteins are well characterized and binding partners known, to date the highly conserved carboxy-terminal domains of the three proteins have lacked functional definition. In this study, we have determined that the carboxy-terminal domain of HEF1 contains a divergent helix-loop-helix (HLH) motif. This motif mediates HEF1 homodimerization and HEF1 heterodimerization with a recognition specificity similar to that of the transcriptional regulatory HLH proteins Id2, E12, and E47. We had previously demonstrated that the HEF1 carboxy-terminus expressed as a separate domain in yeast reprograms cell division patterns, inducing constitutive pseudohyphal growth. Here we show that pseudohyphal induction by HEF1 requires an intact HLH, further supporting the idea that this motif has an effector activity for HEF1, and implying that HEF1 pseudohyphal activity derives in part from interactions with yeast helix-loop-helix proteins. These combined results provide initial insight into the mode of function of the HEF1 carboxy-terminal domain and suggest that the HEF1 protein may interact with cellular proteins which control differentiation.

Adaptor Proteins, Signal Transducing↗
PubMed2001

Maintenance of nucleolar machineries and pre-rRNAs in remnant nucleolus of erythrocyte nuclei and remodeling in Xenopus egg extracts.

The nuclear functions in erythrocytes are almost completely extinct. There is no RNA polymerase I transcription, although a remnant nucleolar structure is still present. The remnant nucleolus of Xenopus laevis erythrocytes maintains a morphologically organized structure, nearly exclusively fibrillar. In this inactive nucleolar remnant, we revealed the presence of a modified form of transcription factor UBF. Several proteins of the processing machinery such as fibrillarin, nucleolin and B23/NO38, snoRNAs U3 and U8, and partially processed preribosomal RNAs colocalized in these remnant structures. Attempts to reprogram these erythrocyte nuclei in Xenopus egg extract showed that import of several nucleolar proteins was induced while the nucleolar remnant was disorganized. UBF became abundant and showed a necklace-like distribution on the decondensed ribosomal genes. Fibrillarin, nucleolin, and snoRNAs U3 and U8, also largely imported from the extract, were associated in large prenuclear bodies scattered in the nucleoplasm. B23/NO38 was present in different small bodies formed only in the most decondensed nuclei. In these remodeled erythrocyte nuclei, there was no imported preribosomal RNA and the initial presence of a residual nucleolar structure containing several partners of ribosome biogenesis was not sufficient to promote reassembly of newly imported nucleolar machineries. These nuclei, which reproduce the early events of nucleogenesis are also transcriptionally silent and thus compare to the early embryonic nuclei of Xenopus laevis.

Animals↗
PubMed2000

Molecular phenotype of the human oocyte by PCR-SAGE.

Consecutive application of PCR and serial analysis of gene expression (SAGE) was used to generate a catalog of approximately 50, 000 SAGEtags from nine human oocytes. Matches for known genes were identified using the National Institutes of Health SAGEtag database. This database links directly to the UniGene database, providing rapid discrimination between SAGEtags that match known genes and expressed sequence tags and those that currently have no match. Matches in the oocyte SAGE catalog were found for surface receptors, second-messenger systems, and cytoskeletal, apoptotic, and secreted proteins. Many of these proteins were not previously known to be expressed in mammalian oocytes. The relative abundances of transcripts for cytoskeletal proteins and proteins known to be in oocytes are consistent with their documented expression, suggesting an absence of representational distortion by the PCR step. The expression profile of the human oocyte may help identify factors that reprogram somatic cell nuclei to totipotency.

Databases, Factual↗