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The influence of triploidy on gene expression in the silkworm, bombyx mori

In Bombyx mori, it is well established that polyploids are easily induced when newly laid eggs are exposed to a variety of conditions, such as high or low temperature, centrifugal force, or chemicals like colchicine. To investigate gene dosage effects by varying the ploidy, the transcription levels of six genes expressed in various tissues were analysed in the diploid and two different genetically produced triploids (PPC and CCP). In the PPC triploid, the transcription level per cell of two genes was directly proportional to the structural gene dosage, whereas two other genes showed the mRNA level expected if compensation occurred. In the CCP triploid, three genes displayed dose-dependent levels of expression, whereas one gene showed the same expression level as the diploid strains. In both triploids, exceptional cases showed a negative correlation of expression with ploidy or a positive correlation greater than expected from the structural gene dosage. Interestingly, the transcription levels of most tested genes were significantly different from the strains which were used as parents of the triploids, and also widely divergent expression patterns were found for some genes in the diploid offspring. In this study, the cause of the unexpected expression patterns observed in the euploid series is discussed in relation to the difference between the two parental strains in expression level of genes and in trans-acting regulatory effects on their target genes.

Journal Article↗

Rescue of the En-1 mutant phenotype by replacement of En-1 with En-2.

The related mouse Engrailed genes En-1 and En-2 are expressed from the one- and approximately five-somite stages, respectively, in a similar presumptive mid-hindbrain domain. However, mutations in En-1 and En-2 produce different phenotypes. En-1 mutant mice die at birth with a large mid-hindbrain deletion, whereas En-2 mutants are viable, with cerebellar defects. To determine whether these contrasting phenotypes reflect differences in temporal expression or biochemical activity of the En proteins, En-1 coding sequences were replaced with En-2 sequences by gene targeting. This rescued all En-1 mutant defects, demonstrating that the difference between En-1 and En-2 stems from their divergent expression patterns.

Animals↗

Transforming growth factor-betas and related gene products in mosquito vectors of human malaria parasites: signaling architecture for immunological crosstalk.

The participation of a divergent mosquito transforming growth factor-beta (TGF-beta) and mammalian TGF-beta1 in the Anopheles stephensi response to malaria parasite development [Infect. Genet. Evol. 1 (2001) 131-141; Infect. Immun. 71 (2003) 3000-3009] suggests that a network of Anopheles TGF-beta ligands and signaling pathways figure prominently in immune defense of this important vector group. To provide a basis for identifying the roles of these proteins in Anopheles innate immunity, we identified six predicted TGF-beta ligand-encoding genes in the Anopheles gambiae genome, including two expressed, diverged copies of 60A, the first evidence of ligand gene duplication outside of chordates. In addition to five predicted type I and II receptors, we identified three Smad genes in the A. gambiae genome that would be predicted to support both TGF-beta/Activin- and bone morphogenetic protein (BMP)-like signaling. All three Smad genes are expressed in an immunocompetent A. stephensi cell line and in the A. stephensi midgut epithelium, confirming that a conserved signaling architecture is in place to support signaling by divergent exogenous and endogenous TGF-beta superfamily proteins.

Amino Acid Sequence↗

Pharmacological and genetic influences on hole-board behaviors in mice.

Head dipping on a hole-board is frequently used as an indicator of exploratory tendencies in rodent studies. Drugs with diverse pharmacological properties alter head dipping suggesting that many neurotransmitter systems are involved in the expression of exploratory behavior. The aim of the current experiments was to determine the effects of several drugs from different classes on head dipping, and to compare the effects of some of these agents in lines of mice that have been selectively bred for divergent expression of head dipping on a hole-board. In the current experiments, the effects on head dipping of three doses each of fluoxetine, desipramine, GBR-12909, methamphetamine, pentylenetetrazol, and diazepam were evaluated in genetically heterogeneous mice. Most drugs altered the number of head dips in a predictable manner, but the effects on locomotion were generally as large as those seen for head dipping. Locomotion could completely account for the effects of fluoxetine and pentylenetetrazol, and to a lesser extent, diazepam. We have also developed replicate lines of mice selectively bred for high (High Exploratory Behavior: HEB) or low (Low Exploratory Behavior: LEB) head dipping on a hole-board and evaluated the effects of diazepam and methamphetamine on hole-board behaviors in these mice. Diazepam increased head dipping and locomotion equivalently in both lines of mice, but methamphetamine stimulated locomotion in HEB mice more than in LEB mice. These results broadly suggest that the effects of most drugs we tested are not specific for head dipping, since almost all drugs tested affected head dipping and locomotion equivalently. However, the results with the genetically heterogeneous mice and HEB and LEB mice suggest that some aspects of the dopaminergic system are involved in head dipping.

Animals↗

Loss of Methylthioadenosine Phosphorylase (MTAP) Expression: A Potentially Useful Tool for Distinguishing Sarcomatoid Urothelial Carcinoma From Inflammatory Myofibroblastic Tumor.

Inflammatory myofibroblastic tumor (IMT) and sarcomatoid urothelial carcinoma (SarUC) can have striking histologic overlap but have significantly different prognoses and clinical management paradigms. Loss of methylthioadenosine phosphorylase (MTAP) protein expression by immunohistochemistry (IHC) serves as a useful surrogate for homozygous 9p21 deletion, a recurrent genomic alteration in urothelial carcinoma (UC). We analyzed MTAP expression by IHC in 65 SarUCs and 27 urinary tract IMTs to evaluate its utility in navigating this challenging differential diagnosis. Overall, MTAP loss was significantly more frequent in SarUC (55%) compared with IMT (4%) (P < .0001). Among 46 biphasic SarUCs with independently evaluable epithelial and mesenchymal components, divergent expression patterns were frequent. The most common pattern was retention of MTAP staining in both epithelial and mesenchymal components (19/46; 41% of cases), followed by selective retention of MTAP in the epithelial component and loss in the mesenchymal component (16/46; 35% of cases). MTAP loss was observed in both the epithelial and mesenchymal components in 11 out of 46 (24%) SarUC cases. None of the 46 biphasic SarUC cases showed selective MTAP loss in the epithelial component but retention in the mesenchymal component. MTAP IHC was also particularly valuable in assessing clonal relationships in 2 challenging biphasic cases in which the differential diagnosis included a collision between a noninvasive low-grade papillary UC and an IMT versus a subtle IMT-like SarUC arising in association with an overlying noninvasive low-grade papillary UC. Next-generation sequencing on a subset of cases (n = 11) was useful for confirming 9p deletion in cases with MTAP loss by IHC, and for demonstrating molecular hallmarks of urothelial neoplasia thereby providing additional diagnostic support for morphologically challenging SarUC cases with IMT-like morphology. Therefore, MTAP IHC can be useful in evaluating spindle cell lesions of the urinary tract, as loss is significantly more common in SarUC than in IMT, and enriched in the mesenchymal component of biphasic SarUC. However, MTAP loss can be seen in both entities, and the diagnosis of IMT-like spindle cell tumors in the urinary tract requires careful integration of morphologic, immunohistochemical, and molecular data.

Humans↗

Comparison of in vitro and in vivo infectivity of different clade B HIV-1 envelope chimeric simian/human immunodeficiency viruses in Macaca mulatta.

The use of HIV-1 env/SIVmac chimeric viruses expressing divergent HIV-1 envelopes of clinical isolates, facilitates homologous and heterologous evaluation of various recombinant HIV-1 envelope vaccine candidates in lower primates. In this study we compare the in vitro and in vivo infectivity, via intravenous (IV) and intravaginal (IVAG) routes of infection, of stocks of chimeric viruses expressing env from four different clade B HIV-1 isolates. The TCID50/ml was 7.1 x 10(4), 1.0 x 10(4), 6.3 x 10(4), and 1.2 x 10(3) for SHIVsf13, SHIVHan2, SHIVNM-3rn, and SHIVW6.1D, respectively, with a MID50/ml upon IV inoculation of 3.2 x 10(3), 3.2 x 10(4), 3.2 x 10(4), and 3.2 x 10(3), respectively. The same SHIVsf13 stock was infectious after IVAG administration, requiring a 300-fold higher virus dose. Plasma antigenemia and cell-associated viremia were generally highest at weeks 2 or 4 after infection and decreased to subdetectable levels after 8-12 weeks. All infected animals tested developed anti-HIV-1 gp120 antibodies. Inoculated virus dose showed no (linear) quantitative correlation with cellular virus load, duration of viremia, plasma antigenemia, and anti-gp120 antibody titers. No significant changes in peripheral blood CD4 cell levels were observed and none of the animals has shown evidence of disease progression to date (i.e., 13 months postinfection). Four in vivo passages of cell-associated SHIVW6.1D did not result in increased virulence. Vaccine development studies in macaques monkeys have become feasible with the use of various clade B HIV-1 env SHIV chimeras.

Animals↗

Cellular transcriptomics -- the next phase of endocrine expression profiling.

Transcriptome analysis, or global gene expression profiling, has become a commonly used and valuable tool in both basic and clinical endocrine research. Novel endocrine regulators have 'surfaced' and greater consideration is now given to understanding function at the level of gene networks. Recent developments have shown that the transcriptome is considerably larger and more divergently expressed than was previously thought. Endocrine cells express a great variety of coding and noncoding RNAs in a highly cell-specific manner. If further value is to be taken from this research area, then steps towards defined cellular transcriptomics must be taken. New sampling techniques that utilize novel genetic models are a key first step.

Animals↗

Cell density-dependent modulation of the Vibrio fischeri luminescence system in the absence of autoinducer and LuxR protein.

Expression of the Vibrio fischeri luminescence genes (luxR and luxICDABEG) in Escherichia coli requires autoinducer (N-3-oxohexanoyl homoserine lactone) and LuxR protein, which activate transcription of luxICDABEG (genes for autoinducer synthase and the luminescence enzymes), and cyclic AMP (cAMP) and cAMP receptor protein (CRP), which activate transcription of the divergently expressed luxR gene. In E. coli and in V. fischeri, the autoinducer-LuxR protein-dependent induction of luxICDABEG transcription (called autoinduction) is delayed by glucose, whereas it is promoted by iron restriction, but the mechanisms for these effects are not clear. To examine in V. fischeri control of lux gene expression by autoinducer, cAMP, glucose, and iron, lux::Mu dI(lacZ) and lux deletion mutants of V. fischeri were constructed by conjugation and gene replacement procedures. beta-Galactosidase synthesis in a luxC::lacZ mutant exhibited autoinduction. In a luxR::lacZ mutant, complementation by the luxR gene was necessary for luminescence, and addition of cAMP increased beta-galactosidase activity four- to sixfold. Furthermore, a luxI::lacZ mutant produced no detectable autoinducer but responded to its addition with induced synthesis of beta-galactosidase. These results confirm in V. fischeri key features of lux gene regulation derived from studies with E. coli. However, beta-galactosidase specific activity in the luxI::lacZ mutant, without added autoinducer, exhibited an eight- to tenfold decrease and rise back during growth, as did beta-galactosidase and luciferase specific activities in the luxR::lacZ mutant and luciferase specific activity in a delta(luxR luxICD) mutant. The presence of glucose delayed the rise back in beta-galactosidase and luciferase specific activities in these strains, whereas iron restriction promoted it. Thus, in addition to transcriptional control by autoinducer and LuxR protein, the V. fischeri lux system exhibits a cell density-dependent modulation of expression that does not require autoinducer, LuxR protein, or known lux regulatory sites. The response of autoinducer-LuxR protein-independent modulation to glucose and iron may account for how these environmental factors control lux gene expressions.

Cyclic AMP↗

Genome-wide characterization of the FOX gene family reveals sex-biased expression and FoxO-associated regulation during gonadal development in Bellamya aeruginosa.

Forkhead box (FOX) transcription factors are important regulators of development and reproduction, but their roles in molluscan gonadal development remain unclear. In this study, the FOX gene family was systematically identified in the freshwater gastropod Bellamya aeruginosa, and comparative gonadal transcriptomic analyses were performed across sexes and developmental stages.A total of 35 FOX genes were identified and classified into 19 subfamilies. Phylogenetic and synteny analyses indicated that the FOX gene family is generally conserved among mollusks, whereas FoxG and FoxL2 showed lineage-specific expansion. Structural analyses demonstrated that most BaeFOX proteins retained the conserved Forkhead domain architecture. Transcriptomic analyses revealed that gene expression divergence between testes and ovaries was markedly greater than that between developmental stages within the same gonad, indicating that sexual dimorphism is the major source of gonadal transcriptional variation. Functional enrichment consistently identified the FoxO signaling pathway in sex-biased comparisons. Several FOX genes also displayed clear gonad-biased expression patterns, and network analyses suggested that BaeFoxO, BaeFoxL2, and BaeFoxG may play central regulatory roles in gonadal development. These findings provide the first comprehensive characterization of the FOX gene family in B. aeruginosa and suggest that FOX-related regulatory networks potentially participate in gonadal development in gastropod mollusks.

Animals↗

Insulin regulation of gene expression through the forkhead transcription factor Foxo1 (Fkhr) requires kinases distinct from Akt.

Insulin inhibits expression of certain liver genes through the phosphoinositol (PI) 3-kinase/Akt pathway. However, whether Akt activity is both necessary and sufficient to mediate these effects remains controversial. The forkhead proteins (Foxo1, Foxo3, and Foxo4, previously known as Fkhr or Afx) are transcriptional enhancers, the activity of which is inhibited by insulin through phosphorylation-dependent translocation and nuclear exclusion. Others and we have previously shown that the forkhead protein Foxo1 is phosphorylated at three different sites: S(253), T(24), and S(316). We have also shown that T(24) fails to be phosphorylated in hepatocytes lacking insulin receptors, and we have suggested that this residue is targeted by a kinase distinct from Akt. In this study, we have further analyzed the ability of Akt to phosphorylate different Foxo1 sites in control and insulin receptor-deficient hepatocytes. Expression of a dominant negative Akt (Akt-AA) in control hepatocytes led to complete inhibition of endogenous Akt, but failed to inhibit Foxo1 T(24) phosphorylation and, consequently, insulin suppression of IGFBP-1 promoter activity. Conversely, expression of a constitutively active Akt (Akt-Myr) in insulin receptor-deficient hepatocytes led to an overall increase in the level of Foxo1 phosphorylation, but failed to induce T(24) and S(316) phosphorylation. These data indicate that the Foxo1 T(24) and S(316) kinases are distinct from Akt, and suggest that the pathways required for insulin regulation of hepatic gene expression diverge downstream of PI 3-kinase.

Animals↗

[The genetic differentiation of mammalian taxa: their assessment by biochemical genetic markers].

A review of data on genetic differentiation of mammalian taxa has been made on the basis of estimating the percent of fixed gene differences (PFD). The results substantiate the existence of evident differences in the scale of genetic divergence between taxa in different mammalian orders. Among smaller mammals (marsupials, insectivores, chiropterans, myomorph and sciuromorph rodents, african mole rats, and elephant shrews) interspecific differences within a genus involve the average of 25-40% of investigated loci. At the genetic level the value is 50-60%, whereas at the familial level the differences are beyond the resolution capacity of the method (PFD = 60-80%). Orders of larger mammals can be divided into two subgroups. One of them that includes carnivores, artiodactylans, and hystricomorph rodents is characterised by PFD values of 10-14%, 30-50%, and 69-70% at respective levels. The other subgroup composed of proboscideans, primates, pinnipeds, and toothed whales, has a low level of genetic divergence expressed by PFD values of 0-3%, 7-36%, and 50-60% at species, generic and familial levels, respectively. Insufficiency of data on baleen whales and perissodactyls does not allow to cluster them ultimately with any of these groups. There are three possible, but not necessarily alternative, causes for the observed differences in genetic divergence: 1) over-ranking of genera in larger mammals; 2) different paleontological age of orders; 3) unequal rates of molecular evolution.

Animals↗

A novel binary adenovirus-based dual-regulated expression system for independent transcription control of two different transgenes.

BACKGROUND: Stringent multitransgene control is a prerequisite for future gene-therapy and tissue-engineering scenarios and requires constant improvements in design to achieve optimal conditional transcription profiles. METHODS: We have pioneered a variety of recombinant adenoviruses which (i) enable streptogramin-responsive transgene transduction in a compact autoregulated one-virus format, (ii) manage independent streptogramin- and tetracycline-responsive control of two different transgenes from a single divergent expression unit, and (iii) control sense and antisense expression of the human cyclin-dependent kinase inhibitor p27(Kip1) to engineer conditional positive (enforced S-phase entry, p27(Kip1)-antisense expression) or negative (G1-phase-specific growth arrest, p27(Kip1)-sense expression) growth control in mammalian cell lines and human primary cells. RESULTS: The transgene control performance of all adenoviral expression configurations has been rigorously optimized for tight, balanced and maximum expression levels and was validated for intracellular as well as for secreted product in a variety of biotechnologically relevant cell lines (Chinese hamster ovary cells [CHO-K1], baby hamster kidney cells [BHK-21]) as well as in human cell lines (human fibrosarcoma cells [HT-1080]) and primary cells (human aortic fibroblasts [HAFs]). CONCLUSIONS: We believe that multiregulated multigene-controlled adenoviruses are important assets for successful therapeutic reprogramming of mammalian cells in clinically relevant scenarios.

Adenoviridae↗

Genomic sequence and spatiotemporal expression comparison of zebrafish mbx1 and its paralog, mbx2.

The expression of midbrain homeobox-1 (mbx1) defines a discrete region in the vertebrate neural plate that will give rise to the mesencephalon, as well as subregions of the diencephalon and retinal field. Here, we report on the identification and cloning of a second Mbx gene in zebrafish, termed mbx2. Genomic sequence comparison suggests that mbx1 and mbx2 are derived from the duplication of a single putative ancestral gene that is conserved in other vertebrates as a single copy gene. Furthermore, phylogenetic analyses indicate that the mbx genes belong to a novel subgroup of paired-like homeobox genes. Finally, quantitative reverse transcriptase-PCR and whole mount in situ hybridization experiments revealed a pattern of partial spatiotemporal expression divergence between the mbx paralogs that correlates with sequence divergence in noncoding regulatory domains. Our data support a subfunctionalization model that may explain the retention of duplicate mbx genes in teleosts.

Amino Acid Sequence↗

A LexA-related protein regulates redox-sensitive expression of the cyanobacterial RNA helicase, crhR.

Expression of the cyanobacterial DEAD-box RNA helicase, crhR, is regulated in response to conditions, which elicit reduction of the photosynthetic electron transport chain. A combination of electrophoretic mobility shift assay (EMSA), DNA affinity chromatography and mass spectrometry identified that a LexA-related protein binds specifically to the crhR gene. Transcript analysis indicates that lexA and crhR are divergently expressed, with lexA and crhR transcripts accumulating differentially under conditions, which respectively oxidize and reduce the electron transport chain. In addition, expression of the Synechocystis lexA gene is not DNA damage inducible and its amino acid sequence lacks two of three residues required for activity of prototypical LexA proteins, which repress expression of DNA repair genes in a range of prokaryotes. A direct effect of recombinant LexA protein on crhR expression was confirmed from the observation that LexA reduces crhR expression in a linear manner in an in vitro transcription/translation assay. The results indicate that the Synechocystis LexA-related protein functions as a regulator of redox-responsive crhR gene expression, and not DNA damage repair genes.

Amino Acid Sequence↗

Basic fibroblast growth factor regulates type I collagen and collagenase gene expression in human smooth muscle cells.

Basic fibroblast growth factor (bFGF) is a multifunctional peptide well known for angiogenic, neurotropic, and mesoderm-inducing effects. In the present study, we have investigated the effects of bFGF on collagen and collagenase gene expression in human iliac arterial smooth muscle cells. We report that bFGF inhibits type I collagen gene expression and collagen biosynthesis, with concomitant stimulation of collagenase gene expression. The smooth muscle cells incubated with human recombinant bFGF decreased the mRNA steady state levels of pro-alpha 1(I) type I collagen by as much as 72%. [3H]Hydroxyproline synthesis was also suppressed by 59% compared with untreated control cultures. Indirect immunofluorescence confirmed corresponding changes at the protein level. In contrast to the down-regulation of type I collagen gene expression, collagenase gene expression was found to be up-regulated severalfold by bFGF. The data suggest that bFGF is capable of regulating collagen and collagenase gene expression divergently in human smooth muscle cells and that the effects appear to be mediated at a pretranslational level.

Cells, Cultured↗

Comparative immunohistochemical analysis of the expression of cytokeratins, vimentin and alpha-smooth muscle actin in human foetal mesonephros and metanephros.

The human mesonephros is currently regarded as a simplified version of the foetal metanephros, primarily due to the close morphological resemblance between these two structures. The aim of the present study was to define whether human mesonephric and foetal metanephric nephrons share immunophenotypical traits in their corresponding structures (glomeruli, proximal and distal tubules). For this purpose we first investigated immunohistochemically the overall expression and topographical distribution of cytokeratins 7, 8, 18, 19, and 20, vimentin and alpha-smooth muscle actin in mature mesonephric nephrons and compared the results with those obtained in maturing-stage foetal metanephric nephrons. No expression of cytokeratins 7 and 20 was found. Cytokeratins 8, 18, and 19 and vimentin showed a restricted and basically coincident expression along the different components of both mesonephric and metanephric nephrons. These findings indicate that the intermediate filament protein profile of human mature mesonephric nephrons closely recapitulates that observed in developing metanephros and thereby strengthens the concept that human mesonephros, a transient ontogenic structure, is largely similar to the foetal metanephros. The sole difference between human mesonephros and foetal metanephros was the divergent expression of alpha-smooth muscle actin. This protein exhibited an increasingly accentuated mesangial expression paralleling the morphological maturation of metanephric glomerulus, whereas it was absent from the mesonephric one. This would suggest that the mesangial cells in these two renal structures have a different function during the foetal life.

Actins↗

Interaction-dependent gene expression in Mla-specified response to barley powdery mildew.

Plant recognition of pathogen-derived molecules influences attack and counterattack strategies that affect the outcome of host-microbe interactions. To ascertain the global framework of host gene expression during biotrophic pathogen invasion, we analyzed in parallel the mRNA abundance of 22,792 host genes throughout 36 (genotype x pathogen x time) interactions between barley (Hordeum vulgare) and Blumeria graminis f. sp hordei (Bgh), the causal agent of powdery mildew disease. A split-split-plot design was used to investigate near-isogenic barley lines with introgressed Mla6, Mla13, and Mla1 coiled-coil, nucleotide binding site, Leu-rich repeat resistance alleles challenged with Bgh isolates 5874 (AvrMla6 and AvrMla1) and K1 (AvrMla13 and AvrMla1). A linear mixed model analysis was employed to identify genes with significant differential expression (P value < 0.0001) in incompatible and compatible barley-Bgh interactions across six time points after pathogen challenge. Twenty-two host genes, of which five were of unknown function, exhibited highly similar patterns of upregulation among all incompatible and compatible interactions up to 16 h after inoculation (hai), coinciding with germination of Bgh conidiospores and formation of appressoria. By contrast, significant divergent expression was observed from 16 to 32 hai, during membrane-to-membrane contact between fungal haustoria and host epidermal cells, with notable suppression of most transcripts identified as differentially expressed in compatible interactions. These findings provide a link between the recognition of general and specific pathogen-associated molecules in gene-for-gene specified resistance and support the hypothesis that host-specific resistance evolved from the recognition and prevention of the pathogen's suppression of plant basal defense.

Carrier Proteins↗

The two-component signal transduction system RR06/HK06 regulates expression of cbpA in Streptococcus pneumoniae.

Streptococcus pneumoniae encounters a number of environmental niches in the body, including the nasopharynx, lungs, blood, middle ear, and brain. Recent studies have identified 13 putative two-component signal-transduction systems in S. pneumoniae, which are likely to be important for gene regulation in response to external stimuli. Here, we present conclusive evidence for the regulation of choline binding protein A (CbpA), a major pneumococcal virulence factor and protective antigen, by one of these two-component signal-transduction systems. We have demonstrated divergent expression of cbpA in unmarked hk06 and rr06 deletion mutants relative to wild-type S. pneumoniae D39 by using Western immunoblotting and real-time RT-PCR. Electrophoretic mobility-shift and solid-phase binding assays have demonstrated the binding of RR06 to the promoter region of cbpA, suggesting that RR06/HK06 directly regulates cbpA transcription. We have also shown that this system is important for the ability of the pneumococcus to adhere to epithelial cells in vitro and to survive and proliferate in an in vivo mouse model. Thus, the RR06/HK06 system has a significant role in pathogenesis, both in colonization and invasive disease.

Animals↗