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At least 1,009 records · Page 56Linked to original sources
PubMed1999

A direct repeat sequence at the Rasgrf1 locus and imprinted expression.

Genomic imprinting is an epigenetic modification that can lead to parental-specific monoallelic expression of specific autosomal genes. While methylation of CpG dinucleotides is thought to be a strong candidate for this epigenetic modification, little is known about the establishment or maintenance of parental origin-specific methylation patterns. We have recently identified a portion of mouse chromosome 9 containing a paternally methylated region associated with a paternally expressed imprinted gene, Ras protein-specific guanine nucleotide-releasing factor 1 (Rasgrf1). This area of chromosome 9 also contains a short, direct tandem repeat in close proximity to a paternally methylated NotI site 30 kb upstream of Rasgrf1. Short, direct tandem repeats have been found associated with other imprinted genes and may act as important regulatory structures. Here we demonstrate that two rodent species (Mus and Rattus) contain a similar direct repeat structure associated with a region of paternal-specific methylation. In both species, the Rasgrf1 gene shows paternal-specific monoallelic expression in neonatal brain. A more divergent rodent species (Peromyscus) appears to lack a similar repeat structure based on Southern Blot analysis. Peromyscus animals show biallelic expression of Rasgrf1 in neonatal brain. These results suggest that direct repeat elements may play an important role in the imprinting process.

Animals↗
PubMed2003

Hematogenous macrophages express CD8 and distribute to regions of lesion cavitation after spinal cord injury.

Historically, CD4 and CD8 antigens have been used to designate functionally distinct T-lymphocyte subsets. However, these antigens also have been described on macrophages in the normal and pathologic central nervous system (CNS). Signaling through CD4 or CD8 may impart unique functions in macrophage subsets that express these antigens. In the current study, the distribution and temporal patterns of expression of CD4 and CD8 were evaluated on various cell types within the traumatically injured spinal cord. The data reveal divergent patterns of CD4 and CD8 expression on unique macrophage populations. Specifically, we show sustained elevations of CD4 expression on microglia and macrophages throughout the lesion site and spared white matter. In contrast, CD8 is predominantly associated with hematogenous macrophages that are recruited from the blood during the first week postinjury. The distribution of CD8-positive cells is restricted to areas of necrotic cavitation. Differential signaling of resident and recruited macrophages through CD4 or CD8 may explain the apparent dichotomy of CNS-macrophage-mediated injury and repair.

Animals↗
PubMed1996

Expression of sialic acid and polysialic acid in serogroup B Neisseria meningitidis: divergent transcription of biosynthesis and transport operons through a common promoter region.

We studied capsule-defective (Cap-) serogroup B meningococcal mutants created through Tn916 or omega-fragment mutagenesis. The Cap- phenotypes were the results of insertions in three of four linked genes (synX, synC, and synD) involved in CMP-N-acetylneuraminic acid and polysialic acid capsule biosynthesis, and in ctrA the first of four linked genes involved in capsule membrane transport. Mutations in the CMP-N-acetylneuraminic acid biosynthesis genes synX and synC caused defects in lipooligosaccharide sialylation but not mutations in the putative (alpha2 -> 8)-linked polysialyltransferase (synD) or in ctrA. Reverse transcriptase PCR studies indicated that the four biosynthesis genes (synX to -D) and the capsule transport genes (ctr to -D) were separately transcribed as operons. The operons were separated by a 134-bp intergenic region. Primer extension of synX and ctrA demonstrated that transcription of the operons was divergently initiated from adjacent start sites present in the intergenic region. Both transcriptional start sites were preceded by a perfect -10 Pribnow promoter binding region. The synX to -D, but not the ctrA to -D, transcriptional start site was preceded by a sequence bearing strong homology to the consensus sigma 70 -35 promoter binding sequence. Both promoters showed transcriptional activity when cloned behind a lacZ reporter gene in Escherichia coli. Our results confirm the intrinsic relationship between polysialic acid capsule biosynthesis and lipooligosaccharide sialylation pathways in group B Neisseria meningitidis. Our study also suggests that the intergenic region separating the synX to -D and ctrA to -D operons is an important control point for the regulation of group B capsule expression through coordinated transcriptional regulation of the synX to -D and drA to -D promoters.

Bacterial Capsules↗
PubMed2005

Blastocladiella emersonii expresses a centrin similar to Chlamydomonas reinhardtii isoform not found in late-diverging fungi.

Centrins are members of the calcium-binding EF-hand protein superfamily which can be divided into two subfamilies, probably associated with different functions: one related to Chlamydomonas reinhardtii centrin, CrCenp, and the other, represented by Saccharomyces cerevisiae isoform, ScCdc31p. ESTs encoding the two isoforms (BeCen1 and BeCen3) from the chytridiomycete Blastocladiella emersonii were isolated, and expression of the CrCenp-type centrin, BeCen1, was analyzed throughout the fungus life cycle. Becen1 mRNA levels increase transiently during sporulation and protein levels present a similar pattern. Immunolocalization studies seem to localize BeCen1 at the basal body zone and in the cytoplasm surrounding the nuclear cap, a zoospore organelle.

Amino Acid Sequence↗
PubMed2001

Organization, expression, and function of Caulobacter crescentus genes needed for assembly and function of the flagellar hook.

This paper reports on the organization, expression, and function of the divergently transcribed flbG and flaN operons in the hook gene cluster of Caulobacter crescentus. The transcription initiation site of flbG was determined previously, and in this work the transcription map was completed by locating the 3' end of the mRNA using nuclease S1 protection assays. A previous genetic study had suggested that the flbG operon is comprised of four genes; however, the nucleotide sequence revealed three tandemly arranged ORFs that correspond to 5'-flbG, flbH, and flgE. FlbG is similar to FliK proteins which are required for termination of hook synthesis, FlbH is similar to FlgD proteins which are essential scaffolding proteins that cap the hook during its assembly, and FlgE corresponds to the hook structural protein. The divergently transcribed flaN gene codes for a hook associated protein I homolog based on its inferred amino acid sequence similarity to FlgK proteins. Based on the amino acid sequence similarities and phenotypes of mutants, flbG, flbH, and flaN have been renamed fliK, flgD, and flgK, FlgD, FlgE, and FlgK proteins, with apparent molecular masses of 23, 68, and 41 kDa, respectively, were expressed from plasmids in a cell-free coupled transcription-translation system, and a protein corresponding to FliK was identified as part of a 190-kDa FliK-LacZ fusion protein. We present evidence showing that, in addition to its role in termination of hook synthesis, FliK is also required for initiation of hook assembly.

Amino Acid Sequence↗
PubMed2004

Expression patterns of Xenopus FGF receptor-like 1/nou-darake in early Xenopus development resemble those of planarian nou-darake and Xenopus FGF8.

Fibroblast growth factors (FGFs) mediate many cell-to-cell signaling events during early development. Nou-darake (ndk), a gene encoding an FGF receptor (FGFR)-like molecule, was found to be highly and specifically expressed in the head region of the planarian Dugesia japonica, and its functional analyses provided strong molecular evidence for the existence of a brain-inducing circuit based on the FGF signaling pathway. To analyze the role of ndk during vertebrate development, we isolated the Xenopus ortholog of ndk, the vertebrate FGFR-like 1 gene (XFGFRL1). Expression of XFGFRL1/Xndk was first detected in the anterior region at the late gastrula stage and dramatically increased at the early neurula stage in an overall anterior mesendodermal region, including the prechordal plate, paraxial mesoderm, anterior endoderm, and archenteron roof. This anterior expression pattern resembles that of ndk in planarians, suggesting that the expression of FGFRL1/ndk is conserved in evolution between these two distantly diverged organisms. During the tail bud stages, XFGFRL1/Xndk expression was detected in multiple regions, including the forebrain, eyes, midbrain-hindbrain boundary, otic vesicles, visceral arches, and somites. In many of these regions, XFGFRL1/Xndk was coexpressed with XFGF8, indicating that XFGFRL1/Xndk is a member of the XFGF8 synexpression group, which includes sprouty, sef, and isthmin.

Amino Acid Sequence↗
PubMed2000

Patterning the early zebrafish by the opposing actions of bozozok and vox/vent.

Fish and frog embryos are patterned along the dorsal-ventral axis during the gastrula stage by opposing gradients of Bmps and Bmp inhibitory proteins. Three transcriptional repressors with partially overlapping expression domains have been proposed to be important mediators of Bmp function in Xenopus. We find that two related factors are expressed in the early zebrafish embryo. Although these factors are considerably divergent from the related Xenopus genes, they are expressed in domains similar to those of their Xenopus relatives throughout embryogenesis. Both of the zebrafish genes, which we have named vox and vent, are potent ventralizing factors in both zebrafish and Xenopus embryos. Using mutants in the Bmp pathway, we find that there are Bmp-dependent and Bmp-independent domains of vox expression, whereas vent is mostly dependent upon Bmp signaling. We show that ectopic vox or vent negatively regulates expression of the early dorsal gene bozozok (boz) and that ectopic boz eliminates vox and vent expression. Moreover, the normal exclusion of vox and vent from the organizer region is lost in boz mutant embryos. Our results show that boz and vox/vent are mutually antagonistic and indicate that the early establishment of the size of the organizer domain is dependent on an interplay between these early expressed transcriptional repressors.

Amino Acid Sequence↗
PubMed2004

Memory effects in collective dynamics of Brownian suspensions.

We obtain macroscopic equations for average suspension velocity and particle current in a Brownian suspension valid on long time scales for which the memory effects are important. The coefficients in these equations depend solely on local properties of the medium. This formalism allows one to obtain well-defined theoretical expressions for transport coefficients, free of the integrals diverging with the size of the system. As an example, the expression for long-time collective diffusion coefficient is derived and the memory contribution to this coefficient is estimated.

Journal Article↗
PubMed1985

Characterization of the multigene family encoding the mouse S16 ribosomal protein: strategy for distinguishing an expressed gene from its processed pseudogene counterparts by an analysis of total genomic DNA.

Two genes from the family encoding mouse ribosomal protein S16 were cloned, sequenced, and analyzed. One gene was found to be a processed pseudogene, i.e., a nonfunctional gene presumably derived from an mRNA intermediate. The other S16 gene contained introns and had exonic sequences identical to those of a cloned S16 cDNA. The expression of this gene was demonstrated by Northern blot analysis of nuclear poly(A)+ RNA with cDNA and unique sequence intron probes. Each S16 intron contains a well-preserved remnant of the TACTAAC motif, which is ubiquitous in yeast introns and known to play a critical role in intron splicing. A sequence comparison with two other mouse ribosomal protein genes analyzed in our laboratory, L30 and L32, revealed common structural features which might be involved in the control and coordination of ribosomal protein gene expression. These include the lack of a canonical TATA box in the -20 to -30 region and a remarkably similar 12-nucleotide pyrimidine sequence (CTTCCYTYYTC) that spans the cap site and is flanked by C + G-rich sequences. The nature of the other members of the S16 family was evaluated by three types of experiment: a DNase I sensitivity analysis to measure the extent of chromatin condensation; an analysis of the thermal stability of cDNA-gene hybrids to estimate the extent of divergence of each gene sequence from that of the expressed gene; and a restriction fragment analysis which distinguishes intron-containing genes from intronless processed genes. The results of these analyses show that all genes except the expressed S16 gene are in a condensed chromatin configuration associated with transcriptional quiescence; that most of the genes within the S16 family have sequences greater than 7% divergent from the expressed S16 gene; and that at least 7 of the 10 S16 genes lack introns. We conclude that the ribosomal protein S16 multigene family contains one expressed intron-containing gene and nine inactive pseudogenes, most or all of which are of the processed type.

Animals↗
PubMed2003

A family of acr-coregulated Mycobacterium tuberculosis genes shares a common DNA motif and requires Rv3133c (dosR or devR) for expression.

Previous work has shown that the divergently transcribed Mycobacterium tuberculosis genes acr (hspX, Rv2031c) and acg (Rv2032) are induced under conditions of shallow standing culture and low oxygen and intracellularly within macrophages. We used a combination of computational and experimental methods to identify promoters for eight additional genes that are regulated in a similar manner and that comprise an acr-coregulated promoter (ACP) family. Transcriptional regulation of these ACP family members was evaluated by using a plasmid-based promoter-green fluorescent protein fusion system and flow cytometry. All promoters showed increased expression in shallow standing versus shaking cultures, in low- versus high-oxygen conditions, and intracellularly within macrophages versus extracellularly in tissue culture medium. However, there were quantitative differences in expression among promoters and among conditions for each promoter. A conserved 18-bp palindromic sequence motif was identified in all ACPs by Gibbs sampling-based computational analyses. Two such motifs overlap regions in the acr and acg promoters that were previously shown to be required for their expression. In addition, we found that 5% carbon dioxide was required for growth of Mycobacterium bovis BCG under microaerophilic (1.3% O(2)) culture conditions and fully prevented the growth cessation typically associated with rapid removal of oxygen. These findings are likely to be relevant to the in vivo environment and will contribute to our understanding of the pathogenesis of tuberculosis infection.

Bacteriological Techniques↗
PubMed2005

Chicken RFamide-related peptide (GnIH) and two distinct receptor subtypes: identification, molecular characterization, and evolutionary considerations.

RFamide-related peptides (RFRPs) regulate the release of various pituitary hormones in vertebrates. It is completely unknown how the functions of RFRPs vary among animal classes and whether vertebrate RFRPs are orthologous to each other and belong to the same peptide family. This report concerns identification of avian RFRP (gonadotropin-inhibitory hormone, GnIH) from the chicken. Chromosome-wide synteny conservation demonstrated the orthologous relationships among vertebrate RFRPs. The consensus motif for RFRP was modified to Pro-Xaa-Arg-Phe-NH2. We also describe the first identification of two distinct types of receptors for non-mammalian RFRP (RFRPR and NPFFR) from the chicken. Amino acid comparison revealed substantial differences in both termini of receptors among classes of vertebrates. The 5'-flanking regions of chicken RFRPR and NPFFR suggested their expressions in the pituitary gland, and this was confirmed by the RT-PCR analysis. Localizations of both chicken RFRP and its receptors were distinct from those of mammals. These results indicated that avian RFRP, unlike the mammalian one, directly acts on the pituitary gland via receptors to regulate gonadotropin release. It was also suggested that functional differences, especially between avian and mammalian RFRPs, are substantially due to divergences in the structures and expression sites of their receptors.

Amino Acid Sequence↗
PubMed1995

Divergent differentiation in choroid plexus papilloma. An immunohistochemical study of five cases.

Intermediate filament and S100 expression was studied in five cases of choroid plexus papilloma. All the cases showed positivity for S100 and Nimentin. Cytokeratin and glial fibrillary protein (GFAP) intermediate filaments were present in 80 pc of the cases. None of the cases expressed epithelial membrane antigen. These results confirm the divergent differentiation of choroid plexus tumours.

Adolescent↗
PubMed2004

Trout CC chemokines: comparison of their sequences and expression patterns.

Several thousand EST sequences were recently made available in the EMBL sequence database from the rainbow trout Oncorhynchus mykiss. BLAST based searches were utilised to identify sequences resembling mammalian CC chemokines within these ESTs. Fifteen new and unique CC chemokine-like sequences were identified for trout, bringing the total of known CC chemokine sequences in trout to 18 when including those already published. Some of these trout chemokines appeared highly related (in pairs) suggesting recent duplication events or tight evolutionary constraints. Phylogenetically, the trout chemokine sequences grouped with both inducible and constitutive mammalian CC chemokine subtypes, suggesting early divergence of these functional groups. Expression analyses on gill and head kidney show constitutive expression of many of these trout CC chemokines in these lymphoid-rich tissues. However, induction of some of the chemokines structurally related to 'inducible' CC chemokines was observed in a trout macrophage-like cell line (RTS-11) in response to stimulation with recombinant TNFalpha.

Amino Acid Sequence↗
PubMed1991

Detection of a gene encoding a phosphatidylinositol-specific phospholipase C that is co-ordinately expressed with listeriolysin in Listeria monocytogenes.

A phosphatidylinositol-specific phospholipase C (PI-PLC) that is unique to the pathogenic Listeria species L. monocytogenes and L. ivanovii has been detected. Deletion analysis performed with Escherichia coli recombinants expressing PI-PLC activity together with maxicell analysis showed that a 34 kDa polypeptide was responsible for this activity. Nucleotide sequencing revealed that the gene encoding this polypeptide comprises 317 amino acid residues with a 22-amino-acid signal peptide. This gene, designated pic for phosphatidylinositol-specific phospholipase C, is located back to back with the listeriolysin gene on the chromosome of L. monocytogenes where these genes are transcribed by divergent non-overlapping promoters. Expression of the pic gene is dependent on the product of the prfA gene, which also regulates expression of the listeriolysin gene in L. monocytogenes.

Amino Acid Sequence↗
PubMed1998

A divergent member of the transforming growth factor beta receptor family from Schistosoma mansoni is expressed on the parasite surface membrane.

To optimize reproductive success under the limitations determined by conditions within an individual host, parasitic helminths have evolved mechanisms that allow them to detect and respond to host factors such as species, age, sex, reproductive condition, and immune status. Using the model helminth Schistosoma mansoni, we have explored the possibility that parasitic helminths express signal-transducing receptor molecules on their surfaces. Here, we present the identification of a schistosome member of the transforming growth factor beta receptor family of cell-surface receptors, the first member of this family to be identified in a platyhelminth. The putative protein kinase domain of the schistosome receptor displays up to 58% amino acid identity to kinase domains of other type I receptor serine-threonine kinases, and contains a potential "GS domain," suggesting it is a divergent member of the type I receptor subfamily. This receptor is expressed on the surface of the parasite's syncytial tegument and expression of receptor messenger RNA and protein is up-regulated following infection of the mammalian host. The receptor protein can be isolated in a phosphorylated form from adult parasites, which together with its surface location, suggests that it functions in transducing signals across the parasite surface membrane.

Amino Acid Sequence↗
PubMed1995

Gene structure, chromosomal localization, and expression of the murine homologue of human proteinase inhibitor 6 (PI-6) suggests divergence of PI-6 from the ovalbumin serpins.

Human proteinase inhibitor 6 (PI-6) is a recently described protein belonging to the serine proteinase inhibitor (serpin) superfamily. Sequence similarity suggests that PI-6 most resembles the ovalbumin (ov) serpins which include plasminogen activator inhibitor-2, the squamous cell carcinoma antigen, monocyte/neutrophil elastase inhibitor, and maspin. Although these proteins are associated with carcinomas and inflammation, they appear to have diverse functions and little is known of their physiological roles. In this study we have characterized cDNA and genomic clones encoding mouse PI-6 in order to analyze the localization, structure, and expression of the gene. The reactive center residues (Arg-Cys) are conserved in the mouse molecule, and recombinant mouse PI-6 was shown to bind thrombin, indicating that it has similar inhibitory properties to its human counterpart. Using reverse transcriptase-polymerase chain reaction assays on RNA isolated from 15-day-old embryos and adult mice, we have shown that mouse PI-6 expression is developmentally regulated, and that, unlike human PI-6, it is absent from the placenta. The mouse homologue of the human PI-6 gene has been designated Spi3 and was mapped to chromosome 13 between the Pl1 and ctla2 alpha genes. It spans 20 kilobases, consists of 7 exons and 6 introns, and contains a TATA motif 24 nucleotides upstream of the transcriptional start site. A 680-base pair DNA fragment containing this motif and 31 nucleotides of the 5'-untranslated region of the structural gene directed transcription of a bacterial cat gene, demonstrating the presence of a functional promoter. The PI-6 gene lacks an intron present in the ovalbumin and PAI-2 genes; otherwise it is identical in terms of the numbers, position, and phasing of the intron/exon boundaries. These results suggest that PI-6 and the ov-serpin genes have diverged and do not belong to the same subgroup.

Amino Acid Sequence↗
PubMed2004

Functional divergence in tandemly duplicated Arabidopsis thaliana trypsin inhibitor genes.

In multigene families, variation among loci and alleles can contribute to trait evolution. We explored patterns of functional and genetic variation in six duplicated Arabidopsis thaliana trypsin inhibitor (ATTI) loci. We demonstrate significant variation in constitutive and herbivore-induced transcription among ATTI loci that show, on average, 65% sequence divergence. Significant variation in ATTI expression was also found between two molecularly defined haplotype classes. Population genetic analyses for 17 accessions of A. thaliana showed that six ATTI loci arranged in tandem within 10 kb varied 10-fold in nucleotide diversity, from 0.0009 to 0.0110, and identified a minimum of six recombination events throughout the tandem array. We observed a significant peak in nucleotide and indel polymorphism spanning ATTI loci in the interior of the array, due primarily to divergence between the two haplotype classes. Significant deviation from the neutral equilibrium model for individual genes was interpreted within the context of intergene linkage disequilibrium and correlated patterns of functional differentiation. In contrast to the outcrosser Arabidopsis lyrata for which recombination is observed even within ATTI loci, our data suggest that response to selection was slowed in the inbreeding, annual A. thaliana because of interference among functionally divergent ATTI loci.

Amino Acid Sequence↗
PubMed1999

Discoordinate regulation of different K channels in cultured rat skeletal muscle by nerve growth factor.

We investigated the effects of nerve growth factor (NGF) on expression of K+ channels in cultured skeletal muscle. The channels studied were (1) charybdotoxin (ChTx)-sensitive channels by using a polyclonal antibody raised in rabbits against ChTx, (2) Kv1.5 voltage-sensitive channels, and (3) apamin-sensitive (afterhyperpolarization) channels. Crude homogenates were prepared from cultures made from limb muscles of 1-2-day-old rat pups for identification of ChTx-sensitive and Kv1.5 channels by Western blotting techniques. Apamin-sensitive K+ channels were studied by measurement of specific [125I]-apamin binding by whole cell preparations. ChTx-sensitive channels display a fusion-related increase in expression, and NGF downregulates these channels in both myoblasts and myotubes. Voltage-dependent Kv1.5 channel expression is low in myoblasts and increases dramatically with fusion; NGF induces early expression of these channels and causes expression after fusion to increase even further. NGF downregulates apamin-sensitive channels. NGF increases the rate of fall of the action potential recorded intracellularly from single myotubes with intracellular microelectrodes. The results confirm and extend those of previous studies in showing a functional role for NGF in the regulation of membrane properties of skeletal muscle. Moreover, the findings demonstrate that the different K+ channels in this preparation are regulated in a discoordinate manner. The divergent effects of NGF on expression of different K+ channels, however, do not appear sufficient to explain the NGF-induced increase in the rate of fall of the action potential. The changes during the falling phase may rather be due to increases in channel properties or may result from an increased driving force on the membrane potential secondary to the NGF-induced hyperpolarization.

Action Potentials↗