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PubMed1986

Evolution of cytochrome c genes and pseudogenes.

A statistical analysis of the nucleotide sequences of cytochrome c genes from four species of animals and two of yeast and of cytochrome c pseudogenes from rat, mouse, and human was conducted. It was estimated that animals and yeast diverged 1.2 billion years ago, that the two duplicated genes DC3 and DC4 in Drosophila diverged 520 million years ago, and that the two duplicated genes Iso-1 and Iso-2 in the yeast Saccharomyces cerevisiae diverged 200 million years ago. DC3 is expressed at a low level and has evolved 3 times faster than DC4. This observation supports the neutralist view that relaxation of functional constraints is a more likely cause of accelerated evolution following gene duplication than is advantageous mutation. All the rodent pseudogenes examined appear to be processed pseudogenes derived directly from the functional genes, and most of them apparently arose after the mouse-rat split. No event of gene conversion could be detected between any pair of the rodent pseudogenes. Our analysis suggests that the human cytochrome c gene has evolved at a rate comparable to the average rate for pseudogenes, whereas some human cytochrome c pseudogenes have evolved at an exceptionally low rate.

Animals↗
PubMed2006

Evolution of the metazoan protein phosphatase 2C superfamily.

Members of the protein phosphatase 2C (PP2C) superfamily are Mg(2+)/Mn(2+)-dependent serine/threonine phosphatases, which are essential for regulation of cell cycle and stress signaling pathways in cells. In this study, a comprehensive genomic analysis of all available metazoan PP2C sequences was conducted. The phylogeny of PP2C was reconstructed, revealing the existence of 15 vertebrate families which arose following a series of gene duplication events. Relative dating of these duplications showed that they occurred in two active periods: before the divergence of bilaterians and before vertebrate diversification. PP2C families which duplicated during the first period take part in different signaling pathways, whereas PP2C families which diverged in the second period display tissue expression differences yet participate in similar signaling pathways. These differences were found to involve variation of expression in tissues which show higher complexity in vertebrates, such as skeletal muscle and the nervous system. Further analysis was performed with the aim of identifying the functional domains of PP2C. The conservation pattern across the entire PP2C superfamily revealed an extensive domain of more than 50 amino acids which is highly conserved throughout all PP2C members. Several insertion or deletion events were found which may have led to the specialization of each PP2C family.

Animals↗
PubMed2006

Coexistence of the loss of heterozygosity at the PTEN locus and HER2 overexpression enhances the Akt activity thus leading to a negative progesterone receptor expression in breast carcinoma.

Serine/threonine kinase Akt/PKB is known to regulate divergent cellular processes, including apoptosis, proliferation, differentiation, and metabolism. Akt is activated by a variety of stimuli, through such growth factor receptors as HER2, in phosphoinositide-3-OH kinase (PI3K)-dependent manner. A loss of phosphatase and tensin homolog deleted on chromosome 10 (PTEN) function also activates Akt. It has recently been shown that Akt activation is associated with a worse outcome among endocrine treated breast cancer patients and that it also inhibits the progesterone receptor (PR) expression via the PI3K/Akt pathway in breast cancer cells. Therefore, the PI3K/Akt signaling pathway has recently attracted considerable attention as a new target for effective therapeutic strategies. In the present study, we investigated the relationship between Akt activation and either HER2 overexpression or PTEN gene alteration, as well as the PR expression. We analyzed the incidence of LOH at the PTEN locus in 138 breast cancer patients, using our new system for microsatellite analysis, called high-resolution fluorescent microsatellite analysis (HRFMA). We showed Akt activation to significantly correlate with HER2 overexpression or LOH at the PTEN gene locus while inversely correlating with the PR expression. In addition, when LOH at the PTEN gene locus and HER2 overexpression occurred simultaneously, the incidence of Akt activation and reduced PR expression was significant. The association between Akt activation and PR negative expression was observed even in the ER-positive cases. Our results suggest that simultaneous PTEN LOH and HER2 overexpression enhances Akt activation and may thus lead to a negative PR expression.

Breast Neoplasms↗
PubMed2005

Immunophenotypic and ultrastructural validation of a new human glioblastoma cell line.

1. A human glioma cell line, NG97, was established by Grippo et al. in 2001 from tissue obtained from a grade III astrocytoma (WHO, 2000). In this first study, the cell line grew as two morphologically distinct subpopulations: dendritic/spindle cells and small round cells. The injection of NG97 cells into nude mice induced an aggressive tumor characterized by: severe cytological atypia, vascular proliferation and pseudopalisading necrosis (glioblastoma multiforme features). 2. The purpose of the present study was to characterize the immunophenotype and ultrastructural aspects of this cell line, using the parental tumor, cultured cells and the xenotransplant, in order to assess its glial nature and possible divergent differentiation. 3. NG97 cells and xenotransplant expressed the main neuroglial markers (GFAP, S-100 protein, NSE and Leu-7) and showed no aberrant expression of other histogenetic markers. GFAP was similarly expressed in the parental tumor and in the cells in culture, but decreased in the xenotransplant. NSE expression was reduced in NG97 cells, but substantially recovered in the xenotransplant. This variability in expression of GFAP and NSE was interpreted as either a phenomenon of dedifferentiation or to microenvironmental selection of specific subclones. S-100 was equally expressed in the three contexts. The xenotransplant's ultrastructural features were those of a highly undifferentiated tumor. No significant immunophenotypic or ultrastructural differences between the two morphologically distinct populations were found. 4. Thus, our data demonstrate that NG97 cells constitute a pure glial-committed cell line, which may prove useful as a malignant glioma model in studies addressing pathophysiological, diagnostic and therapeutic issues.

Animals↗
PubMed1995

The steroidogenic acute regulatory protein is induced by angiotensin II and K+ in H295R adrenocortical cells.

Adrenal steroid hormone biosynthesis can be activated by the protein kinase A pathway by ACTH, the protein kinase C pathway by angiotensin II (AII), or by increasing intracellular Ca2+ levels by AII or K+. Although their mechanisms of action are not known, each of these pathways is dependent upon the de novo synthesis of a protein that is required for the acute production of steroids. We have recently proposed the steroidogenic acute regulatory (StAR) protein as this required protein, therefore, we examined the effect of different agonists on StAR's expression in H295R human adrenocortical carcinoma cells. (Bu)2cAMP, AII, K+, BAYK8644 (a calcium channel agonist) and TPA are all shown to induce StAR. Aldosterone synthesis was stimulated by all the agonists with the exception of TPA, indicating that AII-stimulated steroid production is mediated by increases in intracellular calcium. Thus, these data suggest that regulation of StAR expression may represent a common mechanism for divergent pathways to acutely control adrenal steroidogenesis.

3-Pyridinecarboxylic acid, 1,4-dihydro-2,6-dimethy↗
PubMed2005

Human and murine glycerol kinase: influence of exon 18 alternative splicing on function.

Glycerol kinase (GK) is a key enzyme in glycerol metabolism with two alternatively spliced forms-one with an 87bp insertion corresponding to exon 18 (GK+EX18), and one lacking exon 18 (GK-EX18). We report the expression of GK+/-EX18 in various tissues and cell lines, as well as their enzymatic characteristics and subcellular localization. RT-PCR revealed differential expression in tissues and cell lines. Northern blot analysis revealed that both forms of the murine ortholog, Gyk, were highly expressed in murine heart and increased during embryonic development. K(m) values for glycerol for GK+/-EX18 were not significantly different, although GK-EX18 had a higher V(max) for glycerol. GK-EX18 had a lower K(m) and V(max) for ATP than GK+EX18. Immunofluorescence experiments showed that GK+EX18 co-localized to the mitochondria and the perinuclear region while GK-EX18 had a diffuse expression pattern. These data suggest specific and divergent roles for GK+EX18 and GK-EX18 in cellular metabolism and development.

Alternative Splicing↗
PubMed2004

Polymorphisms in human MDR1 (P-glycoprotein): recent advances and clinical relevance.

Drug transporters are increasingly recognized to be important to drug disposition and response. P-glycoprotein, the encoded product of the human MDR1 (ABCB1) gene, is of particular clinical relevance in that this transporter has broad substrate specificity, including a variety of structurally divergent drugs in clinical use today. Moreover, expression of this efflux transporter in certain tissue compartments such as the gastrointestinal tract and brain capillary endothelial cells limits oral absorption and central nervous system entry of many drugs. Recently, a number of single-nucleotide polymorphisms (SNPs) in MDR1 have been identified. An increasing number of studies have also implicated certain commonly occurring SNPs in MDR1 in problems including altered drug levels and host susceptibility to diseases such as Parkinson's disease, inflammatory bowel disease, refractory seizures, and CD4 cell recovery during human immunodeficiency virus therapy. However, in many such cases, the reported effects of MDR1 SNPs have been inconsistent and, in some cases, conflicting. In this review SNPs in MDR1 in relation to population frequencies, drug levels, and phenotypes are outlined. In addition, issues relating to MDR1 haplotypes, environmental factors, and study design, as potential confounding factors of the observed MDR1 polymorphism effect in vivo, are also discussed.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2006

A set of recombineering plasmids for gram-negative bacteria.

We have constructed a set of plasmids that can be used to express recombineering functions in some gram-negative bacteria, thereby facilitating in vivo genetic manipulations. These plasmids include an origin of replication and a segment of the bacteriophage lambda genome comprising the red genes (exo, bet and gam) under their native control. These constructs do not require the anti-termination event normally required for Red expression, making their application more likely in divergent species. Some of the plasmids have temperature-sensitive replicons to simplify curing. In creating these vectors we developed two useful recombineering applications. Any gene linked to a drug marker can be retrieved by gap-repair using only a plasmid origin and target homologies. A plasmid origin of replication can be changed to a different origin by targeted replacement, to potentially alter its copy number and host range. Both these techniques will prove useful for manipulation of plasmids in vivo. Most of the Red plasmid constructs catalyzed efficient recombination in E. coli with a low level of uninduced background recombination. These Red plasmids have been successfully tested in Salmonella, and we anticipate that that they will provide efficient recombination in other related gram-negative bacteria.

Bacteriophage lambda↗
PubMed2005

Handling calcium signaling: Arabidopsis CaMs and CMLs.

The Arabidopsis genome harbors seven calmodulin (CAM) and 50 CAM-like (CML) genes that encode potential calcium sensors. The CAMs encode only four protein isoforms. Selective pressure to maintain multiple CAMs indicates nonredundancy. Sequence divergence, even in the EF hand calcium-binding motif, exists among the CMLs and, therefore, divergent functions are likely to have evolved. Expression data recently available from Massively Parallel Signature Sequencing and Genevestigator compilation of microarrays are reviewed. The seven Arabidopsis CAMs are highly and relatively uniformly expressed. Differential expression is evident among the distinct CMLs over developmental stages, in various organs and in response to many different stimuli. In spite of the potential importance in mediating plant calcium signaling, the physiological functions of the Arabidopsis CaMs and CMLs remain largely unknown.

Amino Acid Sequence↗
PubMed1999

Perceptions of health care professionals and patients about the risk of HIV transmission through oral sex: a qualitative study.

We explored health care professionals' beliefs and methods for counseling patients about risks for transmitting human immunodeficiency virus (HIV) through oral sex and HIV-seropositive patients' beliefs and practices regarding oral sex behavior. Health care professionals used divergent counseling strategies, avoided specific recommendations, and expressed ambivalence about recommending barrier protection for oral sex. Patients expressed differing beliefs about oral sex risk; the majority have engaged in unprotected oral sex since diagnosis. Few professionals or patients mentioned oral sex risk for other sexually transmitted diseases (STDs), which can be cofactors for HIV. Although scientific evidence indicates a potential risk for transmitting HIV via oral sex, and patients in our sample want more information about this risk, the health care professionals we interviewed have adopted a largely noncommittal approach to communicating potential risk to patients. Health care professionals should consider discussing more specifically with patients the oral sex risk for transmission of HIV and other sexually transmitted diseases.

Adult↗
PubMed2003

The SELF-PRUNING gene family in tomato.

The SELF PRUNING (SP) gene controls the regularity of the vegetative-reproductive switch along the compound shoot of tomato and thus conditions the 'determinate' (sp/sp) and 'indeterminate' (SP_) growth habits of the plant. SP is a developmental regulator which is homologous to CENTRORADIALIS (CEN) from Antirrhinum and TERMINAL FLOWER 1 (TFL1) and FLOWERING LOCUS T (FT) from Arabidopsis. Here we report that SP is a member of a gene family in tomato composed of at least six genes, none of which is represented in the tomato EST collection. Sequence analysis of the SP gene family revealed that its members share homology along their entire coding regions both among themselves and with the six members of the Arabidopsis family. Furthermore, members of the gene family in the two species display a common genomic organization (intron-exon pattern). In tomato, phylogenetically close homologues diverged considerably with respect to their organ expression patterns while SP2I and its closest homologue from Arabidopsis (MFT) exhibited constitutive expression. This research focusing on a plant of sympodial growth habit sets the stage for a functional analysis of this weakly expressed gene family which plays a key role in determining plant architecture.

Amino Acid Sequence↗
PubMed2005

A genome-wide comparison of recent chimpanzee and human segmental duplications.

We present a global comparison of differences in content of segmental duplication between human and chimpanzee, and determine that 33% of human duplications (> 94% sequence identity) are not duplicated in chimpanzee, including some human disease-causing duplications. Combining experimental and computational approaches, we estimate a genomic duplication rate of 4-5 megabases per million years since divergence. These changes have resulted in gene expression differences between the species. In terms of numbers of base pairs affected, we determine that de novo duplication has contributed most significantly to differences between the species, followed by deletion of ancestral duplications. Post-speciation gene conversion accounts for less than 10% of recent segmental duplication. Chimpanzee-specific hyperexpansion (> 100 copies) of particular segments of DNA have resulted in marked quantitative differences and alterations in the genome landscape between chimpanzee and human. Almost all of the most extreme differences relate to changes in chromosome structure, including the emergence of African great ape subterminal heterochromatin. Nevertheless, base per base, large segmental duplication events have had a greater impact (2.7%) in altering the genomic landscape of these two species than single-base-pair substitution (1.2%).

Animals↗
PubMed2005

The Polo kinase Plk4 functions in centriole duplication.

The human Polo-like kinase 1 (PLK1) and its functional homologues that are present in other eukaryotes have multiple, crucial roles in meiotic and mitotic cell division. By contrast, the functions of other mammalian Polo family members remain largely unknown. Plk4 is the most structurally divergent Polo family member; it is maximally expressed in actively dividing tissues and is essential for mouse embryonic development. Here, we identify Plk4 as a key regulator of centriole duplication. Both gain- and loss-of-function experiments demonstrate that Plk4 is required--in cooperation with Cdk2, CP110 and Hs-SAS6--for the precise reproduction of centrosomes during the cell cycle. These findings provide an attractive explanation for the crucial function of Plk4 in cell proliferation and have implications for the role of Polo kinases in tumorigenesis.

Cell Cycle↗
PubMedDate not supplied

Developmental system drift and flexibility in evolutionary trajectories.

The comparative analysis of homologous characters is a staple of evolutionary developmental biology and often involves extrapolating from experimental data in model organisms to infer developmental events in non-model organisms. In order to determine the general importance of data obtained in model organisms, it is critical to know how often and to what degree similar phenotypes expressed in different taxa are formed by divergent developmental processes. Both comparative studies of distantly related species and genetic analysis of closely related species indicate that many characters known to be homologous between taxa have diverged in their morphogenetic or gene regulatory underpinnings. This process, which we call "developmental system drift" (DSD), is apparently ubiquitous and has significant implications for the flexibility of developmental evolution of both conserved and evolving characters. Current data on the population genetics and molecular mechanisms of DSD illustrate how the details of developmental processes are constantly changing within evolutionary lineages, indicating that developmental systems may possess a great deal of plasticity in their responses to natural selection.

Animals↗
PubMedDate not supplied

Hox gene duplication and deployment in the annelid leech Helobdella.

The segmented leeches are members of the phylum Annelida within the Lophotrochozoa. Here, we describe the isolation of a new Hox gene, Lox18, in the leech Helobdella triserialis. Phylogenetic analysis indicates that Lox18 is a Deformed (Dfd) ortholog. H. triserialis has at least two Dfd orthologs, Lox18 and the previously described Lox6 (Kourakis et al. 1997; Wong and Macagno 1998), indicating that these genes duplicated after the last common ancestor of annelids and arthropods. Although the temporal appearance of Lox18 message is similar to that of Lox6, the spatial pattern is different. Lox18 does not have a sharply defined anterior border of expression in the second neuromere of the subesophageal ganglion of the central nervous system (CNS) as does Lox6, but is expressed uniformly in a small subset of cells in the longitudinal connectives and lateral roots in every segment of the CNS along the entire anterior-posterior (AP) axis. Even though Lox18 shares greater sequence similarity within the homeodomain and flanking regions to Drosophila Dfd than to the previously isolated Lox6, its expression pattern suggests that its function has diverged from the ancestral Hox function. Previous sampling has indicated that the last common ancestor of protostomes and deuterostomes had as many as 10 clustered Hox genes representing distinct paralogy groups (Irvine et al. 1997; de Rosa et al. 1999); leech Hox genes may have undergone subsequent and independent cluster or genome-wide duplication. These results point to the need for total genome level understanding for key members of the Lophotrochozoa.

Amino Acid Sequence↗
PubMed1993

Myelin protein zero gene mutated in Charcot-Marie-tooth type 1B patients.

Autosomal dominant of Charcot-Marie-Tooth disease (CMT), whose gene is type 1B (CMT1B), has slow nerve conduction with demyelinated Schwann cells. In this study the abundant peripheral myelin protein zero (MPZ) gene, MPZ, was mapped 130 kb centromeric to the Fc receptor immunoglobulin gene cluster in band 1q22, and a major MPZ point mutation was found to cosegregate with CMT1B in one large CMT1B family. The MPZ point mutation in 18 of 18 related CMT1B pedigree 1 patients converts a positively charged lysine in codon 96 to a negatively charged glutamate. The same MPZ locus cosegregates with the CMT1B disease gene in a second CMT1B family [total multipoint logarithm of odds (lod) = 11.4 at theta = 0.00] with a splice junction mutation. Both mutations occur in MPZ protein regions otherwise conserved identically in human, rat, and cow since these species diverged 100 million years ago. MPZ protein, expressed exclusively in myelinated peripheral nerve Schwann cells, constitutes > 50% of myelin protein. These mutations are anticipated to disrupt homophilic MPZ binding and result in CMT1B peripheral nerve demyelination.

Animals↗
PubMed1996

The embAB genes of Mycobacterium avium encode an arabinosyl transferase involved in cell wall arabinan biosynthesis that is the target for the antimycobacterial drug ethambutol.

The antimycobacterial compound ethambutol [Emb; dextro-2,2'-(ethylenediimino)-di-1-butanol] is used to treat tuberculosis as well as disseminated infections caused by Mycobacterium avium. The critical target for Emb lies in the pathway for the biosynthesis of cell wall arabinogalactan, but the molecular mechanisms for drug action and resistance are unknown. The cellular target for Emb was sought using drug resistance, via target overexpression by a plasmid vector, as a selection tool. This strategy led to the cloning of the M. avium emb region which rendered the otherwise susceptible Mycobacterium smegmatis host resistant to Emb. This region contains three complete open reading frames (ORFs), embR, embA, and embB. The translationally coupled embA and embB genes are necessary and sufficient for an Emb-resistant phenotype which depends on gene copy number, and their putative novel membrane proteins are homologous to each other. The predicted protein encoded by embR, which is related to known transcriptional activators from Streptomyces, is expendable for the phenotypic expression of Emb resistance, but an intact divergent promoter region between embR and embAB is required. An Emb-sensitive cell-free assay for arabinan biosynthesis shows that overexpression of embAB is associated with high-level Emb-resistant arabinosyl transferase activity, and that embR appears to modulate the in vitro level of this activity. These data suggest that embAB encode the drug target of Emb, the arabinosyl transferase responsible for the polymerization of arabinose into the arabinan of arabinogalactan, and that overproduction of this Emb-sensitive target leads to Emb resistance.

Amino Acid Sequence↗
PubMed2003

Comparison of the A2 gene locus in Leishmania donovani and Leishmania major and its control over cutaneous infection.

In Old World Leishmania infections, Leishmania donovani is responsible for fatal visceral leishmaniasis, and L. major is responsible for non-fatal cutaneous leishmaniasis in humans. The genetic differences between these species which govern the pathology or site of infection are not known. We have therefore carried out detailed analysis of the A2 loci in L. major and L. donovani because A2 is expressed in L. donovani but not L. major, and A2 is required for survival in visceral organs by L. donovani. We demonstrate that although L. major contains A2 gene regulatory sequences, the multiple repeats that exist in L. donovani A2 protein coding regions are absent in L. major, and the remaining corresponding A2 sequences appear to represent non-expressed pseudogenes. It was possible to restore amastigote-specific A2 expression to L. major, confirming that A2 regulatory sequences remain functional in L. major. Although L. major is a cutaneous parasite in rodents and humans, restoring A2 expression to L. major inhibited its ability to establish a cutaneous infection in susceptible BALB/c or resistant C57BL6 mice, a phenotype typical of L. donovani. There was no detectable cellular immune response against L. major after cutaneous infection with A2-expressing L. major, suggesting that the lack of growth was not attributable to acquired host resistance but to an A2-mediated suppression of parasite survival in skin macrophages. These observations argue that the lack of A2 expression in L. major contributed to its divergence from L. donovani with respect to the pathology of infection.

3' Untranslated Regions↗