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PubMed1994

Complementary deletions in expressed potato U2snRNA gene variants support the hypothesis that stem-loop IIb is dispensable for splicing.

A polymerase chain reaction (PCR) strategy designed to amplify DNA sequences between closely linked U2snRNA genes has generated extensive coding and 5' regulatory sequence information on the potato U2snRNA multigene family. Two of the U2snRNA coding sequences isolated differed substantially from normal U2snRNAs by containing both complementary deletions and regions of novel sequence. However, sequences such as Sm-binding sites and loops of stem-loops III and IV, which are some of the most highly conserved regions in U2snRNA, remain highly conserved in these genes. The complementary deletions would effectively remove stem-loop IIb which has been shown in yeast to be unnecessary for pre-mRNA splicing. Transcripts from one of the genes have been detected by reverse transcriptase-PCR (RT-PCR) in total RNA. These novel U2snRNA genes represent the first reported example of naturally occurring structural variants and provide support for the proposed non-essential role of U2snRNA stem-loop IIb.

Base Sequence↗

PubMed2004

Structure-activity relationships for substrate recognition by the human dopamine transporter.

Information is available on the structure-activity relationships for dopamine as a substrate for uptake by the dopamine transporter. However, dopamine transport is a complex process involving substrate binding, translocation, release as well as transporter reorientation. The present study examines only the substrate recognition step by assessment of the potency of various dopamine-related compounds in inhibiting the binding of the cocaine analog [3H]2beta-carbomethoxy-3beta-(4-fluorophenyl)tropane ([3H]WIN 35,428) to human dopamine transporters expressed in HEK-293 cells. alpha-Methylation of the side chain, the presence of the amine, and the 2-carbon-length of the side chain were found to be important for binding affinity, whereas beta-hydroxylation of the side chain and methoxylation at the phenyl ring generated weaker compounds. In addition, the presence of both m- and p-OH at the phenyl ring bestowed an increase in potency but the presence of p-OH alone a decrease. N-alkylation (propylation or methylation) had little or an even slightly beneficial effect on affinity, whereas alpha-carbonylation and alpha-methanoylation reduced affinity. Amino naphthalene compounds with a fused benzenoid ring system retained some potency consonant with the extended (i.e. beta-rotameric) trans (=anti) form of the side chain in dopamine when interacting with the transporter. In a second series of experiments, the interaction between dopamine and structural variants was assessed by monitoring the capability of a compound to shift the dopamine inhibition curve to the right as expected for a competitive inhibitor acting at the same site. Appreciable deviation from competitive interaction was observed by removal of the amine from the side chain, by alpha-carbonylation, and by alpha-methanoylation. Two blocker-type compounds, semi-rigid variants of cocaine, also displayed significant deviation. A substrate-based compound, inhibiting cocaine analog binding without interfering with dopamine recognition, could be a cocaine antagonist allowing conformational changes to occur during dopamine uptake.

Binding, Competitive↗

PubMed1980

Defective synthesis of HbE is due to reduced levels of beta E mRNA.

Haemoglobin E (alpha 2 beta 2(26)Glu leads to Lys) is one of the commonest haemoglobin variants. There are an estimated 30 million carriers of the beta E gene in South-East Asia, where they comprise more than 50% of the population in some areas; however, the reasons for this high frequency have never been adequately explained. Homozygotes for HbE may be midly anaemic, but they do not have any clinical disability. However, individuals heterozygous for both beta E and beta thalassaemia (HbE/beta thalassaemia) have a severe clinical disorder which in some cases may approach that seen in homozygous beta thalassaemia and which is by far the commonest form of symptomatic thalassaemia in the Indian subcontinent and South-East Asia. Haemoglobin E is the only common structural variant which interacts with beta thalassaemia to produce a severe disorder and the underlying mechanism of the interaction is not known. We have studied several homozygotes and heterozygotes for HbE and show here that the beta E chain is inefficiently synthesized and produces the phenotype of a mild form of beta thalassaemia; hence, when inherited together with beta thalassaemia it causes a marked beta-chain deficit. Furthermore, the mechanism for the defective production of beta E chains seems to be a reduction of beta E mRNA, a most unexpected finding in a disorder caused by a single amino acid substitution and presumably by a single nucleotide change in the DNA of the beta globin gene.

Globins↗

PubMed1996

Combined cytogenetic and molecular genetic analyses of fifty-nine untreated human prostate carcinomas.

G-banding analyses and molecular genetic investigations (fluorescence in situ hybridization (FISH) and loss of heterozygosity (LOH) studies) were performed in 59 tumor and nontumorous samples of human prostate carcinoma. Clonal chromosome aberrations were detected in 16 tumors of which nine were poorly differentiated (G3) and 11 in an advanced stage (pT3). Six cases showed numerical chromosome aberrations. The most common numerical aberrations were trisomy 7 and loss of the Y chromosome each present in three tumors. Clonal structural aberrations were detected in 12 tumors. Deletions could be observed in two cases affecting chromosome 6q23 and in two cases affecting chromosomal region 16q. A structural variant of the pericentromeric heterochromatin of chromosome 9 became apparent in six cases. The Y chromosome was involved in clonal translocations in two cases, additionally an inversion occurred on chromosome 19 in one case. All clonal chromosomal changes were found exclusively in the tumor sample. For an analysis of the pericentromeric heterochromatin of chromosome 9, FISH using a chromosome 9-specific sat III DNA probe was carried out on metaphase preparations of tumor and nontumorous tissues of two cases showing var(9)(qh). The FISH data suggest a deletion in the pericentromeric heterochromatin. Loss of heterozygosity studies on chromosomal regions 10q and 16q were carried out because both chromosomes were frequently affected by nonclonal structural aberrations. Loss of heterozygosity could be verified in 11 cases.

Aged↗

PubMed2001

Catalytic cleavage of cis- and trans-acting antigenomic delta ribozymes in the presence of various divalent metal ions.

Catalytic activity of four structural variants of the antigenomic delta ribozyme, two cis- and two trans-acting, has been compared in the presence of selected divalent metal ions that effectively support catalysis. The ribozymes differ in regions that are not directly involved in formation of the ribozyme active site: the region immediately preceding the catalytic cleavage site, the P4 stem and a stretch of the viral RNA sequence extending the minimal ribozyme sequence at its 3'-terminus. The variants show high cleavage activity in the presence of Mg(2+), Ca(2+) and Mn(2+), lower with Co(2+) and Sr(2+) and some variants are also active with Cd(2+) and Zn(2+) ions. In the presence of a particular metal ion the ribozymes cleave, however with different initial rates, according to pseudo-first or higher order kinetics and to different final cleavage extents. On the other hand, relatively small differences are observed in the reactions induced by various metal ions. The cleavage of trans-acting ribozymes induced by Mg(2+) is partially inhibited in the presence of Na(+), spermidine and some other divalent metal ions. The inert Co(NH(3))(6)(3+) complex is unable to support catalysis, as reported earlier for the genomic ribozyme. The results are discussed in terms of the influence of structural elements peripheral to the ribozyme active site on its cleavage rate and efficiency as well as the role of metal ions in the cleavage mechanism. Some implications concerning further studies and possible applications of delta ribozymes are also considered.

Base Sequence↗

PubMed1997

Animal lectins.

Protein and lipid glycosylation is no longer considered as a topic whose appeal is restricted to a limited number of analytical experts perseveringly pursuing the comprehensive cataloguing of structural variants. It is in fact arousing curiosity in various areas of basic and applied bioscience. Well founded by the conspicuous coding potential of the sugar part of cellular glycoconjugates which surpasses the storage capacity of oligonucleotide- or oligopeptide-based code systems, recognition of distinct oligosaccharide ligands by endogenous receptors, i.e. lectins and sugar-binding enzymes or antibodies, is increasingly being discovered to play salient roles in animal physiology. Having inevitably started with a descriptive stage, research on animal lectins has now undubitably reached maturity. Besides listing the current categories for lectin classification and providing presentations of the individual families and their presently delineated physiological significance, this review places special emphasis on tracing common structural and functional themes which appear to reverberate in nominally separated lectin and animal categories as well as lines of research which may come to fruition for medical sciences.

Animals↗

PubMed2002

Synthesis and cytotoxicity of 9-alkoxy-1,5-dichloroanthracene derivatives in murine and human cultured tumor cells.

9-Alkoxy-1,5-dichloroanthracenes were successfully prepared. Their cytotoxicity was evaluated in vitro on rat glioma C6 cell lines and human hepatoma G2 cell lines, respectively. Alkylation of 1,5-dichloro-9(10H)-anthracenone with either the appropriate alcohols or alkyl chlorides in the presence of sulfuric acid or sodium hydride, respectively, furnished this structural class of anthracenes. Contrary to mitoxantrone, cytotoxic properties were observed as documented by the reactivity of the novel compounds and potent in vitro activity against C6 cells and hep G2 cells over a wide range of structural variants. Among these compounds, 5c, 5h, 5l and 5n are potent cytotoxins. They inhibit C6 cell growth in culture, indicated by using 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide sodium salt (XTT) colorimetric assay. By using this assay it was also shown that 5c, 5d and 5l possess potent cytotoxicity on hep G2 cells. The most active compound displaying in vitro cytotoxicity was the 9-butoxy derivative 5h with IC50 values 0.02 microM against C6 cells, as compared with mitoxantrone with IC50 values 0.07 microM. The most active compound displaying in vitro cytotoxicity against hep G2 cells was 5c with IC50 values 1.7 microM (mitoxantrone: 0.8 microM). Structure-activity relationships (SAR) of these compounds with respect to the nature of the alkoxy substitution in the 9 position are discussed for both cell lines.

Animals↗

PubMed2000

Analogues and derivatives of ciproxifan, a novel prototype for generating potent histamine H3-receptor antagonists.

Novel derivatives of the highly potent and selective histamine H3-receptor antagonist ciproxifan (3) with different chain lengths as well as with structural variants of the cyclopropyl ketone moiety have been prepared and screened for their antagonist H3-receptor potencies in vitro and in vivo. Some derivatives (2, 6-8, 12) containing other functionalities were effective in vitro in the same (sub)nanomolar concentration range and in vivo in a remarkably low oral dose.

Animals↗

PubMed2004

Gonadotropin-releasing hormone receptors.

GnRH and its analogs are used extensively for the treatment of hormone-dependent diseases and assisted reproductive techniques. They also have potential as novel contraceptives in men and women. A thorough delineation of the molecular mechanisms involved in ligand binding, receptor activation, and intracellular signal transduction is kernel to understanding disease processes and the development of specific interventions. Twenty-three structural variants of GnRH have been identified in protochordates and vertebrates. In many vertebrates, three GnRHs and three cognate receptors have been identified with distinct distributions and functions. In man, the hypothalamic GnRH regulates gonadotropin secretion through the pituitary GnRH type I receptor via activation of G(q). In-depth studies have identified amino acid residues in both the ligand and receptor involved in binding, receptor activation, and translation into intracellular signal transduction. Although the predominant coupling of the type I GnRH receptor in the gonadotrope is through productive G(q) stimulation, signal transduction can occur via other G proteins and potentially by G protein-independent means. The eventual selection of intracellular signaling may be specifically directed by variations in ligand structure. A second form of GnRH, GnRH II, conserved in all higher vertebrates, including man, is present in extrahypothalamic brain and many reproductive tissues. Its cognate receptor has been cloned from various vertebrate species, including New and Old World primates. The human gene homolog of this receptor, however, has a frame-shift and stop codon, and it appears that GnRH II signaling occurs through the type I GnRH receptor. There has been considerable plasticity in the use of different GnRHs, receptors, and signaling pathways for diverse functions. Delineation of the structural elements in GnRH and the receptor, which facilitate differential signaling, will contribute to the development of novel interventive GnRH analogs.

Amino Acid Sequence↗

PubMed1999

[Characteristics of quantitative karyotypic variability in cell line of kidney from rat kangaroo (Potorous tridactylis)].

The goal of this work was to investigate the numeral karyotypic variability in different sublines (MT, M2). These sublines are formed spontaneously from the main cell line (M) and have modal number of chromosomes 9 and 10, MSVK (main structural variant karyotype)--3 + 3 + 1 + 2 and 3 + 4 + 2 + 1. There are general regulations which were originally got for the line M. In particular: 1) nonrandom character of cell distribution according to the number of chromosomal deviations from MSVK; 2) specific character of deviations of each chromosome from MSVK; 3) presence of significant connections between separate chromosomes by simultaneous, mainly single directed numeral deviations. These three lines (M, MT, M2) were compared and some differences were found: 1) different frequencies of deviations from MSVK; 2) the same chromosomes have tendency to different numeral deviation; 3) the specificity of some significant connections between separate chromosomes by simultaneous numeral deviations. These results lead us to a conclusion that the balance of numerical karyotypic structure in cell populations depends on the regulations connected with the character of deviations according to the number of chromosomes from MSVK which has the largest selected advantage. Each line has its own specific limits of karyotypic variability.

Animals↗

PubMed1994

[The effect of mycoplasmal contamination of cultures of skin fibroblasts from the Indian muntjac and of the subsequent decontamination of the cultures using ciprofloxacin on the karyotypic structure of the cell line].

The karyotypic variability of Indian muntjac skin fibroblast cell line, cultured for 95-168 days after contamination with Acholeplasma laidlawii strain PG-8, has been investigated. The contaminated cultures differ from noncontaminated ones in cell distribution for chromosome number. The noncontaminated cultures have modal number of chromosomes equal to 7 with the main structure variant of the karyotype (SVK) 2+2+1+1+1. In the contaminated cultures the cell number with 7 chromosomes and the main SVK 2+2+1+1+1 decreased, whereas the cell number with 6 chromosomes increased along with the main SVK 2+2+1+1 resulting from the loss of chromosome Y1. The treatment of cells with ciprofloxacin for mycoplasma decontamination did not restore the normal cell distribution for chromosome number. The frequency of chromosomal aberrations, mainly dicentrics, due to telomeric associations, increased after 95-168 days of cultivation of contaminated cells. Chromosomes 1 and 2 and their combination are mainly involved in dicentric formations. The treatment of contaminated cells with ciprofloxacin restores the initial frequency of chromosomal aberrations. Chromosomes with altered structures have not been demonstrated. It has been shown that cells became mycoplasma-free after 15 days of treatment with ciprofloxacin. The role of aneuploidy and dicentrics in cell adaptation to culture conditions is discussed.

Acholeplasma laidlawii↗

PubMed2004

The NC1 domain of human collagen IV is necessary to initiate triple helix formation.

Type IV collagen is a heterotrimeric molecule, which contains the N-terminal 7S, a central triple-helical domain, and the globular C-terminal NC1 domain. A zipper-like mechanism of triple helix formation, starting from the C-terminus, has been proposed for most collagens but for collagen type IV there has only been indirect evidence so far. In this study we expressed trimeric human collagen type IV to compare the effects of different structural variants on the formation of collagen IV molecules. Our data show that the NC1 but not 7S domain is essential for the chain association and initiation of triple helix formation. This strongly suggests an N-to-C terminal mechanism of triple helix formation. Additionally, we could show that the human alpha2(IV) chain can form chimeric alpha1.alpha1.alpha2(IV) heterotrimers with mouse subunits when expressed in PF-HR9 cells.

Animals↗

PubMed1984

Technetium-99m benzimidazolyl iminodiacetic acid hepatobiliary radiopharmaceuticals: structure biodistribution studies.

The biodistribution of fifteen structural variants of the hepatobiliary radiopharmaceutical, technetium-99m benzimidazolyl iminodiacetic acid (BIMIDA) were determined 1 h after i.v. injection into rats. The best compounds with respect to hepatobiliary excretion were those with halogen substituents in the benzene ring of the BIMIDA ligand. The cholescintigraphic properties of the BIMIDA compounds compared favourably with those of technetium-99m acetanilido iminodiacetic acid (HIDA) radiopharmaceuticals.

Animals↗

PubMed1998

An Arg/Lys-rich core peptide mimics TRBP binding to the HIV-1 TAR RNA upper-stem/loop.

TRBP is a cellular protein that binds to the HIV-1 leader RNA, TAR. Circular dichroism experiments have shown that a 24 amino acid peptide (TR1), located within a dsRNA binding domain (dsRBD) of TRBP, binds TAR with a 3:1 stoichiometry, eliciting a conformational change involving base unstacking. The binding characteristics of synthetic structural variants of TAR indicate that guanine residues play a key role in the TR1-RNA interaction and that binding sites exist in the upper-stem/loop and lower stem region of TAR. Deletion analysis of TR1 has led to the identification of a 15 amino acid subpeptide (TR13) which is necessary and sufficient to bind to the high affinity upper-stem/loop binding site of TAR. Alanine scanning of TR13 has revealed that mutations in either Lys or Arg residues result in altered TAR-binding, and molecular modelling/docking experiments have shown that the two Arg residues of TR13 can interact with two appropriately spaced guanine residues in the upper-stem/loop of TAR. The TR13 lysine residues appear to be essential for maintaining structural integrity and the correct positioning of the Arg side-chains. We propose that TRBP binds TAR by means of a "2-G hook" motif and that the binding specificity of this particular member of the family of double-stranded RNA-binding proteins lies within the highly conserved dsRBD core motif. Finally, our results also suggest that TRBP may function in vivo by modifying the tertiary structure of TAR RNA.

Amino Acid Sequence↗

PubMed2003

Screening for mutations in human alpha-globin genes by nonradioactive single-strand conformation polymorphism.

Point mutations and small insertions or deletions in the human alpha-globin genes may produce alpha-chain structural variants and alpha-thalassemia. Mutations can be detected either by direct DNA sequencing or by screening methods, which select the mutated exon for sequencing. Although small (about 1 kb, 3 exons and 2 introns), the alpha-globin genes are duplicate (alpha2 and alpha1) and highly G-C rich, which makes them difficult to denature, reducing sequencing efficiency and causing frequent artifacts. We modified some conditions for PCR and electrophoresis in order to detect mutations in these genes employing nonradioactive single-strand conformation polymorphism (SSCP). Primers previously described by other authors for radioactive SSCP and phast-SSCP plus denaturing gradient gel electrophoresis were here combined and the resultant fragments (6 new besides 6 original per alpha-gene) submitted to silver staining SSCP. Nine structural and one thalassemic mutations were tested, under different conditions including two electrophoretic apparatus (PhastSystem and GenePhor, Amersham Biosciences), different polyacrylamide gel concentrations, run temperatures and denaturing agents, and entire and restriction enzyme cut fragments. One hundred percent of sensitivity was achieved with four of the new fragments formed, using the PhastSystem and 20% gels at 15 degree C, without the need of restriction enzymes. This nonradioactive PCR-SSCP approach showed to be simple, rapid and sensitive, reducing the costs involved in frequent sequencing repetitions and increasing the reliability of the results. It can be especially useful for laboratories which do not have an automated sequencer.

DNA Mutational Analysis↗

PubMed2006

Chromosome polymorphism in Astyanax fasciatus (Teleostei, Characidae). 1. Karyotype analysis, Ag-NORs and mapping of the 18S and 5S ribosomal genes in sympatric karyotypes and their possible hybrid forms.

Astyanax fasciatus may be characterized as a chromosomally diversified 'species' presenting distinct cytotypes, each with its specific variants. The sympatric and syntopic occurrence of different cytotypes reinforces the hypothesis in which A. fasciatus may represent a group of species currently placed under a single common designation. Specimens from three collection points spread along the Mogi-Guaçu River in southeast Brazil were examined in the present work: (1) near its headwaters (Ouro Fino--MG), (2) in the middle region of the river (Cachoeira de Emas, Pirassunun ga--SP) and (3) close to its confluence with the Pardo River (Barrinha--SP). The 2n = 48 chromosomes cytotype was found in all sampling points, while cytotype 2n = 46 was only encountered in Barrinha and Cachoeira de Emas. In the latter locality, cytotype 2n = 46 predominated; nevertheless, other karyotype forms with 2n = 45 and 47 chromosomes also occurred, besides a structural variant of cytotype 2n = 46. One specimen with 2n = 47 chromosomes was also found in Ouro Fino. The Ag-NOR analysis, as well as the location of the 18S and 5S ribosomal genes, were conserved in all cytotypes. The data indicate that the variant karyotypes are a consequence of interbreeding between the standard cytotypes (2n = 46 and 48) and/or its descendants. This suggests a karyotype plasticity for this species, where at least a few variant karyotypes would not have deleterious effects on their bearers.

Animals↗

PubMed1984

Use of JH4 joining segment gene by an anti-arsonate antibody that bears the major A-strain cross-reactive idiotype but displays diminished antigen binding.

One of the antibody families utilized by the A/J mouse in its response to p-azophenylarsonate (Ars) is characterized by the expression of the major anti-arsonate cross-reactive idiotype (CRI) of the A strain. This family has been termed the Ars-A family. A hybridoma antibody (HP 101F11 ) obtained after immunization of an A/J mouse with Ars was identified initially as displaying the CRI, but was subsequently found to bind antigen at a level much lower than most members of the Ars-A family. The results of binding studies suggested that HP 101F11 possesses reduced avidity for antigen. When isolated light and heavy chains were allowed to recombine with the heavy and light chains of a strongly antigen-binding, strongly CRI-positive antibody of the Ars-A family (HP 93G7 ), the low level of antigen binding by HP 101F11 was found to be due to a structurally variant heavy chain. Whereas antibodies of the Ars-A family with normal avidity for antigen had been shown to use the JH2 joining segment gene, amino acid sequence analysis of HP 101F11 revealed that this antibody has a JH segment with a sequence identical to that encoded by a portion of a different JH gene, JH4 . The implication that 101F11 uses the JH4 gene instead of JH2 was supported by the observation that the productively rearranged gene is associated with an Eco R1 restriction fragment 0.95 Kb smaller than the corresponding fragments of Ars-A hybridomas with normal avidity for antigen. The size difference of 0.95 Kb corresponds exactly to the known distance between the JH2 and JH4 genes in BALB/c germline DNA. In addition to the structural differences immediately attributable to the use of JH4 , HP 101F11 has shown an amino acid interchange in the DH segment, and a single amino acid deletion at the DH-JH boundary. These results show that variation among members of the Ars-A family in the DH and/or JH segments provides alternative structural forms of Ars-A antibodies upon which selective processes can operate during the course of an immune response.

Amino Acid Sequence↗

PubMed1995

Precision substrate targeting of protein kinases v-Abl and c-Src.

The active site substrate specificities of v-Abl and c-Src are compared and contrasted. Both enzymes catalyze the phosphorylation of a broad assortment of peptide-bound aliphatic and aromatic alcohols, such as achiral and simple straight chain residues. In addition, both protein kinases exhibit a "dual specificity" with respect to the ability to utilize D- and L-configurational isomers as substrates. However, c-Src and v-Abl are extremely inefficient as catalysts for certain structural arrangements, including secondary alcohols and primary alcohols containing large substituents in close proximity to the hydroxyl moiety. In addition to these similarities, these enzymes also display noteworthy differences in catalytic behavior. Whereas c-Src exhibits a modest preference for aromatic versus aliphatic alcohols, v-Abl does not. Most dramatic is the ability of c-Src to utilize short chain alcohols as substrates, an activity virtually absent from the catalytic repertoire of v-Abl. The implications of these observations are 2-fold. First, because both enzymes are able to accommodate a wide variety of structural variants within their respective active site regions, there exists a substantial degree of flexibility with respect to inhibitor design. Second, because these enzymes exhibit disparate active site specificities, it is possible that other tyrosine-specific protein kinases will display unique substrate specificities as well. Consequently, it may ultimately be possible to exploit these differences to generate inhibitors that precisely target specific protein kinases.

Amino Acid Sequence↗