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At least 19 recordsLinked to original sources
PubMed2026

Polyploidy Arithmetic.

Polyploidy occurs in plants and animals, and is an important force in speciation and genome evolution. The main focus of this paper is the following fundamental question that was recently posed by Huber and Maher: Given the ploidy numbers of a collection of extant species, or their ploidy profile, what is the smallest number of hybridizations needed in any evolutionary history for these species to completely represent these numbers? In this paper, we shall show that this question can be rephrased in terms of addition chains and the closely related addition sequences, which have been studied for over a century in mathematics and computer science. These are sequences of natural numbers that start with 1, so that each number in the sequence larger than 1 is the sum of two other numbers arising earlier in the sequence. In our first main result, we show that finding the smallest number of hybridization events to explain a ploidy profile, or the hybrid number, is equivalent to solving the so-called addition sequence problem. This immediately implies that computing the hybridization number is computationally intractable. Even so, it also leads to new connections to representing polyploid evolution using networks. More specifically, in our second main result we show that ploidy profiles representable by tree-child networks are exactly the addition chains, implying a polynomial-time algorithm for identifying these profiles. We then consider beaded tree-child networks, which permit the representation of autopolyploidy events, and in our third main result we provide a greedy polynomial-time algorithm to decide whether a given profile can be realized by such a network. We expect that our results can be leveraged in future work through, for example, making use of known algorithms for computing short addition sequences to give bounds for the hybrid number, and in guiding network reconstruction for polyploid species.

Polyploidy↗
PubMed1992

An additional carbohydrate chain in the variant thyroxine-binding globulin-Gary (TBGAsn-96) impairs its secretion.

The T4-binding globulin-Gary (TBG-G) variant has severely impaired T4 binding, is unstable at 37 C, and presents an apparent anodal shift of all isoforms when submitted to isoelectric focusing. Inheritance of this abnormal TBG produces a profound decrease in the serum levels of native TBG with reciprocal changes in its denatured form, causing thyroid hormone concentrations to be as low as those found in complete TBG deficiency. The TBG-G gene possesses a single nucleotide substitution replacing the normal IIe96 (ATC) with Asn (AAC), thus creating a new site for N-linked glycosylation. In order to determine whether TBG-G contains an additional carbohydrate chain as indirectly suggested by the isoelectric focusing results, cDNAs containing the normal TBG (TBG-N), and TBG-G were inserted in the appropriate vectors to allow their expression in mammalian cells (COS-1) and in amphibian (Xenopus) oocytes. In both systems, expression of TBG-G yielded a larger molecule than TBG-N when analyzed by polyacrylamide gel electrophoresis under denaturing conditions. However, both were identical in size when synthesized in COS-1 cells in the presence of tunicamycin or when deglycosylated after their synthesis in Xenopus oocytes. Pulse chase experiments revealed impaired secretion and excessive overall intracellular degradation of TBG-G relative to TBG-N. As expected from studies on serum from affected subjects, in vitro expressed TBG-G had a 10-fold lower affinity for T4. These studies prove that the new site for potential glycosylation created by the point mutation in TBG-G is indeed glycosylated.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1977

Multiple hemoglobin alpha-chains in the sika deer (Cervus nippon).

Investigation of the hemoglobin alpha-chains of an Asiatic deer, the sika (Cervus nippon), was prompted by the heterogenity of alpha-chain gene loci in the Virginia white-tailed deer (Odocoileus virginianus). Although electrophoresis of hemoglobin chains from 10 sika revealed only a single alpha-chain band, peptide mapping demonstrated variations in the alpha-TPIII and alpha-TPIV peptides. Substitutions at positions 15, 20, and 22 produced a minimum of five alpha-chains; two possible additional chains could noy be proven because of inseparability of the whole alpha-chains. The most common chain contains Asp-15, Lys-20 and Pro-22 but in other chains glycine is present at position 15, Asx at position 20, and either serine or Asx at position 22. The probable explanation for the large number of alpha-chains is gene duplication which may have been produced by breedings between subspecies from different geographical areas. Comparison with the alpha-chain structure of the white-tailed deer suggests that the sika may have evolved from the lineage which produced the white tailed-deer after the alpha-chain genes of the latter species had duplicated. In addition, these data provide further examples of the unusual variability of this portion of the alpha-chain.

Amino Acid Sequence↗
PubMed1992

Molecular cloning, expression and characterization of the ovine IL-2R alpha chain.

Interleukin-2 (IL-2) stimulates the proliferation of activated antigen-specific T cells through its interaction with high affinity receptors. This event is largely regulated by the inducible expression of the alpha-chain (CD25) which, in combination with the beta-chain and possibly additional chains, forms the high affinity IL-2 receptor (IL-2R) complex. From a concanavalin A (Con A)-activated ovine T-cell complementary DNA (cDNA) library we have isolated two cDNA clones which together constitute a 2650 base pair (bp) messenger RNA (mRNA) species encoding the ovine IL-2R alpha chain. The nucleotide sequence has high homology with analogous cDNA from other species and predicts a mature protein of 254 amino acids. In addition to the predominate 2.6 kilobase (kb) ovine IL-2R alpha chain mRNA species. Northern blot analysis of activated T-cell RNA revealed two larger mRNA species. The ovine IL-2R alpha chain cDNA was transfected into CHO cells and low affinity binding of human recombinant IL-2 demonstrated. Polyclonal antisera generated against the transfected cells cross-reacted with Con A-activated ovine lymphocytes. In addition these antisera were used to immunoprecipitate a unique 50,000 MW protein from the transfected cells. It is likely that this protein represents the expressed ovine IL-2R alpha chain cDNA which is heavily glycosylated as distinct from the 30,869 MW primary translation product. Southern blot analysis of ovine genomic DNA suggests that the ovine IL-2R alpha chain is encoded by a single copy gene.

Animals↗
PubMed1992

Molecular analyses of a human sex hormone-binding globulin variant: evidence for an additional carbohydrate chain.

Genomic DNA was isolated from an individual who is homozygous for a sex hormone-binding globulin (SHBG) variant that resolves into three molecular weight forms of 56K, 52K, and 48K during electrophoresis under denaturing conditions (sodium dodecyl sulfate-polyacrylamide gel electrophoresis). This material was amplified using intron-specific oligonucleotide primers in a polymerase chain reaction to obtain the eight exons encoding SHBG. Sequence analysis of these exons revealed a point mutation encoding an amino acid substitution (Asp --> Asn) at residue 327 in the SHBG polypeptide, and the same mutation was identified in three siblings who also appear to be homozygous for this trait. This mutation introduces an additional consensus site for N-glycosylation at this position, and to confirm its utilization we introduced it into a human SHBG complementary DNA. The mutated complementary DNA was inserted into the pRc/CMV expression vector, and transfected into Chinese hamster ovary (CHO) cells. The product was secreted normally but proportionally less of it (54%) bound to concanavalin A when compared to normal SHBG produced by CHO cells (85%), or SHBG in the serum of either a normal individual or those who produce an electrophoretic variant (98%). Furthermore, when subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting, the SHBG variant produced by CHO cells consisted of a 60K subunit as well as the heavy (52K) and light (48K) subunits associated with normal SHBG produced by CHO cells or in serum. This additional subunit is larger than the variant in serum and probably reflects a greater degree of complexity in the carbohydrate structures added to recombinant SHBG during synthesis in CHO cells. Nevertheless, its steroid-binding affinity was equal to normal SHBG produced by CHO cells or SHBG in serum.

Amino Acid Sequence↗
PubMed1992

Carboxy-terminal-extended variant of the human fibrinogen alpha subunit: a novel exon conferring marked homology to beta and gamma subunits.

Similarities between the N-terminal regions of the three subunits of the clotting protein fibrinogen--(alpha beta gamma)2--suggest that they evolved from a common progenitor. However, to date no human alpha chain has been found with the strong C-terminal homology shared by the beta and gamma chains. Here we examine the natural product of a novel fibrinogen alpha chain transcript bearing a separate open reading frame that supplies the missing C-terminal homology to the other chains. Additional splicing leads to the use of this extra sequence as a sixth exon elongating the alpha chain by 35%. Since the extended alpha chain (alpha E) is assembled into fibrinogen molecules and its synthesis is enhanced by interleukin-6, it suggests participation in both the acute phase response and normal physiology.

Amino Acid Sequence↗
PubMed1978

Primary and secondary tryptic cleavages of human IgM at high temperature.

Previously it was shown that the tryptic digestion of human IgM at 65 C yield Fc'mu fragments in addition to Fabmu and (Fc)5mu fragments. This Fc'mu was found to be derived from the Cmu4 domain of the mu-chain. Additional studies were done on the effects of tryptic digestion time and temperature on the proteolytic process of IgM, IgM digestion by 2% trypsin at 65 C produced (Fc)8mu and Fc'mu in approximately a 3:2 ratio. While an appreciable amount of intact (Fc)5mu was present along with Fc'mu in the IgM digest, no residual "(Fc)5mu fragment" with its C-terminal segment missing was found. If the temperature of digestion is held constant at either 56 C or 60 C and the digestion time is varied from 20 to 90 min, there is also progressive cleavage of IgM with a concomitant increase in the yield of Fc'mu. It appears that the tryptic digestion of IgM is a stepwise process and that the primary cleavage of IgM occurs at Arg-325(2) of all ten mu-chains and the (Fc)5mu is subsequently degraded to Fc'mu fragments by secondary cleavage.

Alkylation↗
PubMed1975

Ribosome inactivation by the toxic lectins abrin and ricin. Kinetics of the enzymic activity of the toxin A-chains.

A sensitive test system for toxin-treated ribosomes was worked out by treating rabbit reticulocyte ribosomes with abrin A-chain, ricin A-chain or ricinus agglutinin A-chain, adding neutralizing amounts of specific antitoxins and testing for polyphenylalanine-synthesizing activity in a system where the concentration of elongation factors and ribosomes were varied. The strongest inhibition was obtained in the presence of low concentrations of elongation factor (EF-2). The activity of the ribosomes decreased with time of incubation with the toxin A-chains. Addition of anti-toxins stopped further inactivation. In systems containing untreated and toxin-treated ribosomes the ability to polymerize phenylalanine was proportional to the concentration of untreated ribosomes. There was a linear relationship between toxin A-chain concentration and the number of ribosomes inactivated per minute. The inactivation rate increased with temperature, and the estimated activation energy was 10.6 kcal (44.3 kJ). Linewaver-Burk plots of the data obtained by incubating various ribosome concentrations with toxins indicated a molecular activity of about 1500 ribosomes/minute for abrin and ricin A-chains and 100 ribosomes/minute for ricinus agglutinin A-chain. The apparent Michaelis constant was 0.1-0.2 muM for all three A-chains. The activity of the A-chains in the intact cell is discussed.

Abrin↗
PubMed1978

Studies on IgM polymerization: reassociation to non-covalently and covalently linked Fc5mu fragments.

Fc5mu fragments were purified from a trypsin digest of native IgM by gel filtration and isoelectric focusing. Polyacrylamide gel electrophoresis of Fc5mu fragments in sodium dodecyl sulphate disclosed a major and a minor band with molecules of 320,000 and 285,000 daltons, respectively. The mu chain fragments showed a molecular weight of 34,500. After reduction of the Fc5mu fragments to free mu chain fragments and J chain removal of the reducing agent by dialysis for 24 h under nitrogen in the presence of Zn ions gave non-covalently linked Fc5mu fragments. This shows that the non-covalent interactions operating between the mu chains of non-covalently linked native IgM are present in the C-terminal part of the mu chains. Additional dialysis in the presence of Zn and Cu ions resulted in the formation of covalently linked Fc5mu fragments.

Alkylation↗
PubMed1992

Expression and modulation of the vitronectin receptor on human dermal microvascular endothelial cells.

Microvascular endothelial cells express a variety of cell-surface integrins in vivo and in vitro with varying affinities for matrix proteins. The vitronectin receptor (VnR), a complex of the alpha v and beta 3 integrin chains, is capable of binding to a variety of matrix proteins that are deposited in injured tissues, including vitronectin, fibrinogen, and thrombin. Staining of frozen sections of human skin with antibodies recognizing the VnR and examination by immunofluorescence microscopy demonstrates staining in a vascular pattern suggesting in vivo expression of the vitronectin receptor on endothelial cells. Examination of pure cultures of human dermal microvascular endothelial cells (HDMEC) by flow-cytometric analysis and enzyme-linked immunosorbent assay confirmed that HDMEC also express cell surface VnR complex in vitro. Stimulation of human dermal microvascular endothelial cells in vitro with agents that stimulate protein kinase C resulted in dose- and time-dependent increases in expression of alpha v and beta 3 integrin chains. Additionally, stimulation with basic fibroblast growth factor induced similar increases, but stimulation with transforming growth factor-beta or interleukin-1 alpha failed to increase VnR expression. Increases in cell-surface VnR expression also correlated with an increased ability of microvascular endothelial cells to bind to vitronectin, but not fibronectin-coated surfaces. Although increases in cell-surface expression of beta 3 paralleled increases in expression of cell-surface alpha v, regulation of mRNA expression was distinct for each chain. These data suggests that microvascular endothelial cells express the VnR complex in vivo, that the cell-surface expression of this integrin on dermal microvascular endothelial cells can be regulated, and that this regulation may be important in cell adherence, cell migration, and wound healing.

Blotting, Northern↗
PubMed1992

Cutaneous T-cell lymphoma: utility of antibodies to the variable regions of the human T-cell antigen receptor.

BACKGROUND: The clonotypic 90 kd Ti heterodimer of the human T-cell antigen receptor is composed of two distinct chains (alpha beta or rarely tau delta) that result from the recombination of variable (V), constant, joining, and, in the case of beta chains, additional diversity regions. OBJECTIVE: The variable region expression of human cutaneous T-cell lymphoma (CTCL) was studied. METHODS: Biopsy specimens from 13 patients with CTCL (7 plaque, 3 tumor stage, 3 Sézary syndrome) were examined immunohistochemically by a panel of seven commercially available monoclonal V-region antibodies. RESULTS: Two patients had significant anti-V-region staining. One patient with Sézary syndrome had two lesions, subjected to biopsy 4 months apart, that reacted with beta V5(a), a specificity previously documented by flow cytometry of leukemic cells. A patient with plaque-stage CTCL, negative for T-cell gene rearrangement by Southern blot, demonstrated reactivity with beta V5(c) largely limited to epidermotropic lymphocytes. CONCLUSION: Panels of V-region antibodies should be useful reagents for diagnosis and follow-up of CTCL.

Adult↗
PubMed1979

Yeast tRNA Leu UAG. Purification, properties and determination of the nucleotide sequence by radioactive derivative methods.

A second major species of leucine tRNA, tRNA Leu UAG (formerly designated tRNA Leu CUA) was purified from baker's yeast in a three-step procedure entailing BD-cellulose chromatography in the presence and absence of Mg2+ and Sephadex G-100 gel filtration. Results of aminoacylation and partial RNase T1 digestion experiments showed that this tRNA retains a native conformation under conditions that denature yeast tRNA Leu m5CAA (tRNA3 Leu). The primary structure of baker's yeast tRNA Leu UAG was elucidated by application of sensitive radioactive isotope derivative ("postlabeling") methods. Complete RNase T1 and A and partial RNase U2 fragments, prepared from non-radioactive tRNA and 5'-half and 3'-half molecules, were separated by two-dimensional polyethyleneimine-cellulose anion-exchange thin-layer chromatography and isolated by a novel micropreparative procedure affording high yields of these compounds in sufficient purity for subsequent tritium derivative analysis. Base composition and sequence of oligonucleotides were analyzed by tritium derivative methods. Molar ratios of the fragments were determined from the radioactivity of 3H-labeled nucleoside trialcohols in combination with base analysis. 2'-O-Methylated guanosine was characterized using the [gamma-32P]ATP/polynucleotide kinase reaction. The analysis of classical complete and partial RNase digests by the tritium derivative methods yielded the complete nucleotide sequence of the tRNA. A total of about 20 A260 units of the RNA was used for analysis, i.e. considerably less material than required for conventional spectrophotometric analysis. A different sequencing approach, consisting of a combination of "readout sequencing" with tritium sequencing of complete RNase T1 and A fragments, was applied to the 3'-half molecule. The 3'-half molecule was labeled with 32P at its 5' terminus, partially degraded with RNase T1, U2, and Phy1 and with alkali, and subjected to polyacrylamide gel electrophoresis. The sequence was read off the gel on the basis of cleavage patterns and size of the fragments. While the readout procedure provided only the positions of A, U, C, and G residues in the chain, additional information from tritium derivative analysis was utilized to define the positions of the modified nucleosides. The readout sequencing procedure was found to require less than 0.01 A260 unit of RNA and the analysis of the complete fragments about 6 A260 units. Interesting structural features of tRNA Leu UAG are (a) the location of unique, leucine tRNA iso-acceptor-specific sequences next to U-8, a constant nucleotide participating in synthetase recognition, (b) the occurrence of 1-methyladenosine in the T loop, a modification not present in the structurally related tRNA Leu m5CAA, and (c) the unusual presence of an unmodified uridine in the first position of the anticodon, which may be related to the unusual coding properties reported for this tRNA.

Adenine↗
PubMed1977

Specific and non-specific interactions of two carcinogenic mycotoxins, luteoskyrin and rugulosin with nucleic acids.

(-) Luteoskyrin and (+) Rugulosin are 2 hepatotoxic and carcinogenic anthraquinone-like pigments from Penicillia which contaminate rice and other foodstuffs. They inhibit in vivo and in vitro replication, transcription and DNA repair of Protocaryots and Eucaryots presumably by forming chelate-complexes with nucleic acids. In the present work, characterization, specificity and structure of binary polychelates (pigment-metal)n and ternary complexes (pigment-metal-nucleic acids) are successively reported: whereas, unspecific complex II with double-stranded polynucleotides is shown to result from simple adsorption of polychelate onto the double helix, complex I is specific for single-stranded DNA (or polypurine nucleotides) and results from electrostatic association of separate pigment-metal units with the polyphosphate chain. Additional stabilization is obtained by hydrophobic interaction between stacked aromatic moieties of pigment and purine units. A model of interaction is proposed for both complexes I and II.

Carcinogens↗
PubMed1992

Polymerase chain reaction with additional primers allows identification of amplified DNA and recognition of specific alleles.

The use of additional primers in the standard two primer polymerase chain reaction (PCR) is described. This modification allows detection of a target gene in a single reaction, and identification of the amplification product obtained or recognition of a specific allele. The oligonucleotides used are internal to the original amplification primers and amplification-compatible with one of the original primers. Annealing of an additional primer to the target gene as well as to the primary amplification product will lead to the appearance of an additional smaller amplification fragment upon agarose gel electrophoresis of PCR products. Use of one or more allele-specific oligonucleotides as additional primers, in addition to two gene-specific primers, will allow recognition of different alleles of the target gene in a single PCR without further analysis except gel electrophoresis. The general applicability of the method was determined with several PCR assays for the detection of pathogenic bacteria.

Alleles↗
PubMed1992

Effects of temperature variation and phenethyl alcohol addition on acyl chain order and lipid organization in Escherichia coli derived membrane systems. A 2H- and 31P-NMR study.

Using 2H- and 31P-NMR techniques the effects of temperature variation and phenethyl alcohol addition were investigated on lipid acyl chain order and on the macroscopic lipid organization of membrane systems derived from cells of the Escherichia coli fatty acid auxotrophic strain K1059, which was grown in the presence of [11,11-2H2]oleic acid. Membranes of intact cells showed a gel to liquid-crystalline phase transition in the range of 4-20 degrees C, which was similar to that observed for the total lipid extract and for the dominant lipid species phosphatidylethanolamine (PE). Phosphatidylglycerol (PG) remained in a fluid bilayer throughout the whole temperature range (4-70 degrees C). At 30 degrees C acyl chain order was highest in PE, followed by the total lipid extract, PG, intact cells, and isolated inner membrane vesicles. Acyl chain order in E. coli PE and PG was much higher than in the corresponding dioleoylphospholipids. E. coli PE was found to maintain a bilayer organization up to about 60 degrees C, whereas in the total lipid extract as well as in intact E. coli cells bilayer destabilization occurred already at about 42 degrees C. It is proposed that the regulation of temperature at which the bilayer-to-non-bilayer transition occurs may be important for membrane functioning in E. coli. Addition of phenethyl alcohol did not affect the macroscopic lipid organization in E. coli cells or in the total lipid extract, but caused a large reduction in chain order of about 70% at 1 mol% of the alcohol in both membrane systems. It is concluded that while both increasing temperature and addition of phenethyl alcohol can affect membrane integrity, in the former case this is due to the induction of non-bilayer lipid structures, whereas in the latter case this is caused by an increase in membrane fluidity.

Escherichia coli↗
PubMed1976

Intracytoplasmic and surface-bound immunoglobulins in "nonsecretory" and Bence-Jones myeloma.

Immunoglobulins were studied at the cellular level by direct immunofluorescence in twenty-five patients with 'nonsecretory' myeloma and thirty-six patiens with Bence-Jones (BJ) myeloma. The results were compared with those obtained in a control group of thirty-six patients with common secretory myeloma. A monoclonal Ig (IgG in eighteen, IgA in three and kappa chains only in three cases) was found in the cytoplasm of the plasma cells from all the patients with 'nonsecretory' myeloma, with a striking dysbalance in the staining brightness for the heavy and the light chains. A similar dysbalance in staining was also observed for plasma cell surface Ig chains but in the opposite way. In twenty patients with BJ myeloma studied for cytoplasmic Ig only, determinants of a heavy chain were clearly found in four cases. When surface Ig were studied also, the production of gamma chains in addition to the light chain could be ascertained in six of sixteen cases. In addition, IgM with the same light chain type as the BJ protein was detected at the cell surface on plasma cells and lymphocytes in two of these sixteen patients. 'Monoclonal' populations of B lymphocytes bearing the same Ig chains as those produced by the myeloma cells were detectable in five of eleven 'nonsecretory' myeloma and in five of sixteen BJ myeloma patients. Normal blood B lymphocytes were in decreased number, particularly when a 'monoclonal' lymphocytic population was detected. Data are discussed which suggest that plasma cells from most patients with 'nonsecretory' myeloma might synthesize and secrete Ig molecules with structurally abnormal chains that are then quickly degraded.

Bence Jones Protein↗
PubMed1978

Collagen polymorphism in mature rabbit cornea.

Sequential extraction of mature rabbit corneal stroma with NaCl-Tris buffer and acetic acid solubilized only 12% of the total corneal collagen. Pepsin (E:S 1:10,4 degrees C, 48 hr) in 0.4 M acetic acid solubilized 91% to 95% of the total collagen in the residue. Approximately 68% of the solubilized material could be precipitated at 2.5M NaCl and a further 3% to 9% at 3.5M NaCl. The collagenous material precipitating at 2.5M NaCl contained alpha, beta, gamma, and some higher molecular weight components and had a CNBr profile similar to bovine type I skin collagen. It had an hydroxylysine/lysine (OHLys/Lys) ratio of 0.43, similar to that of skin collagen, but unlike skin collagen was 52% glycosyled. Although the 3.5M NaCl precipitate had a CNBr peptide profile similar to that of type I collagen, it contained two additional collagen chains of molecular weight approximately 140,000 and 100,000 daltons, had an OHLys/Lys ratio of 0.62, and was 66% glycosylated. Individual chains were separated from the collagen precipitates by gel electrophoresis,and the additional collagen chains were shown to be carbohydrate rich. These additional collagen chains may be derived from one or more molecular species which are physiologically important in the maintenance of the unique organization of corneal collagen.

Amino Acids↗