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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↗
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↗
PubMed1979

Purification and characterization of a single chain precursor C3-protein (pro-C3) from normal human plasma.

Fresh human plasma was treated with proteinase inhibitors and passed through an immunoadsorbent column of Sepharose anti-C3 globulin. The insolubilized C3 was eluted with 5 M guanidine and, after extensive dialysis, was reduced with 0.2 M 2-mercaptoethanol and electrophoresed on SDS-polyacrylamide gels. The bulk of the eluted C3 dissociated into two major protein bands, m.w. 125,000 and 75,000 corresponding to the alpha- and beta-chains of C3. In addition, a nonreducible single polypeptide chain (SPC) with a m.w. value of 197,000 +/- 2,000 similar to the apparent m.w. of unreduced C3 was consistently present. SPC has been purified by elution from SDS (SPC) and found to remain a single polypeptide chain upon re-electrophoresis on SDS gels in the presence of 0.2 M 2-mercaptoethanol. The purified SPC reacted with antisera to denatured C3, C3alpha, and C3beta chains. Additionally, antisera to SPC, also reacted with denatured C3, C3alpha-, and C3beta-chains, revealed a reaction identity between SPC and C3, and detected partial identity between SPC and C3alpha- as well as C3beta-chains. This suggested that SPC and C3 are antigenically related. The amino acid compositions and tryptic peptide maps of SPC and C3 were similar. Based on these findings, it is suggested that SPC must represent a single-chain precursor C3 (pro-C3) in plasma that escaped post-synthetic proteolytic cleavage into a two-subunit chain C3 molecule.

Amino Acids↗
PubMed1975

Comparative studies on monotypic IgMlambda and IgGkappa from an individual patient. I. Evidence for shared VH idiotypic determinants.

A comparative idiotypic antigenic analysis of an IgMlambda and an IgGkappa paraprotein obtained from sera of an individual patient, Br, revealed the presence of very similar idiotypic determinants associated with the VH regions of the Br mu- and gamma-chains. In addition, the IgGkappa protein expressed light (L) chain-associated idiotypic determinants which were not evident on the IgMlambda protein or its isolated L chains. Extensive tests of specificity revealed that the shared VH idiotypic determinants were not present in large weight amounts of heterologous nonspecific IgM and IgG, nor on Ig molecules contained in a large number of normal and myeloma sera.

Animals↗
PubMed1979

Cell-free synthesis and segregation of beta 2-microglobulin.

beta2-Microglobulin has been synthesized in vitro by using a rabbit reticulocyte lysate system and mRNA from the mouse tumor cell line EL4. The molecule is synthesized as a precursor with an NH2-terminal extension of 19 amino acids: Ser-X-Ser-Val-X-Leu-Val-Phe-Leu-Val-Leu-Val-Ser-Leu-X-Gly-Leu-Tyr-X. The processing and segregation of this peripheral membrane protein are directly comparable to those of secretory proteins and integral membrane proteins: addition of dog pancreas microsomal membranes during translation caused conversion to the processed chain, but addition of membranes after synthesis did not; only the processed chain sedimented with the membrane vesicles and was protected from proteolysis by the vesicles; and processing of nascent beta 2-microglobulin was blocked by competitive inhibitors that prevent processing and segregation of secretory and integral membrane proteins. These results suggest that the signal sequences of secretory proteins, integral membrane proteins, and peripheral membrane proteins have a common function and a common receptor on the cytoplasmic face of dog pancreas microsomal membranes. This system also provides a means for studying in vitro the expression and function of the major histocompatibility antigens that are associated with beta 2-microglobulin on cell surfaces.

Amino Acid Sequence↗
PubMed1978

Monoclonal IgM cryoglobulinemia associated with gamma-3 heavy chain disease: immunochemical and biochemical studies.

A patient (Mia) with a monoclonal IgM(kappa) cryoglobulin (cryo IgM) developed additional heavy chain disease proteins of the gamma3 subclass 8 years later. Biochemical studies of the cryo IgM indicated that the heavy chain was VHI, but the NH2-terminal amino acid sequence of the light chain did not permit a definite assignment of its Vkappa subgroup. Two major fragments of the gamma3 chain were distinguishable by electrophoresis in sodium dodecyl sulfate polyacrylamide gel. The smaller component (designated Mia F) had a molecular weight of approximately 30 000 and the larger component (designated Mia S) 35 000. Both fragments had G3m(21) and G3m(27) allotypic determinants. These data and the NH2-terminal amino acid sequence of the gamma chain fragments suggested that Mia S consists of the major part of the gamma3 hinge region plus the CH2 and CH3 domains of the gamma3 chain, whereas Mia F may be derived from the former as a result of postsynthetic cleavage. The partial amino acid sequence of the Mia S fragment is homologous to the hinge region amino acid sequence of human gamma3 chains reported in the literature, with only one amino acid difference out of the 11 residues compared. This difference may represent an allotypic difference within the gamma3 subclass. Alternatively, the production of Mia S may have resulted from the accidental derepression of a "silent" constant region gene not expressed in normal individuals.

Amino Acid Sequence↗
PubMed1975

An investigation into the site of termination of static gamma fibres within muscle spindles of the cat peroneus longus muscle.

1. The distribution of static fusimotor fibres to intrafusal muscle fibres of cat peroneus longus muscle spindles was investigated using the glycogen-depletion technique of Edström & Kugelberg (1968). Single static gamma fibres were stimulation intermittently at high rates for 3 hr with the blood supply occluded for some of this time. Subsequently the portion of muscle containing the activated spindles was fixed, sectioned and stained for glycogen with the periodic acid-Schiff (PAS) method. 2. Ten static axons caused depletion in eleven spindles. In five of these the only glycogen-depleted fibres were nuclear chain fibres. In the other six spindles one nuclear bag fibre was depleted in addition to chain fibres and this was always the larger of the two within the spindle. 3. These results on a medium-sized hind limb muscle are compared with findings concerning the distribution of static gamma fibre axons previously investigated only in very small muscles. The results agree in showing that nearly all static gamma fibres innervate nuclear chain fibres but that in 50-75% of the times in which static gamma fibres innervate spindles the distribution is to bag fibres as well as to chain fibres. The interpretation to be put upon this is uncertain. One possibility with which the results from peroneus longus are consistent is that the bag fibres which are usually innervated by static axons are the 'intermediate' bag fibres whose ultrastructure has recently been shown to resemble that of chain fibres.

Animals↗
PubMed1976

Nuclear magnetic resonance studies of sperm whale myoglobin specifically enriched with 13C in the methionine methyl groups.

The Cepsilon methyl group of the 2 methionine residues in sperm whale myoglobin was enriched with respect to 13C. This was accomplished by treatment of the apomyoglobin at pH 4 at room temperature with a 100-fold proportion of 13CH3I to form an intermediate containing enriched S-methylmethionine. Unselective demethylation to regain the apomyoglobin structure was accomplished by treatment at pH 10.5 with 0.5 M dithioerythritol at 37 degrees for 18 h. Reagents were removed at each stage by dialysis against dilute sodium azide solution. Hemin was reincorporated to form the holoprotein in a way that avoided the presence of an excess of the small molecule. After chromatographic purification the enriched myoglobin was obtained in a yield of between 29 and 60%. The composition, absorbance spectrum, circular dichroism spectrum, isoionic point, electrophoretic behavior, and oxygen-binding behavior following reduction were all indistinguishable from those of the virgin protein. NMR measurements were made at 15.1, 25.2, and 67.9 MHz at 27-30 degrees. The two enriched loci are represented by separate resonances that appear slightly downfield of the spectral position of the corresponding resonance in free methionine. The positions of these resonances are sensitive to pH and to the ligand bound at the heme group which is approximately 17 A distant from each methionine Cepsilon. On the basis of two separate types of experiment the downfield resonance was assigned to methionine 55 and the upfield resonance to methionine 131. Part of the observed variations in chemical shift could be treated as arising from pseudocontact interactions but part was ascribed to structural changes communicated to the environment of each methionine residue as a result of changes in heme ligand, pH, or temperature. The linewidths of the methionine Cepsilon resonances are narrowed by increasing temperature according to an Arrhenius energy of activation of nearly 3 kcal. The spin-lattice relaxation times, T1, of the two methionine Cepsilon resonances at the three spectrometer frequencies were interpreted to indicate the existence of rotational motions in each side chain in addition to that about the Sdelta-Cepsilon bond. The results as a whole show that the two methionine side chains undergo continuous variations in environment, and that these variations are controlled by events at a distance within the protein structure. It is suggested that the structural lability serves the function of facilitating conformational variations and adjustments within the heme pocket.

Amino Acids↗
PubMed1976

Purification and translation of an immunoglobulin lambda chain messenger RNA from mouse myeloma.

Here we describe the 500-fold purification of an mRNA encoding an immunoglobulin lambda light chain derived from the mouse myeloma tumor, RPC-20. Purification involves the isolation of membrane-bound polysomes, oligo(dT)-cellulose chromatography, and sucrose gradient centrifugation under conditions favoring denaturation of polynucleotide complexes. The mRNA purified in this way directs the cell-free synthesis of a polypeptide which is five or six amino acids longer than the mature form of RPC-20 light chain. In addition to directing the synthesis of a precursor-like polypeptide, the mRNA migrates on electrophoresis as a band containing approximately 1150 nucleotides, about 500 more than required to encode the mature form of the light chain.

Cell Line↗
PubMed1979

Middle East lymphoma and alpha-chain disease. An immunohistochemical study.

An immunoperoxidase study of the small intestinal mucosa of three patients with alpha-chain disease showed heavy infiltration of the mucosa by plasma cells containing alpha-heavy chain and J-chain but no light chains. An additional band-like and nodular mucosal infiltrate was also present and consisted of cells showing no evidence of cytoplasmic immunoglobulin synthesis. The cells comprising this infiltrate invaded and destroyed intestinal crypts, and immunoperoxidase staining showed them to be sharply distinct from the alpha-chain-containing plasma cells. In two cases of Middle East lymphoma, immunohistochemistry revealed a normal plasma cell population in the lamina propria of the small intestine. These results show that alpha-chain disease can be diagnosed in routine paraffin sections which should permit clarification of its true incidence in Middle East lymphoma. The demonstration of sharp distinction between the two types of mucosal infiltrate in alpha-chain disease is in contrast to previous immunofluorescence results and enables more ready identification of mucosal changes that may be important in the management of the disease.

Child, Preschool↗
PubMed1979

Heat-induced fragmentation of human alpha 2-macroglobulin.

Previous studies have demonstrated that human plasma alpha 2-macroglobulin (alpha 2 M) possesses a single subunit chain (Mr approximately 185,000) when incubated with dodecyl sulfate and dithiothreitol at 37 degrees C and analyzed by dodecyl sulfate-gel electrophoresis. The present study details the observation that heating alpha 2 M to 90 degrees C under identical conditions produces at least two additional polypeptide chains, termed bands II and III, with apparent molecular weights of 125,00 and 62,000. The generation of these fragments is enhanced by increasing the time of incubation. The appearance of band II composition of the buffer, dodecyl sulfate concentrations, or alpha 2 M protein concentration in the incubation mixture. The electrophoretic bands II and III of alpha 2 M have dissimilar 125I-labeled tryptic peptide digests and also differ in their amino acid composition. The heat-induced fragmentation of alpha 2M is not affected by the inclusion of a variety of low molecular weight protease inhibitors, suggesting that the appearance of bands II and III is not due to enzyme-catalyzed hydrolysis. When the subunit chain of alpha 2M is first cleaved by trypsin into the previously described Mr = 85,000 derivative, neither band II nor III material, nor other lower molecular weight products are generated by heat treatment. Furthermore, preincubation of alpha 2M with methylamine prevents fragmentation of the subunit chain. These results indicate that these fragments are neither pre-existing subunits of alpha 2M nor derivatives formed prior to treatment for gel analysis. These data provide evidence that a covalent bond in the alpha 2M molecule is unusually susceptible to heat-induced cleavage.

Amino Acids↗
PubMed1976

Membrane adenosine triphosphatase of Micrococcus lysodeikticus. ISolation of two forms of the enzyme complex and correlation between ezymatic stability, latency and activity.

Two new forms of the plasma membrane ATP-ase of Micrococcus lysodeikticus NCTC 2665 were isolated from a sub-strain of the microorganism by polyacrylamide gel electrophoresis. One of them had a mol.wt of 368,000 and a very low specific activity (0.80 mumol.min-1.mg protein-1) that could not be stimulated by trypsin. This form has been called B1 (strain B, inactive). If the elctrophoresis was carried out in the presence of reducing agents (i.e., dithiothreitol) and the pH of the effluent maintained at a value of 8.5 another form of the enzyme was obtained. This had a mol.wt of 385,000 and a specific activity of 2.5-5.0 mumol.min-1.mg protein-1 that could be stimulated by trypsin to 5-10 mumol.min-1.mg protein-1. This preparation of the ATPase has been called from BA (strain B, enzyme active). The subunit composition of both forms has been studied by sodium dodecyl sulphate and urea gel electrophoresis and compared to that of the enzyme previously purified from the original strain (form A). The three forms of the enzyme had similar beta and delta subunits, with mol.wt of about 50,000 and 30,000 dalton, respectively. They also had in common the component(s) of relative mobility 1.0, whose status as true subunit(s) of the enzyme remains yet to be established. However, subunit alpha, that had a mol.wt of about a 52,500 in form A (ANDREU et al. Eur. J. Biochem. (1973) 37, 505-515), had a mol.wt similar to beta in form B1 and about 60,000 in form BA. Furthermore BA usually showed two types of this subunit (alpha' and alpha") and an additional peptide chain E) with a mol.wt of about 25,000 dalton. This latter subunit seemed to account for the stimulation by trypsin of form BA. Forms BA could be converted to B1 by storage and freezing and thawing. Conventional protease activity could not be detected in any of the purified ATPase forms and addition of protease inhibitors to form BA failed to prevent its conversion to form B1. The low activity form (B1) was more stable than the active forms of the enzyme and also differeed in its circular dichroism. These results show that M. lysodeikticus ATPase can be isolated in several forms. Although these variations may be artifacts caused by the purification procedures, they provide model systems for understanding the structural and functional relationships of the enzyme and for drawing some speculations about its function in vivo.

Adenosine Triphosphatases↗
PubMed1979

Anaerobic respiration and energy conservation in Paracoccus denitrificans. Functioning of iron-sulfur centers and the uncoupling effect of nitrite.

1. Electron paramagnetic resonance spectra at 8-60 K of NADH-reduced membrane particles prepared from Paracoccus denitrificans grown anaerobically with nitrate as terminal electron acceptor show the presence of iron-sulfur centers 1-4 in the NADH-ubiquinone segment of the respiratory chain. In addition resonance lines at g = 2.058, g = 1.953 and g = 1.88 are detectable in the spectra of succinate-reduced membranes at 15 K, which are attributed to the iron-sulfur-containing nitrate reductase. 2. Sulphate-limited growth under anaerobic conditions does not affect the iron-sulfur pattern of NADH dehydrogenase or nitrate reductase. Furthermore respiratory chain-linked electron transport and its inhibition by rotenone are not influenced. These results contrast those observed for sulphate-limited growth of P. denitrificans under aerobic conditions [Eur. J. Biochem. (1977) 81, 267-275]. 3. Proton translocation studies of whole cells indicate that nitrite increases the proton conductance of the cytoplasmic membrane, resulting in a collapse of the proton gradient across the membrane. Nitrite accumulates under anaerobic growth conditions with nitrate as terminal electron acceptor; the extent of accumulation depends on the specific growth conditions. Thus the low efficiencies of respiratory chain-linked energy conservation observed during nitrate respiration [Arch. Microbiol. (1977) 112, 17-23] can be explained by the uncoupling action of nitrite.

Anaerobiosis↗
PubMed1978

k Chain variable regions from three galactan binding myeloma proteins.

A series of seven BALB/c myeloma proteins has been identified with binding specificity for antigens containing beta(1 leads to 6)-D-galactopyranosyl moieties. We have determined the primary amino acid sequence of the first 108 residues from the light chains of three of these proteins. The framework portions of the variable regions of these three light chains are identical with residue 100 at which position three different amino acids are found in the three chains. An additional interchange was found at position 106 in one of the proteins. Based on recent DNA sequence studies suggesting that the variable region ends at residue 97, these substitutions indicate the possible existance of multiple genes coding for the region beginning at residue 98 and continuing toward the carboxy terminus. A single amino acid interchange was observed in complementarity determining regions occurring in L3. This substitution (Ile-Trp) would require changes in all three codon bases to produce the respective amino acids if one were derived from the other. Two of these chains are thus indistinguishable for their first 100 amino acids and are the first pair of k chains to exhibit complete identity over their variable regions.

Amino Acid Sequence↗
PubMed1979

Sequences of five potential recombination sites encoded close to an immunoglobulin kappa constant region gene.

Immunoglobulin kappa chain gene formation involves site-specific somatic recombination between one of several hundred germ-line variable region genes and a joining site (or "J segment") encoded close to the constant region gene. We have cloned and determined the nucleotide sequence of major portions of the recombination region of the mouse kappa gene and discovered a series of five such J segments spread out along a segment of DNA 2.4 kilobases from the kappa constant region gene. These J segments encode the 13 COOH-terminal amino acids of the variable region, probably including amino acids involved in the antigen combining site and in heavy/light chain contacts. The J segments also display striking sequence homology to one another in both their coding and immediately flanking sequences. Major elements of a short palindrome--CAC(TA)GTG--are preserved adjacent to the recombination sites of both variable and J region genes and constitute inverted repeats at both ends of the sequences to be joined. These palindromes can be written as a hypothetical stem structure that draws variable and J regions together, providing a possible molecular basis for the DNA joining event. Four of the J segments that we have discovered encode amino acid sequences already found in myeloma proteins. By altering the frame of recombination, we can account for additional light chain amino acid sequences, suggesting that the V/J joining event might generate antibody diversity somatically both by using different combinations of variable and J region genes and by using alternative joining frames.

Animals↗
PubMed1979

Differences in the expression of histocompatibility antigens on mouse lymphocytes and tumor cells: immunochemical studies.

Immunochemical studies have shown that labeled, detergent-solubilized extracts of SL2 (H-2d) lymphoma cells contain components reactive with several anti-H-2 alloantisera of restricted specificity. Anti-H-2k and anti-H-2ja as well as anti-H-2d sera precipitated labeled polypeptides of a molecular weight similar to that of H-2 heavy chains. In addition, all antisera tested precipitated a component of 70000 daltons molecular weight, which is antigenically related to gp 69/71 of Friend murine leukemia virus. Reactions with antisera directed against haplotypes other than H-2d could be blocked by addition of unlabeled, detergent-solubilized extracts of H-2d lymphocytes, or by H-2 antigens against which the antiserum was directed. Sequential immunoprecipitations initially using antisera against the K, D, or L region gene products to remove individual known H-2d antigens have made possible the identification of some molecules responsible for these reactions. The results show that antisera against haplotypes other than H-2d which react with SL2 cells, cross-react with normal H-2d antigens. Quantitative absortion of these antisera with intact or solubilized cells has shown that lymphocytes and tumor cells differ in their expression of some H-2 determinants. The antibodies bind only weakly to intact H-2d lymphocytes, but strongly to the corresponding detergent-solubilized antigens. These results do not, therefore, support the derepression hypothesis put forward earlier.

Animals↗
PubMed1978

Poly(adenosine dephosphate ribose) metabolism and regulation of myocardial cell growth by oxygen.

Control of the rate of cardiac cell division by oxygen occurs most probably by altering the redox state of a control substance, e.g. NAD(+)right harpoon over left harpoonNADH. NAD(+) (and not NADH) forms poly(ADP-ribose), an inhibitor of DNA synthesis, in a reaction catalysed by poly(ADP-ribose) polymerase. Lower partial pressure of oxygen, which increases the rate of division, would shift NAD(+)-->NADH, decrease poly(ADP-ribose) synthesis, and increase DNA synthesis. Chick-embryo heart cells grown in culture in 20% O(2) (in which they divide more slowly than in 5% O(2)) did exhibit greater poly(ADP-ribose) polymerase activity (+83%, P<0.001) than when grown in 5% O(2). Reaction product was identified as poly(ADP-ribose) by its insensitivity to deoxyribonuclease, ribonuclease, NAD glycohydrolase, Pronase, trypsin and micrococcal nuclease, and by its complete digestion with snake-venom phosphodiesterase to phosphoribosyl-AMP and AMP. Isolation of these digestion products by Dowex 1 (formate form) column chromatography and paper chromatography allowed calculation of average poly(ADP-ribose) chain length, which was 15-26% greater in 20% than in 5% O(2). Thus in 20% O(2) the increase in poly(ADP-ribose) formation results from chain elongation. Formation of new chains also occurs, probably to an even greater degree than chain elongation. Additionally, poly(ADP-ribose) polymerase has very different K(m) and V(max.) values and pH optima in 20% and 5% O(2). These data suggest that poly(ADP-ribose) metabolism participates in the regulation of heart-cell division by O(2), probably by several different mechanisms.

Animals↗
PubMed1978

Interaction of cortisol-21-palmitate with liposomes examined by differential scanning calorimetry.

Liposomes have been suggested as carriers for corticosteroids in the local treatment of arthritis by intra-articular injection. The long chain 21-esters of cortisol such as the palmitate or octanoate are taken up and retained by liposomes in higher concentration than cortisol itself. Differential scanning calorimetry has been used to show that the cortisol ester is anchored in the liposome phospholipid bilayer by the acyl side chain. In addition, the limiting concentration of cortisol-21-palmitate which can be incorporated into dipalmitolyl phosphatidylcholine liposomes has been measured by observing changes in the DSC spectrum at different steroid concentrations. Steroid in excess of this concentration limit forms a separate phase which can be identified by nuclear magnetic resonance. For optimum effect, the treatment of arthritis with liposomes must be carried out with liposomes containing steroid below the limiting concentration.

Arthritis, Rheumatoid↗