bluuebunny/crossref_metadata_2025 huggingface dataset:
Alteration of substrate specificity for the endoribonucleolytic cleavage of RNA by the Tetrahymena ribozyme.
Authors: Murphy F L , Cech T R
Published: May 2006

A shortened form of the intervening sequence of the self-splicing RNA from Tetrahymena thermophila catalyzes sequence-specific cleavage of RNA. Cleavage site selection involves a base-pairing interaction between the substrate RNA and a binding site within the intervening sequence. Single-base changes in this binding site were previously shown to alter substrate specificity in a predictable manner. To examine the generality with which substrate specificity can be altered, six variant catalytic RNAs (ribozymes) have been produced with two- or three-base changes in the active site. Each ribozyme cleaves its predicted substrate. The conditions required for good reactivity and for discrimination against cleavage at mismatched sites vary and were independently determined for each ribozyme.
Modeling antibody hypervariable loops: a combined algorithm.
Authors: Martin A C , Cheetham J C , Rees A R
Published: May 2006

To be of any value, a predicted model of an antibody combining site should have an accuracy approaching that of antibody structures determined by x-ray crystallography (1.6-2.7 A). A number of modeling protocols have been proposed, which fall into two main categories--those that adopt a knowledge-based approach and those that attempt to construct the hypervariable loop regions of the antibody ab initio. Here we present a combined algorithm requiring no arbitrary decisions on the part of the user, which has been successfully applied to the modeling of the individual loops in two systems: the anti-lysozyme antibody HyHel-5, the crystal structure of which is as a complex with lysozyme [Sheriff, S., Silverton, E. W., Padlan, E. A., Cohen, G. H., Smith-Gill, S. J., Finzel, B. C. & Davies, D. R. (1987) Proc. Natl. Acad. Sci. USA 84, 8075-8079], and the free antigen binding fragment (Fab) of the anti-lysozyme peptide antibody, Gloop2. This protocol may be used with a high degree of confidence to model single-loop replacements, insertions, deletions, and side-chain replacements. In addition, it may be used in conjunction with other modeling protocols as a method by which to model particular loops whose conformations are predicted poorly by these methods.
Interaction of a nuclear location signal with isolated nuclear envelopes and identification of signal-binding proteins by photoaffinity labeling.
Authors: Benditt J O , Meyer C , Fasold H , Barnard F C , Riedel N
Published: May 2006

The nuclear envelope (NE) separates the two major compartments of eukaryotic cells, the nucleus and the cytoplasm. Recent studies suggest that the uptake of nuclear proteins into the nucleus is initiated by binding of nuclear location signals (NLSs) contained within these proteins to receptors in the NE, followed by translocation through the nuclear pore complex. To examine the binding step without interference from intranuclear events, we have used a system consisting of (i) purified rat liver NEs fixed onto glass slides and (ii) the prototype simian virus 40 large T antigen (SV40 T) NLS conjugated to nonnuclear carrier proteins, and we have visualized the receptor-ligand interaction by indirect immunofluorescence. In this system, incubation of isolated NEs with the wild-type SV40 T NLS conjugate with carrier proteins resulted in binding that was signal sequence-dependent, could be competitively blocked with excess conjugated and unconjugated wild-type peptide, did not require ATP, and was not affected by the transport-inhibiting lectin wheat germ agglutinin. In contrast, only minimal binding was observed with a mutant SV40 T NLS conjugate. These results are consistent with those obtained in other, more complex in vitro systems and suggest that binding of the SV40 T NLS is receptor-mediated. Binding is largely abolished by extraction of the NE with the nonionic detergent Triton X-100, suggesting that the receptor is soluble in detergent. We find in the Triton X-100 supernatant four major NLS-binding proteins with apparent molecular masses of 76, 67, 59, and 58 kDa by photoaffinity labeling with a highly specific crosslinker, azido-NLS. The reduced complexity of the system described here should be useful for the functional study of other potential NLSs for the identification and isolation of their binding sites and for the screening of antibodies raised against these binding sites.
Targeted gene mutations in Drosophila.
Authors: Ballinger D G , Benzer S
Published: May 2006

A cloned gene can be of interest because of its expression in a particular tissue or at a certain developmental stage, or because of homology to an interesting gene from another organism. In Drosophila its location in the genome is readily determined by in situ hybridization to the banded larval salivary gland polytene chromosomes, but it is more difficult to isolate mutations that may reveal its function. This paper describes a general method for detecting transposable element insertions into the gene in question. This "reverse genetics" then offers the possibility of observing a consequent mutant phenotype, providing a key to the normal function of the gene. The sensitivity of the polymerase chain reaction makes it possible to detect the occurrence of a single appropriate P-element transposon insertion among a population of mutagenized flies. This is accomplished by the use of oligonucleotide primers--one a sequence from within the cloned gene and the other homologous to the terminal sequence of the P-element DNA--to prime synthesis into the DNA flanking an insertion site. A segment of DNA, bounded by the two primers, will be a target for amplification only in a fly in which a P-element has inserted within about 2 kilobases of the gene primer. This technique has been used to detect P-element insertions near a gene expressed in the Drosophila compound eye. Potential problems with the technique and possible refinements in the screen are discussed. In principle, it could be utilized to detect insertion of a foreign element into any gene for which at least a partial sequence is known and could be extended to other organisms.
Lithium chloride potentiates tumor necrosis factor-mediated cytotoxicity in vitro and in vivo.
Authors: Beyaert R , Vanhaesebroeck B , Suffys P , Van Roy F , Fiers W
Published: May 2006

Tumor necrosis factor (TNF) is cytotoxic for several transformed cell lines in vitro. In the presence of LiCl, the murine fibrosarcoma cell lines L929 and WEHI 164 clone 13 became greater than 10 times more sensitive to TNF-mediated cytotoxicity. The human tumor cell lines BT20 and HeLa D98/AH2 were also responsive to the cytotoxicity-enhancing effect of LiCl. Other monovalent or divalent cations did not affect TNF-mediated cytotoxicity. The potentiating effect of LiCl on TNF cytotoxicity was largely independent of transcription, and LiCl could be added to the cells as early as 2 hr before or as late as 4 hr after TNF without loss of effectiveness. The mechanism by which LiCl increases the cytotoxic response seems to differ from the sensitizing effect of actinomycin D or interferon gamma, since the latter treatments overcame TNF resistance of several cell lines, whereas LiCl did not. Evidence is presented that LiCl acts, either directly or indirectly, via the TNF-activated phospholipase A2 pathway. In nude mice, a combination of TNF and LiCl led to hemorrhagic necrosis and growth inhibition of L929 tumors, whereas little effect was observed when TNF was administered alone. HeLa D98/AH2 tumors also were sensitive to the potentiating effect of LiCl in vivo. We conclude that LiCl enhances the effectiveness of TNF in vitro and in vivo, results that may have therapeutic implications.
Circumscribed changes of the cerebral cortex in neuropsychiatric disorders of later life.
Authors: Bowen D M , Najlerahim A , Procter A W , Francis P T , Murphy E
Published: May 2006

The extent and distribution of biochemical abnormalities thought to reflect disorders of subpopulations of neurons have been determined in the cerebral cortex from brains of patients with Alzheimer-type dementia and depressive illness who died of natural causes. In dementia, loss of gray matter from areas of the parietal and temporal lobes is most obvious. In depression, these areas are not affected, but the pars opercularis and temporal pole are smaller than in controls. Results expressed per unit mass of total protein indicate selective reductions in both disorders of serotonin 2 recognition sites in all areas examined and of somatostatin content in only the temporal pole of the six areas examined. In dementia alone a selective loss was found of somatostatin content of the superior parietal lobule and of serotonin 1A sites and choline acetyltransferase activity in all areas examined. Results for depression expressed per entire area indicate additionally reduced somatostatin content and serotonin 1A sites in the pars opercularis and serotonin 1A sites in the temporal pole. These multiple analyses performed on each sample provide further support for a prominent disorder of pyramidal neurons in dementia as well as more evidence for alterations in cortical neurons in depression, either as a result of the disease itself or its treatment.
Epstein-Barr virus nuclear protein 2 is a key determinant of lymphocyte transformation.
Authors: Cohen J I , Wang F , Mannick J , Kieff E
Published: May 2006

Epstein-Barr virus (EBV) efficiently transforms B lymphocytes to perpetual proliferation. The EBV laboratory strain P3HR-1 is transformation-incompetent and lacks a DNA segment that includes the EBV nuclear antigen 2 (EBNA-2) gene and a portion of the EBNA leader protein (EBNA-LP) gene. These two genes are expressed in transformed B lymphocytes. Recombinant transformation-competent EBVs were produced by transfecting P3HR-1-infected cells with a cosmid containing the DNA deleted in P3HR-1. Deletion of 105 nucleotides from the middle of the EBNA-2 gene had no discernible affect on transformation. Two larger EBNA-2 deletions abolished transformation but did not affect EBNA-2 nuclear localization. Two naturally occurring EBV variants (EBV types 1 and 2) differ extensively in their growth-transformation phenotype and in their EBNA-LP, EBNA-2, and EBNA-3A, -3B, and -3C genes. Recombinant P3HR-1 carrying EBV-1 EBNA-2 has many of the EBV-1 in vitro growth-transforming effects; recombinant P3HR-1, isogenic except for EBV-2 EBNA-2, has many of the EBV-2 growth-transforming effects including slow emergence of transformants, growth in tight clumps with few surrounding viable cells, and early sensitivity to dilution with fresh medium. Thus, EBNA-2 is an essential molecule in lymphocyte growth transformation by EBV and a major determinant of the differences between EBV-1 and EBV-2 in lymphocyte growth transformation.
Antisense RNA complementary to 3' coding and noncoding sequences of creatine kinase is a potent inhibitor of translation in vivo.
Authors: Ch'ng J L , Mulligan R C , Schimmel P , Holmes E W
Published: May 2006

Antisense RNA is a potentially powerful tool for creating dominant negative mutations, but one of the limitations of this strategy has been the relative inefficiency of antisense transcripts in blocking target gene expression. To identify more effective target sequences, helper-free retrovirus-mediated gene transfer was used to introduce antisense RNAs complementary to multiple functional regions of the human creatine kinase B (CK-B) mRNA into U937 cells. Antisense RNA complementary to the last third of the coding and all of the noncoding regio of this mRNA is highly effective; one or two antisense transcripts is sufficient to block the expression of one CK-B mRNA. In contrast, antisense RNA from which sequences complementary to the last 17 codons and all the 3' noncoding region have been deleted has no effect on CK-B expression. Neither antisense RNA alters the abundance of the target message, processing of the primary transcript, egress of the CK-B message from the nucleus, or the polysome profile of CK-B mRNA in sucrose gradients. These results point to a direct effect of the antisense transcript on translation and suggest that this effect may be explained at least in part by an inhibition of elongation or termination as a consequence of the duplex formed in the distal coding and/or 3' noncoding region.
A humanized antibody that binds to the interleukin 2 receptor.
Authors: Queen C , Schneider W P , Selick H E , Payne P W , Landolfi N F , Duncan J F , Avdalovic N M , Levitt M , Junghans R P , Waldmann T A
Published: May 2006

The anti-Tac monoclonal antibody is known to bind to the p55 chain of the human interleukin 2 receptor and to inhibit proliferation of T cells by blocking interleukin 2 binding. However, use of anti-Tac as an immunosuppressant drug would be impaired by the human immune response against this murine antibody. We have therefore constructed a "humanized" antibody by combining the complementarity-determining regions (CDRs) of the anti-Tac antibody with human framework and constant regions. The human framework regions were chosen to maximize homology with the anti-Tac antibody sequence. In addition, a computer model of murine anti-Tac was used to identify several amino acids which, while outside the CDRs, are likely to interact with the CDRs or antigen. These mouse amino acids were also retained in the humanized antibody. The humanized anti-Tac antibody has an affinity for p55 of 3 x 10(9) M-1, about 1/3 that of murine anti-Tac.
Cooperation of c-raf-1 and c-myc protooncogenes in the neoplastic transformation of simian virus 40 large tumor antigen-immortalized human bronchial epithelial cells.
Authors: Pfeifer A M , Mark G E , Malan-Shibley L , Graziano S , Amstad P , Harris C C
Published: May 2006

Overexpression of c-raf-1 and the myc family of protooncogenes is primarily associated with small cell carcinoma, which accounts for approximately 25% of human lung cancer. To determine the functional significance of the c-raf-1 and/or c-myc gene expression in lung carcinogenesis and to delineate the relationship between protooncogene expression and tumor phenotype, we introduced both protooncogenes, alone or in combination, into human bronchial epithelial cells. Two retroviral recombinants, pZip-raf and pZip-myc, containing the complete coding sequences of the human c-raf-1 and murine c-myc genes, respectively, were constructed and transfected into simian virus 40 large tumor antigen-immortalized bronchial epithelial cells (BEAS-2B); this was followed by selection for G418 resistance. BEAS-2B cells expressing both the transfected c-raf-1 and c-myc sequences formed large cell carcinomas in athymic nude mice with a latency of 4-21 weeks, whereas either pZip-raf- or pZip-myc-transfected cells were nontumorigenic after 12 months. Cell lines established from tumors (designated RMT) revealed the presence of the cotransfected c-raf-1 and c-myc sequences and expressed morphological, chromosomal, and isoenzyme markers, which identified BEAS-2B cells as the progenitor line of the tumors. A significant increase in the mRNA levels of neuron-specific enolase was detected in BEAS-2B cells containing both the c-raf-1 and c-myc genes and derived tumor cell lines. The data demonstrate that the concomitant expression of the c-raf and c-myc protooncogenes causes neoplastic transformation of human bronchial epithelial cells resulting in large cell carcinomas with certain neuroendocrine markers. The presented model system should be useful in studies of molecular events involved in multistage lung carcinogenesis.
Regression of adjuvant-induced arthritis in rats following bone marrow transplantation.
Authors: van Bekkum D W , Bohre E P , Houben P F , Knaan-Shanzer S
Published: May 2006

Total body irradiation followed by bone marrow transplantation was found to be an effective treatment for adjuvant arthritis induced in rats. This treatment is most effective when applied shortly after the clinical manifestation of arthritis--i.e., 4-7 weeks after administration of Mycobacterium tuberculosis. Transplantation of bone marrow at a later stage results in a limited recovery, in that the inflammatory reaction regresses but the newly formed excessive bone is not eliminated. Local irradiation of the affected joints had no effect on the disease. It could also be excluded that the recovery of arthritis following marrow transplantation is due to lack of available antigen. Transplantation of syngeneic bone marrow is as effective as that of allogeneic bone marrow from a rat strain that is not susceptible to induction of adjuvant arthritis. The beneficial effect of this treatment cannot be ascribed to the immunosuppressive effect of total body irradiation, since treatment with the highly immunosuppressive drug Cyclosporin A resulted in a regression of the joint swelling but relapse occurred shortly after discontinuation of the treatment.
Canine hemophilia B resulting from a point mutation with unusual consequences.
Authors: Evans J P , Brinkhous K M , Brayer G D , Reisner H M , High K A
Published: May 2006

We have used the polymerase chain reaction to amplify the entire coding region of canine factor IX from a hemophilia B animal. When the sequence was compared to that which codes for normal canine factor IX, a single missense mutation was identified. This mutation (G----A at nucleotide 1477) results in the substitution of glutamic acid for glycine-379 in the catalytic domain of the molecule. The mutation creates a new restriction site that allowed confirmation of the abnormal sequence in both hemophilic and carrier animals. Amino acid 379 in canine factor IX corresponds to position 381 in human factor IX, a location at which no human mutations have been described. Moreover, it occurs at one of the few amino acids that have been rigorously conserved among the trypsin-like serine proteases throughout evolution. The mutation responsible for canine hemophilia B results in a complete lack of circulating factor IX in the affected animals. As it is unusual for a missense mutation to result in a complete absence of protein product, structural modeling of the mutant and normal proteins was pursued. These studies suggest that the observed mutation would have major adverse effects on the tertiary structure of the aberrant factor IX molecule. The elucidation of this mutation sheds light on structure-function relationships in factor IX and should facilitate future experiments directed toward gene therapy of this disease.
Localization of the receptor site for alpha-scorpion toxins by antibody mapping: implications for sodium channel topology.
Authors: Thomsen W J , Catterall W A
Published: May 2006

Site-directed and monoclonal antibodies recognizing different extracellular regions of the RII sodium channel alpha subunit have been used to determine the sequences that comprise the receptor for alpha-scorpion toxins by evaluating the effect of antibody on voltage-dependent binding of radio-labeled toxin isolated from Leiurus quinquestriatus to both reconstituted rat brain sodium channel and rat brain synaptosomes. Of six antibodies tested, two recognizing amino acid residues 355-371 and 382-400 located on an extracellular loop between transmembrane segments S5 and S6 of domain I and one recognizing residues 1686-1703 of a similar loop of domain IV inhibit binding by 30-55%. Inhibition is concentration-(EC50 = 0.4-2 microM) and time- (t1/2 = 40-80 min) dependent. Five different monoclonal antibodies recognizing the same extracellular loop in domain I inhibit binding completely with similar EC50 values as observed for site-directed antibodies. Kinetic studies of the antibody effect are consistent with a slowly reversible competition for the toxin receptor site. Our results suggest that the extracellular loops between segments S5 and S6 of domains I and IV comprise at least part of the alpha-scorpion toxin receptor site and support the membrane topology models in which domains I and IV are adjacent in the tertiary structure of the channel protein and six transmembrane sequences are contained in each of the four homologous domains.
Transcriptional activity of the human thymidine kinase gene determined by a method using the polymerase chain reaction and an intron-specific probe.
Authors: Lipson K E , Baserga R
Published: May 2006

We have used the technique of reverse transcription coupled to the polymerase chain reaction to detect mRNA precursors [heterogeneous nuclear RNA (hnRNA)] transcribed from the thymidine kinase (TK) gene of human diploid fibroblasts. With this method, the amplification products of both hnRNA (containing the introns) and mature mRNA can be detected on Southern blots with appropriate hybridization probes. With the experimental conditions used, the sensitivity of the technique is such that TK mRNA can be detected in as few as 20 S-phase cells. TK hnRNA is maximally expressed early in the S phase of the cell cycle after quiescent human fibroblasts are stimulated to proliferate. At this point, the ratio of TK hnRNA to TK mRNA is 1:155. A small amount of TK hnRNA can be detected in populations of cells that appear to be quiescent. However, the presence of the precursor in these populations correlates with the number of cells still cycling. No TK hnRNA can be detected in truly quiescent human diploid fibroblasts, suggesting that in these cells, the TK gene is not transcribed in G0.
An ochre mutation in the vitamin D receptor gene causes hereditary 1,25-dihydroxyvitamin D3-resistant rickets in three families.
Authors: Ritchie H H , Hughes M R , Thompson E T , Malloy P J , Hochberg Z , Feldman D , Pike J W , O'Malley B W
Published: May 2006

Hereditary 1,25-dihydroxyvitamin D3-resistant rickets is a rare autosomal-recessive disease resulting from target-organ resistance to the action of the active hormonal form of vitamin D. Four affected children from three related families with the classical syndrome of hereditary 1,25-dihydroxyvitamin D3-resistant rickets and the absence of detectable binding to the vitamin D receptor (VDR) in cultured fibroblasts or lymphoblasts were examined for genetic abnormalities in the VDR gene. Genomic DNA from Epstein-Barr virus-transformed lymphoblasts of eight family members was isolated and amplified by polymerase chain reaction techniques. Amplified fragments containing the eight structural exons encoding the VDR protein were sequenced. The DNA from all affected children exhibited a single C----A base substitution within exon 7 at nucleotide 970 that resulted in the conversion of the normal codon for tyrosine (TAC) into a premature termination codon (TAA) at amino acid 292. This mutation causes a truncation of the VDR protein thereby deleting a large portion of the steroid hormone binding domain (amino acids 292-424). Although the affected children were all homozygotic for the mutation, the four parents tested all exhibited both wild-type and mutant alleles, indicating a heterozygous state. The functional consequences of this mutation were confirmed after expression of the recreated mutant VDR cDNA in mammalian cells. Recreated mutant receptor exhibited no specific 1,25-[3H]dihydroxyvitamin D3 binding and failed to activate a cotransfected VDR promoter-reporter gene construct. Thus these findings identify an ochre mutation in a human steroid hormone receptor in patients with hereditary 1,25-dihydroxyvitamin D3-resistant rickets.
T-cell receptor delta-chain diversity in peripheral lymphocytes.
Authors: Lacy M J , McNeil L K , Roth M E , Kranz D M
Published: May 2006

A small percentage (approximately 5%) of the cells in the adult thymus expresses a heterodimeric receptor, gamma delta, that exhibits extensive clonal diversity. The specificity and function of these cells are unclear. Furthermore, it is not known if their role in the immune system is primarily one that operates within the thymus during the selection of the T-cell repertoire or if they function primarily in an antigen-recognition capacity in the peripheral lymphoid system. To examine if gamma delta+ T cells in the periphery are as diverse as those in the thymus, we used the polymerase chain reaction to amplify delta-chain transcripts from polyclonal populations of thymic and splenic lymphocytes (the latter were derived from allogeneic mixed lymphocyte cultures). The nucleotide sequences of delta chains from the spleen, like those from the thymus, were all different. Most of the diversity was present in the region between the variable (V) and joining (J) gene segments and was generated through the use of the two known diversity (D) elements, D delta 1 and D delta 2, and by the addition or deletion of bases at the V delta D delta 1, D delta 1D delta 2, and D delta 2J delta junctions. The extensive gamma delta repertoire among peripheral cells suggests that they have the potential to recognize an array of ligands that could be as diverse as those recognized by alpha beta+ cells. The amplification strategy described here can be used to analyze rapidly the diversity exhibited by any of the members of the immunoglobulin-like gene families that undergo rearrangement.
Structural characterization of toxic cyclic peptides from blue-green algae by tandem mass spectrometry.
Authors: Krishnamurthy T , Szafraniec L , Hunt D F , Shabanowitz J , Yates J R , Hauer C R , Carmichael W W , Skulberg O , Codd G A , Missler S
Published: May 2006

Combined use of chemical degradation, derivatization, and tandem mass spectrometry for rapid structural characterization of toxic cyclic peptides from blue-green algae at the nanomole level is described. Previously, all blue-green algal toxins were thought to belong to a family of seven-residue cyclic peptides, having the general structure cyclo-D-Ala-L-Xaa-erythro-beta-methyl-D-isoaspartic acid-L-Yaa-Adda-D-isoglutamic acid-N-methyldehydroalanine, where Xaa and Yaa represent variable amino acids of the L configuration and Adda is 3-amino-9-methoxy-2,6,8-trimethyl-10-phenyl-deca-4,6-dienoic acid. Structural characterization of two additional toxins indicates that further variability can exist within this family of naturally occurring toxic cyclic peptides. Isoaspartic acid and dehydroalanine can substitute for beta-methylisoaspartic acid and N-methyldehydroalanine, respectively.
Specific postendocytic proteolysis of apolipoprotein B in oocytes does not abolish receptor recognition.
Authors: Nimpf J , Radosavljevic M , Schneider W J
Published: May 2006

Upon receptor-mediated transfer of plasma very low density lipoprotein (VLDL) particles into growing chicken oocytes, their major apolipoprotein (apo) component, apoB, is proteolytically cleaved. apoB fragmentation appears to be catalyzed by cathepsin D or a similar pepstatin A-sensitive protease and results in the presence of a characteristic set of polypeptides on yolk VLDL particles. The nicks introduced into the apoB backbone during postendocytic processing occur in yolk platelets and appear to prepare internalized VLDL for storage in yolk. Since yolk VLDL binds to chicken receptors specific for apoB-containing lipoproteins in identical fashion to plasma VLDL, the possibility exists that the developing embryo utilizes yolk VLDL as a nutrient by way of receptor-mediated endocytosis.
Milk and fat production in dairy cattle influenced by advanced subclinical bovine leukemia virus infection.
Authors: Wu M C , Shanks R D , Lewin H A
Published: May 2006

Genetic potentials (pedigree-estimated breeding value) for milk and for fat were compared in cows grouped according to subclinical stage of bovine leukemia virus infection. Genetic potential for milk production was significantly greater in seropositive cows with persistent lymphocytosis (622 +/- 72 kg) and in seropositive hematologically normal cows (554 +/- 34 34 kg) than in seronegative herdmates (418 +/- 53 kg). When 305-day twice-daily-milking mature equivalent milk production records for the current lactation were adjusted for genetic potential, bovine leukemia virus-infected cows that were hematologically normal had significantly greater milk production than did seronegative herdmates, suggesting that early bovine leukemia virus infection was positively associated with milk yield. Genetic potential for fat production was significantly greater for cows with persistent lymphocytosis (21 +/- 2 kg) than for other seropositive (16 +/- 1 kg) and seronegative herdmates (13 +/- 2 kg); however, 305-day twice-daily-milking mature equivalent fat production for the current lactation was not significantly different between the groups. Thus, cows with persistent lymphocytosis did not produce fat according to their genetic potential. As an apparent consequence of tendencies for greater milk yield and less fat production, milk fat percentage was significantly reduced in cows with persistent lymphocytosis (3.33 +/- 0.09%) and other seropositive cows (3.48 +/- 0.05%) relative to seronegative herdmates (3.67 +/- 0.07%). These results suggest a need to reevaluate the economic impact of bovine leukemia virus infection on the dairy industry.
Identification of covalently linked trimeric and tetrameric D domains in crosslinked fibrin.
Authors: Mosesson M W , Siebenlist K R , Amrani D L , DiOrio J P
Published: May 2006

Following proteolytic conversion of fibrinogen to fibrin, clot assembly commences with formation of double-stranded fibrils that subsequently branch extensively in forming a three-dimensional network. Plasmin digests of fibrin clots that had first been covalently crosslinked by plasma transglutaminase (factor XIIIa) contained multimeric proteolytic fragments composed of crosslinked outer (D) domains of neighboring fibrin molecules. Two of these were larger than the well-known "D dimer" fragment and corresponded to D trimers and D tetramers, respectively. Whereas D dimers originate from crosslinked D domains at bimolecular junctions within two-stranded fibrils, D trimers and D tetramers evidently arise through crosslinking of contiguous D domains at trimolecular and tetramolecular junctions or at fibril branch points, respectively. Measurement of the widths of fibrils comprising trifunctional branches in thin fiber networks revealed tetramolecular branch points, which are formed by bifurcation of two double-stranded fibrils. In addition, another type of trifunctional structure, which we term the trimolecular branch point, was composed of three double-stranded fibrils. Crosslinking of D domains to form trimers may occur at this type of junction. These findings add to our understanding of the crosslinking arrangements that stabilize fibrin clot structure and the ways that fibrin molecules polymerize to form branches in the clot matrix.
Binding of hormone accelerates the kinetics of glucocorticoid and progesterone receptor binding to DNA.
Authors: Schauer M , Chalepakis G , Willmann T , Beato M
Published: May 2006

Steroid hormone receptors induce genes by virtue of their interaction with DNA regulatory sequences. The hormonal response of a particular gene in vivo correlates with binding of the hormone to the receptor and supposedly reflects the degree of occupancy of the corresponding DNA regulatory sequences. However, in vitro the steroid-free glucocorticoid and progesterone receptors bind specifically to the regulatory sequences of mouse mammary tumor virus, thus raising questions on the role of the hormone in DNA binding in vivo. By using monoclonal antibodies, gel retardation assays, and filter binding techniques we show here that binding of a functional steroid to either the glucocorticoid or the progesterone receptors influences the kinetics of the protein-DNA interaction in vitro. In the presence of hormone the on rate of receptor binding to DNA fragments with or without regulatory sequences is accelerated 2- to 5-fold, and the off rate is accelerated 10- to 20-fold. The receptors complexed to an antihormone bind to DNA with kinetics intermediate between those of the steroid-free and the hormone-bound protein. Thus, ligand binding accelerates the kinetics of receptor binding to DNA and this could partly account for the behavior of the hormone receptor observed in vivo.
Identifying protein-binding sites from unaligned DNA fragments.
Authors: Stormo G D , Hartzell G W
Published: May 2006

The ability to determine important features within DNA sequences from the sequences alone is becoming essential as large-scale sequencing projects are being undertaken. We present a method that can be applied to the problem of identifying the recognition pattern for a DNA-binding protein given only a collection of sequenced DNA fragments, each known to contain somewhere within it a binding site for that protein. Information about the position or orientation of the binding sites within those fragments is not needed. The method compares the "information content" of a large number of possible binding site alignments to arrive at a matrix representation of the binding site pattern. The specificity of the protein is represented as a matrix, rather than a consensus sequence, allowing patterns that are typical of regulatory protein-binding sites to be identified. The reliability of the method improves as the number of sequences increases, but the time required increases only linearly with the number of sequences. An example, using known cAMP receptor protein-binding sites, illustrates the method.
Identification of an assembly domain in the small subunit of ribulose-1,5-bisphosphate carboxylase.
Authors: Wasmann C C , Ramage R T , Bohnert H J , Ostrem J A
Published: May 2006

The mature small subunit (SSU) of ribulose-1,5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39) in higher plants contains a highly conserved sequence of 16 amino acids that is absent in the SSUs of cyanobacteria. To determine whether this region of the SSU of higher plants has a specific function, portions of the SSU genes (rbcS) of pea (Pisum sativum) and the cyanobacterium Anacystis nidulans were fused to create chimeric genes that either lacked or contained the coding sequence for the 16 conserved amino acids. Precursor proteins synthesized in vitro from the chimeric genes were incubated with isolated pea chloroplasts to assay import and assembly into the holoenzyme. Fusion proteins lacking the 16-amino acid sequence were imported and processed but failed to assemble with endogenous large subunit. Addition of the region from a pea rbcS containing the 16 amino acids to the rbcS of Anacystis enabled the imported SSU fusion protein to assemble with pea large subunit. This 16-amino acid sequence is encoded by a separate exon in certain rbcS genes of higher plants. We propose that the conserved 16-amino acid sequence constitutes a domain acquired to facilitate assembly of the eukaryotic holoenzyme.
Early nodulin genes are induced in alfalfa root outgrowths elicited by auxin transport inhibitors
Authors: Hirsch A. M. , Bhuvaneswari T. V. , Torrey J. G. , Bisseling T.
Published: May 2006

Rhizobium nod
genes are essential for root hair deformation and cortical cell division, early stages in the development of nitrogen-fixing root nodules. Nod
-
mutants are unable to initiate nodules on legume roots. We observed that
N
-(1-naphthyl)phthalamic acid and 2,3,5-triiodobenzoic acid, compounds known to function as auxin transport inhibitors, induced nodule-like structures on alfalfa roots. The nodule-like structures (pseudonodules) were white, devoid of bacteria, and resembled nodules elicited by
Rhizobium meliloti
exopolysaccharide (
exo
) mutants at both the histological and molecular level. Two nodulin genes, ENOD2 and Nms-30, were expressed. RNA isolated from the nodule-like structures hybridized to pGmENOD2, a soybean early nodulin cDNA clone. RNA isolated from roots did not hybridize. We determined by
in vitro
translations of total RNA that the alfalfa nodulin transcript Nms-30 was also expressed in the nodule-like structures. The late expressed nodulin genes, such as the leghemoglobin genes, were not transcribed. Because
N
-(1-naphthyl)phthalamic acid and 2,3,5-triiodobenzoic acid induce the development of nodules on alfalfa roots, we suggest that the auxin transport inhibitors mimic the activity of compound(s) made upon the induction of the
Rhizobium nod
genes.
Targeting of a chromosomal protein to the nucleus and to lampbrush chromosome loops.
Authors: Roth M B , Gall J G
Published: May 2006

We have isolated a cDNA clone (SE5A) that encodes a protein on lampbrush chromosome loops of the newt Notophthalmus. In vitro-synthesized transcripts of this clone were injected into Xenopus oocytes, where they were efficiently translated. Most of the translated protein was imported into the oocyte nucleus, and some of it appeared on the chromosome loops. The translation product must contain information that permits its appropriate targeting first to the nucleus and then to the chromosome loops.
Sulfation of tyrosine residues increases activity of the fourth component of complement.
Authors: Hortin G L , Farries T C , Graham J P , Atkinson J P
Published: May 2006

Sulfation of tyrosine residues recently has been recognized as a biosynthetic modification of many plasma proteins and other secretory proteins. Effects of this site-specific modification on protein function are not known, but the activity of several peptides such as cholecystokinin is greatly augmented by sulfation. Here, we examine the role of sulfation in the processing and activity of C4 (the fourth component of complement), one of the few proteins in which sites and stoichiometry of tyrosine sulfation have been characterized. Our results, with C4 as a paradigm, suggest that sulfation of tyrosine residues can have major effects on the activity of proteins participating in protein-protein interactions. Sulfation of C4 synthesized by Hep G2 cells was blocked by incubating the cells with NaClO3 and guaiacol. These sulfation inhibitors did not alter secretion or other steps in the processing of C4. However, hemolytic activity of C4 was decreased more than 50%. The inhibitors' effect on C4 activity was prevented by adding Na2SO4 to restore sulfation of C4. Activity of C3, a complement component homologous to C4 but lacking tyrosine sulfate residues, was minimally reduced (19%) by the inhibitors. Decreased hemolytic activity of nonsulfated C4 apparently resulted from impaired interaction with complement subcomponent C1s (EC 3.4.21.42), the protease that physiologically activates C4. Purified C1s was able to cleave nonsulfated C4, but approximately 10-fold higher concentrations of C1s were required for that cleavage than to yield equivalent cleavage of sulfated C4. Our results suggest that activation of C4, a central component in the classical pathway of complement activation, is influenced by the level of sulfation of the protein. Thus, sulfation of C4 provides a potential locus for physiological or pharmacological modulation of complement-mediated opsonization and inflammation.
Human muscle glycogen synthase cDNA sequence: a negatively charged protein with an asymmetric charge distribution.
Authors: Browner M F , Nakano K , Bang A G , Fletterick R J
Published: May 2006

The cDNA for human muscle glycogen synthase encodes a protein of 737 amino acids. The primary structure of glycogen synthase is not related either to bacterial glycogen synthase or to any glycogen phosphorylase. All nine of the serines that are phosphorylated in the rabbit muscle enzyme in vivo are conserved in the human muscle sequence. The amino- and carboxyl-terminal fragments, which contain all the phosphorylation sites, are very negatively charged. Overall the unphosphorylated protein has a charge of -13, while the fully phosphorylated inactive protein has a net charge of -31. The importance of the asymmetrical charge distribution is discussed.
Phosphorylation and glycosylation of the luteinizing hormone receptor.
Authors: Minegishi T , Delgado C , Dufau M L
Published: May 2006

Purified testicular and ovarian luteinizing hormone/human chorionic gonadotropin (hCG) receptors are phosphorylated at serine and threonine residues by the catalytic subunit of the cAMP-dependent protein kinase (protein kinase A). Occupancy of the receptors by hCG significantly increased the rate but not the extent of phosphorylation. However, prolonged preincubation of receptors with hCG reduced the subsequent rate of receptor phosphorylation. Identical phosphopeptide maps were obtained for the phosphorylated ovarian and testicular receptors. The phosphorylated receptor, like the native receptor, bound to wheat germ lectin and hCG-Sepharose and migrated as a single band of Mr 90,000 (testis) and Mr 85,000 (ovary) on NaDodSO4/PAGE. Neuraminidase treatment of receptors caused reductions of molecular weight to 82,000 (testis) and 77,000 (ovary), and further treatment with O-Glycanase had minimal effect on molecular size. However, deglycosylation with N-Glycosidase and endoglycosidase F produced a single labeled polypeptide of Mr 59,000 for both gonadal receptors. Treatment of native receptors with neuraminidase caused no apparent change in binding of gonadotropin to blotted receptors, whereas deglycosylated receptors showed a major reduction in hormone binding. These results indicate that luteinizing hormone/hCG receptors are sialoglycoproteins with predominantly N-linked glycosyl residues that account for the size difference between testicular and ovarian receptors and that may participate in the interaction with gonadotropin. Receptor occupancy by agonist leads to a conformational change that facilitates its phosphorylation during initial binding and reduces the rate of phosphorylation after more prolonged exposure to hCG.
Comparative study of optical absorption and circular dichroism of bacteriochlorophyll oligomers in Triton X-100, the antenna pigment B850, and the primary donor P-860 of photosynthetic bacteria indicates that all are similar dimers of bacteriochlorophyll a
Authors: Scherz A. , Rosenbach-Belkin V.
Published: May 2006

Dimers of bacteriochlorophyll a (Bchl
a
) with optical absorption maximum at 853 nm and a nonconservative circular dichroism spectrum are formed in a solution of formamide/water that contains micelles of Triton X-100. The apparent equilibrium constant and the corresponding Gibbs energy change for the Bchl self-organization are 4.9 × 10
6
M
-1
and -9.2 kcal/mol, respectively. The experimental absorption and circular dichroism spectra of the
in vitro
Bchl dimer (termed Bchl-853) are similar to the spectra of the bacterial light-harvesting complex B850 and the primary electron donor P-860 and probably point to a common structural motif. Indeed, simulation of the dimers' spectra (optical absorption and circular dichroism), achieved by using an extended version of the exciton theory, suggests the same geometry as recently elucidated for P-860 by x-ray diffraction crystallography. The proposed geometry is predicted to have the minimum energy in the gas phase. In conclusion, the spectral properties of the bathochromically shifted forms of Bchl
a
are likely a result of strong dipolar interactions in self-organized structures of Bchls.
Anticancer activities of adenine nucleotides in mice are mediated through expansion of erythrocyte ATP pools.
Authors: Rapaport E , Fontaine J
Published: May 2006

ATP and AMP exhibit significant anticancer activities against established footpad CT26 colon adenocarcinoma in CB6F1 mice. Adenosine, inorganic phosphate, and inorganic pyrophosphate were without such effects under identical conditions. Daily intraperitoneal injections of adenine nucleotides in large volumes of saline, starting after the tumors became palpable, resulted in inhibition of tumor growth and a few "cures." The treatment was not toxic to the host as determined by changes in body weights. Weight loss observed in animals upon progression of the fast-growing CT26 tumors was slowed markedly in adenine nucleotide-treated mice. The inhibition of weight loss in tumor-bearing mice was shown to be neither the cause nor the effect of the inhibition of tumor growth. Intraperitoneal injections of AMP or ATP but not of adenosine yielded expansions of erythrocyte ATP pools in host animals. The expanded erythrocyte ATP pools are stable over a period of hours, while slowly releasing micromolar amounts of ATP into the blood plasma compartment, leading to several-fold increases in plasma (extracellular) ATP levels. Based on previous studies in which 1-5 microM extracellular ATP effectively inhibited the growth of a variety of tumor cells in several in vitro systems, it is suggested that similar levels of ATP in blood plasma account for the anticancer activities observed in a murine host.
An in vitro system for infection with hepatitis B virus that uses primary human fetal hepatocytes.
Authors: Ochiya T , Tsurimoto T , Ueda K , Okubo K , Shiozawa M , Matsubara K
Published: May 2006

An in vitro culture of human fetal hepatocytes has been employed for infection by hepatitis B virus (HBV) virions that are produced by an established human hepatoma cell line, HB 611. HBV surface antigen and e antigen were released into the medium 3-4 days after infection, and production continued thereafter. RNA synthesis with similar kinetics was observed. Viral DNA replication started 2 days after infection, and replicative HBV DNA that included relaxed circles, single-stranded minus strands, and closed circles accumulated during 16 days of incubation. Immunofluorescent study using fluorescein isothiocyanate-labeled rabbit antisera directed against HBV core antigen revealed that this antigen is present in the nuclei in 12% of the infected cells. Particles containing HBV DNA were detected in the culture medium and were infectious. Thus, this in vitro infection system closely mimics infection in vivo and it allows detailed studies on early events associated with human HBV entry into cells and subsequent replication and integration.
Somatostatin analogues inhibit growth of pancreatic cancer by stimulating tyrosine phosphatase.
Authors: Liebow C , Reilly C , Serrano M , Schally A V
Published: May 2006

Several analogues of somatostatin were examined in the Mia PaCa-2 human pancreatic cancer cell line for their ability to promote tyrosine phosphatase activity affecting the receptors for the epidermal growth factor. The inhibition of growth of the Mia PaCa-2 cells in culture was also evaluated to determine the mechanism of action of somatostatin analogues and their relative effectiveness in inhibiting cancer growth. Of the analogues tested D-Phe-Cys-Tyr-D-Trp-Lys-Val-Cys-Trp-NH2 (RC-160) caused the greatest stimulation of tyrosine phosphatase activity. Analogue D-Phe-Cys-Tyr-D-Trp-Lys-Val-Cys-Thr-NH2 (RC-121) had less effect but was more potent than somatostatin-14. Analogue D-Phe-Cys-Phe-D-Trp-Lys-Thr-Cys-Thr(ol) (SMS 201-995) produced no significant dephosphorylation. The analogues displayed the same order of activity in assays on growth inhibition of Mia PaCa-2 cells in cultures. Analogue (SMS-201-995) caused virtually no tyrosine phosphatase stimulation or growth inhibition in this cancer cell line, although it possesses a much higher antisecretory activity than somatostatin-14 in normal tissues. These observations indicate that somatostatin and some of its analogues can act as growth inhibitors in cancer cells through the activation of tyrosine phosphatase. These data reinforce the view that somatostatin analogue RC-160 and related compounds could be used for treatment of pancreatic cancer.
Two sodium-channel genes in Drosophila: implications for channel diversity.
Authors: Ramaswami M , Tanouye M A
Published: May 2006

We describe two Drosophila melanogaster transcription units that are highly homologous to a rat Na+-channel cDNA. They appear to encode the major subunits of two distinct Na+-channel proteins. One of these maps to the second chromosome and is identical to a Na+-channel gene whose partial sequence has been previously reported [Salkoff, L., Butler, A., Wei, A., Scavarda, N., Giffen, K., Ifune, K., Goodman, R. & Mandel, G. (1987) Science 237, 744-749]. The other transcription unit maps to position 14C/D, on the X chromosome, close to the paralyzed (para) gene. Mutations in para affect membrane excitability in Drosophila neurons [Ganetzky, B. & Wu, C.F. (1986) Annu. Rev. Genet. 20, 13-44]. Sequence comparisons suggest that two Na+-channel genes arose early in evolution, before the divergence of vertebrate and invertebrate lines.