bluuebunny/crossref_metadata_2025 huggingface dataset:
Induction of manganese-containing superoxide dismutase in anaerobic Escherichia coli by diamide and 1,10-phenanthroline: sites of transcriptional regulation.
Authors: Privalle C T , Kong S E , Fridovich I
Published: May 2006

Transcriptional regulation of the sodA gene, a member of the soxRS regulon encoding the manganese-containing superoxide dismutase (MnSOD; superoxide:superoxide oxidoreductase, EC 1.15.1.1) of Escherichia coli, was examined in a variety of regulatory mutants. Diamide, an oxidant that causes the anaerobic biosynthesis of the MnSOD polypeptide and also facilitates insertion of manganese at the active site, was found to anaerobically induce MnSOD in both soxRS and fur arcA fnr strains. Metal chelating agents also caused anaerobic induction of MnSOD in a fur arcA fnr triple mutant; however, this induction of MnSOD and of glucose-6-phosphate dehydrogenase (G6PD) by 1,10-phenanthroline was dependent on an intact soxRS locus. A strain of E. coli bearing a fusion of the soxS promoter to lacZ was used to demonstrate that both diamide and 1,10-phenanthroline caused anaerobic activation of soxS transcription. These results indicate that (i) both diamide and 1,10-phenanthroline induce the soxRS regulon anaerobically by stimulation of soxS transcription; (ii) diamide, but not metal chelators, also induces MnSOD biosynthesis by a soxRS-independent mechanism, perhaps mediated by effects on fur, arcA, or fnr-mediated repression of sodA; and (iii) the soxRS locus contains a metal-binding component and is responsive to the redox status of the cell.
Dissociation of glucose-regulated protein Grp78 and Grp78-IgE Fc complexes by ATP.
Authors: Toledo H , Carlino A , Vidal V , Redfield B , Nettleton M Y , Kochan J P , Brot N , Weissbach H
Published: May 2006

Recent studies have shown that ATP can dissociate dimers of the glucose-regulated protein Grp78 to monomers. In the present study, we have used purified recombinant Grp78 from Escherichia coli to investigate this reaction in more detail. During the course of the Grp78 dimer-monomer conversion, a stable Grp78 monomer-ATP complex is formed. Upon removal of the ATP, the Grp78 dimer is reformed. ADP, nonhydrolyzable ATP analogues, and GTP do not effect the dissociation of Grp78 dimers. A cell line that overproduces IgE Fc has been used to examine the nature of the Grp78-IgE Fc complexes present and the effect of ATP on them. Grp78-IgE Fc complexes ranging from 100 kDa to 300 kDa were observed by sucrose gradient analysis, suggesting that aggregate forms of Grp78 may be present in some of these complexes. Treatment of the extracts with ATP resulted in release of a Grp78 monomer from the complex. These results suggest that the dissociation of Grp78 oligomers by ATP may be involved in the function of Grp78 in protein translocation through the endoplasmic reticulum.
Chromosomal structure of Rhodobacter capsulatus strain SB1003: cosmid encyclopedia and high-resolution physical and genetic map.
Authors: Fonstein M , Haselkorn R
Published: May 2006

A combination of cosmid genome walking and pulsed-field gel electrophoresis was used to construct a high-resolution physical and genetic map of the 3.8-megabase (Mb) genome of Rhodobacter capsulatus SB1003. The mapping was done by hybridization of pulsed-field gel blots and by grouping and further mapping of the cosmids and bacteriophages from genomic libraries. Cosmid clones formed two uninterrupted and ordered groups, one corresponding to the chromosome of R. capsulatus, the other to its 134-kb plasmid. Cos site end-labeling and partial EcoRV digestion of cosmids were used to construct a high-resolution EcoRV map of the genome. Overlapping of the cosmids was confirmed by the resemblance of the cosmid restriction maps and by direct end-to-end hybridization with SP6- and T7-specific transcripts. Twenty-three previously cloned genes and eight groups of repeated sequences, revealed in this work, were located in the ordered gene library and mapped with an accuracy of 1-10 kb. Blots of a minimal set of 192 cosmids, covering the chromosome and the plasmid with the known map position of each cosmid, give to R. capsulatus the same advantages that the Kohara phage panel gives to E. coli.
Neurotrophin 3 supports the survival of developing muscle sensory neurons in culture.
Authors: Hory-Lee F , Russell M , Lindsay R M , Frank E
Published: May 2006

Target-dependent cell death of different sub-populations of sensory neurons may be regulated by different trophic factors. To investigate this possibility, we have taken advantage of the fact that the fractions of muscle sensory and cutaneous sensory neurons in chicken dorsal root ganglia (DRG) are probably different at different segmental levels, and we have compared the responses of chicken DRG from levels that do and do not innervate limb tissue to various growth factors in vitro. Nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF) both supported neurite outgrowth from DRG explanted from all segmental levels. In contrast, neurotrophin 3 (NT-3) supported robust neurite growth only from DRG explanted from the cervical or lumbar levels, which innervate limb muscles. Similarly, NGF and BDNF both promoted survival of dissociated neurons from limb and nonlimb segmental levels, whereas NT-3 promoted survival of more neurons from limb compared to nonlimb levels. This suggests that muscle sensory neurons, which are probably more prevalent at the cervical and lumbar levels, may be specifically affected by NT-3. To evaluate this possibility directly, we compared the survival of retrogradely labeled muscle and cutaneous neurons in NGF, BDNF, and NT-3. Identified muscle sensory neurons survived best in vitro in the presence of NT-3, while the survival of identified cutaneous sensory neurons was greatest in NGF. This work provides direct evidence for a potential role of NT-3 versus NGF in the survival of a specific subpopulation of DRG neurons.
En bloc substitution of the Src homology region 2 domain activates the transforming potential of the c-Abl protein tyrosine kinase.
Authors: Muller A J , Pendergast A M , Parmar K , Havlik M H , Rosenberg N , Witte O N
Published: May 2006

Src homology region 2 (SH2) domains are present in many proteins involved in signal transduction. In nonreceptor protein tyrosine kinases the SH2 domain has been implicated in regulation of tyrosine kinase activity and in mediating interactions involved in downstream signaling. Different SH2 domains exhibit distinct binding specificities for both phosphotyrosine- and phosphoserine/phosphothreonine-containing proteins. We show that different SH2 domains are not functionally equivalent within the context of the c-ABL1b protooncogene. c-ABL1b, altered by replacement of its SH2 domain with the N-terminal SH2 domain of Ras GTPase-activating protein, exhibited activated transforming capability, caused intracellular tyrosine phosphorylation of p62, and was relocalized from nucleus to cytoplasm. This en bloc substitution apparently uncouples two distinct functions of the SH2 domain so that c-ABL escapes normal regulatory control while it retains the capability to elicit signals that promote transformation. The SH2 domain of the ARG protein tyrosine kinase, which shares high amino acid-sequence homology with the SH2 domain of ABL, was less effective in activating the oncogenic potential of c-ABL. The effects that the N-terminal SH2 domain of Ras GTPase-activating protein has in the context of c-ABL resemble the effects of deleting the SH3 domain. Thus, the SH2 and SH3 domains may have coordinate roles as regulatory control elements within the context of c-ABL.
Bidirectional transport of glucocorticoid receptors across the nuclear envelope.
Authors: Madan A P , DeFranco D B
Published: May 2006

We have used transient interspecies heterokaryons to analyze nucleocytoplasmic shuttling of glucocorticoid receptor (GR) and demonstrated that receptors that accumulate within nuclei upon ligand binding are not statically confined to that compartment, but rather have the capacity to reversibly transverse the nuclear envelope. The ability of various GR mutants to shuttle between nuclei of heterokaryons excluded transcriptional activation and DNA binding as prerequisites for nucleocytoplasmic shuttling of GR. However, a constitutively nuclear GR derivative that has fused at its amino terminus the simian virus 40 large tumor antigen nuclear localization signal sequence was unable to efficiently export from nuclei unless ligand-bound. These results uncover an unexpected effect of ligand binding to GR--i.e., the overriding of a dominant negative effect on nuclear export of a heterologous nuclear import signal sequence. Furthermore, they demonstrate that a nuclear import signal sequence can influence nuclear processing pathways that culminate in efficient nuclear export.
Stimulation by phospholipids of a protein-tyrosine-phosphatase containing two src homology 2 domains.
Authors: Zhao Z , Shen S H , Fischer E H
Published: May 2006

PTP1C, a protein-tyrosine-phosphatase (protein-tyrosine-phosphate phosphohydrolase, EC 3.1.3.48) containing two src homology 2 domains, is poorly active when assayed with various protein substrates in vitro. Its activity is stimulated > 1000-fold by anionic phospholipids when myelin basic protein or mitogen-activated protein kinase is used as substrate but reduced in the presence of several other substrates. Data are presented to indicate a direct interaction of the enzyme with phospholipids. Enzyme stimulation directed only toward certain specific substrates is interpreted by assuming that these compounds also bind to the phospholipid vesicles where they will be subjected to rapid enzymatic attack. A possible regulation of PTP1C by its translocation to the cell membrane is hypothesized.
Ala-->Gly mutation in the putative catalytic loop confers temperature sensitivity on Ros, insulin receptor, and insulin-like growth factor I receptor protein-tyrosine kinases.
Authors: Chen J , Hanafusa T , Wang L H
Published: May 2006

Temperature-sensitive mutations in the avian sarcoma virus UR2 oncogene ros, encoding a receptor protein-tyrosine kinase (PTK), were identified. The Ala385-->Gly change mapping within the highly conserved RDLAARN motif in the Ros kinase domain was responsible for the temperature-sensitive phenotype. Based on the sequence homology of all known protein kinases and the crystalline structure of the cAMP-dependent protein kinase, this conserved region probably represents the PTK catalytic loop. The same mutation when introduced into the human insulin and insulin-like growth factor I receptors made these PTKs temperature sensitive in both biological function and kinase activity. Our results support the presumed catalytic role of this highly conserved sequence in PTKs. Due to its highly conserved nature, we predict that the same mutation would probably confer temperature sensitivity on other PTKs.
Early auxin-induced genes encode short-lived nuclear proteins.
Authors: Abel S , Oeller P W , Theologis A
Published: May 2006

The plant growth hormone indoleacetic acid (IAA) transcriptionally activates gene expression in plants. Some of the genes whose expression is induced by IAA encode a family of proteins in pea (PS-IAA4 and PS-IAA6) and Arabidopsis (IAA1 and IAA2) that contain putative nuclear localization signals that direct a beta-glucuronidase reporter protein into the nucleus. Pulse-chase and immunoprecipitation experiments have defined the t1/2 of the PS-IAA4 and PS-IAA6 proteins to be 8 and 6 min, respectively. Their most prominent feature is the presence of a beta alpha alpha motif similar to the beta-sheet DNA-binding domain found in prokaryotic repressors of the Arc family. Based on these data, we suggest that plant tissues express short-lived nuclear proteins as a primary response to IAA. We propose that these proteins act as activators or repressors of genes responsible for mediating the various auxin responses.
Gene transfer into hematopoietic stem cells: long-term maintenance of in vitro activated progenitors without marrow ablation.
Authors: Bienzle D , Abrams-Ogg A C , Kruth S A , Ackland-Snow J , Carter R F , Dick J E , Jacobs R M , Kamel-Reid S , Dubé I D
Published: May 2006

Adoptive transfer of genetically modified somatic cells will play an increasingly important role in the management of a wide spectrum of human diseases. Among the most appealing somatic cells as potential gene transfer vehicles are hematopoietic cells, because of their wide distribution and their well-characterized capacities for proliferation, differentiation, and self-renewal. Genes can be readily transferred into short-lived and lineage-restricted hematopoietic cells, but there remains a need to develop reliable methods for gene transfer into hematopoietic stem cells in large animals. In this work, we used a gene transfer approach in which hematopoietic cells in long-term marrow cultures were exposed to the replication-defective retrovirus N2, bearing the reporter gene neo, on multiple occasions during 21 days of culture. Genetically marked cultured autologous cells were infused into 18 canine recipients in the absence of marrow-ablative conditioning. neo was detected by Southern blotting and/or the polymerase chain reaction in the marrow, blood, marrow-derived granulocyte/macrophage and erythroid progenitors, and cultured T cells in dogs after infusion. In most dogs, the proportion of long-term marrow culture cells contributing to hematopoiesis rose during the first 3 months after infusion and peaked within the first 6. The maximal levels attained were between 10% and 30% G418-resistant (neo-positive) granulocyte/macrophage progenitors. At 12 months, five dogs maintained greater than 10% G418-resistant progenitors, and for two of them this level exceeded 20%. Two dogs had greater than 5% G418-resistant hematopoietic progenitors at 24 months after infusion. Our data suggest that very primitive hematopoietic progenitors are maintained in long-term marrow cultures, where they can be triggered into entering the cell cycle. In vivo, these activated cells likely continue normal programs of proliferation, differentiation, and self-renewal. Their progeny can be maintained at clinically relevant levels for up to 2 years without the requirement that endogenous hematopoiesis be suppressed through chemo- or radiotherapy prior to adoptive transfer. Long-term marrow culture cells may thus be ideal targets for gene therapy involving adoptive transfer of transduced hematopoietic cells.
DNA bound by the Oxytricha telomere protein is accessible to telomerase and other DNA polymerases.
Authors: Shippen D E , Blackburn E H , Price C M
Published: May 2006

Macronuclear telomeres in Oxytricha exist as DNA-protein complexes in which the termini of the G-rich strands are bound by a 97-kDa telomere protein. During telomeric DNA replication, the replication machinery must have access to the G-rich strand. However, given the stability of telomere protein binding, it has been unclear how this is accomplished. In this study we investigated the ability of several different DNA polymerases to access telomeric DNA in Oxytricha telomere protein-DNA complexes. Although DNA bound by the telomere protein is not degraded by micrococcal nuclease or labeled by terminal deoxynucleotidyltransferase, this DNA serves as an efficient primer for the addition of telomeric repeats by telomerase, a specialized RNA-dependent DNA polymerase (ribonucleoprotein reverse transcriptase), EC 2.7.7.49. Moreover, in the presence of a suitable complementary C-rich DNA template, AMV reverse transcriptase and the E. coli Klenow fragment will also elongate DNA bound by the telomere protein. These findings indicate that the 3' terminus and the Watson-Crick base pairing positions are exposed in the protein complex. We propose that the telomere protein can serve a dual role at the telomere by protecting the DNA phosphate backbone from degradation while simultaneously exposing the DNA bases for replication.
Alternative splicing of RNA transcripts encoded by the murine p105 NF-kappa B gene generates I kappa B gamma isoforms with different inhibitory activities.
Authors: Grumont R J , Gerondakis S
Published: May 2006

The gene encoding the 105-kDa protein (p105) precursor of the p50 subunit of transcription factor NF-kappa B also encodes a p70 I kappa B protein, I kappa B gamma, which is identical to the C-terminal 607 amino acids of p105. Here we show that alternative RNA splicing generates I kappa B gamma isoforms with properties different from those of p70. One 63-kDa isoform, termed I kappa B gamma-1, which lacks 59 amino acids C-terminal to ankyrin repeat 7, has a novel 35-amino acid C terminus encoded by an alternative reading frame of the p105 gene. A 55-kDa isoform, I kappa B gamma-2, lacks the 190 C-terminal amino acids of p70I kappa B gamma. In contrast to p70I kappa B gamma, which is a cytoplasmic protein, I kappa B gamma-1 is found in both the cytoplasm and nucleus, whereas I kappa B gamma-2 is predominantly nuclear. The I kappa B gamma isoforms also display differences in specificity and affinity for Rel/NF-kappa B proteins. While p70I kappa B gamma inhibits p50-, p65-, and c-Rel-mediated transactivation and/or DNA binding, both I kappa B gamma-1 and I kappa B gamma-2 are specific for p50 and have different affinities for this subunit. The absence in I kappa B gamma-1 and I kappa B gamma-2 of a protein kinase A site whose phosphorylation modulates p70I kappa B gamma inhibitory activity suggests that alternative RNA splicing may be used to generate I kappa B gamma isoforms that respond differently to intracellular signals.
Two Mhc class I and two Mhc class II genes map to the chicken Rfp-Y system outside the B complex.
Authors: Miller M M , Goto R , Bernot A , Zoorob R , Auffray C , Bumstead N , Briles W E
Published: May 2006

Gene sequences highly similar to major histocompatibility complex (Mhc) class I and class II genes were recently recognized as mapping to a site in the genome of the chicken separate from the Mhc class I, class II, and B-G genes of the major histocompatibility (B) complex. The present study was undertaken to see whether this complex of Mhc-like genes designated as restriction fragment pattern Y (Rfp-Y) might reside in one of three clusters of cosmid clones contained within the molecular map of chicken Mhc genes, since only two of the three clusters can be assigned to the B system. To determine whether the third cluster (cluster II/IV) might contain Rfp-Y, a subclone (18.1) from within cluster II/IV near a polymorphic lectin gene was used to analyze the DNA of families in which Rfp-Y haplotypes are known to be segregating. The restriction fragment polymorphisms revealed by the 18.1 probe were found to segregate in parallel with the restriction fragment polymorphisms defining the Rfp-Y haplotypes, thus establishing the location of Rfp-Y within cosmid cluster II/IV. Two of six Mhc class I genes and two of five Mhc class II genes map to cosmid cluster II/IV, so a substantial fraction of chicken Mhc genes, including at least one that may be expressed, are located in a chromosomal region separate from the B system. In further linkage analyses, Rfp-Y was found to assort independently from more than 400 markers in the present linkage map of the chicken genome.
Top-down construction of an ordered Schizosaccharomyces pombe cosmid library.
Authors: Grothues D , Cantor C R , Smith C L
Published: May 2006

A very rapid and efficient method for sorting and ordering large numbers of clones is presented. This top-down mapping approach divides the entire ordering problem into many smaller tasks and analyzes in parallel a gridded membrane array of clones by hybridization with probe pools. The strategy was tested on a 15-fold-coverage Schizosaccharomyces pombe cosmid library. About 1600 clones were assigned to chromosomes and to regions defined by the Not I and Sfi I restriction maps. Then, the clones were ordered into 20 contigs, which is consistent with statistical expectations for the degree of genome coverage used. The parallel ordering of clones and the computer-based analysis of digitized images make this approach very efficient; it is about 8-fold faster than existing methods. Only 61 hybridizations were needed to order 1600 clones.
Simulated responses of cerebellar Purkinje cells are independent of the dendritic location of granule cell synaptic inputs.
Authors: De Schutter E , Bower J M
Published: May 2006

Cerebellar Purkinje cell responses to granule cell synaptic inputs were examined with a computer model including active dendritic conductances. Dendritic P-type Ca2+ channels amplified postsynaptic responses when the model was firing at a physiological rate. Small synchronous excitatory inputs applied distally on the large dendritic tree resulted in somatic responses of similar size to those generated by more proximal inputs. In contrast, in a passive model the somatic postsynaptic potentials to distal inputs were 76% smaller. The model predicts that the somatic firing response of Purkinje cells is relatively insensitive to the exact dendritic location of synaptic inputs. We describe a mechanism of Ca2+-mediated synaptic amplification, based on the subspiking threshold recruitment of P-type Ca2+ channels in the dendritic branches surrounding the input site.
Posttranscriptional mRNA processing as a mechanism for regulation of human A1 adenosine receptor expression.
Authors: Ren H , Stiles G L
Published: May 2006

The human A1 adenosine receptor gene contains six exons with exons 1, 2, 3, 4, and part of 5 representing 5' untranslated regions. Reverse transcription-PCR with exon-specific primers showed two distinct transcripts containing either exons 3, 5, and 6 or exons 4, 5, and 6, with exons 3 and 4 being mutually exclusive. No mature mRNAs containing exons 1 and 2 have been detected. All human tissues that express any A1 receptors contain mRNA with exons 4, 5, and 6. Tissues which express high levels of A1 receptors contain mRNA with exons 3, 5, and 6. Exon 4 contains two upstream ATG codons whereas exon 3 contains none. COS cells transfected with expression vectors containing exon 4 (exons 1-6, 3-6, or Ex4-6) express much lower levels of A1 receptors than vectors without exon 4 (exons 3, 5, and 6). Mutation of upstream ATG codons in exon 4 leads to 3- to 7-fold increased A1 receptor expression, up to the level seen with the construct containing exons 3, 5, and 6. Thus, in human tissues "basal" levels of A1 receptors can be expressed by use of mRNA containing exons 4, 5, and 6, but when high levels are needed, alternative transcripts with exons 3, 5, and 6 are produced.
Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro.
Authors: Skripkin E , Paillart J C , Marquet R , Ehresmann B , Ehresmann C
Published: May 2006

The diploid genome of all retroviruses is made of two homologous copies of RNA intimately associated near their 5' end, in a region called the dimer linkage structure. Dimerization of genomic RNA is thought to be important for crucial functions of the retroviral life cycle (reverse transcription, translation, encapsidation). Previous in vitro studies mapped the dimer linkage structure of human immunodeficiency virus type 1 (HIV-1) in a region downstream of the splice donor site, containing conserved purine tracts that were postulated to mediate dimerization, through purine quartets. However, we recently showed that dimerization of HIV-1 RNA also involves sequences upstream of the splice donor site. Here, we used chemical modification interference to identify nucleotides that are required in unmodified form for dimerization of a RNA fragment containing nucleotides 1-707 of HIV-1 RNA. These nucleotides map exclusively in a restricted area upstream of the splice donor site and downstream of the primer binding site. They are centered around a palindromic sequence (GUGCAC279) located in a hairpin loop. Our results support a model in which dimer formation is initiated by the annealing of the palindromic sequences, possibly by a loop-loop interaction between the two monomers. Further experiments show that the deletion of the stem-loop or base substitutions in the loop abolish dimerization, despite the presence of the previously postulated dimer linkage structure. On the other hand, deletions of the purine tracts downstream of the splice donor site do not prevent dimerization. Therefore, we conclude that the palindromic region represents the dimerization initiation site of genomic RNA.
Circadian expression of the luciferin-binding protein correlates with the binding of a protein to the 3' untranslated region of its mRNA.
Authors: Mittag M , Lee D H , Hastings J W
Published: May 2006

The circadian-expressed luciferin-binding protein from the dinoflagellate Gonyaulax polyedra is regulated at the translational level. We detected a protein, apparently a dimer, that binds specifically to the 3' untranslated region of its mRNA. Its binding site was localized within a 22-nt region in the 3' untranslated region containing seven UG repeats. The binding activity of this protein cycles on a daily basis, decreasing at the beginning of the night when synthesis of luciferin-binding protein starts and increasing at the end of the night when synthesis of luciferin-binding protein stops. This suggests that it functions as a clock-controlled repressor, preventing the translation of lbp mRNA during the day.
Estradiol causes the rapid accumulation of cAMP in human prostate.
Authors: Nakhla A M , Khan M S , Romas N P , Rosner W
Published: May 2006

Androgens are widely acknowledged to be central to the pathogenesis of benign prostatic hypertrophy (BPH). However, BPH increases in prevalence as men age, at precisely the stage of life when plasma androgens are decreasing. The decrease in total plasma androgens is amplified by an age-related increase in plasma sex hormone-binding globulin (SHBG) that results in a relatively greater decrease in free androgens than in total androgens. In addition, estrogens have long been suspected to be important in BPH, but a direct effect on the human prostate has never been demonstrated. We present data that are consistent with a role for estradiol, and for a decrease in androgens and an increase in SHBG, in the pathogenesis of BPH. We show that estradiol, but not dihydrotestosterone, acts in concert with SHBG to produce an 8-fold increase in intracellular cAMP in human BPH tissue. This increase is not blocked by an antiestrogen and is not provoked by an estrogen (diethylstilbestrol) that does not bind to SHBG, thus excluding the classic estrogen receptor as being operative in these events. Conversely, dihydrotestosterone, which blocks the binding of estradiol to SHBG, completely negates the effect of estradiol. Finally, we demonstrate that the SHBG-steroid-responsive second-messenger system is primarily localized to the prostatic stromal cells and not to the prostatic epithelial cells. Thus, we have shown a cell-specific, powerful, nontranscriptional effect of estradiol on the human prostate.
Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics.
Authors: Saghai Maroof M A , Biyashev R M , Yang G P , Zhang Q , Allard R W
Published: May 2006

This study was undertaken to assess the extent of genetic variation in barley simple sequence repeats (SSRs) and to study the evolutionary dynamics of SSR alleles. SSR polymorphisms were resolved by the polymerase chain reaction with four pairs of primers. In total, 71 variants were observed in a sample of 207 accessions of wild and cultivated barley. Analyses of wheat-barley addition lines and barley doubled haploids identified these variants (alleles) with four loci, each located on a different chromosome. The numbers of alleles detected at a locus corresponded to the number of nucleotide repeats in the microsatellite sequences. The numbers of alleles at two loci were 28 and 37; to our knowledge these are the largest numbers of alleles for single Mendelian loci reported in plants. Three alleles were resolved by each of the other two loci. Allelic diversity was greater in wild than in cultivated barley and surveys of two generations (F8 and F53) of Composite Cross II, an experimental population of cultivated barley, showed that few of the alleles present in the 28 parents survived into generation F53, whereas some infrequent alleles reached high frequencies. Such changes in frequency indicate that the chromosomal segments marked by the SSR alleles are under the influence of natural selection. The SSR variants allow specific DNA sequences to be followed through generations. Thus, the great resolving power of SSR assays may provide clues regarding the precise targets of natural and man-directed selection.
Identification of the prfC gene, which encodes peptide-chain-release factor 3 of Escherichia coli.
Authors: Mikuni O , Ito K , Moffat J , Matsumura K , McCaughan K , Nobukuni T , Tate W , Nakamura Y
Published: May 2006

The termination of protein synthesis in bacteria requires two codon-specific polypeptide release factors, RF-1 and RF-2. A third factor, RF-3, which stimulates the RF-1 and RF-2 activities, was originally identified in Escherichia coli, but it has received little attention since the 1970s. To search for the gene encoding RF-3, we selected nonsense-suppressor mutations by random insertion mutagenesis on the assumption that a loss of function of RF-3 would lead to misreading of stop signals. One of these mutations, named tos-1 (for transposon-induced opal suppressor), mapped to the 99.2 min region on the E. coli chromosome and suppressed all three stop codons. Complementation studies and analyses of the DNA and protein sequences revealed that the tos gene encodes a 59,442-Da protein, with sequence homology to elongation factor EF-G, including G-domain motifs, and that the tos-1 insertion eliminated the C-terminal one-fifth of the protein. Extracts containing the overproduced Tos protein markedly increased the formation of ribosomal termination complexes and stimulated the RF-1 or RF-2 activity in the codon-dependent in vitro termination assay. The stimulation was significantly reduced by GTP, GDP, and the beta,gamma-methylene analog of GTP, but not by GMP. These results fit perfectly with those described in the original publications on RF-3, and the tos gene has therefore been designated prfC. A completely null prfC mutation made by reverse genetics affected the cell growth under the limited set of physiological and strain conditions.
Mitochondrial minicircle DNA supports plasmid replication and maintenance in nuclei of Trypanosoma brucei.
Authors: Metzenberg S , Agabian N
Published: May 2006

In a search for trypanosome DNA sequences that permit replication and stable maintenance of extrachromosomal elements, a 1-kilobase-pair (kbp) fragment from a mitochondrial kinetoplast DNA (kDNA) minicircle of Trypanosoma brucei was isolated and characterized. The plasmid pTbo-1, carrying the kDNA element, is maintained in T. brucei as a supercoiled concatemer containing approximately seven to nine pTbo-1 monomer units (5.6 kbp each) in a head-to-tail orientation. The concatemer is found in approximately one copy per cell when procyclic trypanosomes are cultured in the presence of 100 micrograms of hygromycin per ml; however, in the absence of continuous hygromycin selection, the plasmid is lost from the population with a t1/2 of approximately 8.7 days (17 cell generations). A second unrelated kDNA minicircle was also able to serve as an autonomously replicating sequence (ARS) element in T. brucei, suggesting that this is a general property of kDNA minicircles. Replication of mitochondrial DNA in the nucleus may be due to either a specific consensus sequence (such as in yeast ARS elements) or nonspecific sequence characteristics (such as the degree of A&T-richness or bent DNA).
Agalactosyl glycoforms of IgG autoantibodies are pathogenic.
Authors: Rademacher T W , Williams P , Dwek R A
Published: May 2006

The glycosylation of IgG results in many different glycoforms. A large body of correlative data (including remission of arthritis during pregnancy) has suggested that IgG molecules lacking galactose were associated with rheumatoid arthritis. We now demonstrate that agalactosyl IgG glycoforms are directly associated with pathogenicity in murine collagen-induced arthritis. We show that passive transfer of an acute synovitis in T-cell-primed mice can be enhanced by using IgG containing autoantibodies to type II collagen when the antibodies are present as the agalactosyl glycoform. Thus, nonpathogenic doses of autoantibodies can be made pathogenic by altering their glycosylation state.
Ca2+ triggers premature inactivation of the cdc2 protein kinase in permeabilized sea urchin embryos.
Authors: Suprynowicz F A , Prusmack C , Whalley T
Published: May 2006

Exit from mitosis requires inactivation of the cyclin B-p34cdc2 protein kinase complex. Since increased cytosolic Ca2+ has been implicated as a potential trigger of mitotic progression, we directly tested the possibility that Ca2+ triggers the pathway responsible for inactivating the cdc2 kinase, using sea urchin embryos permeabilized at various stages of the cell cycle. In cells permeabilized during late interphase and prophase, micromolar Ca2+ induced premature inactivation of the cdc2 kinase without affecting the absolute amount of p34cdc2 protein. Inactivation was selective for the cdc2 kinase, as elevated Ca2+ had no effect on cAMP-dependent protein kinase activity. Premature cdc2 kinase inactivation did not require cyclin B destruction, but did coincide with the dissociation of cyclin B-p34cdc2 complexes. In cells permeabilized during prometaphase and metaphase, cdc2 kinase inactivation was Ca(2+)-independent, presumably because at these later times the inactivating pathway had been enabled prior to permeabilization. This work provides evidence that Ca2+ is the physiological trigger enabling cdc2 kinase inactivation during mitosis.
Mutator phenotypes in human colorectal carcinoma cell lines.
Authors: Bhattacharyya N P , Skandalis A , Ganesh A , Groden J , Meuth M
Published: May 2006

Recent studies have revealed that tumors in patients with hereditary nonpolyposis colon cancer are associated with high-frequency alterations of microsatellite sequences. To investigate the mechanisms and consequences of this form of genetic instability, we identified three colorectal carcinoma cell lines that express dinucleotide-repeat instability like that found in hereditary nonpolyposis colon cancer tumors and show increased rates of spontaneous mutation at selectable loci. However, the pattern of hypermutation in these cell lines differed significantly. In one line (HCT116), microsatellite mutations occurred at a remarkably high rate (approximately 10(-2) mutations per cell per generation), whereas this rate was considerably lower in the two other lines (DLD-1 and HCT15). The rate of mutation at the locus encoding hypoxanthine guanine phosphoribosyltransferase was substantially elevated (200- to 600-fold) in all three tumor cell lines, yet the types of mutations arising differed. A specific frame-shift hotspot accounted for 24% of hypoxanthine guanine phosphoribosyltransferase mutations in HCT116. The frequency of mutations at this site was reduced significantly in DLD-1 and HCT15 lines. These data suggest that the mutatw phenotypes in the colorectal carcinoma cell lines could be the consequence of mutator genes affecting different repair or error-avoidance pathways.
Expression of an auxin- and cytokinin-regulated gene in cambial region in Zinnia.
Authors: Ye Z H , Varner J E
Published: May 2006

The expression patterns of a cDNA clone, p48h-10, of an auxin-induced gene were examined in isolated mesophyll cells of Zinnia and in the organs of Zinnia plants. In the isolated mesophyll cells, the mRNA accumulates in 48 hr of culture with 1-naphthaleneacetic acid alone. Because the first cell division occurs before 36 hr of culture, the gene probably is not involved in cell division. Benzyladenine does not induce expression of this gene, but the combination of 1-naphthaleneacetic acid and benzyladenine induces the mRNA accumulation about 24 hr earlier than does 1-naphthaleneacetic acid alone. Tissue print hybridization shows that the mRNA is present predominantly in the cambial region in stems, leaves, and roots and in the vascular bundles in flower buds but does not occur in the apical regions of shoot or root. The characteristics of the gene expression, including auxin- and cytokinin-regulated induction and cambial region localization, encourage us to suggest that the gene is involved in the early process of vascular differentiation.
The history of a genetic system.
Authors: Popadić A , Anderson W W
Published: May 2006

Although the chromosomal polymorphism for inversions in Drosophila pseudoobscura is one of the best studied systems in population genetics, the identity of the ancestral gene arrangement has remained unresolved for more than 50 years. There are more than 40 gene arrangements, and 4 of them (Standard, Hypothetical, Santa Cruz, and Tree Line) have been considered as candidates for the ancestral type. We propose a framework of competing hypotheses to distinguish among the alternatives. Two conclusions come from contrasting each hypothesis with the results from DNA sequencing and restriction mapping. First, not only Standard but also Hypothetical can be excluded as the ancestral gene arrangement. Second, although either Tree Line or Santa Cruz could be the ancestral type, the available data provide greater support for Santa Cruz.
Snapshot blotting: transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to grids for electron microscopy.
Authors: Jett S D , Bear D G
Published: May 2006

We present a technique, "snapshot blotting," for the electrophoretic transfer of nucleic acids and nucleoprotein complexes in gel electrophoresis bands onto highly stable carbon film-coated grids for imaging by electron microscopy. The method permits structural analysis of macromolecular species that have been resolved by a gel mobility-shift assay. To demonstrate the efficiency and integrity of the transfer process for a multiprotein-DNA assembly, we have imaged various species of a prokaryotic transcription complex, using the cleavage-defective EcoRI(Q111) protein as an orientation marker and as a blockade of transcription elongation. Snapshot blotting should be of great utility in the structural characterization of nucleic acids and protein-nucleic acid interactions.
Male ornament size as a reliable cue to enhanced offspring viability in the barn swallow.
Authors: Møller A P
Published: May 2006

Many extravagant secondary sexual characters are assumed to have evolved as a result of female choice, either because they attract females or because they reliably reflect the quality of males. Females mating with the most ornamented individuals with a superior genotype are expected to benefit by producing more viable offspring. A viability advantage associated with mate choice can be demonstrated only if (i) parent ornament size reliably reflects parent viability and (ii) offspring viability is directly related to the expression of the ornament of the parent. Barn swallows (Hirundo rustica) are monogamous passerine birds, which are sexually size dimorphic in tail length. Previous experiments and observations have shown that females prefer males with the largest tail ornaments and that male survivors have larger tail ornaments than nonsurvivors. Here I demonstrate that offspring longevity is positively related to ornament size of the male parent and that the longevity of sons is a trait with a statistically significant resemblance to that of their fathers. The viability effects could be entirely due to differences in quality of parental care. However, relative paternal provisioning of offspring was negatively related to the tail length of males, while total provisioning rate by both pair members, and thus offspring body size, body mass, and body condition, was unrelated to male tail length. Therefore, females may, through their mate choice, gain an indirect fitness advantage in terms of enhanced offspring viability.
Platelet-derived growth factor alpha receptor gene expression: isolation and characterization of the promoter and upstream regulatory elements.
Authors: Wang C , Stiles C D
Published: May 2006

Receptors for the platelet-derived growth factors (PDGFs) are expressed conditionally in developing embryos and adult tissues. Aberrant expression of PDGF receptors is a molecular marker for proliferative disorders such as atherosclerosis, myofibrosis, and malignant astrocytoma. We isolated genomic clones that encompass the 5' end of the mouse PDGF alpha receptor mRNA transcript and extend 10 kb into the upstream flanking region of the gene. Using these clones, we constructed a partial genomic map that locates the promoter and transcription start sites of the gene. One of our genomic clones contains cis-acting regulatory elements that drive expression of reporter gene constructs selectively in cells that express PDGF alpha receptors.
A decentralized process for finding equilibria given by linear equations.
Authors: Reiter S
Published: May 2006

I present a decentralized process for finding the equilibria of an economy characterized by a finite number of linear equilibrium conditions. The process finds all equilibria or, if there are none, reports that, in a finite number of steps at most equal to the number of equations. The communication and computational complexity compare favorably with other decentralized processes. The process may also be interpreted as an algorithm for solving a distributed system of linear equations. Comparisons with the Linpack program for LU (lower and upper triangular decomposition of the matrix of the equation system, a version of Gaussian elimination) are presented.
Dissection of an antibody-catalyzed reaction.
Authors: Stewart J D , Krebs J F , Siuzdak G , Berdis A J , Smithrud D B , Benkovic S J
Published: May 2006

Antibody 43C9 accelerates the hydrolysis of a p-nitroanilide by a factor of 2.5 x 10(5) over the background rate in addition to catalyzing the hydrolysis of a series of aromatic esters. Since this represents one of the largest rate accelerations achieved with an antibody, we have undertaken a series of studies aimed at uncovering the catalytic mechanism of 43C9. The immunogen, a phosphonamidate, was designed to mimic the geometric and electronic characteristics of the tetrahedral intermediate that forms upon nucleophilic attack by hydroxide on the amide substrate. Further studies, however, revealed that the catalytic mechanism is more complex and involves the fortuitous formation of a covalent acyl-antibody intermediate as a consequence of complementary side chain residues at the antibody-binding site. Several lines of evidence indicate that the catalytic mechanism involves two key residues: His-L91, which acts as a nucleophile to form the acyl-antibody intermediate, and Arg-L96, which stabilizes the anionic tetrahedral moieties. Support for this mechanism derives from the results of site-directed mutagenesis experiments and solvent deuterium isotope effects as well as direct detection of the acyl-antibody by electrospray mass spectrometry. Despite its partial recapitulation of the course of action of enzymic counterparts, the reactivity of 43C9, like other antibodies, is apparently limited by its affinity for the inducing immunogen. To go beyond this level, one must introduce additional catalytic functionality, particularly general acid-base catalysis, through either improvements in transition-state analog design or site-specific mutagenesis.
Chromatographic resolution of in vivo phosphorylated and nonphosphorylated eukaryotic translation initiation factor eIF-4E: increased cap affinity of the phosphorylated form.
Authors: Minich W B , Balasta M L , Goss D J , Rhoads R E
Published: May 2006

Eukaryotic translation initiation factor eIF-4E plays a central role in the recognition of the 7-methylguanosine-containing cap structure of mRNA and the formation of initiation complexes during protein synthesis. eIF-4E exists in both phosphorylated and nonphosphorylated forms, and the primary site of phosphorylation has been identified. Previous studies have suggested that eIF-4E phosphorylation facilitates its participation in protein synthesis. However, the biochemical basis for the functional difference between the two forms of eIF-4E is unknown. To address this directly, we have developed a method for the separation of phosphorylated and nonphosphorylated eIF-4E from rabbit reticulocytes by chromatography on rRNA-Sepharose. Using the resultant purified forms, we have studied the protein's interaction with the cap analogs m7GTP and m7GpppG and with the cap of globin mRNA by fluorescence quenching of tryptophan residues. It was found that phosphorylated eIF-4E had 3- to 4-fold greater affinity for cap analogs and mRNA than nonphosphorylated eIF-4E. The equilibrium binding constants (x 10(5), expressed as M-1) for the interaction of phosphorylated eIF-4E with m7GTP, m7GpppG, and globin mRNA were 20.0 +/- 0.1, 16.4 +/- 0.1, and 31.0 +/- 0.1, respectively, whereas those for the nonphosphorylated form were 5.5 +/- 0.4, 4.3 +/- 0.4, and 10.0 +/- 0.1, respectively. Treatment with potato acid phosphatase converted the phosphorylated form to the nonphosphorylated form and decreased the binding constant for m7GTP by a factor of 3. The increased affinity for mRNA caps may account for the in vivo and in vitro correlations between eIF-4E phosphorylation and accelerated protein synthesis and cell growth.
Circadian clock locus frequency: protein encoded by a single open reading frame defines period length and temperature compensation.
Authors: Aronson B D , Johnson K A , Dunlap J C
Published: May 2006

The frequency (frq) locus encodes a key component, a state variable, in a cellular oscillator generating circadian rhythmicity. Two transcripts have been mapped to this region, and data presented here are consistent with the existence of a third transcript. Analysis of cDNA clones and clock mutants from this region focuses attention on one transcript encoding a protein. FRQ, which is a central clock component: (i) mutations in all of the semidominant frq alleles are the result of single amino acid substitutions and map to the open reading frame (ORF) encoding FRQ; (ii) deletion of this ORF, or a frameshift mutation within it, results in a strain with a recessive clock phenotype characterized by the loss of rhythm stability and compensation. Single amino acid substitutions within, or disruption of, this single ORF are thus sufficient to drive major alterations in both period length and temperature compensation, two canonical characteristics of circadian systems. The 989-amino acid FRQ protein species the circadian function of frq in the assembly of the Neurospora biological clock.
Antisense phosphorothioate oligonucleotides: selective killing of the intracellular parasite Leishmania amazonensis.
Authors: Ramazeilles C , Mishra R K , Moreau S , Pascolo E , Toulmé J J
Published: May 2006

We targeted the mini-exon sequence, present at the 5' end of every mRNA of the protozoan parasite Leishmania amazonensis, by phosphorothioate oligonucleotides. A complementary 16-mer (16PS) was able to kill amastigotes--the intracellular stage of the parasite--in murine macrophages in culture. After 24 hr of incubation with 10 microM 16PS, about 30% infected macrophages were cured. The oligomer 16PS acted through antisense hybridization in a sequence-dependent way; no effect on parasites was observed with noncomplementary phosphorothioate oligonucleotides. The antisense oligonucleotide 16PS was a selective killer of the protozoans without any detrimental effect to the host macrophage. Using 16PS linked to a palmitate chain, which enabled it to complex with low density lipoproteins, improved the leishmanicidal efficiency on intracellular amastigotes, probably due to increased endocytosis. Phosphorothioate oligonucleotides complementary to the intron part of the mini-exon pre-RNA were also effective, suggesting that antisense oligomers could prevent trans-splicing in these parasites.