bluuebunny/crossref_metadata_2025 huggingface dataset:
Evidence for gene conversion in genes for cell-adhesion molecules.
Authors: Gally J A , Edelman G M
Published: May 2006

The genomic sequences encoding a chicken Ca(2+)-dependent cell adhesion molecule (K-CAM) were recently found to be located approximately 600 base pairs upstream from the translation initiation site of a homologous protein, liver CAM. The sizes of 11 exons of the K-CAM gene are almost identical to those in the L-CAM (liver cell-adhesion molecule) gene with exon-intron junctions occurring at exactly equivalent positions. The sizes and sequences of most introns were, however, much more dissimilar. More detailed comparisons of these two genes reveal that the sequences of the last two exons (exons 15 and 16) are far more alike than are any of the other exons; they are, in fact, almost identical. The introns that separate these exons in the two genes likewise resemble one another far more than do any other corresponding introns. This degree of similarity appears to be far greater than can be accounted for by selection for protein structure, and it strongly suggests that a gene conversion event occurred between these two genes subsequent to their duplication and divergence to perform different biological functions.
Biochemical analysis of UV mutagenesis in Escherichia coli by using a cell-free reaction coupled to a bioassay: identification of a DNA repair-dependent, replication-independent pathway.
Authors: Cohen-Fix O , Livneh Z
Published: May 2006

Incubation of UV-irradiated plasmid DNA with a protein extract prepared from Escherichia coli cells led to the production of mutations in the cro gene residing on the plasmid. The mutations were detected in a subsequent bioassay step, which involved transformation of an indicator strain with the plasmid DNA that was retrieved from the reaction mixture, followed by plating on lactose/MacConkey plates. UV mutations produced in this cell-free reaction required the recA and umuC gene products and were prevented by rifampicin, an inhibitor of RNA polymerase, which inhibited plasmid replication. Removal of pyrimidine photodimers from the plasmid by enzymatic photoreactivation after the in vitro stage, but prior to transformation, increased plasmid survival as expected. Surprisingly, it also caused a large increase in the frequency of UV mutations detected in the bioassay. This photoreactivation-stimulated in vitro UV mutagenesis was dependent on the excision repair genes uvrA, uvrB, and uvrC and occurred in the absence of DNA replication. This suggests that two distinct UV mutagenesis pathways occurred in vitro: a replication-dependent pathway (type I) and a repair-dependent pathway (type II). DNA sequence analysis of type II UV mutations revealed a spectrum similar to that of in vivo UV mutagenesis. When the photoreactivation step was included in the protocol, type II UV mutagenesis did not require the RecA and UmuC proteins. These results are in agreement with the in vivo delayed photoreactivation phenomenon, where the removal of photodimers after an incubation period eliminated the requirement for RecA and UmuC in UV mutagenesis. The above system will enable the biochemical analysis of UV mutagenesis and the isolation of proteins involved in the process.
Construction of small-insert genomic DNA libraries highly enriched for microsatellite repeat sequences.
Authors: Ostrander E A , Jong P M , Rine J , Duyk G
Published: May 2006

We describe an efficient method for the construction of small-insert genomic libraries enriched for highly polymorphic, simple sequence repeats. With this approach, libraries in which 40-50% of the members contain (CA)n repeats are produced, representing an approximately 50-fold enrichment over conventional small-insert genomic DNA libraries. Briefly, a genomic library with an average insert size of less than 500 base pairs was constructed in a phagemid vector. Amplification of this library in a dut ung strain of Escherichia coli allowed the recovery of the library as closed circular single-stranded DNA with uracil frequently incorporated in place of thymine. This DNA was used as a template for second-strand DNA synthesis, primed with (CA)n or (TG)n oligonucleotides, at elevated temperatures by a thermostable DNA polymerase. Transformation of this mixture into wild-type E. coli strains resulted in the recovery of primer-extended products as a consequence of the strong genetic selection against single-stranded uracil-containing DNA molecules. In this manner, a library highly enriched for the targeted microsatellite-containing clones was recovered. This approach is widely applicable and can be used to generate marker-selected libraries bearing any simple sequence repeat from cDNAs, whole genomes, single chromosomes, or more restricted chromosomal regions of interest.
Gibberellic acid and abscisic acid coordinately regulate cytoplasmic calcium and secretory activity in barley aleurone protoplasts.
Authors: Gilroy S , Jones R L
Published: May 2006

The effects of gibberellic acid (GA3) and abscisic acid (ABA) on the temporal and spatial dynamics of cytosolic calcium concentration ([Ca2+]i) in aleurone protoplasts of barley (Hordeum vulgare L. cv. Himalaya) were measured by using fluorescence ratio analysis and confocal microscopy. After 4-6 h of treatment, GA3 induced a sustained increase in [Ca2+]i from 50 to 150 nM in aleurone protoplasts. The increase in [Ca2+]i preceded the GA3-induced increase in alpha-amylase synthesis and secretion by 4 h. The elevation of [Ca2+]i was highest in the peripheral cytoplasm and may play a role in coordinating the secretory events there. Reducing Ca2+ levels in the incubation medium to below 500 microM inhibited the increase in [Ca2+]i and the GA3-induced stimulation of alpha-amylase synthesis and secretion. These data suggest that GA3 may increase [Ca2+]i by increasing the influx of Ca2+ at the plasma membrane. ABA reversed the effect of GA3 on [Ca2+]i within 3 h, 2 h before its effect on alpha-amylase production could be detected. Thus changes in [Ca2+]i may play a role in mediating the effects of GA3 and ABA on the synthesis and secretion of alpha-amylase in the aleurone cell.
No stop codons in the antisense strands of the genes for nylon oligomer degradation.
Authors: Yomo T , Urabe I , Okada H
Published: May 2006

Genes for nylon oligomer-degrading enzymes are unique in the sense that the enzymes encoded by them are found not to have any appropriate substrates during most of the period of their evolution. Furthermore, these nylB genes form a family not related to any other known gene families. The base sequences of these genes were examined and a common characteristic was found: a long stretch of sequence without chain-terminating base triplets, defined as a nonstop frame (NSF), is being maintained on the antisense strand. Moreover, a certain coding frame is open for both the sense and the antisense sequences, while the other frames have many stop codons. The probability of the presence of these NSFs on the antisense strand of a gene is very small (0.0001-0.0018). In addition, another gene for nylon oligomer degradation was found to have a NSF on its antisense strand, and this gene is phylogenically independent of the nylB genes. Therefore, the presence of these NSFs is very rare and improbable. Even if the common ancestral gene of the nylB family was originally endowed with a NSF on its antisense strand, the probability of this original NSF persisting in one of its descendants of today is only 0.007. Unless an unknown force was maintaining the NSF, it would have quickly disappeared by random emergences of chain terminators. Therefore, the presence of such rare NSFs on all three antisense strands of the nylB gene family suggests that there is some special mechanism for protecting these NSFs from mutations that generate the stop codons. Such a mechanism may enable NSFs to evolve into new functional genes and hence seems to be a basic mechanism for the birth of new enzymes.
Importance of specific purine amino and hydroxyl groups for efficient cleavage by a hammerhead ribozyme.
Authors: Fu D J , McLaughlin L W
Published: May 2006

Eight modified ribozymes of 19 residues have been prepared with individual purine amino or hydroxyl groups excised. The modified ribozymes were chemically synthesized with the substitution of a single 2'-deoxyadenosine, 2'-deoxyguanosine, inosine, or purine riboside for residues G10, A11, G13, or A14. Five of the modified ribozymes cleaved the 24-mer substrate with little change in rate as monitored by simple first-order kinetics. However, deletion of the 2-amino group at G10 (replacement with inosine) or deletion of either of the 2'-hydroxyls at G10 or G13 (replacement with 2'-deoxyguanosine) resulted in ribozymes with a drastic decrease in cleavage efficiency. Increasing the concentration of the Mg2+ cofactor from 10 mM to 50 mM significantly enhanced cleavage efficiency by these three derivatives. Steady-state kinetic assays for these three ribozymes indicated that the modifications result in both an increase in Km and a decrease in kcat. These results suggest that the exocyclic amino group at-G10 and the hydroxyls at G10 and G13 are important both for ribozyme-substrate binding and for the Mg(2+)-catalyzed cleavage reaction.
P-element homologous sequences are tandemly repeated in the genome of Drosophila guanche.
Authors: Miller W J , Hagemann S , Reiter E , Pinsker W
Published: May 2006

In Drosophila guanche, P-homologous sequences were found to be located in a tandem repetitive array (copy number: 20-50) at a single genomic site. The cytological position on the polytene chromosomes was determined by in situ hybridization (chromosome O: 85C). Sequencing of one complete repeat unit (3.25 kilobases) revealed high sequence similarity between the central coding region comprising exons 0 to 2 and the corresponding section of the Drosophila melanogaster P element. The rest of the sequence has diverged considerably. Exon 3 has no coding function and the inverted repeats have disappeared. The P homologues of D. guanche apparently have lost their mobility but have retained the coding capacity for a protein similar to the 66-kDa P-element repressor of D. melanogaster. Divergence between different repeat units indicates early amplification of the sequence at this particular genomic site. The presence of a common P-element site at 85C in Drosophila subobscura, Drosophila madeirensis, and D. guanche suggests that clustering of the sequence at this location took place before the phylogenetic radiation of the three species.
Graviton scattering and matter distribution.
Authors: Britten R J
Published: May 2006

In this model gravitation results from the emission and absorption of quanta (gravitons) that are scattered a few times in crossing a typical galaxy. Many features of the universe can be explained in terms of this model, although theoretical justification for the scattering of gravitons is lacking. Gravitons follow a random walk and diffuse through the outer regions of a galaxy. As a result the force of attraction follows a 1/R law, matching observed galactic rotation curves and explaining galactic dynamics without the need of dark matter. The model makes predictions regarding early stages in the expansion of the universe and the establishment of the mass distribution. It may be assumed that a nearly uniform expanding cloud of gas was present that was subject to collapse under gravitational forces. The 1/R law of attraction due to graviton diffusion is orders of magnitude more effective for initiation of collapse than the inverse square law, and it applies to blocks of gas larger than the graviton mean free path. Delay in the spread of gravitational attraction by diffusion sets a time-dependent range beyond which the attractive force is zero. In the model this causes arrays of matter to collapse locally into zones with a spacing set by the length of the range of the attractive force. An initial examination indicates that under these conditions the background radiation could have been released from a nearly uniform distribution at the time of decoupling of radiation and matter, followed by gravitational collapse into blocks of galactic mass. In the model the diffusion of gravitons continued and collapse became possible on a larger scale, initiating the formation of galactic clusters and still larger structures. The slow rate of diffusion then prevented the largest structures from attracting each other and permitted the formation of the voids on a very large scale. The model predicts that on the largest scale there is a three-dimensional repeated array of structures separated by voids. Ultimately structures larger than galactic clusters outran the diffusion of the gravitons and have since been freely expanding.
Expression of the epidermal growth factor receptor gene is regulated in mouse blastocysts during delayed implantation.
Authors: Paria B C , Das S K , Andrews G K , Dey S K
Published: May 2006

The delayed implantation model was used to study epidermal growth factor receptor(s) (EGF-R) in the mouse blastocyst. Delayed implantation and blastocyst dormancy were induced by ovariectomy on day 4 of pregnancy and were maintained by daily (days 5-7) injections of progesterone (P4). Blastocyst activation and implantation were initiated by coinjection of estradiol-17 beta (E2) with P4 on the 3rd day of delay. Immunostaining of EGF-R, autoradiographic detection of 125I-labeled EGF binding, and measurement of EGF-inducible subcellular protein tyrosine phosphorylation demonstrated the loss of EGF-R from blastocysts (dormant) recovered 24 h after ovariectomy or on the 3rd day of P4-maintained delay. However, increased EGF-R levels were detected in blastocysts (activated) recovered 12 or 24 h after E2 injection. Blastocyst EGF-R mRNA levels were quantitated by reverse transcriptase (RT)-PCR and distribution of this mRNA was examined by in situ hybridization. To provide a homologous probe for these studies, a mouse EGF-R partial cDNA was cloned and used as the template for synthesis of antisense- and sense-strand EGF-R RNA. Quantitative RT-PCR demonstrated an 8- to 10-fold reduction in EGF-R mRNA copies per cell in dormant blastocysts. In contrast, an 8-fold increase in EGF-R mRNA copies per cell was detected in activated blastocysts 8 h after injection of E2. In situ hybridization detected EGF-R mRNA in most cells of normal day 4 blastocysts but not in those of dormant blastocysts. These studies establish that expression of the EGF-R gene in mouse blastocysts is tightly regulated by maternal steroid hormonal status.
Pivotal role of amino acid at position 138 in the allosteric hinge reorientation of cAMP receptor protein.
Authors: Ryu S , Kim J , Adhya S , Garges S
Published: May 2006

The cAMP receptor protein (CRP) of Escherichia coli needs cAMP for an allosteric change to regulate gene expression by binding to specific DNA sites. The hinge region connecting the DNA-binding domain to the cAMP-binding domain has been proposed to participate in the cAMP-induced allosteric change necessary to adjust C and D alpha-helices for movement of the DNA-binding F alpha-helix away from the protein surface. The role of the hinge region for a conformation change in CRP was tested by studying the effects of single amino acid substitutions at residue 138 located within the hinge. Physiological studies of wild-type and mutant cells and biochemical analysis of purified wild-type and mutant CRP revealed at least three groups of altered CRPs: (i) CRP that behaves like wild type (CRP+); (ii) CRP that binds cAMP but does not complete the structural changes required for specific DNA binding, proteolytic cleavage, and transcription activation (CRPallo); and (iii) CRP that shows some or all of these conformational changes without cAMP (CRP*). These results show a pivotal role of position 138 from which change emanates and provide further evidence that a hinge reorientation involving residue 138 is involved in the interhelical adjustments.
Substitution of the 3' terminal adenosine residue of transfer RNA in vivo.
Authors: Reuven N B , Deutscher M P
Published: May 2006

We have altered by site-directed mutagenesis the 3' terminal adenosine residue of a tRNA(Tyrsu3+) gene encoded on a single-copy plasmid and examined the consequences of these substitutions on suppressor activity in vivo. Our data show that mutant su3 genes containing 3'-CCC, -CCG, or -CCU termini instead of -CCA can be efficiently transcribed and processed in Escherichia coli to generate functional suppressor tRNAs. However, in contrast to normal tRNA genes, both tRNA nucleotidyltransferase and exoribonuclease activities are required to obtain suppression by the mutant tRNAs, indicating that removal of the incorrect 3' terminal residue and resynthesis of the normal -CCA terminus are occurring in this situation. In addition, a low level of suppressor activity and tRNA repair was found in cells devoid of tRNA nucleotidyltransferase, suggesting that an additional activity able to partially repair the 3' end of tRNA is present in E. coli. The use of mutant strains lacking one or several exoribonucleases revealed that the various RNAses have very different specificities for removal of incorrect 3' residues and that these differ greatly from their action on CCA-ending tRNA. These data show that the 3' terminal adenosine residue is necessary for tRNA function in vivo and that cells can compensate for its alteration by changes in the normal pathway of tRNA metabolism.
Transmembrane signaling by an insulin receptor lacking a cytoplasmic beta-subunit domain.
Authors: Sasaoka T , Takata Y , Kusari J , Anderson C M , Langlois W J , Olefsky J M
Published: May 2006

To assess the function of the cytoplasmic domain of the insulin receptor (IR) beta subunit, we have studied a mutant IR truncated by 365 aa (HIR delta 978), thereby deleting > 90% of the cytoplasmic domain. HIR delta 978 receptors were processed normally to homodimers that were expressed at the cell surface where they bind insulin with normal affinity. Although these truncated IRs were inactive with respect to ligand-induced internalization and autophosphorylation, insulin stimulated endogenous substrate (pp185) phosphorylation significantly more in HIR delta 978 cells than in untransfected Rat1 cells. Importantly, despite absence of the beta-subunit cytoplasmic domain, fibroblasts expressing HIR delta 978 receptors displayed enhanced sensitivity to insulin for stimulation of glucose incorporation into glycogen, alpha-aminoisobutyric acid uptake, thymidine incorporation, and S6 kinase activity compared with parental fibroblasts. Insulin also induced the expression of the protooncogene c-fos and the early growth response gene Egr-1 in HIR delta 978 cells far greater than in parental Rat1 fibroblasts. Furthermore, an agonistic monoclonal antibody specific for the human IR stimulated insulin action in fibroblasts expressing wild-type human IR but had no effect on HIR delta 978 cells. In conclusion, the HIR delta 978 truncated IRs appear to confer enhanced insulin sensitivity by augmenting the signaling properties of the endogenous rodent IRs.
Production of tumor necrosis factor and other proinflammatory cytokines by human mononuclear phagocytes stimulated with myelin P2 protein.
Authors: Baron P , Constantin G , D'Andrea A , Ponzin D , Scarpini E , Scarlato G , Trinchieri G , Rossi F , Cassatella M A
Published: May 2006

In this study we examined the effect of myelin P2 protein on some proinflammatory functions exerted by human mononuclear phagocytes. Northern blot analysis demonstrated that P2 protein selectively induced in monocytes and macrophages mRNA accumulation of tumor necrosis factor (TNF), interleukin 1 beta (IL-1 beta), and interleukin 8 (IL-8) in a time-dependent manner. Natural killer stimulating factor (IL-12) mRNA and protein secretion was strongly induced by lipopolysaccharide but not by P2 protein. Supernatants harvested from P2-stimulated monocytes contained significant amounts of TNF, IL-1 beta, and IL-8, whereas those from macrophages contained only TNF and IL-8. The effect of the P2 protein on TNF and IL-8 mRNA accumulation and secretion was not affected by polymyxin B, which, on the other hand, almost completely abolished the effect of lipopolysaccharide. Finally, P2 protein did not directly trigger hydrogen peroxide release but, through the induced release of TNF, potentiated monocyte respiratory burst capability. Since P2 protein is the antigen responsible for the induction of experimental allergic neuritis, these findings identify a potential mechanism involved in the inflammatory reaction and myelin damage during experimental allergic neuritis.
Changing Epstein-Barr viral ZEBRA protein into a more powerful activator enhances its capacity to disrupt latency.
Authors: Baumann R , Grogan E , Ptashne M , Miller G
Published: May 2006

The Epstein-Barr viral transcriptional activator ZEBRA induces expression of viral early lytic genes when introduced into cells bearing latent Epstein-Barr virus. We show here that a ZEBRA-herpes simplex viral protein 16 (VP16) fusion protein induces early viral lytic gene expression in Epstein-Barr virus-containing cells more efficiently than does wild-type ZEBRA. The fusion protein is also a more powerful transcriptional activator in these cells, as assayed with reporter constructs. Our experiments also suggest that ZEBRA manifests a function required for full activity on certain natural promoters but not on promoters bearing oligomerized ZEBRA binding sites; this function cannot be provided by VP16.
Phylogenetic analysis of rbcL sequences identifies Acorus calamus as the primal extant monocotyledon.
Authors: Duvall M R , Learn G H , Eguiarte L E , Clegg M T
Published: May 2006

The identity of the oldest lineage of monocotyledons is a subject of debate. Alternative interpretations of morphological homologies are variously consistent with proposals that species of Alismatanae, Dioscoreales, or Melanthiales were the earliest descendants of the first monocotyledons. We present phylogenetic analyses based on DNA sequences of the plastid locus rbcL in which Acorus calamus, an herb with unspecialized floral features and of uncertain affinities, is supported as a member of the oldest extant lineage of monocotyledons. This conclusion is consistent with a substantial body of morphological, anatomical, and embryological evidence and offers an explanation for the failure to identify any close relationship between Acorus and other genera.
University of california at Santa Barbara Anisotropy Program: degree scale results from the South Pole 1990-1991.
Authors: Gaier T , Schuster J , Gundersen J , Meinhold P , Lubin P
Published: May 2006

We report on the preliminary result of a search for anisotropy in the cosmic background radiation (CBR). Our receiver operates with four equally spaced channels from 25 to 35 GHz with a beam size of approximately 1.5 degrees full width at half maximum. The system operated successfully for 500 hr at the South Pole during 1990-1991 austral summer. The data from one region, representing 25 hr after editing, are presented here. A strong signal is present in the lower-frequency channels with a spectrum unlike CBR fluctuations. The highest-frequency channel has the smallest contribution from this signal and has been used to set a 95% confidence level upper limit DeltaT/T </= 1.4 10-5.
Is the velocity-distance relation for galaxies linear?
Authors: van den Bergh S
Published: May 2006

Diameters of ScI galaxies, the luminosities of supernovae of type Ia at maximum light, and the brightness of central galaxies in rich clusters are examined as potential yardsticks or standard candles for study of the velocity-distance relationship. Both supergiant ScI galaxies and supernovae Ia (which have luminosities that differ by up to a factor of approximately 10) are found to be unsuitable for such a study. The remarkably small luminosity dispersion of first-ranked cluster galaxies (which is not yet understood physically) suggests that deviations from a linear velocity-distance relationship are less, approximately 20% out to red shifts of approximately 40,000 km.s-1.
The redshift-distance relation.
Authors: Segal I E
Published: May 2006

Key predictions of the Hubble law are inconsistent with direct observations on equitable complete samples of extragalactic sources in the optical, infrared, and x-ray wave bands-e.g., the predicted dispersion in apparent magnitude is persistently greatly in excess of its observed value, precluding an explanation via hypothetical perturbations or irregularities. In contrast, the predictions of the Lundmark (homogeneous quadratic) law are consistent with the observations. The Lundmark law moreover predicts the deviations between Hubble law predictions and observation with statistical consistency, while the Hubble law provides no explanation for the close fit of the Lundmark law. The flux-redshift law F [symbol, see text] (1 + z)/z appears consistent with observations on equitable complete samples in the entire observed redshift range, when due account is taken of flux limits by an optimal statistical method. Under the theoretical assumption that space is a fixed sphere, as in the Einstein universe, this law implies the redshift-distance relation z = tan2(r/2R), where R is the radius of the spherical space. This relation coincides with the prediction of chronometric cosmology, which estimates R as 160 +/- 40 Mpc (1 parsec = 3.09 x 10(16) m) from the proper motion to redshift relation of superluminal sources. Tangential aspects, including statistical methodology, fundamental physical theory, bright cluster galaxy samples, and proposed luminosity evolution, are briefly considered.
Tests of the long and short extragalactic distance scales.
Authors: de Vaucouleurs G
Published: May 2006

Distances on the short and long scales of 12 nearby galaxies, one group, and three clusters are compared with recent estimates by independent methods and researchers. All comparisons show a close agreement [within 0.3 magnitude (mag) in the distance modulus (DM)] between the short-scale moduli and the new estimates by others at all distances from the Large Magellanic Cloud [Delta (distance) = 0.05 megaparsec (Mpc); 1 pc = 3.09 x 10(16) m] to the Coma cluster (Delta = 83 Mpc). The mean systematic difference (short - others) is only -0.04 mag with no evidence for a significant Malmquist bias in the short scale. The long scale differs systematically from all the others by about +0.25 mag within the Local Group (DM < 26) and by +1.1 outside (26 < DM < 35). Accidental errors are also much larger in the long-scale moduli (0.5 mag) than in the other two scales (0.1 mag). The mean value of the Hubble expansion ratio for the test objects is  = 86 +/- 1 km.sec-1. Mpc-1.
Studies on leukemia developing spontaneously in an inbred family of rats.
Authors: Gross L , Dreyfuss Y
Published: May 2006

This study is a continuation of our recently reported observations on leukemia and lymphomas developing spontaneously in a subline of Sprague-Dawley rats bred by brother-to-sister mating in our laboratory. The previous preliminary report described our observations made in the course of the initial 12 generations of our leukemic subline. The current study reviews the data collected during 8 additional generations and results of experimental and morphologic studies. There was no problem in transmitting the spontaneously developing leukemia by inoculation of suspensions of leukemic cells into newborn or very young suckling Sprague-Dawley rats. Attempts to transmit the disease by inoculation of cell-free, filtered leukemic extracts gave thus far positive results only in one experiment in which two of six inoculated rats developed leukemia and a third one developed an angiosarcoma on the neck. In six additional experiments, of a total of 37 rats inoculated with leukemic filtrates, none developed leukemia and 9 females developed mammary fibroadenomas. Reviews of microscopic slides of blood and of sections of lymphoid tumors, livers, spleens, kidneys, and fragments of bone marrow of the leukemic animals are discussed as well as electron microscopic studies.
Evolution of nest construction in swallows (Hirundinidae): a molecular phylogenetic perspective.
Authors: Winkler D W , Sheldon F H
Published: May 2006

Nest construction is more diverse in the Hirundinidae than in any other family of oscine birds. To explore the evolution of this diversity, we superimposed nest data on a DNA-hybridization phylogeny of 17 swallow species. Nest construction is tightly linked to the inferred evolutionary history. Burrowing appears to be the primitive nesting mode, and burrowing ancestors gave rise to cavity-adopting and mud-nesting clades. Obligate cavity adoption is mostly confined to a monophyletic clade in the New World, and the diversification of obligate nest adopters appears to be tied to the richness of forest habitats and recent active mountain building there. Construction of mud nests originated only once in the history of the group, and mud-nesters have diversified principally in Africa, where a drier climatic history has favored their mode of nesting. The use of pure mud to construct a hanging nest is unique among all birds, and we infer that mud nests have increased in complexity during evolution from simple mud cups to fully enclosed retort-shaped nests. This increased complexity appears to have been the critical precursor for the evolution of high-density colonial mud-nesters.
Accelerated tumor development in interferon-treated B6.C-Hyal-1 a mice.
Authors: De Maeyer-Guignard J , Lauret E , Eusèbe L , De Maeyer E
Published: May 2006

The Hyal-1 locus, which we have previously described and mapped to mouse chromosome 9, influences the serum levels and molecular weight forms of hyaluronidase. We have also shown that the growth of two transplantable tumors, the 3LL carcinoma and the B16F10 melanoma, is influenced by the alleles at Hyal-1, in that the tumors develop more slowly in congenic B6.C-Hyal-1a (also called HW23) mice than in the parental Hyal-1b C57BL/6 mice. Here we present evidence that tumor development is stimulated and mortality is accelerated in B6.C-Hyal-1a mice grafted with 3LL carcinoma cells when treated with alpha/beta interferon (IFN-alpha/beta) or with IFN-beta, whereas in IFN-treated C57BL/6 mice 3LL tumor growth is inhibited. Likewise, in B6.C-Hyal-1a mice grafted with B16F10 melanoma cells, IFN-alpha/beta treatment results in stimulation of tumor growth, whereas in IFN-treated C57BL/6 mice tumor growth, whereas in IFN-treated C57BL/6 mice tumor growth is inhibited and mortality delayed. Thus, IFN-alpha/beta treatment of B6.C-Hyal-1a mice results in stimulation of tumor development and sometimes in accelerated mortality. This is the opposite of the usually described effect of IFN treatment in mice, which is inhibition of tumor development and delayed mortality, as was indeed observed in the C57BL/6 mice in the present experiments. These results provide the first indication that host genes can up- or down-regulate the antitumor activity of IFN and that, on some genetic backgrounds, IFN treatment enhances rather than inhibits tumor development. This may help to explain the apparent discordance between mouse model studies, which hitherto have consistently reported inhibition of tumor formation by IFN, and the clinical trials, in which only a limited percentage of individuals show tumor regression while others have no beneficial effect or even have progression of disease in spite of the IFN treatment.
Analysis of the ground-state band and a closely related intercalated band of 235(92)U143 by the two-revolving-cluster model with consideration of symmetric and antisymmetric resonance of the two dissimilar clusters.
Authors: Pauling L , Kamb B
Published: May 2006

The reported ground-state band of 235(92)U143 extending from J = 7/2- to 51/2- is found to be two intercalated bands, one beginning with 7/2- and the other with 9/2-, each with DeltaJ = 2. Analysis by the two-resonating-cluster model leads to 3875 Da.fm2 for the moment of inertia for the first few levels, then increasing by centrifugal stretching. This value is interpreted by the structure p70n112 for the central sphere with clusters p11n16 and p11n15 with radius of revolution R = 8.55 fm. The major principal axis of the Poinsot ellipsoid is taken to be determined by an unquantized number K, with vector intermediate in orientation between L and J. The values of K are found by empirical analysis to equal L + 0.28, with the theory of rotation of the ellipsoid giving L + 0.28 for 7/2-, slowly decreasing to L + 0.251 for 51/2-. The 7/2- band is based on odd values of L (negative parity) and the 9/2- band on even values (positive parity). Negative parity for both bands is achieved by symmetric resonance of the two dissimilar clusters in the 7/2- band and antisymmetric resonance in the 9/2- band.
Cytokine induction of an alternatively spliced murine vascular cell adhesion molecule (VCAM) mRNA encoding a glycosylphosphatidylinositol-anchored VCAM protein.
Authors: Terry R W , Kwee L , Levine J F , Labow M A
Published: May 2006

VCAM-1 is an immunoglobulin superfamily member that mediates adhesion of a variety of leukocytes to endothelial cells. VCAM expression has been associated with a variety of disease states and has been implicated in a number of normal processes. The predominant form of VCAM produced in human endothelial cells is a transmembrane protein containing seven immunoglobulin domains. In this study the murine VCAM gene has been characterized to allow the function(s) of VCAM to be studied in a small genetically accessible animal. While expression of an mRNA encoding a seven-immunoglobulin-domain transmembrane VCAM protein was seen in most tissues, the predominant change in VCAM expression upon interleukin 1 beta treatment was the induction of an alternatively spliced VCAM mRNA containing only the first three immunoglobulin domains. This message encodes a glycosylphosphatidylinositol (GPI)-anchored form of VCAM, VCAMGPI. VCAMGPI was efficiently cleaved from the cell surface by phosphatidylinositol-specific phospholipase C, mediated adhesion to leukocytes in a very late antigen 4-dependent manner, and was produced by mouse endothelial cell lines in culture. These data demonstrate that alternate forms of VCAM are produced under different physiological conditions and suggest that VCAMGPI may have a distinct role in inflammatory processes.
Two transmembrane signaling mechanisms control expression of the cAMP receptor gene CAR1 during Dictyostelium development.
Authors: Louis J M , Saxe C L , Kimmel A R
Published: May 2006

Dictyostelium discoideum is among the best characterized organisms for the study of receptor/guanine nucleotide binding protein-mediated control of differentiation. Dictyostelium grow unicellularly but form fully differentiated multicellular organisms through a developmental program regulated by secreted cAMP activating specific cell-surface receptors. Dictyostelium respond differentially to cAMP at different developmental stages. During early development, expression of certain genes is induced by low-level oscillations of extracellular cAMP. Later, continuous, high cAMP concentrations will promote expression of specific genes in multicellular structures. Here, we show that the cAMP receptor gene CAR1, which is essential for development, utilizes two promoters that are activated at distinct stages of development and respond to different extracellular cAMP conditions. One promoter is active with low-level oscillations of cAMP; exposure to high cAMP concentrations will repress this promoter and induce a second promoter. The CAR1 mRNAs are alternatively spliced but encode identical proteins. Thus, through differential sensitivity to its own ligand, cAMP, two promoters and alternative splicing regulate CAR1 expression during Dictyostelium development.
The 3'-terminal end (NCCA) of tRNA determines the structure and stability of the aminoacyl acceptor stem.
Authors: Limmer S , Hofmann H P , Ott G , Sprinzl M
Published: May 2006

We have done a systematic study on the contribution of the single-stranded NCCA end (where N is any nucleotide) to the stability of the aminoacyl stem of tRNA. A 7-bp RNA duplex with the single-strand ACCA 3' terminus derived from the aminoacyl stem of Escherichia coli tRNA(Ala) and several chemically synthesized sequence variants are characterized by proton NMR and thermodynamic parameters. The single-stranded 3' terminus noticeably stabilizes the duplex in a sequence-dependent manner. Though the largest contribution to the stability gain due to the ACCA end is provided by the first dangling 3' nucleotide, the influence of even the fourth nucleotide is measurable. The nature of the N73 discriminator base influences the stem structure and stability, which may be important for the recognition of tRNA by aminoacyl-tRNA synthetase. The stepwise attachment of the nucleotides to the 3' tail improves the stacking of the unpaired bases over the helix stem. Hence, the ACCA end appears to be structured. Replacing Mg2+ with Mn2+ causes broadening of certain imino proton peaks in the NMR spectrum, indicating a specific divalent metal ion binding site in the vicinity of the major identity element of the duplex (G3-U70) that is required for its recognition by the Ala-tRNA synthetase.
Coexpression of neurotrophins and their receptors in neurons of the central nervous system.
Authors: Kokaia Z , Bengzon J , Metsis M , Kokaia M , Persson H , Lindvall O
Published: May 2006

Nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF) are neuronal survival molecules which utilize the Trk family of tyrosine kinase receptors. Using double-label in situ hybridization, we demonstrate that mRNAs for BDNF and its high-affinity receptor TrkB are coexpressed in hippocampal and cortical neurons. Also, a large number of neurons in these areas coexpress NGF and BDNF mRNAs. Epileptic seizures lead to increased levels of both BDNF/TrkB and NGF/BDNF mRNAs in double-labeled cells. Our results show that individual neurons of the central nervous system can coexpress neurotrophins and their receptors and produce two neurotrophic factors. These factors could support neuronal survival after brain insults, not only via retrograde transport but also through autocrine mechanisms.
Alloantibodies can discriminate class I major histocompatibility complex molecules associated with various endogenous peptides.
Authors: Sherman L A , Chattopadhyay S , Biggs J A , Dick R F , Bluestone J A
Published: May 2006

Molecules encoded by a single major histocompatibility complex class I gene can associate with any one of a large number of peptide ligands. T-cell receptors have the capacity to discriminate among these peptide-class I complexes and in many cases bind only a single peptide-class I complex with sufficient affinity to trigger effector function. In contrast, it is generally assumed that class I-specific alloantibodies are indifferent to peptide heterogeneity, being directed toward allele-specific determinants on the molecule. In this report, three monoclonal antibodies were used to precipitate Kb molecules from cell lysates. Surprisingly, in each case a different set of peptides was found to be associated with Kb as detected by peptide-dependent Kb-specific alloreactive cytolytic T lymphocytes or by biochemical resolution. These results demonstrate that the affinity of binding by alloantibodies can be affected by the endogenous peptide ligand.
Can a protein influence the fate of its own coding sequence?: the amino- and carboxyl-terminal regions of H1 histone.
Authors: Ohno S , Becak M L
Published: May 2006

The amino- and carboxyl-terminal regions of H1 histone are afforded an opportunity to bind to their own coding segments. While such binding is of no consequence to the type of H1 histone that is expressed only in terminally differentiated cells (here referred to as H5), the same binding occurring in H1 of proliferating cells might affect the course of evolution of its amino- and carboxyl-terminal regions. With the above in mind, amino acid sequences of H5 from three species were compared with those of H1 from five species. The spherical core was more conserved in H1 than in H5, whereas the amino- and carboxyl-terminal regions of both were hypervariable. A distinct evolutionary pattern, however, was observed only in these regions of H1 but not of H5. Tandem repeats of short palindromes often generated nearly identical long palindromes in distantly related species. Thus, as far as the 37-residue-long amino-terminal region was concerned, the greatest homology was between the rat and human rather than between the rat and the mouse. With regard to the last 25 residues in the carboxyl-terminal region, the greatest homology was between the chicken and the rainbow trout; the next was between the mouse and the trout. Successions of long palindromes populating the amino- and carboxyl-terminal regions of H1 might be the direct consequence of the autologous binding between peptides and their coding sequence.
Insight into the relationship of chlorophyll a fluorescence yield to the concentration of its natural quenchers in oxygenic photosynthesis.
Authors: Shinkarev V P , Govindjee
Published: May 2006

Fluorescence of chlorophyll a (Chla) is a noninvasive and very sensitive intrinsic probe of photosynthesis. It monitors the composition and organization of the photosystems, the exciton energy transfer, the photochemistry, and the effects of various types of stress on plants. It is the most used as well as the most abused tool in photosynthesis. Thus, an understanding of its relationship to photosynthesis has been of paramount importance. Both the oxidized primary plastoquinone, QA, and the oxidized primary reaction-center Chla, P680+ (for short, P+), are known to be quenchers of Chla fluorescence yield (phi f) of photosystem II. Flash-number dependence of Chla fluorescence yield shows either a period 4, due to the four-step charge-accumulation process of water oxidation (donor side), or period 2 behavior, due to the two-step reduction of the plastoquinone QB (acceptor side) of photosystem II reaction centers. We provide here a further insight into the relationship of variable Chla fluorescence yield (phi f) to the concentration of the two quenchers. The observed time dependence of the ratio of psi f after flash 3 to that after flash 1 (or flash 5) in spinach thylakoids at pH 6 can be explained if we suggest that 1/psi f approximately equals a[PQA] + c, where a, b, and c are constants. From this it follows that the quenching of Chla fluorescence by P680+ after a flash is dependent on QA: for low [QA] (when most reaction centers are closed, [PQA] is low) the quenching of Chla fluorescence by P680+ predominates, while for high [QA] (when most reaction centers are open), the quenching of Chla fluorescence is due predominantly to the increased concentration of the reduced form of P680 ([P+] is low).
Evidence for adaptive evolution of the G6pd gene in the Drosophila melanogaster and Drosophila simulans lineages.
Authors: Eanes W F , Kirchner M , Yoon J
Published: May 2006

Proponents of the neutral theory argue that evolution at the molecular level largely reflects a process of random genetic drift of neutral mutations. Under this theory, levels of interspecific divergence and intraspecific polymorphism are expected to be correlated across classes of nucleotide or amino acid sequences with different degrees of functional constraint, such as synonymous and replacement sites. Nucleotide sites with reduced polymorphism should show comparably reduced levels of interspecific divergence. To examine this hypothesis, we have sequenced 32 and 12 copies of the glucose-6-phosphate dehydrogenase (G6pd) gene in Drosophila melanogaster and Drosophila simulans, respectively. Both species exhibit similar levels of nucleotide polymorphism at synonymous sites. D. melanogaster shows two amino acid polymorphisms, one associated with the cosmopolitan allozyme polymorphism and a second with an allozyme polymorphism endemic to European and North African populations. In contrast, D. simulans shows no replacement polymorphism. While synonymous divergence between species is 10%, which is typical of other genes, there are 21 replacement differences. This level of amino acid sequence divergence, when contrasted with levels of amino acid polymorphism, silent polymorphism, and divergence, is in 10-fold excess over that expected under the neutral model of molecular evolution. We propose that this excess divergence reflects episodes of natural selection on G6pd resulting in fixation of advantageous amino acid mutations in these two recently separated lineages.
Identification and characterization of an essential, activating regulatory element of the human SIS/PDGFB promoter in human megakaryocytes.
Authors: Jin H M , Brady M L , Fahl W E
Published: May 2006

The SIS/PDGFB gene, encoding the B polypeptide of platelet-derived growth factor (PDGF-B), is transcriptionally activated (> 50 fold) in human K562 erythroleukemia cells when they are induced to differentiate into megakaryocytic cells by treatment with phorbol 12-myristate 13-acetate ("tetradecanoylphorbol acetate," TPA). A 250-bp PDGF-B gene promoter attached to a reporter gene was shown to reproduce this TPA-induced activation. In a series of mutants that we constructed, a 10-bp linker sequence was systematically moved across the 250-bp PDGF-B promoter sequence, and the effect upon luciferase reporter activity was measured to identify a site through which this TPA-induced transcriptional activation occurred. We identified a site, which we named the SIS proximal element (SPE), at positions -58 to -39 relative to the PDGF-B mRNA initiation site that was essential for the TPA-induced activation. The SPE site contains two repeated sequences (TCTC and CACC) arranged in an ABBA configuration. The SPE sequence was not found in the existing list of consensus sequences for transcription factor binding sites. Gel mobility-shift assays using an SPE oligonucleotide and K562 cell nuclear extracts showed three shifted complexes, one of which was formed only following TPA treatment of K562 cells. In a time-course study, TPA induction of the endogenous PDGF-B mRNA and formation of the TPA-inducible complex occurred over the same time frame, and both events were specifically blocked by the addition of cycloheximide. The 20-bp SPE sequence was highly conserved (19/20) in both the cat and the mouse PDGF-B promoter, and conserved portions of the SPE sequence were also found at two sites within the human PDGF-A promoter. The role of the SPE in regulating the concurrent expression of the PDGF-B and PDGF-A genes in megakaryocytes, as well as various human tumor cells, is considered.
The rRNA-encoding DNA array has an altered structure in topoisomerase I mutants of Saccharomyces cerevisiae.
Authors: Christman M F , Dietrich F S , Levin N A , Sadoff B U , Fink G R
Published: May 2006

All the chromosomes from isogenic TOP1 and top1 strains have similar mobility on pulsed-field gels except for chromosome XII, which fails to migrate into the gels in top1 mutants. Chromosome XII contains the tandem repeats of rRNA-encoding DNA (rDNA). When a segment of chromosome XII containing only rDNA is transferred to chromosome III by a recombination event, chromosome III fails to enter a pulsed-field gel in extracts from top1 strains, indicating that the aberrant migration of chromosome XII in top1 mutants is caused by the presence of rDNA. Failure of chromosome XII to migrate into a pulsed-field gel occurs only in preparations from exponentially growing top1 cultures and not in preparations from stationary-phase top1 cultures. rDNA from a top1 strain does enter the gel if it is cut with an enzyme (Pst I) that cuts the tandem rDNA array into single 9-kb repeat units, indicating that more than a single repeat unit is required to maintain the aberrant structure.