bluuebunny/crossref_metadata_2025 huggingface dataset:
Evidence for incorporation of intact dietary pyrimidine (but not purine) nucleosides into hepatic RNA.
Authors: Berthold H K , Crain P F , Gouni I , Reeds P J , Klein P D
Published: May 2006

The absorption and metabolism of dietary nucleic acids have received less attention than those of other organic nutrients, largely because of methodological difficulties. We supplemented the rations of poultry and mice with the edible alga Spirulina platensis, which had been uniformly labeled with 13C by hydroponic culture in 13CO2. The rations were ingested by a hen for 4 wk and by four mice for 6 days; two mice were fed a normal diet and two were fed a nucleic acid-deficient diet. The animals were killed and nucleosides were isolated from hepatic RNA. The isotopic enrichment of all mass isotopomers of the nucleosides was analyzed by selected ion monitoring of the negative chemical ionization mass spectrum and the labeling pattern was deconvoluted by reference to the enrichment pattern of the tracer material. We found a distinct difference in the 13C enrichment pattern between pyrimidine and purine nucleosides; the isotopic enrichment of uniformly labeled [M + 9] isotopomers of pyrimidines exceeded that of purines [M + 10] by > 2 orders of magnitude in the avian nucleic acids and by 7- and 14-fold in the murine nucleic acids. The purines were more enriched in lower mass isotopomers, those less than [M + 3], than the pyrimidines. Our results suggest that large quantities of dietary pyrimidine nucleosides and almost no dietary purine nucleosides are incorporated into hepatic nucleic acids without hydrolytic removal of the ribose moiety. In addition, our results support a potential nutritional role for nucleosides and suggest that pyrimidines are conditionally essential organic nutrients.
Development of a safe live Leishmania vaccine line by gene replacement.
Authors: Titus R G , Gueiros-Filho F J , de Freitas L A , Beverley S M
Published: May 2006

Vaccination with live Leishmania major has been shown to yield effective immunization in humans; however, this has been discontinued because of problems associated with virulence of the available vaccine lines. To circumvent this, we tested the ability of a dhfr-ts- null mutant of L. major, obtained by gene targeting, to infect and then to vaccinate mice against challenge with virulent L. major. Survival and replication of dhfr-ts- in macrophages in vitro were dependent upon thymidine, with parasites differentiating into amastigotes prior to destruction. dhfr-ts- parasites persisted in BALB/c mice for up to 2 months, declining with a half-life of 2-3 days. Nonetheless, dhfr-ts- was incapable of causing disease in both susceptible and immunodeficient (nu/nu) BALB/c mice. Animal infectivity could be partially restored by thymidine supplementation. When inoculated by the i.v., s.c., or i.m. routes into mice, dhfr-ts- could elicit substantial resistance to a subsequent challenge with virulent L. major. Thus, Leishmania bearing auxotrophic gene knockouts can be safe and induce protective immunity. Potentially, dhfr-ts- could be used as a platform for delivery of immunogens relevant to other diseases.
Chloroplast DNA variation and the recent radiation of the giant senecios (Asteraceae) on the tall mountains of eastern Africa.
Authors: Knox E B , Palmer J D
Published: May 2006

Chloroplast DNA restriction-site variation was surveyed among 40 accessions representing all 11 species of giant senecios (Dendrosenecio, Asteraceae) at all but one known location, plus three outgroup species. Remarkably little variation (only 9 variable sites out of roughly 1000 sites examined) was found among the 40 giant senecio accessions, yet as a group they differ significantly (at 18 sites) from Cineraria deltoidea, the closest known relative. This pattern indicates that the giant senecios underwent a recent dramatic radiation in eastern Africa and evolved from a relatively isolated lineage within the Senecioneae. Biogeographic interpretation of the molecular phylogeny suggests that the giant senecios originated high on Mt. Kilimanjaro, with subsequent dispersion to the Aberdares, Mt. Kenya, and the Cherangani Hills, followed by dispersion westward to the Ruwenzori Mountains, and then south to the Virunga Mountains, Mt. Kahuzi, and Mt. Muhi, but with dispersion back to Mt. Elgon. Geographic radiation was an important antecedent to the diversification in eastern Africa, which primarily involved repeated altitudinal radiation, both up and down the mountains, leading to morphological parallelism in both directions. In general, the plants on a given mountain are more closely related to each other than they are to plants on other mountains, and plants on nearby mountains are more closely related to each other than they are to plants on more distant mountains. The individual steps of the geographic radiation have occurred at various altitudes, some clearly the result of intermountain dispersal. The molecular evidence suggests that two species are extant ancestors to other species on the same or nearby mountains.
The role of voice input for human-machine communication.
Authors: Cohen P R , Oviatt S L
Published: May 2006

Optimism is growing that the near future will witness rapid growth in human-computer interaction using voice. System prototypes have recently been built that demonstrate speaker-independent real-time speech recognition, and understanding of naturally spoken utterances with vocabularies of 1000 to 2000 words, and larger. Already, computer manufacturers are building speech recognition subsystems into their new product lines. However, before this technology can be broadly useful, a substantial knowledge base is needed about human spoken language and performance during computer-based spoken interaction. This paper reviews application areas in which spoken interaction can play a significant role, assesses potential benefits of spoken interaction with machines, and compares voice with other modalities of human-computer interaction. It also discusses information that will be needed to build a firm empirical foundation for the design of future spoken and multimodal interfaces. Finally, it argues for a more systematic and scientific approach to investigating spoken input and performance with future language technology.
Speech recognition technology: a critique.
Authors: Levinson S E
Published: May 2006

This paper introduces the session on advanced speech recognition technology. The two papers comprising this session argue that current technology yields a performance that is only an order of magnitude in error rate away from human performance and that incremental improvements will bring us to that desired level. I argue that, to the contrary, present performance is far removed from human performance and a revolution in our thinking is required to achieve the goal. It is further asserted that to bring about the revolution more effort should be expended on basic research and less on trying to prematurely commercialize a deficient technology.
Training and search methods for speech recognition.
Authors: Jelinek F
Published: May 2006

Speech recognition involves three processes: extraction of acoustic indices from the speech signal, estimation of the probability that the observed index string was caused by a hypothesized utterance segment, and determination of the recognized utterance via a search among hypothesized alternatives. This paper is not concerned with the first process. Estimation of the probability of an index string involves a model of index production by any given utterance segment (e.g., a word). Hidden Markov models (HMMs) are used for this purpose [Makhoul, J. & Schwartz, R. (1995) Proc. Natl. Acad. Sci. USA 92, 9956-9963]. Their parameters are state transition probabilities and output probability distributions associated with the transitions. The Baum algorithm that obtains the values of these parameters from speech data via their successive reestimation will be described in this paper. The recognizer wishes to find the most probable utterance that could have caused the observed acoustic index string. That probability is the product of two factors: the probability that the utterance will produce the string and the probability that the speaker will wish to produce the utterance (the language model probability). Even if the vocabulary size is moderate, it is impossible to search for the utterance exhaustively. One practical algorithm is described [Viterbi, A. J. (1967) IEEE Trans. Inf. Theory IT-13, 260-267] that, given the index string, has a high likelihood of finding the most probable utterance.
Integration of speech with natural language understanding.
Authors: Moore R C
Published: May 2006

The integration of speech recognition with natural language understanding raises issues of how to adapt natural language processing to the characteristics of spoken language; how to cope with errorful recognition output, including the use of natural language information to reduce recognition errors; and how to use information from the speech signal, beyond just the sequence of words, as an aid to understanding. This paper reviews current research addressing these questions in the Spoken Language Program sponsored by the Advanced Research Projects Agency (ARPA). I begin by reviewing some of the ways that spontaneous spoken language differs from standard written language and discuss methods of coping with the difficulties of spontaneous speech. I then look at how systems cope with errors in speech recognition and at attempts to use natural language information to reduce recognition errors. Finally, I discuss how prosodic information in the speech signal might be used to improve understanding.
The angiotensin II type 2 (AT2) receptor antagonizes the growth effects of the AT1 receptor: gain-of-function study using gene transfer.
Authors: Nakajima M , Hutchinson H G , Fujinaga M , Hayashida W , Morishita R , Zhang L , Horiuchi M , Pratt R E , Dzau V J
Published: May 2006

The type 1 angiotensin II (AT1) receptor is well characterized but the type 2 (AT2) receptor remains an enigma. We tested the hypothesis that the AT2 receptor can modulate the growth of vascular smooth muscle cells by transfecting an AT2 receptor expression vector into the balloon-injured rat carotid artery and observed that overexpression of the AT2 receptor attenuated neointimal formation. In cultured smooth muscle cells, AT2 receptor transfection reduced proliferation and inhibited mitogen-activated protein kinase activity. Furthermore, we demonstrated that the AT2 receptor mediated the developmentally regulated decrease in aortic DNA synthesis at the latter stages of gestation. These results suggest that the AT2 receptor exerts an antiproliferative effect, counteracting the growth action of AT1 receptor.
The hypocone as a key innovation in mammalian evolution.
Authors: Hunter J P , Jernvall J
Published: May 2006

The hypocone, a cusp added to the primitively triangular upper molar teeth of therian mammals, has evolved convergently > 20 times among mammals during the Cenozoic. Acquisition of the hypocone itself involves little phenotypic change, but subsequent diversification of groups possessing the hypocone may be greatly enhanced. Our analysis of the Cenozoic mammalian radiations, including the Recent fauna, shows that high species diversity of mammals with hypocones and association of the hypocone with herbivory strongly support recognition of the hypocone as a key innovation that has allowed invasion of, and diversification within, herbivorous adaptive zones. In contrast, mammals lacking hypocones show no marked increase in species diversity during the Cenozoic.
Genomic structure of human microtubule-associated protein 2 (MAP-2) and characterization of additional MAP-2 isoforms.
Authors: Kalcheva N , Albala J , O'Guin K , Rubino H , Garner C , Shafit-Zagardo B
Published: May 2006

We have determined that the gene for human microtubule-associated protein 2 (MAP-2) spans 19 exons, including 6 exons identified in this study, 1-4, 8, and 13; all six of these exons are transcribed. The alternative splicing of coding exons generates a greater diversity of MAP-2 transcripts and isoforms. The first three exons encode alternate 5' untranslated regions that can be spliced to additional untranslated sequences contained in exons 4 and 5. Exons 8 and 13 are transcribed in human fetal spinal cord, adult brain, MSN cells, and rat brain, and each exon maintains an open reading frame with both high and low molecular weight MAP-2 isoforms. Antibodies generated to synthetic peptides of exons 8 and 13 demonstrate that these exons are translated and MAP-2 isoforms containing these exons are generated.
Turbulent diffusion phase transition is due to singular energy spectrum.
Authors: Wallstrom T C
Published: May 2006

The phase transition for turbulent diffusion, reported by Avellaneda and Majda [Avellaneda, M. & Majda, A. J. (1994) Philos. Trans. R. Soc. London A 346, 205-233, and several earlier papers], is traced to a modeling assumption in which the energy spectrum of the turbulent fluid is singularly dependent on the viscosity in the inertial range. Phenomenological models of turbulence and intermittency, by contrast, require that the energy spectrum be independent of the viscosity in the inertial range. When the energy spectrum is assumed to be consistent with the phenomenological models, there is no phase transition for turbulent diffusion.
Grs 1915+105: a superluminal source in the Galaxy.
Authors: Rodríguez L F , Mirabel I F
Published: May 2006

We present the results of additional observations of the high energy source GRS 1915+105, which produces ejecta with apparent superluminal motions. The observations reported here were carried out with the Very Large Array at 3.5 cm and 20 cm. The 3.5-cm observations made during 1994 May allowed us to continue following the proper motions of the bright 1994 March 19 ejecta, as well as those of a subsequent, fainter ejection. The proper motions of the 1994 March 19 ejecta continued to be ballistic (i.e., constant) over the period of about 75 days where they remained detectable. From the observations in 1994 March-May we have identified three ejections of pairs of plasma clouds moving ballistically in approximately the same direction on the sky with similar proper motions. The 20-cm observations made during 1994 November and December were used to search, yet unsuccessfully, for extended jets or lobes associated with GRS 1915+105.
Possible links between BL Lacertae objects and quasars from very long baseline interferometry radio data.
Authors: Gabuzda D C
Published: May 2006

Systematic differences in the very long baseline interferometry (VLBI) radio polarization structure and average VLBI component speeds of BL Lacertae objects and quasars support the view that the observational distinction between these classes, based in large part on the strength of their optical line emission, is meaningful; in other words, this distinction reflects significant differences in the physical conditions in these sources. Possible models providing a link between the optical and VLBI properties of BL Lacertae objects and quasars are discussed. Most VLBI polarization observations to date have been global observations made at 6 cm; recent results suggest that the VLBI polarization structure of some sources may change dramatically on scales smaller than those probed by these 6-cm observations.
The case for unification.
Authors: Gopal-Krishna
Published: May 2006

I investigate the issue of whether the various subclasses of radio-loud galaxies are intrinsically the same but have been classified differently mainly due to their being viewed from different directions. Evidence for the two key elements of this popular version of the "unified scheme (US)," relativistic jets and nuclear tori, is updated. The case for the torus opening angle increasing with the radio luminosity of the active galactic nucleus (AGN) is freshly argued. Radio-loud AGN are particularly suited for testing the US, since their structures and polarization properties on different scales, as well as their overall radio sizes, provide useful statistical indicators of the relative orientations of their various subclasses. I summarize recent attempts to bring under a single conceptual framework the USs developed for radio-moderate [Fanaroff-Riley type I (FRI)] and radio-powerful (FRII) AGN. By focusing on FRII radio sources, I critically examine the recent claims of conflict with the US, based on the statistics of radio-size measurements for large, presumably orientation-independent, samples with essentially complete optical identifications. Possible ways of reconciling these results, and also the ones based on very-long-baseline radio interferometry polarimetric observations, with the US are pointed out. By incorporating a highly plausible temporal evolution of radio source properties into the US, I outline a scenario that allows the median linear size of quasars to approach, or even exceed, that of radio galaxies, as samples with decreasing radio luminosity are observed. Thus, even though a number of issues remain to be fully resolved, the scope of unified models continues to expand.
Unification and large-scale structure.
Authors: Laing R A
Published: May 2006

The hypothesis of relativistic flow on parsec scales, coupled with the symmetrical (and therefore subrelativistic) outer structure of extended radio sources, requires that jets decelerate on scales observable with the Very Large Array. The consequences of this idea for the appearances of FRI and FRII radio sources are explored.
Optical evidence for the unification of active galactic nuclei and quasi-stellar objects.
Authors: Miller J S
Published: May 2006

There is a variety of optical evidence for some unification of different types of active galactic nuclei and quasi-stellar objects (QSOs). The case is very strong for the unification of at least some Seyfert galaxies, where polarization data show that the type assigned to the Seyfert galaxy must depend on viewing direction. It has been proposed that Fanaroff-Riley type 2 (FR2) radio galaxies are quasars seen in a direction from which the quasar is obscured, and there is some limited direct evidence for this picture. The broad absorption line QSOs may be normal QSOs seen from a special direction. Some of the sources observed to have high luminosities in the far infrared could be obscured QSOs and active nuclei. Mergers and interactions are likely to play an important role in nuclear activity, and active galaxies and QSOs could change their apparent types through these encounters followed by subsequent evolution.
Gravitational lensing of active galactic nuclei.
Authors: Hewitt J N
Published: May 2006

Most of the known cases of strong gravitational lensing involve multiple imaging of an active galactic nucleus. The properties of lensed active galactic nuclei make them promising systems for astrophysical applications of gravitational lensing; in particular, they show structure on scales of milliseconds of arc to tens of seconds of arc, they are variable, and they are polarized. More than 20 cases of strong gravitational lenses are now known, and about half of them are radio sources. High-resolution radio imaging is making possible the development of well-constrained lens models. Variability studies at radio and optical wavelengths are beginning to yield results of astrophysical interest, such as an independent measure of the distance scale and limits on source sizes.
Studies of group B streptococcal infection in mice deficient in complement component C3 or C4 demonstrate an essential role for complement in both innate and acquired immunity.
Authors: Wessels M R , Butko P , Ma M , Warren H B , Lage A L , Carroll M C
Published: May 2006

Group B streptococci (GBS) cause sepsis and meningitis in neonates and serious infections in adults with underlying chronic illnesses. Specific antibodies have been shown to be an important factor in protective immunity for neonates, but the role of serum complement is less well defined. To elucidate the function of the complement system in immunity to this pathogen, we have used the approach of gene targeting in embryonic stem cells to generate mice totally deficient in complement component C3. Comparison of C3-deficient mice with mice deficient in complement component C4 demonstrated that the 50% lethal dose for GBS infection was reduced by approximately 50-fold and 25-fold, respectively, compared to control mice. GBS were effectively killed in vitro by human blood leukocytes in the presence of specific antibody and C4-deficient serum but not C3-deficient serum. The defective opsonization by C3-deficient serum in vitro was corroborated by in vivo studies in which passive immunization of pregnant dams with specific antibodies conferred protection from GBS challenge to normal and C4-deficient pups but not C3-deficient pups. These results indicate that the alternative pathway is sufficient to mediate effective opsonophagocytosis and protective immunity to GBS in the presence of specific antibody. In contrast, the increased susceptibility to infection of non-immune mice deficient in either C3 or C4 implies that the classical pathway plays an essential role in host defense against GBS infection in the absence of specific immunity.
Evidence for DNA phosphate backbone alkylation and cleavage by pyrrolo[1,2-a]benzimidazoles: small molecules capable of causing base-pair-specific phosphodiester bond hydrolysis.
Authors: Schulz W G , Nieman R A , Skibo E B
Published: May 2006

This report presents evidence that a reduced pyrrolo[1,2-a]benzimidazole (PBI) cleaves DNA as a result of phosphate alkylation followed by hydrolysis of the resulting phosphate triester. The base-pair specificity of the phosphate alkylation results from Hoogsteen-type hydrogen bonding of the reduced PBI in the major groove at only A.T and G.C base pairs. Alkylated phosphates were detected by 31P NMR and the cleavage products were detected by 1H NMR and HPLC. Evidence is also presented that a reduced PBI interacts with DNA in the major groove rather than in the minor groove or by intercalation.
Sleep electroencephalogram delta-frequency amplitude, night plasma levels of tumor necrosis factor alpha, and human immunodeficiency virus infection.
Authors: Darko D F , Miller J C , Gallen C , White J , Koziol J , Brown S J , Hayduk R , Atkinson J H , Assmus J , Munnell D T
Published: May 2006

We tested the hypothesis that increases in tumor necrosis factor alpha (TNF-alpha) induced by human immunodeficiency virus (HIV) are associated with the increases in slow-wave sleep seen in early HIV infection and the decrease with sleep fragmentation seen in advanced HIV infection. Nocturnal sleep disturbances and associated fatigue contribute to the disability of HIV infection. TNF-alpha causes fatigue in clinical use and promotes slow-wave sleep in animal models. With slow progress toward a vaccine and weak effects from current therapies, efforts are directed toward extending productive life of HIV-infected individuals and shortening the duration of disability in terminal illness. We describe previously unrecognized nocturnal cyclic variations in plasma levels of TNF-alpha in all subjects. In 6 of 10 subjects (1 control subject, 3 HIV-seropositive patients with CD4+ cell number > 400 cells per microliters, and 2 HIV-positive patients with CD4+ cell number < 400 cells per microliters), these fluctuations in TNF-alpha were coupled to the known rhythm of electroencephalogram delta amplitude (square root of power) during sleep. This coupling was not present in 3 HIV-positive subjects with CD4+ cell number < 400 cells per microliters and 1 control subject. In 5 HIV subjects with abnormally low CD4+ cell counts ( < 400 cells per microliters), the number of days since seroconversion correlated significantly with low correlation between TNF-alpha and delta amplitude. We conclude that a previously unrecognized normal, physiological coupling exists between TNF-alpha and delta amplitude during sleep and that the lessened likelihood of this coupling in progressive HIV infection may be important in understanding fatigue-related symptoms and disabilities.
Temporally and spectrally resolved subpicosecond energy transfer within the peripheral antenna complex (LH2) and from LH2 to the core antenna complex in photosynthetic purple bacteria.
Authors: Hess S , Chachisvilis M , Timpmann K , Jones M R , Fowler G J , Hunter C N , Sundström V
Published: May 2006

We report studies of energy transfer from the 800-nm absorbing pigment (B800) to the 850-nm absorbing pigment (B850) of the LH2 peripheral antenna complex and from LH2 to the core antenna complex (LH1) in Rhodobacter (Rb.) sphaeroides. The B800 to B850 process was studied in membranes from a LH2-reaction center (no LH1) mutant of Rb. sphaeroides and the LH2 to LH1 transfer was studied in both the wild-type species and in LH2 mutants with blue-shifted B850. The measurements were performed by using approximately 100-fs pulses to probe the formation of acceptor excitations in a two-color pump-probe measurement. Our experiments reveal a B800 to B850 transfer time of approximately 0.7 ps at 296 K and energy transfer from LH2 to LH1 is characterized by a time constant of approximately 3 ps at 296 K and approximately 5 ps at 77 K. In the blue-shifted B850 mutants, the transfer time from B850 to LH1 becomes gradually longer with increasing blue-shift of the B850 band as a result of the decreasing spectral overlap between the antennae. The results have been used to produce a model for the association between the ring-like structures that are characteristic of both the LH2 and LH1 antennae.
Differentiation of immortal cells inhibits telomerase activity.
Authors: Sharma H W , Sokoloski J A , Perez J R , Maltese J Y , Sartorelli A C , Stein C A , Nichols G , Khaled Z , Telang N T , Narayanan R
Published: May 2006

Telomerase, a ribonucleic acid-protein complex, adds hexameric repeats of 5'-TTAGGG-3' to the ends of mammalian chromosomal DNA (telomeres) to compensate for the progressive loss that occurs with successive rounds of DNA replication. Although somatic cells do not express telomerase, germ cells and immortalized cells, including neoplastic cells, express this activity. To determine whether the phenotypic differentiation of immortalized cells is linked to the regulation of telomerase activity, terminal differentiation was induced in leukemic cell lines by diverse agents. A pronounced downregulation of telomerase activity was produced as a consequence of the differentiated status. The differentiation-inducing agents did not directly inhibit telomerase activity, suggesting that the inhibition of telomerase activity is in response to induction of differentiation. The loss of telomerase activity was not due to the production of an inhibitor, since extracts from differentiated cells did not cause inhibition of telomerase activity. By using additional cell lineages including epithelial and embryonal stem cells, down-regulation of telomerase activity was found to be a general response to the induction of differentiation. These findings provide the first direct link between telomerase activity and terminal differentiation and may provide a model to study regulation of telomerase activity.
Genetic heterogeneity in isogenic homozygous clonal zebrafish.
Authors: Buth D G , Gordon M S , Plaut I , Drill S L , Adams L G
Published: May 2006

The C32 isogenic homozygous diploid (IHD) strain of the zebrafish (Danio rerio) was found to be polyallelic at a malate dehydrogenase locus (sMdh-A). A variant allele is thought to have arisen via mutation within the past 10 bisexual generations that have maintained the strain since its last gynogenetic cloning event; this unique allele now predominates at the sMdh-A locus. The estimated mutation rate in this species is sufficiently high that long-term genetic homogeneity of its IHD clones cannot be assumed. Researchers using such bisexually maintained clones should be aware that they are not necessarily using genetically uniform subjects. Genetic uniformity of cloned IHD zebrafish will be maximized if experimental subjects are obtained soon after a cloning event.
A light-dependent complementation system for analysis of NADPH:protochlorophyllide oxidoreductase: identification and mutagenesis of two conserved residues that are essential for enzyme activity.
Authors: Wilks H M , Timko M P
Published: May 2006

Protochlorophyllide reductase (NADPH:protochlorophyllide oxidoreductase; EC 1.6.99.1) catalyzes the light-dependent reduction of protochlorophyllide to chlorophyllide, a key regulatory step in the chlorophyll biosynthetic pathway. We have developed an expression system in which the protochlorophyllide reductase from pea (Pisum sativum L.) is used to complement protochlorophyllide reduction mutants in the photosynthetic bacterium Rhodobacter capsulatus, allowing analysis of wild-type and mutant forms of the enzyme. By protein sequence comparisons, we have identified the plant protochlorophyllide reductases as belonging to the family of short-chain alcohol dehydrogenases. Based on our protein sequence alignments, we have identified and mutated two conserved residues (Tyr-275 and Lys-279) within the proposed active site of the enzyme and shown that they are critical for activity. A model of the enzyme reaction mechanism for light-dependent protochlorophyllide reduction is proposed.
Abnormal calcium homeostasis and mitochondrial polarization in a human encephalomyopathy.
Authors: Moudy A M , Handran S D , Goldberg M P , Ruffin N , Karl I , Kranz-Eble P , DeVivo D C , Rothman S M
Published: May 2006

Patients with several inherited human encephalomyopathies exhibit systemic and neurological symptoms in association with specific mitochondrial mutations. The mechanisms by which these mitochondrial mutations result in cellular injury have not been elucidated. One potential cause of neuronal vulnerability is an inability to effectively buffer intracellular calcium. We report that fibroblasts from patients with one specific inherited encephalomyopathy, MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) syndrome, have elevated levels of ionized calcium and cannot normally sequester calcium influxes. Quantitative fluorescence imaging demonstrated that this abnormality was associated with a relative decrease in mitochondrial membrane potential compared to control fibroblasts. This documentation of pathological calcium homeostasis in a genetic neurological disease extends the calcium hypothesis of toxic cell injury to human mitochondrial encephalomyopathies.
Dimensionless invariants from foraging theory's marginal value theorem.
Authors: Charnov E L , Parker G A
Published: May 2006

Copula duration (t) decreases, and proportional rate of sperm transfer (c) increases, with larger male body size in dung flies, so their dimensionless product (c. t) is approximately constant (approximately 2.2). The most recent copulating male fertilizes about 89% of the eggs laid (= 1 - e(-c.t) = 1 - e(-2.2)), independent of his body size. The conditions under which natural selection favors this phenotypic invariance are studied with fitness optimization models. The dimensionless rules for optimal patch residence times are then generalized to cover phenotypic variation in other foraging cases.
Transient protein kinase C activation primes long-term depression and suppresses long-term potentiation of synaptic transmission in hippocampus.
Authors: Stanton P K
Published: May 2006

Activity-dependent long-lasting plasticity in hippocampus and neocortex includes long-term potentiation (LTP) and long-term depression (LTD) of synaptic strength. Recent studies have confirmed theoretical predictions that the sensitivity of LTP- and LTD-inducing mechanisms is dynamically regulated by previous synaptic history. In particular, prior induction of either repeated short-term potentiations or LTP lowers the threshold for induction of LTD and raises the threshold for LTP. In the current study, transient activation of protein kinase C with phorbol 12,13-diacetate was able to substitute for synaptic activity in priming synapses to exhibit enhanced homosynaptic LTD and to suppress the induction of LTP at Schaffer collateral synapses in area CA1 of hippocampal slices. This priming lasted 30 min, but not 3 hr, following phorbol 12,13-diacetate bath application. These data suggest that a protein kinase C-sensitive phosphorylation site may be an activity-sensitive target mediating the rapid expression of LTP and LTD.
The N-terminal portion of domain E of retinoic acid receptors alpha and beta is essential for the recognition of retinoic acid and various analogs.
Authors: Ostrowski J , Hammer L , Roalsvig T , Pokornowski K , Reczek P R
Published: May 2006

Utilizing a strategy involving domain exchange between retinoic acid receptors alpha and beta (RAR alpha and RAR beta) and monitoring the transcriptional activity of the resulting chimeric receptors with receptor-selective retinoids, we identified a 70-aa region within the N-terminal portion of the RAR alpha and -beta domain E which is important for an RAR alpha- or RAR beta-specific response. Two amino acid residues within this region, serine-232 (S232) and threonine-239 (T239) in RAR alpha and the corresponding alanine-225 (A225) and isoleucine-232 (I232) in RAR beta, were found to be essential for this effect. In addition, binding studies using the chimeric receptors expressed in Escherichia coli showed that the N-terminal portion of domain E was also important for the characteristic binding profile of t-RA and various retinoids with RAR alpha or RAR beta. Structural predictions of the primary amino acid sequence in this region indicate the presence of an amphipathic helix-turn-helix structure with five hydrophobic amino acids that resemble a leucine zipper motif. The amino acid residues identified by domain swapping, S232 and T239 in RAR alpha and A225 and I232 in RAR beta, were found within the hydrophobic face of an alpha-helix in close proximity to this zipper motif, suggesting that the ligand may interact with the receptor in the region adjacent to a surface involved in protein-protein interactions. This finding may link ligand binding to other processes important for transcriptional activation.
beta-Glucosidase: an elicitor of herbivore-induced plant odor that attracts host-searching parasitic wasps.
Authors: Mattiacci L , Dicke M , Posthumus M A
Published: May 2006

Cabbage plants respond to caterpillar (Pieris brassicae) herbivory by releasing a mixture of volatiles that makes them highly attractive to parasitic wasps (Cotesia glomerata) that attack the herbivores. Cabbage leaves that are artificially damaged and subsequently treated with gut regurgitant of P. brassicae caterpillars release a volatile blend similar to that of herbivore-damaged plants. We demonstrate the presence of beta-glucosidase in P. brassicae regurgitant. Leaves treated with commercial beta-glucosidase (from almonds) release a volatile blend similar to that of leaves treated with P. brassicae regurgitant. In a flight bioassay, leaves treated with almond beta-glucosidase are highly attractive to the parasitic wasp C. glomerata. Furthermore, the wasps do not discriminate between cabbage leaves treated with almond beta-glucosidase and leaves treated with larval regurgitant. beta-Glucosidase was also recorded in cabbage leaf extract, but this is not as effective as caterpillar beta-glucosidase in eliciting the volatile production. Caterpillars that feed on a beta-glucosidase-free diet secrete the enzyme, and their regurgitant is an effective elicitor of the plant response. These findings show that beta-glucosidase is a P. brassicae-secreted elicitor of the defense response of cabbage plants to herbivore injury, inducing the emission of volatiles that are used by parasitoids of the herbivore to locate their victims.
Bcp1, a gene required for male fertility in Arabidopsis.
Authors: Xu H , Knox R B , Taylor P E , Singh M B
Published: May 2006

Male fertility in flowering plants is dependent on production of viable pollen grains within the anther. Genes expressed exclusively in the anther are likely to include those that control male fertility. On the basis of their tissue specificity, such genes have been isolated, yet in none of them has this function been demonstrated. Here we report that one such gene, Bcp1, is active in both diploid tapetum and haploid microspores and is required for pollen fertility. Perturbation of this gene in either tapetum or microspores prevents production of fertile pollen in transgenic Arabidopsis plants. When tapetum expression of this gene is perturbed, mature anthers contain dead shriveled pollen. On the other hand, when microspore expression is perturbed, anthers show 1:1 segregation of viable/aborted pollen. These findings identify a class of sporophytic/gametophytic genes controlling male fertility and, hence, reproduction in flowering plants.
Antiparallel, intramolecular triplex DNA stimulates homologous recombination in human cells.
Authors: Rooney S M , Moore P D
Published: May 2006

The DNA motif 5'-AAGGGAGAAXGGGTATAGGGYAAGAGGGAA-3' (named XY32) is an H-palindrome and has been shown to undergo a superhelix-induced, pH-dependent structural transition to H-form (pyrimidine purineo pyrimidine triplex) DNA when X = Y = A (AA32) or X = Y = G (GG32), but when X = A and Y = G (AG32) or X = G and Y = A (GA32), the transition is much more difficult [Mirkin, S. (1987) Nature (London) 330, 495-497]. Furthermore, AA32, GG32, and GA32 triplexes have the proper sequence structure to potentially form pyrimidineopurineopurine (*H-form) triplexes, but AG32 does not [Beal, P. A. & Dervan, P. B. (1992) Nucleic Acids Res. 20, 2773-2776]. Using an in vivo plasmid-plasmid recombination assay system in cultured human cells, we have found that AA32, GA32, and GG32 stimulate homologous recombination between plasmids 3- to 5-fold when both recombination substrates contain these triplex-forming sequences, whereas AG32, which differs from the others by only 1 or 2 bp, does not significantly affect the frequency of recombination. Double-strand breaks, which destroy supercoiling, nullify the stimulation. Therefore, stimulation of homologous recombination between plasmids containing these sequences correlates with their triplex-forming potential. Crosses in which the triplex-forming sequence is inserted into only one substrate exhibit an intermediate stimulation, suggesting that the inserts are acting alone as intramolecular triplexes.
Expression of tobacco genes for light-harvesting chlorophyll a/b binding proteins of photosystem II is controlled by two circadian oscillators in a developmentally regulated fashion.
Authors: Kolar C , Adám E , Schäfer E , Nagy F
Published: May 2006

Light-induced expression of genes encoding the light-harvesting chlorophyll a/b binding proteins of photosystem II (Cab) was shown to be controlled by a circadian oscillator coupled to the red-light-absorbing plant photoreceptor phytochrome. Here we show that a red-light-insensitive oscillator is also involved in regulating the expression of the Cab genes. We provide evidence that germination leads, in a light-independent manner, to the setting and/or synchronization of endogenous oscillators and that it induces the expression of Cab genes in a circadian fashion. This circadian oscillator is not coupled to phytochrome, as it cannot be reset by red light for at least 44 h after sowing. Short red light pulses given between 12 and 44 h after sowing, however, induce new rhythms without perturbing the already free-running red-light-independent circadian oscillation. At this stage of development, the phytochrome-coupled and uncoupled circadian rhythms coexist. Both circadian rhythms are expressed and exhibit period lengths close to 24 h but are phased differently. At later stages of development (60 h or later after sowing), red light treatments synchronized these free-running rhythms and led to the appearance of a single new circadian oscillation. These data indicate that during early development the expression of single tobacco Cab genes, particularly expression of the Cab21 and Cab40 genes, is controlled in a developmentally dependent manner by two circadian oscillators.
Gas-phase folding and unfolding of cytochrome c cations.
Authors: Wood T D , Chorush R A , Wampler F M , Little D P , O'Connor P B , McLafferty F W
Published: May 2006

Water is thought to play a dominant role in protein folding, yet gaseous multiply protonated proteins from which the water has been completely removed show hydrogen/deuterium (H/D) exchange behavior similar to that used to identify conformations in solution. Indicative of the gas-phase accessibility to D2O, multiply-charged (6+ to 17+) cytochrome c cations exchange at six (or more) distinct levels of 64 to 173 out of 198 exchangeable H atoms, with the 132 H level found at charge values 8+ to 17+. Infrared laser heating and fast collisions can apparently induce ions to unfold to exchange at a higher distinct level, while charge-stripping ions to lower charge values yields apparent folding as well as unfolding.
Radial and tangential dispersion patterns in the mouse retina are cell-class specific.
Authors: Reese B E , Harvey A R , Tan S S
Published: May 2006

The retina is derived from a pseudostratified germinal zone in which the relative position of a progenitor cell is believed to determine the position of the progeny aligned in the radial axis. Such a developmental mechanism would ensure that radial arrays of cells which comprise functional units in the mature central nervous system are also clonally related. The present study has tested this hypothesis by using X chromosome-inactivation transgenic mosaic mice. We report that the retina shows a conspicuous distinction for clonally related neuroblasts of different laminar and functional fates: the rod photoreceptor, Müller, and bipolar cells are aligned in the radial axis, whereas the cone photoreceptor, horizontal, amacrine, and ganglion cells are tangentially displaced with respect to them. These results indicate that the dispersion of cell classes across the retinal surface is differentially constrained. Some classes of retinal neuroblast exhibit a significant tangential, as well as radial, component in their dispersion from the germinal zone, whereas others disperse only in the radial dimension. Consequently, the majority of radial columns within the mature retina must be derived from multiple progenitors. Because the cone photoreceptor, horizontal, amacrine, and ganglion cells establish nonrandom matrices in their cellular distributions within the respective retinal layers, tangential dispersion may be the means by which these matrices are constructed.
Use of Saccharomyces cerevisiae for patch-clamp analysis of heterologous membrane proteins: characterization of Kat1, an inward-rectifying K+ channel from Arabidopsis thaliana, and comparison with endogeneous yeast channels and carriers.
Authors: Bertl A , Anderson J A , Slayman C L , Gaber R F
Published: May 2006

Transport-deficient strains of the yeast Saccharomyces cerevisiae have recently proven useful for cloning, by functional complementation, of cDNAs encoding heterologous membrane transporters: specifically, H(+)-amino acid symporters and K+ channels from the higher plant Arabidopsis thaliana. The present study uses whole-cell patch-clamp experiments to show that yeast strains which grow poorly on submillimolar K+ due to the deletion of two K(+)-transporter genes (TRK1 and TRK2) are in fact missing a prominent K+ inward current present in wild-type cells. Rescue of such strains for growth on low K+ by transformation with a gene (KAT1) encoding an inward-rectifying K+ channel from Arabidopsis is accompanied by the appearance of an inward current whose characteristics are in qualitative agreement with previous studies in the Xenopus oocyte system, but differ in quantitative details. The ability to make such measurements directly on Saccharomyces should facilitate structure-function studies of any electrogenic or electrophoretic ion transporters which can be expressed in the plasma membrane (or tonoplast) of that organism.
Comprehensive allelotyping of human renal cell carcinomas using microsatellite DNA probes.
Authors: Thrash-Bingham C A , Greenberg R E , Howard S , Bruzel A , Bremer M , Goll A , Salazar H , Freed J J , Tartof K D
Published: May 2006

The von Hippel-Lindau locus on chromosome 3p is a tumor suppressor gene known to be involved in nonpapillary renal cell carcinoma. A previous loss of heterozygosity (LOH) study aimed at determining the allelotype of kidney tumors has indicated that in addition to 3p, chromosome arms 5q, 6q, 10q, 11q, 17p, and 19p may also harbor tumor suppressor genes. However, cytogenetic studies reveal that chromosomes 3p, 6q, 8p, 9pq, and 14q most frequently undergo karyotypic changes in renal tumors. To resolve these differences, a collection of microsatellite DNA probes has been used to scan for LOH so that 90% of individual tumor genomes were rendered informative for allele loss. The assay is capable of detecting quantitative genomic alterations in tumor cells as well. We find that LOH is most frequent for chromosome arm 3p. However, in no tumor is 3p exclusively affected. LOH for 6q, 8p, 9pq, and 14q is also distinctly elevated for both nonpapillary as well as papillary tumors and suggest that many of the tumor suppressor loci involved may be common to the etiology of both forms of kidney cancer.
Prolactin-immunoglobulin G complexes from human serum act as costimulatory ligands causing proliferation of malignant B lymphocytes.
Authors: Walker A M , Montgomery D W , Saraiya S , Ho T W , Garewal H S , Wilson J , Lorand L
Published: May 2006

Several lines of evidence indicate that immunoglobulin-bound prolactin found in human serum is not a conventional complex between an anti-prolactin antibody and prolactin but a different type of association of prolactin with the Fab portion of IgG heavy chains. The complex of prolactin with IgG was purified from serum by anti-human prolactin affinity chromatography and was shown to contain close to 1 mole of N epsilon-(gamma-glutamyl)lysine crosslinks per mole of complex, a characteristic feature in structures crosslinked by transglutaminase. Interestingly, the complex caused a proliferation of cells from a subset of patients with chronic lymphocytic leukemia, while it was inactive in a cell proliferation prolactin bioassay. By contrast, human prolactin stimulated the proliferation of cells in the bioassay but had no effect on the complex-responsive cells from the patients. Competition studies with prolactin and free Fc fragment of IgG demonstrated a necessity for engaging both the prolactin and the immunoglobulin receptors for proliferation. More importantly, competition for the growth response by free prolactin and IgG suggests both possible reasons for the slow growth of this neoplasm as well as avenues for control of the disease.