bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of two nuclear mammalian homologous DNA-pairing activities that do not require associated exonuclease activity.
Authors: Akhmedov A T , Bertrand P , Corteggiani E , Lopez B S
Published: May 2006

We have developed an assay to study homologous DNA-pairing activities in mammalian nuclear extracts. This assay is derived from the POM blot assay, described earlier, which was specific for RecA activity in bacterial crude extracts. In the present work, proteins from mammalian nuclear extracts were resolved by electrophoresis on SDS/polyacrylamide gels and then electrotransferred onto a nitrocellulose membrane coated with circular single-stranded DNA (ssDNA). The blot obtained was incubated with a labeled homologous double-stranded DNA (dsDNA). Homologous pairing between the ssDNA and the labeled dsDNA was detected by autoradiography as a radioactive spot on the membrane. In nuclear extracts from mammalian cells, we found two major polypeptides of 100 and 75 kDa, able to promote the formation of stable plectonemic joints. Joint molecule formation required at least one homologous end on the dsDNA, but either end of the dsDNA could be recruited to initiate the reaction. For each polypeptide, the reaction required divalent cations such as Mg2+, Ca2+, or Mn2+. Although ATP was not necessary, ADP was inhibitory in each case. Unlike most of the known eukaryotic DNA-pairing proteins, both activities identified here were able to promote the formation of joint molecules without requiring an associated exonuclease activity. In addition, these two proteins were detected in cell lines from different tissues and from different mammalian species (human, mouse, and hamster).
Quantitative measurement of regional blood flow with gadolinium diethylenetriaminepentaacetate bolus track NMR imaging in cerebral infarcts in rats: validation with the iodo[14C]antipyrine technique.
Authors: Wittlich F , Kohno K , Mies G , Norris D G , Hoehn-Berlage M
Published: May 2006

NMR bolus track measurements were correlated with autoradiographically determined regional cerebral blood flow (rCBF). The NMR method is based on bolus infusion of the contrast agent gadolinium diethylenetriaminepentaacetate and high-speed T*2-sensitive NMR imaging. The first pass of the contrast agent through the image plane causes a transient decrease of the signal intensity. This time course of the signal intensity is transformed into relative concentrations of the contrast agent in each pixel. The mean transit time and relative blood flow and volume are calculated from such indicator dilution curves. We investigated whether this NMR technique correctly expresses the relative rCBF. The relative blood flow data, calculated from NMR bolus track experiments, and the absolute values of iodo[14C]antipyrine autoradiography were compared. A linear relationship was observed, indicating the proportionality of the transient NMR signal change with CBF. Excellent interindividual reproducibility of calibration constants is observed (r = 0.963). For a given NMR protocol, bolus track measurements calibrated with autoradiography after the experiment allow determination of absolute values for rCBF and regional blood volume.
Activation of a neurofilament kinase, a tau kinase, and a tau phosphatase by decreased ATP levels in nerve growth factor-differentiated PC-12 cells.
Authors: Bush M L , Miyashiro J S , Ingram V M
Published: May 2006

Brain pathology in Alzheimer disease and in aged controls shows hyperphosphorylation of tau and of neurofilament proteins. Roder and Ingram [Roder, H.M. & Ingram, V.M. (1991) J. Neurosci. 11, 3325-3343 and Roder, H.M., Eden, P.A. & Ingram, V.M. (1993) Biochem. Biophys. Res. Commun. 193, 639-647] previously reported that the brain protein kinase PK40erk can hyperphosphorylate both tau and neurofilaments and interestingly, is strongly inhibited by ATP uncomplexed with Mg2+. We now report that the mitochondrial uncoupler carbonyl cyanide p-trifluoro-methoxyphenylhydrazone decreases ATP levels in rat pheochromacytoma (PC-12) cells differentiated with nerve growth factor and activates a neurofilament kinase, a tau kinase, and, unexpectedly, a tau phosphatase--either PP1 or PP2A. Such aberrant modulation of protein phosphorylation patterns could be the common biochemical basis for senile dementia and for Alzheimer disease and could explain the late-onset etiology of both conditions.
Ethanol enhances growth factor activation of mitogen-activated protein kinases by a protein kinase C-dependent mechanism.
Authors: Roivainen R , Hundle B , Messing R O
Published: May 2006

Excessive alcohol consumption alters neuronal growth and causes striking elongation of axons and dendrites in several brain regions. This could result from increased sensitivity to neurotrophic factors, since ethanol markedly enhances nerve growth factor (NGF)- and basic fibroblast growth factor (bFGF)-stimulated neurite outgrowth in the neural cell line PC12. The mechanism by which ethanol enhances growth factor responses was investigated by examining activation of mitogen-activated protein kinases (MAP kinases), a key event in growth factor signaling. Ethanol (100 mM) increased NGF- and bFGF-induced activation of MAP kinases. This increase, like ethanol-induced increases in neurite outgrowth, was prevented by down regulation of beta, delta, and epsilon protein kinase C (PKC) isozymes. Since chronic ethanol exposure specifically upregulates delta and epsilon PKC, these findings suggest that ethanol promotes neurite growth by enhancing growth factor signal transduction through a delta or epsilon PKC-regulated pathway.
Human liver mitochondrial carnitine palmitoyltransferase I: characterization of its cDNA and chromosomal localization and partial analysis of the gene.
Authors: Britton C H , Schultz R A , Zhang B , Esser V , Foster D W , McGarry J D
Published: May 2006

Using the cDNA for rat liver mitochondrial carnitine palmitoyltransferase I (CPT I; EC 2.3.1.21) as a probe, we isolated its counterpart as three overlapping clones from a human liver cDNA library. Both the nucleotide sequence of the human cDNA and the predicted primary structure of the protein (773 aa) proved to be very similar to those of the rat enzyme (82% and 88% identity, respectively). The CPT I mRNA size was also found to be the same (approximately 4.7 kb) in both species. Screening of a human genomic library with the newly obtained cDNA yielded a positive clone of approximately 6.5 kb which, upon partial analysis, was found to contain at least two complete exons linked by a 2.3-kb intron. Oligonucleotide primers specific to upstream and downstream regions of one of the exon/intron junctions were tested in PCRs with DNA from a panel of somatic cell hybrids, each containing a single human chromosome. The results allowed unambiguous assignment of the human liver CPT I gene to the q (long) arm of chromosome 11. Additional experiments established that liver and fibroblasts express the same isoform of mitochondrial CPT I, legitimizing the use of fibroblast assays in the differential diagnosis of the "muscle" and "hepatic" forms of CPT deficiency. The data provide insights into the structure of a human CPT I isoform and its corresponding gene and establish unequivocally that CPT I and CPT II are distinct gene products. Availability of the human CPT I cDNA should open the way to an understanding of the genetic basis of inherited CPT I deficiency syndromes, how the liver CPT I gene is regulated, and which tissues other than liver express this particular variant of the enzyme.
Voltage-dependent gating of an asymmetric gramicidin channel.
Authors: Oiki S , Koeppe R E , Andersen O S
Published: May 2006

In an effort to understand the molecular mechanisms of voltage activation of ion channels, we have chosen a system of known structure and examined the properties of heterodimeric channels formed between [Val1]gramicidin A ([Val1]gA) and [F6Val1]gramicidin A ([F6Val1]gA). Gramicidin channels are usually not voltage-dependent; but the introduction of a single symmetry-breaking dipolar F6Val1 residue into a ([Val1]gA)2 dimer to form the [F6Val1]gA/[Val1]gA heterodimer induces voltage-dependent transitions between two conducting states: a high-conductance state and a zero conductance (closed) state. The distribution between these states varies as a function of the applied potential but is not dependent on the nature of the permeant ion (H+ or Cs+). The permeating ions do not seem to contribute to the apparent gating charge.
Influence of interleukin 12 on p53 peptide vaccination against established Meth A sarcoma.
Authors: Noguchi Y , Richards E C , Chen Y T , Old L J
Published: May 2006

BALB/c murine sarcoma Meth A is known to have three missense point mutations in p53. We previously reported that a nonamer peptide containing the codon 234 mutational product (designated 234CM) elicited 234CM-specific cytotoxic T cells and that immunization with 234CM in adjuvant before tumor challenge inhibited Meth A growth. Because interleukin 12 (IL-12) has been shown to have antitumor activity against established tumors and immuno-modulatory activities, we analyzed its effect on p53 peptide immunization and Meth A growth. Multiple injections of IL-12 alone (4 times a week for 2 weeks) caused regression of established Meth A sarcoma, and this effect was dose dependent. IL-12 treatment prior to Meth A challenge had little or no antitumor activity. To evaluate the effect of IL-12 on the generation of 234CM-specific cytotoxic T lymphocytes, spleen cells from BALB/c mice immunized with 234CM in adjuvant and injected with various doses of IL-12 were sensitized with 234CM in vitro. Multiple injections of 1 ng of IL-12 induced the highest cytotoxicity against target cells pulsed with 234CM. Higher doses of IL-12 suppressed 234CM-specific cytotoxic T-cell generation. Mice immunized with 234CM in QS-21 adjuvant and treated with 1 ng of IL-12 rejected established Meth A sarcoma. Mice comparably treated with 1 ng of IL-12 but immunized with 234CW peptide (the wild-type counterpart to 234CM) in QS-21 or with QS-21 alone showed progressive tumor growth.
Myoblast differentiation during mammalian somitogenesis is dependent upon a community effect.
Authors: Cossu G , Kelly R , Di Donna S , Vivarelli E , Buckingham M
Published: May 2006

The differentiation potential of early mammalian myogenic cells was tested under clonal culture conditions. Cells were isolated from paraxial mesoderm and limb buds of transgenic mouse embryos at 9.5 days after conception and grown in culture at clonal density either on collagen-coated dishes or on various feeder cell layers. The transgene used contained a reporter gene encoding beta-galactosidase with a nuclear localization signal under the control of regulatory sequences from the gene for fast myosin light chain 3, so that beta-galactosidase staining indicated the presence of differentiated muscle cells. After 5 days in culture, the number and size of beta-galactosidase-positive (beta-gal+) clones were recorded. Cells isolated from somites I-V (the last five somites to have formed) or from unsegmented paraxial mesoderm did not give rise to any beta-gal+ clones. Cells isolated from somites VI-X or from the forelimb bud gave rise to beta-gal+ clones, but only on feeder cells. Cells from somites XI or older gave rise to beta-gal+ clones independently of the substrate. However, when cells isolated from unsegmented paraxial mesoderm or somites I-V were cultured with nontransgenic cells from the trunk (including neural tube and notochord), differentiation occurred on condition that the cells were in a three-dimensional aggregate, even though their specific position in the somite had been lost. By culturing explants ranging in size from 1 to < 100 cells in the presence of an inhibitor of cell division, we determined that a minimal number of 30-40 cells is required for mesodermal cells to differentiate.
Molecular cloning and characterization of chitinase genes from Candida albicans.
Authors: McCreath K J , Specht C A , Robbins P W
Published: May 2006

Chitinase (EC 3.2.1.14) is an important enzyme for the remodeling of chitin in the cell wall of fungi. We have cloned three chitinase genes (CHT1, CHT2, and CHT3) from the dimorphic human pathogen Candida albicans. CHT2 and CHT3 have been sequenced in full and their primary structures have been analyzed: CHT2 encodes a protein of 583 aa with a predicted size of 60.8 kDa; CHT3 encodes a protein of 567 aa with a predicted size of 60 kDa. All three genes show striking similarity to other chitinase genes in the literature, especially in the proposed catalytic domain. Transcription of CHT2 and CHT3 was greater when C. albicans was grown in a yeast phase as compared to a mycelial phase. A transcript of CHT1 could not be detected in either growth condition.
Pancreatic digestive enzyme secretion in the rabbit: rapid cyclic variations in enzyme composition.
Authors: Adelson J W , Clarizio R , Coutu J A
Published: May 2006

The role and mechanism of nonparallel pancreatic secretion of digestive enzymes, in which enzyme proportions change in rapidly regulated fashion, remain controversial. Secretion was collected from male 2.2-kg New Zealand rabbits in 5-min intervals for 3 h under basal conditions or constant stimulation with cholecystokinin (CCK; 0.1 microgram per kg per h i.v.) or methacholine chloride (MCh; 40 micrograms per kg per h i.v.). Both CCK and MCh produced an 8-fold stimulation of protein output. Enzymes were separated by SDS/PAGE and quantitated by densitometry of Coomassie blue-stained gels. Under both basal conditions and constant MCh infusion, rapid neurosecretory-like 12-min cyclic changes occurred in the proportions of amylase, lipase I, chymotrypsinogen, and trypsinogen. During constant infusion their percentages changed as much as 10-fold, and their ratios cycled by as much as 30-fold. The mean percentage for the entire infusion period for lipase I declined > 25% with CCK or MCh, for amylase it rose approximately 30%, and for chymotrypsinogen and trypsinogen it doubled (for all, P < 0.05). CCK and MCh elicited subtly but significantly different mean enzyme percentages and enzyme ratios (P < 0.05) for amylase, chymotrypsinogen, and trypsinogen; these differences were also confirmed by regression and correlation analyses. The changes in enzyme percentages and ratios were explicitly consistent with secretagogue-caused shifts in the intrapancreatic enzyme secretory sources. Nonparallel secretion of digestive enzymes occurs routinely, even during constant stimulation, and is due to cyclic neurosecretory-like secretion from heterogeneous intrapancreatic sources.
Evidence suggesting that the odortypes of pregnant women are a compound of maternal and fetal odortypes.
Authors: Beauchamp G K , Katahira K , Yamazaki K , Mennella J A , Bard J , Boyse E A
Published: May 2006

Odortypes--namely, body odors that distinguish one individual from another on the basis of genetic polymorphism at the major histocompatibility complex and other loci--are a fundamental element in the social life and reproductive behavior of the mouse, including familial imprinting, mate choice, and control of early pregnancy. Odortypes are strongly represented in urine. During mouse pregnancy, an outcrossed mother's urine acquires fetal major histocompatibility complex odortypes of paternal origin, an observation that we took as the focus of a search for odortypes in humans, using a fully automated computer-programmed olfactometer in which trained rats are known to distinguish precisely the odortypes of another species. Five women provided urine samples before and after birth, which in each case appropriately trained rats were found to distinguish in the olfactometer. Whether this olfactory distinction of mothers' urine before and after birth reflects in part the odortype and hence genotype of the fetus, and not just the state of pregnancy per se, was tested in a second study in which each mother's postpartum urine was mixed either with urine from her own infant or with urine of a different, same-aged infant. Responses of trained rats were more positive with respect to the former (congruous) mixtures than to the latter (incongruous) mixtures, implying that, as in the mouse, human fetal odortypes of paternal genomic origin are represented in the odortype of the mother, doubtless by circulatory transfer of the pertinent odorants.
Kinetics of hydrogen bond breakage in the process of unfolding of ribonuclease A measured by pulsed hydrogen exchange.
Authors: Kiefhaber T , Baldwin R L
Published: May 2006

A sensitive test for kinetic unfolding intermediates in ribonuclease A (EC 3.1.27.5) is performed under conditions where the enzyme unfolds slowly (10 degrees C, pH 8.0, 4.5 M guanidinium chloride). Exchange of peptide NH protons (2H-1H) is used to monitor structural opening of individual hydrogen bonds during unfolding, and kinetic models are developed for hydrogen exchange during the process of protein unfolding. The analysis indicates that the kinetic process of unfolding can be monitored by EX1 exchange (limited by the rate of opening) for ribonuclease A in these conditions. Of the 49 protons whose unfolding/exchange kinetics was measured, 47 have known hydrogen bond acceptor groups. To test whether exchange during unfolding follows the EX2 (base-catalyzed) or the EX1 (uncatalyzed) mechanism, unfolding/exchange was measured both at pH 8.0 and at pH 9.0. A few faster-exchanging protons were found that undergo exchange by both EX1 and EX2 processes, but the 43 slower-exchanging protons at pH 8 undergo exchange only by the EX1 mechanism, and they have closely similar rates. Thus, it is likely that all 49 protons undergo EX1 exchange at the same rate. The results indicate that a single rate-limiting step in unfolding breaks the entire network of peptide hydrogen bonds and causes the overall unfolding of ribonuclease A. The additional exchange observed for some protons that follows the EX2 mechanism probably results from equilibrium unfolding intermediates and will be discussed elsewhere.
Substitution of a highly basic helix/loop sequence into the RNase H domain of human immunodeficiency virus reverse transcriptase restores its Mn(2+)-dependent RNase H activity.
Authors: Keck J L , Marqusee S
Published: May 2006

Human immunodeficiency virus (HIV) reverse transcriptase (RT) is a multifunctional protein, containing both DNA polymerase and RNase H activity. The RNase H activity of HIV RT catalyzes the hydrolysis of the RNA strand of RNA.DNA hybrids. While the domain that carries out the RNase H activity in HIV RT can be expressed as an independent, folded polypeptide, it is inactive as an RNase H. Here, we report the overexpression and purification of an active, recombinant HIV RNase H domain in which the sequence corresponding to the Escherichia coli RNase H1 basic helix/loop has been substituted for the corresponding sequence of HIV RNase H. The resulting polypeptide (RNH102) has Mn(2+)-dependent RNase H activity and is more stable than the independently expressed wild-type HIV RNase H domain.
Diverse incidences of individual oligopeptides (dipeptidic to hexapeptidic) in proteins of human, bakers' yeast, and Escherichia coli origin registered in the Swiss-Prot data base.
Authors: Doi H , Kitajima M , Watanabe I , Kikuchi Y , Matsuzawa F , Aikawa S , Takiguchi K , Ohno S
Published: May 2006

Oligopeptidic permutations of the 20 amino acid residues give rise to proteins of diverse functions. Our long-term goal is to produce a lexicon of oligopeptides, classifying them into at least five categories: (i) ubiquitous, (ii) function specific, (iii) group specific, (iv) species specific, and (v) nonexistent. To begin with, we report on the varying frequencies of individual oligopeptides (dipeptidic to hexapeptidic in length) found among 2862 human proteins, 1942 Saccharomyces cerevisiae proteins, and 2672 Escherichia coli proteins registered in the Swiss-Prot data base (version 29.0, released in June 1994). At all lengths (dipeptides to hexapeptides), homooligopeptides were very prominent among the most frequently occurring varieties in proteins of human and bakers' yeast origins. However, this was not the case with E. coli. While all of the expected 20(3) varieties of tripeptides were found among human proteins, three tripeptides (Cys-Cys-Trp, Trp-Trp-Cys, and Trp-Trp-His) were missing from the bakers' yeast proteins. Three tripeptides (Cys-Ile-Trp, Cys-Met-Tyr, and Cys-Trp-Trp) were also absent from E. coli proteins. Inasmuch as the Swiss-Prot data base already contained 67% of the expected total of 4000 E. coli proteins, it is virtually certain that 96,000 varieties of hexapeptides containing at least one or another of the three missing tripeptides noted above shall be nonexistent in E. coli. Furthermore, the observation of missing tripeptides in the bakers' yeast proteins suggests that nonexistent hexapeptides shall be highly phylum specific. Because of the sample size, only a small fraction of the 20(6) varieties of hexapeptides were expected to be encountered in the present survey. Indeed, only 1.2-1.5% of the possible hexapeptides were found, and the average copy number of observed hexapeptides varied between 1.06 and 1.25. Nevertheless, 33 varieties of hexapeptides occurred in 102-169 copies among human proteins. Furthermore, 15 of the 33 varieties contained such rarely used residues as Tyr, His, Cys, and Trp.
Evolutionary importance for the membrane enhancement of the production of vitamin D3 in the skin of poikilothermic animals.
Authors: Holick M F , Tian X Q , Allen M
Published: May 2006

The photoproduction of vitamin D in the skin was essential for the evolutionary development of terrestrial vertebrates. During exposure to sunlight, previtamin D3 formed in the skin is isomerized to vitamin D3 (calciol) by a temperature-dependent process. Since early land vertebrates were poikilothermic, the relatively slow conversion of previtamin D3 to vitamin D3 at ambient temperature put them at serious risk for developing vitamin D deficiency, thus leading to a poorly mineralized skeleton that could have ultimately halted further evolutionary development of vertebrates on land. We evaluated the rate of isomerization of previtamin D3 to vitamin D3 in the skin of iguanas and found the isomerization rate was enhanced by 1100% and 1700% at 25 degrees C and 5 degrees C, respectively. It is likely that the membrane entrapment of previtamin D3 in its s-cis,s-cis conformation is responsible for the markedly enhanced conversion of previtamin D3 to vitamin D3. The membrane-enhanced production of vitamin D3 ensures the critical supply of vitamin D3 to poikilothermic animals such as iguanas.
Sustained delivery of erythropoietin in mice by genetically modified skin fibroblasts.
Authors: Naffakh N , Henri A , Villeval J L , Rouyer-Fessard P , Moullier P , Blumenfeld N , Danos O , Vainchenker W , Heard J M , Beuzard Y
Published: May 2006

We have examined whether the secretion of erythropoietin (Epo) from genetically modified cells could represent an alternative to repeated injections of the recombinant hormone for treating chronic anemias responsive to Epo. Primary mouse skin fibroblasts were transduced with a retroviral vector in which the murine Epo cDNA is expressed under the control of the murine phosphoglycerate kinase promoter. "Neo-organs" containing the genetically modified fibroblasts embedded into collagen lattices were implanted into the peritoneal cavity of mice. Increased hematocrit (> 80%) and elevated serum Epo concentration (ranging from 60 to 408 milliunits/ml) were observed in recipient animals over a 10-month observation period. Hematocrit values measured in recipient mice varied according to the number of implanted Epo-secreting fibroblasts (ranging from 2.5 to 20 x 10(6)). The implantation of neo-organs containing Epo-secreting fibroblasts appeared, therefore, as a convenient method to achieve permanent in vivo delivery of the hormone. We estimated that the biological efficacy of the approach may be relevant for the treatment of human hemoglobinopathies.
Crystallization and preliminary x-ray studies of NADPH-cytochrome P450 reductase.
Authors: Djordjevic S , Roberts D L , Wang M , Shea T , Camitta M G , Masters B S , Kim J J
Published: May 2006

NADPH-cytochrome P450 reductase (CPR; NADPH:ferrihemoprotein reductase, EC 1.6.2.4) catalyzes the transfer of electrons to all known microsomal cytochromes P450. CPR is unique in that it is one of only two mammalian enzymes known to contain both flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN), the other being the various isoforms of nitric oxide synthase. Similarities in amino acid sequence and in functional domain arrangement with other key flavoproteins, including nitric oxide synthase, make CPR an excellent prototype for studies of interactions between two flavin cofactors. We have obtained diffraction-quality crystals of rat liver CPR, expressed in Escherichia coli and solubilized by limited proteolysis with trypsin. The crystals were grown in Hepes buffer (pH 7.0), containing polyethylene glycol 4500 and NaCl. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit cell dimensions a = 103.3 A, b = 116.1 A, and c = 120.4 A. If we assume that there are two molecules of the 72-kDa CPR polypeptide per asymmetric unit, the calculated value of Vm is 2.54 A3/Da.
Suppression and promotion of tumor growth by monoclonal antibodies to ErbB-2 differentially correlate with cellular uptake.
Authors: Hurwitz E , Stancovski I , Sela M , Yarden Y
Published: May 2006

Amplification and overexpression of the erbB-2/neu protooncogene are frequently associated with aggressive clinical course of certain human adenocarcinomas, and therefore the encoded surface glycoprotein is considered a candidate target for immunotherapy. We previously generated a series of anti-ErbB-2 monoclonal antibodies (mAbs) that either accelerate or inhibit the tumorigenic growth of erbB-2-transformed murine fibroblasts. The present study extended this observation to a human tumor cell line grown as xenografts in athymic mice and addressed the biochemical differences between the two classes of mAbs. We show that the inhibitory effect is dominant in an antibody mixture, and it depends on antibody bivalency. By using radiolabeled mAbs we found that all of three tumor-inhibitory mAbs became rapidly inaccessible to acid treatment when incubated with tumor cells. However, a tumor-stimulatory mAb remained accessible to extracellular treatments, indicating that it did not undergo endocytosis. In addition, intracellular fragments of the inhibitory mAbs, but not of the stimulatory mAb, were observed. Electron microscopy of colloidal gold-antibody conjugates confirmed the absence of endocytosis of the stimulatory mAb but detected endocytic vesicles containing an inhibitory mAb. We conclude that acceleration of cell growth by ErbB-2 correlates with cell surface localization, whereas inhibition of tumor growth is associated with an intrinsic ability of anti-ErbB-2 mAbs to induce endocytosis. These conclusions are relevant to the selection of optimal mAbs for immunotherapy and may have implications for the mechanism of cellular transformation by an overexpressed erbB-2 gene.
Cytokine-mediated survival from lethal herpes simplex virus infection: role of programmed neuronal death.
Authors: Geiger K D , Gurushanthaiah D , Howes E L , Lewandowski G A , Reed J C , Bloom F E , Sarvetnick N E
Published: May 2006

The mechanisms responsible for cytokine-mediated antiviral effects are not fully understood. We approached this problem by studying the outcome of intraocular herpes simplex (HSV) infection in transgenic mice that express interferon gamma in the photoreceptor cells of the retina. These transgenic mice showed selective survival from lethal HSV-2 infection manifested in both eyes, the optic nerve, and the brain. Although transgenic mice developed greater inflammatory responses to the virus in the eyes, inflammation and viral titers in their brains were equivalent to nontransgenic mice. However, survival of transgenic mice correlated with markedly lower numbers of central neurons undergoing apoptosis. The protooncogene Bcl2 was found to be induced in the HSV-2-infected brains of transgenic mice, allowing us to speculate on its role in fostering neuronal survival in this model. These observations imply a complex interaction between cytokine, virus, and host cellular factors. Our results suggest a cytokine-regulated salvage pathway that allows for survival of infected neurons.
The photoreceptor sensory rhodopsin I as a two-photon-driven proton pump.
Authors: Haupts U , Haupts C , Oesterhelt D
Published: May 2006

Proton translocation experiments with intact cells of Halobacterium salinarium overproducing sensory rhodopsin I (SRI) revealed transport activity of SRI in a two-photon process. The vectoriality of proton translocation depends on pH, being outwardly directed above, and inwardly directed below, pH 5.7. Activation of the transport cycle requires excitation of the initial dark state of SRI, SRI590, to form the intermediate SRI380. Action spectra identify the photocycle intermediates SRI380 and SRI520 as the two photochemically reactive species in the outwardly directed transport process. As shown by flash photolysis experiments, SRI520 undergoes a so-far unknown photochemical reaction to SRI380 with a half-time of <200 micros. Mutation of SRI residue Asp-76, the residue which is equivalent to the proton acceptor Asp-85 in bacteriorhodopsin, to asparagine leads to inactivation of proton translocation. This demonstrates that the underlying mechanisms of proton transport in both retinal proteins share similar features. However, SRI is to our knowledge the first case where photochemical reactions between two thermally unstable photoproducts of a retinal protein constitute a catalytic ion transport cycle.
Repressible cation-phosphate symporters in Neurospora crassa.
Authors: Versaw W K , Metzenberg R L
Published: May 2006

The filamentous fungus Neurospora crassa possesses two nonhomologous high-affinity phosphate permeases, PHO-4 and PHO-5. We have isolated separate null mutants of these permeases, allowing us to study the remaining active transporter in vivo in terms of phosphate uptake and sensitivity to inhibitors. The specificity for the cotransported cation differs for PHO-4 and PHO-5, suggesting that these permeases employ different mechanisms for phosphate translocation. Phosphate uptake by PHO-4 is stimulated 85-fold by the addition of Na+, which supports the idea that PHO-4 is a Na(+)-phosphate symporter. PHO-5 is unaffected by Na+ concentration but is much more sensitive to elevated pH than is PHO-4. Presumably, PHO-5 is a H(+)-phosphate symporter. Na(+)-coupled symport is usually associated with animal cells. The finding of such a system in a filamentous fungus is in harmony with the idea that the fungal and animal kingdoms are more closely related to each other than either is to the plant kingdom.
Functional interactions between the retinoblastoma (Rb) protein and Sp-family members: superactivation by Rb requires amino acids necessary for growth suppression.
Authors: Udvadia A J , Templeton D J , Horowitz J M
Published: May 2006

The transient expression of the retinoblastoma protein (Rb) regulates the transcription of a variety of growth-control genes, including c-fos, c-myc, and the gene for transforming growth factor beta 1 via discrete promoter sequences termed retinoblastoma control elements (RCE). Previous analyses have shown that Sp1 is one of three RCE-binding proteins identified in nuclear extracts and that Rb functionally interacts with Sp1 in vivo, resulting in the "superactivation" of Sp1-mediated transcription. By immunochemical and biochemical criteria, we report that an Sp1-related transcription factor, Sp3, is a second RCE-binding protein. Furthermore, in transient cotransfection assays, we report that Rb "superactivates" Sp3-mediated RCE-dependent transcription in vivo and that levels of superactivation are dependent on the trans-activator (Sp1 or Sp3) studied. Using expression vectors carrying mutated Rb cDNAs, we have identified two portions of Rb required for superactivation: (i) a portion of the Rb "pocket" (amino acids 614-839) previously determined to be required for physical interactions between Rb and transcription factors such as E2F-1 and (ii) a novel amino-terminal region (amino acids 140-202). Since both of these regions of Rb are targets of mutation in human tumors, our data suggest that superactivation of Sp1/Sp3 may play a role in Rb-mediated growth suppression and/or the induction of differentiation.
Regulation of CD45 engagement by the B-cell receptor CD22.
Authors: Sgroi D , Koretzky G A , Stamenkovic I
Published: May 2006

The B-cell receptor CD22 binds sialic acid linked alpha-2-6 to terminal galactose residues on N-linked oligosaccharides associated with several cell-surface glycoproteins. The first of these sialoglycoproteins to be identified was the receptor-linked phosphotyrosine phosphatase CD45, which is required for antigen/CD3-induced T-cell activation. In the present work, we examine the effect of interaction between the extracellular domain of CD45 and CD22 on T-cell activation. Using soluble CD22-immunoglobulin fusion proteins and T cells expressing wild-type and chimeric CD45 forms, we show that engagement of CD45 by soluble CD22 can modulate early T-cell signals in antigen receptor/CD3-mediated stimulation. We also show that addition of sialic acid by beta-galactoside alpha-2,6-sialyltransferase to the CD22 molecule abrogates interactions between CD22 and its ligands. Together, these observations provide direct evidence for a functional role of the interaction between the extracellular domain of CD45 and a natural ligand and suggest another regulatory mechanism for CD22-mediated ligand engagement.
Differential activation of proliferation and cytotoxicity in human T-cell lymphotropic virus type I Tax-specific CD8 T cells by an altered peptide ligand.
Authors: Höllsberg P , Weber W E , Dangond F , Batra V , Sette A , Hafler D A
Published: May 2006

Human T-cell leukemia virus type I (HTLV-I) gives rise to a neurologic disease known as HTLV-I-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Although the pathogenesis of the disease is unknown, the presence of a remarkably high frequency of Tax-specific, cytotoxic CD8 T cells may suggest a role of these cells in the development of HAM/TSP. Antigen-mediated signaling in a CD8 T-cell clone specific for the Tax(11-19) peptide of HTLV-I was studied using analog peptides substituted in their T-cell receptor contact residues defined by x-ray crystallographic data of the Tax(11-19) peptide in the groove of HLA-A2. CD8 T-cell stimulation with the wild-type peptide antigen led to activation of p56lck kinase activity, interleukin 2 secretion, cytotoxicity, and clonal expansion. A Tax analog peptide with an alanine substitution of the T-cell receptor contact residue tyrosine-15 induced T-cell-mediated cytolysis without activation of interleukin 2 secretion or proliferation. Induction of p56lck kinase activity correlated with T-cell-mediated cytotoxicity, whereas interleukin 2 secretion correlated with [3H]thymidine incorporation and proliferation. Moreover, Tax peptide analogs that activated the tyrosine kinase activity of p56lck could induce unresponsiveness to secondary stimulation with the wild-type peptide. These observations show that a single amino acid substitution in a T-cell receptor contact residue of Tax can differentially signal CD8 T cells and further demonstrate that primary activation has functional consequences for the secondary response of at least some Tax-specific CD8 T cells to HTLV-I-infected target cells.
Regulatory region in choline acetyltransferase gene directs developmental and tissue-specific expression in transgenic mice.
Authors: Lönnerberg P , Lendahl U , Funakoshi H , Arhlund-Richter L , Persson H , Ibáñez C F
Published: May 2006

Acetylcholine, one of the main neurotransmitters in the nervous system, is synthesized by the enzyme choline acetyltransferase (ChAT; acetyl-CoA:choline O-acetyltransferase, EC 2.3.1.6). The molecular mechanisms controlling the establishment, maintenance, and plasticity of the cholinergic phenotype in vivo are largely unknown. A previous report showed that a 3800-bp, but not a 1450-bp, 5' flanking segment from the rat ChAT gene promoter directed cell type-specific expression of a reporter gene in cholinergic cells in vitro. Now we have characterized a distal regulatory region of the ChAT gene that confers cholinergic specificity on a heterologous downstream promoter in a cholinergic cell line and in transgenic mice. A 2342-bp segment from the 5' flanking region of the ChAT gene behaved as an enhancer in cholinergic cells but as a repressor in noncholinergic cells in an orientation-independent manner. Combined with a heterologous basal promoter, this fragment targeted transgene expression to several cholinergic regions of the central nervous system of transgenic mice, including basal forebrain, cortex, pons, and spinal cord. In eight independent transgenic lines, the pattern of transgene expression paralleled qualitatively and quantitatively that displayed by endogenous ChAT mRNA in various regions of the rat central nervous system. In the lumbar enlargement of the spinal cord, 85-90% of the transgene expression was targeted to the ventral part of the cord, where cholinergic alpha-motor neurons are located. Transgene expression in the spinal cord was developmentally regulated and responded to nerve injury in a similar way as the endogenous ChAT gene, indicating that the 2342-bp regulatory sequence contains elements controlling the plasticity of the cholinergic phenotype in developing and injured neurons.
Rubellimicrobium thermophilum gen. nov., sp. nov., a red-pigmented, moderately thermophilic bacterium isolated from coloured slime deposits in paper machines
Authors: Denner Ewald B. M. , Kolari Marko , Hoornstra Douwe , Tsitko Irina , Kämpfer Peter , Busse Hans-Jürgen , Salkinoja-Salonen Mirja
Published: May 2006

Six red-pigmented strains of the Alphaproteobacteria with optimal growth between 45 and 54 °C were previously isolated from coloured biofilms in two fine-paper machines and one pulp dryer. The strains were found to be resistant to 15 p.p.m. 2,2-dibromo-3-nitrilopropionamide, a common industrial biocide. 16S RNA gene sequence similarity of the isolates was 99.7–100 %. Ribotyping using the restriction enzymes PvuII and EcoRI showed that four of the isolates (C-lvk-R2A-1, C-lvk-R2A-2T, C-R2A-52d and C-R2A-5d) belong to a single species. 16S rRNA gene-based phylogenetic analysis revealed that, together with Rhodobacter blasticus ATCC 33485T, the isolates form a deep line of descent (94.7–94.9 % sequence similarity) within the family Rhodobacteraceae loosely affiliated with the Rhodobacter/Paracoccus clade. The isolates were strictly aerobic and oxidase-positive (catalase was weakly positive) and utilized a wide range of substrates including pentoses, hexoses, oligosaccharides and sugar alcohols. The predominant constituents in their cellular fatty acid profiles were C19 : 0 cyclo ω8c (39–44 %), C18 : 0 (21–24 %) and C16 : 0 (21–23 %). Fatty acids present in smaller amounts included C18 : 1
ω7c, C10 : 0 3-OH, C18 : 1
ω7c 11-methyl, C20 : 2
ω6,9c and C17 : 0 cyclo, amongst others. Polar lipids included diphosphatidylglycerol, phosphatidylcholine and an unidentified aminolipid, but not phosphatidylethanolamine. Carotenoid pigments were synthesized but bacteriochlorophyll a was not. The polyamine patterns consisted of the major compounds putrescine, spermidine and sym-homospermidine. The major respiratory lipoquinone was ubiquinone Q-10. The DNA G+C content was 69.4–70.2 mol%. On the basis of the phylogenetic and phenotypic evidence, the biofilm isolates were classified in a new genus, Rubellimicrobium gen. nov.; four of the isolates are assigned to the type species, Rubellimicrobium thermophilum gen. nov., sp. nov. Strain C-lvk-R2A-2T (=CCUG 51817T=DSM 16684T=HAMBI 2421T) is the type strain of Rubellimicrobium thermophilum.
Psychrobacter cryohalolentis sp. nov. and Psychrobacter arcticus sp. nov., isolated from Siberian permafrost
Authors: Bakermans Corien , Ayala-del-Río Héctor L. , Ponder Monica A. , Vishnivetskaya Tatiana , Gilichinsky David , Thomashow Michael F. , Tiedje James M.
Published: May 2006

Three Gram-negative, non-motile, non-pigmented, oxidase-positive coccobacilli capable of growth at temperatures from −10 to 30 °C and salinities of 0 to 1.7 M NaCl were isolated from Siberian permafrost and characterized. Both 16S rRNA andgyrBgene sequencing studies placed the isolates in theGammaproteobacteriawithin the genusPsychrobacter. However, with higher bootstrap values and reproducible tree topologies,gyrBrepresented a more reliable phylogenetic marker for the taxonomy ofPsychrobacterspecies. DNA–DNA hybridization data supportedgyrBtree topologies and established two relatedness groups within the three isolates; neither of these groups was related at the species level to any previously describedPsychrobacterspecies. The two groups of isolates could be differentiated phenotypically from 13 previously describedPsychrobacterspecies using API strips. These results support the existence of two novel species ofPsychrobacter, for which we propose the namesPsychrobacter cryohalolentissp. nov. (type strain K5T=DSM 17306T=VKM B-2378T) andPsychrobacter arcticussp. nov. (type strain 273-4T=DSM 17307T=VKM B-2377T).
‘Candidatus Streptomyces philanthi’, an endosymbiotic streptomycete in the antennae of Philanthus digger wasps
Authors: Kaltenpoth Martin , Goettler Wolfgang , Dale Colin , Stubblefield J. William , Herzner Gudrun , Roeser-Mueller Kerstin , Strohm Erhard
Published: May 2006

Symbiotic interactions with bacteria are essential for the survival and reproduction of many insects. The European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae) engages in a highly specific association with bacteria of the genus Streptomyces that appears to protect beewolf offspring against infection by pathogens. Using transmission and scanning electron microscopy, the bacteria were located in the antennal glands of female wasps, where they form dense cell clusters. Using genetic methods, closely related streptomycetes were found in the antennae of 27 Philanthus species (including two subspecies of P. triangulum from distant localities). In contrast, no endosymbionts could be detected in the antennae of other genera within the subfamily Philanthinae (Aphilanthops, Clypeadon and Cerceris). On the basis of morphological, genetic and ecological data, ‘Candidatus Streptomyces philanthi’ is proposed. 16S rRNA gene sequence data are provided for 28 ecotypes of ‘Candidatus Streptomyces philanthi’ that reside in different host species and subspecies of the genus Philanthus. Primers for the selective amplification of ‘Candidatus Streptomyces philanthi’ and an oligonucleotide probe for specific detection by fluorescence in situ hybridization (FISH) are described.
Kineococcus marinus sp. nov., isolated from marine sediment of the coast of Jeju, Korea
Authors: Lee Soon Dong
Published: May 2006

A novel marine actinomycete, designated strain KST3-3T, which was isolated from a sediment sample of the coast of Jeju, Korea, was subjected to a polyphasic taxonomic characterization. The organism was characterized morphologically by the formation of motile, coccoid cells. A phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the organism was related to the generaKineosporiaandKineococcus, and members of the suborderFrankineae, and occupied the deepest branch outside a taxon encompassing members of the genusKineococcus. The organism showed relatively low levels of 16S rRNA gene sequence similarity to members of the generaKineococcus(93.0–93.4 %) andKineosporia(93.1–93.8 %). The morphological and chemotaxonomic characteristics, albeit with a slightly higher level of sequence similarity to members of the genusKineosporia, supported its classification within the genusKineococcus. On the basis of the polyphasic data presented, it was evident that the organism should be assigned to a novel species of the genusKineococcus, for which the nameKineococcus marinussp. nov. is proposed. The type strain is strain KST3-3T(=KCCM 42250T=NRRL B-24439T).
Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi
Authors: Yamada Takeshi , Sekiguchi Yuji , Hanada Satoshi , Imachi Hiroyuki , Ohashi Akiyoshi , Harada Hideki , Kamagata Yoichi
Published: May 2006

One thermophilic (strain IMO-1T) and two mesophilic (strains KIBI-1Tand YMTK-2T) non-spore-forming, non-motile, Gram-negative, multicellular filamentous micro-organisms, which were previously isolated as members of the tentatively named class ‘Anaerolineae’ of the phylumChloroflexi, were characterized. All isolates were strictly anaerobic micro-organisms. The length of the three filamentous isolates was greater than 100 μm and the width was 0.3–0.4 μm for strain IMO-1T, 0.4–0.5 μm for strain KIBI-1Tand thinner than 0.2 μm for strain YMTK-2T. Strain IMO-1Tcould grow at pH 6.0–7.5 (optimum growth at pH 7.0). The optimal temperature for growth of strain IMO-1Twas around 50 °C (growth occurred between 42 and 55 °C). Growth of the mesophilic strains KIBI-1Tand YMTK-2Toccurred at pH 6.0–7.2 with optimal growth at pH 7.0. Both of the mesophilic strains were able to grow in a temperature range of 25–50 °C with optimal growth at around 37 °C. Yeast extract was required for growth of all three strains. All the strains could grow with a number of carbohydrates in the presence of yeast extract. The G+C contents of the DNA of strains IMO-1T, KIBI-1Tand YMTK-2Twere respectively 53.3, 59.5 and 48.2 mol%. Major fatty acids for thermophilic strain IMO-1Twere anteiso-C17 : 0, iso-C15 : 0, C16 : 0and anteiso-C15 : 0, whereas those for mesophilic strains KIBI-1Tand YMTK-2Twere branched C14 : 0, iso-C15 : 0, C16 : 0and branched C17 : 0, and branched C17 : 0, C16 : 0, C14 : 0and C17 : 0, respectively. Detailed phylogenetic analyses based on their 16S rRNA gene sequences indicated that the isolates belong to the class-level taxon ‘Anaerolineae’ of the bacterial phylumChloroflexi, which for a long time had been considered as a typical uncultured clone cluster. Their morphological, physiological, chemotaxonomic and genetic traits strongly support the conclusion that these strains should be described as three novel independent taxa in the phylumChloroflexi. Here,Anaerolinea thermolimosasp. nov. (type strain IMO-1T=JCM 12577T=DSM 16554T),Levilinea saccharolyticagen. nov., sp. nov. (type strain KIBI-1T=JCM 12578T=DSM 16555T) andLeptolinea tardivitalisgen. nov., sp. nov. (type strain YMTK-2T=JCM 12579T=DSM 16556T) are proposed. In addition, we formally propose to subdivide the tentative class-level taxon ‘Anaerolineae’ intoAnaerolineaeclassis nov. andCaldilineaeclassis nov. We also propose the subordinate taxaAnaerolinealesord. nov.,Caldilinealesord. nov.,Anaerolineaceaefam. nov. andCaldilineaceaefam. nov.