Chrysanthemum chlorotic mottle viroid: Unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes

The causal agent of chrysanthemum chlorotic mottle (CChM) disease has been identified, cloned, and sequenced. It is a viroid RNA (CChMVd) of 398–399 nucleotides. In vitro transcripts with the complete CChMVd sequence were infectious and induced the typical symptoms of the CChM disease. CChMVd can form hammerhead structures in both polarity strands. Plus and minus monomeric CChMVd RNAs self-cleaved during in vitro transcription and after purification as predicted by these structures, which are stable and most probably act as single hammerhead structures as in peach latent mosaic viroid (PLMVd), but not in avocado sunblotch viroid (ASBVd). Moreover, the plus CChMVd hammerhead structure also appears to be active in vivo, because the 5′ terminus of the linear plus CChMVd RNA isolated from infected tissue is that predicted by the corresponding hammerhead ribozyme. Both hammerhead structures of CChMVd display some peculiarities: the plus self-cleaving domain has an unpaired A after the conserved A9 residue, and the minus one has an unusually long helix II. The most stable secondary structure predicted for CChMVd is a branched conformation that does not fulfill the rod-like or quasi-rod-like model proposed for the in vitro structure of most viroids with the exception of PLMVd, whose proposed secondary structure of lowest free energy also is branched. The unusual conformation of CChMVd and PLMVd is supported by their insolubility in 2 M LiCl, in contrast to ASBVd and a series of representative non-self-cleaving viroids that are soluble under the same high salt conditions. These results support the classification of self-cleaving viroids into two subgroups, one formed by ASBVd and the other one by PLMVd and CChMVd.

Identification of an ATP-binding cassette transporter involved in bicarbonate uptake in the cyanobacterium Synechococcus sp. strain PCC 7942

Exposure of cells of cyanobacteria (blue–green algae) grown under high-CO2 conditions to inorganic C-limitation induces transcription of particular genes and expression of high-affinity CO2 and HCO3− transport systems. Among the low-CO2-inducible transcription units of Synechococcus sp. strain PCC 7942 is the cmpABCD operon, encoding an ATP-binding cassette transporter similar to the nitrate/nitrite transporter of the same cyanobacterium. A nitrogen-regulated promoter was used to selectively induce expression of the cmpABCD genes by growth of transgenic cells on nitrate under high CO2 conditions. Measurements of the initial rate of HCO3− uptake after onset of light, and of the steady-state rate of HCO3− uptake in the light, showed that the controlled induction of the cmp genes resulted in selective expression of high-affinity HCO3− transport activity. The forced expression of cmpABCD did not significantly increase the CO2 uptake capabilities of the cells. These findings demonstrated that the cmpABCD genes encode a high-affinity HCO3− transporter. A deletion mutant of cmpAB (M42) retained low CO2-inducible activity of HCO3− transport, indicating the occurrence of HCO3− transporter(s) distinct from the one encoded by cmpABCD. HCO3− uptake by low-CO2-induced M42 cells showed lower affinity for external HCO3− than for wild-type cells under the same conditions, showing that the HCO3− transporter encoded by cmpABCD has the highest affinity for HCO3− among the HCO3− transporters present in the cyanobacterium. This appears to be the first unambiguous identification and description of a primary active HCO3− transporter.

Integrin activation controls metastasis in human breast cancer

Metastasis is the primary cause of death in human breast cancer. Metastasis to bone, lungs, liver, and brain involves dissemination of breast cancer cells via the bloodstream and requires adhesion within the vasculature. Blood cell adhesion within the vasculature depends on integrins, a family of transmembrane adhesion receptors, and is regulated by integrin activation. Here we show that integrin αvβ3 supports breast cancer cell attachment under blood flow conditions in an activation-dependent manner. Integrin αvβ3 was found in two distinct functional states in human breast cancer cells. The activated, but not the nonactivated, state supported tumor cell arrest during blood flow through interaction with platelets. Importantly, activated αvβ3 was expressed by freshly isolated metastatic human breast cancer cells and variants of the MDA-MB 435 human breast cancer cell line, derived from mammary fat pad tumors or distant metastases in severe combined immunodeficient mice. Expression of constitutively activated mutant αvβ3D723R, but not αvβ3WT, in MDA-MB 435 cells strongly promoted metastasis in the mouse model. Thus breast cancer cells can exhibit a platelet-interactive and metastatic phenotype that is controlled by the activation of integrin αvβ3. Consequently, alterations within tumors that lead to the aberrant control of integrin activation are expected to adversely affect the course of human breast cancer.

ATP-dependent Membrane Assembly of F-Actin Facilitates Membrane Fusion

We recently established an in vitro assay that monitors the fusion between latex-bead phagosomes and endocytic organelles in the presence of J774 macrophage cytosol (Jahraus et al., 1998). Here, we show that different reagents affecting the actin cytoskeleton can either inhibit or stimulate this fusion process. Because the membranes of purified phagosomes can assemble F-actin de novo from pure actin with ATP (Defacque et al., 2000a), we focused here on the ability of membranes to nucleate actin in the presence of J774 cytosolic extracts. For this, we used F-actin sedimentation, pyrene actin assays, and torsional rheometry, a biophysical approach that could provide kinetic information on actin polymerization and gel formation. We make two major conclusions. First, under our standard in vitro conditions (4 mg/ml cytosol and 1 mM ATP), the presence of membranes actively catalyzed the assembly of cytosolic F-actin, which assembled into highly viscoelastic gels. A model is discussed that links these results to how the actin may facilitate fusion. Second, cytosolic actin paradoxically polymerized more under ATP depletion than under high-ATP conditions, even in the absence of membranes; we discuss these data in the context of the well described, large increases in F-actin seen in many cells during ischemia.

GenEST, a powerful bidirectional link between cDNA sequence data and gene expression profiles generated by cDNA-AFLP

The release of vast quantities of DNA sequence data by large-scale genome and expressed sequence tag (EST) projects underlines the necessity for the development of efficient and inexpensive ways to link sequence databases with temporal and spatial expression profiles. Here we demonstrate the power of linking cDNA sequence data (including EST sequences) with transcript profiles revealed by cDNA-AFLP, a highly reproducible differential display method based on restriction enzyme digests and selective amplification under high stringency conditions. We have developed a computer program (GenEST) that predicts the sizes of virtual transcript-derived fragments (TDFs) of in silico-digested cDNA sequences retrieved from databases. The vast majority of the resulting virtual TDFs could be traced back among the thousands of TDFs displayed on cDNA-AFLP gels. Sequencing of the corresponding bands excised from cDNA-AFLP gels revealed no inconsistencies. As a consequence, cDNA sequence databases can be screened very efficiently to identify genes with relevant expression profiles. The other way round, it is possible to switch from cDNA-AFLP gels to sequences in the databases. Using the restriction enzyme recognition sites, the primer extensions and the estimated TDF size as identifiers, the DNA sequence(s) corresponding to a TDF with an interesting expression pattern can be identified. In this paper we show examples in both directions by analyzing the plant parasitic nematode Globodera rostochiensis. Various novel pathogenicity factors were identified by combining ESTs from the infective stage juveniles with expression profiles of ∼4000 genes in five developmental stages produced by cDNA-AFLP.

The Cia5 gene controls formation of the carbon concentrating mechanism in Chlamydomonas reinhardtii

Wild-type Chlamydomonas reinhardtii cells shifted from high concentrations (5%) of CO2 to low, ambient levels (0.03%) rapidly increase transcription of mRNAs from several CO2-responsive genes. Simultaneously, they develop a functional carbon concentrating mechanism that allows the cells to greatly increase internal levels of CO2 and HCO\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document}. The cia5 mutant is defective in all of these phenotypes. A newly isolated gene, designated Cia5, restores transformed cia5 cells to the phenotype of wild-type cells. The 6,481-bp gene produces a 5.1-kb mRNA that is present constitutively in light in high and low CO2 both in wild-type cells and the cia5 mutant. It encodes a protein that has features of a putative transcription factor and that, likewise, is present constitutively in low and high CO2 conditions. Complementation of cia5 can be achieved with a truncated Cia5 gene that is missing the coding information for 54 C-terminal amino acids. Unlike wild-type cells or cia5 mutants transformed with an intact Cia5 gene, cia5 mutants complemented with the truncated gene exhibit constitutive synthesis of mRNAs from CO2-responsive genes in light under both high and low CO2 conditions. These discoveries suggest that posttranslational changes to the C-terminal domain control the ability of CIA5 to act as an inducer and directly or indirectly control transcription of CO2-responsive genes. Thus, CIA5 appears to be a master regulator of the carbon concentrating mechanism and is intimately involved in the signal transduction mechanism that senses and allows immediate responses to fluctuations in environmental CO2 and HCO\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document} concentrations.

A deletion mutant in the human cytomegalovirus gene encoding IE1(491aa) is replication defective due to a failure in autoregulation.

Human cytomegalovirus (CMV) replication begins with the expression of two regulatory proteins, IE1(491aa) and IE2(579aa), produced from differentially spliced transcripts under control of the ie1/ie2 promoter-enhancer. A deletion mutation removing all 406 IE1(491aa)-specific amino acids was engineered into the viral genome and this mutant (RC303 delta Acc) was propagated on an IE1(491aa)-expressing human fibroblast cell line (ihfie1.3). RC303 delta Acc failed to replicate on normal human fibroblasts at low multiplicities of infection (mois). At mois > 3 plaque-forming units per cell, virus replication and production of progeny were comparable to wild type. However, at mois between 0.01 and 1, mutant virus replicated slowly on normal fibroblasts, a pattern that suggested initiation of productive infection required multiple hits. Replication of RC303 delta Acc correlated with the ability to express IE2(579aa), consistent with a role for IE1(491aa) in positive autoregulation of the ie1/ie2 promoter-enhancer and with data suggesting that virion transactivators compensate for the lack of IE1(491aa) under high moi conditions. ie1-deficient CMV should be completely avirulent, suggesting its utility as a gene therapy vector for hematopoietic progenitors that are normal sites of CMV latency.

Polimerização em emulsão de estireno em microrreator.

A polimerização em emulsão de estireno em um microrreator Syrris de 250 µL com misturador estático junção \"T\" foi estudada em duas etapas. Primeiro somente a fluidodinâmica deste dispositivo não convencional foi avaliada, depois, foi desenvolvida a reação de polimerização de forma a observar como este fator influencia no sistema. Os experimentos foram realizados procurando se atingir maiores conversões, mas mantendo a estabilidade da emulsão. Foi um trabalho exploratório, portanto se assemelha mais a um processo de evolução (evolutionary process). Foram verificados a partir de qual relação das vazões dos dois fluidos ocorre a formação de gotas, e que com o aumento da vazão da fase contínua, aquosa (Qc), mantendo constante a vazão da fase dispersa (Qd), foi verificado uma diminuição do diâmetro das gotas e um regime de fluxo laminar. Posteriormente, realizou-se a polimerização em emulsão do estireno no microrreator, porém com restrições para altas vazões. Os parâmetros de processo testados foram a proporção Qc e Qd, a temperatura e a concentração do iniciador para então verificar o efeito que a variação destas ocasionam na conversão de monômero, no diâmetro e número de partículas e nas massas moleculares médias. A polimerização foi feita para soma das vazões Qc e Qd da ordem de 100 µ L/min, com 15% de monômero na formulação e com o maior tempo de residência possível de 2,5 minutos. Para maiores concentrações de monômero, acima de 15% foi verificado entupimento do canal do microrreator. A taxa de conversão de monômero aumentou com o aumento da temperatura e com o aumento da concentração do iniciador, mas o maior valor atingido foi de apenas 37% devido ao baixo tempo de residência. Nos casos de maiores taxas de conversão, as massas moleculares obtidas foram as menores conforme o esperado pela teoria. Finalmente, os índices de polidispersão (PDI), obtidos foram da ordem de 2,5 a 3,5.

Nitrogen regulation of protein–protein interactions and transcript levels of GlnK PII regulator and AmtB ammonium transporter homologs in Archaea

Gene homologs of GlnK PII regulators and AmtB-type ammonium transporters are often paired on prokaryotic genomes, suggesting these proteins share an ancient functional relationship. Here, we demonstrate for the first time in Archaea that GlnK associates with AmtB in membrane fractions after ammonium shock, thus, providing a further insight into GlnK-AmtB as an ancient nitrogen sensor pair. For this work, Haloferax mediterranei was advanced for study through the generation of a pyrE2-based counterselection system that was used for targeted gene deletion and expression of Flag-tagged proteins from their native promoters. AmtB1-Flag was detected in membrane fractions of cells grown on nitrate and was found to coimmunoprecipitate with GlnK after ammonium shock. Thus, in analogy to bacteria, the archaeal GlnK PII may block the AmtB1 ammonium transporter under nitrogen-rich conditions. In addition to this regulated protein–protein interaction, the archaeal amtB-glnK gene pairs were found to be highly regulated by nitrogen availability with transcript levels high under conditions of nitrogen limitation and low during nitrogen excess. While transcript levels of glnK-amtB are similarly regulated by nitrogen availability in bacteria, transcriptional regulators of the bacterial glnK promoter including activation by the two-component signal transduction proteins NtrC (GlnG, NRI) and NtrB (GlnL, NRII) and sigma factor σN (σ54) are not conserved in archaea suggesting a novel mechanism of transcriptional control.

Fate and Transport of Naproxen in a Sandy Aquifer Material: Saturated Column Studies and Model Evaluation

Naproxen-C14H14O3 is a nonsteroidal anti-inflammatory drug which has been found at detectable concentrations in wastewater, surface water, and groundwater. Naproxen is relatively hydrophilic and is in anionic form at pH between 6 and 8. In this study, column experiments were performed using an unconsolidated aquifer material from an area near Barcelona (Spain) to assess transport and reaction mechanisms of Naproxen in the aquifer matrix under different pore water fluxes. Results were evaluated using HYDRUS-1D, which was used to estimate transport parameters. Batch sorption isotherms for Naproxen conformed with the linear model with a sorption coefficient of 0.42 (cm3 g−1), suggesting a low sorption affinity. Naproxen breakthrough curves (BTCs) measured in soil columns under steady-state, saturated water flow conditions displayed similar behavior, with no apparent hysteresis in sorption or dependence of retardation (R, 3.85-4.24) on pore water velocities. Soil sorption did not show any significant decrease for increasing flow rates, as observed from Naproxen recovery in the effluent. Sorption parameters estimated by the model suggest that Naproxen has a low sorption affinity to aquifer matrix. Most sorption of Naproxen occurred on the instantaneous sorption sites, with the kinetic sorption sites representing only about 10 to 40% of total sorption.

(Table 1) Soil physical parameters of sediments obtained in the Lüchow-Dannenberg district, Lower Saxony

The mobility of the radionuclides of the elements Sr, I, Cs and Ce were investigated for three typical sands of Northern Germany under simulated natural, undersaturated flow conditions. The laboratory experiments include the determination of the flow parameters of the seepwater movement as well as the transport velocities of the radionuclides in the sands. For the three selected sands, the following mobility sequence/order has been established for the radionuclides: I < Sr < Cs < Ce

(Table 1) Abundances of Discoaster species in ODP Hole 130-806C

Members of the calcareous nannofossil genus Discoaster have been used extensively to subdivide Tertiary deep-sea sediments into biostratigraphic zones or subzones (e.g., Martini, 1971; Bukry, 1973). Haq and Lohmann (1976) mapped biogeographic migrations of this group through time and over latitude. They suggested that expansions and contractions of Discoaster-dominated assemblages across latitudes reflect sea-surface temperature changes. Subsequently, late Pliocene Discoaster species were counted at closely spaced sample intervals from various Atlantic sites (Backman et al., 1986; Backman and Pestiaux, 1987; Chepstow-Lusty et al., 1989, 1991), and Indian Ocean as well as Pacific Ocean sites (Chepstow-Lusty, 1990). In addition to the biostratigraphic information revealing positions and the precision by which the different late Pliocene Discoaster species can be determined, these studies also demonstrated that discoasters strongly fluctuate in abundance as a function of time. These abundance variations occur in equatorial as well as temperate temperature regimes, and show periodicities that reflect orbital frequencies. Chepstow-Lusty et al. (1989, 1991) also suggested that the oscillating abundances partly represent productivity pressure, because discoasters tend to show low abundances under high productivity conditions and vice versa. In the Pacific Ocean, counts showing late Pliocene Discoaster abundances exist from three sites, namely Ocean Drilling Program (ODP) Site 677 in the eastern equatorial upwelling region, Core V28-179 from the central equatorial region, and Core V32-127 from the mid-latitude Hess Rise. The two Vema cores are condensed and show sedimentation rates below 0.5 cm/1000 yr, thus offering a poorly resolved stratigraphy. Hole 806C from the Ontong Java Plateau provided an opportunity to establish a highly resolved Discoaster record from the western extreme of the equatorial Pacific under an environmental setting that differed from ODP Site 677 by being less influenced by intense upwelling. The Discoaster counting technique is described by Backman and Shackleton (1983).

Foraminifera species in the CO2 vents near Ischia, Italy, 2010

The seas around the island of Ischia (Italy) have a lowered pH as a result of volcanic gas vents that emit carbon dioxide from the sea floor at ambient seawater temperatures. These areas of acidified seawater provide natural laboratories in which to study the long-term biological response to rising CO2 levels. Benthic foraminifera (single-celled protists) are particularly interesting as they have short life histories, are environmentally sensitive and have an excellent fossil record. Here, we examine changes in foraminiferal assemblages along pH gradients at CO2 vents on the coast of Ischia and show that the foraminiferal distribution, diversity and nature of the fauna change markedly in the living assemblages as pH decreases.

Transport of dredged sediment placed in the nearshore zone--Currituck sand-bypass study (phase I) /

New dredge-disposal techniques may serve the dual role of aiding sand by-passing across coastal inlets, and beach nourishment, provided the dredged sediments placed seaward of the surf zone move shoreward into that zone. During the summer of 1976, 26,750 cubic meters of relatively coarse sediment was dredged from New River Inlet, North Carolina, moved down coast by a split-hull barge, and placed in a 215-meter coastal reach between the 2- and 4-meter depth contours. Bathymetric changes on the disposal piles and in the adjacent beach and nearshore area were studied for a 13-week period (August to November 1976) to determine the modification of the surrounding beach and nearshore profile, and the net transport direction of the disposal sediment. The sediment piles initially created a local shoal zone with minimum depths of 0.6 meter. Disposal sediment was coarser (Mn = 0.49 millimeter) than the native sand at the disposal site (Mn = 0.14 millimeter) and coarser than the composite mean grain size of the entire profile (Mn = 0.21 millimeter). Shoaling and breaking waves caused rapid erosion of the pile tops and a gradual coalescing of the piles to form a disposal bar located seaward (= 90 meters) of a naturally occurring surf zone bar. As the disposal bar relief was reduced, the disposal bar-associated breaker zone was restricted to low tide times or periods of high wave conditions.

Series of articles on compressor and fan design written by German engineers.

Composed primarily of articles written by Bruno Eckert's group, Forschungsinstitut für Kraftfahrwesen und Fahrzeugmotoren, Technische Hochschule, Stuttgard. Translated by various groups and individuals both in and out of the Navy Dept. Preliminary translation done by German prisoners of war.