The role of conserved region 1 of Escherichia coli sigma-70 in transcription initiation

The sigma (σ) subunit of eubacterial RNA polymerase is essential for initiation of transcription at promoter sites. σ factor directs the RNA polymerase core subunits ( a2bb′ ) to the promoter consensus elements and thereby confers selectivity for transcription initiation. The N-terminal domain (region 1.1) of Escherichia coli σ70 has been shown to inhibit DNA binding by the C-terminal DNA recognition domains when σ is separated from the core subunits. Since DNA recognition by RNA polymerase is the first step in transcription, it seemed plausible that region 1 might also influence initiation processes subsesquent to DNA binding. This study explores the functional roles of regions 1.1 and 1.2 of σ70 in transcription initiation. Analysis in vitro of the transcriptional properties of a series of N-terminally truncated σ70 derivates revealed a critical role for region 1.1 at several key stages of initiation. Deletion of the first 75 to 100 amino acids of σ70 (region 1.1) resulted in both a slow rate of transition from a closed promoter complex to a DNA-strand-separated open complex, as well as a reduced efficiency of transition from the open complex to a transcriptionally active open complex. These effects were partially reversed by addition of a polypeptide containing region 1.1 in trans. Therefore, region 1.1 not only modulates DNA binding but is important for efficient transcription initiation, once a closed complex has formed. A deletion of the first 133 amino acids which removes both regions 1.1 and 1.2 resulted in arrest of initiation at the earliest closed complex, suggesting that region 1.2 is required for open complex formation. Mutagenesis of region 1.1 uncovered a mechanistically important role for isoleucine at position 53 (I53). Substitution of I53 with alanine created a σ factor that associated with the core subunits to form holoenzyme, but the holoenzyme was severely deficient for promoter binding. The I53A phenotype was suppressed in vivo by truncation of five amino acids from the C-terminus of σ 70. These observations are consistent with a model in which σ 70I53A fails to undergo a critical conformational change upon association with the core subunits, which is needed to expose the DNA-binding domains and confer promoter recognition capability upon holoenzyme. To understand the basis of the autoinhibitory properties of the σ70 N-terminal domain, in the absence of core RNA polymerase, a preliminary physical assessment of the interdomain interactions within the σ70 subunit was launched. Results support a model in which N-terminal amino acids are in close proximity to residues in the C-terminus of the σ 70 polypeptide. ^

Loop formulation of the supersymmetric nonlinear O(N) sigma model

We derive the fermion loop formulation for the supersymmetric nonlinear O(N) sigma model by performing a hopping expansion using Wilson fermions. In this formulation the fermionic contribution to the partition function becomes a sum over all possible closed non-oriented fermion loop configurations. The interaction between the bosonic and fermionic degrees of freedom is encoded in the constraints arising from the supersymmetry and induces flavour changing fermion loops. For N ≥ 3 this leads to fermion loops which are no longer self-avoiding and hence to a potential sign problem. Since we use Wilson fermions the bare mass needs to be tuned to the chiral point. For N = 2 we determine the critical point and present boson and fermion masses in the critical regime.

Computer vision profiling of neurite outgrowth dynamics reveals spatiotemporal modularity of Rho GTPase signaling

Rho guanosine triphosphatases (GTPases) control the cytoskeletal dynamics that power neurite outgrowth. This process consists of dynamic neurite initiation, elongation, retraction, and branching cycles that are likely to be regulated by specific spatiotemporal signaling networks, which cannot be resolved with static, steady-state assays. We present NeuriteTracker, a computer-vision approach to automatically segment and track neuronal morphodynamics in time-lapse datasets. Feature extraction then quantifies dynamic neurite outgrowth phenotypes. We identify a set of stereotypic neurite outgrowth morphodynamic behaviors in a cultured neuronal cell system. Systematic RNA interference perturbation of a Rho GTPase interactome consisting of 219 proteins reveals a limited set of morphodynamic phenotypes. As proof of concept, we show that loss of function of two distinct RhoA-specific GTPase-activating proteins (GAPs) leads to opposite neurite outgrowth phenotypes. Imaging of RhoA activation dynamics indicates that both GAPs regulate different spatiotemporal Rho GTPase pools, with distinct functions. Our results provide a starting point to dissect spatiotemporal Rho GTPase signaling networks that regulate neurite outgrowth.

Spatio-temporal Rho GTPase signaling - where are we now?

Rho-family GTPases are molecular switches that transmit extracellular cues to intracellular signaling pathways. Their regulation is likely to be highly regulated in space and in time, but most of what is known about Rho-family GTPase signaling has been derived from techniques that do not resolve these dimensions. New imaging technologies now allow the visualization of Rho GTPase signaling with high spatio-temporal resolution. This has led to insights that significantly extend classic models and call for a novel conceptual framework. These approaches clearly show three things. First, Rho GTPase signaling dynamics occur on micrometer length scales and subminute timescales. Second, multiple subcellular pools of one given Rho GTPase can operate simultaneously in time and space to regulate a wide variety of morphogenetic events (e.g. leading-edge membrane protrusion, tail retraction, membrane ruffling). These different Rho GTPase subcellular pools might be described as 'spatio-temporal signaling modules' and might involve the specific interaction of one GTPase with different guanine nucleotide exchange factors (GEFs), GTPase-activating proteins (GAPs) and effectors. Third, complex spatio-temporal signaling programs that involve precise crosstalk between multiple Rho GTPase signaling modules regulate specific morphogenetic events. The next challenge is to decipher the molecular circuitry underlying this complex spatio-temporal modularity to produce integrated models of Rho GTPase signaling.

Understanding Molecular Orbitals; Sigma Orbitals

Various plots of sigma molecular orbitals in diatomic molecules are discussed.

An analysis of the function of region 1.2 of the primary sigma factor, sigma 70, from Escherichia coli

The sigma (σ) subunit of eubacterial RNA polymerase is required for recognition of and transcription initiation from promoter DNA sequences. One family of sigma factors includes those related to the primary sigma factor from E. coli, σ70. Members of the σ70 family have four highly conserved domains, of which regions 2 through 4 are present in all members. Region 1 can be subdivided into regions 1.1 and 1.2. Region 1.1 affects DNA binding by σ 70 alone, as well as transcription initiation by holoenzyme. Region 1.2, present and highly conserved in most sigma factors, has not yet been assigned a putative function, although previous work demonstrated that it is not required for either association with the core subunits of RNA polymerase or promoter specific binding by holoenzyme. This study primarily investigates the functional role of region 1.2 during transcription initiation. In vivo and in vitro characterization of thirty-two single amino acid substitutions targeted to region 1.2 of E. coli σ70 as well as a deletion of region 1.2, revealed that mutations in region 1.2 can affect promoter binding, open complex formation, initiated complex formation, and the transition from abortive transcription to elongation. The relative degree of solvent exposure of several positions in region 1.2 has been determined, with positions 116 and 122 likely to be located near the surface of σ70. ^ During the course of this study, the existence of two “wild type” variants of E. coli σ70 was discovered. The identity of amino acid 149 has been reported variably as either arginine or aspartic acid in published articles and in online databases. In vivo and in vitro characterization of the two reported variations of E. coli σ70 (N149 and D149) has determined that the two variants are functionally equivalent. However, in vivo and in vitro characterization of single amino acid substitutions and a region 1.2 deletion in the context of each variant background revealed that the behavior of some mutations are greatly affected by the identity of amino acid 149. ^

An extracytoplasmic function sigma factor operon regulates Myxococcus xanthus developmental gene expression

Myxococcus xanthus is a Gram-negative soil bacterium that undergoes multicellular development when high-density cells are starved on a solid surface. Expression of the 4445 gene, predicted to encode a periplasmic protein, commences 1.5 h after the initiation of development and requires starvation and high density conditions. Addition of crude or boiled supernatant from starving high-density cells restored 4445 expression to starving low-density cells. Addition of L-threonine or L-isoleucine to starving low-density cells also restored 4445 expression, indicating that the high-density signaling activity present in the supernatant might be composed of extracellular amino acids or small peptides. To investigate the circuitry integrating these starvation and high-density signals, the cis- and trans-acting elements controlling 4445 expression were identified. The 4445 transcription start site was determined by primer extension analysis to be 58 by upstream of the predicted translation start site. The promoter region contained a consensus sequence characteristic of e&barbelow;xtrac&barbelow;ytoplasmic f&barbelow;unction (ECF) sigma factor-dependent promoters, suggesting that 4445 expression might be regulated by an ECF sigma factor-dependent pathway, which are known to respond to envelope stresses. The small size of the minimum regulatory region, identified by 5′-end deletion analysis as being only 66 by upstream of the transcription start site, suggests that RNA polymerase could be the sole direct regulator of 4445 expression. To identify trans-acting negative regulators of 4445 expression, a strain containing a 4445-lacZ was mutagenized using the Himar1-tet transposon. The four transposon insertions characterized mapped to an operon encoding a putative ECF sigma factor, ecfA; an anti-sigma factor, reaA; and a negative regulator, reaB. The reaA and the reaB mutants expressed 4445 during growth and development at levels almost 100-fold higher than wild type, indicating that these genes encode negative regulators. The ecfA mutant expressed 4445-lacZ at basal levels, indicating that ecfA is a positive regulator. High Mg2+ concentrations over-stimulated this ecfA pathway possibly due to the depletion of exopolysaccharides and assembled type IV pili. These data indicate that the ecfA operon encodes a new regulatory stress pathway that integrates and transduces starvation and cell density cues during early development and is also responsive to cell-surface alterations.^

Zircons, isotope ratios and element analyses from tonalite and oxide gabbro of the mid-ocean ridge from ODP Hole 176-735B

A limiting factor in the accuracy and precision of U/Pb zircon dates is accurate correction for initial disequilibrium in the 238U and 235U decay chains. The longest-lived-and therefore most abundant-intermediate daughter product in the 235U isotopic decay chain is 231Pa (T1/2 = 32.71 ka), and the partitioning behavior of Pa in zircon is not well constrained. Here we report high-precision thermal ionization mass spectrometry (TIMS) U-Pb zircon data from two samples from Ocean Drilling Program (ODP) Hole 735B, which show evidence for incorporation of excess 231Pa during zircon crystallization. The most precise analyses from the two samples have consistent Th-corrected 206Pb/238U dates with weighted means of 11.9325 ± 0.0039 Ma (n = 9) and 11.920 ± 0.011 Ma (n = 4), but distinctly older 207Pb/235U dates that vary from 12.330 ± 0.048 Ma to 12.140 ± 0.044 Ma and 12.03 ± 0.24 to 12.40 ± 0.27 Ma, respectively. If the excess 207Pb is due to variable initial excess 231Pa, calculated initial (231Pa)/(235U) activity ratios for the two samples range from 5.6 ± 1.0 to 9.6 ± 1.1 and 3.5 ± 5.2 to 11.4 ± 5.8. The data from the more precisely dated sample yields estimated DPazircon/DUzircon from 2.2-3.8 and 5.6-9.6, assuming (231Pa)/(235U) of the melt equal to the global average of recently erupted mid-ocean ridge basaltic glasses or secular equilibrium, respectively. High precision ID-TIMS analyses from nine additional samples from Hole 735B and nearby Hole 1105A suggest similar partitioning. The lower range of DPazircon/DUzircon is consistent with ion microprobe measurements of 231Pa in zircons from Holocene and Pleistocene rhyolitic eruptions (Schmitt (2007; doi:10.2138/am.2007.2449) and Schmitt (2011; doi:10.1146/annurev-earth-040610-133330)). The data suggest that 231Pa is preferentially incorporated during zircon crystallization over a range of magmatic compositions, and excess initial 231Pa may be more common in zircons than acknowledged. The degree of initial disequilibrium in the 235U decay chain suggested by the data from this study, and other recent high precision datasets, leads to resolvable discordance in high precision dates of Cenozoic to Mesozoic zircons. Minor discordance in zircons of this age may therefore reflect initial excess 231Pa and does not require either inheritance or Pb loss.

Método Seis Sigma

Trabajo de investigación orientado a verificar si se puede lograr una mejora significativa y sustentable en los procesos de una empresa aplicando el método Seis Sigma.

Chemial and isotope compositions of rocks from the West Antarctic

The paper is devoted to a marine geophysical-geological research in the West Antarctic. This researche contributed to establishing the base geodesic network of the West Antarctic and supplemented geokinematic monitoring based on this network with geophysical and geologic information on structure and features of geomorphological and tectonic development of the South Ocean floor. Collected materials allow to conclude about the inhomogeneity of the Scotia Sea floor and about combination of fragments of a continental massif with young rift structures in conditions of the upwelling mantle. The ancient continental bridge, faunal connections between the South America and the West Antarctic has been destroyed by processes of destruction, taphrogeny and sea floor spreading. Structures of the Scotia and Caribbean Seas, North Fiji and Arctic Basins are similar.

Fission track age determinations of rocks from north Greenland

Apatite fission track (FT) ages and length characteristics of samples obtained from Cambrian to Paleocene-aged sandstones collected along the margin of Nares Strait in Ellesmere Island in the Canadian Arctic Archipelago are dominated by a thermal history related to Paleogene relative plate movements between Greenland and Ellesmere Island. A preliminary inverse FT thermal model for a Cambrian (Archer Fiord Formation) sandstone in the hanging wall of the Rawlings Bay thrust at Cape Lawrence is consistent with Paleocene exhumational cooling, likely as a result of erosion of the thrust. This suggests that thrusting at Cape Lawrence occurred prior to the onset of Eocene compression, likely due to transpression during earlier strikeslip along the strait. Models for samples from volcaniclastic sandstones of the Late Paleocene Pavy Formation (from Cape Back and near Pavy River), and a sandstone from the Late Paleocene Mount Lawson Formation (at Split Lake, near Makinson Inlet) are also consistent with minor burial heating following known periods of basaltic volcanism in Baffin Bay and Davis Strait (c. 61-59 Ma), or related tholeiitic volcanism and intrusive activity (c. 55-54 Ma). Thermal models for samples from sea level dykes from around Smith Sound suggest a period of Late Cretaceous - Paleocene heating prior to final cooling during Paleocene time. These model results imply that Paleocene tectonic movements along Nares Strait were significant, and provide limited support for the former existence of the Wegener Fault. Apatite FT data from central Ellesmere Island suggest however, that cooling there occurred during Early Eocene time (c. 50 Ma), which was likely a result of erosion of thrusts during Eurekan compression. This diachronous cooling suggests that Eurekan deformation was partitioned at discrete intervals across Ellesmere Island, and thus it is likely that displacements along the strait were much less than the 150 km that has been previously suggested for the Wegener Fault.

Physical oceanography during five ECOMARGE cruises

The first experiment of the ECOMARGE programme (ECOsystèmes de MARGE continentale) was initiated in 1983-1984, in the Gulf of Lions (northwestern Mediterranean Sea). The objectives of the ECOMARGE-I experiment were: to quantify the transfer of particulate matter, in general, and of organic carbon, in particular, from its introduction to and formation in the waters of the continental shelf-to its consumption or sedimentation on the shelf or its transfer to the slope and deep sea; and to understand the processes involved in that transfer, consumption and sedimentation together with their variability in space and time. The results of that experiment, from 1983 to 1988, are presented in this Special Issue. The highlights of the results are summarised in this paper. These results indicate that, of the particles formed in the waters of the continental shelf and those introduced by rivers, some are deposited as sediments on the shelf. A portion is transported offshore, however, to the slope and deep sea. The Rho^ne River, in the northeastern part of the study area, is the major source of continental material; this is transported to sea in a benthic nepheloid layer and, mostly, alongshore to the southwest. Here, it largely leaves the shelf through the canyons, especially the Lacaze-Duthiers Canyon. In the offshore waters, particle concentrations and distributions show surficial, intermediate and benthic nepheloid layers. These turbid structures increase towards the southwest, corresponding to the seaward shift of the front between the coastal waters and the Liguro-Provençal cyclonic gyre, a major forcing function in the Gulf of Lions. Considering the source and fate of particles (largely biogenic from the euphotic zone and abiogenic from deeper waters) a layered system is described, which is emphasized by the concentrations of natural and artificial elements and compounds. Of the flux of particles to the Lacaze-Duthiers Canyon, on a decadal scale, about 30% (as a minimum) is estimated to be stored as sediment; the remainder is transported down-canyon, towards the deep sea. The temporal variability of processes affecting this net seaward transport, of both biogenic and abiogenic material, is from hours, days to seasonal, and probably interannual, time scales. The response of the system to these variations is rapid, with pulses of increased discharge of particles from the adjacent shelf being detected in sediment traps in the Lacaze-Duthiers Canyon in less than 16 days (the temporal resolution of the traps). Based upon the study of tracers of particulate matter and environmental factors (i.e. river discharge and climatic conditions), it appears that the contribution from the Rho^ne River and its adjacent area is maximal during the winter; at this time, the flow of the Liguro-Provençal Current also increases. In contrast, the maximum relative contribution of the adjacent southwesterly area to the flux in the Lacaze-Duthiers Canyon occurs in summer, during storm events.

Geochemical composition of bentonite layers and U-Pb ages of detrital zircons from the Paleogene Basilika Formation (Svalbard) and Mount Lawson Formation (Ellesmere Island)

Major and trace element composition as well as Sm-Nd isotopes of whole-rock samples and clay fractions (<2 µm) of bentonite layers and U-Pb ages of detrital zircons from the Paleogene Basilika Formation (Svalbard) and Mount Lawson Formation (Ellesmere Island).