Stimulation of bacteriophage T4 middle transcription by the T4 proteins MotA and AsiA occurs at two distinct steps in the transcription cycle

The bacteriophage T4 encodes proteins that are responsible for tightly regulating mRNA synthesis throughout phage development in Escherichia coli. The three classes of T4 promoters (early, middle, and late) are utilized sequentially by the host RNA polymerase as a result of phage-induced modifications. One such modification is the tight binding of the T4 AsiA protein to the σ70 subunit of the RNA polymerase. This interaction is pivotal for the transition between T4 early and middle transcription, since it both inhibits recognition of host and T4 early promoters and stimulates T4 middle mode synthesis. The activation of T4 middle transcription also requires the T4 MotA protein, bound specifically to its recognition sequence, the “Mot box,” which is centered at position −30 of these promoters. Accordingly, the two T4 proteins working in concert are sufficient to effectively switch the transcription specificity of the RNA polymerase holoenzyme. Herein, we investigate the mechanism of transcription activation and report that, while the presence of MotA and AsiA increases the initial recruitment of RNA polymerase to a T4 middle promoter, it does not alter the intrinsic stability of the discrete complexes formed. In addition, we have characterized the RNA polymerase-promoter species by UV laser footprinting and followed their evolution from open into initiating complexes. These data, combined with in vitro transcription assays, indicate that AsiA and MotA facilitate promoter escape, thereby stimulating the production of full-length transcripts.

Carbohydrates in Individual Cells of Epidermis, Mesophyll, and Bundle Sheath in Barley Leaves with Changed Export or Photosynthetic Rate1

Carbohydrate metabolism of barley (Hordeum vulgare) leaves induced to accumulate sucrose (Suc) and fructans was investigated at the single-cell level using single-cell sampling and analysis. Cooling of the root and shoot apical meristem of barley plants led to the accumulation of Suc and fructan in leaf tissue. Suc and fructan accumulated in both mesophyll and parenchymatous bundle-sheath (PBS) cells because of the reduced export of sugars from leaves under cooling and to increased photosynthesis under high photon fluence rates. The general trends of Suc and fructan accumulation were similar for mesophyll and PBS cells. The fructan-to-Suc ratio was higher for PBS cells than for mesophyll cells, suggesting that the threshold Suc concentration needed for the initiation of fructan synthesis was lower for PBS cells. Epidermal cells contained very low concentrations of sugar throughout the cooling experiment. The difference in Suc concentration between control and treated plants was much less if compared at the single-cell level rather than the whole-tissue level, suggesting that the vascular tissue contains a significant proportion of total leaf Suc. We discuss the importance of analyzing complex tissues at the resolution of individual cells to assign molecular mechanisms to phenomena observed at the whole-plant level.

Gas-phase folding and unfolding of cytochrome c cations.

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.

Collective effects in light scattering from cold strontium clouds

A cold atomic cloud is a versatile object, because it offers many handles to control and tune its properties. This facilitates studies of its behavior in various circumstances, such as sample temperature, size and density, composition, dimensionality and coherence time. The range of possible experiments is constrained by the specifications of the atomic species used. In this thesis presents the work done in the experiment for laser cooling of strontium atoms, focusing on its stability, which should provide cold and ultracold samples for the study of collective effects in light scattering. From the initial apparatus, innumerous changes were performed. The vacuum system got improved and now reached lower ultra high vacuum due to the pre-baking done to its parts and adding a titanium-sublimation stage. The quadrupole trap were improved by the design and construction of a new pair of coils. The stability of the blue, green and red laser systems and the loss prevention of laser light were improved, giving rise to a robust apparatus. Another important point is the development of homemade devices to reduce the costs and to be used as a monitor of different parts of an cold atoms experiment. From this homemade devices, we could demonstrate a dramatic linewidth narrowing by injection lock of an low cost 461 nm diode laser and its application to our strontium experiment. In the end, this improved experimental apparatus made possible the study of a new scattering effect, the mirror assisted coherent back-scattering (mCBS).

Portable 3D laser-camera calibration system with color fusion for SLAM

Nowadays, the use of RGB-D sensors have focused a lot of research in computer vision and robotics. These kinds of sensors, like Kinect, allow to obtain 3D data together with color information. However, their working range is limited to less than 10 meters, making them useless in some robotics applications, like outdoor mapping. In these environments, 3D lasers, working in ranges of 20-80 meters, are better. But 3D lasers do not usually provide color information. A simple 2D camera can be used to provide color information to the point cloud, but a calibration process between camera and laser must be done. In this paper we present a portable calibration system to calibrate any traditional camera with a 3D laser in order to assign color information to the 3D points obtained. Thus, we can use laser precision and simultaneously make use of color information. Unlike other techniques that make use of a three-dimensional body of known dimensions in the calibration process, this system is highly portable because it makes use of small catadioptrics that can be placed in a simple manner in the environment. We use our calibration system in a 3D mapping system, including Simultaneous Location and Mapping (SLAM), in order to get a 3D colored map which can be used in different tasks. We show that an additional problem arises: 2D cameras information is different when lighting conditions change. So when we merge 3D point clouds from two different views, several points in a given neighborhood could have different color information. A new method for color fusion is presented, obtaining correct colored maps. The system will be tested by applying it to 3D reconstruction.

Portable 3D laser-camera calibration system with color fusion for SLAM

Paper submitted to the 43rd International Symposium on Robotics (ISR2012), Taipei, Taiwan, Aug. 29-31, 2012.

Targetless image-based method for measuring displacements and strains on concrete surfaces with a consumer camera

Measurement of concrete strain through non-invasive methods is of great importance in civil engineering and structural analysis. Traditional methods use laser speckle and high quality cameras that may result too expensive for many applications. Here we present a method for measuring concrete deformations with a standard reflex camera and image processing for tracking objects in the concretes surface. Two different approaches are presented here. In the first one, on-purpose objects are drawn on the surface, while on the second one we track small defects on the surface due to air bubbles in the hardening process. The method has been tested on a concrete sample under several loading/unloading cycles. A stop-motion sequence of the process has been captured and analyzed. Results have been successfully compared with the values given by a strain gauge. Accuracy of our methods in tracking objects is below 8 μm, in the order of more expensive commercial devices.

Organic distributed feedback laser to monitor solvent extraction upon thermal annealing in solution-processed polymer films

Solution-processed polymer films are used in multiple technological applications. The presence of residual solvent in the film, as a consequence of the preparation method, affects the material properties, so films are typically subjected to post-deposition thermal annealing treatments aiming at its elimination. Monitoring the amount of solvent eliminated as a function of the annealing parameters is important to design a proper treatment to ensure complete solvent elimination, crucial to obtain reproducible and stable material properties and therefore, device performance. Here we demonstrate, for the first time to our knowledge, the use of an organic distributed feedback (DFB) laser to monitor with high precision the amount of solvent extracted from a spin-coated polymer film as a function of the thermal annealing time. The polymer film of interest, polystyrene in the present work, is doped with a small amount of a laser dye as to constitute the active layer of the laser device and deposited over a reusable DFB resonator. It is shown that solvent elimination translates into shifts in the DFB laser wavelength, as a consequence of changes in film thickness and refractive index. The proposed method is expected to be applicable to other types of annealing treatments, polymer-solvent combinations or film deposition methods, thus constituting a valuable tool to accurately control the quality and reproducibility of solution-processed polymer thin films.

Stable oxygen and carbon isotope of foraminifera from DSDP Leg 90 sites

High-resolution oxygen and carbon isotope stratigraphy is presented for Miocene to early Pliocene sequences at three DSDP sites from the Lord Howe Rise, southwest Pacific, at water depths ranging from 1,300 to 2,000 m. Site 588 is located in the warm subtropics (~26°S), whereas Sites 590 and 591 are positioned in transitional (northern temperate) water masses (~31°S). Benthic foraminiferal oxygen and carbon isotope analyses were conducted on all sites; planktonic foraminiferal isotope data were generated for Site 590 only. Sample resolution in these sequences is on the order of 50,000 yr. or better. The chronological framework employed in this study is based largely upon ages assigned to Neogene calcareous nannoplankton boundaries. The benthic oxygen isotope record exhibits several major features during the Neogene. During most of the early Miocene, delta18O values were relatively low, reaching minimum values in the late early Miocene (19.5 to 16.5 Ma), and recording the climax of Neogene warmth. This was followed by a major increase in benthic delta18O values between ~16.5 and 13.5 Ma, which is interpreted as representing major, permanent accumulation of the East Antarctic ice sheet and cooling of bottom waters. During the 3 m.y. 18O enrichment, surface waters at these middle latitudes warmed between 16 and 14.5 Ma. During the remainder of the middle and late Miocene, benthic delta18O values exhibit distinct fluctuations, but the average value remained unchanged. The isotopic data show two distinct episodes of climatic cooling close to the middle/late Miocene boundary. The earliest of these events occurred between 12.5 and 11.5 Ma in the latest middle Miocene. The second cooling event occurred from 11 to 9 Ma, and is marked by some of the highest delta18O values of the entire Miocene. This was followed by relative warmth during the middle part of the late Miocene. The latest Miocene and earliest Pliocene (6.2 to 4.5 Ma) were marked by relatively high delta18O values, indicating increased cooling and glaciation. During the middle Pliocene, at about 3.4 Ma, a 0.4 per mil increase in benthic delta18O documents a net increase in average global ice volume and cooling of bottom waters. During this interval of increased glaciation, surface waters warmed by 2-3°C in southern middle-latitude regions. During the late Pliocene, between 2.6 and 2.4 Ma, a further increase in delta18O occurred; this has been interpreted by previous workers as heralding the onset of Northern Hemisphere glaciation. Surface-water warming in the middle latitudes occurred in association with major high-latitude glacial increases in the early middle Miocene (16-14 Ma), middle Pliocene (-3.5 Ma), and late Pliocene (~2.4 Ma). These intervals were also marked by increases in the vertical temperature gradient in the open ocean. Intersite correlation is enhanced by using carbon isotope stratigraphy. The great similarity of the delta13C time-series records within and between ocean basins and with water depth clearly indicates that changes in oceanwide average delta13C of [HCO3]- in seawater dominated the records, rather than local effects. Broad changes in the Neogene delta13C record were caused largely by transfer of organic carbon between continental and oceanic reservoirs. These transfers were caused by marine transgressions and regressions on the continental margins. The dominant feature of Neogene delta13C stratigraphy is a broad late early to early middle Miocene increase of about lâ between ~19 and 14.5 Ma. This trend occurred contemporaneously with a period of maximum coastal onlap (transgression) and maximum Neogene climatic warmth. The delta13C trend terminated during the expansion of the Antarctic ice sheet and associated marine regression. The latest Miocene carbon isotope shift (of up to - 0.75 per mil) at 6.2 Ma is clearly recorded in all sites examined and was followed by relatively low values during the remainder of the Neogene. This shift was caused by a glacioeustatic sealevel lowering that exposed continental margins via regression and ultimately increased the flux of organic carbon to the deep sea. An increase in delta13C values during the early Pliocene (~5 to 4 Ma) resulted from marine transgression during a time of global warmth.

Foraminiferal oxygen and carbon isotopic measurements from 5 sites of southern Atlantic and Pacific

The stratigraphy and paleoceanography of the late Miocene and early Pliocene have been examined at six sites in the South Atlantic and southwest Pacific oceans: Deep Sea Drilling Project (DSDP) sites 284, 516A, 519, 588, and 590 and two piston cores from Chain cruise 115. A consistent stratigraphy was developed among sites using graphic correlation, which resulted in age models for all sites that are tied to the revised paleomagnetic time scale of Berggren et al. (1985). Applying these chronologies, we assessed latitudinal and interocean contrasts in the stratigraphic ranges of late Miocene-early Pliocene planktonic foraminiferal and nanno - fossil datums. Salient stratigraphic results include (1) The last appearance datum (LAD) of Globoquadrina dehiscens is a late Miocene (approx. 6.4 Ma) event in the subtropics and is not useful for the placement of the Miocene/Pliocene (M/P) boundary in this biogeographic province. (2) The first appearance datum (FAD) of Globorotalia crassaformis occurred at 5.1 Ma in the South Atlantic near the M/P boundary, suggesting that Gr. crassaformis may have first evolved in the South Atlantic and later migrated to other regions. (3) In the southwest Pacific, the FADs of Gr. margaritae (5.97 Ma), Gr. puncticulata (5.09 Ma), and Gr. crassaformis (4.87 Ma) are significantly time transgressive between temperate and warm subtropical regions. Time lags of 1.0 m.y. were required for these species to adapt to physical and/or biotic conditions peripheral to their endemic biogeographic provinces. (4) Between the subtropics of the South Atlantic and southwest Pacific, many planktonic foraminiferal datums (FAD of Dentogloboquadrina altispira, Gr. cibaoensis, Gr. conomiozea, Gr. margaritae, and Gq. dehiscens and LAD of Gr. cibaoensis) markedly depart from the correlation suggested by magnetostratigraphy, indicating that these datum levels are unreliable for correlation between these ocean basins. (5) In contrast, available calcareous nannofossil datum levels fall on or near the paleomagnetic correlation line, indicating synchroneity of events within the subtropics. (6) Biostratigraphic, magnetic, and 87Sr/86Sr correlation between sites 588 and 519 and the M/P neostratotype at Capo Rossello, Sicily, suggests that the base of the Zanclean stratotype occurs at 5.1-5.0 Ma in the lower reversed subchron of the Gilbert, about 2-3 * 10**5 years above the Gilbert/Chron 5 boundary. Oxygen isotopic results from DSDP sites 284, 519, and CH115 piston cores confirm a prolonged benthic d18O increase in the latest Miocene between 5.6 and 5.0 Ma, as originally proposed by Shackleton and Kennett (1975). At DSDP site 588, the benthic d18O record in the latest Miocene is marked by high-frequency fluctuations with amplitude variations of 0.5per mill, and a long-period wavelength component of 400,000 years. Maximum d18O values, however, occurred during the late Miocene (Kapitean Stage) between 5.5 and 5.1 Ma. The late Miocene d18O changes resulted from mid- and high-latitude cooling and pulses of ice sheet expansion and contraction. Glacial events were most intense during the latest Miocene (Kapitean Stage), and occurred at 5.50-5.35 Ma and at 5.10 Ma. Glacial events are estimated to have lowered sea level by 40 to 60 m and contributed to the isolation and desiccation of the Mediterranean Basin during the late Messinian. Interglacial conditions prevailed at 5.2 Ma and between 5.0 and 4.1 Ma in the early Pliocene. The beginning of the Pliocene was marked by changes in many proxy climatic indicators at all sites, suggesting a prolonged interval of warm, interglacial conditions between 5.0 and 4.1 Ma during the earliest Pliocene.

Late Neogene benthic foraminifera and stable carbon isotope record of the blake Outer Ridge

Carbon isotope and benthic foraminiferal data from Blake Outer Ridge, a sediment drift in the western North Atlantic (Ocean Drilling Program Sites 994 and 997, water depth ~ 2800 m), document variability in the relative volume of Southern Component (SCW) and Northern Component Waters (NCW) over the last 7 Ma. SCW was dominant before ~5.0 Ma, at ~3.6-2.4 Ma, and 1.2-0.8 Ma, whereas NCW dominated in the warm early Pliocene (5.0-3.6 Ma), and at 2.4-1.2 Ma. The relative volume of NCW and SCW fluctuated strongly over the last 0.8 Ma, with strong glacial-interglacial variability. The intensity of the Western Boundary Undercurrent was positively correlated to the relative volume of NCW. Values of Total Organic Carbon (TOC) were > 1.5% in sediments older than ~ 3.8 Ma, and not correlated to high primary productivity indicators, thus may reflect lateral transport of organic matter. TOC values decreased during the intensification of the Northern Hemisphere Glaciation (NHG, 3.8-1.8 Ma). Benthic foraminiferal assemblages underwent major changes when the sites were dominantly under SCW (3.6-2.4 and 1.2-0.8 Ma), coeval with the 'Last Global Extinction' of elongate, cylindrical deep-sea benthic foraminifera, which has been linked to cooling, increased ventilation and changes in the efficiency of the biological pump. These benthic foraminiferal turnovers were neither directly associated with changes in dominant bottom water mass nor with changes in productivity, but occurred during global cooling and increased ventilation of deep waters associated with the intensification of the NHG.

Late Eocene to early Oligocene carbonate and barite accumulation rates in the Pacific Basin

The late Eocene through earliest Oligocene (40-32 Ma) spans a major transition from greenhouse to icehouse climate, with net cooling and expansion of Antarctic glaciation shortly after the Eocene/Oligocene (E/O) boundary. We investigated the response of the oceanic biosphere to these changes by reconstructing barite and CaCO3 accumulation rates in sediments from the equatorial and North Pacific Ocean. These data allow us to evaluate temporal and geographical variability in export production and CaCO3 preservation. Barite accumulation rates were on average higher in the warmer late Eocene than in the colder early Oligocene, but cool periods within the Eocene were characterized by peaks in both barite and CaCO3 accumulation in the equatorial region. We infer that climatic changes not only affected deep ocean ventilation and chemistry, but also had profound effects on surface water characteristics influencing export productivity. The ratio of CaCO3 to barite accumulation rates, representing the ratio of particulate inorganic C accumulation to Corg export, increased dramatically at the E/O boundary. This suggests that long-term drawdown of atmospheric CO2 due to organic carbon deposition to the seafloor decreased, potentially offsetting decreasing pCO2 levels and associated cooling. The relatively larger increase in CaCO3 accumulation compared to export production at the E/O suggests that the permanent deepening of the calcite compensation depth (CCD) at that time stems primarily from changes in deep water chemistry and not from increased carbonate production.

Benthic oxygen isotope and dust flux record from ODP Site 108-659 in the North Atlantic

High-resolution benthic oxygen isotope and dust flux records from Ocean Drilling Program site 659 have been analyzed to extend the astronomically calibrated isotope timescale for the Atlantic from 2.85 Ma back to 5 Ma. Spectral analysis of the delta18O record indicates that the 41-kyr period of Earth's orbital obliquity dominates the Pliocene record. This is shown to be true regardless of fundamental changes in the Earth's climate during the Pliocene. However, the cycles of Sahelian aridity fluctuations indicate a shift in spectral character near 3 Ma. From the early Pliocene to 3 Ma, the periodicities were dominantly precessional (19 and 23 kyr) and remained strong until 1.5 Ma. Subsequent to 3 Ma, the variance at the obliquity period (41 kyr) increased. The timescale tuned to precession suggests that the Pliocene was longer than previously estimated by more than 0.5 m.y. The tuned ages for the magnetic boundaries Gauss/Gilbert and Top Cochiti are about 6-8% older than the ages of the conventional timescale. A major phase of Pliocene northern hemisphere ice growth occurred between 3.15 Ma and 2.5 Ma. This was marked by a gradual increase in glacial Atlantic delta18O values of 1per mil and an increase in amplitude variations by up to 1.5 per mil, much larger than in the Pacific deepwater record (site 846). The first maxima occured in cold stages G6-96 between 2.7 Ma and 2.45 Ma. Prior to 3 Ma, the isotope record is characterized by predominantly low amplitude fluctuations (< 0.7 per mil). When obliquity forcing was at its minimum between 4.15 and 3.6 Ma and during the Kaena interval, delta18O amplitude fluctuations were minimal. From 4.9 to 4.3 Ma, the delta18O values decreased by about 0.5 per mil, reaching a long-term minimum at 4.15 Ma, suggesting higher deepwater temperatures or a deglaciation. Deepwater cooling and/or an increase in ice volume is indicated by a series of short-term delta18O fluctuations between 3.8 and 3.6 Ma.

Mineralogy at DSDP Site 82-558 and Hole 82-563

Downhole bulk-sample and clay-mineral analytical results for Sites 558 and 563 are presented in this chapter. These results show a Tertiary climatic and hydrologic evolution similar to that at other DSDP drill sites in the northeastern Atlantic Ocean (Sites 398, 403-406, 548-550, 552-555). The sediments recovered at both sites are primarily calcareous and chalky oozes characterized by >90% carbonate and minor quartz and plagioclase feldspar. Clay minerals smectite, kaolinite, illite, and chlorite are present throughout the cores; upsection, illite increases at the expense of smectite. The clay mineralogy suggests climatic cooling and increased ocean circulation during the Miocene. Intervals rich in very fine grained (<2 µm) quartz suggest times of increased eolian input. This could have resulted from development, during Oligocene and late Miocene time, of an arid, desertlike sediment provenance that lasted until the present day.

Miocene microflora and palaeoclimate reconstructions from three sites in Bulgaria

In this study we reconstruct quantitatively the Middle to Upper Miocene climate evolution in the southern Forecarpathian Basin (Central Paratethys area, Northwest Bulgaria) by applying the coexistence approach to 101 well-dated palynofloras isolated from three cores. The climatic evolution is compared with changes in vegetation and palaeogeography. The Middle Miocene was a period of a subtropical/warm-temperate humid climate with mean annual temperature (MAT) between 16 and 18°C and mean annual precipitation (MAP) between 1100 and 1300 mm. Thereby, during the entire Middle Miocene a trend of slightly decreasing temperatures is observed and only small climate fluctuations occur which are presumably related to palaeogeographic reorganisations. The vegetation shows a corresponding trend with a decrease in abundance of palaeotropic and thermophilous elements. The Upper Miocene is characterised by more diverse climatic conditions, probably depending on palaeogeographic and global climatic transformations. The beginning of this period is marked by a slight cooling and a significant drying of the climate, with MAT 13.3-17°C and MAP 652-759 mm. After that, fluctuations of all palaeoclimate parameters occur displaying cycles of humid/dryer and warmer/cooler conditions, which are again well reflected in the vegetation. Our study provides a first quantitative model of the Middle-Upper Miocene palaeoclimate evolution in Southeastern Europe and is characterised by a relatively high precision and resolution with respect to the climate data and stratigraphy.