Gait modulation in <i>C. Elegans</i>: it's not a choice, it's a reflex!

A commentary on 'Shared strategies for behavioral switching: understanding how locomotor patterns are turned on and off' by Mesce, K. A., and Pierce-Shimomura, J. T. (2010). Front. Behav. Neurosci. 4:49

Vibronic interactions in the visible and near-infrared spectra of C60− anions

Electron-phonon coupling is an important factor in understanding many properties of the C60 fullerides. However, there has been little success in quantifying the strength of the vibronic coupling in C60 ions, with considerable disagreement between experimental and theoretical results. We will show that neglect of quadratic coupling in previous models for C60- ions results in a significant overestimate of the linear coupling constants. Including quadratic coupling allows a coherent interpretation to be made of earlier experimental and theoretical results which at first sight are incompatible

Escherichia coli MW005: lambda Red-mediated recombineering and copy-number induction of oriV-equipped constructs in a single host

<p>Abstract</p> <p>Background</p> <p><it>Escherichia coli </it>strain EL350 contains chromosomally integrated phage lambda Red recombinase genes enabling this strain to be used for modifying the sequence of resident clones <it>via </it>recombineering. BAC and fosmid clones are highly suitable for modification by recombineering but, because they are present at low (1-2) copies per cell, the DNA is difficult to isolate in high yield and purity. To overcome this limitation vectors, e.g. pCC1FOS, have been constructed that contain the additional replication origin, <it>oriV</it>, which permits copy-number to be induced transiently when propagated in a suitable host strain, e.g. EPI300, that supplies the cognate <it>trans</it>-replication protein TrfA. Previously, we used EL350 and EPI300 sequentially to recombineer <it>oriV</it>-equipped fosmid genomic clones and, subsequently, to induce copy-number of the resulting recombinant clone. To eliminate these intervening DNA isolation and transformation steps we retrofitted EL350 with a <it>P</it>_BAD-driven <it>trfA </it>gene generating strain MW005 that supports, independently, both recombineering and copy-number induction.</p> <p>Results</p> <p>The <it>P</it>_BAD-driven copy of <it>cre </it>in EL350 was replaced seamlessly with a copy of <it>trfA</it>, PCR-amplified from EPI300 chromosomal DNA, to generate MW005. This new strain has been used to both generate, via recombineering, a number of reporter gene fusions directly from pCC1FOS-based <it>Caenorhabditis elegans </it>genomic clones and to transiently induce copy-number of fosmid and BAC clones prior to DNA preparation.</p> <p>Conclusions</p> <p>By retrofitting EL350, an established 'recombineering' <it>E. coli </it>strain, with a tightly regulated copy of <it>trfA </it>we have produced a new strain, MW005, which combines recombineering capacity with the useful ability to transiently induce copy-number of <it>oriV</it>-equipped clones. By coupling these two steps in a single strain, use of MW005 will enable the more rapid recombineering-mediated production of recombinant clones in the yield and quality necessary for many downstream purposes.</p

Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns

BACKGROUND: The C. elegans Promoterome is a powerful resource for revealing the regulatory mechanisms by which transcription is controlled pan-genomically. Transcription factors will form the core of any systems biology model of genome control and therefore the promoter activity of Promoterome inserts for C. elegans transcription factor genes was examined, in vivo, with a reporter gene approach. RESULTS: Transgenic C. elegans strains were generated for 366 transcription factor promoter/gfp reporter gene fusions. GFP distributions were determined, and then summarized with reference to developmental stage and cell type. Reliability of these data was demonstrated by comparison to previously described gene product distributions. A detailed consideration of the results for one C. elegans transcription factor gene family, the Six family, comprising ceh-32, ceh-33, ceh-34 and unc-39 illustrates the value of these analyses. The high proportion of Promoterome reporter fusions that drove GFP expression, compared to previous studies, led to the hypothesis that transcription factor genes might be involved in local gene duplication events less frequently than other genes. Comparison of transcription factor genes of C. elegans and Caenorhabditis briggsae was therefore carried out and revealed very few examples of functional gene duplication since the divergence of these species for most, but not all, transcription factor gene families. CONCLUSION: Examining reporter expression patterns for hundreds of promoters informs, and thereby improves, interpretation of this data type. Genes encoding transcription factors involved in intrinsic developmental control processes appear acutely sensitive to changes in gene dosage through local gene duplication, on an evolutionary time scale

Observation of ultrafast internal conversion in fullerene anions in solution

The ultrafast decay rates of photoexcited View the MathML source ions have been measured in the condensed phase. The mechanism for decay is internal conversion, and the decay rate is a strong function of the charge on the ion. A bottleneck in the ground state recovery has also been detected, and its interpretation is discussed

Exploring the Potential of Using Carbonyl Sulfide to Track the Urban Biosphere Signal

Unidad de excelencia María de Maeztu CEX2019-000940-MCities are implementing additional urban green as a means to capture CO and become more carbon neutral. However, cities are complex systems where anthropogenic and natural components of the CO budget interact with each other, and the ability to measure the efficacy of such measures is still not properly addressed. There is still a high degree of uncertainty in determining the contribution of the vegetation signal, which furthermore confounds the use of CO mole fraction measurements for inferring anthropogenic emissions of CO. Carbonyl sulfide (OCS) is a tracer of photosynthesis which can aid in constraining the biosphere signal. This study explores the potential of using OCS to track the urban biosphere signal. We used the Sulfur Transport and dEposition Model (STEM) to simulate the OCS concentrations and the Carnegie Ames Stanford Approach ecosystem model to simulate global CO fluxes over the Bay Area of San Francisco during March 2015. Two observation towers provided measurements of OCS and CO: The Sutro tower in San Francisco (upwind from the area of study providing background observations), and a tower located at Sandia National Laboratories in Livermore (downwind of the highly urbanized San Francisco region). Our results show that the STEM model works better under stable marine influence, and that the boundary layer height and entrainment are driving the diurnal changes in OCS and CO at the downwind Sandia site. However, the STEM model needs to better represent the transport and boundary layer variability, and improved estimates of gross primary productivity for characterizing the urban biosphere signal are needed

A first version of the Caenorhabditis elegans Promoterome

An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such localizome maps should provide information on where (in what cells or tissues) and when (at what stage of development or under what conditions) genes are expressed. They should also indicate in what cellular compartments the corresponding proteins are localized. Caenorhabditis elegans is particularly suited for the development of a localizome map since all its 959 adult somatic cells can be visualized by microscopy, and its cell lineage has been completely described. Here we address one of the challenges of C. elegans localizome mapping projects: that of obtaining a genome-wide resource of C. elegans promoters needed to generate transgenic animals expressing localization markers such as the green fluorescent protein (GFP). To ensure high flexibility for future uses, we utilized the newly developed MultiSite Gateway system. We generated and validated version 1.1 of the Promoterome: a resource of approximately 6000 C. elegans promoters. These promoters can be transferred easily into various Gateway Destination vectors to drive expression of markers such as GFP, alone (promoter::GFP constructs), or in fusion with protein-encoding open reading frames available in ORFeome resources (promoter::ORF::GFP)

Current- and Wave-Generated Bedforms on Mixed Sand–Clay Intertidal Flats:A New Bedform Phase Diagram and Implications for Bed Roughness and Preservation Potential

The effect of bedforms on frictional roughness felt by the overlying flow is crucial to the regional modelling of estuaries and coastal seas. Bedforms are also a key marker of palaeoenvironments. Experiments have shown that even modest biotic and abiotic cohesion in sand inhibits bedform formation, modifies bedform size, and slows bedform development, but this has rarely been tested in nature. The present study used a comprehensive dataset recorded over a complete spring–neap cycle on an intertidal flat to investigate bedform dynamics controlled by a wide range of wave and current conditions, including the effects of wave–current angle and bed cohesion. A detailed picture of different bedform types and their relationship to the flow, be they equilibrium, non-equilibrium, or relict, was produced, and captured in a phase diagram that integrates wave-dominated, current-dominated, and combined wave–current bedforms. This bedform phase diagram incorporates a substantially wider range of flow conditions than previous phase diagrams, including bedforms related to near-orthogonal wave–current angles, such as ladderback ripples. Comparison with laboratory-derived bedform phase diagrams indicates that washed-out ripples, lunate interference ripples and upper-stage plane beds replace the subaqueous dune field; such bedform distributions may be a key characteristic of intertidal flats. The field data also provide a means of predicting the dimensions of these bedforms, which can be transferred to other areas and grain sizes. We show that an equation for the prediction of equilibrium bedform size is sufficient to predict the roughness, even though the bedforms are highly variable in character and only in equilibrium with the flow for approximately half the time. Whilst the effect of cohesive clay is limited under more active spring conditions, clay does play a role in reducing the bedform dimensions under more quiescent neap conditions. We also investigated which combinations of waves, currents, and bed clay contents in the intertidal zone have the highest potential for bedform preservation in the geological record. This shows that combined wave–current bedforms have the lowest preservation potential and equilibrium current ripples have the highest preservation potential, even in the presence of moderate and storm waves. Hence, the absence of wave ripples and combined-flow bedforms and their primary stratification in sedimentary successions cannot be taken as evidence that waves were absent at the time of deposition