589 research outputs found
Direct visualization of mucus production by the cold-water coral <i>Lophelia pertusa</i> with digital holographic microscopy
<i>Lophelia pertusa</i> is the dominant reef-building organism of cold-water coral reefs, and is known to produce significant amounts of mucus, which could involve an important metabolic cost. Mucus is involved in particle removal and feeding processes, yet the triggers and dynamics of mucus production are currently still poorly described because the existing tools to study these processes are not appropriate. Using a novel microscopic technique—digital holographic microscopy (DHM)–we studied the mucus release of <i>L</i>. <i>pertusa</i> under various experimental conditions. DHM technology permits µm-scale observations and allows the visualization of transparent mucoid substances in real time without staining. Fragments of <i>L</i>. <i>pertusa</i> were first maintained in flow-through chambers without stressors and imaged with DHM, then exposed to various stressors (suspended particles, particulate food and air exposure) and re-imaged. Under non-stressed conditions no release of mucus was observed, whilst mucus strings and sheaths were produced in response to suspended particles (activated charcoal and drill cuttings sediment) i.e. in a stressed condition. Mucus strings and so-called ‘string balls’ were also observed in response to exposure to particulate food (brine shrimp <i>Artemia salina</i>). Upon air-exposure, mucus production was clearly visible once the fragments were returned to the flow chamber. Distinct optical properties such as optical path length difference (OPD) were measured with DHM in response to the various stimuli suggesting that different mucus types are produced by <i>L</i>. <i>pertusa</i>. Mucus produced to reject particles is similar in refractive index to the surrounding seawater, suggesting that the energy content of this mucus is low. In contrast, mucus produced in response to either food particle addition or air exposure had a higher refractive index, suggesting a higher metabolic investment in the production of these mucoid substances. This paper shows for the first time the potential of DHM technology for the detection, characterization and quantification of mucus production through OPD measurements in <i>L</i>. <i>pertusa</i>
Imaging-in-flow: digital holographic microscopy as a novel tool to detect and classify nanoplanktonic organisms
Traditional taxonomic identification of planktonic organisms is based on light microscopy, which is both time-consuming and tedious. In response, novel ways of automated (machine) identification, such as flow cytometry, have been investigated over the last two decades. To improve the taxonomic resolution of particle analysis, recent developments have focused on "imaging-in-flow," i.e., the ability to acquire microscopic images of planktonic cells in a flow-through mode. Imaging-in-flow systems are traditionally based on classical brightfield microscopy and are faced with a number of issues that decrease the classification performance and accuracy (e. g., projection variance of cells, migration of cells out of the focus plane). Here, we demonstrate that a combination of digital holographic microscopy (DHM) with imaging-in-flow can improve the detection and classification of planktonic organisms. In addition to light intensity information, DHM provides quantitative phase information, which generates an additional and independent set of features that can be used in classification algorithms. Moreover, the capability of digitally refocusing greatly increases the depth of field, enables a more accurate focusing of cells, and reduces the effects of position variance. Nanoplanktonic organisms similar in shape were successfully classified from images captured with an off-axis DHM with partial coherence. Textural features based on DHM phase information proved more efficient in separating the three tested phytoplankton species compared with shape-based features or textural features based on light intensity. An overall classification score of 92.4% demonstrates the potential of holographic-based imaging-in-flow for similar looking organisms in the nanoplankton range
Long-distance electron transport occurs globally in marine sediments
Recently, long filamentous bacteria have been reported conducting electrons over centimetre distances in marine sediments. These so-called cable bacteria perform an electrogenic form of sulfur oxidation, whereby long-distance electron transport links sulfide oxidation in deeper sediment horizons to oxygen reduction in the upper millimetres of the sediment. Electrogenic sulfur oxidation exerts a strong impact on the local sediment biogeochemistry, but it is currently unknown how prevalent the process is within the seafloor. Here we provide a state-of-the-art assessment of its global distribution by combining new field observations with previous reports from the literature. This synthesis demonstrates that electrogenic sulfur oxidation, and hence microbial long-distance electron transport, is a widespread phenomenon in the present-day seafloor. The process is found in coastal sediments within different climate zones (off the Netherlands, Greenland, the USA, Australia) and thrives on a range of different coastal habitats (estuaries, salt marshes, mangroves, coastal hypoxic basins, intertidal flats). The combination of a widespread occurrence and a strong local geochemical imprint suggests that electrogenic sulfur oxidation could be an important, and hitherto overlooked, component of the marine cycle of carbon, sulfur and other elements
Mineral formation induced by cable bacteria performing long-distance electron transport in marine sediments
Cable bacteria are multicellular, filamentous microorganisms that are capable
of transporting electrons over centimeter-scale distances. Although recently
discovered, these bacteria appear to be widely present in the seafloor, and
when active they exert a strong imprint on the local geochemistry. In
particular, their electrogenic metabolism induces unusually strong pH
excursions in aquatic sediments, which induces considerable mineral
dissolution, and subsequent mineral reprecipitation. However, at present, it
is unknown whether and how cable bacteria play an active or direct role in
the mineral reprecipitation process. To this end we present an explorative
study of the formation of sedimentary minerals in and near filamentous cable
bacteria using a combined approach of electron microscopy and spectroscopic
techniques. Our observations reveal the formation of polyphosphate granules
within the cells and two different types of biomineral formation directly
associated with multicellular filaments of these cable bacteria: (i)Â the
attachment and incorporation of clay particles in a coating surrounding the
bacteria and (ii) encrustation of the cell envelope by iron minerals. These
findings suggest a complex interaction between cable bacteria and the
surrounding sediment matrix, and a substantial imprint of the electrogenic
metabolism on mineral diagenesis and sedimentary biogeochemical cycling. In
particular, the encrustation process leaves many open questions for further
research. For example, we hypothesize that the complete encrustation of
filaments might create a diffusion barrier and negatively impact the
metabolism of the cable bacteria.</p
Natural occurrence of microbial sulphur oxidation by long-range electron transport in the seafloor
Recently, a novel mode of sulphur oxidation was described in marine sediments, in which sulphide oxidation in deeper anoxic layers was electrically coupled to oxygen reduction at the sediment surface. Subsequent experimental evidence identified that long filamentous bacteria belonging to the family Desulfobulbaceae likely mediated the electron transport across the centimetre-scale distances. Such long-range electron transfer challenges some long-held views in microbial ecology and could have profound implications for sulphur cycling in marine sediments. But, so far, this process of electrogenic sulphur oxidation has been documented only in laboratory experiments and so its imprint on the seafloor remains unknown. Here we show that the geochemical signature of electrogenic sulphur oxidation occurs in a variety of coastal sediment environments, including a salt marsh, a seasonally hypoxic basin, and a subtidal coastal mud plain. In all cases, electrogenic sulphur oxidation was detected together with an abundance of Desulfobulbaceae filaments. Complementary laboratory experiments in intertidal sands demonstrated that mechanical disturbance by bioturbating fauna destroys the electrogenic sulphur oxidation signal. A survey of published geochemical data and 16S rRNA gene sequences identified that electrogenic sulphide oxidation is likely present in a variety of marine sediments with high sulphide generation and restricted bioturbation, such as mangrove swamps, aquaculture areas, seasonally hypoxic basins, cold sulphide seeps and possibly hydrothermal vent environments. This study shows for the first time that electrogenic sulphur oxidation occurs in a wide range of marine sediments and that bioturbation may exert a dominant control on its natural distribution
Multidimensional chemical control of CRISPR–Cas9
Cas9-based technologies have transformed genome engineering and the interrogation of genomic functions, but methods to control such technologies across numerous dimensions-including dose, time, specificity, and mutually exclusive modulation of multiple genes-are still lacking. We conferred such multidimensional controls to diverse Cas9 systems by leveraging small-molecule-regulated protein degron domains. Application of our strategy to both Cas9-mediated genome editing and transcriptional activities opens new avenues for systematic genome interrogation
Does rumination mediate the relationship between emotion regulation ability and posttraumatic stress disorder?
Background and objectives: Trauma-related rumination has been suggested to be involved in the maintenance of posttraumatic stress disorder (PTSD). This view has empirically been supported by extensive evidence using cross-sectional, prospective, and experimental designs. However, it is unclear why trauma survivors engage in rumination despite its negative consequences. The current study aimed to explore the hypothesis that low emotion regulation ability underlies trauma-related rumination. Methods: Emotion regulation ability and trauma-related rumination were assessed in 93 road traffic accident survivors 2 weeks post-trauma. In addition, symptom levels of PTSD were assessed at 2 weeks as well as 1, 3, and 6 months follow-up. Results: Emotion regulation ability was significantly related to trauma-related rumination as well as levels of PTSD symptoms. In addition, the association between low emotion regulation ability and PTSD was mediated by rumination. Conclusions: The findings support the view that rumination is used as a dysfunctional emotion regulation strategy by trauma survivors
Measurement of the proton and deuteron structure functions, F2p and F2d, and of the ratio sigma(L)/sigma(T)
The muon-proton and muon-deuteron inclusive deep inelastic scattering cross
sections were measured in the kinematic range 0.002 < x < 0.60 and 0.5 < Q2 <
75 GeV2 at incident muon energies of 90, 120, 200 and 280 GeV. These results
are based on the full data set collected by the New Muon Collaboration,
including the data taken with a small angle trigger. The extracted values of
the structure functions F2p and F2d are in good agreement with those from other
experiments. The data cover a sufficient range of y to allow the determination
of the ratio of the longitudinally to transversely polarised virtual photon
absorption cross sections, R= sigma(L)/sigma(T), for 0.002 < x < 0.12 . The
values of R are compatible with a perturbative QCD prediction; they agree with
earlier measurements and extend to smaller x.Comment: In this replacement the erroneously quoted R values in tables 3-6 for
x>0.12, and R1990 values in tables 5-6 for all x, have been corrected, and
the cross sections in tables 3-4 have been adapted. Everything else,
including the structure functions F2, remained unchanged. 22 pages, LateX,
including figures, with two .sty files, and three separate f2tab.tex files
for the F2-tables. Accepted for publication in Nucl.Phys.B 199
Measurement of inclusive D*+- and associated dijet cross sections in photoproduction at HERA
Inclusive photoproduction of D*+- mesons has been measured for photon-proton
centre-of-mass energies in the range 130 < W < 280 GeV and a photon virtuality
Q^2 < 1 GeV^2. The data sample used corresponds to an integrated luminosity of
37 pb^-1. Total and differential cross sections as functions of the D*
transverse momentum and pseudorapidity are presented in restricted kinematical
regions and the data are compared with next-to-leading order (NLO) perturbative
QCD calculations using the "massive charm" and "massless charm" schemes. The
measured cross sections are generally above the NLO calculations, in particular
in the forward (proton) direction. The large data sample also allows the study
of dijet production associated with charm. A significant resolved as well as a
direct photon component contribute to the cross section. Leading order QCD
Monte Carlo calculations indicate that the resolved contribution arises from a
significant charm component in the photon. A massive charm NLO parton level
calculation yields lower cross sections compared to the measured results in a
kinematic region where the resolved photon contribution is significant.Comment: 32 pages including 6 figure
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