601 research outputs found
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
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) 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
Red Deer Browsing Decelerates Shrub Regrowth Despite Increasing Wolf Presence
Semi-natural open habitats in Europe have been shaped by traditional land use practices, such as extensive mowing or livestock grazing. However, socio-economic transformations have led to the abandonment of many grassland and heathland areas and conservation management is now required to maintain these biodiverse habitats. Grazing by wild red deer (Cervus elaphus) can be a convenient alternative to laborious mechanical management or livestock grazing. Yet it remains unclear if free-ranging ungulates can counteract shrub growth sufficiently to maintain open habitats—especially with natural predators, i.e. wolves (Canis lupus), recolonizing Europe. To assess red deer effects on shrub regrowth after clearance, we installed a cohort of open and fenced plots (17 pairs) in 2016, when wolf presence in our study area (Grafenwöhr military training area, DE) was negligible. When wolf presence had become frequent in 2020, we set up a second cohort (41 paired plots). For both cohorts, the vegetation in the shrub and herb layer was significantly higher in fenced than open plots already after one year. Shrub height increased continuously and dead herbaceous biomass accumulated under red deer exclusion. Consequently, wild red deer can slow down shrub succession in open habitats even under increasing predation pressure. Regardless of wolf presence, a wildlife management that enables red deer to forage in open landscapes could thus reduce the required frequency of conservation management interventions
Crystal Structure of Staphylococcus aureus Cas9
Summary The RNA-guided DNA endonuclease Cas9 cleaves double-stranded DNA targets with a protospacer adjacent mot if (PAM) and complementarity to the guide RNA. Recently, we harnessed Staphylococcus aureus Cas9 (SaCas9), which is significantly smaller than Streptococcus pyogenes Cas9 (SpCas9), to facilitate efficient in vivo genome editing. Here, we report the crystal structures of SaCas9 in complex with a single guide RNA (sgRNA) and its double-stranded DNA targets, containing the 5′-TTGAAT-3′ PAM and the 5′-TTGGGT-3′ PAM, at 2.6 and 2.7 Å resolutions, respectively. The structures revealed the mechanism of the relaxed recognition of the 5′-NNGRRT-3′ PAM by SaCas9. A structural comparison of SaCas9 with SpCas9 highlighted both structural conservation and divergence, explaining their distinct PAM specificities and orthologous sgRNA recognition. Finally, we applied the structural information about this minimal Cas9 to rationally design compact transcriptional activators and inducible nucleases, to further expand the CRISPR-Cas9 genome editing toolbox.National Institute of General Medical Sciences (U.S.) (Grant T32GM007753)National Institutes of Health (U.S.) (Award 1DP1-MH100706
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
Measurement of the diffractive structure function in deep inelastic scattering at HERA
This paper presents an analysis of the inclusive properties of diffractive
deep inelastic scattering events produced in interactions at HERA. The
events are characterised by a rapidity gap between the outgoing proton system
and the remaining hadronic system. Inclusive distributions are presented and
compared with Monte Carlo models for diffractive processes. The data are
consistent with models where the pomeron structure function has a hard and a
soft contribution. The diffractive structure function is measured as a function
of \xpom, the momentum fraction lost by the proton, of , the momentum
fraction of the struck quark with respect to \xpom, and of . The \xpom
dependence is consistent with the form \xpoma where
in all bins of and
. In the measured range, the diffractive structure function
approximately scales with at fixed . In an Ingelman-Schlein type
model, where commonly used pomeron flux factor normalisations are assumed, it
is found that the quarks within the pomeron do not saturate the momentum sum
rule.Comment: 36 pages, latex, 11 figures appended as uuencoded fil
Measurement of Jet Shapes in Photoproduction at HERA
The shape of jets produced in quasi-real photon-proton collisions at
centre-of-mass energies in the range GeV has been measured using the
hadronic energy flow. The measurement was done with the ZEUS detector at HERA.
Jets are identified using a cone algorithm in the plane with a
cone radius of one unit. Measured jet shapes both in inclusive jet and dijet
production with transverse energies GeV are presented. The jet
shape broadens as the jet pseudorapidity () increases and narrows
as increases. In dijet photoproduction, the jet shapes have been
measured separately for samples dominated by resolved and by direct processes.
Leading-logarithm parton-shower Monte Carlo calculations of resolved and direct
processes describe well the measured jet shapes except for the inclusive
production of jets with high and low . The observed
broadening of the jet shape as increases is consistent with the
predicted increase in the fraction of final state gluon jets.Comment: 29 pages including 9 figure
Angular and Current-Target Correlations in Deep Inelastic Scattering at HERA
Correlations between charged particles in deep inelastic ep scattering have
been studied in the Breit frame with the ZEUS detector at HERA using an
integrated luminosity of 6.4 pb-1. Short-range correlations are analysed in
terms of the angular separation between current-region particles within a cone
centred around the virtual photon axis. Long-range correlations between the
current and target regions have also been measured. The data support
predictions for the scaling behaviour of the angular correlations at high Q2
and for anti-correlations between the current and target regions over a large
range in Q2 and in the Bjorken scaling variable x. Analytic QCD calculations
and Monte Carlo models correctly describe the trends of the data at high Q2,
but show quantitative discrepancies. The data show differences between the
correlations in deep inelastic scattering and e+e- annihilation.Comment: 26 pages including 10 figures (submitted to Eur. J. Phys. C
Plastisol Foaming Process. Decomposition of the Foaming Agent, Polymer Behavior in the Corresponding Temperature Range and Resulting Foam Properties
The decomposition of azodicarbonamide, used as foaming agent in PVC - plasticizer (1/1) plastisols was studied by DSC. Nineteen different plasticizers, all belonging to the ester family, two being polymeric (polyadipates), were compared. The temperature of maximum decomposition rate (in anisothermal regime at 5 K min-1 scanning rate), ranges between 434 and 452 K. The heat of decomposition ranges between 8.7 and 12.5 J g -1. Some trends of variation of these parameters appear significant and are discussed in terms of solvent (matrix) and viscosity effects on the decomposition reactions. The shear modulus at 1 Hz frequency was determined at the temperature of maximum rate of foaming agent decomposition, and differs significantly from a sample to another. The foam density was determined at ambient temperature and the volume fraction of bubbles was used as criterion to judge the efficiency of the foaming process. The results reveal the existence of an optimal shear modulus of the order of 2 kPa that corresponds roughly to plasticizer molar masses of the order of 450 ± 50 g mol-1. Heavier plasticizers, especially polymeric ones are too difficult to deform. Lighter plasticizers such as diethyl phthalate (DEP) deform too easily and presumably facilitate bubble collapse
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