110 research outputs found
Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions
Background: Cytosine methylation in plant genomes is important for the regulation of gene transcription and transposon activity. Genome-wide methylomes are studied upon mutation of the DNA methyltransferases, adaptation to environmental stresses or during development. However, from basic biology to breeding programs, there is a need to monitor multiple samples to determine transgenerational methylation inheritance or differential cytosine methylation. Methylome data obtained by sodium hydrogen sulfite (bisulfite)-conversion and next-generation sequencing (NGS) provide genome- wide information on cytosine methylation. However, a profiling method that detects cytosine methylation state dispersed over the genome would allow high-throughput analysis of multiple plant samples with distinct epigenetic signatures. We use specific restriction endonucleases to enrich for cytosine coverage in a bisulfite and NGS-based profiling method, which was compared to whole-genome bisulfite sequencing of the same plant material.
Methods: We established an effective methylome profiling method in plants, termed plant-reduced representation bisulfite sequencing (plant-RRBS), using optimized double restriction endonuclease digestion, fragment end repair, adapter ligation, followed by bisulfite conversion, PCR amplification and NGS. We report a performant laboratory protocol and a straightforward bioinformatics data analysis pipeline for plant-RRBS, applicable for any reference-sequenced plant species.
Results: As a proof of concept, methylome profiling was performed using an Oryza sativa ssp. indica pure breeding line and a derived epigenetically altered line (epiline). Plant-RRBS detects methylation levels at tens of millions of cytosine positions deduced from bisulfite conversion in multiple samples. To evaluate the method, the coverage of cytosine positions, the intra-line similarity and the differential cytosine methylation levels between the pure breeding line and the epiline were determined. Plant-RRBS reproducibly covers commonly up to one fourth of the cytosine positions in the rice genome when using MspI-DpnII within a group of five biological replicates of a line. The method predominantly detects cytosine methylation in putative promoter regions and not-annotated regions in rice.
Conclusions: Plant-RRBS offers high-throughput and broad, genome- dispersed methylation detection by effective read number generation obtained from reproducibly covered genome fractions using optimized endonuclease combinations, facilitating comparative analyses of multi-sample studies for cytosine methylation and transgenerational stability in experimental material and plant breeding populations
The Arabidopsis thaliana F-Box Protein FBL17 Is Essential for Progression through the Second Mitosis during Pollen Development
In fungi and metazoans, the SCF-type Ubiquitin protein ligases (E3s) play a critical role in cell cycle regulation by degrading negative regulators, such as cell cycle-dependent kinase inhibitors (CKIs) at the G1-to-S-phase checkpoint. Here we report that FBL17, an Arabidopsis thaliana F-box protein, is involved in cell cycle regulation during male gametogenesis. FBL17 expression is strongly enhanced in plants co-expressing E2Fa and DPa, transcription factors that promote S-phase entry. FBL17 loss-of-function mutants fail to undergo pollen mitosis II, which generates the two sperm cells in mature A. thaliana pollen. Nonetheless, the single sperm cell-like cell in fbl17 mutants is functional but will exclusively fertilize the egg cell of the female gametophyte, giving rise to an embryo that will later abort, most likely due to the lack of functional endosperm. Seed abortion can, however, be overcome by mutations in FIE, a component of the Polycomb group complex, overall resembling loss-of-function mutations in the A. thaliana cyclin-dependent kinase CDKA;1. Finally we identified ASK11, as an SKP1-like partner protein of FBL17 and discuss a possible mechanism how SCFFBL17 may regulate cell division during male gametogenesis
Diabetes mellitus in dogs attending UK primary-care practices: frequency, risk factors and survival
Background: Diabetes mellitus (DM) is an important endocrine disorder of dogs. The objectives of this study were to estimate prevalence and incidence of DM in dogs, and to explore risk factors for DM and the survival of DM cases in primary-care clinics in the UK.
Results: A case-control study nested in the cohort of dogs (n = 480,469) aged ≥3 years presenting at 430 VetCompass clinics was used to identify risk factors for DM, using multivariable logistic regression. Overall 409 new and 863 pre-existing DM cases (total 1272) were identified in 2016, giving an apparent annual prevalence of 0.26% (95% confidence interval (CI): 0.25–0.28%), and an annual incidence risk of 0.09% (95%CI: 0.08–0.09%) in dogs aged ≥3 years. Factors associated with increased odds for DM diagnosis were all age categories > 8 years, female entire dogs (odds ratio (OR): 3.03, 95% CI 1.69–5.44, p < 0.001) and male neutered dogs (OR: 1.99, 95% CI 1.18–3.34, p = 0.010) compared to male entire dogs, Border Terriers (OR: 3.37, 95% CI 1.04–10.98, p = 0.043) and West Highland White Terriers (WHWT) (OR: 2.88, 95% CI 1.49–5.56, p = 0.002) compared to crossbreeds. Dogs that had received previous glucocorticoid treatment (OR: 2.19, 95% CI 1.02–4.70, p = 0.044) and those with concurrent conditions (documented obese, pancreatitis, hyperadrenocorticism) also had increased odds for DM diagnosis.
Cox regression modelling was used to evaluate factors associated with survival in the 409 incident DM cases in 2016. Increased hazard of death following diagnosis of DM was shown in dogs that were ≥ 10 years age, Cocker Spaniels (HR: 2.06, 95% CI 1.06–4.01, p = 0.034) compared to crossbreeds, had a blood glucose (BG) level at
diagnosis > 40 mmol/L (HR: 2.73, 95% CI 1.35–5.55, p = 0.005) compared to < 20 mmol/L at diagnosis, or had received previous glucocorticoid treatment (HR: 1.86, 95% CI 1.21–2.86, p = 0.005). Dogs at reduced hazard of death included neutered dogs (HR: 0.58, 95% CI 0.42–0.79, p = 0.001), Border Collies (HR: 0.39, 95% CI 0.17–0.87, p = 0.022) and those starting insulin treatment (HR: 0.08 95% CI 0.05–0.12, p < 0.001). Conclusions: Certain breeds and concurrent health conditions are associated with an increased risk of DM. In addition to certain signalment factors, a high BG level at diagnosis and prior glucocorticoid treatment were adversely associated with survival of dogs with DM.
Keywords: Diabetes mellitus, Risk factors, Survival, Case-control study, Benchmarking, VetCompas
Endoreplication Controls Cell Fate Maintenance
Cell-fate specification is typically thought to precede and determine cell-cycle regulation during differentiation. Here we show that endoreplication, also known as endoreduplication, a specialized cell-cycle variant often associated with cell differentiation but also frequently occurring in malignant cells, plays a role in maintaining cell fate. For our study we have used Arabidopsis trichomes as a model system and have manipulated endoreplication levels via mutants of cell-cycle regulators and overexpression of cell-cycle inhibitors under a trichome-specific promoter. Strikingly, a reduction of endoreplication resulted in reduced trichome numbers and caused trichomes to lose their identity. Live observations of young Arabidopsis leaves revealed that dedifferentiating trichomes re-entered mitosis and were re-integrated into the epidermal pavement-cell layer, acquiring the typical characteristics of the surrounding epidermal cells. Conversely, when we promoted endoreplication in glabrous patterning mutants, trichome fate could be restored, demonstrating that endoreplication is an important determinant of cell identity. Our data lead to a new model of cell-fate control and tissue integrity during development by revealing a cell-fate quality control system at the tissue level
Event-by-event correlations between () hyperon global polarization and handedness with charged hadron azimuthal separation in Au+Au collisions at from STAR
Global polarizations () of () hyperons have been
observed in non-central heavy-ion collisions. The strong magnetic field
primarily created by the spectator protons in such collisions would split the
and global polarizations (). Additionally, quantum chromodynamics (QCD) predicts
topological charge fluctuations in vacuum, resulting in a chirality imbalance
or parity violation in a local domain. This would give rise to an imbalance
() between left- and right-handed
() as well as a charge separation along the magnetic field,
referred to as the chiral magnetic effect (CME). This charge separation can be
characterized by the parity-even azimuthal correlator () and
parity-odd azimuthal harmonic observable (). Measurements of
, , and have not led to definitive
conclusions concerning the CME or the magnetic field, and has not
been measured previously. Correlations among these observables may reveal new
insights. This paper reports measurements of correlation between and
, which is sensitive to chirality fluctuations, and correlation
between and sensitive to magnetic field in Au+Au
collisions at 27 GeV. For both measurements, no correlations have been observed
beyond statistical fluctuations.Comment: 10 pages, 10 figures; paper from the STAR Collaboratio
Hyperon polarization along the beam direction relative to the second and third harmonic event planes in isobar collisions at = 200 GeV
The polarization of and hyperons along the beam
direction has been measured relative to the second and third harmonic event
planes in isobar Ru+Ru and Zr+Zr collisions at = 200 GeV. This
is the first experimental evidence of the hyperon polarization by the
triangular flow originating from the initial density fluctuations. The
amplitudes of the sine modulation for the second and third harmonic results are
comparable in magnitude, increase from central to peripheral collisions, and
show a mild dependence. The azimuthal angle dependence of the
polarization follows the vorticity pattern expected due to elliptic and
triangular anisotropic flow, and qualitatively disagree with most hydrodynamic
model calculations based on thermal vorticity and shear induced contributions.
The model results based on one of existing implementations of the shear
contribution lead to a correct azimuthal angle dependence, but predict
centrality and dependence that still disagree with experimental
measurements. Thus, our results provide stringent constraints on the thermal
vorticity and shear-induced contributions to hyperon polarization. Comparison
to previous measurements at RHIC and the LHC for the second-order harmonic
results shows little dependence on the collision system size and collision
energy.Comment: 6 pages, 5 figures, Published in Physical Review Letter
Observation of the electromagnetic field effect via charge-dependent directed flow in heavy-ion collisions at the Relativistic Heavy Ion Collider
The deconfined quark-gluon plasma (QGP) created in relativistic heavy-ion
collisions enables the exploration of the fundamental properties of matter
under extreme conditions. Non-central collisions can produce strong magnetic
fields on the order of Gauss, which offers a probe into the
electrical conductivity of the QGP. In particular, quarks and anti-quarks carry
opposite charges and receive contrary electromagnetic forces that alter their
momenta. This phenomenon can be manifested in the collective motion of
final-state particles, specifically in the rapidity-odd directed flow, denoted
as . Here we present the charge-dependent measurements of
near midrapidities for , , and
in Au+Au and isobar (Ru+Ru and
Zr+Zr) collisions at 200 GeV, and
in Au+Au collisions at 27 GeV, recorded by the STAR detector at the
Relativistic Heavy Ion Collider. The combined dependence of the signal on
collision system, particle species, and collision centrality can be
qualitatively and semi-quantitatively understood as several effects on
constituent quarks. While the results in central events can be explained by the
and quarks transported from initial-state nuclei, those in peripheral
events reveal the impacts of the electromagnetic field on the QGP. Our data put
valuable constraints on the electrical conductivity of the QGP in theoretical
calculations
Tomography of Ultra-relativistic Nuclei with Polarized Photon-gluon Collisions
A linearly polarized photon can be quantized from the Lorentz-boosted
electromagnetic field of a nucleus traveling at ultra-relativistic speed. When
two relativistic heavy nuclei pass one another at a distance of a few nuclear
radii, the photon from one nucleus may interact through a virtual
quark-antiquark pair with gluons from the other nucleus forming a short-lived
vector meson (e.g. ). In this experiment, the polarization was
utilized in diffractive photoproduction to observe a unique spin interference
pattern in the angular distribution of decays.
The observed interference is a result of an overlap of two wave functions at a
distance an order of magnitude larger than the travel distance
within its lifetime. The strong-interaction nuclear radii were extracted from
these diffractive interactions, and found to be fm () and fm (), larger than the nuclear charge
radii. The observable is demonstrated to be sensitive to the nuclear geometry
and quantum interference of non-identical particles
Observation of Global Spin Alignment of and Vector Mesons in Nuclear Collisions
The strong force, as one of the four fundamental forces at work in the
universe, governs interactions of quarks and gluons, and binds together the
atomic nucleus. Notwithstanding decades of progress since Yukawa first
developed a description of the force between nucleons in terms of meson
exchange, a full understanding of the strong interaction remains a major
challenge in modern science. One remaining difficulty arises from the
non-perturbative nature of the strong force, which leads to the phenomenon of
quark confinement at distance scales on the order of the size of the proton.
Here we show that in relativistic heavy-ion collisions, where quarks and gluons
are set free over an extended volume, two species of produced vector (spin-1)
mesons, namely and , emerge with a surprising pattern of global
spin alignment. In particular, the global spin alignment for is
unexpectedly large, while that for is consistent with zero. The
observed spin-alignment pattern and magnitude for the cannot be
explained by conventional mechanisms, while a model with strong force fields
accommodates the current data. This is the first time that the strong force
field is experimentally supported as a key mechanism that leads to global spin
alignment. We extract a quantity proportional to the intensity of the field of
the strong force. Within the framework of the Standard Model, where the strong
force is typically described in the quark and gluon language of Quantum
Chromodynamics, the field being considered here is an effective proxy
description. This is a qualitatively new class of measurement, which opens a
new avenue for studying the behaviour of strong force fields via their imprint
on spin alignment
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