1,554 research outputs found
The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing
DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, is an evolutionarily conserved epigenetic mark involved in a number of different biological functions in eukaryotes, including transcriptional regulation, chromatin structural organization, cellular differentiation and development. In the social amoeba Dictyostelium, previous studies have shown the existence of a DNA methyltransferase (DNMA) belonging to the DNMT2 family, but the extent and function of 5-methylcytosine in the genome are unclear. Here, we present the whole genome DNA methylation profile of Dictyostelium discoideum using deep coverage replicate sequencing of bisulfite-converted gDNA extracted from post-starvation cells. We find an overall very low number of sites with any detectable level of DNA methylation, occurring at significant levels in only 303-3432 cytosines out of the ∼7.5 million total cytosines in the genome depending on the replicate. Furthermore, a knockout of the DNMA enzyme leads to no overall decrease in DNA methylation. Of the identified sites, significant methylation is only detected at 11 sites in all four of the methylomes analyzed. Targeted bisulfite PCR sequencing and computational analysis demonstrate that the methylation profile does not change during development and that these 11 cytosines are most likely false positives generated by protection from bisulfite conversion due to their location in hairpin-forming palindromic DNA sequences. Our data therefore provide evidence that there is no significant DNA methylation in Dictyostelium before fruiting body formation and identify a reproducible experimental artifact from bisulfite sequencing. © 2023 The Author(s). Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics
Evaluation of a chiral cubane-based Schiff base ligand in asymmetric catalysis reactions
Recently, a novel chiral cubane-based Schiff base ligand was reported to yield modest enantioselectivity in the Henry reaction. To further explore the utility of this ligand in other asymmetric organic transformations, we evaluated its stereoselectivity in cyclopropanation and Michael addition reactions. Although there was no increase in stereocontrol, upon computational evaluation using both M06L and B3LYP calculations, it was revealed that a pseudo six-membered ring exists, through H-bonding of a cubyl hydrogen to the copper core. This decreases the steric bulk above the copper center and limits the asymmetric control with this ligand.The authors thank the Niagara University Academic Center for Integrated Science and the Rochester Academy of Science for their financial support. MLI would like to thank the Barbara S. Zimmer Memorial Research Award for financial aid. MLC gratefully acknowledges generous allocations of supercomputing time from the Australian National Computational Infrastructure, support from the Australian Research Council under its Centers of Excellence program, and an ARC Future Fellowship. RP would also like to thank Western New England University, College of Pharmacy for generous financial support
Rationally designed immunogens enable immune focusing following SARS-CoV-2 spike imprinting
Eliciting antibodies to surface-exposed viral glycoproteins can generate protective responses that control and prevent future infections. Targeting conserved sites may reduce the likelihood of viral escape and limit the spread of related viruses with pandemic potential. Here we leverage rational immunogen design to focus humoral responses on conserved epitopes. Using glycan engineering and epitope scaffolding in boosting immunogens, we focus murine serum antibody responses to conserved receptor binding motif (RBM) and receptor binding domain (RBD) epitopes following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike imprinting. Although all engineered immunogens elicit a robust SARS-CoV-2-neutralizing serum response, RBM-focusing immunogens exhibit increased potency against related sarbecoviruses, SARS-CoV, WIV1-CoV, RaTG13-CoV, and SHC014-CoV; structural characterization of representative antibodies defines a conserved epitope. RBM-focused sera confer protection against SARS-CoV-2 challenge. Thus, RBM focusing is a promising strategy to elicit breadth across emerging sarbecoviruses without compromising SARS-CoV-2 protection. These engineering strategies are adaptable to other viral glycoproteins for targeting conserved epitopes
Status Report of the DPHEP Study Group: Towards a Global Effort for Sustainable Data Preservation in High Energy Physics
Data from high-energy physics (HEP) experiments are collected with
significant financial and human effort and are mostly unique. An
inter-experimental study group on HEP data preservation and long-term analysis
was convened as a panel of the International Committee for Future Accelerators
(ICFA). The group was formed by large collider-based experiments and
investigated the technical and organisational aspects of HEP data preservation.
An intermediate report was released in November 2009 addressing the general
issues of data preservation in HEP. This paper includes and extends the
intermediate report. It provides an analysis of the research case for data
preservation and a detailed description of the various projects at experiment,
laboratory and international levels. In addition, the paper provides a concrete
proposal for an international organisation in charge of the data management and
policies in high-energy physics
Bi-allelic Variants in the GPI Transamidase Subunit PIGK Cause a Neurodevelopmental Syndrome with Hypotonia, Cerebellar Atrophy, and Epilepsy
Glycosylphosphatidylinositol (GPI)-anchored proteins are critical for embryogenesis, neurogenesis, and cell signaling. Variants in several genes participating in GPI biosynthesis and processing lead to decreased cell surface presence of GPI-anchored proteins (GPI-APs) and cause inherited GPI deficiency disorders (IGDs). In this report, we describe 12 individuals from nine unrelated families with 10 different bi-allelic PIGK variants. PIGK encodes a component of the GPI transamidase complex, which attaches the GPI anchor to proteins. Clinical features found in most individuals include global developmental delay and/or intellectual disability, hypotonia, cerebellar ataxia, cerebellar atrophy, and facial dysmorphisms. The majority of the individuals have epilepsy. Two individuals have slightly decreased levels of serum alkaline phosphatase, while eight do not. Flow cytometric analysis of blood and fibroblasts from affected individuals showed decreased cell surface presence of GPI-APs. The overexpression of wild-type (WT) PIGK in fibroblasts rescued the levels of cell surface GPI-APs. In a knockout cell line, transfection with WT PIGK also rescued the GPI-AP levels, but transfection with the two tested mutant variants did not. Our study not only expands the clinical and known genetic spectrum of IGDs, but it also expands the genetic differential diagnosis for cerebellar atrophy. Given the fact that cerebellar atrophy is seen in other IGDs, flow cytometry for GPI-APs should be considered in the work-ups of individuals presenting this feature
Inclusive Search for Anomalous Production of High-pT Like-Sign Lepton Pairs in Proton-Antiproton Collisions at sqrt{s}=1.8 TeV
We report on a search for anomalous production of events with at least two
charged, isolated, like-sign leptons with pT > 11 GeV/c using a 107 pb^-1
sample of 1.8 TeV ppbar collisions collected by the CDF detector. We define a
signal region containing low background from Standard Model processes. To avoid
bias, we fix the final cuts before examining the event yield in the signal
region using control regions to test the Monte Carlo predictions. We observe no
events in the signal region, consistent with an expectation of
0.63^(+0.84)_(-0.07) events. We present 95% confidence level limits on new
physics processes in both a signature-based context as well as within a
representative minimal supergravity (tanbeta = 3) model.Comment: 15 pages, 4 figures. Minor textual changes, cosmetic improvements to
figures and updated and expanded reference
Double Diffraction Dissociation at the Fermilab Tevatron Collider
We present results from a measurement of double diffraction dissociation in
collisions at the Fermilab Tevatron collider. The production cross
section for events with a central pseudorapidity gap of width
(overlapping ) is found to be [] at [630]
GeV. Our results are compared with previous measurements and with predictions
based on Regge theory and factorization.Comment: 10 pages, 4 figures, using RevTeX. Submitted to Physical Review
Letter
Search for Gluinos and Scalar Quarks in Collisions at TeV using the Missing Energy plus Multijets Signature
We have performed a search for gluinos (\gls) and squarks (\sq) in a data
sample of 84 pb of \ppb collisions at = 1.8 TeV, recorded by
the Collider Detector at Fermilab, by investigating the final state of large
missing transverse energy and 3 or more jets, a characteristic signature in
R-parity-conserving supersymmetric models. The analysis has been performed
`blind', in that the inspection of the signal region is made only after the
predictions from Standard Model backgrounds have been calculated. Comparing the
data with predictions of constrained supersymmetric models, we exclude gluino
masses below 195 \gev (95% C.L.), independent of the squark mass. For the case
\msq \approx \mgls, gluino masses below 300 \gev are excluded.Comment: 7 pages, 3 figure
Search for Narrow Diphoton Resonances and for gamma-gamma+W/Z Signatures in p\bar p Collisions at sqrt(s)=1.8 TeV
We present results of searches for diphoton resonances produced both
inclusively and also in association with a vector boson (W or Z) using 100
pb^{-1} of p\bar p collisions using the CDF detector. We set upper limits on
the product of cross section times branching ratio for both p\bar
p\to\gamma\gamma + X and p\bar p\to\gamma\gamma + W/Z. Comparing the inclusive
production to the expectations from heavy sgoldstinos we derive limits on the
supersymmetry-breaking scale sqrt{F} in the TeV range, depending on the
sgoldstino mass and the choice of other parameters. Also, using a NLO
prediction for the associated production of a Higgs boson with a W or Z boson,
we set an upper limit on the branching ratio for H\to\gamma\gamma. Finally, we
set a lower limit on the mass of a `bosophilic' Higgs boson (e.g. one which
couples only to \gamma, W, and Z$ bosons with standard model couplings) of 82
GeV/c^2 at 95% confidence level.Comment: 30 pages, 11 figure
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