1,261 research outputs found
Mitochondria Are Related to Synaptic Pathology in Alzheimer's Disease
Morphological alterations of mitochondria may play an important role in the pathogenesis of Alzheimer's disease, been associated with oxidative stress and Aβ-peptide-induced toxicity. We proceeded to estimation of mitochondria on electron micrographs of autopsy specimens of Alzheimer's disease. We found substantial morphological and morphometric changes of the mitochondria in the neurons of the hippocampus, the neocortex, the cerebellar cortex, the thalamus, the globus pallidus, the red nucleus, the locus coeruleus, and the climbing fibers. The alterations consisted of considerable changes of the cristae, accumulation of osmiophilic material, and modification of the shape and size. Mitochondrial alterations were prominent in neurons, which showed a depletion of dendritic spines and loss of dendritic branches. Mitochondrial alterations are not related with the accumulation of amyloid deposits, but are prominent whenever fragmentation of the Golgi apparatus exists. Morphometric analysis showed also that mitochondria are significantly reduced in neurons, which demonstrated synaptic pathology
Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay
Learning to read and write the transcriptional regulatory code is of central importance to progress in genetic analysis and engineering. Here we describe a massively parallel reporter assay (MPRA) that facilitates the systematic dissection of transcriptional regulatory elements. In MPRA, microarray-synthesized DNA regulatory elements and unique sequence tags are cloned into plasmids to generate a library of reporter constructs. These constructs are transfected into cells and tag expression is assayed by high-throughput sequencing. We apply MPRA to compare >27,000 variants of two inducible enhancers in human cells: a synthetic cAMP-regulated enhancer and the virus-inducible interferon-β enhancer. We first show that the resulting data define accurate maps of functional transcription factor binding sites in both enhancers at single-nucleotide resolution. We then use the data to train quantitative sequence-activity models (QSAMs) of the two enhancers. We show that QSAMs from two cellular states can be combined to design enhancer variants that optimize potentially conflicting objectives, such as maximizing induced activity while minimizing basal activity.National Human Genome Research Institute (U.S.) (grant R01HG004037)National Science Foundation (U.S.) ((NSF) grant PHY-0957573)National Science Foundation (U.S.) (NSF grant PHY-1022140)Broad Institut
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
August 1, 2010Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution,
providing a robust platform for molecular diagnostics. Here, we optimize bisulfite sequencing for
genome-scale analysis of clinical samples. Specifically, we outline how restriction digestion
targets bisulfite sequencing to hotspots of epigenetic regulation; we show that 30ng of DNA are
sufficient for genome-scale analysis; we demonstrate that our protocol works well on formalinfixed,
paraffin-embedded (FFPE) samples; and we describe a statistical method for assessing
significance of altered DNA methylation patterns.National Institutes of Health (U.S.) (Grant R01HG004401)National Institutes of Health (U.S.) (Grant U54HG03067)National Institutes of Health (U.S.) (Grant U01ES017155
Strongly magnetized pulsars: explosive events and evolution
Well before the radio discovery of pulsars offered the first observational
confirmation for their existence (Hewish et al., 1968), it had been suggested
that neutron stars might be endowed with very strong magnetic fields of
-G (Hoyle et al., 1964; Pacini, 1967). It is because of their
magnetic fields that these otherwise small ed inert, cooling dead stars emit
radio pulses and shine in various part of the electromagnetic spectrum. But the
presence of a strong magnetic field has more subtle and sometimes dramatic
consequences: In the last decades of observations indeed, evidence mounted that
it is likely the magnetic field that makes of an isolated neutron star what it
is among the different observational manifestations in which they come. The
contribution of the magnetic field to the energy budget of the neutron star can
be comparable or even exceed the available kinetic energy. The most magnetised
neutron stars in particular, the magnetars, exhibit an amazing assortment of
explosive events, underlining the importance of their magnetic field in their
lives. In this chapter we review the recent observational and theoretical
achievements, which not only confirmed the importance of the magnetic field in
the evolution of neutron stars, but also provide a promising unification scheme
for the different observational manifestations in which they appear. We focus
on the role of their magnetic field as an energy source behind their persistent
emission, but also its critical role in explosive events.Comment: Review commissioned for publication in the White Book of
"NewCompStar" European COST Action MP1304, 43 pages, 8 figure
Gravitational waves from single neutron stars: an advanced detector era survey
With the doors beginning to swing open on the new gravitational wave
astronomy, this review provides an up-to-date survey of the most important
physical mechanisms that could lead to emission of potentially detectable
gravitational radiation from isolated and accreting neutron stars. In
particular we discuss the gravitational wave-driven instability and
asteroseismology formalism of the f- and r-modes, the different ways that a
neutron star could form and sustain a non-axisymmetric quadrupolar "mountain"
deformation, the excitation of oscillations during magnetar flares and the
possible gravitational wave signature of pulsar glitches. We focus on progress
made in the recent years in each topic, make a fresh assessment of the
gravitational wave detectability of each mechanism and, finally, highlight key
problems and desiderata for future work.Comment: 39 pages, 12 figures, 2 tables. Chapter of the book "Physics and
Astrophysics of Neutron Stars", NewCompStar COST Action 1304. Minor
corrections to match published versio
Subunit asymmetry and roles of conformational switching in the hexameric AAA+ ring of ClpX
The hexameric AAA+ ring of Escherichia coli ClpX, an ATP-dependent machine for protein unfolding and translocation, functions with the ClpP peptidase to degrade target substrates. For efficient function, ClpX subunits must switch between nucleotide-loadable (L) and nucleotide-unloadable (U) conformations, but the roles of switching are uncertain. Moreover, it is controversial whether working AAA+-ring enzymes assume symmetric or asymmetric conformations. Here, we show that a covalent ClpX ring with one subunit locked in the U conformation catalyzes robust ATP hydrolysis, with each unlocked subunit able to bind and hydrolyze ATP, albeit with highly asymmetric position-specific affinities. Preventing UâL interconversion in one subunit alters the cooperativity of ATP hydrolysis and reduces the efficiency of substrate binding, unfolding and degradation, showing that conformational switching enhances multiple aspects of wild-type ClpX function. These results support an asymmetric and probabilistic model of AAA+-ring activity.National Institutes of Health (U.S.) (Grant GM-101988)Massachusetts Institute of Technology (Poitras Predoctoral Fellowship
Defending the genome from the enemy within:mechanisms of retrotransposon suppression in the mouse germline
The viability of any species requires that the genome is kept stable as it is transmitted from generation to generation by the germ cells. One of the challenges to transgenerational genome stability is the potential mutagenic activity of transposable genetic elements, particularly retrotransposons. There are many different types of retrotransposon in mammalian genomes, and these target different points in germline development to amplify and integrate into new genomic locations. Germ cells, and their pluripotent developmental precursors, have evolved a variety of genome defence mechanisms that suppress retrotransposon activity and maintain genome stability across the generations. Here, we review recent advances in understanding how retrotransposon activity is suppressed in the mammalian germline, how genes involved in germline genome defence mechanisms are regulated, and the consequences of mutating these genome defence genes for the developing germline
Medical students' and facilitators' experiences of an Early Professional Contact course: Active and motivated students, strained facilitators
Background: Today, medical students are introduced to patient contact, communication skills, and clinical examination in the preclinical years of the curriculum with the purpose of gaining clinical experience. These courses are often evaluated from the student perspective. Reports with an additional emphasis on the facilitator perspective are scarce. According to constructive alignment, an influential concept from research in higher education, the learning climate between students and teachers is also of great importance. In this paper, we approach the learning climate by studying both students' and facilitators' course experiences.\ud
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In 2001, a new "Early Professional Contact" longitudinal strand through term 1â4, was introduced at the Sahlgrenska Academy, University of Gothenburg, Sweden. General practitioners and hospital specialists were facilitators.\ud
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The aim of this study was to assess and analyse students' and clinical facilitators' experiences of the Early Professional Contact course and to illuminate facilitators' working conditions.\ud
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Methods: Inspired by a Swedish adaptation of the Course Experience Questionnaire, an Early Professional Contact Questionnaire was constructed. In 2003, on the completion of the first longitudinal strand, a student and facilitator version was distributed to 86 students and 21 facilitators. In the analysis, both Chi-square and the Mann-Whitney tests were used.\ud
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Results: Sixty students (70%) and 15 facilitators (71%) completed the questionnaire. Both students and facilitators were satisfied with the course. Students reported gaining [inspiration] for their future work as doctors along with increased confidence in meeting patients. They also reported increased motivation for biomedical studies. Differences in attitudes between facilitators and students were found. Facilitators experienced a greater workload, less reasonable demands and less support, than students.\ud
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Conclusion: In this project, a new Early Professional Contact course was analysed from both student and facilitator perspectives. The students experienced the course as providing them with a valuable introduction to the physician's professional role in clinical practice. In contrast, course facilitators often experienced a heavy workload and lack of support, despite thorough preparatory education. A possible conflict between the clinical facilitator's task as educator and member of the workplace is suggested. More research is needed on how doctors combine their professional tasks with work as facilitators
Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV
The performance of muon reconstruction, identification, and triggering in CMS
has been studied using 40 inverse picobarns of data collected in pp collisions
at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection
criteria covering a wide range of physics analysis needs have been examined.
For all considered selections, the efficiency to reconstruct and identify a
muon with a transverse momentum pT larger than a few GeV is above 95% over the
whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4,
while the probability to misidentify a hadron as a muon is well below 1%. The
efficiency to trigger on single muons with pT above a few GeV is higher than
90% over the full eta range, and typically substantially better. The overall
momentum scale is measured to a precision of 0.2% with muons from Z decays. The
transverse momentum resolution varies from 1% to 6% depending on pseudorapidity
for muons with pT below 100 GeV and, using cosmic rays, it is shown to be
better than 10% in the central region up to pT = 1 TeV. Observed distributions
of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO
Performance of CMS muon reconstruction in pp collision events at sqrt(s) = 7 TeV
The performance of muon reconstruction, identification, and triggering in CMS
has been studied using 40 inverse picobarns of data collected in pp collisions
at sqrt(s) = 7 TeV at the LHC in 2010. A few benchmark sets of selection
criteria covering a wide range of physics analysis needs have been examined.
For all considered selections, the efficiency to reconstruct and identify a
muon with a transverse momentum pT larger than a few GeV is above 95% over the
whole region of pseudorapidity covered by the CMS muon system, abs(eta) < 2.4,
while the probability to misidentify a hadron as a muon is well below 1%. The
efficiency to trigger on single muons with pT above a few GeV is higher than
90% over the full eta range, and typically substantially better. The overall
momentum scale is measured to a precision of 0.2% with muons from Z decays. The
transverse momentum resolution varies from 1% to 6% depending on pseudorapidity
for muons with pT below 100 GeV and, using cosmic rays, it is shown to be
better than 10% in the central region up to pT = 1 TeV. Observed distributions
of all quantities are well reproduced by the Monte Carlo simulation.Comment: Replaced with published version. Added journal reference and DO
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