62 research outputs found
Photodisintegration of He into p+t
The two-body photodisintegration of He into a proton and a triton has
been studied using the CEBAF Large-Acceptance Spectrometer (CLAS) at Jefferson
Laboratory. Real photons produced with the Hall-B bremsstrahlung-tagging system
in the energy range from 0.35 to 1.55 GeV were incident on a liquid He
target. This is the first measurement of the photodisintegration of He
above 0.4 GeV. The differential cross sections for the He
reaction have been measured as a function of photon-beam energy and
proton-scattering angle, and are compared with the latest model calculations by
J.-M. Laget. At 0.6-1.2 GeV, our data are in good agreement only with the
calculations that include three-body mechanisms, thus confirming their
importance. These results reinforce the conclusion of our previous study of the
three-body breakup of He that demonstrated the great importance of
three-body mechanisms in the energy region 0.5-0.8 GeV .Comment: 13 pages submitted in one tgz file containing 2 tex file and 22
postscrip figure
Exclusive electroproduction on the proton at CLAS
The reaction has been measured, using the 5.754
GeV electron beam of Jefferson Lab and the CLAS detector. This represents the
largest ever set of data for this reaction in the valence region. Integrated
and differential cross sections are presented. The , and
dependences of the cross section are compared to theoretical calculations based
on -channel meson-exchange Regge theory on the one hand and on quark handbag
diagrams related to Generalized Parton Distributions (GPDs) on the other hand.
The Regge approach can describe at the 30% level most of the features
of the present data while the two GPD calculations that are presented in this
article which succesfully reproduce the high energy data strongly underestimate
the present data. The question is then raised whether this discrepancy
originates from an incomplete or inexact way of modelling the GPDs or the
associated hard scattering amplitude or whether the GPD formalism is simply
inapplicable in this region due to higher-twists contributions, incalculable at
present.Comment: 29 pages, 29 figure
Stem Cell Factor SALL4 Represses the Transcriptions of PTEN and SALL1 through an Epigenetic Repressor Complex
Background The embryonic stem cell (ESC) factor, SALL4, plays an essential role in both development and leukemogenesis. It is a unique gene that is involved in self-renewal in ESC and leukemic stem cell (LSC).Methodology/Principal Findings To understand the mechanism(s) of SALL4 function(s), we sought to identify SALL4-associated proteins by tandem mass spectrometry. Components of a transcription repressor Mi-2/Nucleosome Remodeling and Deacetylase (NuRD) complex were found in the SALL4-immunocomplexes with histone deacetylase (HDAC) activity in ESCs with endogenous SALL4 expression and 293T cells overexpressing SALL4. The SALL4-mediated transcriptional regulation was tested on two potential target genes: PTEN and SALL1. Both genes were confirmed as SALL4 downstream targets by chromatin-immunoprecipitation, and their expression levels, when tested by quantitative reverse transcription polymerase chain reaction (qRT-PCR), were decreased in 293T cells overexpressing SALL4. Moreover, SALL4 binding sites at the promoter regions of PTEN and SALL1 were co-occupied by NuRD components, suggesting that SALL4 represses the transcriptions of PTEN and SALL1 through its interactions with the Mi-2/NuRD complex. The in vivo repressive effect(s) of SALL4 were evaluated in SALL4 transgenic mice, where decreased expressions of PTEN and SALL1 were associated with myeloid leukemia and cystic kidneys, respectively.Conclusions/Significance In summary, we are the first to demonstrate that stem cell protein SALL4 represses its target genes, PTEN and SALL1, through the epigenetic repressor Mi-2/NuRD complex. Our novel finding provides insight into the mechanism(s) of SALL4 functions in kidney development and leukemogenesis
DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing
Tissue specific patterns of methylated cytosine residues vary with age, can be altered by environmental factors, and are often abnormal in human disease yet the cellular consequences of DNA methylation are incompletely understood. Although the bodies of highly expressed genes are often extensively methylated in plants, the relationship between intragenic methylation and expression is less clear in mammalian cells. We performed genome-wide analyses of DNA methylation and gene expression to determine how the pattern of intragenic methylation correlates with transcription and to assess the relationship between methylation of exonic and intronic portions of the gene body. We found that dense exonic methylation is far more common than previously recognized or expected statistically, yet first exons are relatively spared compared to more downstream exons and introns. Dense methylation surrounding the transcription start site (TSS) is uncoupled from methylation within more downstream regions suggesting that there are at least two classes of intragenic methylation. Whereas methylation surrounding the TSS is tightly linked to transcriptional silencing, methylation of more downstream regions is unassociated with the magnitude of gene expression. Notably, we found that DNA methylation downstream of the TSS, in the region of the first exon, is much more tightly linked to transcriptional silencing than is methylation in the upstream promoter region. These data provide direct evidence that DNA methylation is interpreted dissimilarly in different regions of the gene body and suggest that first exon methylation blocks transcript initiation, or vice versa. Our data also show that once initiated, downstream methylation is not a significant impediment to polymerase extension. Thus, the consequences of most intragenic DNA methylation must extend beyond the modulation of transcription magnitude
Disease- and age-related changes in histone acetylation at gene promoters in psychiatric disorders
Increasing evidence suggests that epigenetic factors have critical roles in gene
regulation in neuropsychiatric disorders and in aging, both of which are
typically associated with a wide range of gene expression abnormalities. Here,
we have used chromatin immunoprecipitation-qPCR to measure levels of acetylated
histone H3 at lysines 9/14 (ac-H3K9K14), two epigenetic marks associated
with transcriptionally active chromatin, at the promoter regions of eight
schizophrenia-related genes in n=82 postmortem prefrontal
cortical samples from normal subjects and those with schizophrenia and bipolar
disorder. We find that promoter-associated ac-H3K9K14 levels are correlated with
gene expression levels, as measured by real-time qPCR for several genes,
including, glutamic acid decarboxylase 1 (GAD1), 5-hydroxytryptamine
receptor 2C (HTR2C), translocase of outer mitochondrial membrane 70
homolog A (TOMM70A) and protein phosphatase 1E (PPM1E).
Ac-H3K9K14 levels of several of the genes tested were significantly negatively
associated with age in normal subjects and those with bipolar disorder, but not
in subjects with schizophrenia, whereby low levels of histone acetylation were
observed in early age and throughout aging. Consistent with this observation,
significant hypoacetylation of H3K9K14 was detected in young subjects with
schizophrenia when compared with age-matched controls. Our results demonstrate
that gene expression changes associated with psychiatric disease and aging
result from epigenetic mechanisms involving histone acetylation. We further find
that treatment with a histone deacetylase (HDAC) inhibitor alters the expression
of several candidate genes for schizophrenia in mouse brain. These findings may
have therapeutic implications for the clinical use of HDAC inhibitors in
psychiatric disorders
First measurement of target and double spin asymmetries for polarized e- polarized p --> e p pi0 in the nucleon resonance region above the Delta(1232)
The exclusive channel polarized proton(polarized e,e prime p)pi0 was studied
in the first and second nucleon resonance regions in the Q2 range from 0.187 to
0.770 GeV2 at Jefferson Lab using the CEBAF Large Acceptance Spectrometer
(CLAS). Longitudinal target and beam-target asymmetries were extracted over a
large range of center-of-mass angles of the pi0 and compared to the unitary
isobar model MAID, the dynamic model by Sato and Lee, and the dynamic model
DMT. A strong sensitivity to individual models was observed, in particular for
the target asymmetry and in the higher invariant mass region. This data set,
once included in the global fits of the above models, is expected to place
strong constraints on the electrocoupling amplitudes A_{1/2} and S_{1/2} for
the Roper resonance N(1400)P11, and the N(1535)S11 and N(1520)D13 states.Comment: 13 pages, 13 figure
Oxidative protein labeling in mass-spectrometry-based proteomics
Oxidation of proteins and peptides is a common phenomenon, and can be employed as a labeling technique for mass-spectrometry-based proteomics. Nonspecific oxidative labeling methods can modify almost any amino acid residue in a protein or only surface-exposed regions. Specific agents may label reactive functional groups in amino acids, primarily cysteine, methionine, tyrosine, and tryptophan. Nonspecific radical intermediates (reactive oxygen, nitrogen, or halogen species) can be produced by chemical, photochemical, electrochemical, or enzymatic methods. More targeted oxidation can be achieved by chemical reagents but also by direct electrochemical oxidation, which opens the way to instrumental labeling methods. Oxidative labeling of amino acids in the context of liquid chromatography(LC)–mass spectrometry (MS) based proteomics allows for differential LC separation, improved MS ionization, and label-specific fragmentation and detection. Oxidation of proteins can create new reactive groups which are useful for secondary, more conventional derivatization reactions with, e.g., fluorescent labels. This review summarizes reactions of oxidizing agents with peptides and proteins, the corresponding methodologies and instrumentation, and the major, innovative applications of oxidative protein labeling described in selected literature from the last decade
Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design
Changes to the Fossil Record of Insects through Fifteen Years of Discovery
The first and last occurrences of hexapod families in the fossil record are compiled from publications up to end-2009. The major features of these data are compared with those of previous datasets (1993 and 1994). About a third of families (>400) are new to the fossil record since 1994, over half of the earlier, existing families have experienced changes in their known stratigraphic range and only about ten percent have unchanged ranges. Despite these significant additions to knowledge, the broad pattern of described richness through time remains similar, with described richness increasing steadily through geological history and a shift in dominant taxa, from Palaeoptera and Polyneoptera to Paraneoptera and Holometabola, after the Palaeozoic. However, after detrending, described richness is not well correlated with the earlier datasets, indicating significant changes in shorter-term patterns. There is reduced Palaeozoic richness, peaking at a different time, and a less pronounced Permian decline. A pronounced Triassic peak and decline is shown, and the plateau from the mid Early Cretaceous to the end of the period remains, albeit at substantially higher richness compared to earlier datasets. Origination and extinction rates are broadly similar to before, with a broad decline in both through time but episodic peaks, including end-Permian turnover. Origination more consistently exceeds extinction compared to previous datasets and exceptions are mainly in the Palaeozoic. These changes suggest that some inferences about causal mechanisms in insect macroevolution are likely to differ as well
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