Constraining the evolution of the unstable accretion disk in SMC X-1 with NICER

Neutron star high mass X-ray binaries with superorbital modulations in luminosity host warped inner accretion disks that occult the neutron star during precession. In SMC X-1, the instability in the warped disk geometry causes superorbital period "excursions:" times of instability when the superorbital period decreases from its typical value of 55 days to $\sim$40 days. Disk instability makes SMC X-1 an ideal system in which to investigate the effects of variable disk geometry on the inner accretion flow. Using the high resolution spectral and timing capabilities of the Neutron Star Interior Composition Explorer (NICER) we examined the high state of four different superorbital cycles of SMC X-1 to search forchanges in spectral shape and connections to the unstable disk geometry. We performed pulse phase-averaged and phase-resolved spectroscopy to closely compare the changes in spectral shape and any cycle-to-cycle variations. While some parameters including the photon index and absorbing column density show slight variations with superorbital phase, these changes are most evident during the intermediate state of the supeorbital cycle. Few spectral changes are observed within the high state of the superorbital cycle, possibly indicating the disk instability does not significantly change SMC X-1's accretion process.Comment: 11 pages, 5 figures. Accepted to Ap

The Tumor Suppressor HHEX Inhibits Axon Growth when Prematurely Expressed in Developing Central Nervous System Neurons

Neurons in the embryonic and peripheral nervoussystem respond to injury by activating transcriptional programs supportive of axon growth, ultimately resulting in functional recovery. In contrast, neurons in the adult central nervous system (CNS) possess a limited capacity to regenerate axons after injury, fundamentally constraining repair. Activating pro-regenerative gene expression in CNS neurons is a promising therapeutic approach, but progress is hampered by incomplete knowledge of the relevant transcription factors. An emerging hypothesis is that factors implicated in cellular growth and motility outside the nervous system may also control axon growth in neurons. We therefore tested sixty-nine transcription factors, previously identified as possessing tumor suppressive or oncogenic properties in non-neuronal cells, in assays of neurite outgrowth. This screen identified YAP1 and E2F1 as enhancers of neurite outgrowth, and PITX1, RBM14, ZBTB16, and HHEX as inhibitors. Follow-up experiments are focused on the tumor suppressor HHEX, one of the strongest growth inhibitors. HHEX is widely expressed in adult CNS neurons, including corticospinal tract neurons after spinal injury, but is present only in trace amounts in immature cortical neurons and adult peripheral neurons. HHEX overexpression in early postnatal cortical neurons reduced both initial axonogenesis and the rate of axon elongation, and domain deletion analysis strongly implicated transcriptional repression as the underlying mechanism. These findings suggest a role for HHEX in restricting axon growth in the developing CNS, and substantiate the hypothesis that previously identified oncogenes and tumor suppressors can play conserved roles in axon extension

Novel sequential ChIP and simplified basic ChIP protocols for promoter co-occupancy and target gene identification in human embryonic stem cells

<p>Abstract</p> <p>Background</p> <p>The investigation of molecular mechanisms underlying transcriptional regulation, particularly in embryonic stem cells, has received increasing attention and involves the systematic identification of target genes and the analysis of promoter co-occupancy. High-throughput approaches based on chromatin immunoprecipitation (ChIP) have been widely used for this purpose. However, these approaches remain time-consuming, expensive, labor-intensive, involve multiple steps, and require complex statistical analysis. Advances in this field will greatly benefit from the development and use of simple, fast, sensitive and straightforward ChIP assay and analysis methodologies.</p> <p>Results</p> <p>We initially developed a simplified, basic ChIP protocol that combines simplicity, speed and sensitivity. ChIP analysis by real-time PCR was compared to analysis by densitometry with the ImageJ software. This protocol allowed the rapid identification of known target genes for SOX2, NANOG, OCT3/4, SOX17, KLF4, RUNX2, OLIG2, SMAD2/3, BMI-1, and c-MYC in a human embryonic stem cell line. We then developed a novel Sequential ChIP protocol to investigate <it>in vivo </it>promoter co-occupancy, which is basically characterized by the absence of antibody-antigen disruption during the assay. It combines centrifugation of agarose beads and magnetic separation. Using this Sequential ChIP protocol we found that c-MYC associates with the SOX2/NANOG/OCT3/4 complex and identified a novel RUNX2/BMI-1/SMAD2/3 complex in BG01V cells. These two TF complexes associate with two distinct sets of target genes. The RUNX2/BMI-1/SMAD2/3 complex is associated predominantly with genes not expressed in undifferentiated BG01V cells, consistent with the reported role of those TFs as transcriptional repressors.</p> <p>Conclusion</p> <p>These simplified basic ChIP and novel Sequential ChIP protocols were successfully tested with a variety of antibodies with human embryonic stem cells, generated a number of novel observations for future studies and might be useful for high-throughput ChIP-based assays.</p

Constraining the Evolution of the Unstable Accretion Disk in SMC X-1 with NICER

Neutron star high-mass X-ray binaries with superorbital modulations in luminosity host warped inner accretion disks that occult the neutron star during precession. In SMC X-1, the instability in the warped disk geometry causes superorbital period “excursions”: times of instability when the superorbital period decreases from its typical value of 55 to ∼40 days. Disk instability makes SMC X-1 an ideal system in which to investigate the effects of variable disk geometry on the inner accretion flow. Using the high-resolution spectral and timing capabilities of the Neutron Star Interior Composition Explorer, we examined the high state of four different superorbital cycles of SMC X-1 to search for changes in spectral shape and connections to the unstable disk geometry. We performed pulse phase-averaged and phase-resolved spectroscopy to closely compare the changes in spectral shape and any cycle-to-cycle variations. While some parameters, including the photon index and absorbing column density, show slight variations with superorbital phase, these changes are most evident during the intermediate state of the superorbital cycle. Few spectral changes are observed within the high state of the superorbital cycle, possibly indicating the disk instability does not significantly change SMC X-1's accretion process

Fluctuations of functionally distinct CD8+ T-cell clonotypes demonstrate flexibility of the HIV-specific TCR repertoire

T-cell receptor (TCR) diversity of virus-specific CD8+ T cells likely helps prevent escape mutations in chronic viral infections. To understand the dynamics of the virus-specific T cells in more detail, we followed the evolution of the TCR repertoire specific for a dominant HLA-B*08–restricted epitope in Nef (FLKEKGGL) in a cohort of subjects infected with HIV. Epitope-specific CD8+ T cells used structurally diverse TCR repertoires, with different TCRβ variable regions and with high amino acid diversity within antigen recognition sites. In a longitudinal study, distinct Vβ populations within the HIV-specific TCR repertoire expanded simultaneously with changes in plasma viremia, whereas other Vβ populations remained stable or even decreased. Despite antigenic variation in some subjects, all subjects had the consensus sequence present during the study period. Functional analysis of distinct Vβ populations revealed differences in HIV-specific IFN-γ secretion ex vivo as well as differences in tetramer binding, indicating functional heterogeneity among these populations. This contrasts with findings in a subject on antiretroviral therapy with suppression of viremia to less than 50 copies/mL, where we observed long-term persistence of a single clonotype. Our findings illustrate the flexibility of a heterogeneous HIV-1–specific CD8+ TCR repertoire in subjects with partial control of viremia