Detection of erbB2 copy number variations in plasma of patients with esophageal carcinoma

<p>Abstract</p> <p>Background</p> <p>Mortality is high in patients with esophageal carcinoma as tumors are rarely detected before the disease has progressed to an advanced stage. Here, we sought to isolate cell-free DNA released into the plasma of patients with esophageal carcinoma, to analyze copy number variations of marker genes in the search for early detection of tumor progression.</p> <p>Methods</p> <p>Plasma of 41 patients with esophageal carcinoma was prospectively collected before tumor resection and chemotherapy. Our dataset resulted heterogeneous for clinical data, resembling the characteristics of the tumor. DNA from the plasma was extracted to analyze copy number variations of the <it>erbB2 </it>gene using real-time PCR assays.</p> <p>Results</p> <p>The real-time PCR assays for <it>erbB2 </it>gene showed significant (<it>P </it>= 0.001) copy number variations in the plasma of patients with esophageal carcinoma, as compared to healthy controls with high sensitivity (80%) and specificity (95%). These variations in <it>erbB2 </it>were negatively correlated to the progression free survival of these patients (<it>P </it>= 0.03), and revealed a further risk category stratification of patients with low VEGF expression levels.</p> <p>Conclusion</p> <p>The copy number variation of <it>erbB2 </it>gene from plasma can be used as prognostic marker for early detection of patients at risk of worse clinical outcome in esophageal cancer.</p

Systematic NMR Analysis of Stable Isotope Labeled Metabolite Mixtures in Plant and Animal Systems: Coarse Grained Views of Metabolic Pathways

BACKGROUND: Metabolic phenotyping has become an important 'bird's-eye-view' technology which can be applied to higher organisms, such as model plant and animal systems in the post-genomics and proteomics era. Although genotyping technology has expanded greatly over the past decade, metabolic phenotyping has languished due to the difficulty of 'top-down' chemical analyses. Here, we describe a systematic NMR methodology for stable isotope-labeling and analysis of metabolite mixtures in plant and animal systems. METHODOLOGY/PRINCIPAL FINDINGS: The analysis method includes a stable isotope labeling technique for use in living organisms; a systematic method for simultaneously identifying a large number of metabolites by using a newly developed HSQC-based metabolite chemical shift database combined with heteronuclear multidimensional NMR spectroscopy; Principal Components Analysis; and a visualization method using a coarse-grained overview of the metabolic system. The database contains more than 1000 (1)H and (13)C chemical shifts corresponding to 142 metabolites measured under identical physicochemical conditions. Using the stable isotope labeling technique in Arabidopsis T87 cultured cells and Bombyx mori, we systematically detected >450 HSQC peaks in each (13)C-HSQC spectrum derived from model plant, Arabidopsis T87 cultured cells and the invertebrate animal model Bombyx mori. Furthermore, for the first time, efficient (13)C labeling has allowed reliable signal assignment using analytical separation techniques such as 3D HCCH-COSY spectra in higher organism extracts. CONCLUSIONS/SIGNIFICANCE: Overall physiological changes could be detected and categorized in relation to a critical developmental phase change in B. mori by coarse-grained representations in which the organization of metabolic pathways related to a specific developmental phase was visualized on the basis of constituent changes of 56 identified metabolites. Based on the observed intensities of (13)C atoms of given metabolites on development-dependent changes in the 56 identified (13)C-HSQC signals, we have determined the changes in metabolic networks that are associated with energy and nitrogen metabolism

Co-Orientation of Replication and Transcription Preserves Genome Integrity

In many bacteria, there is a genome-wide bias towards co-orientation of replication and transcription, with essential and/or highly-expressed genes further enriched co-directionally. We previously found that reversing this bias in the bacterium Bacillus subtilis slows replication elongation, and we proposed that this effect contributes to the evolutionary pressure selecting the transcription-replication co-orientation bias. This selection might have been based purely on selection for speedy replication; alternatively, the slowed replication might actually represent an average of individual replication-disruption events, each of which is counter-selected independently because genome integrity is selected. To differentiate these possibilities and define the precise forces driving this aspect of genome organization, we generated new strains with inversions either over ∼1/4 of the chromosome or at ribosomal RNA (rRNA) operons. Applying mathematical analysis to genomic microarray snapshots, we found that replication rates vary dramatically within the inverted genome. Replication is moderately impeded throughout the inverted region, which results in a small but significant competitive disadvantage in minimal medium. Importantly, replication is strongly obstructed at inverted rRNA loci in rich medium. This obstruction results in disruption of DNA replication, activation of DNA damage responses, loss of genome integrity, and cell death. Our results strongly suggest that preservation of genome integrity drives the evolution of co-orientation of replication and transcription, a conserved feature of genome organization

Search for continuous gravitational wave emission from the Milky Way center in O3 LIGO--Virgo data

We present a directed search for continuous gravitational wave (CW) signals emitted by spinning neutron stars located in the inner parsecs of the Galactic Center (GC). Compelling evidence for the presence of a numerous population of neutron stars has been reported in the literature, turning this region into a very interesting place to look for CWs. In this search, data from the full O3 LIGO--Virgo run in the detector frequency band $[10,2000]\rm~Hz$ have been used. No significant detection was found and 95$\%$ confidence level upper limits on the signal strain amplitude were computed, over the full search band, with the deepest limit of about $7.6\times 10^{-26}$ at $\simeq 142\rm~Hz$. These results are significantly more constraining than those reported in previous searches. We use these limits to put constraints on the fiducial neutron star ellipticity and r-mode amplitude. These limits can be also translated into constraints in the black hole mass -- boson mass plane for a hypothetical population of boson clouds around spinning black holes located in the GC.Comment: 25 pages, 5 figure

Search for subsolar-mass binaries in the first half of Advanced LIGO’s and Advanced Virgo’s third observing run

We report on a search for compact binary coalescences where at least one binary component has a mass between 0.2 M_\odot and 1.0 M_\odot in Advanced LIGO and Advanced Virgo data collected between 1 April 2019 1500 UTC and 1 October 2019 1500 UTC. We extend previous analyses in two main ways: we include data from the Virgo detector and we allow for more unequal mass systems, with mass ratio q \geq 0.1. We do not report any gravitational-wave candidates. The most significant trigger has a false alarm rate of 0.14 \mathrm{yr}^-1. This implies an upper limit on the merger rate of subsolar binaries in the range [220–24200] \mathrm{Gpc}^{-3} \, \mathrm{yr}^{-1}, depending on the chirp mass of the binary. We use this upper limit to derive astrophysical constraints on two phenomenological models that could produce subsolar-mass compact objects. One is an isotropic distribution of equal-mass primordial black holes. Using this model, we find that the fraction of dark matter in primordial black holes is f_\mathrm{PBH}\equiv \Omega_\mathrm{PBH}/\Omega_\mathrm{DM}\lesssim 6\%. The other is a dissipative dark matter model, in which fermionic dark matter can collapse and form black holes. The upper limit on the fraction of dark matter black holes depends on the minimum mass of the black holes that can be formed: the most constraining result is obtained at M_\mathrm{min}=1 M_\odot, where f_\mathrm{DBH}\equiv \Omega_\mathrm{PBH}/\Omega_\mathrm{DM}\lesssim 0.003\%. These are the tightest limits on spinning subsolar-mass binaries to date

All-sky search for gravitational wave emission from scalar boson clouds around spinning black holes in LIGO O3 data

This paper describes the first all-sky search for long-duration, quasimonochromatic gravitational-wave signals emitted by ultralight scalar boson clouds around spinning black holes using data from the third observing run of Advanced LIGO. We analyze the frequency range from 20 to 610 Hz, over a small frequency derivative range around zero, and use multiple frequency resolutions to be robust towards possible signal frequency wanderings. Outliers from this search are followed up using two different methods, one more suitable for nearly monochromatic signals, and the other more robust towards frequency fluctuations. We do not find any evidence for such signals and set upper limits on the signal strain amplitude, the most stringent being ≈10−25 at around 130 Hz. We interpret these upper limits as both an “exclusion region” in the boson mass/black hole mass plane and the maximum detectable distance for a given boson mass, based on an assumption of the age of the black hole/boson cloud system

Aggressiveness of cancer-care near the end-of-life in Korea

Objective: The aim of this study was to examine the appropriateness of chemotherapy and care in Korean cancer patients near the end-of-life. Methods: We designed a retrospective cohort composed of patients diagnosed as having metastatic cancer and who received palliative chemotherapy at Seoul National University Hospital in 2002. Two hundred and ninety-eight patients who died of cancer were evaluated in terms of the appropriateness of the cancer-care they received, including chemotherapy. Results: Median duration of chemotherapy was 6.02 months compared with 8.67 months for median overall survival. The median period between last chemotherapy and death was 2.02 months. Of the 298 patients, 50.3% received chemotherapy during the last 2 months of life. Furthermore, 17 patients (5.7%) died within 2 weeks after receiving chemotherapy. The proportion who visited an emergency room (ER) more than once during the last months of life was 33.6%, and the average number of ER visits after a diagnosis of cancer was 1.72. Only 9.1% of patients were referred to a hospice consultation service and only 11.7% of patients agreed with written DNR. Conclusions: Among patients who died of cancer, significant proportions were found to have received chemotherapy up to the end-of-life and to have visited ERs. Hospice referrals and discussions about DNR were not conducted well during the end-of-life period in Korea.This study was supported by grants of the Korea Health 21 R&D Project, Ministry of Health & Welfare (0412-CR01-0704-0001) and of the Innovative Research Institute for Cell Therapy (A062260), Republic of Korea.