Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Tracing sources of ammonium in reducing groundwater in a well field in Hanoi (Vietnam) by means of stable nitrogen isotope (d15N) values

In the Southern part of Hanoi, high ammonium (NH4 + ) concentrations in reducing groundwater have been an issue over the last 25 years. Elevated NH4 + concentrations in groundwater, in general, are an indicator of influences from anthropogenic sources, but the buried peat layers in the Red River delta formation are also hypothesized to contribute to the high NH4 + levels (up to 100 mg/l). We traced the sources of NH4 + at the Nam Du well field of the Hanoi water works by means of isotope ratios (15N/14N). The d15N values were determined for total sedimentary N and exchangeable NH4 + of the peat material, and for NH4 + dissolved in deep and shallow groundwater, sewage, and surface water. Groundwater NH4 + of the upper (Holocene) and the lower (Pleistocene) aquifers had higher d15N values than did total N and NH4 + of the sediments, and were somewhat higher than the d15N values of NH4 + in sewage and surface water. We conclude that the present conditions of temperature and pH tend to promote deprotonation of NH4 + to ammonia (NH3), which eventually degasses from the groundwater table to the unsaturated pore space. This can cause an enrichment of 15N in the remaining NH4 + , as the lighter 14N inNH3 is volatilized at a slightly faster rate. The intermediate d15N values within the Pleistocene aquifer can be explained by the recharge thereto, which is a mixture of the high d15N values of the Holocene aquifer and the low d15N values of water infiltrating from the Red River into the Pleistocene aquifer. Some part of the increased groundwater NH4 + is likely to arise from anthropogenic activities, as supported by several indications: a large drawdown in the Pleistocene aquifer caused by Hanoi’s extensive water abstraction and subsequent downward gradient from the upper Holocene aquifer; the presence of coliforms in groundwater; and a positive correlation between ammonium and DOC, Cl, Br and Ni, but a lack of correlation with As. However, the much higher concentrations of NH4 + in the groundwater compared to the potential Surface sources, the positive correlation between NH4 + and DOC, the abundance of natural organic matter (OM), the amount of exchangeable NH4 + in the sediments, and the highly reducing conditions in the aquifers indicate that N-mineralization of organic N from the peat contribute substantially to the high NH4 + levels in groundwater of the Nam Du well field

Arsenic mobilisation in a new well-field for drinking water production along the Red River, Nam Du, Hanoi.

Arsenic enrichment of groundwater in the Red River (Song Hong) delta in Vietnam was discovered in 1998. Several studies performed in this area found concentrations of As exceeding the WHO-guideline of 10 lg/L. This study focuses on an area south of Hanoi city, Nam Du, where a new well field came into operation in 2004. The new well field is situated on the bank along the Red River in order to facilitate induced infiltration. The Nam Du area receives surface water with a high load of nutrients and organic matter from the Hanoi sewage system, and is subject to recently increased groundwater extraction from the Pleistocene aquifer system. The objective of the study was (1) to assess the situation in the Nam Du area by mapping the distribution of As, (2) to identify possible sources of As in the groundwater and (3) to investigate the mobilisation processes releasing As into the groundwater. Two main field campaigns were carried out, in 2006 and 2007, both during the dry season. Groundwater and surface water levels were measured and water- and sediment samples were collected. The water in the Pleistocene aquifer shows the same water-level variations as the Red River at a distance of 2.5 km from the riverbank, while the Holocene aquifer heads are recharged by surface water ponds and show less seasonal variation. The concentration of As in the groundwater in Nam Du exceeded the WHO provisional guideline value at all sampled locations. The main conclusions are summarised as (i) the distribution of As is highly variable but the zones with the highest concentrations of As are near the Red River in the Holocene aquifer and just down gradient from this in the Pleistocene aquifer, (ii) the sediments within the aquifers are considered to be the source of the As, where the Holocene aquifer is believed to act as the main source of As into the Pleistocene aquifer as reduced groundwater containing As from the Holocene aquifer is flowing downwards due to the downward gradient, and (iii) two different processes appear to take part in the mobilisation process. In the Holocene aquifer, reductive dissolution of FeOOH and the release of adsorbed As appear to be the main mobilisation processes. In the Pleistocene, however, mobilisation of adsorbed As due to competition from HCO3 ions for surface sites on FeOOH may be a major mechanism of As mobilisation. It is suggested that the drinking water supplier undertakes the following actions to ensure acceptable levels of As in the treated drinking water: (a) to implement a long-term monitoring program, (b) implement alternative treatment technologies; and (c) to possibly consider an alternative drinking water source

A simple high-throughput approach identifies actionable drug sensitivities in patient-derived tumor organoids.

Tumor organoids maintain cell-cell interactions, heterogeneity, microenvironment, and drug response of the sample they originate from. Thus, there is increasing interest in developing tumor organoid models for drug development and personalized medicine applications. Although organoids are in principle amenable to high-throughput screenings, progress has been hampered by technical constraints and extensive manipulations required by current methods. Here we introduce a miniaturized method that uses a simplified geometry by seeding cells around the rim of the wells (mini-rings). This allows high-throughput screenings in a format compatible with automation as shown using four patient-derived tumor organoids established from two ovarian and one peritoneal high-grade serous carcinomas and one carcinosarcoma of the ovary. Using our automated screening platform, we identified personalized responses by measuring viability, number, and size of organoids after exposure to 240 kinase inhibitors. Results are available within a week from surgery, a timeline compatible with therapeutic decision-making

A simple high-throughput approach identifies actionable drug sensitivities in patient-derived tumor organoids

Nhan Phan et al. present a high-throughput approach to screen tumor organoids by seeding cells in mini-rings. They apply their method to cell lines and patient-derived tumor organoids representing four different cancers, and identified personalized responses for each organoid within a clinically relevant timeline

Reciprocal Activation of Transcription Factors Underlies the Dichotomy between Proliferation and Invasion of Glioma Cells

<div><p>Histology of malignant glioma depicts dense proliferative areas rich in angiogenesis as well as dissemination of neoplastic cells into adjacent brain tissue. Although the mechanisms that trigger transition from proliferative to invasive phenotypes are complex, the dichotomy of cell proliferation and migration, the “Go or Grow” hypothesis, argues for specific and coordinated regulation of these phenotypes. We investigated transcriptional elements that accompany the phenotypes of migration and proliferation, and consider the therapeutic significance of the “Go or Grow” hypothesis. Interrogation of matched core and rim regions from human glioblastoma biopsy specimens <i>in situ</i> (n = 44) revealed higher proliferation (Ki67 labeling index) in cells residing at the core compared to the rim. Profiling activated transcription factors in a panel of migration-activated versus migration-restricted GBM cells portrayed strong NF-κB activity in the migratory cell population. In contrast, increased c-Myc activity was found in migration-restricted proliferative cells. Validation of transcriptional activity by NF-κB- or c-Myc-driven GFP or RFP, respectively, showed an increased NF-κB activity in the active migrating cells, whereas the proliferative, migration restricted cells displayed increased c-Myc activity. Immunohistochemistry on clinical specimens validated a robust phosphorylated c-Myc staining in tumor cells at the core, whereas increased phosphorylated NF-κB staining was detected in the invasive tumor cells at the rim. Functional genomics revealed that depletion of c-Myc expression by siRNA oligonucleotides reduced cell proliferation <i>in vitro</i>, but surprisingly, cell migration was enhanced significantly. Conversely, inhibition of NF-κB by pharmacological inhibitors, SN50 or BAY-11, decreased both cell migration <i>in vitro</i> and invasion <i>ex vivo</i>. Notably, inhibition of NF-κB was found to have no effect on the proliferation rate of glioma cells. These findings suggest that the reciprocal and coordinated suppression/activation of transcription factors, such as c-Myc and NF-κB may underlie the shift of glioma cells from a “growing-to-going” phenotype.</p></div

Inhibition of NF-κB function suppresses glioma cell migration in vitro and invasion ex vivo.

<p>Treatment with 50 µM SN50 peptide inhibitor suppresses migration of (A) T98G and SNB19 glioma cells in a radial migration assay when compared with untreated (NT) or scrambled peptide treated (SN50M) cells (*; p<0.0001). (B) SNB19 glioma cells stably expressing GFP were implanted into the bilateral putamen on rat organotypic brain slices. Implanted cells were then treated with SN50 peptide inhibitor, scrambled peptide (SN50M) or left untreated (NT) and observed at 48 hrs. Depth of invasion was then calculated from Z-axis images collected by confocal laser scanning microscopy. The mean value of the depth of invasion was obtained from four independent experiments (*; p<0.0001). Treatment with 20 µM NF-κB functional inhibitor (BAY-11-7082) suppresses migration of (C) T98G and SNB19 glioma cells in a radial migration assay when compared with untreated (NT) or DMSO treated (VC) cells (*; p<0.0001). (D) Similar ex vivo brain slice invasion assay as described in B with NF-κB functional inhibitor (BAY-11-7082) demonstrated reduced invasion of T98G and SNB19 glioma cells. The mean value of the depth of invasion was obtained from four independent experiments (*; p<0.0001).</p