De novo assembly and phasing of a Korean human genome.

Advances in genome assembly and phasing provide an opportunity to investigate the diploid architecture of the human genome and reveal the full range of structural variation across population groups. Here we report the de novo assembly and haplotype phasing of the Korean individual AK1 (ref. 1) using single-molecule real-time sequencing, next-generation mapping, microfluidics-based linked reads, and bacterial artificial chromosome (BAC) sequencing approaches. Single-molecule sequencing coupled with next-generation mapping generated a highly contiguous assembly, with a contig N50 size of 17.9 Mb and a scaffold N50 size of 44.8 Mb, resolving 8 chromosomal arms into single scaffolds. The de novo assembly, along with local assemblies and spanning long reads, closes 105 and extends into 72 out of 190 euchromatic gaps in the reference genome, adding 1.03 Mb of previously intractable sequence. High concordance between the assembly and paired-end sequences from 62,758 BAC clones provides strong support for the robustness of the assembly. We identify 18,210 structural variants by direct comparison of the assembly with the human reference, identifying thousands of breakpoints that, to our knowledge, have not been reported before. Many of the insertions are reflected in the transcriptome and are shared across the Asian population. We performed haplotype phasing of the assembly with short reads, long reads and linked reads from whole-genome sequencing and with short reads from 31,719 BAC clones, thereby achieving phased blocks with an N50 size of 11.6 Mb. Haplotigs assembled from single-molecule real-time reads assigned to haplotypes on phased blocks covered 89% of genes. The haplotigs accurately characterized the hypervariable major histocompatability complex region as well as demonstrating allele configuration in clinically relevant genes such as CYP2D6. This work presents the most contiguous diploid human genome assembly so far, with extensive investigation of unreported and Asian-specific structural variants, and high-quality haplotyping of clinically relevant alleles for precision medicine.

Kinetics of polystyrene nanoplastic deposition on SiO2 and Al2O3 surfaces: Ionic strength effects.

Nanoplastic pollution is an emerging environmental threat to the critical zone. The transport of nanoplastic particles in subsurface environments can be determined mainly by soil minerals because they provide surfaces that interact with nanoplastic particles. However, the interactions between mineral surfaces and nanoplastics are poorly understood. In this study, the deposition kinetics of polystyrene-nanoplastic particles onto representative oxide surfaces SiO2 and Al2O3 at circumneutral pH were investigated using a quartz crystal microbalance, with variations in the ionic strength (0.1-100 mM) of the well-dispersed nanoplastic particles suspension. While polystyrene-nanoplastic particles deposited minimally on the SiO2 surface at an ionic strength of < 100 mM (∼10 ng/cm2), substantial deposition occurred at 100 mM (3.7 ± 0.4 µg/cm2). On the Al2O3 surface, a significant amount of polystyrene-nanoplastic particle was deposited from the lowest ionic strength (4.5 ± 0.8 µg/cm2). The deposition mass at 100 mM NaCl was two times higher (7.2 ± 0.2 µg/cm2) than on the SiO2 surface, while the deposition rates were similar between the two surfaces (10-15 Hz/min). Our results indicate that alumina most likely exerts a stronger influence than quartz on the transport of nanoplastic particles in soils and groundwater aquifers. The deposition kinetics strongly depends on the mineral surface and solution ionic strength, and these quantitative results can serve as validation data in developing transport modeling of nanoplastic in subsurface environments.

Toward a mechanistic understanding of cesium adsorption to todorokite: A molecular dynamics simulation study.

A mechanistic understanding of cesium (Cs) adsorption to soil mineral phases is essential for effective mitigation of Cs mobility in the subsurface environment. Todorokite, a common tunnel-structured manganese oxide in soil, exhibits sorption capacity for Cs comparable to the capacities of clay minerals. However, the adsorption sites and molecular species of Cs+ adsorbed to todorokite remain uncertain in comparison with those of clay minerals. In this study, we explored adsorption of Cs+ to hydrated todorokite surfaces via atomistic molecular dynamics (MD) simulations. We performed the first MD simulations based on atomic pair potentials for Mn-oxide edge surfaces interfaced with an aqueous solution. MD simulations predicted that Cs+ forms only inner-sphere (IS) complexes within todorokite tunnels; however, Cs+ forms both IS and outer-sphere (OS) complexes at the external (010) and (100)/(001) external surfaces. On the (010) surface, the positions between IS and OS complexes of Cs+ were interchangeable during MD simulations. Detailed molecular structures of IS and OS Cs+ surface complexes are compared to those of Cs+ in an aqueous solution. The current MD simulation results can be used as an atomistic structural proxy for spectroscopic analysis of adsorbed metal speciation and surface complexation modeling of metal adsorption to Mn oxides.

Complete genome sequence of Klebsiella oxytoca M1, isolated from Manripo area of South Korea.

Here we report the full genome sequence of Klesiella oxytoca M1, isolated from Manripo area of South Korea. The strain K. oxytoca M1 is able to produce either 2,3-butanediol or acetoin selectively by controlling the pH and temperature.

TDAG51 deficiency promotes oxidative stress-induced apoptosis through the generation of reactive oxygen species in mouse embryonic fibroblasts.

Apoptosis has an important role in maintaining tissue homeostasis in cellular stress responses such as inflammation, endoplasmic reticulum stress, and oxidative stress. T-cell death-associated gene 51 (TDAG51) is a member of the pleckstrin homology-like domain family and was first identified as a pro-apoptotic gene in T-cell receptor-mediated cell death. However, its pro-apoptotic function remains controversial. In this study, we investigated the role of TDAG51 in oxidative stress-induced apoptotic cell death in mouse embryonic fibroblasts (MEFs). TDAG51 expression was highly increased by oxidative stress responses. In response to oxidative stress, the production of intracellular reactive oxygen species was significantly enhanced in TDAG51-deficient MEFs, resulting in the activation of caspase-3. Thus, TDAG51 deficiency promotes apoptotic cell death in MEFs, and these results indicate that TDAG51 has a protective role in oxidative stress-induced cell death in MEFs.