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Lipopolysaccharides (LPS) are a major component of the outer membrane of Gram-negative bacteria and are pathogen-associated molecular patterns recognized by the TLR4/MD2 complex that induces an inflammatory response. Recently, the cytosolic receptors caspase-4/-5/-11 that bind LPS inside the cell and trigger inflammasome activation or pyroptosis, have been identified. Despite the important roles of caspase-4 in human immune responses, few studies have investigated its biochemical characteristics and interactions with LPS. Since caspase-4 (C258A) purified from an Escherichia coli host forms aggregates, monomeric proteins including full-length caspase-4, caspase-4 (C258A), and the CARD domain of caspase-4 have been purified from the insect cell system. Here, we report the overexpression and purification of monomeric caspase-4 (C258A) and CARD domain from E . coli and demonstrate that purified caspase-4 (C258A) and CARD domain bind large LPS micelles and disaggregate them to small complexes. As the molar ratio of caspase-4 to LPS increases, the size of the caspase-4/LPS complex decreases. Our results present a new function of caspase-4 and set the stage for structural and biochemical studies, and drug discovery targeting LPS/caspase-4 interactions by establishing a facile purification method to obtain large quantities of purified caspase-4 (C258A) and the CARD domain.

The role of matrix metalloproteinase-2 (MMP-2) in tumor cell migration has been widely studied, however, the characteristics and effects of MMP-2 in clinical sample of metastatic colorectal cancer (CRC) remain poorly understood. Here, in order to unveil the perturbed proteomic signal during MMP-2 induced cancer progression, we analyzed plasma proteome of CRC patients according to disease progression, HCT116 cancer secretome upon MMP-2 knockdown, and publicly available CRC tissue proteome data. Collectively, the integrative analysis of multi-layered proteomes revealed that a protein cluster containing EMT (Epithelial-to-Mesenchymal Transition)-associated proteins such as CD9-integrin as well as MMP-2. The proteins of the cluster were regulated by MMP-2 perturbation and exhibited significantly increased expressions in tissue and plasma as disease progressed from TNM (Tumor, Node, and Metastasis) stage I to II. Furthermore, we also identified a plausible association between MMP-2 up-regulation and activation of focal adhesion kinase signaling in the proteogenomic analysis of CRC patient tissues. Based on these comparative and integrative analyses, we suggest that the high invasiveness in the metastatic CRC resulted from increased secretion of MMP-2 and CD9-integrin complex mediated by FAK signaling activation.

The Tibetan Plateau is regarded as the Earth's Third Pole, which is the source region of several major rivers that impact more 20% the world population. This high‐altitude region is reported to have been undergoing much greater rate of weather changes under global warming, but the existing reanalysis products are inadequate for depicting the state of the atmosphere, particularly with regard to the amount of precipitation and its diurnal cycle. An ensemble Kalman filter (EnKF) data assimilation system based on the limited‐area Weather Research and Forecasting (WRF) model was evaluated for use in developing a regional reanalysis over the Tibetan Plateau and the surrounding regions. A 3‐month prototype reanalysis over the summer months (June−August) of 2015 using WRF‐EnKF at a 30‐km grid spacing to assimilate nonradiance observations from the Global Telecommunications System was developed and evaluated against independent sounding and satellite observations in comparison to the ERA‐Interim and fifth European Centre for Medium‐Range Weather Forecasts Reanalysis (ERA5) global reanalysis. Results showed that both the posterior analysis and the subsequent 6‐ to 12‐hr WRF forecasts of the prototype regional reanalysis compared favorably with independent sounding observations, satellite‐based precipitation versus those from ERA‐Interim and ERA5 during the same period. In particular, the prototype regional reanalysis had clear advantages over the global reanalyses of ERA‐Interim and ERA5 in the analysis accuracy of atmospheric humidity, as well as in the subsequent downscale‐simulated precipitation intensity, spatial distribution, diurnal evolution, and extreme occurrence. Key Points A pilot reanalysis over the Tibetan Plateau using the PSU WRF‐EnKF system was developed and evaluated against independent soundings and satellite observations as well as ERA‐Interim and ERA5 The pilot reanalysis had clear advantage in atmospheric humidity than existing global reanalysis The subsequent downscaled precipitation forecasts from the pilot reanalysis compared favorably against those from the global reanalyses of ERA‐Interim and ERA5

In this study, the East Asia Regional Reanalysis (EARR) is developed for the period 2013–14 and characteristics of the EARR are examined in comparison with ERA-Interim (ERA-I) reanalysis. The EARR is based on the Unified Model with 12-km horizontal resolution, which has been an operational numerical weather prediction model at the Korea Meteorological Administration since being adopted from the Met Office in 2011. Relative to the ERA-I, in terms of skill scores, the EARR performance for wind, temperature, relative humidity, and geopotential height improves except for mean sea level pressure, the lower-troposphere geopotential height, and the upper-air relative humidity. In a similar way, RMSEs of the EARR are smaller than those of ERA-I for wind, temperature, and relative humidity, except for the upper-air meridional wind and the upper-air relative humidity in January. With respect to the near-surface variables, the triple collocation analysis and the correlation coefficients confirm that EARR provides a much improved representation when compared with ERA-I. In addition, EARR reproduces the finescale features of near-surface variables in greater detail than ERA-I does, and the kinetic energy (KE) spectra of EARR agree more with the canonical atmospheric KE spectra than do the ERA-I KE spectra. On the basis of the fractions skill score, the near-surface wind of EARR is statistically significantly better simulated than that of ERA-I for all thresholds, except for the higher threshold at smaller spatial scales. Therefore, although special care needs to be taken when using the upper-air relative humidity from EARR, the near-surface variables of the EARR that were developed are found to be more accurate than those of ERA-I.

As the need for regional reanalyses emerged around the world, a short period of the East Asia Regional Reanalysis (EARR) system was recently developed based on the Unified Model (UM). In this study, the quality of the EARR is evaluated by comparing the short-range precipitation reforecasts against reforecasts of ERA-Interim (ERA-I) reanalysis and operational forecasts of the Korea Meteorological Administration (OPER). For the verification, two different periods are selected for 14 days in the summer (July 2013, denoted as 201307) and winter (February 2014, denoted as 201402). The equitable threat score (ETS) of EARR and OPER is generally greater than that of ERA-I. The frequency bias index (FBI) of EARR and OPER is overall closer to 1 than that of ERA-I for all thresholds, which indicates that EARR and OPER are much closer to the observation compared to ERA-I. For the period 201307, the ERA-I FBI is greater than 1 for lower thresholds and the probability of detection (POD) and false alarm ratio (FAR) of ERA-I are high, implying that ERA-I tends to overforecast light precipitation. In addition, using the same Weather Research and Forecasting (WRF)Model, the 6-h precipitation forecasts are integrated every 12 h (initialized from 0000/1200 UTC) for 4 months for the summer and winter season. Although the differences of ETS and FBI between EARR and ERA-I are not distinct for the summer season, overall EARRETS is higher than ERA-I ETS, and EARR FBI is closer to 1 than ERA-I FBI. Based on several evaluations, the precipitation reforecasts of EARR are confirmed to be more accurate than those of OPER and ERA-I in East Asia.

A generalized platform for introducing a diverse range of biomolecules into living cells in high-throughput could transform how complex cellular processes are probed and analyzed. Here, we demonstrate spatially localized, efficient, and universal delivery of biomolecules into immortalized and primary mammalian cells using surface-modified vertical silicon nanowires. The method relies on the ability of the silicon nanowires to penetrate a cell's membrane and subsequently release surface-bound molecules directly into the cell's cytosol, thus allowing highly efficient delivery of biomolecules without chemical modification or viral packaging. This modality enables one to assess the phenotypic consequences of introducing a broad range of biological effectors (DNAs, RNAs, peptides, proteins, and small molecules) into almost any cell type. We show that this platform can be used to guide neuronal progenitor growth with small molecules, knock down transcript levels by delivering siRNAs, inhibit apoptosis using peptides, and introduce targeted proteins to specific organelles. We further demonstrate codelivery of siRNAs and proteins on a single substrate in a microarray format, highlighting this technology's potential as a robust, monolithic platform for high-throughput, miniaturized bioassays.

Recognition of intracellular lipopolysaccharide (LPS) by Caspase-4 (Casp-4) is critical for host defense against Gram-negative pathogens. LPS binds to the N-terminal caspase activation and recruitment domain (CARD) of procaspase-4, leading to auto-proteolytic activation followed by pro-inflammatory cytokine release and pyroptotic cell death. Aberrant hyper-activation of Casp-4 leads to amplification of the inflammatory response linked to sepsis. While the active site of a caspase has been targeted with peptide inhibitors, inhibition of LPS–Casp-4 interaction is an emerging strategy for the development of selective inhibitors with a new mode of action for treating infectious diseases and sepsis induced by LPS. In this study, a high-throughput screening (HTS) system based on fluorescence polarization (FP) was devised to identify inhibitors of the LPS and Casp-4 interaction. Using HTS and IC50 determination and subsequently showing inhibited Casp-4 activity, we demonstrated that the LPS–Casp-4 interaction is a druggable target for Casp-4 inhibition and possibly a non-canonical inflammatory pathway.

This Analysis reports the development and assessment of 645 multiple reaction monitoring (MRM) mass spectrometry assays to quantify 319 targeted human breast cancer proteins. The results of this pilot project coordinated among three individual groups suggest that an organized international effort to generate MRM assays to the human proteome will be possible. Multiple reaction monitoring (MRM) mass spectrometry has been successfully applied to monitor targeted proteins in biological specimens, raising the possibility that assays could be configured to measure all human proteins. We report the results of a pilot study designed to test the feasibility of a large-scale, international effort for MRM assay generation. We have configured, validated across three laboratories and made publicly available as a resource to the community 645 novel MRM assays representing 319 proteins expressed in human breast cancer. Assays were multiplexed in groups of >150 peptides and deployed to quantify endogenous analytes in a panel of breast cancer–related cell lines. The median assay precision was 5.4%, with high interlaboratory correlation ( R 2 > 0.96). Peptide measurements in breast cancer cell lines were able to discriminate among molecular subtypes and identify genome-driven changes in the cancer proteome. These results establish the feasibility of a large-scale effort to develop an MRM assay resource.

The East Asia Regional Reanalysis (EARR) system is developed based on the advanced hybrid gain data assimilation method (AdvHG) using the Weather Research and Forecasting (WRF) model and conventional observations. Based on EARR, the high-resolution regional reanalysis and reforecast fields are produced with 12 km horizontal resolution over East Asia for 2010–2019. The newly proposed AdvHG is based on the hybrid gain approach, weighting two different analyses for an optimal analysis. The AdvHG differs from the hybrid gain in that (1) E3DVAR is used instead of EnKF, (2) 6 h forecast of ERA5 is used to be more consistent with WRF, and (3) the preexisting, state-of-the-art reanalysis is used. Thus, the AdvHG can be regarded as an efficient approach for generating regional reanalysis datasets thanks to cost savings as well as the use of the state-of-the-art reanalysis. The upper-air variables of EARR are verified with those of ERA5 for January and July 2017 and the 10-year period 2010–2019. For upper-air variables, ERA5 outperforms EARR over 2 years, whereas EARR outperforms (shows comparable performance to) ERA-I and E3DVAR for January 2017 (July 2017). EARR represents precipitation better than ERA5 for January and July 2017. Therefore, although the uncertainties of upper-air variables of EARR need to be considered when analyzing them, the precipitation of EARR is more accurate than that of ERA5 for both seasons. The EARR data presented here can be downloaded from https://doi.org/10.7910/DVN/7P8MZT (Yang and Kim, 2021b) for data on pressure levels and https://doi.org/10.7910/DVN/Q07VRC (Yang and Kim, 2021c) for precipitation.

The sensitivities of meteorological forecast errors associated with Asian dust transport events to changes in the initial state were evaluated for 46 occurrences that affected the Korean Peninsula from 2005 to 2010. Adjoint-based sensitivities were used to determine these sensitivities. Sensitive regions were located primarily over two regions upstream from the Korean Peninsula: the northern source region, including areas of Mongolia and northern China, and the Tibetan Plateau. Depending on transport trajectories, month, and year, the sensitive regions were located over either the northern source regions or the Tibetan Plateau. That is, the Asian dust forecast in Korea was found to be sensitive to the meteorological fields over the northern source regions, but also those over the Tibetan Plateau even though the latter is not a dust source region or an upstream area according to the transport trajectories. Employing additional observations at existing instrumentation sites or developing new observational sites in both sensitive regions could be beneficial in reducing the atmospheric circulation forecast errors in East Asia, thus improving the accuracy of transport forecasts of Asian dust events affecting the Korean Peninsula.