Natural peloids originating from subsea depths of 200 m in the hupo basin, South Korea: physicochemical properties for potential pelotherapy applications.

The present study firstly reports surface sediment from the subsea depth of 200 m as a potential natural peloid. The fine-silt sediment exhibited a consistent clay mineral composition dominated by illite, chlorite, kaolinite, and diatomite. The most abundant clay mineral was illite/mica, with other minerals loosely packed in a face-to-face orientation. The thermal conductivity, specific heat capacity, and cation-exchange capacity of the sediment were in the range 0.855-0.885 W/m K, 2.718-2.821 J/g °C, and 23.06-32.96 cmol/kg, respectively. The concentrations of most toxic elements in the sediment were considerably lower than the limits set by domestic cosmetic regulations and other international standards. The analyzed samples exhibited similar properties to those of previously reported peloids, thus making them suitable for use in the field of pelotherapy; furthermore, the consistency in data across a wide peloid-distribution area is expected to enable economically viable mining. Future investigations should aim to to evaluate the long-term effects on the skin, the bioavailability of potentially hazardous substances, and the therapeutic efficacy for various skin conditions.

The 2023 Report on the Proteome from the HUPO Human Proteome Project.

Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1-4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.

Hu'po Anshen decoction promotes fracture healing in mice with traumatic brain injury through BMP2-COX2-ATF4 signaling pathway.

Hu'po Anshen decoction (HPASD), a traditional Chinese medicine used to treat concussion and fracture, could regulate the expression of bone morphogenetic protein 2 (BMP2). However, whether HPASD affects the fracture healing of traumatic brain injury (TBI) combined with a fracture through BMP2 and its downstream signals remains obscure. The chondrocyte-specific BMP2 conditional knockout mice and chondrocyte-specific cyclooxygenase-2 (COX2) overexpression mice were generated. BMP2 conditional knockout mice were treated with fracture surgery, fracture combined with TBI, or fracture combined with TBI followed by different doses of HPASD (2.4, 4.8, and 9.6 g/kg), respectively. TBI was induced by Feeney's weight-drop technique. The fracture callus formation and fracture sites were determined by X-ray, micro-CT, and histological analyses. The expressions of chondrocyte-, osteoblast-, and BMP2/COX2 signal-related targets were determined by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and western blot assays. The specific absence of BMP2 in chondrocytes led to the prolonged formation of cartilage callus, a delay in the osteogenesis initiation and the downregulation of RUNX2, Smad1/5/9, EP4, ERK1/2, RSK2, ATF4. Overexpression of COX2 partially reverses the effects of chondrocyte-specific BMP2 knockout mice. HPASD promoted cartilage callus formation and osteogenesis initiation, as accompanied by upregulated expression levels of RUNX2, Smad1/5/9, EP4, ERK1/2, RSK2, and ATF4 in a time-dependent and concentration-dependent manner in chondrocyte-specific BMP2 knockout mice. Overall, our findings demonstrated that HPASD induced COX2 transcription through the BMP2-Smad1/5/9-RUNX2 axis, and then affected fracture healing through the COX2-mediated EP4-ERK1/2-RSK2-ATF4 axis.

Mercury contamination of sediments in an open coastal area of the Hupo Basin, East Sea, Korea.

Mercury (Hg) contamination in open coastal areas has attracted public concern regarding safe fish consumption and management of the coastal environment, especially in areas of accidental Hg spills on inland coasts. This study investigated the temporal and spatial distribution of Hg in sediments of Youngil Bay and the Hupo Basin, East Sea, Korea; it also discussed the sources and transport of anthropogenic Hg. Hg hot spots were found in the northern Hupo Basin (elevated by 2-3×) and the river mouth area in Youngil Bay (elevated by approximately 70×). The river mouth contamination resulted from the destruction of a dam impounding landfill waste, while the basin contamination was attributed to atmospheric deposition and Hg enrichment associated with increased organic carbon concentrations driven by high biological production in the coastal upwelling area. Spilled Hg was transported to open coastal areas up to 36.6°N.

Hu'po Anshen Decoction Accelerated Fracture-Healing in a Rat Model of Traumatic Brain Injury Through Activation of PI3K/AKT Pathway.

Hu'po Anshen decoction (HPASD) is a traditional Chinese medicine formula comprising five herbal medicines for the treatment of concussion and fracture healing, but its pharmacological mechanism is still unclear. Ultra-performance liquid chromatography coupled with quadrupole time of flight mass spectrometry (UPLC/Q-TOF MS) was used to analyze the main active components of HPASD. Rats were randomly assigned to fracture group, fracture combined with traumatic brain injury (TBI) group (FBI) and FBI combined with HPASD treatment group (FBIH). Rats in the FBIH group were given oral doses of HPASD (2.4 g/kg, 4.8 g/kg and 9.6 g/kg) for 14 or 21 consecutive days. The fracture callus formation and fracture sites were determined by radiographic analysis and micron-scale computed tomography (micro-CT) analysis. Hematoxylin and eosin (H&E) staining and a three-point bending test were applied to assess histological lesions and biomechanical properties, respectively. The levels of cytokines-/protein-related to bone formation and differentiation as well as PI3K/AKT pathway-related proteins were determined by Enzyme-linked immunosorbent assay (ELISA), quantitative reverse transcription-polymerase chain reaction (qRT-PCR), or western blot assays, respectively. UPLC-Q/TOF-MS-based serum metabolomic analysis was also performed to investigate the therapeutic effects of HPASD in the treatment of FBI. UPLC/Q-TOF MS analysis showed the chemical components in HPASD, including flavonoids, amino acids, saponins, and phenylpropanoid constituents, etc. HPASD dose-dependently promoted callus formation, increased bone density, improved mechanical parameters and morphological scores, and facilitated the expressions of VEGF, PDGF, bFGF, VEGFA, CoL1A1, RUNX2, BMP2, and Aggrecan, inhibited the expression of MMP13, and activated PI3K/AKT pathway. Metabolomics analysis revealed abnormalities of malate-aspartate shuttle and glucose-alanine. HPASD accelerates fracture healing by promoting bone formation and regulating the malate-aspartate shuttle and glucose-alanine cycle, which might be associated with the activation of the PI3K/AKT pathway.

Fictibacillus marinisediminis sp. nov., a nitrate-reducing bacterium isolated from marine sediment in Hupo Basin, Republic of Korea.

An isolate, designated strain KIGAM418T was isolated from marine mud below 192 m depth in the Hupo Basin, Republic of Korea. Strain KIGAM418T was Gram-stain positive, spore-forming, rod-shaped, facultatively anaerobic, and grew at 10‒45 °C, in 0‒2% (w/v) NaCl at pH 4.0‒12.0. The strain tested positive for catalase, oxidase, and motility. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain KIGAM418T was related to the genus Fictibacillus. The strain showed the highest similarity to Fictibacillus rigui WPCB074T (98.0-98.1%) and Fictibacillus solisalsi YC1T (97.2-97.8%). The diagnostic diamino acid of the cell wall was meso-diaminopimelic acid. The major fatty acids were characterized as anteiso-C15:0 and iso-C15:0. Strain KIGAM418T possessed diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine as the major polar lipids and menaquinone-7 as the predominant menaquinone. The genome size and G + C content were 4.56 Mb and 43.2 mol%, respectively. According to predicted functional genes of the genome, the category of amino acid transport and metabolism was mainly distributed. Based on the polyphasic taxonomic data, strain KIGAM418T represents a novel species of the genus Fictibacillus, for which the name Fictibacillus marinisediminis sp. nov. is proposed. The type strain is KIGAM418T (= KCTC 43291 T = JCM 34437 T).

The status of proteomics as we enter the 2020s: Towards personalised/precision medicine.

The last decade has seen many major advances in proteomics, with over 70,000 publications in the field since 2010. A comprehensive omics toolbox has been developed facilitating rapid in depth analysis of the human proteome. Such studies are advancing our understanding of the biology of both health and disease. The combination of proteomics with other omics platforms (the omics pipeline), in particular proteogenomics, is giving important insights to the molecular changes leading to disease, covering the spectrum from genotype to phenotype and identifying potential biomarkers for disease detection, surveillance and monitoring, and revealing potential new drug targets. Discovery-based finding are now being translated to clinical application, supporting the rollout of precision/personalised medicine. This perspective has focused on twelve areas of importance that have fuelled the field. Recent exemplars are given to illustrate this and show how, together with some emerging technologies, they are anticipated to lead to further advances in the field. However, hurdles still remain to be overcome, especially in the area of Big Data analysis.

Proteomics, Personalized Medicine and Cancer.

As of 2020 the human genome and proteome are both at >90% completion based on high stringency analyses. This has been largely achieved by major technological advances over the last 20 years and has enlarged our understanding of human health and disease, including cancer, and is supporting the current trend towards personalized/precision medicine. This is due to improved screening, novel therapeutic approaches and an increased understanding of underlying cancer biology. However, cancer is a complex, heterogeneous disease modulated by genetic, molecular, cellular, tissue, population, environmental and socioeconomic factors, which evolve with time. In spite of recent advances in treatment that have resulted in improved patient outcomes, prognosis is still poor for many patients with certain cancers (e.g., mesothelioma, pancreatic and brain cancer) with a high death rate associated with late diagnosis. In this review we overview key hallmarks of cancer (e.g., autophagy, the role of redox signaling), current unmet clinical needs, the requirement for sensitive and specific biomarkers for early detection, surveillance, prognosis and drug monitoring, the role of the microbiome and the goals of personalized/precision medicine, discussing how emerging omics technologies can further inform on these areas. Exemplars from recent onco-proteogenomic-related publications will be given. Finally, we will address future perspectives, not only from the standpoint of perceived advances in treatment, but also from the hurdles that have to be overcome.

Asia-Oceania HUPO: Past, Present, and Future.

The Asia-Oceania Human Proteome Organization (AOHUPO; www.aohupo.org) was officially founded on June 7, 2001, by Richard J. Simpson (Australia), Akira Tsugita (Japan), and Young-Ki Paik (Korea) and launched on October 1-4, 2001, at the second scientific meeting of the International Proteomics Conference held in Canberra, Australia. Inaugural council members of the AOHUPO elected were Richard J. Simpson (Australia, president), Qi-Chang Xia (China), Kazuyuki Nakamura (Japan), Akira Tsugita (Japan, VIce President), Young-Ki Paik (Korea, secretary general), Mike Hubbard (New Zealand), Max C. M. Chung (Singapore), Shui-Tien Chen (Taiwan), and John Bennett (Philippines). The first AOHUPO conference was held on March 26-27, 2002, at the Seoul National University, Seoul, Korea, conjointly with the second Annual Meeting of KHUPO. Since then, biennial AOHUPO conferences have been held in Taipei (2004), Singapore (2006), Cairns (2008), Hyderabad (2010), Beijing (2012), Bangkok (2014), Sun Moon Lake (2016), and Osaka (2018). The 10th AOHUPO conference is scheduled to be held in Busan on June 30 to July 2, 2021, to celebrate our 20th anniversary.

The separation sciences, the front end to proteomics: An historical perspective.

It is now over 25 years since the term proteomics (analysis of the entire protein complement of a cell, tissue, or organism under a specific, defined set of conditions) was originally coined. Since then, the field has advanced rapidly and there are now more than 135,500 publications addressing the field. With current instrumentation it is possible to detect over 10,000 protein forms in a single experiment. The separation of proteins and peptides has been a key component of many of these studies for both sample concentration and enrichment and to reduce the complexity of the samples under analysis, allowing deeper mining of the individual proteomes. In this review, the roles of chromatography, electrophoresis, and other allied techniques in the advancement of the field will be investigated. Key technologies will be presented, and examples given of their application showing how the field has now advanced to a stage where it is enhancing our understanding of the human biology underlying health and disease, and clinical translation, supporting precision/personalized medicine, is now feasible. Clearly the separation sciences have played a key role in many of these advances.