The first Chromosomal-level genome assembly of Sageretia thea using Nanopore long reads and Pore-C technology

Sageretia thea, a notable species within the mock buckthorn genus, is recognized for its intriguing biogeographical distribution and diverse medicinal properties. Despite this significance, genomic studies on S. thea are still in the nascent stages. We present the first chromosome-level genome assembly of S. thea that was generated using a combination of Oxford Nanopore long-read and Illumina short-read sequencing technologies complemented by Pore-C chromatin conformation capture. The genome assembly had a size of 197.8 Mb with 12 chromosomal scaffolds and a scaffold N50 length of 15.9 Mb. A total of 25,434 protein-coding genes were identified and functionally annotated, and the gene model indicated 96.5% complete eukaryotic BUSCOs. Additionally, orthologous gene profiling and synteny analysis were performed to elucidate the evolutionary relationships within the Rhamnaceae family and Rosales. This high-quality chromosomal genome is the first genomic view of S. thea, which will serve as the basis for future studies on its biological and medicinal properties, and evolutionary history.

Ordovician origin and subsequent diversification of the brown algae

Brown algae are the only group of heterokont protists exhibiting complex multicellularity. Since their origin, brown algae have adapted to various marine habitats, evolving diverse thallus morphologies and gamete types. However, the evolutionary processes behind these transitions remain unclear due to a lack of a robust phylogenetic framework and problems with time estimation. To address these issues, we employed plastid genome data from 138 species, including heterokont algae, red algae, and other red-derived algae. Based on a robust phylogeny and new interpretations of algal fossils, we estimated the geological times for brown algal origin and diversification. The results reveal that brown algae first evolved true multicellularity, with plasmodesmata and reproductive cell differentiation, during the late Ordovician Period (ca. 450 Ma), coinciding with a major diversification of marine fauna (the Great Ordovician Biodiversification Event) and a proliferation of multicellular green algae. Despite its early Paleozoic origin, the diversification of major orders within this brown algal clade accelerated only during the Mesozoic Era, coincident with both Pangea rifting and the diversification of other heterokont algae (e.g., diatoms), coccolithophores, and dinoflagellates, with their red algal-derived plastids. The transition from ancestral isogamy to oogamy was followed by three simultaneous reappearances of isogamy during the Cretaceous Period. These are concordant with a positive character correlation between parthenogenesis and isogamy. Our new brown algal timeline, combined with a knowledge of past environmental conditions, shed new light on brown algal diversification and the intertwined evolution of multicellularity and sexual reproduction.

Selective induction of Rab9-dependent alternative mitophagy using a synthetic derivative of isoquinoline alleviates mitochondrial dysfunction and cognitive deficits in Alzheimer's disease models

Rationale: Promotion of mitophagy is considered a promising strategy for the treatment of neurodegenerative diseases including Alzheimer's disease (AD). The development of mitophagy-specific inducers with low toxicity and defined molecular mechanisms is essential for the clinical application of mitophagy-based therapy. The aim of this study was to investigate the potential of a novel small-molecule mitophagy inducer, ALT001, as a treatment for AD. Methods: ALT001 was developed through chemical optimization of an isoquinolium scaffold, which was identified from a chemical library screening using a mitophagy reporter system. In vitro and in vivo experiments were conducted to evaluate the potential of ALT001 as a mitophagy-targeting therapeutic agent and to investigate the molecular mechanisms underlying ALT001-induced mitophagy. The therapeutic effect of ALT001 was assessed in SH-SY5Y cells expressing mutant APP and mouse models of AD (5×FAD and PS2APP) by analyzing mitochondrial dysfunction and cognitive defects. Results: ALT001 specifically induces mitophagy both in vitro and in vivo but is nontoxic to mitochondria. Interestingly, we found that ALT001 induces mitophagy through the ULK1-Rab9-dependent alternative mitophagy pathway independent of canonical mitophagy pathway regulators such as ATG7 and PINK1. Importantly, ALT001 reverses mitochondrial dysfunction in SH-SY5Y cells expressing mutant APP in a mitophagy-dependent manner. ALT001 induces alternative mitophagy in mice and restores the decreased mitophagy level in a 5×FAD AD model mouse. In addition, ALT001 reverses mitochondrial dysfunction and cognitive defects in the PS2APP and 5×FAD AD mouse models. AAV-mediated silencing of Rab9 in the hippocampus further confirmed that ALT001 exerts its therapeutic effect through alternative mitophagy. Conclusion: Our results highlight the therapeutic potential of ALT001 for AD via alleviation of mitochondrial dysfunction and indicate the usefulness of the ULK1-Rab9 alternative mitophagy pathway as a therapeutic target.

Oligonol ameliorates liver function and brain function in the 5 × FAD mouse model: transcriptional and cellular analysis

Alzheimer's disease (AD) is a common neurodegenerative disease worldwide and is accompanied by memory deficits, personality changes, anxiety, depression, and social difficulties. For treatment of AD, many researchers have attempted to find medicinal resources with high effectiveness and without side effects. Oligonol is a low molecular weight polypeptide derived from lychee fruit extract. We investigated the effects of oligonol in 5 × FAD transgenic AD mice, which developed severe amyloid pathology, through behavioral tests (Barnes maze, marble burying, and nestle shredding) and molecular experiments. Oligonol treatment attenuated blood glucose levels and increased the antioxidant response in the livers of 5 × FAD mice. Moreover, the behavioral score data showed improvements in anxiety, depressive behavior, and cognitive impairment following a 2-month course of orally administered oligonol. Oligonol treatment not only altered the circulating levels of cytokines and adipokines in 5 × FAD mice, but also significantly enhanced the mRNA and protein levels of antioxidant enzymes and synaptic plasticity in the brain cortex and hippocampus. Therefore, we highlight the therapeutic potential of oligonol to attenuate neuropsychiatric problems and improve memory deficits in the early stage of AD.

Bifunctional G-Quadruplex Aptamer Targeting Nucleolin and Topoisomerase 1: Antiproliferative Activity and Synergistic Effect of Conjugated Drugs

As a counterpart to antibody-drug conjugates (ADCs), aptamer-drug conjugates (ApDCs) have been considered a promising strategy for targeted therapy due to the various benefits of aptamers. However, an aptamer merely serves as a targeting ligand in ApDCs, whereas the antibody enables the unexpected therapeutic efficacy of ADCs through antibody-dependent cellular cytotoxicity (ADCC). In this study, we developed a tumor-specific aptamer with an effector function and used it to confirm the feasibility of more potent ApDCs. First, we designed a nucleolin (NCL)-binding G-quadruplex (GQ) library based on the ability of NCL to bind to telomeric sequences. We then identified a bifunctional GQ aptamer (BGA) inhibiting the catalytic activity of topoisomerase 1 (TOP1) by forming an irreversible cleavage complex. Our BGA specifically targeted NCL-positive MCF-7 cells, exhibiting antiproliferative activity, and this suggested that tumor-specific therapeutic aptamers can be developed by using a biased library to screen aptamer candidates for functional targets. Finally, we utilized DM1, which has a synergistic interaction with TOP1 inhibitors, as a conjugated drug. BGA-DM1 exerted an anticancer effect 20-fold stronger than free DM1 and even 10-fold stronger than AS1411 (NCL aptamer)-DM1, highlighting our approach to develop synergistic ApDCs. Therefore, we anticipate that our library might be utilized for the identification of aptamers with effector functions. Furthermore, by employing such aptamers and appropriate drugs, synergistic ApDCs can be developed for targeted cancer therapy in a manner distinct from how ADCs exhibit additional therapeutic efficacy.

Pioglitazone-incorporated microspheres alleviates cardiac dysfunction through macrophage polarization in a rat myocardial infarction model

 

Inflammatory processes are essential for the repair processes after myocardial infarction. Among inflammatory cells involved in this process, macrophages play a critical role through polarization in pro-inflammatory M1 or reparative M2 subtype. Pioglitazone, known as a treatment drug for diabetes mellitus, is reported to regulate macrophage polarization toward reparative M2 subtype. Poly L-lactic-co-glycolic acid (PLGA) has been widely accepted as the delivery carrier in drug delivery system (DDS).

Here, we aimed to validate the therapeutic effects and investigate the mechanisms of DDS-based treatment using pioglitazone to left ventricular remodeling after myocardial infarction.

Pioglitazone-incorporated PLGA microspheres (PGZ-MS) were prepared and the drug release profile was evaluated. The concentration of interleukin-10 secreted from murine bone marrow derived macrophages incubated with PGZ-MS was quantified in the culture supernatant. To validate the therapeutic potential of PGZ-MS in vivo, Sprague-Dawley rats were subjected to permanent left coronary artery ligation to induce myocardial infarction. Mock-MS (100 μg) or PGZ-MS (100 μg) was injected to the infarct region just after induction (n=9–11/group). Cardiac function and left ventricular size were assessed by echocardiography. At 28-day after surgery, rats were sacrificed, and excised hearts were evaluated histologically.

PGZ-MS released 1.8±0.3% of incorporated PGZ within 24 hours and 29.5±1.2% within 14 days indicating sustained release of PGZ in vitro. PGZ-MS augmented Interleukin-10 release from bone marrow derived macrophages, indicating polarization toward reparative M2 subtype. PGZ-MS significantly ameliorated cardiac function after myocardial infarction (fractional shortening: MI vs MI+Mock-MS vs MI+PGZ-MS, 24.4±1.1 vs 24.3±1.6 vs 32.2±1.4%; P=0.0035) with reverse remodeling (wall thickness: MI vs MI+Mock-MS vs MI+PGZ-MS, 0.69±0.12 vs 0.71±0.13 vs 1.06±0.09; P=0.03). Immunohistochemical analyses revealed that PGZ-MS enhanced macrophage polarization toward reparative M2 subtype (ratio of reparative M2 macrophages: 0.39±0.03 vs 0.42±0.02 vs 0.54±0.02; P=0.0004) and attenuated apoptosis of cardiomyocytes in the ischemic border zone (MI vs MI+Mock-MS vs MI+PGZ-MS, 2.6±0.2 vs 1.9±0.2 vs 1.2±0.2 cells/field; P=0.002).

In the present study, we confirmed that PGZ-MS could realize sustained release of pioglitazone which resulted in sustained effect of macrophage polarization and attenuated left ventricular remodeling accompanied with the amelioration of cardiac dysfunction and cardiomyocytes apoptosis. The strategy of DDS-based macrophage polarization might serve as a promising strategy in cardiac regenerative therapy for ischemic heart disease in the future.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Grants-in-Aid for Scientific Research from the Ministry of Education, Science, Sports and Culture of Japan

Hepatic steatosis changes after early gastric cancer surgery

Background: Nonalcoholic fatty liver disease dramatically improves after bariatric surgery, primarily due to improvements in hepatic insulin sensitivity. Since the procedure for gastric cancer surgery is very similar to that for bariatric surgery, we investigated changes in fatty liver following gastrectomy for gastric cancer according to the type of surgery.Methods: We evaluated hepatic steatosis in 212 early gastric cancer patients using Hounsfield units (HUs) on non-contrast computed tomography preoperatively and 6, 12, and 24 months after surgery. We compared the preoperative and postoperative liver-to-spleen HU ratio according to the type of surgery: Billroth I, Billroth II, and total gastrectomy with Roux-en-Y reconstruction. Results: The initial results (liver/spleen HUs and the liver-to-spleen HU ratio) did not significantly differ according to surgical group. After surgery, only patients who underwent total gastrectomy with Roux-en-Y exhibited significant changes in the liver-to-spleen HU ratio at 6 months. In 26 patients who had higher initial HU levels of the spleen than the liver, the liver-to-spleen HU ratio significantly increased from 0.836 to 1.115 at 6 months, 1.109 at 12 months, and 1.102 at 24 months (P<0.01). Conclusion: Significant changes in hepatic steatosis were found in even normal patients (with higher liver than spleen HU values) who underwent total gastrectomy with Roux-en-Y. Patients who initially had fatty liver also showed a significant increase in the liver-to-spleen HU ratio. These results suggest that total gastrectomy with Roux-en-Y reconstruction can have a positive effect on the improvement of hepatic steatosis.

Oat Extract Avenanthramide-C Reverses Hippocampal Long-Term Potentiation Decline in Tg2576 Mice

Memory deterioration in Alzheimer’s disease (AD) is thought to be underpinned by aberrant amyloid β (Aβ) accumulation, which contributes to synaptic plasticity impairment. Avenanthramide-C (Avn-C), a polyphenol compound found predominantly in oats, has a range of biological properties. Herein, we performed methanolic extraction of the Avns-rich fraction (Fr. 2) from germinated oats using column chromatography, and examined the effects of Avn-C on synaptic correlates of memory in a mouse model of AD. Avn-C was identified in Fr. 2 based on ¹H-NMR analysis. Electrophysiological recordings were performed to examine the effects of Avn-C on the hippocampal long-term potentiation (LTP) in a Tg2576 mouse model of AD. Avn-C from germinated oats restored impaired LTP in Tg2576 mouse hippocampal slices. Furthermore, Avn-C-facilitated LTP was associated with changes in the protein levels of phospho-glycogen synthase kinase-3β (p-GSK3β-S9) and cleaved caspase 3, which are involved in Aβ-induced synaptic impairment. Our findings suggest that the Avn-C extract from germinated oats may be beneficial for AD-related synaptic plasticity impairment and memory decline.

Exendin-4 improves long-term potentiation and neuronal dendritic growth in vivo and in vitro obesity condition

Metabolic syndrome, which increases the risk of obesity and type 2 diabetes has emerged as a significant issue worldwide. Recent studies have highlighted the relationship between metabolic imbalance and neurological pathologies such as memory loss. Glucagon-like peptide 1 (GLP-1) secreted from gut L-cells and specific brain nuclei plays multiple roles including regulation of insulin sensitivity, inflammation and synaptic plasticity. Although GLP-1 and GLP-1 receptor agonists appear to have neuroprotective function, the specific mechanism of their action in brain remains unclear. We investigated whether exendin-4, as a GLP-1RA, improves cognitive function and brain insulin resistance in metabolic-imbalanced mice fed a high-fat diet. Considering the result of electrophysiological experiments, exendin-4 inhibits the reduction of long term potentiation (LTP) in high fat diet mouse brain. Further, we identified the neuroprotective effect of exendin-4 in primary cultured hippocampal and cortical neurons in in vitro metabolic imbalanced condition. Our results showed the improvement of IRS-1 phosphorylation, neuronal complexity, and the mature of dendritic spine shape by exendin-4 treatment in metabolic imbalanced in vitro condition. Here, we provides significant evidences on the effect of exendin-4 on synaptic plasticity, long-term potentiation, and neural structure. We suggest that GLP-1 is important to treat neuropathology caused by metabolic syndrome.

The complete mitochondrial genome of Myzus persicae (Sulzer, 1776; Hemiptera: Aphididae) isolated in Korea

We de novo assembled the complete mitochondrial genome of the green peach aphid, Myzus persicae, using its genomic DNA isolated from the bell pepper in Korea. The circular mitogenome of M. persicae is 16,936 bp long and contains the standard 37 genes: 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes, as well as a single control region of 798 bp. Given the high AT ratio (84.1%) of the M. persicae mitogenome, we found, through the comparison of the Chinese M. persicae mitogenomes, that approximately 1.6% of the mitogenome is polymorphic, including 30 single nucleotide polymorphisms (SNPs), 12 insertions and deletions (INDELs), and large sequence variations in the control region. To resolve the phylogenetic position of M. persicae, we analyzed all mitochondrial protein-coding genes from 38 species within the Aphidoidea superfamily, with Adelges laricis as an outgroup. Our M. persicae sample was significantly grouped with three existing M. persicae samples, and the species belonging to the family Aphididae formed a monophyletic clade.

Chemical Use and Associated Health Concerns in the Semiconductor Manufacturing Industry

Background

Research on the status of many chemicals used in the semiconductor industry is needed. The purpose of this study was to describe the overall status of chemical use in the semiconductor industry in Korea and to examine it from a health perspective.

Methods

Data on the status of chemical use and safety data sheets at 11 of 12 major semiconductor workplaces in Korea were collected. The number of chemical products and chemical constituents, quantities of chemicals, and trade secret ingredients used, as well as the health hazards were examined.

Results

On average, 210 chemical products and 135 chemical constituents were used at the surveyed workplaces. Among all chemical products, 33% (range: 16-56%) contained at least one trade secret ingredient. Most of the trade secret ingredients were used in the photolithography process. Several carcinogens, including sulfuric acid, chromic acid, ethylene oxide, crystalline silica, potassium dichromate, and formaldehyde were also used. Only 29% (39 of 135) of the chemical constituents had occupational exposure limits, and more than 60% had no National Fire Protection Association health, safety, and reactivity ratings. Based on the aforementioned results, this study revealed the following. First, many chemical products and constituents are being used in the semiconductor industry and many products contained trade secret ingredients. Second, many products contained significant amounts of carcinogenic, mutagenic, and reproductive toxicant materials.

Conclusion

We conclude that protecting workers in the semiconductor industry against harm from chemical substances will be difficult, due to widespread use of trade secret ingredients and a lack of hazard information. The findings of the status of chemical use and the health and safety risks in semiconductor industry will contribute to epidemiological studies, safe workplace, and worker health protection.

Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists

Microbial communities present in diverse environments from deep seas to human body niches play significant roles in the complex ecosystem and human health. Characterizing their structural and functional diversities is indispensable, and many approaches, such as microscopic observation, DNA fingerprinting, and PCR-based marker gene analysis, have been successfully applied to identify microorganisms. Since the revolutionary improvement of DNA sequencing technologies, direct and high-throughput analysis of genomic DNA from a whole environmental community without prior cultivation has become the mainstream approach, overcoming the constraints of the classical approaches. Here, we first briefly review the history of environmental DNA analysis applications with a focus on profiling the taxonomic composition and functional potentials of microbial communities. To this end, we aim to introduce the shotgun metagenomic sequencing (SMS) approach, which is used for the untargeted ("shotgun") sequencing of all ("meta") microbial genomes ("genomic") present in a sample. SMS data analyses are performed in silico using various software programs; however, in silico analysis is typically regarded as a burden on wet-lab experimental microbiologists. Therefore, in this review, we present microbiologists who are unfamiliar with in silico analyses with a basic and practical SMS data analysis protocol. This protocol covers all the bioinformatics processes of the SMS analysis in terms of data preprocessing, taxonomic profiling, functional annotation, and visualization.

Acute restraint stress reverses impaired LTP in the hippocampal CA1 region in mouse models of Alzheimer's disease

Acute stress facilitates long-term potentiation (LTP) in the mouse hippocampus by modulating glucocorticoid receptors and ion channels. Here, we analysed whether this occurs in mouse models of Alzheimer’s disease (AD) with impaired LTP induction. We found that a brief 30 min restraint stress protocol reversed the impaired LTP assessed with field excitatory postsynaptic potential recordings at cornu ammonis 3-1 (CA3-CA1) synapses in both Tg2576 and 5XFAD mice. This effect was accompanied by increased phosphorylation and surface expression of glutamate A1 (GluA1) -containing α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs). Moreover, enhanced LTP induction and GluA1 phosphorylation were sustained up to 4 h after the stress. Treatment with 200 nM dexamethasone produced similar effects in the hippocampi of these mice, which supports the glucocorticoid receptor-mediated mechanism in these models. Collectively, our results demonstrated an alleviation of impaired LTP and synaptic plasticity in the hippocampal CA1 region following acute stress in the AD mouse models.

A Rapid Colorimetric Sensor for Soluble Interleukin-2 Receptor α, Based on Aptamer-Adsorbed AuNP

The soluble interleukin-2 receptor α (sIL-2Rα) is a broad indicator of clinical disease activity in various inflammatory diseases. Here we have developed, for the first time, a rapid, washing-free colorimetric aptasensor based on a sIL-2Rα aptamer (K_d =1.33 nm). The aptasensor was fabricated with Au nanoparticles (AuNPs) adsorbing sIL-2Rα aptamers. On addition of sIL-2Rα, the aptamers become desorbed from the AuNPs, and this in turn weakens the absorption corresponding to AuNP-catalyzed oxidation of ortho-phenylenediamine (oPD) with H₂ O₂ . The aptasensor was characterized by TEM imaging, ζ potential measurements, dynamic light scattering (DLS) analysis, and UV/Vis spectrometry, followed by further optimization. The fabricated sensor exhibited great analytical performance, with a linear range of 1 to 100 nm and a detection limit of 1 nm both in buffer and in spiked human serum within 25 min. Other proteins, such as bovine serum albumin (BSA), IL-17Rα, IL-5Rα, IL-13Rα₂ , and CD166, showed negligible effects on the aptasensor. Thanks to the great advantages of the aptamers and AuNPs, this aptasensor provides a rapid, simple, and inexpensive process that might offer insights into various diagnostic applications of sIL-2Rα.

Nasal Cavity Administration of Melanin-Concentrating Hormone Improves Memory Impairment in Memory-Impaired and Alzheimer's Disease Mouse Models

Melanin-concentrating hormone (MCH) is a highly conserved neuropeptide known to exhibit important functions in the brain. Some studies have reported that MCH improves memory by promoting memory retention. However, the precise molecular mechanisms by which MCH enhances memory impairment have yet to be fully elucidated. In this study, MCH was administered to the scopolamine-induced memory-impaired mice via the nasal cavity to examine the acute effects of MCH and Alzheimer's disease (AD) mouse models to evaluate the chronic effects of MCH. MCH improved memory impairment in both models and reduced soluble amyloid beta in the cerebral cortex of APP/PS1 transgenic mice. In vitro assays also showed that MCH inhibits amyloid beta-induced cytotoxicity. Furthermore, MCH increased long-term potentiation (LTP) in the hippocampus of wild-type and 5XFAD AD mouse model. To further elucidate the mechanisms of the chronic effect of MCH, the levels of phosphorylated CREB and GSK3β, and the expression of BDNF, TrkB and PSD95 were examined in the cerebral cortex and hippocampus. Our findings indicate that MCH might have neuroprotective effects via downstream pathways associated with the enhancement of neuronal synapses and LTP. This suggests a therapeutic potential of MCH for the treatment of neurodegenerative diseases such as AD.

Conventionally used reference genes are not outstanding for normalization of gene expression in human cancer research

BACKGROUND

The selection of reference genes is essential for quantifying gene expression. Theoretically they should be expressed stably and not regulated by experimental or pathological conditions. However, identification and validation of reference genes for human cancer research are still being regarded as a critical point, because cancerous tissues often represent genetic instability and heterogeneity. Recent pan-cancer studies have demonstrated the importance of the appropriate selection of reference genes for use as internal controls for the normalization of gene expression; however, no stably expressed, consensus reference genes valid for a range of different human cancers have yet been identified.

RESULTS

In the present study, we used large-scale cancer gene expression datasets from The Cancer Genome Atlas (TCGA) database, which contains 10,028 (9,364 cancerous and 664 normal) samples from 32 different cancer types, to confirm that the expression of the most commonly used reference genes is not consistent across a range of cancer types. Furthermore, we identified 38 novel candidate reference genes for the normalization of gene expression, independent of cancer type. These genes were found to be highly expressed and highly connected to relevant gene networks, and to be enriched in transcription-translation regulation processes. The expression stability of the newly identified reference genes across 29 cancerous and matched normal tissues were validated via quantitative reverse transcription PCR (RT-qPCR).

CONCLUSIONS

We reveal that most commonly used reference genes in current cancer studies cannot be appropriate to serve as representative control genes for quantifying cancer-related gene expression levels, and propose in this study three potential reference genes (HNRNPL, PCBP1, and RER1) to be the most stably expressed across various cancerous and normal human tissues.