Regulation of Glutathione S-Transferase Omega 1 Mediated by Cysteine Residues Sensing the Redox Environment

Glutathione S-transferase omega 1 (GstO1) catalyzes deglutathionylation and plays an important role in the protein glutathionylation cycle in cells. GstO1 contains four conserved cysteine residues (C32, C90, C191, C236) found to be mutated in patients with associated diseases. In this study, we investigated the effects of cysteine mutations on the structure and function of GstO1 under different redox conditions. Wild-type GstO1 (WT) was highly sensitive to hydrogen peroxide (H2O2), which caused precipitation and denaturation at a physiological temperature. However, glutathione efficiently inhibited the H2O2-induced denaturation of GstO1. Cysteine mutants C32A and C236A exhibited redox-dependent stabilities and enzyme activities significantly different from those of WT. These results indicate that C32 and C236 play critical roles in GstO1 regulation by sensing redox environments and explain the pathological effect of cysteine mutations found in patients with associated diseases.

Dynamic changes in the plastid and mitochondrial genomes of the angiosperm Corydalis pauciovulata (Papaveraceae)

BACKGROUND

Corydalis DC., the largest genus in the family Papaveraceae, comprises > 465 species. Complete plastid genomes (plastomes) of Corydalis show evolutionary changes, including syntenic arrangements, gene losses and duplications, and IR boundary shifts. However, little is known about the evolution of the mitochondrial genome (mitogenome) in Corydalis. Both the organelle genomes and transcriptomes are needed to better understand the relationships between the patterns of evolution in mitochondrial and plastid genomes.

RESULTS

We obtained complete plastid and mitochondrial genomes from Corydalis pauciovulata using a hybrid assembly of Illumina and Oxford Nanopore Technologies reads to assess the evolutionary parallels between the organelle genomes. The mitogenome and plastome of C. pauciovulata had sizes of 675,483 bp and 185,814 bp, respectively. Three ancestral gene clusters were missing from the mitogenome, and expanded IR (46,060 bp) and miniaturized SSC (202 bp) regions were identified in the plastome. The mitogenome and plastome of C. pauciovulata contained 41 and 67 protein-coding genes, respectively; the loss of genes was a plastid-specific event. We also generated a draft genome and transcriptome for C. pauciovulata. A combination of genomic and transcriptomic data supported the functional replacement of acetyl-CoA carboxylase subunit β (accD) by intracellular transfer to the nucleus in C. pauciovulata. In contrast, our analyses suggested a concurrent loss of the NADH-plastoquinone oxidoreductase (ndh) complex in both the nuclear and plastid genomes. Finally, we performed genomic and transcriptomic analyses to characterize DNA replication, recombination, and repair (DNA-RRR) genes in C. pauciovulata as well as the transcriptomes of Liriodendron tulipifera and Nelumbo nuicifera. We obtained 25 DNA-RRR genes and identified their structure in C. pauciovulata. Pairwise comparisons of nonsynonymous (dN) and synonymous (dS) substitution rates revealed that several DNA-RRR genes in C. pauciovulata have higher dN and dS values than those in N. nuicifera.

CONCLUSIONS

The C. pauciovulata genomic data generated here provide a valuable resource for understanding the evolution of Corydalis organelle genomes. The first mitogenome of Papaveraceae provides an example that can be explored by other researchers sequencing the mitogenomes of related plants. Our results also provide fundamental information about DNA-RRR genes in Corydalis and their related rate variation, which elucidates the relationships between DNA-RRR genes and organelle genome stability.

A Korean Nationwide Cross-Sectional Study Investigating Risk Factors, Prevalence, and Characteristics of Sarcopenia in Men in Early Old Age

The present study investigated the risk factors, prevalence, and characteristics of sarcopenia among men aged 50-64 years. A total of 2868 participants were enrolled in this study. Of these, 328 individuals were classified into a sarcopenia group; the remaining 2540 were assigned to a control group. This study examined several variables, including skeletal muscle mass index, age, height, weight, body mass index, waist circumference, systolic and diastolic blood pressure, fasting glucose, triglyceride and total cholesterol levels, alcohol consumption, and tobacco use. It employed a stratified, clustered, and multistage probability sampling design. Complex sampling was used for the data analysis. The prevalence of sarcopenia was 10.25% (95% CI: 8.98-11.69). All anthropometric measures, including height, weight, BMI, and waist circumference, were significantly different between the two groups (p < 0.05). In terms of blood pressure, only systolic blood pressure (SBP) was significant (p < 0.05), and fasting glucose and triglyceride levels were risk factors for sarcopenia (p < 0.05). Tobacco use differed significantly between the two groups (p < 0.05). This study reported the specific prevalence of sarcopenia and identified its risk factors among men in early old age.

ARiRTN: A Novel Learning-Based Estimation Model for Regressing Illumination

In computational color constancy, regressing illumination is one of the most common approaches to manifesting the original color appearance of an object in a real-life scene. However, this approach struggles with the challenge of accuracy arising from label vagueness, which is caused by unknown light sources, different reflection characteristics of scene objects, and extrinsic factors such as various types of imaging sensors. This article introduces a novel learning-based estimation model, an aggregate residual-in-residual transformation network (ARiRTN) architecture, by combining the inception model with the residual network and embedding residual networks into a residual network. The proposed model has two parts: the feature-map group and the ARiRTN operator. In the ARiRTN operator, all splits perform transformations simultaneously, and the resulting outputs are concatenated into their respective cardinal groups. Moreover, the proposed architecture is designed to develop multiple homogeneous branches for high cardinality, and an increased size of a set of transformations, which extends the network in width and in length. As a result of experimenting with the four most popular datasets in the field, the proposed architecture makes a compelling case that complexity increases accuracy. In other words, the combination of the two complicated networks, residual and inception networks, helps reduce overfitting, gradient distortion, and vanishing problems, and thereby contributes to improving accuracy. Our experimental results demonstrate this model's outperformance over its most advanced counterparts in terms of accuracy, as well as the robustness of illuminant invariance and camera invariance.

Inactivation of the β (1, 2)-xylosyltransferase and the α (1, 3)-fucosyltransferase gene in rice (Oryza sativa) by multiplex CRISPR/Cas9 strategy

KEY MESSAGE

CRISPR/Cas9-mediated OsXylT and OsFucT mutation caused the elimination of plant-specific β1,2-xylose and α1,3-fucose residues on glycoproteins in rice, which is the first report of OsXylT/OsFucT double KO mutation in rice. N-glycosylation pathway is the one of post-translational mechanism and is known as highly conserved in eukaryotes. However, the process for complex-N-glycan modification is different between mammals and plants. In plant-specific manner, β1,2-xylose and α1,3-fucose residues are transferred to N-glycan core structure on glycoproteins by β1,2-xylosyltransferase (β1,2-XylT) and α1,3-fucosyltransferase (α1,3-FucT), respectively. As an effort to use plants as a platform to produce biopharmaceuticals, the plant-specific N-glycan genes of rice (Oryza sativa), β1,2-xylT (OsXylT) and α1,3-FucT (OsFucT), were knocked out using multiplex CRISPR/Cas9 technology. The double knock-out lines were found to have frameshift mutations by INDELs. Both β1,2-xylose and α1,3-fucose residues in the lines were not detected in Western blot analysis. Consistently, there was no peak corresponding to the N-glycans in MALDI-TOF/MS analysis. Although α1,3-fucose and β1,2-xylose residues were not detected in the line, other plant-specific residues of β1,3-galactose and α1,4-fucose were detected. Thus, we suggest that each enzymes working on the process for complex N-glycan biosynthesis might independently act in rice, hence the double knock-out of both OsXylT and OsFucT might be not enough to humanize N-glycan structure in rice.

Cancer-Associated Fibroblast-Induced Resistance to Chemotherapy and Radiotherapy in Gastrointestinal Cancers

In the past few decades, the role of cancer-associated fibroblasts (CAFs) in resistance to therapies for gastrointestinal (GI) cancers has emerged. Clinical studies focusing on GI cancers have revealed that the high expression of CAF-related molecules within tumors is significantly correlated with unfavorable therapeutic outcomes; however, the exact mechanisms whereby CAFs enhance resistance to chemotherapy and radiotherapy in GI cancers remain unclear. The cells of origin of CAFs in GI cancers include normal resident fibroblasts, mesenchymal stem cells, endothelial cells, pericytes, and even epithelial cells. CAFs accumulated within GI cancers produce cytokines, chemokines, and growth factors involved in resistance to therapies. CAF-derived exosomes can be engaged in stroma-related resistance to treatments, and several non-coding RNAs, such as miR-92a, miR-106b, CCAL, and H19, are present in CAF-derived exosomes and transferred to GI cancer cells. The CAF-induced desmoplastic reaction interferes with drug delivery to GI cancer cells, evoking resistance to chemotherapy. However, due to the heterogeneity of CAFs in GI cancers, identifying the exact mechanism underlying CAF-induced resistance may be difficult. Recent advancements in single-cell "omics" technologies could offer clues for revealing the specific subtypes and biomarkers related to resistance.

In Vivo Observation of Endothelial Cell-Assisted Vascularization in Pancreatic Cancer Xenograft Engineering

In this study, for better understanding of patient-derived xenograft (PDX) generation, angiogenic characteristics during PDX cancerous tissue generation was investigated with different initial cell seeding conditions in the hydrogel. We monitored the angiogenic changes during the formation of in vivo cancer cell line xenografts induced by endothelial cells. Our in vivo cancer tissue formation system was designed with the assistance of tissue engineering technology to mimic patient-derived xenograft formation. Endothelial cells and MIA PaCa-2 pancreatic carcinoma cells were encapsulated in fibrin gel at different mixing configurations and subcutaneously implanted into nude mice. To investigate the effect of the initial cancerous cell distribution in the fibrin gel, MIA PaCa-2 cells were encapsulated as a homogeneous cell distribution or as a cell aggregate, with endothelial cells homogeneously distributed in the fibrin gel. Histological observation of the explanted tissues after different implantation periods revealed three different stages: isolated vascular tubes, leaky blood vessels, and mature cancerous tissue formation. The in vivo engineered cancerous tissues had leaky blood vessels with low expression of the vascular tight junction marker CD31. Under our experimental conditions, complex cancer-like tissue formation was most successful when tumorous cells and endothelial cells were homogeneously mixed in the fibrin gel. The present study implies that tumorous xenograft tissue formation can be achieved with a low number of initial cells and that effective vascularization conditions can be attained with a limited volume of patient-derived cancer tissue. Endothelial cell-assisted vascularization can be a potent choice for the effective development of vascularized cancerous tissues for studying patient-derived xenografts, cancer angiogenesis, cancer metastasis, and anticancer drugs.