Protein Transcription Factors Research Articles

CTCF-activated FUCA1 functions as a tumor suppressor by promoting autophagy flux and serum α-L-fucosidase serves as a potential biomarker for prognosis in ccRCC.

Notably, clear cell renal cell carcinoma (ccRCC) is characterized by a distinct metabolic tumor phenotype that involves the reprogramming of multiple metabolic pathways. Although there is increasing evidence linking FUCA1 to malignancies, its specific role and downstream signaling pathways in ccRCC remain poorly understood. Here we found that FUCA1 expression was significantly downregulated in ccRCC tissues, which also predicts poor prognosis of ccRCCpatients. Moreover, enhancing FUCA1 expression resulted in reduced invasion and migration of ccRCC cells, further indicating its protective role. CHIP-qPCR and luciferase assays showed that CTCF was an upstream transcription factor of FUCA1 and could reverse the effects caused by FUCA1 inactivation. The change in FUCA1 led to changes in the results of various autophagy-related proteins and the mRFP-GFP-LC3 dual fluorescence system, indicating that it may play a role in the fusion stage of autophagy. Protein-protein interaction analysis revealed that FUCA2 exhibited the closest interaction with FUCA1 and strongly predicted the prognosis of ccRCC patients. Additionally, serum AFU encoded by FUCA2 could serve as a valuable predictor for survival in ccRCC patients. FUCA1 suppresses invasion and migration of ccRCC cells, with its activity being modulated by CTCF. FUCA1 regulates the autophagy process in ccRCC cells by influencing the fusion between autophagosomes and lysosomes. FUCA2 shares similarities with FUCA1, and elevated serum AFU levels along with increased expression of FUCA2 are indicative of a favorable prognosis in ccRCC.

H2S Donor SPRC Ameliorates Cardiac Aging by Suppression of JMJD3, a Histone Demethylase.

Aims: S-propargyl-cysteine (SPRC) is an endogenous hydrogen sulfide (H2S) donor obtained by modifying the structure of S-allyl cysteine in garlic. This study aims to investigate the effect of SPRC on mitigating cardiac aging and the involvement of jumonji domain-containing protein 3 (JMJD3), a histone demethylase, which represents the primary risk factor in major aging related diseases, in this process, elucidating the preliminary mechanism through which SPRC regulation of JMJD3 occurs. Results: In vitro, SPRC mitigated the elevated levels of reactive oxygen species, senescence-associated β-galactosidase, p53, and p21, reversing the decline in mitochondrial membrane potential, which represented a reduction in cellular senescence. In vivo, SPRC improved Dox-induced cardiac pathological structure and function. Overexpression of JMJD3 accelerated cardiomyocytes and cardiac senescence, whereas its knockdown in vitro reduced the senescence phenotype. The potential binding site of the upstream transcription factor of JMJD3, sheared X box binding protein 1 (XBP1s), was determined using online software. SPRC promoted the expression of cystathionine γ-lyase (CSE), which subsequently inhibited the IRE1α/XBP1s signaling pathway and decreased JMJD3 expression. Innovations: This study is the first to establish JMJD3 as a crucial regulator of cardiac aging. SPRC can alleviate cardiac aging by upregulating CSE and inhibiting endoplasmic reticulum stress pathways, which in turn suppress JMJD3 expression. Conclusions: JMJD3 plays an essential role in cardiac aging regulation, whereas SPRC can suppress the expression of JMJD3 by upregulating CSE, thus delaying cardiac aging, which suggests that SPRC may serve as an aging protective agent, and pharmacological targeting of JMJD3 may also be a promising therapeutic approach in age-related heart diseases.

Genome-wide gene network uncover temporal and spatial changes of genes in auxin homeostasis during fruit development in strawberry (F. × ananassa)

BackgroundThe plant hormone auxin plays a crucial role in regulating important functions in strawberry fruit development. Although a few studies have described the complex auxin biosynthetic and signaling pathway in wild diploid strawberry (Fragaria vesca), the molecular mechanisms underlying auxin biosynthesis and crosstalk in octoploid strawberry fruit development are not fully characterized. To address this knowledge gap, comprehensive transcriptomic analyses were conducted at different stages of fruit development and compared between the achene and receptacle to identify developmentally regulated auxin biosynthetic genes and transcription factors during the fruit ripening process. Similar to wild diploid strawberry, octoploid strawberry accumulates high levels of auxin in achene compared to receptacle.ResultsGenes involved in auxin biosynthesis and conjugation, such as Tryptophan Aminotransferase of Arabidopsis (TAAs), YUCCA (YUCs), and Gretchen Hagen 3 (GH3s), were found to be primarily expressed in the achene, with low expression in the receptacle. Interestingly, several genes involved in auxin transport and signaling like Pin-Formed (PINs), Auxin/Indole-3-Acetic Acid Proteins (Aux/IAAs), Transport Inhibitor Response 1 / Auxin-Signaling F-Box (TIR/AFBs) and Auxin Response Factor (ARFs) were more abundantly expressed in the receptacle. Moreover, by examining DEGs and their transcriptional profiles across all six developmental stages, we identified key auxin-related genes co-clustered with transcription factors from the NAM-ATAF1,2-CUC2/ WRKYGQK motif (NAC/WYKY), Heat Shock Transcription Factor and Heat Shock Proteins (HSF/HSP), APETALA2/Ethylene Responsive Factor (AP2/ERF) and MYB transcription factor groups.ConclusionsThese results elucidate the complex regulatory network of auxin biosynthesis and its intricate crosstalk within the achene and receptacle, enriching our understanding of fruit development in octoploid strawberries.

A novel liquid plasma derivative inhibits melanogenesis through upregulation of Nrf2

Non-thermal plasma (NTP) is an emerging technology with extensive applications in biomedicine, including treatment of abnormal pigmentation. However, very few studies have investigated how plasma induces anti-melanogenesis. Here, liquid plasma was prepared by treating an NTP jet with helium and oxygen (as carrier gases) for 15 min in serum-free culture media. In the zebrafish model, pigmentation ratio was observed with or without liquid plasma. The anti-melanogenic effect of liquid plasma was evaluated in human melanocytes by assessing the expression of melanogenesis-related genes using western blotting, RT-PCR, and immunohistochemistry. Liquid plasma reduced pigmentation in the zebrafish model and inhibited melanin synthesis in primary human melanocytes. Intracellular reactive oxygen species levels decreased and Nrf2 expression increased in liquid plasma–treated melanocytes. Liquid plasma affected microphthalmia-associated transcription factor (MITF) and tyrosinase mRNA and protein levels, tyrosinase activity, and melanin content. Considering the role of Wnt/β-catenin and PI3K/Akt pathways in melanogenesis, the effect of liquid plasma on this pathway was determined; liquid plasma decreased active β-catenin, LEF1/TCF4, MITF, and tyrosinase levels in a time-dependent manner and inhibited the nuclear translocation of β-catenin. This inhibition subsequently suppressed melanogenesis by downregulating MITF and tyrosinase. These results suggest that liquid plasma may be used for treating pigmentary disorders.

The cellular protein phosphatase 2A is a crucial host factor for Marburg virus transcription.

Our study elucidates the crucial role of host protein phosphatase 2A (PP2A) in Marburg virus (MARV) transcription. The regulatory subunit B56 of PP2A facilitates VP30 dephosphorylation, and hence transcription activation, via binding to NP. Our results, together with previous data, reveal a conserved mechanism of filovirus VP30 dephosphorylation by host factor PP2A at the NP interface and provide novel insights into potential pan-filovirus therapies.

MsMIOX2, encoding a MsbZIP53-activated myo-inositol oxygenase, enhances saline-alkali stress tolerance by regulating cell wall pectin and hemicellulose biosynthesis in alfalfa.

Alfalfa is one of the most widely cultivated forage crops worldwide. However, soil salinization restricts alfalfa growth and development and affects global productivity. The plant cell wall is the first barrier against various stresses. Therefore, elucidating the alterations in cell wall architecture is crucial for stress adaptation. This study aimed to clarify the impact of myo-inositol oxygenase 2 (MsMIOX2) on cell wall pectin and hemicellulose biosynthesis under saline-alkali stress and identify the upstream transcription factors that govern MsMIOX2. MsMIOX2 activation induced cell wall pectin and hemicellulose accumulation under saline-alkali stress. The effects of MsMIOX2 in saline-alkali tolerance were investigated by characterizing its overexpression and RNA interference lines. MsMIOX2 overexpression positively regulated the antioxidant system and photosynthesis in alfalfa under saline-alkali stress. MsMIOX2 exhibited myo-inositol oxygenase activity, which increased polysaccharide contents, facilitated pectin and hemicellulose biosynthesis, and extended the cell wall thickness. However, MsMIOX2 RNA interference decreased cell wall thickness and alleviated alfalfa saline-alkali stress tolerance. In addition, MsbZIP53 was identified as an upstream transcriptional MsMIOX2 regulator by yeast one-hybrid, electrophoretic mobility shift assay, dual-luciferase, and beta-glucuronidase assays. MsbZIP53 overexpression increased MsMIOX2 expression, elevated MIOX activity, reinforced the antioxidant system and photosynthesis, and increased saline-alkali stress tolerance in alfalfa. In conclusion, this study presents a novel perspective for elucidating the molecular mechanisms of saline-alkali stress tolerance in alfalfa and emphasizes the potential use of MsMIOX2 in alfalfa breeding.

Circ_0084653 promotes the tumor progression and immune escape in triple-negative breast cancer via the deubiquitination of MYC and upregulation of SOX5

The role of circular RNAs (circRNAs) in cancers is gaining more and more attention, yet related reporters are limited. In triple-negative breast cancer (TNBC), circRNA circ_0084653 originated from COP9 signalosome subunit 5 (COPS5), and COPS5 has been validated to be upregulated in breast cancer before. In our research, COPS5 was also upregulated in TNBC cells, and knockdown of it repressed cell proliferation, invasion, EMT, stemness and PDL-1 protein expression but increased T-cell percentage. Further, circ_0084653 was an aberrantly upregulated circRNA in TNBC cells, and similarly, circ_0084653 silence inhibited TNBC development. Besides, circ_0084653 expression was distributed in both cytoplasm and nucleus. COPS5 overexpression partially rescued the suppressing effects of circ_0084653 depletion in TNBC. Subsequently, circ_0084653 triggered deubiquitination of MYC, the upstream transcription factor of COPS5, via recruiting ubiquitin specific peptidase 36 (USP36). Moreover, circ_0084653 served as the sponge of miR-1323 to release the expression the target gene SRY-box transcription factor 5 (SOX5). SOX5 upregulation completely remedied the inhibiting influence of circ_0084653 downregulation in TNBC. Meanwhile, transcription factor SOX5 activated transcriptionally circ_0084653. To sum up, SOX5-induced circ_0084653 promotes TNBC via the deubiquitination of USP36, which may provide some fresh ideas for TNBC-related molecular mechanisms.

403 Impact of lysine, methionine, and histidine deficiencies on gene expression and upstream transcriptional regulators in bovine mammary epithelial cells: An RNA-sequencing analysis

Abstract Essential (E) amino acids (AA) may alter bovine mammary epithelial cell functions by impacting mRNA expression of genes through their upstream transcription factors. The objective of this research was to study the impact of EAA deficiencies on gene expression and to identify upstream transcriptional factors mediating their effects in bovine mammary epithelial cells. Epithelial cells were collected from the mammary glands of lactating dairy cows and cultured in combined media of DMEM/F12 and Medium 170, differentiated for 5 d, and subsequently treated in triplicate for 60 h with a control medium containing all EAA at normal plasma concentrations for cows (CTL), or a medium with 20 μM Lys (LY), 5 μM Met (LM), or 10 μM His (LH), which are each 25% of normal concentration. RNA was isolated from the cells and sequenced on an Illumina NovaSeq 6000 producing 150 base pair paired-end reads with a minimum sequencing depth of 150 million reads. Reads were cleaned with ‘fastp’ (Chen et al., 2018), aligned to the bovine reference genome (ARS-UCD1.2) using ‘STAR’ aligner (Dobin et al., 2013), and genes counted using ‘featureCounts’ (Liao et al., 2014). Differential expression of genes between treatment pairs was determined using the ‘DESeq2’ package (Love et al., 2014) in R. Genes with an absolute log2 fold change ≥ 1 and a false discovery rate of < 0.05 were considered differentially expressed. The number of differentially expressed genes relative to CTL was 780 for LY, 383 for LH, and 536 for LM. QIAGEN Ingenuity Pathway Analysis (IPA) identified four pathways consistently affected across LY, LM, and LH: kinetochore metaphase signaling, mitotic roles of polo-like kinase, cell cycle: G2/M DNA damage checkpoint regulation, and interferon signaling (Figure 1-3). Notably, the kinetochore metaphase signaling pathway was identified as the most significant across all treatments, suggesting a strong link to cell proliferation and apoptosis during EAA deficiency. The interferon signaling might be related to the Janus kinase 2/signal transducer and activator of transcription 5 (Jak2/STAT5) pathway which can promote the expression of genes encoding milk proteins such as β-casein and β-lactoglobulin. Furthermore, the IPA identified upstream transcription factors related to cell proliferation, apoptosis, autophagy, protein translation, endoplasmic reticulum biogenesis, and amino acid metabolism including NUPR1, FOXM1, MYC, CCND1, TP53, DDIT3, and ATF4 across all treatments. The findings suggest that AA deprivation regulates bovine mammary epithelial cell function by instigating amino acid response pathways and altering secretory cell number.

Endosperm-specific expressed transcription factor protein WRINKLED1-mediated oil accumulative mechanism in woody oil peony Paeonia ostii var. lishizhenii

Paeonia ostii var. lishizhenii exhibits superiority of high α-linolenic acid in seed oils, yet, the low yield highlights the importance of enhancing oil accumulation in seeds for edible oil production. The transcription factor protein WRINKLED1 (WRI1) plays crucial roles in modulating oil content in higher plants; however, its functional characterization remains elusive in P. ostii var. lishizhenii. Herein, based on a correlation analysis of transcription factor transcript levels, FA accumulation rates, and interaction assay of FA biosynthesis associated proteins, a WRI1 homologous gene (PoWRI1) that potentially regulated oil content in P. ostii var. lishizhenii seeds was screened. The PoWRI1 exhibited an endosperm-specific and development-depended expression pattern, encoding a nuclear-localized protein with transcriptional activation capability. Notably, overexpressing PoWRI1 upregulated certain key genes relevant to glycolysis, FA biosynthesis and desaturation, and improved seed development, oil body formation and oil accumulation in Arabidopsis seeds, resulting an enhancement of total seed oil weight by 9.47–18.77 %. The defective impacts on seed phenotypes were rescued through ectopic induction of PoWRI1 in wri1 mutants. Our findings highlight the pivotal role of PoWRI1 in controlling oil accumulation in P. ostii var. lishizhenii, offering bioengineering strategies to increase seed oil accumulation and enhance its potential for edible oil production.

Systems Biology and Machine Learning Identify Genetic Overlaps Between Lung Cancer and Gastroesophageal Reflux Disease.

One Health and planetary health place emphasis on the common molecular mechanisms that connect several complex human diseases as well as human and planetary ecosystem health. For example, not only lung cancer (LC) and gastroesophageal reflux disease (GERD) pose a significant burden on planetary health, but also the coexistence of GERD in patients with LC is often associated with a poor prognosis. This study reports on the genetic overlaps between these two conditions using systems biology-driven bioinformatics and machine learning-based algorithms. A total of nine hub genes including IGHV1-3, COL3A1, ITGA11, COL1A1, MS4A1, SPP1, MMP9, MMP7, and LOC102723407 were found to be significantly altered in both LC and GERD as compared with controls and with pathway analyses suggesting a significant association with the matrix remodeling pathway. The expression of these genes was validated in two additional datasets. Random forest and K-nearest neighbor, two machine learning-based algorithms, achieved accuracies of 89% and 85% for distinguishing LC and GERD, respectively, from controls using these hub genes. Additionally, potential drug targets were identified, with molecular docking confirming the binding affinity of doxycycline to matrix metalloproteinase 7 (binding affinity: -6.8 kcal/mol). The present study is the first of its kind that combines in silico and machine learning algorithms to identify the gene signatures that relate to both LC and GERD and promising drug candidates that warrant further research in relation to therapeutic innovation in LC and GERD. Finally, this study also suggests upstream regulators, including microRNAs and transcription factors, that can inform future mechanistic research on LC and GERD.

Insight into the therapeutic effects of artesunate in relieving metabolic-associated steatohepatitis from transcriptomic and lipidomics analyses.

Artesunate (ART) is a water-soluble derivative of artemisinin, which has shown anti-inflammatory, anti-tumor, and immunomodulating effects. We aimed to investigate the potential therapeutic effects and mechanisms of ART in metabolic dysfunction-associated steatohepatitis (MASH). The mice were randomly divided into the control group, high-fat, high-cholesterol diet-induced MASH group, and the MASH treated with ART (30 mg/kg once daily) group. Liver enzymes, lipids, and histological features were compared among groups. The molecular mechanisms were studied by transcriptomic and lipidomics analyses of liver tissues. The mice of the MASH group had significantly increased hepatic fat deposition and inflammation in terms of biochemical indicators and pathological manifestations than the control group. The ART-treated group had improved plasma liver enzymes and hepatic cholesterol, especially at week 4 of intervention (p < 0.05). A total of 513 differentially expressed genesand 59 differentially expressed lipids were identified in the MASH group and the MASH+ART group. Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment test showed that ART regulated glycerolipid metabolism pathway and enhanced fatty acid degradation. Peroxisome proliferator-activated receptor (PPAR)-α acted as a key transcription factor in the treatment of MASH with ART, which was confirmed by cell experiment. ART significantly improved fat deposition and inflammatory manifestations in MASH mice, with potential therapeutic effects. The mechanism of artemisinin treatment for MASH may involve extensive regulation of downstream genes by upstream transcription factors, such as PPAR-α, to restore hepatic lipid homeostasis.

Transcriptional activation of PINK1 by MyoD1 mediates mitochondrial homeostasis to induce renal calcification in pediatric nephrolithiasis

This study aims to uncover the molecular mechanisms underlying pediatric kidney stone formation induced by renal calcium deposition by utilizing high-throughput sequencing data to reveal the regulation of PINK1 by MyoD1. We performed transcriptome sequencing on peripheral blood samples from healthy children and children with kidney stones to obtain differentially expressed genes (DEGs). Genes related to mitochondrial oxidative stress were obtained from the Genecards website and intersected with DEGs to obtain candidate target genes. Additionally, we conducted protein-protein interaction (PPI) analysis using the STRING database to identify core genes involved in pediatric kidney stone disease (KSD) and predicted their transcription factors using the hTFtarget database. We assessed the impact of MyoD1 on the activity of the PINK1 promoter using dual-luciferase reporter assays and investigated the enrichment of MyoD1 on the PINK1 promoter through chromatin immunoprecipitation (ChIP) experiments. To validate our hypothesis, we selected HK-2 cells and established an in vitro kidney stone model induced by calcium oxalate monohydrate (COM). We evaluated the expression levels of various genes, cell viability, volume of adherent crystals in each group, as well as mitochondrial oxidative stress in cells by measuring mitochondrial membrane potential (Δψm), superoxide dismutase (SOD) activity, reactive oxygen species (ROS), and malondialdehyde (MDA) content. Mitochondrial autophagy was assessed using mtDNA fluorescence staining and Western blot analysis of PINK1-related proteins. Apoptosis-related proteins were evaluated using Western blot analysis, and cell apoptosis was measured using flow cytometry. Furthermore, we developed a rat model of KSD and assessed the expression levels of various genes, as well as the pathologic changes in rat renal tissues using H&E and von Kossa staining, transmission electron microscopy (TEM), and the expression of creatinine, blood urea nitrogen, neutrophil gelatinase-associated lipocalin (NGAL), and kidney injury molecule-1 (KIM-1) to evaluate the mitochondrial oxidative stress in vivo (through measurement of Δψm, SOD activity, ROS, and MDA content). Mitochondrial autophagy was evaluated by Western blot analysis of PINK1-associated proteins. Apoptosis-related proteins were detected using Western blot analysis, and cellular apoptosis was examined using cell flow cytometry and TUNEL staining. Bioinformatics analysis revealed that the PINK1 gene is upregulated and vital in pediatric kidney stone patients. Our in vitro and in vivo experiments demonstrated that silencing PINK1 could inhibit kidney stone formation by suppressing mitochondrial oxidative stress both in vitro and in vivo. We identified MyoD1 as an upstream transcription factor of PINK1 that contributes to the occurrence of pediatric kidney stones through the activation of PINK1. Our in vivo and in vitro experiments collectively confirmed that silencing MyoD1 could inhibit mitochondrial oxidative stress, mitochondrial autophagy, and cellular apoptosis in a rat model of kidney stones by downregulating PINK1 expression, consequently suppressing the formation of kidney stones. In this study, we discovered that MyoD1 may promote kidney stone formation and development in pediatric patients by transcriptionally activating PINK1 to induce mitochondrial oxidative stress.

Modification of Regulatory Tyrosine Residues Biases Human Hsp90α in its Interactions with Cochaperones and Clients

The highly conserved Hsp90 chaperones control stability and activity of many essential signaling and regulatory proteins including many protein kinases, E3 ligases and transcription factors. Thereby, Hsp90s couple cellular homeostasis of the proteome to cell fate decisions. High-throughput mass spectrometry revealed 178 and 169 posttranslational modifications (PTMs) for human cytosolic Hsp90α and Hsp90β, but for only a few of the modifications the physiological consequences are investigated in some detail. In this study, we explored the suitability of the yeast model system for the identification of key regulatory residues in human Hsp90α. Replacement of three tyrosine residues known to be phosphorylated by phosphomimetic glutamate and by non-phosphorylatable phenylalanine individually and in combination influenced yeast growth and the maturation of 7 different Hsp90 clients in distinct ways. Furthermore, wild-type and mutant Hsp90 differed in their ability to stabilize known clients when expressed in HepG2 HSP90AA1−/− cells. The purified mutant proteins differed in their interaction with the cochaperones Aha1, Cdc37, Hop and p23 and in their support of the maturation of glucocorticoid receptor ligand binding domain in vitro. In vivo and in vitro data correspond well to each other confirming that the yeast system is suitable for the identification of key regulatory sites in human Hsp90s. Our findings indicate that even closely related clients are affected differently by the amino acid replacements in the investigated positions, suggesting that PTMs could bias Hsp90s client specificity.

Diarylpropionitrile-stimulated ERβ nuclear accumulation promotes MyoD-induced muscle regeneration in mdx mice by interacting with FOXO3A

Duchenne muscular dystrophy (DMD) is an X-linked recessive progressive degenerative disease of skeletal muscle, characterized by intramuscular inflammation, muscle regeneration disorder and replacement of muscle with fibroadipose tissue. DMD is caused by the absence of normal dystrophy. Impaired self-renew ability and limited differentiation capacity of satellite cells are proved as main reasons for muscle regeneration failure. The deficiency of estrogen impedes the process of muscle regeneration. However, the role of estrogen receptor β (ERβ) in muscle regeneration is still unclear. This study aims to investigate the role and the pharmacological effect of ERβ activation on muscle regeneration in mdx mice. This study showed that mRNA levels of ERβ and myogenic-related genes both witnessed increasing trends in dystrophic context. Our results revealed that treatment with selective ERβ agonist (DPN, diarylpropionitrile) significantly increased myogenic differentiation 1 (MyoD-1) level and promoted muscle regeneration in mdx mice. Similarly, in mdx mice with muscle-specific estrogen receptor α (ERα) ablation, DPN treatment still promoted muscle regeneration. Moreover, we demonstrated that myoblasts differentiation was accompanied by raised nuclear accumulation of ERβ. DPN treatment augmented the nuclear accumulation of ERβ and, thus, contributed to myotubes formation. One important finding was that forkhead box O3A (FOXO3A), as a pivotal transcription factor in Myod-1 transcription, participated in the ERβ-promoted muscle regeneration. Overall, we offered an interesting explanation about the crucial role of ERβ during myogenesis.

An AP2/ERF transcription factor confers chilling tolerance in rice.

Cold stress, a prominent adverse environmental factor, severely hinders rice growth and productivity. Unraveling the complex mechanisms governing chilling tolerance in rice is crucial for molecular breeding of cold-tolerant varieties. Here, we identify an APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factor, OsERF52, as a positive modulator in response to low temperatures. OsERF52 directly regulates the expression of C-Repeat Binding Factor (CBF) genes in rice. In addition, Osmotic Stress/ABA-Activated Protein Kinase 9-mediated phosphorylation of OsERF52 at S261 enhances its stability and interaction with Ideal Plant Architecture 1 and OsbHLH002/OsICE1. This collaborative activation leads to the expression of OsCBFs, thereby initiating the chilling response in rice. Notably, plants with base-edited OsERF52S261D-3HA exhibit enhanced chilling resistance without yield penalty. Our findings unveil the mechanism orchestrated by a regulatory framework involving a protein kinase and transcription factors from diverse families, offering potential genetic resources for developing chilling-tolerant rice varieties.

Investigation of chia seed (Salvia hispanica L.) extract supplementation to extender on post-thawing ram sperm parameters and genes-related antioxidant capacity

Ram semen cryopreservation is not so widely used compared to bull semen. This study was carried out to explore the potential of methanolic chia seed extract (MCSE) in ram semen extender on kinematics, acrosome, apoptosis, antioxidant capacity, genes-related antioxidants, and caspase-3 in post-thawing ram semen. Semen from Rahmani rams (n=5) was collected, pooled, and diluted with Tris-extender (15 % egg yolk, 1 % soybean lecithin and 5 % glycerol) supplemented with MCSE (0, 125, 250, 375, and 500 µg/mL). MCSE had 67.5 % linolenic acid, 17.99 % linoleic acid, total phenolic, and flavonoid compounds. MCSE had higher antioxidant activity by DPPH (2,2-diphenyl-1-picryl-hydrazyl-hydrate) and FRAP (Ferric-reducing antioxidant power) assays. MCSE (500 µg/mL) significantly improved sperm motility (43.6 vs. 30.0 %), vitality (44.0 vs. 30.7 %), and membrane integrity (43.1 vs. 31.3 %) as well as sperm velocity parameters and acrosome integrity (53.4 vs. 36.2 %) after thawing. MCSE at a level of 500 µg/mL increased viability, total antioxidant capacity level, and decreased apoptotic spermatozoa and malondialdehyde levels in post-thawed semen. MCSE at levels of 250, 375, and 500 µg/mL decreased caspase-3 level to 42.8, 35.6, and 30.0 % compared to control (54.6 %) after thawing, and resulted in a clear up-regulation of antioxidant-related genes of superoxide dismutase 1, catalase, glutathione peroxidase 1, and GA-binding protein transcription factor subunit beta-1 (GAPP1). The highest impact was observed for MCSE on GAPP1 as compared to other profiles as well as for MCSE at 500 µg/mL as compared to with other levels. All MCSE levels decreased Caspase-3 mRNA by about 44, 51, 61, and 61 %, respectively. In conclusion, MCSE had higher anti-oxidative activity. Tris-soya bean lecithin extender supplemented with MCSE at a level of 500 µg/mL, as a natural antioxidant, has a vital role in maintaining the freezing ability of ram spermatozoa after cryopreservation.

Multi-omics analysis of the effects of low-temperature storage on chilling injury of bitter gourd

Bitter gourd fruit are susceptible to chilling injury when stored at 4 °C. In this study, bitter gourds were stored at 20 °C to simulate normal ripening and senescence processes, and at 4 °C to induce chilling injury. Transcriptomic, metabolomic, and proteomic analyses were employed to investigate the molecular mechanisms of chilling injury development during low-temperature storage. The results showed that low-temperature storage induced the expression of genes related to proline metabolism (delta-1-pyrroline-5-carboxylate synthase-like, ornithine--oxo-acid transaminase, and proline dehydrogenase2, mitochondrial-like), antioxidants (glutathione peroxidase 2, superoxide dismutase, and L-ascorbate peroxidase 6), and membrane lipid metabolism. Additionally, low-temperature storage affected the ICE-CBF-COR pathway (calcium-binding protein CML15 and transcription factor ICE1). Correspondingly, free fatty acids (9,12,13-trihydroxy-10,15-octadecadienoic acid, 9-hydroperoxy-10E,12,15Z-octadecadienoic acid, γ-linolenic acid, α-linolenic acid*) and phospholipid metabolites LysoPC (18:4, 20:3, 19:1) and LysoPE (20:3, 20:3*, 20:2*) also accumulated during storage. Low-temperature storage increased POD and GPX activities. Overall, chilling injury in bitter gourd was associated with the induction of genes involved in proline metabolism, antioxidant activity, membrane lipid metabolism, cold perception mechanisms, and plant hormone signal transduction.

Impact of oxytosis on the cross-talk of mTORC with mitochondrial proteins in drug-resistant cancer stem cells.

By delivering the environmental inputs to transport nutrients and growth factors, Mechanistic Target of Rapamycin (mTOR) plays a significant role in the growth and metabolism of eukaryotic cells through the regulation of numerous elementary cellular processes such as autophagy, protein synthesis, via translation of mitochondrial protein transcription factor A mitochondrial, mitochondrial ribosomal proteins, and mitochondrial respiratory complexes I &V that are encoded in the nucleus with the help of translation initiation factor 4E-BP. These mitochondrial proteins are involved in cell signaling to regulate proper cell growth, proliferation, and death which are essential for tumor growth and proliferation. This suggests that tumor cells are dependent on mTORC1 for various metabolic pathways. However, this crucial regulator is activated and regulated by calcium homeostasis. Mounting evidence suggests the role of calcium ions in regulating mitochondrial enzymes and proteins. Hence, disrupting calcium homeostasis leads to calcium-dependent cell death called "Oxytosis" through hampering the expression of various mitochondrial proteins. "Oxytosis" is a novel non-apoptotic cell death characterized by glutamate cytotoxicity and ferritin degradation. The present review focuses on the crosstalk between mTORC1 and mitochondrial proteins in the cancer pathophysiology and the impact of calcium ions on disrupting mTORC1 leading to the induction of "Oxytosis."

Integrated analysis reveals NLRC4 as a potential biomarker in sepsis pathogenesis.

Sepsis remains a significant global health burden and contributor to mortality, yet the precise molecular mechanisms underlying the immune response are not fully elucidated. To gain insight into this issue, we performed a comprehensive analysis using a variety of techniques including bulk RNA sequencing, single-cell RNA sequencing, and enzyme-linked immunosorbent assay (ELISA). We performed enrichment analysis of differentially expressed genes in sepsis and healthy individuals by utilizing Gene Ontology (GO) analysis and indicated significant enrichment of immune-related response. Following Weighted Gene Co-Expression Network Analysis (WGCNA) and protein-protein interaction analysis (PPI) were used to identify key immune-related hub genes and validated by ELISA to show that NLRC4 is highly expressed in sepsis. Additionally, an analysis of scRNA-seq data from newly diagnosed sepsis, sepsis diagnosis at 6 hours, and healthy samples demonstrates a significant increase in both the expression levels and proportions of NLRC4 in sepsis monocytes and neutrophils. In addition, using pySCENIC we identified upstream transcription factors that regulate NLRC4. Our study provides valuable insights into the identification of NLRC4 in peripheral blood as a potential candidate gene for the diagnosis and treatment of sepsis.

Characterization and fine mapping of cold-inducible parthenocarpy in cucumber (Cucumis sativus L.)

Cold stress detrimentally influences fruit development, leading to a substantial yield reduction in many fruit-bearing vegetables. Cucumber, a vegetable of subtropical origin, is especially sensitive to cold. Cold-inducible parthenocarpy (CIP) promises fruit yield under cold conditions. Previously, we identified a CIP line EC5 in cucumber, which showed strong parthenocarpy and sustained fruit growth under cold conditions (16°C day/10°C night). However, the candidate gene and genetic mechanism underlying CIP in cucumber remain unknown. In this study, both BSA-seq and conventional QTL mapping strategies were employed on F2 populations to delve into the genetic control of CIP. A single QTL, CIP5.1, was consistently mapped across two winter seasons in 2021 and 2022. Fine mapping delimited the CIP locus into a 38.3 kb region on chromosome 5, harboring 8 candidate genes. Among these candidates, CsAGL11 (CsaV3_5G040370) was identified, exhibiting multiple deletions/insertions in the promoter and 5′UTR region. The CsAGL11 gene encodes a MADS-box transcription factor protein, which is homologous to the genes previously recognized as negative regulators in ovule and fruit development of Arabidopsis and tomato. Correspondingly, cold treatment resulted in decreased expression of CsAGL11 during the early developmental stage of the fruit in EC5. A promoter activity assay confirmed promoter polymorphisms leading to weak transcriptional activation of CsAGL11 under cold conditions. This study deepens our understanding of the genetic characteristics of CIP and elucidates the potential role of the CsAGL11 gene in developing cucumber cultivars with enhanced fruiting under cold conditions.