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1.
ACS Nano ; 18(21): 13618-13634, 2024 May 28.
Article in English | MEDLINE | ID: mdl-38739841

ABSTRACT

Postovulatory aging oocytes usually feature diminished potential for fertilization and poor embryonic development due to enhanced oxidative damage to the subcellular organelles and macromolecules, which stands as a formidable obstacle in assisted reproductive technologies (ART). Here, we developed lipoic acid (LA) and polyethylene glycol (PEG)-modified CeO2 nanoparticles (LA-PEG-CeNPs) with biocompatibility, enzyme-like autocatalytic activity, and free radical scavenging capacity. We further investigated the LA-PEG-CeNPs effect in mouse postovulatory oocytes during in vitro aging. The results showed that LA-PEG-CeNPs dramatically reduced the accumulation of ROS in aging oocytes, improving mitochondrial dysfunction; they also down-regulated the pro-apoptotic activity by rectifying cellular caspase-3, cleaved caspase-3, and Bcl-2 levels. Consistently, this nanoenzyme prominently alleviated the proportion of abnormalities in spindle structure, chromosome alignment, microtubule stability, and filamentous actin (F-actin) distribution in aging oocytes, furthermore decreased oocyte fragmentation, and improved its ability of fertilization and development to blastocyst. Taken together, our finding suggests that LA-PEG-CeNPs can alleviate oxidative stress damage on oocyte quality during postovulatory aging, implying their potential value for clinical practice in assisted reproduction.


Subject(s)
Cerium , Mitochondria , Nanoparticles , Oocytes , Oxidative Stress , Polyethylene Glycols , Thioctic Acid , Animals , Oocytes/drug effects , Oocytes/metabolism , Oxidative Stress/drug effects , Mice , Mitochondria/metabolism , Mitochondria/drug effects , Cerium/chemistry , Cerium/pharmacology , Female , Nanoparticles/chemistry , Thioctic Acid/chemistry , Thioctic Acid/pharmacology , Polyethylene Glycols/chemistry , Polyethylene Glycols/pharmacology , Reactive Oxygen Species/metabolism , Cellular Senescence/drug effects , Ovulation/drug effects , Apoptosis/drug effects
2.
Redox Biol ; 73: 103195, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38781731

ABSTRACT

Accumulating oxidative damage is a primary driver of ovarian reserve decline along with aging. However, the mechanism behind the imbalance in reactive oxygen species (ROS) is not yet fully understood. Here we investigated changes in iron metabolism and its relationship with ROS disorder in aging ovaries of mice. We found increased iron content in aging ovaries and oocytes, along with abnormal expression of iron metabolic proteins, including heme oxygenase 1 (HO-1), ferritin heavy chain (FTH), ferritin light chain (FTL), mitochondrial ferritin (FTMT), divalent metal transporter 1 (DMT1), ferroportin1(FPN1), iron regulatory proteins (IRP1 and IRP2) and transferrin receptor 1 (TFR1). Notably, aging oocytes exhibited enhanced ferritinophagy and mitophagy, and consistently, there was an increase in cytosolic Fe2+, elevated lipid peroxidation, mitochondrial dysfunction, and augmented lysosome activity. Additionally, the ovarian expression of p53, p21, p16 and microtubule-associated protein tau (Tau) were also found to be upregulated. These alterations could be phenocopied with in vitro Fe2+ administration in oocytes from 2-month-old mice but were alleviated by deferoxamine (DFO). In vivo application of DFO improved ovarian iron metabolism and redox status in 12-month-old mice, and corrected the alterations in cytosolic Fe2+, ferritinophagy and mitophagy, as well as related degenerative changes in oocytes. Thereby in the whole, DFO delayed the decline in ovarian reserve and significantly increased the number of superovulated oocytes with reduced fragmentation and aneuploidy. Together, our findings suggest that aging-related disturbance in ovarian iron homeostasis contributes to excessive ROS production and that iron chelation may improve ovarian redox status, and efficiently delay the decline in ovarian reserve and oocyte quality in aging mice. These data propose a novel intervention strategy for preserving the ovarian reserve function in elderly women.


Subject(s)
Aging , Iron , Oocytes , Ovary , Oxidation-Reduction , Reactive Oxygen Species , Animals , Oocytes/metabolism , Mice , Female , Iron/metabolism , Aging/metabolism , Ovary/metabolism , Reactive Oxygen Species/metabolism , Mitochondria/metabolism , Oxidative Stress , Mitophagy , Lipid Peroxidation , Cellular Microenvironment , Ovarian Reserve
3.
Plant J ; 118(6): 2169-2187, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38558472

ABSTRACT

Genome-wide association studies (GWAS) are an effective approach to identify new specialized metabolites and the genes involved in their biosynthesis and regulation. In this study, GWAS of Arabidopsis thaliana soluble leaf and stem metabolites identified alleles of an uncharacterized BAHD-family acyltransferase (AT5G57840) associated with natural variation in three structurally related metabolites. These metabolites were esters of glucuronosylglycerol, with one metabolite containing phenylacetic acid as the acyl component of the ester. Knockout and overexpression of AT5G57840 in Arabidopsis and heterologous overexpression in Nicotiana benthamiana and Escherichia coli demonstrated that it is capable of utilizing phenylacetyl-CoA as an acyl donor and glucuronosylglycerol as an acyl acceptor. We, thus, named the protein Glucuronosylglycerol Ester Synthase (GGES). Additionally, phenylacetyl glucuronosylglycerol increased in Arabidopsis CYP79A2 mutants that overproduce phenylacetic acid and was lost in knockout mutants of UDP-sulfoquinovosyl: diacylglycerol sulfoquinovosyl transferase, an enzyme required for glucuronosylglycerol biosynthesis and associated with glycerolipid metabolism under phosphate-starvation stress. GGES is a member of a well-supported clade of BAHD family acyltransferases that arose by duplication and neofunctionalized during the evolution of the Brassicales within a larger clade that includes HCT as well as enzymes that synthesize other plant-specialized metabolites. Together, this work extends our understanding of the catalytic diversity of BAHD acyltransferases and uncovers a pathway that involves contributions from both phenylalanine and lipid metabolism.


Subject(s)
Acyltransferases , Arabidopsis Proteins , Arabidopsis , Genome-Wide Association Study , Phenylacetates , Arabidopsis/genetics , Arabidopsis/enzymology , Arabidopsis/metabolism , Acyltransferases/genetics , Acyltransferases/metabolism , Phenylacetates/metabolism , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism
4.
Nat Commun ; 15(1): 2492, 2024 Mar 20.
Article in English | MEDLINE | ID: mdl-38509059

ABSTRACT

Biosynthetic enzymes evolutionarily gain novel functions, thereby expanding the structural diversity of natural products to the benefit of host organisms. Diels-Alderases (DAs), functionally unique enzymes catalysing [4 + 2] cycloaddition reactions, have received considerable research interest. However, their evolutionary mechanisms remain obscure. Here, we investigate the evolutionary origins of the intermolecular DAs in the biosynthesis of Moraceae plant-derived Diels-Alder-type secondary metabolites. Our findings suggest that these DAs have evolved from an ancestor functioning as a flavin adenine dinucleotide (FAD)-dependent oxidocyclase (OC), which catalyses the oxidative cyclisation reactions of isoprenoid-substituted phenolic compounds. Through crystal structure determination, computational calculations, and site-directed mutagenesis experiments, we identified several critical substitutions, including S348L, A357L, D389E and H418R that alter the substrate-binding mode and enable the OCs to gain intermolecular DA activity during evolution. This work provides mechanistic insights into the evolutionary rationale of DAs and paves the way for mining and engineering new DAs from other protein families.


Subject(s)
Morus , Morus/genetics , Morus/chemistry , Terpenes , Catalysis , Cycloaddition Reaction
5.
Environ Toxicol ; 39(6): 3710-3720, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38511855

ABSTRACT

Tryptanthrin, an alkaloid applied in traditional Chinese medicine, exhibits a variety of pharmacological activities. This study aimed to investigate the anti-tumor activity of the tryptanthrin derivative (8-cyanoindolo[2,1-b]quinazoline-6,12-dione [CIQ]) in breast cancer cells. In both MDA-MB-231 and MCF-7 breast cancer cells, CIQ inhibited cell viability and promoted caspase-dependent apoptosis. At the concentration- and time-dependent ways, CIQ increased the levels of p-ERK, p-JNK, and p-p38 in breast cancer cells. We found that exposure to the JNK inhibitor or the ERK inhibitor partially reversed CIQ's viability. We also observed that CIQ increased reactive oxygen species (ROS) generation, and upregulated the phosphorylation and expression of H2AX. However, the pretreatment of the antioxidants did not protect the cells against CIQ's effects on cell viability and apoptosis, which suggested that ROS does not play a major role in the mechanism of action of CIQ. In addition, CIQ inhibited the invasion of MDA-MB-231 cells and decreased the expression of the prometastatic factors (MMP-2 and Snail). These findings demonstrated that the possibility of this compound to show promise in playing an important role against breast cancer.


Subject(s)
Antineoplastic Agents , Apoptosis , Breast Neoplasms , Cell Survival , Quinazolines , Female , Humans , Antineoplastic Agents/pharmacology , Apoptosis/drug effects , Breast Neoplasms/drug therapy , Breast Neoplasms/pathology , Cell Line, Tumor , Cell Survival/drug effects , MAP Kinase Signaling System/drug effects , MCF-7 Cells , Quinazolines/pharmacology , Reactive Oxygen Species/metabolism
6.
Autophagy ; : 1-23, 2024 Mar 27.
Article in English | MEDLINE | ID: mdl-38513669

ABSTRACT

PLD1 has been implicated in cytoskeletal reorganization and vesicle trafficking in somatic cells; however, its function remains unclear in oocyte meiosis. Herein, we found PLD1 stably expresses in mouse oocytes meiosis, with direct interaction with spindle, RAB11A+ vesicles and macroautophagic/autophagic vacuoles. The genetic or chemical inhibition of PLD1 disturbed MTOC clustering, spindle assembly and its cortical migration, also decreased PtdIns(4,5)P2, phosphorylated CFL1 (p-CFL1 [Ser3]) and ACTR2, and their local distribution on MTOC, spindle and vesicles. Furthermore in PLD1-suppressed oocytes, vesicle size was significantly reduced while F-actin density was dramatically increased in the cytoplasm, the asymmetric distribution of autophagic vacuoles was broken and the whole autophagic process was substantially enhanced, as illustrated with characteristic changes in autophagosomes, autolysosome formation and levels of ATG5, BECN1, LC3-II, SQSTM1 and UB. Exogenous administration of PtdIns(4,5)P2 or overexpression of CFL1 hyperphosphorylation mutant (CFL1S3E) could significantly improve polar MTOC focusing and spindle structure in PLD1-depleted oocytes, whereas overexpression of ACTR2 could rescue not only MTOC clustering, and spindle assembly but also its asymmetric positioning. Interestingly, autophagy activation induced similar defects in spindle structure and positioning; instead, its inhibition alleviated the alterations in PLD1-depleted oocytes, and this was highly attributed to the restored levels of PtdIns(4,5)P2, ACTR2 and p-CFL1 (Ser3). Together, PLD1 promotes spindle assembly and migration in oocyte meiosis, by maintaining rational levels of ACTR2, PtdIns(4,5)P2 and p-CFL1 (Ser3) in a manner of modulating autophagy flux. This study for the first time introduces a unique perspective on autophagic activity and function in oocyte meiotic development.Abbreviations: ACTR2/ARP2: actin related protein 2; ACTR3/ARP3: actin related protein 3; ATG5: autophagy related 5; Baf-A1: bafilomycin A1; BFA: brefeldin A; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GOLGA2/GM130: golgin A2; GV: germinal vesicle; GVBD: germinal vesicle breakdown; IVM: in vitro maturation; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MI: metaphase of meiosis I; MII: metaphase of meiosis II; MO: morpholino; MTOC: microtubule-organizing center; MTOR: mechanistic target of rapamycin kinase; PB1: first polar body; PLA: proximity ligation assay; PLD1: phospholipase D1; PtdIns(4,5)P2/PIP2: phosphatidylinositol 4,5-bisphosphate; RAB11A: RAB11A, member RAS oncogene family; RPS6KB1/S6K1: ribosomal protein S6 kinase B1; SQSTM1/p62: sequestosome 1; TEM: transmission electron microscopy; TUBA/α-tubulin: tubulin alpha; TUBG/γ-tubulin: tubulin gamma; UB: ubiquitin; WASL/N-WASP: WASP like actin nucleation promoting factor.

7.
Anal Bioanal Chem ; 416(4): 945-957, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38051414

ABSTRACT

Histamine causes allergic reactions and can serve as an indicator for assessing food quality. This study designed and developed a dispersive micro solid-phase extraction (D-µSPE) method that combined the advantages of dispersive liquid-liquid extraction and solid-phase extraction (SPE). Molecularly imprinted polymers (MIPs) were employed as the solid phase in the D-µSPE method to extract histamine in wine samples. We used microwave energy to significantly reduce the synthesis time, achieving an 11.1-fold shorter synthesis time compared to the conventional MIP synthetic method. Under optimized D-µSPE conditions, our results showed that the dispersive solvent could effectively increase the adsorption performance of MIPs in wine samples by 97.7%. To improve the sensitivity of histamine detection in gas chromatography-mass spectrometry, we employed the microwave-assisted tandem derivatization method to reuse excess derivatization reagents and reduce energy consumption and reaction time. Calibration curves were constructed for wine samples spiked with 0-400 nmol histamine using the standard addition method, resulting in good linearity with a coefficient of determination of 0.999. The intra- and inter-batch relative standard deviations of the slope and intercept were < 0.7% and < 5.3%, respectively. The limits of quantitation and detection were 0.4 nmol and 0.1 nmol, respectively. The developed method was successfully applied to analyze the histamine concentration in 10 commercial wine samples. In addition, the AGREEprep tool was used to evaluate the greenness performance of the developed method, which obtained a higher score than the other reported methods.


Subject(s)
Molecular Imprinting , Wine , Wine/analysis , Chromatography, High Pressure Liquid/methods , Histamine/analysis , Polymers/chemistry , Solid Phase Extraction/methods , Molecular Imprinting/methods
8.
Sci Rep ; 13(1): 20368, 2023 11 21.
Article in English | MEDLINE | ID: mdl-37989761

ABSTRACT

Immunotherapy has dramatically changed the landscape of treatment for colorectal cancer (CRC), but currently lack of effective predictive biomarker, especially for tumors with mismatch repair (MMR) proficiency. The response of immunotherapy is associated with the cell-cell interactions in tumor microenvironment, encompassing processes such as cell-cell recognition, binding, and adhesion. However, the function of immunoglobulin superfamily (IGSF) genes in tumor immune microenvironment remains uncharacterized. This study quantified the immune landscape by leveraging a gene expression matrix from publicly accessible databases. The associations between IGSF6 gene expression and immune cell infiltration were assessed. The expression levels of IGSF6, CD8+ T cells, CD4+ T cells and CD68+ macrophage cells in cancer tissues from CRC patients and CRC cell lines were evaluated. IGSF6 was more highly expressed in CRC tumor tissues than adjacent normal tissues. And IGSF6 was significantly correlated with immune cell infiltration in MMR-proficient patients. Remarkably, MMR-proficient patients with high IGSF6 expression showed more sensitive to immunotherapy and chemotherapy than those with low IGSF6 expression. In summary, IGSF6 could be a novel biomarker to evaluate immune infiltration and predict therapeutic effect for MMR-proficient CRC.


Subject(s)
Colorectal Neoplasms , Humans , Colorectal Neoplasms/pathology , DNA Mismatch Repair/genetics , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , CD8-Positive T-Lymphocytes/metabolism , Tumor Microenvironment/genetics
9.
Nutrients ; 15(17)2023 Aug 25.
Article in English | MEDLINE | ID: mdl-37686755

ABSTRACT

Several studies utilizing Rhodiola rosea, which contains a complex mixture of phytochemicals, reported some positive drug-drug interaction (DDI) findings based on in vitro CYP450's enzyme inhibition, MAO-A and MAO-B inhibition, and preclinical pharmacokinetic studies in either rats or rabbits. However, variation in and multiplicity of constituents present in Rhodiola products is a cause for concern for accurately evaluating drug-drug interaction (DDI) risk. In this report, we examined the effects of bioengineered, nature-identical salidroside on the inhibition potential of salidroside on CYP1A2, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, and CYP3A4 utilizing human liver microsomes, the induction potential of salidroside on CYP1A2, CYP2B6 and CYP3A4 in cryopreserved human hepatocytes, the inhibitory potential of salidroside against recombinant human MAO-A and MAO-B, and the OATP human uptake transport inhibitory potential of salidroside using transfected HEK293-OATP1B1 and OATP1B3 cells. The results demonstrate that the bioengineered salidroside at a concentration exceeding the predicted plasma concentrations of <2 µM (based on 60 mg PO) shows no risk for drug-drug interaction due to CYP450, MAO enzymes, or OATP drug transport proteins. Our current studies further support the safe use of salidroside in combination with other drugs cleared by CYP or MAO metabolism or OATP-mediated disposition.


Subject(s)
Cytochrome P-450 Enzyme System , Drug Interactions , Glucosides , Animals , Rabbits , Rats , HEK293 Cells
11.
Biomed Pharmacother ; 166: 115381, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37639744

ABSTRACT

BACKGROUND: The lung microbiome plays a crucial role in human health and disease. Extensive studies have demonstrated that the disturbance of the lung microbiome influences immune response, cognition, and behavior. The goal of this study was to investigate the effect of general anesthetics on lung microbiome. METHODS: Eight-week-old male SD rats received a continuous intravenous infusion of propofol or inhalation of isoflurane for 4 h. 16S rRNA gene amplification from BALF samples was used to investigate the changes in the lung microbiome after interventions. We further performed neurobehavioral assessments to find the differential strains' association with behavior disorder after isoflurane anesthesia. RESULTS: The absolute and relative quantitation of 16S rRNA sequencing data showed that isoflurane altered the diversity and abundance of the lung microbiome in rats more than propofol. Elusimicrobia increased significantly in the isoflurane group. Both EPM and OFT results showed that rats exhibited depression-like behaviors after inhalation of isoflurane. In addition, significant differences were found in the COG/KO/MetaCyc/KEGG pathway enrichment analyses among the groups. CONCLUSION: Continuous inhalation of isoflurane changed the diversity and composition of the lung microbiota in rats, resulting in post-anesthesia depression.


Subject(s)
Isoflurane , Microbiota , Propofol , Humans , Animals , Male , Rats , Rats, Sprague-Dawley , RNA, Ribosomal, 16S , Isoflurane/pharmacology , Propofol/pharmacology , Anesthesia, General
12.
Ann Anat ; 250: 152126, 2023 Oct.
Article in English | MEDLINE | ID: mdl-37364712

ABSTRACT

In mammals, centriole is degenerated during early oogenesis, but it is still not known about the expression and function of centriolar structural components in oocyte meiosis. Here we found that Odf2 (outer dense fiber of sperm tails 2), a key centriolar appendage protein, was stably expressed in mouse oocytes during meiotic progression. Distinct from its single location at centrosomes in somatic mitosis, Odf2 was multiply located at microtubule organizing centers (MTOCs), chromosome centromeres and vesicles in oocyte meiosis. In addition, the vesicle-associated Odf2 disappeared in oocytes treated with the vesicle inhibitor Brefeldin A. Odf2 was mainly co-localized with the mitochondrial sheath in the sperm tail and presented as double spots, similar to γ-tubulin, in the sperm neck region. After fertilization, Odf2 remained on vesicles in embryos from 1-cell to 4-cell stage but was only detected on centrosomes at blastocyst stage. Taken together, Odf2 is expressed precisely in mouse oocytes even in the absence of intact centriole structure, and may regulate oocyte spindle assembly and positioning, additionally, the sperm motility and early embryo development.


Subject(s)
Semen , Sperm Motility , Male , Mice , Animals , Oocytes/physiology , Spermatozoa , Centrosome/physiology , Mammals , Heat-Shock Proteins/metabolism
13.
Chem Biol Interact ; 380: 110538, 2023 Aug 01.
Article in English | MEDLINE | ID: mdl-37164279

ABSTRACT

The enzyme pyruvate kinase M2 (PKM2) is involved in glycolysis, which plays an important role in the regulation of tumor progression. In this study, we investigated the anti-tumor activity of N-(4-(3-(3-(methylamino)-3-oxopropyl)-5-(4'-(trifluoromethyl)-[1,1'-biphenyl]-4-yl)-1H-pyrazol-1-yl)phenyl)propiolamide (MTP), a PKM2 inhibitor, in oral squamous cell carcinoma (OSCC) cells. Our results showed that MTP inhibited cell growth with IC50 values of 0.59 µM and 0.78 µM in SCC2095 and HSC-3 OSCC cells, respectively. MTP induced caspase-dependent apoptosis, which was associated with the modulation of PKM2 and oncogenic biomarkers epidermal growth factor receptor and ß-catenin. In addition, MTP increased the generation of reactive oxygen species (ROS) and modulated the expression of autophagic gene products, including LC3B-II and p62. Western blotting showed that MTP inhibited Janus kinase 2 (JAK2) signaling, and JAK2 overexpression partially reversed MTP-mediated cytotoxicity. Taken together, these data indicate the potential use of MTP as a therapeutic agent for OSCC.


Subject(s)
Carcinoma, Squamous Cell , Head and Neck Neoplasms , Mouth Neoplasms , Humans , Carcinoma, Squamous Cell/metabolism , Squamous Cell Carcinoma of Head and Neck , Janus Kinase 2/metabolism , Mouth Neoplasms/drug therapy , Mouth Neoplasms/metabolism , Cell Line, Tumor , Apoptosis , Autophagy , Cell Proliferation
14.
Acta Pharmacol Sin ; 44(9): 1856-1866, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37193755

ABSTRACT

Psychological stress increases the susceptibility to herpes simplex virus type 1 (HSV-1) infection. There is no effective intervention due to the unknown pathogenesis mechanisms. In this study we explored the molecular mechanisms underlying stress-induced HSV-1 susceptibility and the antiviral effect of a natural compound rosmarinic acid (RA) in vivo and in vitro. Mice were administered RA (11.7, 23.4 mg·kg-1·d-1, i.g.) or acyclovir (ACV, 206 mg·kg-1·d-1, i.g.) for 23 days. The mice were subjected to restraint stress for 7 days followed by intranasal infection with HSV-1 on D7. At the end of RA or ACV treatment, mouse plasma samples and brain tissues were collected for analysis. We showed that both RA and ACV treatment significantly decreased stress-augmented mortality and alleviated eye swelling and neurological symptoms in HSV-1-infected mice. In SH-SY5Y cells and PC12 cells exposed to the stress hormone corticosterone (CORT) plus HSV-1, RA (100 µM) significantly increased the cell viability, and inhibited CORT-induced elevation in the expression of viral proteins and genes. We demonstrated that CORT (50 µM) triggered lipoxygenase 15 (ALOX15)-mediated redox imbalance in the neuronal cells, increasing the level of 4-HNE-conjugated STING, which impaired STING translocation from the endoplasmic reticulum to Golgi; the abnormality of STING-mediated innate immunity led to HSV-1 susceptibility. We revealed that RA was an inhibitor of lipid peroxidation by directly targeting ALOX15, thus RA could rescue stress-weakened neuronal innate immune response, thereby reducing HSV-1 susceptibility in vivo and in vitro. This study illustrates the critical role of lipid peroxidation in stress-induced HSV-1 susceptibility and reveals the potential for developing RA as an effective intervention in anti-HSV-1 therapy.


Subject(s)
Herpes Simplex , Herpesvirus 1, Human , Neuroblastoma , Humans , Animals , Mice , Herpesvirus 1, Human/genetics , Lipid Peroxidation , Acyclovir/pharmacology , Acyclovir/therapeutic use , Herpes Simplex/drug therapy
15.
BMC Bioinformatics ; 24(1): 133, 2023 Apr 04.
Article in English | MEDLINE | ID: mdl-37016291

ABSTRACT

BACKGROUND: RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different software tools. The complexity of these de novo transcriptomics workflows therefore presents a major barrier for researchers to adopt best-practice methods and up-to-date versions of software. RESULTS: Here we present a streamlined and universal de novo transcriptome assembly and annotation pipeline, transXpress, implemented in Snakemake. transXpress supports two popular assembly programs, Trinity and rnaSPAdes, and allows parallel execution on heterogeneous cluster computing hardware. CONCLUSIONS: transXpress simplifies the use of best-practice methods and up-to-date software for de novo transcriptome assembly, and produces standardized output files that can be mined using SequenceServer to facilitate rapid discovery of new genes and proteins in non-model organisms.


Subject(s)
Software , Transcriptome , Sequence Analysis, RNA/methods , RNA-Seq , Gene Expression Profiling , Molecular Sequence Annotation
17.
Nat Commun ; 14(1): 597, 2023 02 03.
Article in English | MEDLINE | ID: mdl-36737607

ABSTRACT

Plants contain rapidly evolving specialized enzymes that support the biosynthesis of functionally diverse natural products. In coumarin biosynthesis, a BAHD acyltransferase-family enzyme COSY was recently discovered to accelerate coumarin formation as the only known BAHD enzyme to catalyze an intramolecular acyl transfer reaction. Here we investigate the structural and mechanistic basis for COSY's coumarin synthase activity. Our structural analyses reveal an unconventional active-site configuration adapted to COSY's specialized activity. Through mutagenesis studies and deuterium exchange experiments, we identify a unique proton exchange mechanism at the α-carbon of the o-hydroxylated trans-hydroxycinnamoyl-CoA substrates during the catalytic cycle of COSY. Quantum mechanical cluster modeling and molecular dynamics further support this key mechanism for lowering the activation energy of the rate-limiting trans-to-cis isomerization step in coumarin production. This study unveils an unconventional catalytic mechanism mediated by a BAHD-family enzyme, and sheds light on COSY's evolutionary origin and its recruitment to coumarin biosynthesis in eudicots.


Subject(s)
Plants , Protons , Isomerism , Plants/metabolism , Acyltransferases/metabolism , Coumarins
18.
Nat Commun ; 14(1): 876, 2023 02 16.
Article in English | MEDLINE | ID: mdl-36797319

ABSTRACT

Grass pea (Lathyrus sativus L.) is a rich source of protein cultivated as an insurance crop in Ethiopia, Eritrea, India, Bangladesh, and Nepal. Its resilience to both drought and flooding makes it a promising crop for ensuring food security in a changing climate. The lack of genetic resources and the crop's association with the disease neurolathyrism have limited the cultivation of grass pea. Here, we present an annotated, long read-based assembly of the 6.5 Gbp L. sativus genome. Using this genome sequence, we have elucidated the biosynthetic pathway leading to the formation of the neurotoxin, ß-L-oxalyl-2,3-diaminopropionic acid (ß-L-ODAP). The final reaction of the pathway depends on an interaction between L. sativus acyl-activating enzyme 3 (LsAAE3) and a BAHD-acyltransferase (LsBOS) that form a metabolon activated by CoA to produce ß-L-ODAP. This provides valuable insight into the best approaches for developing varieties which produce substantially less toxin.


Subject(s)
Amino Acids, Diamino , Lathyrus , Lathyrus/genetics , Lathyrus/metabolism , Amino Acids, Diamino/metabolism , Neurotoxins/metabolism , Genomics
19.
Lung Cancer ; 176: 38-45, 2023 02.
Article in English | MEDLINE | ID: mdl-36592498

ABSTRACT

OBJECTIVES: Using risk models as eligibility criteria for lung screening can reduce race and sex-based disparities. We used data from the International Lung Screening Trial(ILST; NCT02871856) to compare the economic impact of using the PLCOm2012 risk model or the US Preventative Services' categorical age-smoking history-based criteria (USPSTF-2013). MATERIALS AND METHODS: The cost-effectiveness of using PLCOm2012 versus USPSTF-2013 was evaluated with a decision analytic model based on the ILST and other screening trials. The primary outcomes were costs in 2020 International Dollars ($), quality-adjusted life-years (QALY) and incremental net benefit (INB, in $ per QALY). Secondary outcomes were selection characteristics and cancer detection rates (CDR). RESULTS: Compared with the USPSTF-2013 criteria, the PLCOm2012 risk model resulted in $355 of cost savings per 0.2 QALYs gained (INB=$4294 at a willingness-to-pay threshold of $20 000/QALY (95 %CI: $4205-$4383). Using the risk model was more cost-effective in females at both a 1.5 % and 1.7 % 6-year risk threshold (INB=$6616 and $6112, respectively), compared with males ($5221 and $695). The PLCOm2012 model selected more females, more individuals with fewer years of formal education, and more people with other respiratory illnesses in the ILST. The CDR with the risk model was higher in females compared with the USPSTF-2013 criteria (Risk Ratio = 7.67, 95 % CI: 1.87-31.38). CONCLUSION: The PLCOm2012 model saved costs, increased QALYs and mitigated socioeconomic and sex-based disparities in access to screening.


Subject(s)
Lung Neoplasms , Female , Humans , Male , Cost-Benefit Analysis , Early Detection of Cancer/methods , Eligibility Determination , Lung , Lung Neoplasms/diagnosis , Lung Neoplasms/epidemiology , Mass Screening/methods , Quality-Adjusted Life Years
20.
J Org Chem ; 88(1): 513-524, 2023 01 06.
Article in English | MEDLINE | ID: mdl-36545950

ABSTRACT

Herein, the efficient photoredox/nickel dual-catalyzed cyanoalkylation reaction of enamides is illustrated. A wide scope of enamides and cycloketone oxime esters was well-tolerated, affording the synthetically versatile and geometrically defined ß-cyanoalkylated enamide scaffolds. The synthetic practicality of this protocol was revealed by gram-scale reactions, further transformations of enamides, and late-stage modifications of biologically active molecules.


Subject(s)
Amides , Nickel , Molecular Structure , Catalysis
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