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1.
Cell ; 185(18): 3375-3389.e21, 2022 09 01.
Article in English | MEDLINE | ID: mdl-35998627

ABSTRACT

Systemic lupus erythematosus (SLE) is a complex autoimmune disease involving multiple immune cells. To elucidate SLE pathogenesis, it is essential to understand the dysregulated gene expression pattern linked to various clinical statuses with a high cellular resolution. Here, we conducted a large-scale transcriptome study with 6,386 RNA sequencing data covering 27 immune cell types from 136 SLE and 89 healthy donors. We profiled two distinct cell-type-specific transcriptomic signatures: disease-state and disease-activity signatures, reflecting disease establishment and exacerbation, respectively. We then identified candidate biological processes unique to each signature. This study suggested the clinical value of disease-activity signatures, which were associated with organ involvement and therapeutic responses. However, disease-activity signatures were less enriched around SLE risk variants than disease-state signatures, suggesting that current genetic studies may not well capture clinically vital biology. Together, we identified comprehensive gene signatures of SLE, which will provide essential foundations for future genomic and genetic studies.


Subject(s)
Lupus Erythematosus, Systemic , Transcriptome , Humans , Lupus Erythematosus, Systemic/genetics , Sequence Analysis, RNA
2.
Cell ; 184(11): 3006-3021.e17, 2021 05 27.
Article in English | MEDLINE | ID: mdl-33930287

ABSTRACT

Genetic studies have revealed many variant loci that are associated with immune-mediated diseases. To elucidate the disease pathogenesis, it is essential to understand the function of these variants, especially under disease-associated conditions. Here, we performed a large-scale immune cell gene-expression analysis, together with whole-genome sequence analysis. Our dataset consists of 28 distinct immune cell subsets from 337 patients diagnosed with 10 categories of immune-mediated diseases and 79 healthy volunteers. Our dataset captured distinctive gene-expression profiles across immune cell types and diseases. Expression quantitative trait loci (eQTL) analysis revealed dynamic variations of eQTL effects in the context of immunological conditions, as well as cell types. These cell-type-specific and context-dependent eQTLs showed significant enrichment in immune disease-associated genetic variants, and they implicated the disease-relevant cell types, genes, and environment. This atlas deepens our understanding of the immunogenetic functions of disease-associated variants under in vivo disease conditions.


Subject(s)
Gene Expression Regulation/genetics , Gene Expression/immunology , Immune System Diseases/genetics , Adult , Female , Gene Expression/genetics , Gene Expression Regulation/immunology , Genetic Predisposition to Disease/genetics , Genome-Wide Association Study/methods , Humans , Immune System/cytology , Immune System/metabolism , Immune System Diseases/metabolism , Immune System Diseases/physiopathology , Male , Middle Aged , Polymorphism, Single Nucleotide/genetics , Quantitative Trait Loci/genetics , Quantitative Trait Loci/immunology , Transcriptome/genetics , Whole Genome Sequencing/methods
3.
Biochem Biophys Res Commun ; 736: 150491, 2024 Jul 31.
Article in English | MEDLINE | ID: mdl-39142236

ABSTRACT

XRCC8 is a member of the X-ray cross-complementing (XRCC) family, whose responsible gene has not been identified. Previous studies suggested ATM and other genes were potential candidates for XRCC8, but this was not confirmed. In this study, we characterized three V79-derived XRCC8 mutant cells: V-C4, V-E5, and V-G8. Western blot analysis showed reduced expression of the ATM protein in three XRCC8 mutants, and radiation-induced phosphorylated ATM foci were not detected by fluorescence immunocytochemistry. Both ATM knockout cells and XRCC8 mutants exhibited hypersensitivity to camptothecin. Through a cell fusion-based complementation test, we found that XRCC8 mutants were complemented by ATM-proficient cells, but not by ATM knockout cells, in terms of camptothecin sensitivity. Comprehensive sequencing of the ATM genome in XRCC8 mutants revealed unique mutations in each mutant. These results suggest that XRCC8 mutants carry ATM mutations, and their ATM is not properly functional, despite protein expression being detected. This is similar to missense mutations in some Ataxia Telangiectasia patients.

4.
Biochem Biophys Res Commun ; 694: 149386, 2024 01 29.
Article in English | MEDLINE | ID: mdl-38134476

ABSTRACT

Radiation exposure poses a significant threat to cellular integrity by inducing DNA damage through the generation of free radicals and reactive oxygen species. Ascorbic acid, particularly its derivative Palmitoyl Ascorbic Acid 2-Glucoside (PA2G), has demonstrated remarkable radioprotective properties. While previous research focused on its pre-irradiation application, this study explores the post-irradiation radiomitigation potential of PA2G. Our findings reveal that post-irradiation treatment with PA2G enhances cell survival and accelerates DNA repair processes, particularly the non-homologous end-joining (NHEJ) repair pathway. Notably, PA2G treatment reduces the frequency of lethal chromosomal aberrations and micronuclei formation, indicating its ability to enhance the repair of complex DNA lesions. Furthermore, PA2G is shown to play a role in potentially lethal damage repair (PLDR). These radioprotective effects are specific to NHEJ and ATM pathways, as cells deficient in these mechanisms do not benefit from PA2G treatment. This study highlights PA2G as a versatile radioprotector, both pre- and post-irradiation, with significant potential for applications in radiation therapy and protection, offering new insights into its mechanism of action. Further research is required to elucidate the precise molecular mechanisms underlying PA2G's radiomitigation effects and its potential clinical applications.


Subject(s)
DNA Repair , Glucosides , Cell Survival , Glucosides/pharmacology , DNA Damage , Ascorbic Acid/pharmacology , DNA End-Joining Repair
5.
Biochem Biophys Res Commun ; 738: 150517, 2024 Aug 08.
Article in English | MEDLINE | ID: mdl-39146620

ABSTRACT

Here we report that simultaneous inhibition of the three primary DNA damage recognition PI3 kinase-like kinases (PIKKs) -ATM, ATR, and DNA-PK- induces severe combinatorial synthetic lethality in mammalian cells. Utilizing Chinese hamster cell lines CHO and V79 and their respective PIKK mutants, we evaluated effects of inhibiting these three kinases on cell viability, DNA damage response, and chromosomal integrity. Our results demonstrate that while single or dual kinase inhibition increased cytotoxicity, inhibition of all three PIKKs results in significantly higher synergistic lethality, chromosomal aberrations, and DNA double-strand break (DSB) induction as calculated by their synergy scores. These findings suggest that the overlapping redundancy of ATM, ATR, and DNA-PK functions is critical for cell survival, and their combined inhibition greatly disrupts DNA damage signaling and repair processes, leading to cell death. This study provides insights into the potential of multi-targeted DDR kinase inhibition as an effective anticancer strategy, necessitating further research to elucidate underlying mechanisms and therapeutic applications.

6.
Appl Environ Microbiol ; 89(7): e0081223, 2023 07 26.
Article in English | MEDLINE | ID: mdl-37338413

ABSTRACT

Carnivorous pitcher plants are uniquely adapted to nitrogen limitation, using pitfall traps to acquire nutrients from insect prey. Pitcher plants in the genus Sarracenia may also use nitrogen fixed by bacteria inhabiting the aquatic microcosms of their pitchers. Here, we investigated whether species of a convergently evolved pitcher plant genus, Nepenthes, might also use bacterial nitrogen fixation as an alternative strategy for nitrogen capture. First, we constructed predicted metagenomes of pitcher organisms from three species of Singaporean Nepenthes using 16S rRNA sequence data and correlated predicted nifH abundances with metadata. Second, we used gene-specific primers to amplify and quantify the presence or absence of nifH directly from 102 environmental samples and identified potential diazotrophs with significant differential abundance in samples that also had positive nifH PCR tests. Third, we analyzed nifH in eight shotgun metagenomes from four additional Bornean Nepenthes species. Finally, we conducted an acetylene reduction assay using greenhouse-grown Nepenthes pitcher fluids to confirm nitrogen fixation is indeed possible within the pitcher habitat. Results show active acetylene reduction can occur in Nepenthes pitcher fluid. Variation in nifH from wild samples correlates with Nepenthes host species identity and pitcher fluid acidity. Nitrogen-fixing bacteria are associated with more neutral fluid pH, while endogenous Nepenthes digestive enzymes are most active at low fluid pH. We hypothesize Nepenthes species experience a trade-off in nitrogen acquisition; when fluids are acidic, nitrogen is primarily acquired via plant enzymatic degradation of insects, but when fluids are neutral, Nepenthes plants take up more nitrogen via bacterial nitrogen fixation. IMPORTANCE Plants use different strategies to obtain the nutrients that they need to grow. Some plants access their nitrogen directly from the soil, while others rely on microbes to access the nitrogen for them. Carnivorous pitcher plants generally trap and digest insect prey, using plant-derived enzymes to break down insect proteins and generate a large portion of the nitrogen that they subsequently absorb. In this study, we present results suggesting that bacteria living in the fluids formed by Nepenthes pitcher plants can fix nitrogen directly from the atmosphere, providing an alternative pathway for plants to access nitrogen. These nitrogen-fixing bacteria are only likely to be present when pitcher plant fluids are not strongly acidic. Interestingly, the plant's enzymes are known to be more active under strongly acidic conditions. We propose a potential trade-off where pitcher plants sometimes access nitrogen using their own enzymes to digest prey and at other times take advantage of bacterial nitrogen fixation.


Subject(s)
Nitrogen-Fixing Bacteria , Animals , RNA, Ribosomal, 16S/genetics , Insecta , Bacteria/genetics , Nitrogen/analysis , Alkynes
7.
Nucleic Acids Res ; 49(1): e3, 2021 01 11.
Article in English | MEDLINE | ID: mdl-33219668

ABSTRACT

Comparative functional genomics offers a powerful approach to study species evolution. To date, the majority of these studies have focused on the transcriptome in mammalian and yeast phylogenies. Here, we present a novel multi-species proteomic dataset and a computational pipeline to systematically compare the protein levels across multiple plant species. Globally we find that protein levels diverge according to phylogenetic distance but is more constrained than the mRNA level. Module-level comparative analysis of groups of proteins shows that proteins that are more highly expressed tend to be more conserved. To interpret the evolutionary patterns of conservation and divergence, we develop a novel network-based integrative analysis pipeline that combines publicly available transcriptomic datasets to define co-expression modules. Our analysis pipeline can be used to relate the changes in protein levels to different species-specific phenotypic traits. We present a case study with the rhizobia-legume symbiosis process that supports the role of autophagy in this symbiotic association.


Subject(s)
Computational Biology/methods , Gene Regulatory Networks , Plant Proteins/metabolism , Plants/metabolism , Proteome/metabolism , Proteomics/methods , Chromatography, Liquid/methods , Evolution, Molecular , Gene Expression Regulation, Plant , Gene Ontology , Genomics/methods , Phylogeny , Plant Proteins/genetics , Plants/classification , Plants/genetics , Proteome/genetics , Species Specificity , Tandem Mass Spectrometry/methods , Transcriptome/genetics
8.
BMC Biol ; 20(1): 252, 2022 11 09.
Article in English | MEDLINE | ID: mdl-36352404

ABSTRACT

BACKGROUND: Symbiotic associations between bacteria and leguminous plants lead to the formation of root nodules that fix nitrogen needed for sustainable agricultural systems. Symbiosis triggers extensive genome and transcriptome remodeling in the plant, yet an integrated understanding of the extent of chromatin changes and transcriptional networks that functionally regulate gene expression associated with symbiosis remains poorly understood. In particular, analyses of early temporal events driving this symbiosis have only captured correlative relationships between regulators and targets at mRNA level. Here, we characterize changes in transcriptome and chromatin accessibility in the model legume Medicago truncatula, in response to rhizobial signals that trigger the formation of root nodules. RESULTS: We profiled the temporal chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) dynamics of M. truncatula roots treated with bacterial small molecules called lipo-chitooligosaccharides that trigger host symbiotic pathways of nodule development. Using a novel approach, dynamic regulatory module networks, we integrated ATAC-seq and RNA-seq time courses to predict cis-regulatory elements and transcription factors that most significantly contribute to transcriptomic changes associated with symbiosis. Regulators involved in auxin (IAA4-5, SHY2), ethylene (EIN3, ERF1), and abscisic acid (ABI5) hormone response, as well as histone and DNA methylation (IBM1), emerged among those most predictive of transcriptome dynamics. RNAi-based knockdown of EIN3 and ERF1 reduced nodule number in M. truncatula validating the role of these predicted regulators in symbiosis between legumes and rhizobia. CONCLUSIONS: Our transcriptomic and chromatin accessibility datasets provide a valuable resource to understand the gene regulatory programs controlling the early stages of the dynamic process of symbiosis. The regulators identified provide potential targets for future experimental validation, and the engineering of nodulation in species is unable to establish that symbiosis naturally.


Subject(s)
Medicago truncatula , Medicago truncatula/genetics , Medicago truncatula/metabolism , Medicago truncatula/microbiology , Chromatin/genetics , Chromatin/metabolism , Gene Expression Regulation, Plant , Plant Proteins/genetics , Plant Proteins/metabolism , Symbiosis/physiology
9.
Plant Cell ; 31(10): 2386-2410, 2019 10.
Article in English | MEDLINE | ID: mdl-31416823

ABSTRACT

Mycorrhizal fungi form mutualistic associations with the roots of most land plants and provide them with mineral nutrients from the soil in exchange for fixed carbon derived from photosynthesis. The common symbiosis pathway (CSP) is a conserved molecular signaling pathway in all plants capable of associating with arbuscular mycorrhizal fungi. It is required not only for arbuscular mycorrhizal symbiosis but also for rhizobia-legume and actinorhizal symbioses. Given its role in such diverse symbiotic associations, we hypothesized that the CSP also plays a role in ectomycorrhizal associations. We showed that the ectomycorrhizal fungus Laccaria bicolor produces an array of lipochitooligosaccharides (LCOs) that can trigger both root hair branching in legumes and, most importantly, calcium spiking in the host plant Populus in a CASTOR/POLLUX-dependent manner. Nonsulfated LCOs enhanced lateral root development in Populus in a calcium/calmodulin-dependent protein kinase (CCaMK)-dependent manner, and sulfated LCOs enhanced the colonization of Populus by L. bicolor Compared with the wild-type Populus, the colonization of CASTOR/POLLUX and CCaMK RNA interference lines by L. bicolor was reduced. Our work demonstrates that similar to other root symbioses, L. bicolor uses the CSP for the full establishment of its mutualistic association with Populus.


Subject(s)
Calcium Channels/metabolism , Calcium-Calmodulin-Dependent Protein Kinases/metabolism , Calcium/metabolism , Laccaria/metabolism , Lipopolysaccharides/metabolism , Plant Roots/microbiology , Symbiosis/physiology , Calcium-Calmodulin-Dependent Protein Kinases/genetics , Gene Expression Regulation, Plant , Lipopolysaccharides/chemistry , Mycorrhizae/growth & development , Mycorrhizae/metabolism , Mycorrhizae/physiology , Plant Roots/chemistry , Plant Roots/growth & development , Plant Roots/metabolism , Plants, Genetically Modified , Populus/genetics , Populus/metabolism , Signal Transduction
10.
PLoS Biol ; 16(8): e2006352, 2018 08.
Article in English | MEDLINE | ID: mdl-30086128

ABSTRACT

Plants are associated with a complex microbiota that contributes to nutrient acquisition, plant growth, and plant defense. Nitrogen-fixing microbial associations are efficient and well characterized in legumes but are limited in cereals, including maize. We studied an indigenous landrace of maize grown in nitrogen-depleted soils in the Sierra Mixe region of Oaxaca, Mexico. This landrace is characterized by the extensive development of aerial roots that secrete a carbohydrate-rich mucilage. Analysis of the mucilage microbiota indicated that it was enriched in taxa for which many known species are diazotrophic, was enriched for homologs of genes encoding nitrogenase subunits, and harbored active nitrogenase activity as assessed by acetylene reduction and 15N2 incorporation assays. Field experiments in Sierra Mixe using 15N natural abundance or 15N-enrichment assessments over 5 years indicated that atmospheric nitrogen fixation contributed 29%-82% of the nitrogen nutrition of Sierra Mixe maize.


Subject(s)
Microbiota/genetics , Nitrogen Fixation/physiology , Nitrogen/metabolism , Zea mays/metabolism , Mexico , Microbiota/physiology , Phylogeny , Plant Development , Plant Mucilage/metabolism , Plant Roots/metabolism , Polysaccharides/metabolism , Soil , Soil Microbiology
11.
Nature ; 509(7500): 376-80, 2014 May 15.
Article in English | MEDLINE | ID: mdl-24670657

ABSTRACT

Lignin is a phenylpropanoid-derived heteropolymer important for the strength and rigidity of the plant secondary cell wall. Genetic disruption of lignin biosynthesis has been proposed as a means to improve forage and bioenergy crops, but frequently results in stunted growth and developmental abnormalities, the mechanisms of which are poorly understood. Here we show that the phenotype of a lignin-deficient Arabidopsis mutant is dependent on the transcriptional co-regulatory complex, Mediator. Disruption of the Mediator complex subunits MED5a (also known as REF4) and MED5b (also known as RFR1) rescues the stunted growth, lignin deficiency and widespread changes in gene expression seen in the phenylpropanoid pathway mutant ref8, without restoring the synthesis of guaiacyl and syringyl lignin subunits. Cell walls of rescued med5a/5b ref8 plants instead contain a novel lignin consisting almost exclusively of p-hydroxyphenyl lignin subunits, and moreover exhibit substantially facilitated polysaccharide saccharification. These results demonstrate that guaiacyl and syringyl lignin subunits are largely dispensable for normal growth and development, implicate Mediator in an active transcriptional process responsible for dwarfing and inhibition of lignin biosynthesis, and suggest that the transcription machinery and signalling pathways responding to cell wall defects may be important targets to include in efforts to reduce biomass recalcitrance.


Subject(s)
Arabidopsis Proteins/genetics , Arabidopsis/growth & development , Arabidopsis/genetics , Lignin/metabolism , Mediator Complex/genetics , Mutation/genetics , Arabidopsis/metabolism , Arabidopsis Proteins/metabolism , Biofuels , Biomass , Cell Wall/chemistry , Cell Wall/metabolism , Cellulose/metabolism , Gene Expression Regulation, Plant/genetics , Lignin/biosynthesis , Lignin/chemistry , Mediator Complex/chemistry , Mediator Complex/deficiency , Mediator Complex/metabolism , Phenotype , Plants, Genetically Modified , Protein Subunits/genetics , Protein Subunits/metabolism , Transcription, Genetic/genetics
12.
Int J Mol Sci ; 21(18)2020 Sep 10.
Article in English | MEDLINE | ID: mdl-32927807

ABSTRACT

BrdU (bromodeoxyuridine) and EdU (ethynyldeoxyuridine) have been largely utilized as the means of monitoring DNA replication and cellular division. Although BrdU induces gene and chromosomal mutations and induces sensitization to photons, EdU's effects have not been extensively studied yet. Therefore, we investigated EdU's potential cytotoxic and mutagenic effects and its related underlying mechanisms when administered to Chinese hamster ovary (CHO) wild type and DNA repair-deficient cells. EdU treatment displayed a higher cytotoxicity and genotoxicity than BrdU treatment. Cells with defective homologous recombination repair displayed a greater growth delay and severe inhibition of clonogenicity with EdU compared to wild type and other DNA repair-deficient cells. Inductions of sister chromatid exchange and hypoxanthine phosphorybosyl transferase (HPRT) mutation were observed in EdU-incorporated cells as well. Interestingly, on the other hand, EdU did not induce sensitization to photons to the same degree as BrdU. Our results demonstrate that elevated concentrations (similar to manufacturers suggested concentration; >5-10 µM) of EdU treatment were toxic to the cell cultures, particularly in cells with a defect in homologous recombination repair. Therefore, EdU should be administered with additional precautions.


Subject(s)
Deoxyuridine/analogs & derivatives , A549 Cells , Animals , Bromodeoxyuridine , CHO Cells , Cricetulus , DNA Repair , Deoxyuridine/toxicity , Genes, BRCA2 , Humans , Mutagenicity Tests
13.
Plant Cell Physiol ; 60(3): 575-586, 2019 03 01.
Article in English | MEDLINE | ID: mdl-30476329

ABSTRACT

Signals and signaling pathways underlying the symbiosis between legumes and rhizobia have been studied extensively over the past decades. In a previous phosphoproteomic study on the Medicago truncatula-Sinorhizobium meliloti symbiosis, we identified plant proteins that are differentially phosphorylated upon the perception of rhizobial signals, called Nod factors. In this study, we provide experimental evidence that one of these proteins, Early Phosphorylated Protein 1 (EPP1), is required for the initiation of this symbiosis. Upon inoculation with rhizobia, MtEPP1 expression was induced in curled root hairs. Down-regulation of MtEPP1 in M. truncatula roots almost abolished calcium spiking, reduced the expression of essential symbiosis-related genes (MtNIN, MtNF-YB1, MtERN1 and MtENOD40) and strongly decreased nodule development. Phylogenetic analyses revealed that orthologs of MtEPP1 are present in legumes and specifically in plant species able to host arbuscular mycorrhizal fungi, suggesting a possible role in this association too. Short chitin oligomers induced the phosphorylation of MtEPP1 like Nod factors. However, the down-regulation of MtEPP1 affected the colonization of M. truncatula roots by arbuscular mycorrhizal fungi only moderately. Altogether, these findings indicate that MtEPP1 is essential for the establishment of the legume-rhizobia symbiosis but might plays a limited role in the arbuscular mycorrhizal symbiosis.


Subject(s)
Medicago truncatula/metabolism , Plant Proteins/metabolism , Root Nodules, Plant/metabolism , Gene Expression Regulation, Plant/genetics , Gene Expression Regulation, Plant/physiology , Plant Proteins/genetics , Root Nodules, Plant/genetics , Symbiosis/genetics , Symbiosis/physiology
14.
Proc Natl Acad Sci U S A ; 112(31): 9781-6, 2015 Aug 04.
Article in English | MEDLINE | ID: mdl-26199419

ABSTRACT

Rhizobia and arbuscular mycorrhizal fungi produce signals that are perceived by host legume receptors at the plasma membrane and trigger sustained oscillations of the nuclear and perinuclear Ca(2+) concentration (Ca(2+) spiking), which in turn leads to gene expression and downstream symbiotic responses. The activation of Ca(2+) spiking requires the plasma membrane-localized receptor-like kinase Does not Make Infections 2 (DMI2) as well as the nuclear cation channel DMI1. A key enzyme regulating the mevalonate (MVA) pathway, 3-Hydroxy-3-Methylglutaryl CoA Reductase 1 (HMGR1), interacts with DMI2 and is required for the legume-rhizobium symbiosis. Here, we show that HMGR1 is required to initiate Ca(2+) spiking and symbiotic gene expression in Medicago truncatula roots in response to rhizobial and arbuscular mycorrhizal fungal signals. Furthermore, MVA, the direct product of HMGR1 activity, is sufficient to induce nuclear-associated Ca(2+) spiking and symbiotic gene expression in both wild-type plants and dmi2 mutants, but interestingly not in dmi1 mutants. Finally, MVA induced Ca(2+) spiking in Human Embryonic Kidney 293 cells expressing DMI1. This demonstrates that the nuclear cation channel DMI1 is sufficient to support MVA-induced Ca(2+) spiking in this heterologous system.


Subject(s)
Metabolic Networks and Pathways , Mevalonic Acid/metabolism , Signal Transduction , Symbiosis , Arabidopsis/genetics , Calcium Signaling/drug effects , Calcium Signaling/genetics , Cell Nucleus/drug effects , Cell Nucleus/metabolism , Gene Expression Regulation, Plant/drug effects , Gene Silencing/drug effects , HEK293 Cells , Humans , Hydroxymethylglutaryl CoA Reductases/metabolism , Medicago truncatula/drug effects , Medicago truncatula/genetics , Medicago truncatula/microbiology , Metabolic Networks and Pathways/drug effects , Mevalonic Acid/pharmacology , Mutation/genetics , Mycorrhizae/drug effects , Mycorrhizae/physiology , Plant Epidermis/cytology , Plant Epidermis/drug effects , Plant Proteins/metabolism , Plants, Genetically Modified , Signal Transduction/drug effects , Symbiosis/drug effects , Symbiosis/genetics
15.
Int J Mol Sci ; 19(2)2018 Feb 07.
Article in English | MEDLINE | ID: mdl-29414878

ABSTRACT

Suberoylanilide hydroxamic acid (SAHA) is a histone deacetylase inhibitor, which has been widely utilized throughout the cancer research field. SAHA-induced radiosensitization in normal human fibroblasts AG1522 and lung carcinoma cells A549 were evaluated with a combination of γ-rays, proton, and carbon ion exposure. Growth delay was observed in both cell lines during SAHA treatment; 2 µM SAHA treatment decreased clonogenicity and induced cell cycle block in G1 phase but 0.2 µM SAHA treatment did not show either of them. Low LET (Linear Energy Transfer) irradiated A549 cells showed radiosensitization effects on cell killing in cycling and G1 phase with 0.2 or 2 µM SAHA pretreatment. In contrast, minimal sensitization was observed in normal human cells after low and high LET radiation exposure. The potentially lethal damage repair was not affected by SAHA treatment. SAHA treatment reduced the rate of γ-H2AX foci disappearance and suppressed RAD51 and RPA (Replication Protein A) focus formation. Suppression of DNA double strand break repair by SAHA did not result in the differences of SAHA-induced radiosensitization between human cancer cells and normal cells. In conclusion, our results suggest SAHA treatment will sensitize cancer cells to low and high LET radiation with minimum effects to normal cells.


Subject(s)
Histone Deacetylase Inhibitors/pharmacology , Hydroxamic Acids/pharmacology , Neoplasms/radiotherapy , Radiation-Sensitizing Agents/pharmacology , A549 Cells , Biomarkers, Tumor/analysis , Cell Cycle/drug effects , Cell Proliferation/drug effects , Cell Survival/drug effects , DNA Breaks, Double-Stranded/drug effects , DNA Repair/drug effects , Elementary Particles/therapeutic use , Fibroblasts/drug effects , Gamma Rays/therapeutic use , Histone Deacetylase Inhibitors/adverse effects , Humans , Hydroxamic Acids/adverse effects , Photons/therapeutic use , Radiation-Sensitizing Agents/adverse effects , Vorinostat
16.
J Stroke Cerebrovasc Dis ; 26(3): 480-487, 2017 Mar.
Article in English | MEDLINE | ID: mdl-28041902

ABSTRACT

OBJECTIVE: Early rehabilitation for acute stroke patients is widely recommended. We tested the hypothesis that daily intervention by speech therapists promotes safe oral intake of patients with acute stroke. METHODS: We analyzed hospitalized patients who experienced cerebral infarction and cerebral hemorrhage and who underwent rehabilitation between October 2010 and September 2014 at our hospital. In total, 936 patients were analyzed, and 452 patients underwent daily speech therapy. We examined the association of training frequency and eating status. RESULTS: Multiple linear regression analysis indicated that daily speech therapy was correlated significantly and positively with a reduction in the number of days of hospitalization until oral intake commenced (coefficient, -.998; 95% confidence interval, -1.793 to -.202; P < .05), and was not correlated with the cessation of oral intake due to aspiration pneumonia after resuming oral intake. CONCLUSION: Our retrospective cohort study demonstrated that daily intervention by speech therapists in patients with acute stroke shortens the number of days until oral intake without increasing the incidence of aspiration pneumonia.


Subject(s)
Eating , Speech Therapy , Stroke/complications , Aged , Aged, 80 and over , Cohort Studies , Female , Humans , Male , Middle Aged , Outcome Assessment, Health Care , Pneumonia, Aspiration/etiology , Regression Analysis , Stroke Rehabilitation
17.
J Proteome Res ; 15(12): 4403-4411, 2016 12 02.
Article in English | MEDLINE | ID: mdl-27726374

ABSTRACT

Plant science is an important, rapidly developing area of study. Within plant science, one area of study that has grown tremendously with recent technological advances, such as mass spectrometry, is the field of plant-omics; however, plant peptidomics is relatively underdeveloped in comparison with proteomics and metabolomics. Endogenous plant peptides can act as signaling molecules and have been shown to affect cell division, development, nodulation, reproduction, symbiotic associations, and defense reactions. There is a growing need to uncover the role of endogenous peptides on a molecular level. Mass spectrometric imaging (MSI) is a valuable tool for biological analyses as it allows for the detection of thousands of analytes in a single experiment and also displays spatial information for the detected analytes. Despite the prediction of a large number of plant peptides, their detection and imaging with spatial localization and chemical specificity is currently lacking. Here we analyzed the endogenous peptides and proteins in Medicago truncatula using matrix-assisted laser desorption/ionization (MALDI)-MSI. Hundreds of endogenous peptides and protein fragments were imaged, with interesting peptide spatial distribution changes observed between plants in different developmental stages.


Subject(s)
Mass Spectrometry/methods , Medicago truncatula/chemistry , Molecular Imaging/methods , Peptides/analysis , Molecular Imaging/instrumentation , Proteins/analysis , Psychosexual Development , Spatial Analysis , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
18.
Rinsho Byori ; 63(6): 694-9, 2015 Jun.
Article in Japanese | MEDLINE | ID: mdl-26548233

ABSTRACT

We examined how doctors evaluate the results of C. DIFF QUIK CHEK COMPLETE (COMPLETE) in the diagnosis and treatment of Clostridium difficile infection (CDI). A total of 887 stool samples submitted from 2012 to 2013 were examined with COMPLETE. Requested specimens among samples with discrepant results were inoculated onto CCMA plates and incubated under anaerobic conditions for 48 h, then retested by COMPLETE if positive culture results were obtained. Of the 887 specimens, 198 (22.3%) were glutamate dehydrogenase-positive and 73(8.3%) were toxin-positive. Of the 125 specimens yielding discrepant results, 106 specimens were cultured and retested, with 46 (43.4%, 46/106) proving toxin-positive. As a result, the total number of toxin-positive results increased from 73 (8.3%, 73/887) to 119 (13.4%, 119/887). This change was significant (p<0.01). We analyzed the relationship between doctor's decision-making and timing of receiving CD test results in 81 specimens among the discrepant results. Twenty-four patients started treatment just after obtaining the first test result (29.6%, 24/81) and the toxin-positive ratio of the second test was 62.5% (15/24). The decision to start treatment was made after obtaining results of the second test in 48 patients, of whom 13 (16.0%, 13/81) started treatment, and the toxin-positive ratio was 37.5% (18/48). The difference in toxin ratio was significant (p < 0.05). The increase in toxin-positive ratio in the final report facilitates diagnosis in patients with CDL Many doctors, however, started treatment before obtaining results from the second test, suggesting that the 3-day delay in report results represents a drawback for this system.


Subject(s)
Bacterial Toxins/analysis , Clostridioides difficile , Clostridium Infections/diagnosis , Clostridium Infections/drug therapy , Glutamate Dehydrogenase/analysis , Antigens, Bacterial/analysis , Humans , Immunoenzyme Techniques/methods
19.
Mol Cell Proteomics ; 11(9): 724-44, 2012 Sep.
Article in English | MEDLINE | ID: mdl-22683509

ABSTRACT

Symbiotic associations between legumes and rhizobia usually commence with the perception of bacterial lipochitooligosaccharides, known as Nod factors (NF), which triggers rapid cellular and molecular responses in host plants. We report here deep untargeted tandem mass spectrometry-based measurements of rapid NF-induced changes in the phosphorylation status of 13,506 phosphosites in 7739 proteins from the model legume Medicago truncatula. To place these phosphorylation changes within a biological context, quantitative phosphoproteomic and RNA measurements in wild-type plants were compared with those observed in mutants, one defective in NF perception (nfp) and one defective in downstream signal transduction events (dmi3). Our study quantified the early phosphorylation and transcription dynamics that are specifically associated with NF-signaling, confirmed a dmi3-mediated feedback loop in the pathway, and suggested "cryptic" NF-signaling pathways, some of them being also involved in the response to symbiotic arbuscular mycorrhizal fungi.


Subject(s)
Lipopolysaccharides/metabolism , Medicago truncatula/metabolism , Medicago truncatula/microbiology , Mycorrhizae/metabolism , Phosphoproteins/metabolism , Plant Proteins/metabolism , Sinorhizobium meliloti/metabolism , Symbiosis , Medicago truncatula/genetics , Phosphorylation , Rhizobium/metabolism , Signal Transduction/genetics , Sinorhizobium meliloti/genetics , Tandem Mass Spectrometry , Transcriptome
20.
Am J Emerg Med ; 32(7): 812.e1-3, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24440590

ABSTRACT

Anaerobiospirillum succiniciproducens is rarely associated with bacteremia but results in significant mortality. Almost all reported bacteremia cases have occurred in immunocompromised hosts, such as those with alcoholic liver disease, atherosclerosis, recent surgery, malignancies, or acquired immunodeficiency syndrome. We describe here, to our knowledge, the first clinical evidence for A succiniciproducens bacteremia in a healthy man. A 61-year-old man had fallen from a roof and was admitted to our emergency department with severe left flank pain without an external wound. He was given transcatheter arterial embolization for the left kidney injury on the same day, and his condition stabilized. Four days after admission, he had fever without gastrointestinal signs and symptoms. Spiral-shaped, gram-negative anaerobic bacteria were isolated from 2 sets of blood cultures, and the oxidase and catalase test results were negative. The isolated bacteria were different from the Campylobacter spp. On the next day, the bacteria were confirmed as A succiniciproducens by 16S rRNA sequencing. The patient responded to sulbactam/ampicillin. On day 13, the patient was discharged with a 7-day prescription for oral amoxicillin/clavulanate. Six months after admission, the patient was free of recurrent infection. A succiniciproducens bacteremia can occur in healthy adults. When large gram-negative spiral-shaped bacteria are detected, this bacterial species should be considered and differentiated from the Campylobacter spp because A succiniciproducens is often resistant to macrolide antibiotics.


Subject(s)
Anaerobiospirillum/genetics , Bacteremia/microbiology , Gram-Negative Bacterial Infections/microbiology , Immunocompetence , RNA, Bacterial/analysis , RNA, Ribosomal, 16S/analysis , Ampicillin/therapeutic use , Anti-Bacterial Agents/therapeutic use , Bacteremia/diagnosis , Bacteremia/drug therapy , Gram-Negative Bacterial Infections/diagnosis , Gram-Negative Bacterial Infections/drug therapy , Humans , Male , Middle Aged , Sulbactam/therapeutic use
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