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1.
J Environ Manage ; 354: 120456, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38412731

ABSTRACT

The inhibiting effects of ciprofloxacin (CIP) on enhanced biological phosphorus removal (EBPR) were investigated with no change in reactor operation and with increased aeration rate and sludge retention time (SRT) to explore inhibition-alleviating solutions. Additionally, performance recoverability was evaluated. The results showed that the phosphorus removal efficiency in the presence of 0.002-0.092 mg/L CIP for 7 days was only 12.5%. Increasing the aeration rate relieved inhibition (33.5% phosphorus removal efficiency on Day 7), and increasing SRT slowed EBPR performance deterioration. The EBPR performance recovered from CIP inhibition and increases in the aeration rate and SRT resulted in different recovery phenomena. The maximum PO43--P release rate continued to decrease in the first 2 days of the recovery stage and then gradually increased. However, the maximum PO43--P uptake rate immediately increased at different rates among reactors, which might be attributed to variations in the microbial community structure, decreased poly-P content, and enhanced abundances of ABC transporters and quorum sensing. It was found that some microorganisms associated with phosphorus removal were more tolerant to CIP than glycogen accumulating organisms. Moreover, the increased relative abundance of the qepA gene indicated that the microorganisms in the EBPR system had strong antibiotic resistance capacity. The bacterial community structure was significantly affected by CIP and could not recover to the initial structure. The results help to provide technical support for the operation of the EBPR process in the presence of CIP and to increase the understanding of system recoverability.


Subject(s)
Ciprofloxacin , Phosphorus Radioisotopes , Wastewater , Ciprofloxacin/pharmacology , Phosphorus , Bioreactors/microbiology , Sewage
2.
RNA ; 27(9): 1017-1024, 2021 09.
Article in English | MEDLINE | ID: mdl-34131025

ABSTRACT

Connections between distinct catalytic RNA motifs through networks of mutations that retain catalytic function (neutral networks) were likely central to the evolution of biocatalysis. Despite suggestions that functional RNAs collectively form an interconnected web of neutral networks, little evidence has emerged to demonstrate the existence of such intersecting networks in naturally occurring RNAs. Here we show that neutral networks of two naturally occurring, seemingly unrelated endonucleolytic ribozymes, the hammerhead (HH) and hairpin (HP), intersect. Sequences at the intersection of these networks exhibit catalytic functions corresponding to both ribozymes by potentially populating both catalytic folds and enable a smooth crossover between the two. Small and structurally simple endonucleolytic motifs like the HH ribozyme could, through mutational walks along their neutral networks, encounter novel catalytic phenotypes, and structurally flexible, bifunctional sequences at the intersection of these networks could have acted as nodes for evolutionary diversification in an RNA world. Considering the simplicity and small size of the HH ribozyme, we propose that this self-cleaving motif could have been a precursor to other more complex endonucleolytic ribozymes. More generally, our results suggest that RNAs that possess distinct sequences, structures, and catalytic functions, can potentially share evolutionary history through mutational connections in sequence space.


Subject(s)
DNA/genetics , Inverted Repeat Sequences , RNA, Catalytic/metabolism , Transcription, Genetic , Base Pairing , Biocatalysis , Cell-Free System , DNA/metabolism , DNA-Directed RNA Polymerases/genetics , DNA-Directed RNA Polymerases/metabolism , Nucleic Acid Conformation , Nucleotide Motifs , Phosphorus Radioisotopes , Point Mutation , RNA, Catalytic/chemistry , RNA, Catalytic/genetics , Viral Proteins/genetics , Viral Proteins/metabolism
3.
Endoscopy ; 54(1): 75-80, 2022 01.
Article in English | MEDLINE | ID: mdl-33440437

ABSTRACT

BACKGROUND: This study evaluated clinical outcomes of combined chemotherapy and endoscopic ultrasound (EUS)-guided intratumoral radioactive phosphorus-32 (32P) implantation in locally advanced pancreatic adenocarcinoma (LAPC). METHODS: Consecutive patients with newly diagnosed LAPC were recruited over 20 months. Baseline computed tomography and 18F-2-fluoro-2-deoxy-D-glucose (18FDG) positron emission tomography-computed tomography were performed and repeated after 12 weeks to assess treatment response. Following two cycles of conventional chemotherapy, patients underwent EUS-guided 32P implantation followed by six chemotherapy cycles. RESULTS: 12 patients with LAPC (median age 69 years [interquartile range 61.5-73.3]; 8 male) completed treatment. Technical success was 100 % with no procedural complications. At 12 weeks, median reduction in tumor volume was 8.2 cm3 (95 % confidence interval 4.95-10.85; P = 0.003), with minimal or no 18FDG uptake in nine patients (75 %). Tumor downstaging was achieved in six patients (50 %), leading to successful resection in five (42 %), including four R0 resections (80 %). CONCLUSIONS: EUS-guided 32P implantation was feasible, well tolerated, and resulted in a 42 % surgical resection rate. Further evaluation in a larger randomized multicenter trial is warranted.


Subject(s)
Adenocarcinoma , Pancreatic Neoplasms , Adenocarcinoma/diagnostic imaging , Adenocarcinoma/therapy , Aged , Antineoplastic Combined Chemotherapy Protocols , Humans , Male , Pancreatic Neoplasms/diagnostic imaging , Pancreatic Neoplasms/drug therapy , Phosphorus Radioisotopes , Pilot Projects , Ultrasonography, Interventional
4.
J Am Soc Nephrol ; 32(8): 2057-2069, 2021 08.
Article in English | MEDLINE | ID: mdl-34244325

ABSTRACT

BACKGROUND: Reducing intestinal phosphorus absorption is a cornerstone in CKD-MBD management. Yet, knowledge gaps include how CKD pathophysiology affects intestinal phosphorus absorption. In vivo rodent studies suggest that intestinal phosphorus absorption remains inappropriately normal in early-moderate CKD, despite declining 1,25-dihydroxyvitamin D (1,25D). We measured intestinal phosphorus absorption in patients with moderate CKD versus healthy adults using a direct radiotracer method. METHODS: Patients with CKD and healthy adults matched for age, sex, and race were enrolled in this 8-day controlled diet study: the first 6 days outpatient and the final 2 days inpatient. Oral and intravenous doses of 33P and serial blood and urine sampling determined intestinal phosphorus absorption during the final 2 days. Secondary outcomes included fasting biochemistries and 24-hour urine phosphorus (uP). RESULTS: In total, n=8 patients with CKD (eGFR=29-55 ml/min per 1.73 m2) and n=8 matched healthy controls completed the study. On a controlled diet, no difference in fractional intestinal phosphorus absorption was detected between patients with CKD and healthy adults (0.69 versus 0.62, respectively; P=0.52), and this was similar for 24-hour uP (884 versus 935 mg/d, respectively; P=0.70). Fractional intestinal phosphorus absorption was not significantly related to 24-hour uP. Patients with CKD had higher serum intact PTH and intact FGF23 and lower 1,25D. The relationship between 1,25D and fractional intestinal phosphorus absorption was not statistically significant. CONCLUSIONS: Intestinal phosphorus absorption with typical dietary intake did not differ in patients with moderate CKD compared with controls, despite lower serum 1,25D levels. In this setting, a relationship between 24-hour uP and fractional or absolute intestinal absorption was not evident. Further investigation is needed to determine what factors influence intestinal phosphorus absorption in CKD and the apparent lack of compensation by the intestine to limit phosphorus absorption in the face of declining kidney function and reduced 1,25D. Whether this is evident across a range of dietary phosphorus intakes, as well as CKD severity, also needs to be determined. CLINICAL TRIAL REGISTRY NAME AND REGISTRATION NUMBER: Phosphorus Absorption in Healthy Adults and in Patients with Moderate Chronic Kidney Disease, NCT03108222.


Subject(s)
Intestinal Absorption , Phosphorus/metabolism , Renal Insufficiency, Chronic/physiopathology , Adult , Aged , Case-Control Studies , Female , Fibroblast Growth Factor-23 , Fibroblast Growth Factors/blood , Glomerular Filtration Rate , Humans , Male , Middle Aged , Parathyroid Hormone/blood , Phosphorus/urine , Phosphorus Radioisotopes , Radioactive Tracers , Renal Insufficiency, Chronic/blood , Vitamin D/analogs & derivatives , Vitamin D/blood
5.
Rapid Commun Mass Spectrom ; 35(13): e9095, 2021 Jul 15.
Article in English | MEDLINE | ID: mdl-33821547

ABSTRACT

RATIONALE: As a new approach to DNA adductomics, we directly reacted intact, double-stranded (ds)-DNA under warm conditions with an alkylating mass tag followed by analysis by liquid chromatography/mass spectrometry. This method is based on the tendency of adducted nucleobases to locally disrupt the DNA structure (forming a "DNA bubble") potentially increasing exposure of their nucleophilic (including active hydrogen) sites for preferential alkylation. Also encouraging this strategy is that the scope of nucleotide excision repair is very broad, and this system primarily recognizes DNA bubbles. METHODS: A cationic xylyl (CAX) mass tag with limited nonpolarity was selected to increase the retention of polar adducts in reversed-phase high-performance liquid chromatography (HPLC) for more detectability while maintaining resolution. We thereby detected a diversity of DNA adducts (mostly polar) by the following sequence of steps: (1) react DNA at 45°C for 2 h under aqueous conditions with CAX-B (has a benzyl bromide functional group to label active hydrogen sites) in the presence of triethylamine; (2) remove residual reagents by precipitating and washing the DNA (a convenient step); (3) digest the DNA enzymatically to nucleotides and remove unlabeled nucleotides by nonpolar solid-phase extraction (also a convenient step); and (4) detect CAX-labeled, adducted nucleotides by LC/MS2 or a matrix-assisted laser desorption/ionization (MALDI)-MS technique. RESULTS: Examples of the 42 DNA or RNA adducts detected, or tentatively so based on accurate mass and fragmentation data, are as follows: 8-oxo-dGMP, ethyl-dGMP, hydroxyethyl-dGMP (four isomers, all HPLC-resolved), uracil-glycol, apurinic/apyrimidinic sites, benzo[a]pyrene-dGMP, and, for the first time, benzoquinone-hydroxymethyl-dCMP. Importantly, these adducts are detected in a single procedure under a single set of conditions. Sensitivity, however, is only defined in a preliminary way, namely the latter adduct seems to be detected at a level of about 4 adducts in 109 nucleotides (S/N ~30). CONCLUSIONS: CAX-Prelabeling is an emerging new technique for DNA adductomics, providing polar DNA adductomics in a practical way for the first time. Further study of the method is encouraged to better characterize and extend its performance, especially in scope and sensitivity.


Subject(s)
DNA Adducts/analysis , Animals , Benzo(a)pyrene/analysis , Benzyl Compounds , Cations , Cattle , Chromatography, High Pressure Liquid , DNA Adducts/chemistry , DNA Adducts/metabolism , Ethylamines , Guanine/analogs & derivatives , Guanine/analysis , Humans , Nucleotides/metabolism , Phosphorus Radioisotopes , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Uracil/analogs & derivatives , Uracil/analysis
6.
RNA Biol ; 18(sup2): 623-639, 2021 11 12.
Article in English | MEDLINE | ID: mdl-34766865

ABSTRACT

Despite the development of non-radioactive DNA/RNA labelling methods, radiolabelled nucleic acids are commonly used in studies focused on the determination of RNA fate. Nucleic acid fragments with radioactive nucleotide analoguesincorporated into the body or at the 5' or 3' terminus of the molecule can serve as probes in hybridization-based analyses of in vivo degradation and processing of transcripts. Radiolabelled oligoribonucleotides are utilized as substrates in biochemical assays of various RNA metabolic enzymes, such as exo- and endoribonucleases, nucleotidyltransferases or helicases. In some applications, the placement of the label is not a concern, while in other cases it is required that the radioactive mark is located at the 5'- or 3'-end of the molecule. An unsurpassed method for 5'-end RNA labelling employs T4 polynucleotide kinase (PNK) and [γ-32P]ATP. In the case of 3'-end labelling, several different possibilities exist. However, they require the use of costly radionucleotide analogues. Previously, we characterized an untypical nucleotidyltransferase named CutA, which preferentially incorporates cytidines at the 3'-end of RNA substrates. Here, we demonstrate that this unusual feature can be used for the development of a novel, efficient, reproducible and economical method of RNA 3'-end labelling by CutA-mediated cytidine tailing. The labelling efficiency is comparable to that achieved with the most common method applied to date, i.e. [5'-32P]pCp ligation to the RNA 3'-terminus catalysed by T4 RNA ligase I. We show the utility of RNA substrates labelled using our new method in exemplary biochemical assays assessing directionality of two well-known eukaryotic exoribonucleases, namely Dis3 and Xrn1.


Subject(s)
Nucleotidyltransferases/chemistry , RNA/chemistry , Staining and Labeling/methods , Cytidine Triphosphate/chemistry , In Vitro Techniques , Isotope Labeling/methods , Nucleotides/chemistry , Phosphorus Radioisotopes , RNA/genetics , RNA Ligase (ATP)/chemistry , Staining and Labeling/standards , Substrate Specificity , Uridine Triphosphate/chemistry
7.
Biochem J ; 477(14): 2621-2638, 2020 07 31.
Article in English | MEDLINE | ID: mdl-32706850

ABSTRACT

Inositol polyphosphates are ubiquitous molecular signals in metazoans, as are their pyrophosphorylated derivatives that bear a so-called 'high-energy' phosphoanhydride bond. A structural rationale is provided for the ability of Arabidopsis inositol tris/tetrakisphosphate kinase 1 to discriminate between symmetric and enantiomeric substrates in the production of diverse symmetric and asymmetric myo-inositol phosphate and diphospho-myo-inositol phosphate (inositol pyrophosphate) products. Simple tools are applied to chromatographic resolution and detection of known and novel diphosphoinositol phosphates without resort to radiolabeling approaches. It is shown that inositol tris/tetrakisphosphate kinase 1 and inositol pentakisphosphate 2-kinase comprise a reversible metabolic cassette converting Ins(3,4,5,6)P4 into 5-InsP7 and back in a nucleotide-dependent manner. Thus, inositol tris/tetrakisphosphate kinase 1 is a nexus of bioenergetics status and inositol polyphosphate/diphosphoinositol phosphate metabolism. As such, it commands a role in plants that evolution has assigned to a different class of enzyme in mammalian cells. The findings and the methods described will enable a full appraisal of the role of diphosphoinositol phosphates in plants and particularly the relative contribution of reversible inositol phosphate hydroxykinase and inositol phosphate phosphokinase activities to plant physiology.


Subject(s)
Arabidopsis Proteins/metabolism , Arabidopsis/metabolism , Inositol Phosphates/metabolism , Phosphotransferases (Alcohol Group Acceptor)/metabolism , Adenosine Triphosphate/metabolism , Arabidopsis/genetics , Arabidopsis Proteins/genetics , Chromatography, High Pressure Liquid , Chromatography, Ion Exchange/methods , Inositol Phosphates/analysis , Mesylates/chemistry , Mutation , Phosphorus Radioisotopes , Phosphorylation , Phosphotransferases (Alcohol Group Acceptor)/chemistry , Phosphotransferases (Alcohol Group Acceptor)/genetics , Substrate Specificity
8.
Article in English | MEDLINE | ID: mdl-31964798

ABSTRACT

Alphaviruses are arthropod-borne, positive-stranded RNA viruses capable of causing severe disease with high morbidity. Chikungunya virus (CHIKV) is an alphavirus that causes a febrile illness which can progress into chronic arthralgia. The current lack of vaccines and specific treatment for CHIKV infection underscores the need to develop new therapeutic interventions. To discover new antiviral agents, we performed a compound screen in cell culture-based infection models and identified two carbocyclic adenosine analogues, 6'-ß-fluoro-homoaristeromycin (FHA) and 6'-fluoro-homoneplanocin A (FHNA), that displayed potent activity against CHIKV and Semliki Forest virus (SFV) with 50% effective concentrations in the nanomolar range at nontoxic concentrations. The compounds, designed as inhibitors of the host enzyme S-adenosylhomocysteine (SAH) hydrolase, impeded postentry steps in CHIKV and SFV replication. Selection of FHNA-resistant mutants and reverse genetics studies demonstrated that the combination of mutations G230R and K299E in CHIKV nonstructural protein 1 (nsP1) conferred resistance to the compounds. Enzymatic assays with purified wild-type (wt) SFV nsP1 suggested that an oxidized (3'-keto) form, rather than FHNA itself, directly inhibited the MTase activity, while a mutant protein with the K231R and K299E substitutions was insensitive to the compound. Both wt nsP1 and the resistant mutant were equally sensitive to the inhibitory effect of SAH. Our combined data suggest that FHA and FHNA inhibit CHIKV and SFV replication by directly targeting the MTase activity of nsP1, rather than through an indirect effect on host SAH hydrolase. The high potency and selectivity of these novel alphavirus mRNA capping inhibitors warrant further preclinical investigation of these compounds.


Subject(s)
Adenosine/analogs & derivatives , Antiviral Agents/pharmacology , Chikungunya virus/drug effects , Chikungunya virus/physiology , Adenosine/pharmacology , Animals , Chikungunya virus/pathogenicity , Chlorocebus aethiops , Dose-Response Relationship, Drug , Drug Evaluation, Preclinical , Drug Resistance, Viral/drug effects , Drug Resistance, Viral/genetics , Guanosine Monophosphate/metabolism , Mutation , Phosphorus Radioisotopes , Semliki forest virus/drug effects , Vero Cells , Viral Nonstructural Proteins/antagonists & inhibitors , Viral Nonstructural Proteins/genetics , Viral Nonstructural Proteins/metabolism , Virus Replication/drug effects
9.
Methods ; 156: 102-109, 2019 03 01.
Article in English | MEDLINE | ID: mdl-30394295

ABSTRACT

In the growing field of RNA modification, precipitation techniques using antibodies play an important role. However, little is known about their specificities and protocols are missing to assess their effectiveness. Here we present a method to assess enrichment factors after MeRIP-type pulldown experiments, here exemplified with a commercial antibody against N6-methyladenosine (m6A). Testing different pulldown and elution conditions, we measure enrichment factors of 4-5 using m6A-containing mRNAs against an unmodified control of identical sequence. Both types of mRNA carry 32P labels at different nucleotides, allowing their relative quantification in a mixture after digestion to nucleotides, separation by TLC and quantitative phosphorimaging of the labels.


Subject(s)
Adenosine Triphosphate/metabolism , Adenosine/analogs & derivatives , Immunoglobulin G/chemistry , Immunoprecipitation/methods , RNA, Messenger/genetics , Adenosine/chemistry , Adenosine/metabolism , Adenosine Triphosphate/chemistry , Cell-Free System/chemistry , Cell-Free System/metabolism , Chromatography, Thin Layer , DNA-Directed RNA Polymerases/genetics , DNA-Directed RNA Polymerases/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Humans , Immunoglobulin G/genetics , Immunoglobulin G/metabolism , Isotope Labeling/methods , Methylation , Models, Molecular , Phosphorus Radioisotopes , Protein Binding , Protein Interaction Domains and Motifs , Protein Structure, Secondary , RNA, Messenger/chemistry , RNA, Messenger/metabolism , Viral Proteins/genetics , Viral Proteins/metabolism
10.
Nanomedicine ; 27: 102196, 2020 07.
Article in English | MEDLINE | ID: mdl-32272233

ABSTRACT

Bone-targeted therapies have been the choice of treatments for cancer metastases in bone to minimize skeletal morbidity and preserve patients' quality of life. Rhein is of particular interest due to its high bone affinity. Here we reported a novel Rhein- polyethylene glycol (PEG)-nano hydroxyapatite (nHA) conjugate to deliver doxorubicin (DOX) and Phosphorus-32 (32P) simultaneously for enhanced cancer chemo-radiotherapy. The synthetic Rhein-PEG-nHA conjugates were sphere in shape with an average diameter of ~120 nm. Their morphology, drug release and bone affinity were confirmed in vitro. The release profiles of DOX depend on pH condition, but 32P exhibited good stability. Rhein-PEG-nHA also showed high bone affinity in vivo, and the tumor volume decreased after the DOX@Rhein-PEG-nHA and 32P@Rhein-PEG-nHA treatments. Most importantly, the DOX/32P@Rhein-PEG-nHA showed the strongest inhibition on the growth of bone metastases of breast cancer. We revealed the potential of Rhein-PEG-nHA in combined chemo-radiation treatment for bone metastases of breast cancer.


Subject(s)
Bone Neoplasms/drug therapy , Bone Neoplasms/radiotherapy , Breast Neoplasms/drug therapy , Breast Neoplasms/radiotherapy , Drug Delivery Systems , Animals , Anthraquinones/chemistry , Anthraquinones/pharmacology , Bone Neoplasms/pathology , Bone Neoplasms/secondary , Breast Neoplasms/pathology , Cell Line, Tumor , Doxorubicin/chemistry , Doxorubicin/pharmacology , Durapatite/chemistry , Durapatite/pharmacology , Female , Humans , Immunoconjugates/chemistry , Immunoconjugates/pharmacology , Mice , Neoplasm Metastasis , Phosphorus Radioisotopes/chemistry , Phosphorus Radioisotopes/pharmacology , Polyethylene Glycols/chemistry , Xenograft Model Antitumor Assays
11.
Ecol Lett ; 22(9): 1462-1471, 2019 Sep.
Article in English | MEDLINE | ID: mdl-31270952

ABSTRACT

In subtropical oceans phytoplankton carbon: phosphorus (C : P) ratios are high, and these ratios are predicted to increase further with rising ocean temperatures and stratification. Prey stoichiometry may pose a problem for copepod zooplankton nauplii, which have high phosphorus demands due to rapid growth. We hypothesised that nauplii meet this demand by consuming bacteria. Naupliar bacterial and phytoplankton carbon and phosphorus ingestion, assimilation and incorporation were traced using 33 P and 14 C radioisotopes. Bacterial carbon was incorporated four times less efficiently into biomass than phytoplankton carbon. In contrast, bacterial and phytoplankton phosphorus were incorporated at similar efficiencies, and bacteria could meet a substantial amount of naupliar phosphorus requirements. As parts of the ocean become more oligotrophic, bacteria could help sustain naupliar growth and survival under suboptimal stoichiometric conditions. Thus, nauplii may be a shortcut for phosphorus from the microbial loop to the classical food web.


Subject(s)
Bacteria/chemistry , Copepoda/metabolism , Food Chain , Phosphorus/metabolism , Animals , Carbon/metabolism , Carbon Radioisotopes/analysis , Oceans and Seas , Phosphorus Radioisotopes/analysis , Phytoplankton/chemistry
12.
Anal Bioanal Chem ; 411(6): 1253-1260, 2019 Feb.
Article in English | MEDLINE | ID: mdl-30617405

ABSTRACT

Phosphorus (P) research still lacks techniques for rapid imaging of P use and allocation in different soil, sediment, and biological systems in a quantitative manner. In this study, we describe a time-saving and cost-efficient digital autoradiographic method for in situ quantitative imaging of 33P radioisotopes in plant materials. Our method combines autoradiography of the radiotracer applications with additions of commercially available 14C polymer references to obtain 33P activities in a quantitative manner up to 2000 Bq cm-2. Our data show that linear standard regressions for both radioisotopes are obtained, allowing the establishment of photostimulated luminescence equivalence between both radioisotopes with a factor of 9.73. Validating experiments revealed a good agreement between the calculated and applied 33P activity (R2 = 0.96). This finding was also valid for the co-exposure of 14C polymer references and 33P radioisotope specific activities in excised plant leaves for both maize (R2 = 0.99) and wheat (R2 = 0.99). The outlined autoradiographic quantification procedure retrieved 100% ± 12% of the 33P activity in the plant leaves, irrespective of plant tissue density. The simplicity of this methodology opens up new perspectives for fast quantitative imaging of 33P in biological systems and likely, thus, also for other environmental compartments.


Subject(s)
Phosphoric Acids/analysis , Phosphorus Radioisotopes/analysis , Plant Leaves/chemistry , Triticum/chemistry , Zea mays/chemistry , Autoradiography/methods , Carbon Radioisotopes/analysis , Phosphorus/analysis , Polymers/analysis
13.
J Xray Sci Technol ; 27(2): 187-195, 2019.
Article in English | MEDLINE | ID: mdl-30958324

ABSTRACT

OBJECTIVE: To evaluate the potential of synovial membrane volume measurement by MRI in monitoring the effect of radiation synovectomy on patients of Hemophilic Arthropathy (HA). METHODS: We studied 63 diseased joints of 42 HA patients who received hospitalized services at the Hemophilia Diagnosis and Treatment Center of Henan Provincial People's Hospital from May 2011 to January 2015. Unenhanced and enhanced MR scanning of each diseased joint was performed simultaneously. The volumes of synovial membrane of 21 joints from 16 patients before and after being treated with 32P radiation synovectomy (PRS) were measured and compared using image post-processing software and workstation. Two sample matching t test was conducted to analyze the synovial membrane volumes of the same joint measured by unenhanced and enhanced MR, as well as change of MR enhancement ratio after treatments. RESULTS: The synovial membrane volumes measured by unenhanced versus enhanced MR scanning showed no statistical significance. Significant reduction (t = 7.831, p < 0.001) of the synovial membrane volume after treatment (2479.45±46.48 mm3 versus 2983.30±42.87 mm3 before treatment) was observed. MR enhancement ratio of synovial membrane decreased after treatment (0.92±0.06 after vs 1.17±0.07 before treatment) with statistical significance. CONCLUSION: The synovial membrane volume and MR enhancement ratio can be used to monitor patient response to PRS treatment.


Subject(s)
Hemophilia A/complications , Joint Diseases , Magnetic Resonance Imaging/methods , Synovectomy/methods , Synovial Membrane/diagnostic imaging , Adolescent , Adult , Child , Child, Preschool , Follow-Up Studies , Humans , Joint Diseases/diagnostic imaging , Joint Diseases/etiology , Joint Diseases/radiotherapy , Male , Phosphorus Radioisotopes/therapeutic use , Treatment Outcome , Young Adult
14.
New Phytol ; 220(4): 1185-1199, 2018 12.
Article in English | MEDLINE | ID: mdl-29944179

ABSTRACT

Through a mutualistic relationship with woody plant roots, ectomycorrhizal fungi provide growth-limiting nutrients, including inorganic phosphate (Pi), to their host. Reciprocal trades occur at the Hartig net, which is the symbiotic interface of ectomycorrhizas where the two partners are symplasmically isolated. Fungal Pi must be exported to the symbiotic interface, but the proteins facilitating this transfer are unknown. In the present study, we combined transcriptomic, microscopy, whole plant physiology, X-ray fluorescence mapping, 32 P labeling and fungal genetic approaches to unravel the role of HcPT2, a fungal Pi transporter, during the Hebeloma cylindrosporum-Pinus pinaster ectomycorrhizal association. We localized HcPT2 in the extra-radical hyphae and the Hartig net and demonstrated its determinant role for both the establishment of ectomycorrhizas and Pi allocation towards P. pinaster. We showed that the host plant induces HcPT2 expression and that the artificial overexpression of HcPT2 is sufficient to significantly enhance Pi export towards the central cylinder. Together, our results reveal that HcPT2 plays an important role in ectomycorrhizal symbiosis, affecting both Pi influx in the mycelium and efflux towards roots under the control of P. pinaster.


Subject(s)
Fungal Proteins/metabolism , Hebeloma/metabolism , Membrane Transport Proteins/metabolism , Mycorrhizae/physiology , Symbiosis , Fungal Proteins/genetics , Gene Expression Regulation, Fungal , Hebeloma/genetics , Hebeloma/growth & development , Membrane Transport Proteins/genetics , Models, Biological , Mycelium/metabolism , Phosphates/metabolism , Phosphorus Radioisotopes , Pinus/microbiology , Up-Regulation/genetics
15.
Methods ; 113: 72-82, 2017 01 15.
Article in English | MEDLINE | ID: mdl-27729295

ABSTRACT

Phosphorylation of many aminoacyl tRNA synthetases (AARSs) has been recognized for decades, but the contribution of post-translational modification to their primary role in tRNA charging and decryption of genetic code remains unclear. In contrast, phosphorylation is essential for performance of diverse noncanonical functions of AARSs unrelated to protein synthesis. Phosphorylation of glutamyl-prolyl tRNA synthetase (EPRS) has been investigated extensively in our laboratory for more than a decade, and has served as an archetype for studies of other AARSs. EPRS is a constituent of the IFN-γ-activated inhibitor of translation (GAIT) complex that directs transcript-selective translational control in myeloid cells. Stimulus-dependent phosphorylation of EPRS is essential for its release from the parental multi-aminoacyl tRNA synthetase complex (MSC), for binding to other GAIT complex proteins, and for regulating the binding to target mRNAs. Importantly, phosphorylation is the common driving force for the context- and stimulus-dependent release, and non-canonical activity, of other AARSs residing in the MSC, for example, lysyl tRNA synthetase (KARS). Here, we describe the concepts and experimental methodologies we have used to investigate the influence of phosphorylation on the structure and function of EPRS. We suggest that application of these approaches will help to identify new functional phosphorylation event(s) in other AARSs and elucidate their possible roles in noncanonical activities.


Subject(s)
Amino Acyl-tRNA Synthetases/metabolism , Biological Assay , Monocytes/metabolism , Proline/metabolism , Protein Processing, Post-Translational , RNA, Transfer, Pro/metabolism , Amino Acyl-tRNA Synthetases/genetics , Animals , Antibodies/chemistry , Cell Line, Tumor , Cyclin-Dependent Kinase 5/antagonists & inhibitors , Cyclin-Dependent Kinase 5/genetics , Cyclin-Dependent Kinase 5/metabolism , Humans , Interferon-gamma/genetics , Interferon-gamma/metabolism , Macrophages/cytology , Macrophages/metabolism , Mice , Mitogen-Activated Protein Kinase 1/antagonists & inhibitors , Mitogen-Activated Protein Kinase 1/genetics , Mitogen-Activated Protein Kinase 1/metabolism , Monocytes/cytology , Phosphorus Radioisotopes , Phosphorylation , Primary Cell Culture , Protein Binding , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , RNA, Transfer, Pro/genetics
16.
Methods ; 118-119: 41-49, 2017 04 15.
Article in English | MEDLINE | ID: mdl-27871973

ABSTRACT

The study of protein-RNA interactions is critical for our understanding of cellular processes and regulatory circuits controlled by RNA binding proteins (RBPs). Recent next generation sequencing-based approaches significantly promoted our understanding of RNA biology and its importance for cell function. We present a streamlined protocol for Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP), a technique that allows for the characterization of RBP binding sites on target RNAs at nucleotide resolution and transcriptome-wide scale. PAR-CLIP involves irreversible UV-mediated crosslinking of RNAs labeled with photoreactive nucleosides to interacting proteins, followed by stringent purification steps and the conversion of crosslinked RNA into small RNA cDNA libraries compatible with next-generation sequencing. The defining hallmark of PAR-CLIP is a diagnostic mutation at the crosslinking site that is introduced into cDNA during the library preparation process. This feature allows for efficient computational removal of contaminating sequences derived from non-crosslinked fragments of abundant cellular RNAs. In the following, we present two different step-by-step procedures for PAR-CLIP, which differ in the small RNA cDNA library preparation procedure: (1) Standard library preparation involving gel size selections after each enzymatic manipulation, and (2) A modified PAR-CLIP procedure ("on-beads" PAR-CLIP), where most RNA manipulations including the necessary adapter ligation steps are performed on the immobilized RNP. This streamlined procedure reduces the protocol preparation time by three days compared to the standard workflow.


Subject(s)
Gene Library , High-Throughput Nucleotide Sequencing/methods , Immunoprecipitation/methods , RNA-Binding Proteins/genetics , RNA/chemistry , Sequence Analysis, RNA/methods , Thiouridine/metabolism , Antibodies/chemistry , Base Sequence , Binding Sites , Cell Line , Electrophoresis, Agar Gel/methods , Humans , Mutation , Phosphorus Radioisotopes , Protein Binding , RNA/genetics , RNA/metabolism , RNA-Binding Proteins/metabolism , Ribonucleases/chemistry , Software , Thiouridine/chemistry , Transcriptome , Ultraviolet Rays , Y-Box-Binding Protein 1/genetics , Y-Box-Binding Protein 1/metabolism
17.
Methods ; 118-119: 24-40, 2017 04 15.
Article in English | MEDLINE | ID: mdl-27765618

ABSTRACT

Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in combination with next-generation sequencing is a powerful method for identifying endogenous targets of RNA-binding proteins (RBPs). Depending on the characteristics of each RBP, key steps in the PAR-CLIP procedure must be optimized. Here we present a comprehensive step-by-step PAR-CLIP protocol with detailed explanations of the critical steps. Furthermore, we report the application of a new PAR-CLIP data analysis pipeline to three distinct RBPs targeting different annotation categories of cellular RNAs.


Subject(s)
High-Throughput Nucleotide Sequencing/methods , Immunoprecipitation/methods , RNA-Binding Proteins/genetics , RNA/chemistry , Sequence Analysis, RNA/methods , Thiouridine/metabolism , Antibodies/chemistry , Base Sequence , Binding Sites , Cell Line, Tumor , Fragile X Mental Retardation Protein/genetics , Fragile X Mental Retardation Protein/metabolism , Gene Library , HEK293 Cells , Humans , Nucleic Acid Conformation , Phosphoproteins/genetics , Phosphoproteins/metabolism , Phosphorus Radioisotopes , Protein Binding , RNA/genetics , RNA/metabolism , RNA-Binding Protein FUS/genetics , RNA-Binding Protein FUS/metabolism , RNA-Binding Proteins/metabolism , Ribonucleases/chemistry , Sequence Alignment , Thiouridine/chemistry , Ultraviolet Rays
18.
Curr Opin Ophthalmol ; 29(6): 528-534, 2018 Nov.
Article in English | MEDLINE | ID: mdl-30124533

ABSTRACT

PURPOSE OF REVIEW: The pathophysiology of thyroid eye disease (TED) is still not fully understood. However, recently described risk factors and molecular findings have brought new insights into the mechanisms of TED and could lead to the emerging use of more targeted therapies. This article aims to review the clinical findings of TED, and the most recent advances in our understanding of the risk factors and therapeutic options for TED. RECENT FINDINGS: Smoking has been recently shown to have an impact on specific gene expression involved in several disease-related pathways, which seems to be reversible with smoking cessation. This finding further emphasizes the importance of smoking cessation in the prevention and treatment of TED. Selenium deficiency and high-serum cholesterol have been described to be potential independent risk factors for TED and their management could decrease the incidence and severity of TED. In terms of therapeutic options, immunomodulatory medications have shown some promising results for disease control in TED over the past years, but further randomized prospective studies with larger sample sizes are still needed to prove their efficacy. A new technique of P brachytherapy was shown to have quick therapeutic effects on TED without significant side effects and could be a promising therapy for selected cases of TED. SUMMARY: TED is one of the most common autoimmune inflammatory disorders of the orbit. Although its pathophysiology remains unclear, newly described genetic findings and risk factors could help in explaining its occurrence and guide future therapies. Immunosuppressant medications are increasingly used in the management of TED, but further studies are needed to confirm their effectiveness.


Subject(s)
Graves Ophthalmopathy , Brachytherapy/methods , Graves Ophthalmopathy/epidemiology , Graves Ophthalmopathy/physiopathology , Graves Ophthalmopathy/therapy , Humans , Immunomodulation , Phosphorus Radioisotopes/therapeutic use , Risk Factors , Smoking Cessation
19.
Biochem J ; 474(12): 2095-2105, 2017 06 09.
Article in English | MEDLINE | ID: mdl-28487379

ABSTRACT

Magnesium chelatase (Mg-chelatase) inserts magnesium into protoporphyrin during the biosynthesis of chlorophyll and bacteriochlorophyll. Enzyme activity is reconstituted by forming two separate preactivated complexes consisting of a GUN4/ChlH/protoporphyrin IX substrate complex and a ChlI/ChlD enzyme 'motor' complex. Formation of the ChlI/ChlD complex in both Chlamydomonas reinhardtii and Oryza sativa is accompanied by phosphorylation of ChlD by ChlI, but the orthologous protein complex from Rhodobacter capsulatus, BchI/BchD, gives no detectable phosphorylation of BchD. Phosphorylation produces a 1-N-phospho-histidine within ChlD. Proteomic analysis indicates that phosphorylation occurs at a conserved His residue in the C-terminal integrin I domain of ChlD. Comparative analysis of the ChlD phosphorylation with enzyme activities of various ChlI/ChlD complexes correlates the phosphorylation by ChlI2 with stimulation of Mg-chelatase activity. Mutation of the H641 of CrChlD to E641 prevents both phosphorylation and stimulation of Mg-chelatase activity, confirming that phosphorylation at H641 stimulates Mg-chelatase. The properties of ChlI2 compared with ChlI1 of Chlamydomonas and with ChlI of Oryza, shows that ChlI2 has a regulatory role in Chlamydomonas.


Subject(s)
Chlamydomonas reinhardtii/enzymology , Chlorophyll/biosynthesis , Histidine Kinase/metabolism , Lyases/metabolism , Oryza/enzymology , Plant Proteins/metabolism , Protein Processing, Post-Translational , Algal Proteins/agonists , Algal Proteins/chemistry , Algal Proteins/genetics , Algal Proteins/metabolism , Amino Acid Sequence , Amino Acid Substitution , Conserved Sequence , Enzyme Activation , Enzyme Stability , Histidine/metabolism , Histidine Kinase/chemistry , Histidine Kinase/genetics , Hydrogen-Ion Concentration , Lyases/chemistry , Lyases/genetics , Mutation , Phosphorus Radioisotopes , Phosphorylation , Plant Proteins/agonists , Plant Proteins/chemistry , Plant Proteins/genetics , Protein Interaction Domains and Motifs , Protein Multimerization , Proteomics/methods
20.
Exp Parasitol ; 188: 13-20, 2018 May.
Article in English | MEDLINE | ID: mdl-29555416

ABSTRACT

This study was conducted to evaluate the metabolism and phosphorus (P) kinetics in lambs experimentally infected with Trichostrongylus colubriformis using the isotope dilution technique and modelling. Fifteen male lambs (21.1 ±â€¯1.50 kg) of the Santa Inês hair breed of approximately six months old, distributed in the treatments infected (I, n = 8) and control (C, n = 7) were used. The infected lambs received serial infections with 5000 T. colubriformis larvae, three times per week, for 3 weeks (45 000 T. colubriformis total larvae). After 66 days of the last inoculation of infective larvae, 6.6 MBq of 32P were injected in each lamb to evaluate the P kinetics. Blood, faeces and urine samples were collected in the following seven days and the slaughter of lambs were carried out on the last day in order to collect bone and soft tissues (Liver, kidney, heart and muscle) samples. To analyse P flows, the biomathematical model with four compartments (C1 - gastrointestinal tract, C2 - plasma, C3 - bone and C4 - soft tissue) was used. Similar P intake (VI) between treatments (C and I) was verified. Lower absorption of endogenous (Vaf) and dietary P (Vaa), as well as, lower amount of endogenous P (from saliva) that reaches the gastrointestinal tract (VIT), consequently, higher excretion of dietary P (VFD) were verified in infected lambs (P < 0.1). Additionally, in infected lambs, the P bioavailability was lower compared to control lambs. With the lower absorption (VaT) of P in infected lambs, there was, consequently, lower distribution to bones and soft tissues (VeD2) and lower P deposition in the bones (VO+D). It was concluded that P metabolism of lambs infected with T. colubriformis was altered, with reduced intestinal absorption and bioavailability, increased faecal loss and reduced P flow to the bone.


Subject(s)
Phosphorus Radioisotopes/pharmacokinetics , Sheep Diseases/metabolism , Trichostrongylosis/veterinary , Trichostrongylus/physiology , Animals , Biological Availability , Bone and Bones/metabolism , Eating , Feces/chemistry , Feces/parasitology , Gastrointestinal Absorption , Gastrointestinal Tract/metabolism , Kidney/metabolism , Liver/metabolism , Male , Models, Biological , Muscles/metabolism , Myocardium/metabolism , Parasite Egg Count/veterinary , Phosphorus Radioisotopes/administration & dosage , Radioisotope Dilution Technique/veterinary , Random Allocation , Sheep , Sheep Diseases/parasitology , Trichostrongylosis/metabolism
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