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1.
Mol Cell ; 64(2): 376-387, 2016 10 20.
Article in English | MEDLINE | ID: mdl-27720644

ABSTRACT

Nucleotide excision repair (NER) is an evolutionarily conserved mechanism that processes helix-destabilizing and/or -distorting DNA lesions, such as UV-induced photoproducts. Here, we investigate the dynamic protein-DNA interactions during the damage recognition step using single-molecule fluorescence microscopy. Quantum dot-labeled Rad4-Rad23 (yeast XPC-RAD23B ortholog) forms non-motile complexes or conducts a one-dimensional search via either random diffusion or constrained motion. Atomic force microcopy analysis of Rad4 with the ß-hairpin domain 3 (BHD3) deleted reveals that this motif is non-essential for damage-specific binding and DNA bending. Furthermore, we find that deletion of seven residues in the tip of ß-hairpin in BHD3 increases Rad4-Rad23 constrained motion at the expense of stable binding at sites of DNA lesions, without diminishing cellular UV resistance or photoproduct repair in vivo. These results suggest a distinct intermediate in the damage recognition process during NER, allowing dynamic DNA damage detection at a distance.


Subject(s)
DNA Repair , DNA, Fungal/genetics , DNA-Binding Proteins/genetics , Gene Expression Regulation, Fungal , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/radiation effects , Amino Acid Sequence , Base Sequence , Binding Sites , DNA Damage , DNA, Fungal/chemistry , DNA, Fungal/metabolism , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/metabolism , Microscopy, Atomic Force , Microscopy, Fluorescence , Nucleic Acid Conformation , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Quantum Dots/chemistry , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Sequence Deletion , Single Molecule Imaging , Ultraviolet Rays
2.
Ren Fail ; 46(1): 2334396, 2024 Dec.
Article in English | MEDLINE | ID: mdl-38570195

ABSTRACT

OBJECTIVES: Calcium oxalate (CaOx) crystal deposition in acute kidney injury (AKI) patients is under recognized but impacts renal outcomes. This study investigates its determinants and effects. METHODS: We studied 814 AKI patients with native kidney biopsies from 2011 to 2020, identifying CaOx crystal deposition severity (mild: <5, moderate: 5-10, severe: >10 crystals per section). We assessed factors like urinary oxalate, citrate, urate, electrolytes, pH, tubular calcification index, and SLC26A6 expression, comparing them with creatinine-matched AKI controls without oxalosis. We analyzed how these factors relate to CaOx severity and their impact on renal recovery (eGFR < 15 mL/min/1.73 m2 at 3-month follow-up). RESULTS: CaOx crystal deposition was found in 3.9% of the AKI cohort (32 cases), with 72% due to nephrotoxic medication-induced tubulointerstitial nephritis. Diuretic use, higher urinary oxalate-to-citrate ratio induced by hypocitraturia, and tubular calcification index were significant contributors to moderate and/or severe CaOx deposition. Poor baseline renal function, low urinary chloride, high uric acid and urea nitrogen, tubular SLC26A6 overexpression, and glomerular sclerosis were also associated with moderate-to-severe CaOx deposition. Kidney recovery was delayed, with 43.8%, 31.2%, and 18.8% of patients having eGFR < 15 mL/min/1.73 m2 at 4, 12, and 24-week post-injury. Poor outcomes were linked to high urinary α1-microglobulin-to-creatinine (α1-MG/C) ratios and active tubular injury scores. Univariate analysis showed a strong link between this ratio and poor renal outcomes, independent of oxalosis severity. CONCLUSIONS: In AKI, CaOx deposition is common despite declining GFR. Factors worsening tubular injury, not just oxalate-to-citrate ratios, are key to understanding impaired renal recovery.


Subject(s)
Acute Kidney Injury , Calcinosis , Hyperoxaluria , Humans , Calcium Oxalate/chemistry , Creatinine/metabolism , Kidney/pathology , Hyperoxaluria/complications , Oxalates/metabolism , Acute Kidney Injury/pathology , Citrates/metabolism , Citric Acid
3.
Telemed J E Health ; 30(2): 499-508, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37651189

ABSTRACT

Background: The purpose of this research was to compare patient satisfaction between hybrid ophthalmology telemedicine and standard-of-care in-person visits. A retrospective, cross-sectional, case-control analysis of patient satisfaction based on survey data was used. Methods: Responses to the National Research Council Health Patient Survey were retrieved for randomly sampled hybrid ophthalmology telemedicine and in-person visits between March 11, 2020 and December 31, 2021 at a hospital-based eye clinic in Boston, Massachusetts. The primary outcome was based on the question "How likely would you be to recommend this provider to your family and friends?" (0-10 scale) with a score of 9 or 10 coded as satisfied. Two-sample t-tests, Pearson's chi-square tests, and bivariate logistic regressions were used to compare patient satisfaction scores between the hybrid and in-person cohorts. Demographic data, including age, sex, language, and self-reported race and ethnicity, were used as potential predictors of patient satisfaction in a multivariable logistic regression model. Results: There were 49 surveys from hybrid visits and 3,390 surveys from in-person visits. Hybrid visit patients reported high satisfaction scores without significant differences compared to in-person visit patients (hybrid 79% satisfied, in-person 82% satisfied, p = 0.728). Age was significantly associated with satisfaction in the hybrid cohort with the 65+ age group reporting lower satisfaction (below 65 years 100% satisfied, 65+ years 60% satisfied, p = 0.003). No association with age was observed in the in-person cohort. Conclusions: The hybrid ophthalmology telemedicine model can provide effective care without sacrificing patient satisfaction. Older patients may benefit from targeted interventions in future telemedicine models.


Subject(s)
Ophthalmology , Telemedicine , Humans , Aged , Patient Satisfaction , Cross-Sectional Studies , Retrospective Studies , Age Factors
4.
J Transl Med ; 21(1): 680, 2023 09 30.
Article in English | MEDLINE | ID: mdl-37777783

ABSTRACT

BACKGROUND: Metagenomic next-generation sequencing (mNGS) has become a powerful tool for pathogen detection, but the value of human sequencing reads generated from it is underestimated. METHODS: A total of 138 patients with pleural effusion (PE) were diagnosed with tuberculous pleurisy (TBP, N = 82), malignant pleural effusion (MPE, N = 35), or non-TB infection (N = 21), whose PE samples all underwent mNGS analysis. Clinical TB tests including culture, Acid-Fast Bacillus (AFB) test, Xpert, and T-SPOT, were performed. To utilize mNGS for MPE identification, 25 non-MPE samples (20 TBP and 5 non-TB infection) were randomly selected to set human chromosome copy number baseline and generalized linear modeling was performed using copy number variant (CNV) features of the rest 113 samples (35 MPE and 78 non-MPE). RESULTS: The performance of TB detection was compared among five methods. T-SPOT demonstrated the highest sensitivity (61% vs. culture 32%, AFB 12%, Xpert 35%, and mNGS 49%) but with the highest false-positive rate (10%) as well. In contrast, mNGS was able to detect TB-genome in nearly half (40/82) of the PE samples from TBP subgroup, with 100% specificity. To evaluate the performance of using CNV features of the human genome for MPE prediction, we performed the leave-one-out cross-validation (LOOCV) in the subcohort excluding the 25 non-MPE samples for setting copy number standards, which demonstrated 54.1% sensitivity, 80.8% specificity, 71.7% accuracy, and an AUC of 0.851. CONCLUSION: In summary, we exploited the value of human and non-human sequencing reads generated from mNGS, which showed promising ability in simultaneously detecting TBP and MPE.


Subject(s)
Pleural Effusion, Malignant , Pleural Effusion , Tuberculosis, Pleural , Humans , Tuberculosis, Pleural/diagnosis , Pleural Effusion, Malignant/diagnosis , Pleural Effusion, Malignant/genetics , High-Throughput Nucleotide Sequencing , Metagenomics , Sensitivity and Specificity
5.
Neurochem Res ; 48(9): 2881-2894, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37210413

ABSTRACT

Microglia, innate immune cells of the brain, constantly monitor the dynamic changes of the brain microenvironment under physiological conditions and respond in time. Growing evidence suggests that microglia-mediated neuroinflammation plays an important role in the pathogenesis of Alzheimer's disease. In this study, we investigated that the expression of IFITM3 was significantly upregulated in microglia under the Aß treatment, and knockdown of IFITM3 in vitro suppressed the M1-like polarization of microglia. Moreover, IFITM3 was regulated by cGAS-STING signaling in activated microglia, and inhibition of cGAS-STING signaling reduces IFITM3 expression. Taken together, our findings suggested that the cGAS-STING-IFITM3 axis may be involved in Aß-induced neuroinflammation in microglia.


Subject(s)
Alzheimer Disease , Microglia , Humans , Microglia/metabolism , Neuroinflammatory Diseases , Signal Transduction , Nucleotidyltransferases/metabolism , Alzheimer Disease/metabolism , Membrane Proteins/metabolism , RNA-Binding Proteins/metabolism
6.
Nucleic Acids Res ; 48(21): 12348-12364, 2020 12 02.
Article in English | MEDLINE | ID: mdl-33119737

ABSTRACT

XPC/Rad4 initiates eukaryotic nucleotide excision repair on structurally diverse helix-destabilizing/distorting DNA lesions by selectively 'opening' these sites while rapidly diffusing along undamaged DNA. Previous structural studies showed that Rad4, when tethered to DNA, could also open undamaged DNA, suggesting a 'kinetic gating' mechanism whereby lesion discrimination relied on efficient opening versus diffusion. However, solution studies in support of such a mechanism were lacking and how 'opening' is brought about remained unclear. Here, we present crystal structures and fluorescence-based conformational analyses on tethered complexes, showing that Rad4 can indeed 'open' undamaged DNA in solution and that such 'opening' can largely occur without one or the other of the ß-hairpin motifs in the BHD2 or BHD3 domains. Notably, the Rad4-bound 'open' DNA adopts multiple conformations in solution notwithstanding the DNA's original structure or the ß-hairpins. Molecular dynamics simulations reveal compensatory roles of the ß-hairpins, which may render robustness in dealing with and opening diverse lesions. Our study showcases how fluorescence-based studies can be used to obtain information complementary to ensemble structural studies. The tethering-facilitated DNA 'opening' of undamaged sites and the dynamic nature of 'open' DNA may shed light on how the protein functions within and beyond nucleotide excision repair in cells.


Subject(s)
DNA Repair , DNA, Fungal/genetics , DNA-Binding Proteins/genetics , DNA/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Base Sequence , Binding Sites , Crystallography, X-Ray , DNA/chemistry , DNA/metabolism , DNA Damage , DNA, Fungal/chemistry , DNA, Fungal/metabolism , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/metabolism , Kinetics , Molecular Dynamics Simulation , Mutation , Nucleic Acid Conformation , Organophosphorus Compounds/chemical synthesis , Organophosphorus Compounds/metabolism , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae Proteins/metabolism , Spectrometry, Fluorescence , Substrate Specificity , Thermodynamics
7.
Graefes Arch Clin Exp Ophthalmol ; 259(8): 2203-2212, 2021 Aug.
Article in English | MEDLINE | ID: mdl-33566149

ABSTRACT

PURPOSE: To identify risk factors for fellow eye treatment of diabetic retinopathy with Vascular Endothelial Growth Factor (VEGF) injections during the Diabetic Retinopathy Clinical Research Network (DRCR.Net) Protocol T trial METHODS: In this post-hoc analysis of randomized clinical trial data, Cox regression analysis was performed at 52 and 104 weeks to determine risk factors for treatment in 360 fellow eyes. Survival analysis was performed to determine mean time to treatment based upon medication used. RESULTS: Of 360 fellow eyes, 142 (39.4%) required treatment between weeks 4 and 104. Risk factors predicting a lower likelihood of year 1 treatment included older subject age (Hazard Ratio [HR]=0.98, 95% CI 0.96-0.99; p = 0.02) and higher baseline study eye ETDRS score (HR=0.98, 95% CI 0.97-0.99, p = 0.04). Center-involving DME at baseline in the fellow eye was predictive of a higher treatment need at both 52 (HR=1.89, 95% CI 1.42-2.51, p < 0.0001) and 104 weeks (HR=2.68, 95% CI 1.75-4.11, p < 0.0001). Subjects treated in the study eye with aflibercept (HR=0.574, 95% CI 0.371-0.887, p = 0.013) and ranibizumab (HR=0.58, 95%CI 0.36-0.94, p = 0.03) were less likely to require first year fellow eye injection than subjects treated with bevacizumab although this difference was no longer significant at week 104 (aflibercept HR=0.77, 95% CI 0.52-1.16, p = 0.21; ranibizumab HR=0.66, 95% CI 0.43-1.00, p = 0.05). Mean time to treatment was significantly shorter in the bevacizumab group (bevacizumab 25.83 weeks, aflibercept 38.75 weeks, ranibizumab 34.70 weeks (p=0.012)). CONCLUSION: Bilateral treatment with intravitreal anti-VEGF injections was common during the DRCR.net Protocol T. Medication choice may impact the risk of fellow eye treatment.


Subject(s)
Macular Edema , Vascular Endothelial Growth Factor A , Angiogenesis Inhibitors/therapeutic use , Bevacizumab/therapeutic use , Humans , Intravitreal Injections , Macular Edema/drug therapy , Randomized Controlled Trials as Topic , Ranibizumab/therapeutic use , Receptors, Vascular Endothelial Growth Factor/therapeutic use , Recombinant Fusion Proteins/therapeutic use , Risk Factors , Visual Acuity
8.
Graefes Arch Clin Exp Ophthalmol ; 259(1): 45-52, 2021 Jan.
Article in English | MEDLINE | ID: mdl-32813107

ABSTRACT

PURPOSE: A majority of phakic patients undergoing pars plana vitrectomy for epiretinal membrane or macular hole require subsequent cataract surgery within 1-2 years. Combined phaco-vitrectomy eliminates the need for a second surgery and may enable patients to attain their best vision sooner. This study aims to compare the visual outcomes, complication rates, and costs of combined phaco-vitrectomy versus sequential vitrectomy followed by cataract surgery. METHODS: Records were searched by CPT® codes to identify patients with both cataract and vitrectomy surgery at our institution over a 5-year period (2013-2018). Chart review included medical history, demographics, exam findings, operating room records, visual acuity (VA), and clinical outcomes. Statistical analyses were performed with SPSS v19 (IBM). Area under the curve for visual acuity was calculated as the trapezoidal mean of the change in Early Treatment of Diabetic Retinopathy Study letters. RESULTS: After exclusion, 81 eyes of 78 patients underwent both cataract and vitrectomy surgeries at our institution. Thirty-four eyes underwent separate, sequential vitrectomy then phacoemulsification surgery, and 47 eyes had combined phaco-vitrectomy surgery. Total operating room times (120.81 ± 3.41 vs 161.03 ± 5.45 min; p < 0.0001) and associated costs were significantly lower in the combined surgery compared with those in the sequential surgery group. Baseline and final visual acuity were similar between the two groups. Baseline VA was 35.53 letters (~ 20/200) and 32.81 letters (~ 20/220) and increased to final VA of 63.74 (~ 20/53) and 60.91 letters (~ 20/61), in the sequential and combined groups respectively. Area under the curve for vision was greater in the combined surgery group, with subjects gaining an average of + 9.11 ± 3.32 letters from sequential surgery, and + 19.53 ± 3.53 letters in the combined surgery group (p = 0.04). Additionally, patients in the combined group attained their best visual acuity 449 days (15 months) sooner than those receiving sequential surgery. CONCLUSIONS: Combined phaco-vitrectomy surgery resulted in greater area under the curve visual acuity benefit and attainment of best visual acuity 15 months sooner compared with conventional sequential surgeries. There were no significant differences in complication rates or clinical outcomes between the groups, but operative times and costs were lower for combined surgery, supporting a favorable cost-benefit ratio. Graphical abstract.


Subject(s)
Cataract , Epiretinal Membrane , Phacoemulsification , Cataract/complications , Epiretinal Membrane/surgery , Humans , Postoperative Complications/epidemiology , Retrospective Studies , Treatment Outcome , Vitrectomy
9.
Nanotechnology ; 31(9): 095403, 2020 Feb 21.
Article in English | MEDLINE | ID: mdl-31726433

ABSTRACT

Three-dimensional (3D) carbon aerogels with well-defined structures, e.g. high specific surface area (SSA), appropriate pore size distribution, good electrical conductivity and ideal building blocks, have been regarded as promising electrode materials or substrates for incorporation with pseudocapacitive materials for energy storage and conversion applications. Herein, we report a simple and scalable sonochemical method followed by a chemical activation process to transform bacterial cellulose-derived carbon nanofiber aerogels (CNFAs) into 3D graphene nanoribbon aerogels (GNRAs) for supercapacitors. Benefiting from a high SSA, reasonable pore size distribution and good conductivity, the GNRA electrode demonstrates a long cyclability, good rate capability and high charge storage performance for supercapacitors, yielding more than 1.5 times (three-electrode cell) and 2.6 times (two-electrode cell) the gravimetric capacitance of the CNFA electrode. In addition, a hybrid Ni-Co layered double hydroxides (LDHs)@GNRAs electrode achieves an impressive gravimetric capacitance of 968 F g-1 (based on the mass of the active material) at a current density of 1 A g-1. Moreover, an asymmetric supercapacitor device with a remarkable energy density of 29.87 Wh kg-1, wide working voltage windows of 1.6 V and good cycling stability (63.5% retention after 10 000 cycles) is achieved by using the GNRA as an anode and the Ni-Co LDHs@GNRAs as a cathode.

10.
Anal Bioanal Chem ; 412(12): 2731-2741, 2020 May.
Article in English | MEDLINE | ID: mdl-32157359

ABSTRACT

A one-step synthesis using the reversed-phase suspension polymerization method and ultraviolet light curing is proposed for preparing the Raman-encoded suspension array (SA). The encoded microcarriers are prepared by doping the Raman reporter molecules into an aqueous phase, and then dispersing the aqueous phase in an oil phase and curing by ultraviolet light irradiation. The multiplexed biomolecule detection and various concentration experiments confirm the qualitative and quantitative analysis capabilities of the Raman-encoded SA with a limit of detection of 52.68 pM. The narrow bandwidth of the Raman spectrum can achieve a large number of codes in the available spectral range and the independence between the encoding channel and the fluorescent label channel provides the encoding method with high accuracy. This preparation method is simple and easy to operate, low in cost, and high in efficiency. A large number of hydrogel-based encoding microbeads could be quickly obtained with good biocompatibility. Most importantly, concentrating plenty of Raman reporter molecules inside the microbeads increases the signal intensity and means the molecular assembly is not limited by the functional groups; thus, the types of materials available for Raman encoding method are expanded. Furthermore, the signal intensity-related encoding method is verified by doping different proportions of Raman reporter molecules with our proposed synthesis method, which further increases the detection throughput of Raman-encoded SA. Graphical Abstract.

11.
Environ Res ; 182: 109082, 2020 03.
Article in English | MEDLINE | ID: mdl-31891828

ABSTRACT

Restrictions of legacy brominated flame retardants, such as polybrominated diphenyl ether (PBDE) and polybrominated biphenyl (PBB), have resulted in increased usage of alternative halogenated flame retardants (AHFRs). Consequently, AHFRs contamination has caused a major concern in the scientific community. However, there is limited information on their presence in marine mussels. In this study, we investigated the occurrence and distribution of polybrominated biphenyls (PBBs), AHFRs and dehalogenated products in green mussels collected from 22 locations in the northern South China Sea (SCS). Our results revealed that ∑AHFRs were ubiquitous in green mussels with concentrations in the range of 1.08-7.71 ng/g lipid weight (lw). Among target AHFRs, hexabromobenzene (HBB), decabromodiphenyl (DBDPE) and dechlorane plus (DP) were predominant with their mean values of 1.19, 1.00 and 0.82 ng/g lw, respectively. There were negligible stereoisomer enrichments of DP in green mussels based on fanti values, indicating a limited bioaccumulation and metabolism of DP in green mussels. In comparison with other locations, concentrations of the AHFRs in green mussels determined here were at moderate levels. Additionally, there were significant linear relationships between some AHFRs (e.g., HBB and PBEB), suggesting their similar commercial applications and sources in the environment. The estimated daily intakes of AHFRs through consumption of green mussels by the local population in South China were 0.05-0.14 ng/kg body weight/day and 0.17-0.44 ng/kg body weight/day based on the mean and 95th concentrations, respectively. To the best of our knowledge, the present study is the first to report AHFRs and dehalogenated products in green mussels.


Subject(s)
Bivalvia , Flame Retardants , Animals , China , Environmental Monitoring , Halogenated Diphenyl Ethers
12.
Opt Express ; 27(3): 1894-1910, 2019 Feb 04.
Article in English | MEDLINE | ID: mdl-30732236

ABSTRACT

Dual-wavelength digital holographic phase and fluorescence microscopy (DW-DHPFM), combining with Raman spectroscopy, is designed to achieve the detection and analysis of biomolecules with a new dual-channel encoding method. This employs the Raman reporter molecules assembled micro-quartz pieces (MQPs) as microcarriers of suspension array (SA). The dual-wavelength digital holographic phase microscopy (DW-DHPM) and Raman spectroscopy are served as the decoding platforms, and the fluorescence microscopy is used to quantify target analytes. Considering the independence between encoding and label signal, the above two encoding channels could effectively avoid the crosstalk in immunoassay process, and the combination of two encoding methods expand the encoding capacity with a considerable magnitude. Accurate and stable decoding abilities are verified by multiplexed immunoassay experiment and the quantitative analysis of targets with high-sensitivity is confirmed by concentration gradient experiments.

13.
Analyst ; 144(13): 4093-4099, 2019 Jul 07.
Article in English | MEDLINE | ID: mdl-31169834

ABSTRACT

Ion-chelated microbeads (ICMs) for suspension arrays can be prepared by chelating metal ions (MIs), which are used as encoding materials. Stimulating the ICMs, laser induced breakdown spectra (LIBs) can be obtained and the atomic spectra of the chelated ions are chosen as the decoding signals. Our ICMs show digital characteristics with high stability due to the properties of LIBs. And, since there are many available coding materials and different kinds of coding materials can be easily combined, the coding capacity can be considerably enlarged. Further, the background interference in fluoroimmunoassay detection could be avoided, because the ICMs contain no fluorescence emission. In our studies, we achieved a total of 15 types of barcodes by taking full advantage of 4 kinds of ions, then a fluoroimmunoassay was performed to demonstrate the specificity and detection performance of our ICMs in multiplexing and the detection limit could reach 1.49 × 10-10 M, showing promising potential in applications.

14.
Analyst ; 144(14): 4312-4319, 2019 Jul 21.
Article in English | MEDLINE | ID: mdl-31188363

ABSTRACT

A deep learning network called "residual neural network" (ResNet) was used to decode Raman spectra-encoded suspension arrays (SAs). With narrow bandwidths and stable signals, Raman spectra have ideal encoding properties. The different Raman reporter molecules assembled micro-quartz pieces (MQPs) were grafted with various biomolecule probes, which enabled simultaneous detection of numerous target analytes in a single sample. Multiple types of mixed MQPs were measured by Raman spectroscopy and then decoded by ResNet to acquire the type information of analytes. The good classification performance of ResNet was verified by a t-distributed stochastic neighbor embedding (t-SNE) diagram. Compared with other machine learning models, these experiments showed that ResNet was obviously superior in terms of classification stability and training convergence to different datasets. This method simplified the decoding process and the classification accuracy reached 100%.

15.
Anal Bioanal Chem ; 411(21): 5509-5518, 2019 Aug.
Article in English | MEDLINE | ID: mdl-31280475

ABSTRACT

The rapid analysis and detection of biomolecules has become increasingly important in biological research. Hence, here we propose a novel suspension array method that is based on gold nanorod (AuNR)-enhanced Raman spectroscopy and uses micro-quartz pieces (MQPs) as microcarriers. AuNRs and Raman reporter molecules are coupled together by Au-S bonds to obtain surface-enhanced Raman scattering labels (SERS labels). The SERS labels are then assembled on the surfaces of the MQPs via electrostatic interactions, yielding encoded MQPs. Experimental results showed that the encoded MQPs could be decoded using a Raman spectrometer. A multiplex immunoassay experiment demonstrated the validity and specificity of these encoded MQPs when they were used for bioanalysis. In concentration gradient experiments, the proposed method was found to give a linear concentration response to the target biomolecule at target concentrations of 0.46875-30 nM, and the detection limit was calculated to be 1.78 nM. The proposed method utilizes MQPs as carriers rather than conventional microbeads, which allows the interference caused by the background fluorescence of microbeads to be eliminated. The fluorescence of the encoded MQPs can be simply, rapidly, and inexpensively quantified using fluorescence microscopy. By dividing the quantitative and qualitative detection of biomolecules into two independent channels, crosstalk between the encoded signal and the labeled signal is averted and high decoding accuracy and detection sensitivity are guaranteed. Graphical abstract.


Subject(s)
Gold/chemistry , Nanotubes/chemistry , Quartz , Spectrum Analysis, Raman/methods
16.
Proc Natl Acad Sci U S A ; 113(16): E2296-305, 2016 Apr 19.
Article in English | MEDLINE | ID: mdl-27035942

ABSTRACT

DNA damage repair starts with the recognition of damaged sites from predominantly normal DNA. In eukaryotes, diverse DNA lesions from environmental sources are recognized by the xeroderma pigmentosum C (XPC) nucleotide excision repair complex. Studies of Rad4 (radiation-sensitive 4; yeast XPC ortholog) showed that Rad4 "opens" up damaged DNA by inserting a ß-hairpin into the duplex and flipping out two damage-containing nucleotide pairs. However, this DNA lesion "opening" is slow (˜5-10 ms) compared with typical submillisecond residence times per base pair site reported for various DNA-binding proteins during 1D diffusion on DNA. To address the mystery as to how Rad4 pauses to recognize lesions during diffusional search, we examine conformational dynamics along the lesion recognition trajectory using temperature-jump spectroscopy. Besides identifying the ˜10-ms step as the rate-limiting bottleneck towards opening specific DNA site, we uncover an earlier ˜100- to 500-µs step that we assign to nonspecific deformation (unwinding/"twisting") of DNA by Rad4. The ß-hairpin is not required to unwind or to overcome the bottleneck but is essential for full nucleotide-flipping. We propose that Rad4 recognizes lesions in a step-wise "twist-open" mechanism, in which preliminary twisting represents Rad4 interconverting between search and interrogation modes. Through such conformational switches compatible with rapid diffusion on DNA, Rad4 may stall preferentially at a lesion site, offering time to open DNA. This study represents the first direct observation, to our knowledge, of dynamical DNA distortions during search/interrogation beyond base pair breathing. Submillisecond interrogation with preferential stalling at cognate sites may be common to various DNA-binding proteins.


Subject(s)
DNA Damage , DNA, Fungal/chemistry , DNA-Binding Proteins/chemistry , Models, Chemical , Saccharomyces cerevisiae Proteins/chemistry , Saccharomyces cerevisiae/chemistry , DNA, Fungal/genetics , DNA, Fungal/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism
17.
Sensors (Basel) ; 19(24)2019 Dec 09.
Article in English | MEDLINE | ID: mdl-31835375

ABSTRACT

We proposed a coding and decoding method of suspension array (SA) based on micro-quartz pieces (MQPs) with different optical thicknesses. The capture probes (cDNA) were grafted onto the surfaces of MQPs and specifically recognized and combined with the partial sequence of the target DNA (tDNA) to form a MQP-cDNA-tDNA complex. Quantum dot-labeled signal probes were then used to specifically recognize and bind another portion of the tDNA in the complex to form a double-probe sandwich structure. This optical thickness-encoded SA can be decoded and detected by a dual-wavelength digital holographic phase fluorescence microscope system. We conducted a series of DNA molecule detection experiments by using this encoding method. Control experiments confirmed the specificity of optical thickness-encoded SA in DNA detection. The concentration gradient experiments then demonstrated the response of the MQPs based SA to analyte concentration. Finally, we used the encoding method to detect three types of DNA in a single sample and confirmed the feasibility of the proposed optical thickness-encoded SA in multiplexed DNA detection. The detection results are stable, and the detection exhibits high specificity and good repeatability.


Subject(s)
Biosensing Techniques , DNA, Complementary/genetics , DNA/isolation & purification , High-Throughput Screening Assays , DNA/genetics , Fluorescence , Quantum Dots/chemistry , Quartz/chemistry
18.
J Environ Manage ; 250: 109438, 2019 Nov 15.
Article in English | MEDLINE | ID: mdl-31479938

ABSTRACT

A novel MgO-modified magnetic biochar (MgO@MBC) was made by chemical co-precipitation of Mg2+/Fe3+ on anaerobic digestion residue (ADR) and subsequently pyrolyzing at different temperatures. MgO@MBC was used for phosphate recovery from aqueous solution. The physicochemical properties of MgO@MBC were comprehensively investigated using TEM-EDS, FT-IR, XRD, VSM, N2 adsorption-desorption and TGA. Results showed that MgO/γ-Fe2O3 nanoparticles were successfully deposited onto the surface of BC. The effects of reaction temperature, initial solution pH, MgO@MBC dosage, coexisting anions and phosphate concentration on the removal of phosphate by MgO@MBC were researched. Additionally, the adsorption process of phosphate onto MgO@MBC was well described by the pseudo second-order and pseudo first-order models, which indicated a chemisorption and physisorption process. Besides, the maximum adsorption capacity of MgO@MBC for phosphate by the Langmuir model were 149.25 mg/g at 25 °C. Moreover, the thermodynamic study suggested that the adsorption of phosphate onto MgO@MBC was a spontaneous and endothermic process. The adsorption mechanisms including physical absorption, surface electrostatic attraction, surface complexation and precipitation were revealed. It could be concluded that MgO@MBC exhibited high removal efficiency of phosphate and excellent magnetic property for the recovery. MgO@MBC could be utilized as a magnetically recoverable adsorbent to realize phosphate recovery and MgO@MBC after the adsorpion of phosphate could be applied in agricultural production as a fertilizer.


Subject(s)
Phosphates , Water Pollutants, Chemical , Adsorption , Anaerobiosis , Charcoal , Kinetics , Magnesium Oxide , Spectroscopy, Fourier Transform Infrared
19.
Water Sci Technol ; 80(10): 1851-1860, 2019 Nov.
Article in English | MEDLINE | ID: mdl-32144217

ABSTRACT

A novel zerovalen-iron-biochar composite (nZVI/SBC) was synthesized by using FeCl3-laden sorghum straw biomass as the raw material via a facile one-step pyrolysis method without additional chemical reactions (e.g., by NaBH4 reduction or thermochemical reduction). The nZVI/SBC was successfully employed as an activator in phenol degradation by activated persulfate. XRD, SEM, N2 adsorption-desorption and atomic absorption spectrophotometry analysis showed that the nanosized Fe0 was the main component of the 4ZVI/SBC activator, which was a mesopore material with an optimal FeCl3·6H2O/biomass impregnation mass ratio of 2.7 g/g. The 4ZVI/SBC activator showed an efficient degradation of phenol (95.65% for 30 min at 25 °C) with a large specific surface area of 78.669 m2·g-1. The recovery of 4ZVI/SBC activator after the degradation reaction of phenol can be realized with the small amount of dissolved iron in the water. The 4ZVI/SBC activator facilitated the activation of persulfate to degrade phenol into non-toxic CO2 and H2O. The trend of Cl-, SO4 2- and NO3 - affected the removal efficiency of phenol by using the 4ZVI/SBC activator in the following order: NO3 - > SO4 2- > Cl-. The one-step synthesis of the nanosized zerovalent-iron-biochar composite was feasible and may be applied as an effective strategy for controlling organic waste (e.g. phenol) by waste biomass.


Subject(s)
Iron , Water Pollutants, Chemical , Adsorption , Charcoal , Phenols
20.
Retina ; 38(4): 748-754, 2018 Apr.
Article in English | MEDLINE | ID: mdl-28368975

ABSTRACT

PURPOSE: To study the use of ultra-widefield fluorescein angiography (UWF FA) in the detection and management of retinal capillary hemangioblastomas in patients with von Hippel-Lindau disease. METHODS: This is a retrospective study of patients with von Hippel-Lindau disease who underwent UWF FA using the Optos camera at a single center from June 2009 to May 2015. The clinical use of UWF FA was reviewed, and the number of hemangioblastomas identified on UWF FA was compared with ophthalmoscopy and a simulated seven standard field (7SF) FA montage. RESULTS: Twenty eyes of 10 patients were identified. Only 33% of lesions seen on UWF FA were also found on ophthalmoscopy, and 88% of lesions visualized on UWF FA were located outside the 7SF overlay. In 5 eyes that had gaze steering, 18% of lesions could be visualized only on gaze-steered images. For the 14 eyes with data available, 6 had procedures recommended and 8 eyes observed based on data from UWF FA. One of 20 eyes had a lesion on ophthalmoscopy that was missed by imaging. CONCLUSION: Ultra-widefield FA using the Optos camera is helpful for the evaluation and management of patients with von Hippel-Lindau disease. The UWF FA with gaze steering appears to detect more hemangioblastomas than ophthalmoscopy and conventional angiography.


Subject(s)
Diagnostic Techniques, Ophthalmological , Fluorescein Angiography/methods , Hemangioblastoma/diagnostic imaging , Retinal Neoplasms/diagnostic imaging , von Hippel-Lindau Disease/complications , Adolescent , Adult , Child , Early Diagnosis , Female , Hemangioblastoma/etiology , Humans , Male , Middle Aged , Retinal Neoplasms/etiology , Retrospective Studies , Young Adult
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