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1.
Plant J ; 118(6): 1907-1921, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38491869

ABSTRACT

The sex of dioecious plants is mainly determined by genetic factors, but it can also be converted by environmental cues such as exogenous phytohormones. Gibberellic acids (GAs) are well-known inducers of flowering and sexual development, yet the pathway of gibberellin-induced sex conversion in dioecious spinach (Spinacia oleracea L.) remains elusive. Based on sex detection before and after GA3 application using T11A and SSR19 molecular markers, we confirmed and elevated the masculinization effect of GA on a single female plant through exogenous applications of GA3, showing complete conversion and functional stamens. Silencing of GIBBERELLIC ACID INSENSITIVE (SpGAI), a single DELLA family protein that is a central GA signaling repressor, results in similar masculinization. We also show that SpGAI can physically interact with the spinach KNOX transcription factor SHOOT MERISTEMLESS (SpSTM), which is a homolog of the flower meristem identity regulator STM in Arabidopsis. The silencing of SpSTM also masculinized female flowers in spinach. Furthermore, SpSTM could directly bind the intron of SpPI to repress SpPI expression in developing female flowers. Overall, our results suggest that GA induces a female masculinization process through the SpGAI-SpSTM-SpPI regulatory module in spinach. These insights may help to clarify the molecular mechanism underlying the sex conversion system in dioecious plants while also elucidating the physiological basis for the generation of unisexual flowers so as to establish dioecy in plants.


Subject(s)
Flowers , Gene Expression Regulation, Plant , Gibberellins , Plant Proteins , Spinacia oleracea , Gibberellins/metabolism , Plant Proteins/metabolism , Plant Proteins/genetics , Flowers/genetics , Flowers/physiology , Spinacia oleracea/genetics , Spinacia oleracea/physiology , Spinacia oleracea/metabolism , Plant Growth Regulators/metabolism , Transcription Factors/metabolism , Transcription Factors/genetics
2.
Small ; : e2402402, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38949051

ABSTRACT

Doping transition metal oxide spinels with metal ions represents a significant strategy for optimizing the electronic structure of electrocatalysts. Herein, a bimetallic Fe and Ru doping strategy to fine-tune the crystal structure of CoV2O4 spinel for highly enhanced oxygen evolution reaction (OER) is presented performance. The incorporation of Fe and Ru is observed at octahedral sites within the CoV2O4 structure, effectively modulating the electronic configuration of Co. Density functional theory calculations have confirmed that Fe acts as a novel reactive site, replacing V. Additionally, the synergistic effect of Fe, Co, and Ru effectively optimizes the Gibbs free energy of the intermediate species, reduces the reaction energy barrier, and accelerates the kinetics toward OER. As expected, the best-performing CoVFe0.5Ru0.5O4 displays a low overpotential of 240 mV (@10 mA cm-2) and a remarkably low Tafel slope of 38.9 mV dec-1, surpassing that of commercial RuO2. Moreover, it demonstrates outstanding long-term durability lasting for 72 h. This study provides valuable insights for the design of highly active polymetallic spinel electrocatalysts for energy conversion applications.

3.
Brief Bioinform ; 23(2)2022 03 10.
Article in English | MEDLINE | ID: mdl-35189636

ABSTRACT

There is currently a transformed interest toward understanding the impact of fermentation on functional food development due to growing consumer interest on modified health benefits of sustainable foods. In this review, we attempt to summarize recent findings regarding the impact of Next-generation sequencing and other bioinformatics methods in the food microbiome and use prediction software to understand the critical role of microbes in producing fermented foods. Traditionally, fermentation methods and starter culture development were considered conventional methods needing optimization to eliminate errors in technique and were influenced by technical knowledge of fermentation. Recent advances in high-output omics innovations permit the implementation of additional logical tactics for developing fermentation methods. Further, the review describes the multiple functions of the predictions based on docking studies and the correlation of genomic and metabolomic analysis to develop trends to understand the potential food microbiome interactions and associated products to become a part of a healthy diet.


Subject(s)
Fermented Foods , Microbiota , Computational Biology , Fermentation , Food Microbiology , Microbiota/genetics
4.
Bioinformatics ; 39(4)2023 04 03.
Article in English | MEDLINE | ID: mdl-37067488

ABSTRACT

MOTIVATION: A protein can be represented in several forms, including its 1D sequence, 3D atom coordinates, and molecular surface. A protein surface contains rich structural and chemical features directly related to the protein's function such as its ability to interact with other molecules. While many methods have been developed for comparing the similarity of proteins using the sequence and structural representations, computational methods based on molecular surface representation are limited. RESULTS: Here, we describe "Surface ID," a geometric deep learning system for high-throughput surface comparison based on geometric and chemical features. Surface ID offers a novel grouping and alignment algorithm useful for clustering proteins by function, visualization, and in silico screening of potential binding partners to a target molecule. Our method demonstrates top performance in surface similarity assessment, indicating great potential for protein functional annotation, a major need in protein engineering and therapeutic design. AVAILABILITY AND IMPLEMENTATION: Source code for the Surface ID model, trained weights, and inference script are available at https://github.com/Sanofi-Public/LMR-SurfaceID.


Subject(s)
Algorithms , Software , Membrane Proteins
5.
Langmuir ; 2024 Jun 24.
Article in English | MEDLINE | ID: mdl-38914517

ABSTRACT

The pursuit of novel strategies for synthesizing high-performance nanostructures of graphitic carbon nitride (g-C3N4) has garnered increasing scholarly attention in the field of photocatalysis. Herein, we have successfully designed a metal-free photocatalyst by integrating mesoporous carbon nitride (mpg-C3N4) and C60 through a straightforward and innovative method, marking the first instance of such an achievement. Under red light, the C60/mpg-C3N4 composite exhibited a significantly accelerated rhodamine B (RhB) photodecomposition rate, surpassing bulk g-C3N4 by more than 25.8 times and outperforming pure mpg-C3N4 by 7.8 times. The synergistic effect of C60 and the mesoporous structure significantly enhanced the photocatalytic performance of g-C3N4 by adjusting its electronic structure, broadening the light absorption range, increasing the active sites, and reducing the recombination of photogenerated carriers. This work presents a promising avenue for harnessing a metal-free, stable, efficient photocatalyst driven by red light, with potential for enhancing solar energy utilization in environmental remediation.

6.
Inorg Chem ; 63(5): 2655-2662, 2024 Feb 05.
Article in English | MEDLINE | ID: mdl-38247267

ABSTRACT

In an increasing manner, near-infrared phosphor-converted light-emitting diodes (NIR pc-LEDs) are considered to be exemplary light sources owing to their notable attributes of elevated output power, economical nature, and exceptional portability. NIR phosphors are critical components of NIR pc-LEDs. Herein, we report a novel blue light excitable NIR phosphor CaLu2ZrScAl3O12:Cr3+ (CLZSA:Cr3+) as a crucial and efficient broadband NIR emitter. The CLZSA:Cr3+ phosphor displays an intense NIR broadband emission peaking at 776 nm and with a full width at half-maximum (fwhm) of 140 nm. The designed material also exhibits superior resistance to thermal quenching, as the intensity of emission at 423 K remains at 80% of that at room temperature. The constructed NIR pc-LED device based on CLZSA:Cr3+ demonstrates a high total output power of 68.4 mW at a drive current of 100 mA, along with a high photoelectric conversion efficiency of 23.0%. Impressively, the high-power NIR pc-LEDs are utilized as light sources for remote control and non-invasive detection, resulting in the excellent performance and remarkable achievement.

7.
Cell Mol Biol (Noisy-le-grand) ; 70(5): 18-26, 2024 May 27.
Article in English | MEDLINE | ID: mdl-38814239

ABSTRACT

Plastic contamination can cause damage to the water quality of fish farm ponds, and also affect the quality of the final product. Pseudomonas mendocina was found to biodegrade plastics. Our study aimed to investigate the physicochemical properties and drug resistance of P. mendocina isolated from local freshwater aquaculture farms. Firstly, the strain was isolated from aquaculture water and then identified by matrix-assisted flight mass spectrometry and 16S rDNA sequencing. Then, biochemical and antibiotic resistance analyses were performed, and a microbial high-throughput growth detector was used to assess the growth of the strain. Finally, PCR and proteomics analyses were conducted to determine drug-resistance-related genes/proteins. According to the results of the spectrum diagram and sequencing, the isolated bacteria were identified as P. mendocina, and were positive for reactions of ADH, MTE, LAC, MNE, FRU, CIT, MLT, ONPG, and ACE. P. mendocina was sensitive to most of the antibiotics, and its resistance to CHL, MIN, and TIC/CLA was intermediate. Additionally, gyrB was the resistance gene, and mdtA2, mdtA3, mdaB, and emrK1 were closely related to the drug resistance of P. mendocina. Our results show the biochemical properties of P. mendocina in isolated aquaculture water, and provide a new perspective for P. mendocina involved in the biological removal of plastics or microplastics in freshwater aquaculture farms.


Subject(s)
Aquaculture , Fresh Water , Pseudomonas mendocina , Fresh Water/microbiology , Pseudomonas mendocina/genetics , Pseudomonas mendocina/isolation & purification , RNA, Ribosomal, 16S/genetics , Anti-Bacterial Agents/pharmacology , Phylogeny , Farms , Microbial Sensitivity Tests , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Drug Resistance, Bacterial/genetics , Animals
8.
Inorg Chem ; 62(47): 19341-19349, 2023 Nov 27.
Article in English | MEDLINE | ID: mdl-37955404

ABSTRACT

The cation-equivalent substitution strategy has the ability to manipulate the luminescence color of phosphors and enhance their overall luminescence performance. A series of novel yellow feldspar-type 3D layered phosphors (Ca1-ySry)4MgAl2Si3O14:xEu2+ were synthesized using a high-temperature solid-state reaction. The solid solution phosphors belong to a tetragonal crystal system with a space group of P4̅21m and cell parameters of a = b = 7.75407-7.91794 Å, c = 5.04299-5.22543 Å, and V = 303.166-327.602 Å3. Under near-ultraviolet (n-UV) excitation, the luminescence color of the phosphor undergoes modulation from yellow-green (530 nm) to blue (467 nm) as the Sr2+ ion substitution ratio increases. This modulation is attributed to the gradual decrease in crystal field splitting energy. Additionally, both the Stokes shift and the full width of the luminescence spectra decrease. Furthermore, there is an increase in the quantum yield (QY) from 45.50 to 60.73%. Finally, the fabricated white-light-emitting diode devices emitted warm white light and achieved high Ra (Ra = 94, 96.6, 92.7) and low correlated color temperature (CCT = 3486, 3430, 3788 K), indicating that the prepared solid solution phosphors can be used as candidate materials for WLED lighting.

9.
J Stroke Cerebrovasc Dis ; 32(3): 106974, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36587509

ABSTRACT

PURPOSE: Many studies have shown that cytochrome P450 (CYP) gene polymorphisms are usually associated with an increased risk of cardiovascular and cerebrovascular diseases. To explore the association of CYP2C8 and CYP2J2 gene polymorphisms with hypertensive intracerebral hemorrhage (HICH) in the Han Chinese population. METHODS: Forty HICH patients and 40 control subjects were recruited for this study. Two single nucleotide polymorphisms (SNP) (rs1058932, rs2275622) in the CYP2C8 gene and two SNPs (rs2271800, rs1155002) in the CYP2J2 gene were selected for genotyping by direct sequencing. Statistical analysis was applied to examine the effect of genetic variation on HICH. RESULTS: We found that variant alleles of CYP2C8 rs1058932 (A) and rs2275622 (C) were both significantly associated with HICH, especially in females. We also found significant associations of CYP2C8 rs1058932 (A) and rs2275622 (C) variant alleles with poor outcomes in HICH patients, especially in males. CONCLUSIONS: CYP2C8 gene polymorphisms might increase the risk of HICH in the Han Chinese population and might lead to poor outcomes. This finding adds to the body of literature supporting novel therapeutic strategies for HICH.


Subject(s)
Cytochrome P-450 CYP2J2 , Intracranial Hemorrhage, Hypertensive , Male , Female , Humans , Cytochrome P-450 CYP2C8/genetics , Cytochrome P-450 Enzyme System/genetics , Polymorphism, Single Nucleotide
10.
Molecules ; 28(18)2023 Sep 06.
Article in English | MEDLINE | ID: mdl-37764246

ABSTRACT

The shift to an environmentally friendly material economy requires renewable resource exploration. This shift may depend on lignin valorization. Lignin is an aromatic polymer that makes up one-third of total lingo-cellulosic biomass and is separated into large amounts for biofuel and paper manufacture. This renewable polymer is readily available at a very low cost as nearly all the lignin that is produced each year (90-100 million tons) is simply burned as a low-value fuel. Lignin offers potential qualities for many applications, and yet it is underutilized. This Perspective highlights lignin-based material prospects and problems in food packaging, antimicrobial, and agricultural applications. The first half will discuss the present and future studies on exploiting lignin as an addition to improve food packaging's mechanical, gas, UV, bioactive molecules, polyphenols, and antioxidant qualities. Second, lignin's antibacterial activity against bacteria, fungi, and viruses will be discussed. In conclusion, lignin agriculture will be discussed in the food industries.


Subject(s)
Lignin , Nanostructures , Agriculture , Anti-Bacterial Agents/pharmacology , Polymers
11.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 40(10): 1228-1235, 2023 Oct 10.
Article in Zh | MEDLINE | ID: mdl-37730222

ABSTRACT

OBJECTIVE: To assess the association of SLC6A4 gene c.*670T>G polymorphism with the risk for asthma and peripheral blood cytological characteristics among ethnic Zhuang Chinese from Guangxi, China. METHODS: From May 2017 to March 2020, 258 patients diagnosed with asthma and 244 healthy controls were recruited from the Affiliated Hospital of Youjiang Minzhu Medical College and the People's Hospital of Hechi. Genotypes of the c.*670T>G polymorphism were determined by Sanger sequencing. Flow cytometry was used in combination with an electrical impedance method for the counting and classification of peripheral blood cells. RESULTS: Compared with the T allele, the G allele of the c.*670T>G polymorphism was associated with the risk for asthma in the population (OR = 1.54, 95%CI = 1.15-2.06; P = 0.004). Compared with the GT and TT genotypes, homozygous GG genotype also comprised a risk factor (OR = 1.66, 95%CI = 1.16-2.38; P = 0.005). Stratification of the risk factors showed that the homozygous GG genotype has increased the risk of asthma in males and urban residents (P < 0.01). The erythrocyte, hemoglobin and platelet counts of the asthma group were significantly higher than the control group (P < 0.001). The GG, GT and TT genotypes have respectively accounted for 82.35%, 17.65% and 0% of the samples with platelets exceeding the normal value. The overall platelet level of GG genotype was higher than GT+TT genotype (P < 0.05). The significant association was verified by the false positive report probability, and at a prior probability level of 0.1, G vs. T false positive probability was 0.071, and GG vs. GT+TT false positive probability was 0.153. CONCLUSION: The GG genotype of the c.*670T>G polymorphism is associated with the risk for asthma among ethnic Zhuang Chinese from northwest Guangxi. Above finding has also enriched the genotypic data and peripheral blood phenotype for this polymorphism.


Subject(s)
Asthma , East Asian People , Male , Humans , China , Genotype , Alleles , Asthma/genetics , Serotonin Plasma Membrane Transport Proteins
12.
J Chem Phys ; 157(18): 184504, 2022 Nov 14.
Article in English | MEDLINE | ID: mdl-36379802

ABSTRACT

Establishing the structure-property relationship is an important goal of glassy materials, but it is usually impeded by their disordered structure and non-equilibrium nature. Recent studies have illustrated that secondary (ß) relaxation is closely correlated with several properties in a range of glassy materials. However, it has been challenging to identify the pertinent structural features that govern it. In this work, we show that the so-called polyamorphous transition in metallic glasses offers an opportunity to distinguish the structural length scale of ß relaxation. We find that, while the glass transition temperature and medium-range orders (MROs) change rapidly across the polyamorphous transition, the intensity of ß relaxation and the short-range orders (SROs) evolve in a way similar to those in an ordinary reference glass without polyamorphous transition. Our findings suggest that the MRO accounts mainly for the global stiffening of the materials and the glass transition, while the SRO contributes more to ß relaxation per se.

13.
BMC Microbiol ; 21(1): 3, 2021 01 04.
Article in English | MEDLINE | ID: mdl-33397284

ABSTRACT

BACKGROUND: Chlamydia trachomatis is the most common sexually transmitted infection and the bacterial agent of trachoma globally. C. trachomatis undergoes a biphasic developmental cycle involving an infectious elementary body and a replicative reticulate body. Little is currently known about the gene expression dynamics of host cell mRNAs, lncRNAs, and miRNAs at different stages of C. trachomatis development. RESULTS: Here, we performed RNA-seq and miR-seq on HeLa cells infected with C. trachomatis serovar E at 20 h post-infection (hpi) and 44 hpi with or without IFN-γ treatment. Our study identified and validated differentially expressed host cell mRNAs, lncRNAs, and miRNAs during infection. Host cells at 20 hpi showed the most differential upregulation of both coding and non-coding genes while at 44 hpi in the presence of IFN-γ resulted in a dramatic downregulation of a large proportion of host genes. Using RT-qPCR, we validated the top 5 upregulated mRNAs and miRNAs, which are specific for different stages of C. trachomatis development. One of the commonly expressed miRNAs at all three stages of C. trachomatis development, miR-193b-5p, showed significant expression in clinical serum samples of C. trachomatis-infected patients as compared to sera from healthy controls and HIV-1-infected patients. Furthermore, we observed significant upregulation of antigen processing and presentation, and T helper cell differentiation pathways at 20 hpi whereas T cell receptor, mTOR, and Rap1 pathways were modulated at 44 hpi. Treatment with IFN-γ at 44 hpi showed the upregulation of cytokine-cytokine receptor interaction, FoxO signaling, and Ras signaling pathways. CONCLUSIONS: Our study documented transcriptional manipulation of the host cell genomes and the upregulation of stage-specific signaling pathways necessary for the survival of the pathogen and could serve as potential biomarkers in the diagnosis and management of the disease.


Subject(s)
Chlamydia Infections/genetics , Chlamydia trachomatis/growth & development , Gene Expression Profiling/methods , MicroRNAs/genetics , Signal Transduction , Case-Control Studies , Chlamydia Infections/blood , Chlamydia trachomatis/drug effects , Gene Expression Regulation/drug effects , HIV Infections/blood , HIV Infections/genetics , HeLa Cells , Host-Pathogen Interactions , Humans , Interferon-gamma/pharmacology , MicroRNAs/blood , RNA, Long Noncoding/blood , Sequence Analysis, RNA , Signal Transduction/drug effects , Up-Regulation
14.
Langmuir ; 37(11): 3270-3280, 2021 Mar 23.
Article in English | MEDLINE | ID: mdl-33705652

ABSTRACT

Supported Au catalysts are widely used for CO oxidation due to their extremely high activity, and the modification of a support structure is a crucial method to improve catalytic performance. Herein, we prepared gold catalysts supported on flaky TiO2 and on TiO2 hydrogenated at different temperatures (200, 400, and 600 °C). We found that the sample with the support pretreated in hydrogen at 600 °C (0.5Au/TiO2-H600) showed the greatest advantages in activity and stability over the sample with as-prepared TiO2 nanosheets (0.5Au/TiO2-UC). First, calcination at 600 °C changed the exposed surface of TiO2 from {001} to {101}, and gold nanoparticles (2-3 nm) were observed as highly reactive species on 0.5Au/TiO2-H600. Moreover, the increase of oxygen vacancies on the surface of 0.5Au/TiO2-H600 was conducive to oxygen activation and promoted the catalytic activity. Therefore, we emphasized the important role of the support and gave an effective method to improve the catalytic performance by regulating the support structure.

15.
J Vasc Surg ; 71(1): 141-148, 2020 01.
Article in English | MEDLINE | ID: mdl-31327613

ABSTRACT

OBJECTIVE: The purpose of this study was to examine the efficacy and safety of catheter-directed thrombolysis (CDT) for first-line treatment of popliteal and infrapopliteal acute limb ischemia. METHODS: A total of 28 consecutive patients (30 limbs) who underwent CDT for treatment of popliteal and infrapopliteal acute limb ischemia of thromboembolic origin between March 2012 and December 2017 were enrolled in this study. Per the Society for Vascular Surgery, limbs were classified into three runoff score groups: <5, good; 5 to 10, compromised; and >10, poor. The primary end points were primary patency and limb salvage assessed by Kaplan-Meier survival analysis. Secondary end points were technical success and clinical success. The Society for Vascular Surgery-recommended scale for gauging changes in clinical status was used to assess clinical success. Safety of the procedure was evaluated on the basis of periprocedural complications according to the Society of Interventional Radiology classification system. RESULTS: Technical success was achieved in 25 (83.33%) treated limbs. Improved clinical status (grade +3/+2) was achieved in 93.33% of limbs. Primary patency and limb salvage for the entire cohort were 76.67% and 90% at 6 months and 60.0% and 76.67% at 12 months, respectively. The patency rate at 6 months and 12 months was 91.67% and 83.33% for the good runoff group, 80% and 60% for the compromised runoff group, and 50% and 25% for the poor runoff group, respectively. The patency rate of the good runoff group was significantly higher compared with that of the poor runoff group (P = .004). Major amputation rate and mortality rate were 16.67% and 7.14%, respectively, at 12 months. The reintervention rate was 3.57% at 6 months and 21.42% at 12 months. CONCLUSIONS: CDT is safe and effective for revascularization of smaller vessel acute arterial thromboembolism as a primary therapy. However, more studies with a larger sample are warranted.


Subject(s)
Catheterization, Peripheral , Fibrinolytic Agents/administration & dosage , Ischemia/drug therapy , Peripheral Arterial Disease/drug therapy , Popliteal Artery , Thrombolytic Therapy , Acute Disease , Adult , Aged , Amputation, Surgical , Catheterization, Peripheral/adverse effects , Catheterization, Peripheral/mortality , Female , Fibrinolytic Agents/adverse effects , Humans , Ischemia/diagnostic imaging , Ischemia/mortality , Ischemia/physiopathology , Limb Salvage , Male , Middle Aged , Peripheral Arterial Disease/diagnostic imaging , Peripheral Arterial Disease/mortality , Peripheral Arterial Disease/physiopathology , Popliteal Artery/diagnostic imaging , Popliteal Artery/physiopathology , Prospective Studies , Risk Factors , Thrombolytic Therapy/adverse effects , Thrombolytic Therapy/mortality , Time Factors , Treatment Outcome , Vascular Patency
16.
Langmuir ; 36(38): 11196-11206, 2020 Sep 29.
Article in English | MEDLINE | ID: mdl-32787057

ABSTRACT

Copper manganese composite (hopcalite) catalyst has been widely explored for low-temperature CO oxidation reactions. However, the previous reports on the stabilization of such composite catalysts have shown that they deactivated severely under moist conditions. Herein, we developed an α-MnO2 nanorod-supported copper oxide catalyst that is very active and stable for the conditions with or without moisture by the deposition precipitation (DP) method. Incredibly, the CuO/MnO2 DP catalyst (with 5 wt % copper loading) achieves superior activity with a reaction rate of 9.472 µmol-1·gcat-1·s-1 even at ambient temperatures, which is at least double times of that for the reported copper-based catalyst. Additionally, the CuO/MnO2 DP catalyst is significantly more stable than the copper manganese composite catalysts reported in the literature under the presence of 3% water vapor as well as without moisture. A correlation between the catalytic CO oxidation activity and textural characteristics was derived via multitechnique analyses. The results imply that the superior activity of the CuO/MnO2 DP catalyst is associated with the proper adsorption of CO on partially reduced copper oxide as Cu(I)-CO and more surface oxygen species at the interfacial site of the catalyst.

17.
Langmuir ; 36(8): 2030-2036, 2020 03 03.
Article in English | MEDLINE | ID: mdl-32091913

ABSTRACT

Albumin molecules are extensively used as biocompatible coatings, and poly(ethylene glycol) (PEG) materials are widely used for antifouling. PEG materials have excellent antifouling property because of their strong surface hydration. Our previous research indicates that hydration at the PEG/bovine serum albumin solution interface is stronger than that at the PEG/water interface. This research shows that this observation is general for different types of albumin molecules. Different albumins including bovine, porcine, rat, rabbit, and sheep serum albumins were studied in this research. It was found that the hydration at the PEG methacrylate (pOEGMA)/albumin solution interface is always stronger than that at the pOEGMA/water interface. Here, we define "strong interfacial hydration" as "ordered strongly hydrogen-bonded interfacial water". We believe that such a strong hydration is because of the strong hydration on the albumin surface, leading to its biocompatible property. All of the albumin molecules demonstrated stronger hydration on the pOEGMA surface compared to other protein molecules such as lysozyme and fibrinogen. The strong hydration on albumin molecules is related to the high surface coverage of glutamic acid and lysine with similar amounts.


Subject(s)
Polyethylene Glycols , Serum Albumin, Bovine , Adsorption , Animals , Cattle , Methacrylates , Muramidase , Rabbits , Rats , Sheep , Surface Properties , Swine , Water
18.
J Am Chem Soc ; 141(51): 20335-20343, 2019 12 26.
Article in English | MEDLINE | ID: mdl-31774666

ABSTRACT

Graphene-based biosensors have attracted considerable attention due to their advantages of label-free detection and high sensitivity. Many such biosensors utilize noncovalent van der Waals force to attach proteins onto graphene surface while preserving graphene's high conductivity. Maintaining the protein structure without denaturation/substantial conformational change and controlling proper protein orientation on the graphene surface are critical for biosensing applications of these biosensors fabricated with proteins on graphene. Based on the knowledge we obtained from our previous experimental study and computer modeling of amino acid residual level interactions between graphene and peptides, here we systemically redesigned an important protein for better conformational stability and desirable orientation on graphene. In this paper, immunoglobulin G (IgG) antibody-binding domain of protein G (protein GB1) was studied to demonstrate how we can preserve the protein native structure and control the protein orientation on graphene surface by redesigning protein mutants. Various experimental tools including sum frequency generation vibrational spectroscopy, attenuated total refection-Fourier transform infrared spectroscopy, fluorescence spectroscopy, and circular dichroism spectroscopy were used to study the protein GB1 structure on graphene, supplemented by molecular dynamics simulations. By carefully designing the protein GB1 mutant, we can avoid strong unfavorable interactions between protein and graphene to preserve protein conformation and to enable the protein to adopt a preferred orientation. The methodology developed in this study is general and can be applied to study different proteins on graphene and beyond. With the knowledge obtained from this research, one could apply this method to optimize protein function on surfaces (e.g., to enhance biosensor sensitivity).


Subject(s)
Graphite/chemistry , Receptors, GABA-B/chemistry , Biosensing Techniques , Molecular Dynamics Simulation , Protein Conformation
19.
J Am Chem Soc ; 141(25): 9980-9988, 2019 06 26.
Article in English | MEDLINE | ID: mdl-31199639

ABSTRACT

Single layered two-dimensional (2D) materials such as transition metal dichalcogenides (TMDs) show great potential in many microelectronic or nanoelectronic applications. For example, because of extremely high sensitivity, TMD-based biosensors have become promising candidates for next-generation label-free detection. However, very few studies have been conducted on understanding the fundamental interactions between TMDs and other molecules including biological molecules, making the rational design of TMD-based sensors (including biosensors) difficult. This study focuses on the investigations of the fundamental interactions between proteins and two widely researched single-layered TMDs, MoS2, and WS2 using a combined study with linear vibrational spectroscopy attenuated total reflectance FTIR and nonlinear vibrational spectroscopy sum frequency generation vibrational spectroscopy, supplemented by molecular dynamics simulations. It was concluded that a large surface hydrophobic region in a relatively flat location on the protein surface is required for the protein to adsorb onto a monolayered MoS2 or WS2 surface with preferred orientation. No disulfide bond formation between cysteine groups on the protein and MoS2 or WS2 was found. The conclusions are general and can be used as guiding principles to engineer proteins to attach to TMDs. The approach adopted here is also applicable to study interactions between other 2D materials and biomolecules.


Subject(s)
Bacterial Proteins/chemistry , Disulfides/chemistry , Glucosidases/chemistry , Hydrolases/chemistry , Molybdenum/chemistry , Tungsten/chemistry , beta-Glucosidase/chemistry , Adsorption , Clostridium cellulovorans/enzymology , Hydrophobic and Hydrophilic Interactions , Lactococcus lactis/enzymology , Molecular Dynamics Simulation , Spectroscopy, Fourier Transform Infrared , Sphingomonas/enzymology , Surface Properties , Vibration
20.
J Transl Med ; 17(1): 326, 2019 10 01.
Article in English | MEDLINE | ID: mdl-31570096

ABSTRACT

BACKGROUND: To develop a machine learning model for predicting acute respiratory distress syndrome (ARDS) events through commonly available parameters, including baseline characteristics and clinical and laboratory parameters. METHODS: A secondary analysis of a multi-centre prospective observational cohort study from five hospitals in Beijing, China, was conducted from January 1, 2011, to August 31, 2014. A total of 296 patients at risk for developing ARDS admitted to medical intensive care units (ICUs) were included. We applied a random forest approach to identify the best set of predictors out of 42 variables measured on day 1 of admission. RESULTS: All patients were randomly divided into training (80%) and testing (20%) sets. Additionally, these patients were followed daily and assessed according to the Berlin definition. The model obtained an average area under the receiver operating characteristic (ROC) curve (AUC) of 0.82 and yielded a predictive accuracy of 83%. For the first time, four new biomarkers were included in the model: decreased minimum haematocrit, glucose, and sodium and increased minimum white blood cell (WBC) count. CONCLUSIONS: This newly established machine learning-based model shows good predictive ability in Chinese patients with ARDS. External validation studies are necessary to confirm the generalisability of our approach across populations and treatment practices.


Subject(s)
Algorithms , Intensive Care Units , Machine Learning , Models, Theoretical , Respiratory Distress Syndrome/diagnosis , Aged , China , Cohort Studies , Female , Humans , Male , Middle Aged , ROC Curve
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