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1.
Sci Total Environ ; 720: 137566, 2020 Feb 25.
Artigo em Inglês | MEDLINE | ID: mdl-32146395

RESUMO

Anaerobic digestion (AD) with thermal hydrolysis pretreatment has been attracted widespread attention in recent years due to its high efficiency. However, few studies focus on systematical comparison of the downstream AD processes for thermal hydrolyzed sludge and their corresponding microbial community compositions, especially on those at pilot scale and above. Thus, this study systematically compared the long-term performance and microbial communities of two pilot-scale anaerobic reactors for thermal hydrolyzed sludge digestion under mesophilic and thermophilic conditions. The results presented that mesophilic anaerobic digestion (MAD) showed a better performance of methane production than thermophilic anaerobic digestion (TAD). The hydraulic retention time (HRT) needed to be longer than 12 days in MAD while 20 days in TAD to achieve the relatively high methane production, which could be explained by that the ammonia nitrogen accumulation especially the free ammonia determined in TAD was higher than that in MAD at all HRTs, emerging an inhibition of methane yield in TAD. High-throughput Illumina sequencing results demonstrated a more diverse microbial community in MAD than that in TAD. TAD was mediated by a suite of thermophiles, such as Coprothermobacter and Methanothermobacter, while taxa harbored in MAD mostly belonged to Bacteroidetes and relatively broad types of methanogens. In addition, hydrogenotrophic methanogens were the predominant of archaea communities in both digesters probably due to the relatively high concentration of ammonia nitrogen.

2.
J Nutr ; 2020 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-32167145

RESUMO

BACKGROUND: The total and specific types of polyunsaturated fatty acids (PUFAs) related to metabolic syndrome (MetS) remain inconsistent. OBJECTIVE: We assessed the association of erythrocyte n-3 and n-6 PUFAs with MetS and the components of MetS in a cohort population. METHODS: This prospective analysis included 2754 participants (aged 40-75 y) from the Guangzhou Nutrition and Health Study (2008-2019) in China. Erythrocyte PUFAs at baseline were measured using gas chromatography. MetS was assessed every 3 y according to the updated National Cholesterol Education Program Adult Treatment Panel III criteria. Multivariable Cox proportional hazard models were used to evaluate HRs and 95% CIs. RESULTS: We identified 716 incident cases of MetS. The primary analyses showed that the HRs (95% CIs) of MetS (tertile 3 versus 1) were 0.67 (0.56, 0.80) for n-3 PUFAs and 0.70 (0.58, 0.85) for n-6 PUFAs (all Ps trend <0.001). The secondary outcomes showed that, higher erythrocyte very-long-chain (VLC) PUFAs [20:3n-3, docosapentaenoic acid (DPA), docosahexaenoic acid (DHA), arachidonic acid (ARA), and 22:4n-6], but lower α-linolenic acid (ALA) and γ-linolenic acid (GLA), tended to be associated with lower incidences of MetS and its components; among individual MetS components, the associations of PUFAs were more pronounced for hypertriglyceridemia (HTG) and hypertension, followed by low high-density lipoproten (HDL) cholesterol. Significantly higher concentrations of n-3 PUFAs (total, DPA, and DHA) and n-6 PUFAs (total, ARA, and 22:4) were observed in participants with improved (versus progressed) status of MetS (all Ps trend ≤0.003). CONCLUSION: This study reveals that higher erythrocyte VLC n-3 and n-6 PUFAs, but lower 18-carbon PUFAs (ALA and GLA), are associated with lower risks of MetS components (HTG, hypertension, and low HDL cholesterol) and thereby lower MetS incidence in Chinese adults.

3.
Commun Biol ; 3(1): 118, 2020 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-32170157

RESUMO

Abundant life activities are maintained by various biomolecule relationships in human cells. However, many previous computational models only focus on isolated objects, without considering that cell is a complete entity with ample functions. Inspired by holism, we constructed a Molecular Associations Network (MAN) including 9 kinds of relationships among 5 types of biomolecules, and a prediction model called MAN-GF. More specifically, biomolecules can be represented as vectors by the algorithm called biomarker2vec which combines 2 kinds of information involved the attribute learned by k-mer, etc and the behavior learned by Graph Factorization (GF). Then, Random Forest classifier is applied for training, validation and test. MAN-GF obtained a substantial performance with AUC of 0.9647 and AUPR of 0.9521 under 5-fold Cross-validation. The results imply that MAN-GF with an overall perspective can act as ancillary for practice. Besides, it holds great hope to provide a new insight to elucidate the regulatory mechanisms.

4.
Langmuir ; 2020 Mar 26.
Artigo em Inglês | MEDLINE | ID: mdl-32212710

RESUMO

Purification and collection of industrial products from oil-water mixtures are commonly implemented processes. However, the efficiencies of such processes can be severely influenced by the presence of emulsifiers that induce formation of small oil droplets dispersed in the mixtures. Understanding of this emulsifying effect and its counteractions which occur at oil/water interface is therefore necessary for the improvement of designs of these processes. In this article, we investigated the interfacial mechanisms of protein-induced emulsification and the opposing surfactant-induced demulsification related to corn oil refinement. At corn oil/water interfaces, the pH-dependent emulsifying function of zein protein, which is the major storage protein of corn, was elucidated by surface/interface-sensitive sum frequency generation (SFG) vibrational spectroscopy technique. The effective stabilization of corn oil droplets by zein protein was illustrated and correlated to its ordered amide I group at the oil/water interface. Substantial decrease of this ordering with the addition of three industrial surfactants to corn oil-zein solution mixtures was also observed using SFG, which explains the surfactant-induced destabilization and coalescence of small oil droplets. Surfactant-protein interaction was then demonstrated to be the driving force for the disordering of interfacial proteins, either by disrupting protein layers or partially excluding protein molecules from the interface. The ordered zein proteins at the interface were therefore revealed to be the critical factor for the formation of corn oil-water emulsion.

5.
BMC Med Inform Decis Mak ; 20(Suppl 2): 49, 2020 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-32183788

RESUMO

BACKGROUND: The key to modern drug discovery is to find, identify and prepare drug molecular targets. However, due to the influence of throughput, precision and cost, traditional experimental methods are difficult to be widely used to infer these potential Drug-Target Interactions (DTIs). Therefore, it is urgent to develop effective computational methods to validate the interaction between drugs and target. METHODS: We developed a deep learning-based model for DTIs prediction. The proteins evolutionary features are extracted via Position Specific Scoring Matrix (PSSM) and Legendre Moment (LM) and associated with drugs molecular substructure fingerprints to form feature vectors of drug-target pairs. Then we utilized the Sparse Principal Component Analysis (SPCA) to compress the features of drugs and proteins into a uniform vector space. Lastly, the deep long short-term memory (DeepLSTM) was constructed for carrying out prediction. RESULTS: A significant improvement in DTIs prediction performance can be observed on experimental results, with AUC of 0.9951, 0.9705, 0.9951, 0.9206, respectively, on four classes important drug-target datasets. Further experiments preliminary proves that the proposed characterization scheme has great advantage on feature expression and recognition. We also have shown that the proposed method can work well with small dataset. CONCLUSION: The results demonstration that the proposed approach has a great advantage over state-of-the-art drug-target predictor. To the best of our knowledge, this study first tests the potential of deep learning method with memory and Turing completeness in DTIs prediction.

6.
Langmuir ; 36(8): 2030-2036, 2020 Mar 03.
Artigo em Inglês | MEDLINE | ID: mdl-32091913

RESUMO

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.

7.
J Transl Med ; 18(1): 101, 2020 Feb 24.
Artigo em Inglês | MEDLINE | ID: mdl-32093682

RESUMO

BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is a malignancy characterized by metabolic reprogramming. ABAT and ALDH6A1 are metabolic enzymes. In this study, we aim to investigate the associations of ABAT and ALDH6A1 with the malignancy of ccRCC cells. METHODS: The gene expression levels of ABAT and ALDH6A1 in ccRCC were analyzed from gene expression microarray datasets and RNA sequencing data. Clinical information was analyzed from The Cancer Genome Atlas (TCGA) data. The distributions of ABAT and ALDH6A1 in ccRCC clinical tissues were screened by reverse transcription-quantitative polymerase chain reaction (RT-QPCR) and immunohistochemical assays. The effect of overexpression of ABAT or ALDH6A1 was measured by detecting the cell viability, migration ability, and the ratio of lactate and nicotinamide adenine dinucleotide phosphate (NADPH). Chromatin immunoprecipitation (ChIP) and luciferase reporter assays were carried out to investigate the transcript regulation of HNF4A in ABAT and ALDH6A1. RESULTS: Remarkable downregulated ABAT and ALDH6A1 expression levels were observed in ccRCC patients and low expression of ABAT and ALDH6A1 was correlated with poor survival. Overexpression of ABAT or ALDH6A1 significantly attenuated cell proliferation and migration, and impaired lactate production. In ABAT increased ccRCC cells, the ratio of NADPH/NADP+ was reduced. Finally, we demonstrated that ABAT and ALDH6A1 were directly regulated by a tumor suppressor, HNF4A. CONCLUSIONS: These observations identified HNF4A-regulated low-expressed ABAT and ALDH6A1 as promising diagnostic and prognostic biomarkers for ccRCC.

8.
Environ Pollut ; 261: 114140, 2020 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-32062096

RESUMO

Microbial communities in activated sludge (AS) have a significant influence on the functions and stability of aeration tanks in wastewater treatment plants (WWTPs). The microbial community structure is affected by various factors, among which operational parameters outcompeted as the key factors in shaping its structure. However, as an important operational parameter of aeration tank, the mechanisms by which sludge retention time (SRT) affect community properties remain unclear. In this study, 144 AS samples from aeration tanks of 48 full-scale WWTPs operating under different SRT conditions were examined via high-throughput Illumina-MiSeq sequencing technology. The results indicated that SRT significantly affected the diversity, composition, assembly, and co-occurrence patterns of the microbial community in aeration tanks. Moreover, our results provided clear evidence that the microbial communities in aeration tanks operating under SRT of 10-20 days have the highest biodiversity, the lowest stochastic processes influence, the more stable molecular ecological network structure, the lowest risks of filamentous sludge bulking and enhanced nitrogen removal potential. The microbial communities could be more stable and resilient to disturbance when aeration tanks were operated under this SRT condition. The findings of this study provided a reference for the optimization of aeration tanks from an of microbial community perspective.

9.
Biomaterials ; 232: 119668, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31927179

RESUMO

Mitophagy is a specific self-protective autophagic process that degrades damaged or dysfunctional mitochondria, and is generally considered to reduce the effectiveness of mitochondria-targeted therapies. Here, we report an energy depletion-based anticancer strategy by selectively activating excessive mitophagy in cancer cells. We fabricate a type of mitochondria-targeting nanomicelles via the self-assembly of D-α-tocopheryl polyethylene glycol 1000 succinate (TPGS) and dc-IR825 (a near-infrared cyanine dye and a photothermal agent). The TPGS/dc-IR825 nanomicelles enable mitochondrial damage in cancer cells, which, for self-protection, activate two autophagic pathways, (1) mitophagy and (2) adenosine triphosphate (ATP) shortage-triggered autophagy. However, the excessive mitophagy/autophagy activities far surpass the degradative capacity of autolysosomes, leading to the formation of micrometer-sized vacuoles and degradation blockage. Immunofluorescence staining and Western blot analysis reveal that the nanomicelle-treated cancer cells are under severe ATP shortage, which eventually causes substantial cell death. Moreover, the nanomicelles intravenously injected into tumor-bearing mice show high tumor accumulation, long tumor retention, and inhibit the tumor growth by inducing excessive mitophagy/autophagy and energy depletion in tumor cells. Additional near-infrared laser irradiation treatment further enhances the in vitro and in vivo anticancer efficiencies of the nanomicelles, due to the excellent photothermal and photodynamic effects of dc-IR825. We believe that this work highlights the important role of mitophagy/autophagy in treating cancers.

10.
Cancer Lett ; 473: 74-89, 2020 Mar 31.
Artigo em Inglês | MEDLINE | ID: mdl-31904482

RESUMO

Gastrointestinal cancer causes countless deaths every year due to therapeutic resistance. However, whether metabolic alterations contribute to chemoresistance is not well understood. In this study, we report that fatty acid (FA) catabolism was activated in gastrointestinal cancer cells treated with oxaliplatin, which exhibited higher expression of the rate-limiting enzymes carnitine palmitoyltransferase 1B (CPT1B) and CPT2. The clinical analysis also showed that high expression of these enzymes was associated with poor oxaliplatin-based chemotherapy outcomes in patients. Furthermore, genetic or pharmacological inhibition of CPT2 with perhexiline disturbed NADPH and redox homeostasis and increased reactive oxygen species (ROS) generation and cell apoptosis in gastrointestinal cancer cells following oxaliplatin treatment. Specifically, the combination of oxaliplatin and perhexiline significantly suppressed the progression of gastrointestinal cancer in cell-based xenograft and patient-derived xenograft (PDX) models. Mechanistically, CPT2 was transcriptionally upregulated by nuclear factor of activated T cells 3 (NFATc3), which translocated to the nucleus in response to oxaliplatin treatment. In summary, our study suggests that the inhibition of CPT-mediated FA catabolism combined with conventional chemotherapy is a promising therapeutic strategy for patients with gastrointestinal cancers.

11.
Chem Commun (Camb) ; 56(11): 1653-1656, 2020 Feb 06.
Artigo em Inglês | MEDLINE | ID: mdl-31939470

RESUMO

Distinct annexin V binding behaviours in Ca2+-dependent and Ca2+-independent cases were comparatively investigated using sum frequency generation vibrational spectroscopy. It was discovered that binding affected the molecular arrangement of both membrane leaflets, and the initial Ca2+-independent binding went through a transition with annexin V reorientation to a more stable state upon adding Ca2+.


Assuntos
Anexina A5/metabolismo , Cálcio/metabolismo , Bicamadas Lipídicas/metabolismo , 1,2-Dipalmitoilfosfatidilcolina/química , Bicamadas Lipídicas/química , Fosfatidilcolinas/química , Fosfatidilserinas/química , Ligação Proteica , Análise Espectral/métodos , Vibração , Água/química
12.
J Immunol Methods ; 477: 112701, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31705859

RESUMO

INTRODUCTION: ndirect immunofluorescence assay (IFA) using HEp-2 as substrate plays a consolidate role for the detection and measurement of ANA, which is currently considered as the reference method for detection. Manual operation is still very common in China, therefore, the need of standardization and automation for ANA-IFA detecting has been highlighted. OBJECTIVE: The current multi-center study is aimed to evaluate if HELIOS (AESKU Diagnostics, Wendelsheim, Germany) contributes to comparability of ANA screening results among different labs,and establish application specification of HELIOS for standardization of ANA detection. METHODS: ANA detection by manual IFA method and HELIOS on 230 clinical serum samples in eight laboratories. The performance to discriminate positive/negative screening results, endpoint titer estimation and pattern recognition were evaluated in HELIOS and manual visual. RESULTS: The positive coincident rate for ANA detection by manual IFA ranges from 87.7% to 97.8%, the negative coincidence rate ranges from 68.8% to 100%, the correctly estimated titer evaluation were 80 to 171 cases, the correct pattern in 146 to 161 cases, respectively. The positive coincident rate of HELIOS for ANA detection ranges from 91.2% to 97.7%, the negative coincidence rate ranges from 96.5% to 100%, the correctly estimated titer evaluation were 145 to 157 cases, the correct pattern in 123 to 140 cases, respectively. CONCLUSION: HELIOS could provide accurate diagnostic results, this include not only positive/negative results, but also endpoint titer, common patterns. The application of this system can help to promote standardization of ANA detection.

13.
J Cell Mol Med ; 24(1): 79-87, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31568653

RESUMO

LncRNA and miRNA are key molecules in mechanism of competing endogenous RNAs(ceRNA), and their interactions have been discovered with important roles in gene regulation. As supplementary to the identification of lncRNA-miRNA interactions from CLIP-seq experiments, in silico prediction can select the most potential candidates for experimental validation. Although developing computational tool for predicting lncRNA-miRNA interaction is of great importance for deciphering the ceRNA mechanism, little effort has been made towards this direction. In this paper, we propose an approach based on linear neighbour representation to predict lncRNA-miRNA interactions (LNRLMI). Specifically, we first constructed a bipartite network by combining the known interaction network and similarities based on expression profiles of lncRNAs and miRNAs. Based on such a data integration, linear neighbour representation method was introduced to construct a prediction model. To evaluate the prediction performance of the proposed model, k-fold cross validations were implemented. As a result, LNRLMI yielded the average AUCs of 0.8475 ± 0.0032, 0.8960 ± 0.0015 and 0.9069 ± 0.0014 on 2-fold, 5-fold and 10-fold cross validation, respectively. A series of comparison experiments with other methods were also conducted, and the results showed that our method was feasible and effective to predict lncRNA-miRNA interactions via a combination of different types of useful side information. It is anticipated that LNRLMI could be a useful tool for predicting non-coding RNA regulation network that lncRNA and miRNA are involved in.

14.
Shanghai Kou Qiang Yi Xue ; 28(4): 435-438, 2019 Aug.
Artigo em Chinês | MEDLINE | ID: mdl-31792489

RESUMO

PURPOSE: The purpose of this study was to investigate the efficacy of microvascular coupler for arterial anastomosis in head and neck reconstruction during a 2-year period at the Department of Oral and Maxillofacial Surgery, Shandong Provincial Hospital. METHODS: Twenty-one cases of microvascular free flaps from October 2013 through December 2014 were retrospectively reviewed. Flap survival and thrombosis of the arterial anastomoses were determined in these cases. RESULTS: A total of 21 consecutive patients underwent microsurgical head and neck reconstruction, including 7(33.33%) radial forearm, nine(42.86%) fibular and 5(23.81%) anterior lateral thigh free flaps. There was 1 complication related to arterial thrombosis in this series, requiring surgical reexploration and a sutured anastomosis was performed. There were no complications related to technical performance of the coupling device. CONCLUSIONS: Use of a coupler device shows reliability for arterial anastomosis in head and neck reconstruction. With proper vessel selection and sufficient experience using the microvascular coupler, arterial coupling may be performed in an expeditious, safe, and reliable fashion with minimal morbidity. Though not commonly practiced, use of coupling device for arterial anastomosis can significantly save time, which is a viable alternative to sutured anastomosis.


Assuntos
Retalhos de Tecido Biológico , Neoplasias de Cabeça e Pescoço , Procedimentos Cirúrgicos Reconstrutivos , Anastomose Cirúrgica , Humanos , Microcirurgia , Reprodutibilidade dos Testes , Estudos Retrospectivos
16.
Huan Jing Ke Xue ; 40(9): 4143-4151, 2019 Sep 08.
Artigo em Chinês | MEDLINE | ID: mdl-31854879

RESUMO

Two types of biodegradable polymers, polycaprolactone (PCL) and poly-3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV), were used as a denitrification slow-release carbon source and a microbial carrier. By comprehensively comparing their performances in denitrification, carbon release, surface morphology, and material composition as well as their microbial community characteristics, the PHBV was determined as the better performer. It had a shorter denitrification start time, a higher denitrification rate, a lower residual organic matter concentration, and a more stable and sustained denitrification performance than PCL. This is because its surface was rough and contained large amounts of hydrophilic groups such as C-O and C=O, which is easily attached and degraded by microorganisms. As a result, the microorganisms on its surface were diverse. The dominant ones were identified with heterotrophic denitrification potentials, such as Thiothrix, Pseudomonas, Zoogloea, Flavobacterium, and Dechloromonas. Therefore, PHBV is suitable as a carbon source medium for tertiary nitrogen removal.

17.
BMC Genomics ; 20(Suppl 13): 928, 2019 Dec 27.
Artigo em Inglês | MEDLINE | ID: mdl-31881833

RESUMO

BACKGROUND: Identification of protein-protein interactions (PPIs) is crucial for understanding biological processes and investigating the cellular functions of genes. Self-interacting proteins (SIPs) are those in which more than two identical proteins can interact with each other and they are the specific type of PPIs. More and more researchers draw attention to the SIPs detection, and several prediction model have been proposed, but there are still some problems. Hence, there is an urgent need to explore a efficient computational model for SIPs prediction. RESULTS: In this study, we developed an effective model to predict SIPs, called RP-FIRF, which merges the Random Projection (RP) classifier and Finite Impulse Response Filter (FIRF) together. More specifically, each protein sequence was firstly transformed into the Position Specific Scoring Matrix (PSSM) by exploiting Position Specific Iterated BLAST (PSI-BLAST). Then, to effectively extract the discriminary SIPs feature to improve the performance of SIPs prediction, a FIRF method was used on PSSM. The R'classifier was proposed to execute the classification and predict novel SIPs. We evaluated the performance of the proposed RP-FIRF model and compared it with the state-of-the-art support vector machine (SVM) on human and yeast datasets, respectively. The proposed model can achieve high average accuracies of 97.89 and 97.35% using five-fold cross-validation. To further evaluate the high performance of the proposed method, we also compared it with other six exiting methods, the experimental results demonstrated that the capacity of our model surpass that of the other previous approaches. CONCLUSION: Experimental results show that self-interacting proteins are accurately well-predicted by the proposed model on human and yeast datasets, respectively. It fully show that the proposed model can predict the SIPs effectively and sufficiently. Thus, RP-FIRF model is an automatic decision support method which should provide useful insights into the recognition of SIPs.

18.
Environ Int ; 133(Pt A): 105156, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31675532

RESUMO

Sewage sludge from wastewater treatment plants (WWTPs) harbours large amounts of antibiotics, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs), the variation and fate of these emerging pollutants during sludge treatment processes must be thoroughly studied to reduce their potential risks to human health. In this study, 7 pilot-scale CSTR anaerobic digesters were established with the same seed sludge and fed with the same thermal hydrolysis pre-treated sewage sludge, while operating under different conditions. High-throughput quantitative PCR, UPLC-MS/MS and Illumina Hiseq-sequencing were used to systematically evaluate the responses of antibiotics, ARGs, and MGEs in sewage sludge to thermal hydrolysis pre-treatment and various anaerobic digestion (AD) conditions. The results showed that thermal hydrolysis effectively reduced the abundance (>94%) of almost all subtypes of ARGs and MGEs, and it was a powerful technology for reducing tetracyclines, macrolides, and lincosamides. Besides, the abundance of ARGs and MGEs in thermophilic digesters was lower than that in mesophilic digesters, suggesting that thermophilic digesters could be used to avoid the ARGs rebounding. In addition, the thermophilic system further reduced the concentrations of quinolones. For the digesters operated under the mesophilic conditions, a longer hydraulic retention time (HRT) facilitated the removal of antibiotics, ARGs, and MGEs. Furthermore, the microbial community and MGEs had important effects on the persistence and proliferation of ARGs in AD process. The findings of this study provide effective clues for controlling the spread of antibiotic resistance and suggest the optimal operating conditions of digesters.

19.
J Am Chem Soc ; 141(51): 20335-20343, 2019 Dec 26.
Artigo em Inglês | MEDLINE | ID: mdl-31774666

RESUMO

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).

20.
Genes (Basel) ; 10(11)2019 11 12.
Artigo em Inglês | MEDLINE | ID: mdl-31726752

RESUMO

Self-interacting proteins (SIPs) is of paramount importance in current molecular biology. There have been developed a number of traditional biological experiment methods for predicting SIPs in the past few years. However, these methods are costly, time-consuming and inefficient, and often limit their usage for predicting SIPs. Therefore, the development of computational method emerges at the times require. In this paper, we for the first time proposed a novel deep learning model which combined natural language processing (NLP) method for potential SIPs prediction from the protein sequence information. More specifically, the protein sequence is de novo assembled by k-mers. Then, we obtained the global vectors representation for each protein sequences by using natural language processing (NLP) technique. Finally, based on the knowledge of known self-interacting and non-interacting proteins, a multi-grained cascade forest model is trained to predict SIPs. Comprehensive experiments were performed on yeast and human datasets, which obtained an accuracy rate of 91.45% and 93.12%, respectively. From our evaluations, the experimental results show that the use of amino acid semantics information is very helpful for addressing the problem of sequences containing both self-interacting and non-interacting pairs of proteins. This work would have potential applications for various biological classification problems.

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