scholarly journals Corneal proteome and differentially expressed corneal proteins in highly myopic chicks using a label-free SWATH-MS quantification approach

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Byung Soo Kang ◽  
Thomas Chuen Lam ◽  
Jimmy Ka-wai Cheung ◽  
King Kit Li ◽  
Chea-su Kee
Keyword(s):  
High Myopia ◽  
State Of The Art ◽  
Focal Length ◽  
Anterior Segment ◽  
Biomechanical Properties ◽  
Differentially Expressed ◽  
Ocular Tissue ◽  
Label Free ◽  
Ocular Complications ◽  
Axial Dimension

AbstractMyopia, or short-sightedness, is a highly prevalent refractive disorder in which the eye’s focal length is too short for its axial dimension in its relaxed state. High myopia is associated with increased risks of blinding ocular complications and abnormal eye shape. In addition to consistent findings on posterior segment anomalies in high myopia (e.g., scleral remodeling), more recent biometric and biomechanical data in myopic humans and animal models also indicate anterior segment anomalies (e.g., corneal biomechanical properties). Because the cornea is the anterior-most ocular tissue, providing essential refractive power and physiological stability, it is important to understand the biochemical signaling pathway during myopia development. This study first aimed to establish the entire chicken corneal proteome. Then, using the classical form deprivation paradigm to induce high myopia in chicks, state-of-the-art bioinformatics technologies were applied to identify eight differentially expressed proteins in the highly myopic cornea. These results provide strong foundation for future corneal research, especially those using chicken as an animal model for myopia development.

scholarly journals Corneal biomechanical properties in myopic eyes evaluated via Scheimpflug imaging

2020 ◽  
Author(s):  
A-Yong Yu ◽  
Hui Shao ◽  
Anpeng Pan ◽  
Qinmei Wang ◽  
Zixu Huang ◽  
...  
Keyword(s):  
Axial Length ◽  
High Myopia ◽  
Anterior Segment ◽  
Biomechanical Properties ◽  
Corvis St ◽  
Negatively Associated ◽  
Scheimpflug Imaging ◽  
Biomechanical Parameters ◽  
Corneal Biomechanical Properties ◽  
Myopia Control

Abstract Background: To investigate the biomechanical properties of the cornea in myopic eyes using corneal visualization scheimpflug technology (Corvis ST). The relationships between the biomechanical properties of the cornea and the degree of myopia were also investigated.Methods: 265 eyes of 265 subjects were included. Based on spherical equivalent (SE) in diopters (D), participants were divided into four groups: low myopia/control (SE: -0.50 to -3.00D), moderate myopia (SE: -3.00 to -6.00D), high myopia (SE: -6.00 to -10.00D) and severe myopia (SE greater than -10.00D). Axial length (AL), anterior segment parameters, and corneal biomechanical properties were obtained with the Lenstar LS900, Pentacam HR and Corvis ST, respectively.Results: Mean (±SD) SE was -7.29±4.31D (range: -0.63 to -25.75D). Mean AL was 26.31±1.82mm (range: 21.87 to 31.94mm). Significant differences were detected within the four groups in terms of six corneal biomechanical parameters: deformation amplitude (DA), time from start until second applanation (A2-time), length of flattened cornea at the second applanation (A2-length), corneal velocity during the first and second applanation (A2-velocity), time from start to highest concavity (HC-time), and central curvature at highest concavity (HC radius). AL was positively associated with DA whereas negatively associated with A1-velocity and A2-length. SE was positively associated with A2-time, HC-time and A2-velocity, whereas negatively associated with DA. IOP was positively associated with four corneal biomechanical parameters and negatively associated with three parameters.Conclusions: Eyes with severe myopia showed greater DA, lesser A2 time, HC time, and faster A2-velocity compared to low to high myopia. This suggests the cornea becomes weaker and more deformable with elongation of axial length with corresponding increases in myopia. DA, A2-time and A2-velocity could be useful corneal biomechanical indicators in patients with myopia.

Label-Free Mass Spectrometry-Based Plasma Proteomics Identified LY6D, DSC3, CDSN, SERPINB12, and SLURP1,as Novel Protein Biomarkers For Pulmonary Tuberculosis

2019 ◽  
Vol 17 ◽  
Author(s):  
Xiaoli Yu ◽  
Lu Zhang ◽  
Na Li ◽  
Peng Hu ◽  
Zhaoqin Zhu ◽  
...  
Keyword(s):  
Pulmonary Tuberculosis ◽  
Search Algorithm ◽  
Differentially Expressed ◽  
P Value ◽  
Plasma Samples ◽  
Label Free ◽  
Protein Biomarkers ◽  
Protein Database ◽  
Leave One Out ◽  
Potential Biomarkers

Aim: We aimed to identify new plasma biomarkers for the diagnosis of Pulmonary tuberculosis. Background: Tuberculosis is an ancient infectious disease that remains one of the major global health problems. Until now, effective, convenient, and affordable methods for diagnosis of Pulmonary tuberculosis were still lacked. Objective: This study focused on construct a label-free LC-MS/MS based comparative proteomics between six tuberculosis patients and six healthy controls to identify differentially expressed proteins (DEPs) in plasma. Method: To reduce the influences of high-abundant proteins, albumin and globulin were removed from plasma samples using affinity gels. Then DEPs from the plasma samples were identified using a label-free Quadrupole-Orbitrap LC-MS/MS system. The results were analyzed by the protein database search algorithm SEQUEST-HT to identify mass spectra to peptides. The predictive abilities of combinations of host markers were investigated by general discriminant analysis (GDA), with leave-one-out cross-validation. Results: A total of 572 proteins were identified and 549 proteins were quantified. The threshold for differentially expressed protein was set as adjusted p-value < 0.05 and fold change ≥1.5 or ≤0.6667, 32 DEPs were found. ClusterVis, TBtools, and STRING were used to find new potential biomarkers of PTB. Six proteins, LY6D, DSC3, CDSN, FABP5, SERPINB12, and SLURP1, which performed well in the LOOCV method validation, were termed as potential biomarkers. The percentage of cross-validated grouped cases correctly classified and original grouped cases correctly classified is greater than or equal to 91.7%. Conclusion: We successfully identified five candidate biomarkers for immunodiagnosis of PTB in plasma, LY6D, DSC3, CDSN, SERPINB12, and SLURP1. Our work supported this group of proteins as potential biomarkers for pulmonary tuberculosis, and be worthy of further validation.

Assessment of Commercial Off-the-Shelf Tissue Adhesives for Sealing Military-Relevant Corneal Perforation Injuries

2021 ◽  
Author(s):  
Eric J Snider ◽  
Lauren E Cornell ◽  
Brandon M Gross ◽  
David O Zamora ◽  
Emily N Boice
Keyword(s):  
Intraocular Pressure ◽  
High Speed ◽  
Anterior Segment ◽  
Ocular Tissue ◽  
Corneal Tissue ◽  
Corneal Perforation ◽  
Tissue Adhesives ◽  
Open Globe ◽  
Wide Range ◽  
Commercial Off The Shelf

ABSTRACT Introduction Open-globe ocular injuries have increased in frequency in recent combat operations due to increased use of explosive weaponry. Unfortunately, open-globe injuries have one of the worst visual outcomes for the injured warfighter, often resulting in permanent loss of vision. To improve visual recovery, injuries need to be stabilized quickly following trauma, in order to restore intraocular pressure and create a watertight seal. Here, we assess four off-the-shelf (OTS), commercially available tissue adhesives for their ability to seal military-relevant corneal perforation injuries (CPIs). Materials and Methods Adhesives were assessed using an anterior segment inflation platform and a previously developed high-speed benchtop corneal puncture model, to create injuries in porcine eyes. After injury, adhesives were applied and injury stabilization was assessed by measuring outflow rate, ocular compliance, and burst pressure, followed by histological analysis. Results Tegaderm dressings and Dermabond skin adhesive most successfully sealed injuries in preliminary testing. Across a range of injury sizes and shapes, Tegaderm performed well in smaller injury sizes, less than 2 mm in diameter, but inadequately sealed large or complex injuries. Dermabond created a watertight seal capable of maintaining ocular tissue at physiological intraocular pressure for almost all injury shapes and sizes. However, application of the adhesive was inconsistent. Histologically, after removal of the Dermabond skin adhesive, the corneal epithelium was removed and oftentimes the epithelium surface penetrated into the wound and was adhered to inner stromal tissue. Conclusions Dermabond can stabilize a wide range of CPIs; however, application is variable, which may adversely impact the corneal tissue. Without addressing these limitations, no OTS adhesive tested herein can be directly translated to CPIs. This highlights the need for development of a biomaterial product to stabilize these injuries without causing ocular damage upon removal, thus improving the poor vision prognosis for the injured warfighter.

scholarly journals Label-free quantitative proteomic analysis of the inhibition effect of Lactobacillus rhamnosus GG on Escherichia coli biofilm formation in co-culture

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Huiyi Song ◽  
Ni Lou ◽  
Jianjun Liu ◽  
Hong Xiang ◽  
Dong Shang
Keyword(s):  
Escherichia Coli ◽  
Proteomic Analysis ◽  
Biofilm Formation ◽  
Lactobacillus Rhamnosus ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Quantitative Proteomic Analysis ◽  
E Coli ◽  
Protein Ubiquitination

Abstract Background Escherichia coli (E. coli) is the principal pathogen that causes biofilm formation. Biofilms are associated with infectious diseases and antibiotic resistance. This study employed proteomic analysis to identify differentially expressed proteins after coculture of E. coli with Lactobacillus rhamnosus GG (LGG) microcapsules. Methods To explore the relevant protein abundance changes after E. coli and LGG coculture, label-free quantitative proteomic analysis and qRT-PCR were applied to E. coli and LGG microcapsule groups before and after coculture, respectively. Results The proteomic analysis characterised a total of 1655 proteins in E. coli K12MG1655 and 1431 proteins in the LGG. After coculture treatment, there were 262 differentially expressed proteins in E. coli and 291 in LGG. Gene ontology analysis showed that the differentially expressed proteins were mainly related to cellular metabolism, the stress response, transcription and the cell membrane. A protein interaction network and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated that the differentiated proteins were mainly involved in the protein ubiquitination pathway and mitochondrial dysfunction. Conclusions These findings indicated that LGG microcapsules may inhibit E. coli biofilm formation by disrupting metabolic processes, particularly in relation to energy metabolism and stimulus responses, both of which are critical for the growth of LGG. Together, these findings increase our understanding of the interactions between bacteria under coculture conditions.

scholarly journals Alteration of protein expression and spliceosome pathway activity during Barrett’s carcinogenesis

2021 ◽  
Author(s):  
Christoph Stingl ◽  
Angela Bureo Gonzalez ◽  
Coşkun Güzel ◽  
Kai Yi Nadine Phoa ◽  
Michail Doukas ◽  
...  
Keyword(s):  
Micro Rna ◽  
Differentially Expressed ◽  
Epithelial Tissue ◽  
Label Free ◽  
Tissue Samples ◽  
Damage Repair ◽  
Inter Observer Variability ◽  
Stromal Tissue ◽  
The Face ◽  
Abundance And Diversity

Abstract Background Barrett’s esophagus (BE) is a known precursor lesion and the strongest risk factor for esophageal adenocarcinoma (EAC), a common and lethal type of cancer. Prediction of risk, the basis for efficient intervention, is commonly solely based on histologic examination. This approach is challenged by problems such as inter-observer variability in the face of the high heterogeneity of dysplastic tissue. Molecular markers might offer an additional way to understand the carcinogenesis and improve the diagnosis—and eventually treatment. In this study, we probed significant proteomic changes during dysplastic progression from BE into EAC. Methods During endoscopic mucosa resection, epithelial and stromal tissue samples were collected by laser capture microdissection from 10 patients with normal BE and 13 patients with high-grade dysplastic/EAC. Samples were analyzed by mass spectrometry-based proteomic analysis. Expressed proteins were determined by label-free quantitation, and gene set enrichment was used to find differentially expressed pathways. The results were validated by immunohistochemistry for two selected key proteins (MSH6 and XPO5). Results Comparing dysplastic/EAC to non-dysplastic BE, we found in equal volumes of epithelial tissue an overall up-regulation in terms of protein abundance and diversity, and determined a set of 226 differentially expressed proteins. Significantly higher expressions of MSH6 and XPO5 were validated orthogonally and confirmed by immunohistochemistry. Conclusions Our results demonstrate that disease-related proteomic alterations can be determined by analyzing minute amounts of cell-type-specific collected tissue. Further analysis indicated that alterations of certain pathways associated with carcinogenesis, such as micro-RNA trafficking, DNA damage repair, and spliceosome activity, exist in dysplastic/EAC.

scholarly journals Label-Free Comparative Proteomics of Differentially Expressed Mycobacterium tuberculosis Protein in Rifampicin-Related Drug-Resistant Strains

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 607
Author(s):  
Nadeem Ullah ◽  
Ling Hao ◽  
Jo-Lewis Banga Ndzouboukou ◽  
Shiyun Chen ◽  
Yaqi Wu ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Drug Targets ◽  
Control Strategies ◽  
Multidrug Resistant ◽  
Differentially Expressed ◽  
Effective Control ◽  
Drug Resistant ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Candidate Target

Rifampicin (RIF) is one of the most important first-line anti-tuberculosis (TB) drugs, and more than 90% of RIF-resistant (RR) Mycobacterium tuberculosis clinical isolates belong to multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. In order to identify specific candidate target proteins as diagnostic markers or drug targets, differential protein expression between drug-sensitive (DS) and drug-resistant (DR) strains remains to be investigated. In the present study, a label-free, quantitative proteomics technique was performed to compare the proteome of DS, RR, MDR, and XDR clinical strains. We found iniC, Rv2141c, folB, and Rv2561 were up-regulated in both RR and MDR strains, while fadE9, espB, espL, esxK, and Rv3175 were down-regulated in the three DR strains when compared to the DS strain. In addition, lprF, mce2R, mce2B, and Rv2627c were specifically expressed in the three DR strains, and 41 proteins were not detected in the DS strain. Functional category showed that these differentially expressed proteins were mainly involved in the cell wall and cell processes. When compared to the RR strain, Rv2272, smtB, lpqB, icd1, and folK were up-regulated, while esxK, PPE19, Rv1534, rpmI, ureA, tpx, mpt64, frr, Rv3678c, esxB, esxA, and espL were down-regulated in both MDR and XDR strains. Additionally, nrp, PPE3, mntH, Rv1188, Rv1473, nadB, PPE36, and sseA were specifically expressed in both MDR and XDR strains, whereas 292 proteins were not identified when compared to the RR strain. When compared between MDR and XDR strains, 52 proteins were up-regulated, while 45 proteins were down-regulated in the XDR strain. 316 proteins were especially expressed in the XDR strain, while 92 proteins were especially detected in the MDR strain. Protein interaction networks further revealed the mechanism of their involvement in virulence and drug resistance. Therefore, these differentially expressed proteins are of great significance for exploring effective control strategies of DR-TB.

Ocular tissue changes associated with anterior segment opacity in lumpfish ( Cyclopterus lumpus L) eye

2019 ◽  
Vol 42 (10) ◽  
pp. 1401-1408
Author(s):  
Helene Paradis ◽  
Raahyma Ahmad ◽  
James McDonald ◽  
Danny Boyce ◽  
Robert L. Gendron
Keyword(s):  
Anterior Segment ◽  
Ocular Tissue ◽  
Cyclopterus Lumpus ◽  
Tissue Changes

scholarly journals High myopia induced by form deprivation is associated with altered corneal biomechanical properties in chicks

PLoS ONE ◽  
2018 ◽  
Vol 13 (11) ◽  
pp. e0207189 ◽  
Author(s):  
Byung Soo Kang ◽  
Li-Ke Wang ◽  
Yong-Ping Zheng ◽  
Jeremy A. Guggenheim ◽  
William K. Stell ◽  
...  
Keyword(s):  
High Myopia ◽  
Biomechanical Properties ◽  
Corneal Biomechanical Properties

Printable and flexible electronics: from TFTs to bioelectronic devices

2015 ◽  
Vol 3 (48) ◽  
pp. 12347-12363 ◽  
Author(s):  
M. Magliulo ◽  
M. Y. Mulla ◽  
M. Singh ◽  
E. Macchia ◽  
A. Tiwari ◽  
...  
Keyword(s):  
Flexible Electronics ◽  
State Of The Art ◽  
The State ◽  
Label Free ◽  
Electronic Biosensors

This review discusses the state-of-the-art strategies for realizing TFTs by printing compatible techniques, focusing the attention on label-free electronic biosensors.

Quantitative proteomics analysis of FFPE tumor samples reveals the influences of novel targeting nanobubbles conjugated with NET-1 siRNA on tetraspanin protein involved in HCC

2020 ◽  
Author(s):  
Bolin Wu ◽  
Haitao Shang ◽  
Xitian Liang ◽  
Huajing Yang Huajing Yang ◽  
Hui Jing ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Interaction Analysis ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pathway Enrichment Analysis ◽  
Differentially Expressed Proteins ◽  
Label Free ◽  
Protein Protein Interaction ◽  
Study Results ◽  
Ffpe Tumor

Abstract Background: Hepatocellular carcinoma (HCC) poses a severe threat to human health. The NET-1 protein has been proved to be strongly associated with HCC proliferation and metastasis in our previous study. Methods: Here, we developed a label-free proteome mass spectrometry workflow to analyze formalin-fixed and paraffin-embedded HCC xenograft samples collected in our previous study. Results: The result showed that 78 proteins were differentially expressed after NET-1 protein inhibited. Among them, the expression of 61 proteins up-regulated and the expression of 17 proteins were significantly down-regulated. Of the differentially expressed proteins, the vast majority of Gene Ontology enrichment terms belong to the biological process. The KEGG pathway enrichment analysis showed that the 78 differentially expressed proteins significantly enriched in 45 pathways. We concluded that the function of the NET-1 gene is not only to regulate HCC but also to participate in a variety of biochemical metabolic pathways in the human body. Furthermore, the protein-protein interaction analysis indicated that the interactions of differentially expressed proteins are incredibly sophisticated. All the protein-protein interactions happened after the NET-1 gene has been silenced. Conclusions: Finally, our study also provides a useful proposal for targeted therapy based on tetraspanin proteins to treat HCC, and further mechanism investigations are needed to reveal a more detailed mechanism of action for NET-1 protein regulation of HCC.

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