Comprehensive spectral libraries for various rabbit eye tissue proteomes

Washing with buffered vitamin C after corrosive chemical (sodium hypochlorite) exposure reduces ocular depth of injury

Chemical eye injuries occur in home, industrial, and military settings. The standard recommended treatment after exposure of the eyes to chemical toxins is washing with tap water for at least 15 min. An estimated 80 % of ocular toxins are associated with reactive oxygen species and/or extreme pH. Using food-source eyes and a commercially available test kit for depth of injury (IVD EITTM) that measures the depth of dead corneal keratocytes by fragmented DNA staining, washing the eye with a buffered vitamin C solution significantly reduced corneal keratocyte cell death and depth of injury compared to control. When eyes were washed (using a 500-mL eyewash bottle) for 15 min with water after exposure to 32 % sodium hypochlorite (chlorine bleach), the depth of injury was 59.6 ± 3.6 %, a level of damage predicted to cause extreme/permanent eye injury or even blindness in vivo (extreme or irreversible injury, GHS category 1), but washing with 0.2 % buffered vitamin C after bleach exposure reduced damage to13.8 ± 1.4 %, which is significantly less (P < 0.001) and predicted by the IVD EIT method to be reversible irritation (GHS category 2) that will heal within 21 days in vivo.

Ocular tear fluid biomarkers collected by contact lenses

PURPOSE

To collect tear fluid biomarkers from contact lenses (CLs) and determine the impact of CL wear duration.

METHODS

Rabbits were fitted with commercial etafilcon A CLs, which were collected after 1 min, 4 and 8 h (n = 4/time point). Tear fluid proteins and cytokines were extracted from the CLs and quantified. An exploratory comparison was performed between CLs and Schirmer Strips (SS) for a 1 min duration.

RESULTS

The concentration of MUC5AC was significantly higher after 4 h of CL wear. The expression of all investigated cytokines (IL-1α, IL-1β, IL-8, IL-17A, IL-21, Leptin, MIP-1β, MMP-9, NCAM-1, and TNF-α) was detectable after 1 min of CL wear, and over time, all showed significant variations throughout the 8-h CL wear period. Notably, IL-1α significantly increased by 8 h of CL wear, while MMP-9 decreased. Albumin and lysozyme did not show significant variations with CL wear. Differences between CLs and SS after 1 min were statistically significant for albumin, Leptin, TNF-α, IL-1α, IL-1β, and IL-8.

CONCLUSIONS

The duration of CL wear significantly affects the collection of some tear fluid biomarkers. Albumin, MUC5AC, and cytokines may have individual and synergistic diagnostic or prognostic potential. CLs and SS were similar for lysozyme and MUC5AC but differed in the collection of albumin and some cytokines. CLs are a viable tear fluid collection method for biomarker analyses and can be immediately added as a routine clinical test by being FDA-approved medical devices.

Deep Spectral Library of Mice Retina for Myopia Research: Proteomics Dataset generated by SWATH and DIA-NN

The retina plays a crucial role in processing and decoding visual information, both in normal development and during myopia progression. Recent advancements have introduced a library-independent approach for data-independent acquisition (DIA) analyses. This study demonstrates deep proteome identification and quantification in individual mice retinas during myopia development, with an average of 6,263 ± 86 unique protein groups. We anticipate that the use of a predicted retinal-specific spectral library combined with the robust quantification achieved within this dataset will contribute to a better understanding of the proteome complexity. Furthermore, a comprehensive mice retinal-specific spectral library was generated, encompassing a total identification of 9,401 protein groups, 70,041 peptides, 95,339 precursors, and 761,868 transitions acquired using SWATH-MS acquisition on a ZenoTOF 7600 mass spectrometer. This dataset surpasses the spectral library generated through high-pH reversed-phase fractionation by data-dependent acquisition (DDA). The data is available via ProteomeXchange with the identifier PXD046983. It will also serve as an indispensable reference for investigations in myopia research and other retinal or neurological diseases.

Metabolic disruption impairs ribosomal protein levels, resulting in enhanced aminoglycoside tolerance

Aminoglycoside antibiotics target ribosomes and are effective against a wide range of bacteria. Here, we demonstrated that knockout strains related to energy metabolism in Escherichia coli showed increased tolerance to aminoglycosides during the mid-exponential growth phase. Contrary to expectations, these mutations did not reduce the proton motive force or aminoglycoside uptake, as there were no significant changes in metabolic indicators or intracellular gentamicin levels between wild-type and mutant strains. Our comprehensive proteomics analysis unveiled a noteworthy upregulation of proteins linked to the tricarboxylic acid (TCA) cycle in the mutant strains during the mid-exponential growth phase, suggesting that these strains compensate for the perturbation in their energy metabolism by increasing TCA cycle activity to maintain their membrane potential and ATP levels. Furthermore, our pathway enrichment analysis shed light on local network clusters displaying downregulation across all mutant strains, which were associated with both large and small ribosomal binding proteins, ribosome biogenesis, translation factor activity, and the biosynthesis of ribonucleoside monophosphates. These findings offer a plausible explanation for the observed tolerance of aminoglycosides in the mutant strains. Altogether, this research provides valuable insights into the mechanisms of aminoglycoside tolerance, paving the way for novel strategies to combat such cells.

Upconversion nanoparticles doped optical lens: let's see the near-infrared light

The human cannot detect light with a wavelength exceeding 700 nm, primarily due to limitations in the physiological structure of the human eye. However, in certain specific scenarios, the ability to detect near-infrared (NIR) light proves to be extremely valuable. To attain this desired capability, NIR up conversion nanoparticles (UCNPs) were prepared and doped in the optical lens materials, aiming to obtain a NIR light "visible" optical lens. It is demonstrated that the doping of UCNPs in the optical lens materials does not significantly impact on their mechanical properties, optical properties, surface properties and it exhibits excellent biocompatibility in cell and animal experiments. More importantly, the UCNPs doping can convert NIR light into visible light within the material effectively and stably. The eyes can "see" the NIR light after wearing such UCNPs doped optical lens. Such NIR light visible optical lens could have great potential in actual applications.

METABOLIC DISRUPTION IMPAIRS RIBOSOMAL PROTEIN LEVELS, RESULTING IN ENHANCED AMINOGLYCOSIDE TOLERANCE

Aminoglycoside antibiotics display broad-spectrum activity against Gram-negative and Grampositive bacteria by targeting their ribosomes. Herein, we have demonstrated that energy metabolism plays a crucial role in aminoglycoside tolerance, as knockout strains associated with the tricarboxylic acid cycle (TCA) and the electron transport chain (ETC) exhibited increased tolerance to aminoglycosides in the mid-exponential growth phase of Escherichia coli cells. Given that aminoglycoside uptake relies on the energy-driven electrochemical potential across the cytoplasmic membrane, our initial expectation was that these genetic perturbations would decrease the proton motive force (PMF), subsequently affecting the uptake of aminoglycosides. However, our results did not corroborate this assumption. We found no consistent metabolic changes, ATP levels, cytoplasmic pH variations, or membrane potential differences in the mutant strains compared to the wild type. Additionally, intracellular concentrations of fluorophore-labeled gentamicin remained similar across all strains. To uncover the mechanism responsible for the observed tolerance in mutant strains, we employed untargeted mass spectrometry to quantify the proteins within these mutants and subsequently compared them to their wild-type counterparts. Our comprehensive analysis, which encompassed protein-protein association networks and functional enrichment, unveiled a noteworthy upregulation of proteins linked to the TCA cycle in the mutant strains during the mid-exponential growth phase, suggesting that these strains compensate for the perturbation in their energy metabolism by increasing TCA cycle activity to maintain their membrane potential and ATP levels. Furthermore, our pathway enrichment analysis shed light on local network clusters displaying downregulation across all mutant strains, which were associated with both large and small ribosomal binding proteins, ribosome biogenesis, translation factor activity, and the biosynthesis of ribonucleoside monophosphates. These findings offer a plausible explanation for the observed tolerance of aminoglycosides in the mutant strains. Altogether, this research has the potential to uncover mechanisms behind aminoglycoside tolerance, paving the way for novel strategies to combat such cells.

Contact lenses as novel tear fluid sampling vehicles for total RNA isolation, precipitation, and amplification

The tear fluid is a readily accessible, potential source for biomarkers of disease and could be used to monitor the ocular response to contact lens (CL) wear or ophthalmic pathologies treated by therapeutic CLs. However, the tear fluid remains largely unexplored as a biomarker source for RNA-based molecular analyses. Using a rabbit model, this study sought to determine whether RNA could be collected from commercial CLs and whether the duration of CL wear would impact RNA recovery. The results were referenced to standardized strips of filtered paper (e.g., Shirmer Strips) placed in the inferior fornix. By performing total RNA isolation, precipitation, and amplification with commercial kits and RT-PCR methods, CLs were found to have no significant differences in RNA concentration and purity compared to Schirmer Strips. The study also identified genes that could be used to normalize RNA levels between tear samples. Of the potential control genes or housekeeping genes, GAPDH was the most stable. This study, which to our knowledge has never been done before, provides a methodology for the detection of RNA and gene expression changes from tear fluid that could be used to monitor or study eye diseases.

Full-Stokes polarization multispectral images of various stereoscopic objects

Polarization multispectral imaging (PMI) has been applied widely with the ability of characterizing physicochemical properties of objects. However, traditional PMI relies on scanning each domain, which is time-consuming and occupies vast storage resources. Therefore, it is imperative to develop advanced PMI methods to facilitate real-time and cost-effective applications. In addition, PMI development is inseparable from preliminary simulations based on full-Stokes polarization multispectral images (FSPMI). Whereas, FSPMI measurements are always necessary due to the lack of relevant databases, which is extremely complex and severely limits PMI development. In this paper, we therefore publicize abundant FSPMI with 512 × 512 spatial pixels measured by an established system for 67 stereoscopic objects. In the system, a quarter-wave plate and a linear polarizer are rotated to modulate polarization information, while bandpass filters are switched to modulate spectral information. The required FSPMI are finally calculated from designed 5 polarization modulation and 18 spectral modulation. The publicly available FSPMI database may have the potential to greatly promote PMI development and application.

Tear proteomic analysis of young glasses, orthokeratology, and soft contact lens wearers

Contact lens-related ocular surface complications occur more often in teenagers and young adults. The purpose of this study was to determine changes in tear proteome of young patients wearing glasses (GL), orthokeratology lenses (OK), and soft contact lenses (SCL). Twenty-two young subjects (10-26 years of age) who were established GL, OK, and SCL wearers were recruited. Proteomic data were collected using a data-independent acquisition-parallel accumulation serial fragmentation workflow. In total, 3406 protein groups were identified, the highest number of proteins identified in Schirmer strip tears to date. Eight protein groups showed higher abundance, and 11 protein groups showed lower abundance in the SCL group compared to the OK group. In addition, the abundance of 82 proteins significantly differed in children compared to young adult GL wearers, among which 67 proteins were higher, and 15 proteins were lower in children. These 82 proteins were involved in inflammation, immune, and glycoprotein metabolic biological processes. In summary, this work identified over 3000 proteins in Schirmer Strip tears. The results indicated that tear proteomes were altered by orthokeratology and soft contact wear and age, which warrants further larger-scale study on the ocular surface responses of teenagers and young adults separately to contact lens wear. SIGNIFICANCE: In this work, we examined the tear proteomes of young patients wearing glasses, orthokeratology lenses, and soft contact lenses using a data-independent acquisition-parallel accumulation serial fragmentation (diaPASEF) workflow and identified 3406 protein groups in Schirmer strip tears. Nineteen protein groups showed significant abundance changes between orthokeratology and soft contact lens wearers. Moreover, eighty-two protein groups significantly differed in abundance in children and young adult glasses wearers. As a pilot study, this work provides a deep coverage of tear proteome and suggests the need to investigate ocular responses to contact lens wear separately for children and young adults.