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1.
PLoS Genet ; 18(3): e1009841, 2022 03.
Article in English | MEDLINE | ID: mdl-35245286

ABSTRACT

Neural retina leucine zipper (NRL) is an essential gene for the fate determination and differentiation of the precursor cells into rod photoreceptors in mammals. Mutations in NRL are associated with the autosomal recessive enhanced S-cone syndrome and autosomal dominant retinitis pigmentosa. However, the exact role of Nrl in regulating the development and maintenance of photoreceptors in the zebrafish (Danio rerio), a popular animal model used for retinal degeneration and regeneration studies, has not been fully determined. In this study, we generated an nrl knockout zebrafish model via the CRISPR-Cas9 technology and observed a surprising phenotype characterized by a reduced number, but not the total loss, of rods and over-growth of green cones. We discovered two waves of rod genesis, nrl-dependent and -independent at the embryonic and post-embryonic stages, respectively, in zebrafish by monitoring the rod development. Through bulk and single-cell RNA sequencing, we characterized the gene expression profiles of the whole retina and each retinal cell type from the wild type and nrl knockout zebrafish. The over-growth of green cones and mis-expression of green-cone-specific genes in rods in nrl mutants suggested that there are rod/green-cone bipotent precursors, whose fate choice between rod versus green-cone is controlled by nrl. Besides, we identified the mafba gene as a novel regulator of the nrl-independent rod development, based on the cell-type-specific expression patterns and the retinal phenotype of nrl/mafba double-knockout zebrafish. Gene collinearity analysis revealed the evolutionary origin of mafba and suggested that the function of mafba in rod development is specific to modern fishes. Furthermore, the altered photoreceptor composition and abnormal gene expression in nrl mutants caused progressive retinal degeneration and subsequent regeneration. Accordingly, this study revealed a novel function of the mafba gene in rod development and established a working model for the developmental and regulatory mechanisms regarding the rod and green-cone photoreceptors in zebrafish.


Subject(s)
Retinal Degeneration , Zebrafish , Animals , Basic-Leucine Zipper Transcription Factors/genetics , Eye Proteins/metabolism , Mammals/metabolism , Retinal Cone Photoreceptor Cells/metabolism , Retinal Degeneration/genetics , Retinal Degeneration/metabolism , Zebrafish/genetics , Zebrafish/metabolism
2.
Proc Natl Acad Sci U S A ; 118(39)2021 09 28.
Article in English | MEDLINE | ID: mdl-34544860

ABSTRACT

Frozen shoulder is a common fibroproliferative disease characterized by the insidious onset of pain and restricted range of shoulder movement with a significant socioeconomic impact. The pathophysiological mechanisms responsible for chronic inflammation and matrix remodeling in this prevalent fibrotic disorder remain unclear; however, increasing evidence implicates dysregulated immunobiology. IL-17A is a key cytokine associated with inflammation and tissue remodeling in numerous musculoskeletal diseases, and thus, we sought to determine the role of IL-17A in the immunopathogenesis of frozen shoulder. We demonstrate an immune cell landscape that switches from a predominantly macrophage population in nondiseased tissue to a T cell-rich environment in disease. Furthermore, we observed a subpopulation of IL-17A-producing T cells capable of inducing profibrotic and inflammatory responses in diseased fibroblasts through enhanced expression of the signaling receptor IL-17RA, rendering diseased cells more sensitive to IL-17A. We further established that the effects of IL-17A on diseased fibroblasts was TRAF-6/NF-κB dependent and could be inhibited by treatment with an IKKß inhibitor or anti-IL-17A antibody. Accordingly, targeting of the IL-17A pathway may provide future therapeutic approaches to the management of this common, debilitating disease.


Subject(s)
Bursitis/physiopathology , Fibrosis/pathology , Inflammation/pathology , Interleukin-17/immunology , T-Lymphocytes/immunology , Case-Control Studies , Cells, Cultured , Cytokines/metabolism , Female , Fibroblasts/immunology , Fibroblasts/metabolism , Fibroblasts/pathology , Fibrosis/immunology , Fibrosis/metabolism , Humans , Inflammation/immunology , Inflammation/metabolism , Interleukin-17/metabolism , Male , Middle Aged , NF-kappa B/metabolism , Signal Transduction
3.
J Anat ; 242(2): 312-326, 2023 02.
Article in English | MEDLINE | ID: mdl-36087281

ABSTRACT

In limbless fossorial vertebrates such as caecilians (Gymnophiona), head-first burrowing imposes severe constraints on the morphology and overall size of the head. As such, caecilians developed a unique jaw-closing system involving the large and well-developed m. interhyoideus posterior, which is positioned in such a way that it does not significantly increase head diameter. Caecilians also possess unique muscles among amphibians. Understanding the diversity in the architecture and size of the cranial muscles may provide insights into how a typical amphibian system was adapted for a head-first burrowing lifestyle. In this study, we use dissection and non-destructive contrast-enhanced micro-computed tomography (µCT) scanning to describe and compare the cranial musculature of 13 species of caecilians. Our results show that the general organization of the head musculature is rather constant across extant caecilians. However, the early-diverging Rhinatrema bivittatum mainly relies on the 'ancestral' amphibian jaw-closing mechanism dominated by the m. adductores mandibulae, whereas other caecilians switched to the use of the derived dual jaw-closing mechanism involving the additional recruitment of the m. interhyoideus posterior. Additionally, the aquatic Typhlonectes show a greater investment in hyoid musculature than terrestrial caecilians, which is likely related to greater demands for ventilating their large lungs, and perhaps also an increased use of suction feeding. In addition to three-dimensional interactive models, our study provides the required quantitative data to permit the generation of accurate biomechanical models allowing the testing of further functional hypotheses.


Subject(s)
Amphibians , Skull , Animals , Phylogeny , X-Ray Microtomography , Amphibians/anatomy & histology , Skull/anatomy & histology , Muscle, Skeletal
4.
Eur J Neurosci ; 55(8): 1972-1985, 2022 04.
Article in English | MEDLINE | ID: mdl-35357048

ABSTRACT

The human auditory system excels at detecting patterns needed for processing speech and music. According to predictive coding, the brain predicts incoming sounds, compares predictions to sensory input and generates a prediction error whenever a mismatch between the prediction and sensory input occurs. Predictive coding can be indexed in electroencephalography (EEG) with the mismatch negativity (MMN) and P3a, two components of event-related potentials (ERP) that are elicited by infrequent deviant sounds (e.g., differing in pitch, duration and loudness) in a stream of frequent sounds. If these components reflect prediction error, they should also be elicited by omitting an expected sound, but few studies have examined this. We compared ERPs elicited by infrequent randomly occurring omissions (unexpected silences) in tone sequences presented at two tones per second to ERPs elicited by frequent, regularly occurring omissions (expected silences) within a sequence of tones presented at one tone per second. We found that unexpected silences elicited significant MMN and P3a, although the magnitude of these components was quite small and variable. These results provide evidence for hierarchical predictive coding, indicating that the brain predicts silences and sounds.


Subject(s)
Evoked Potentials, Auditory , Evoked Potentials , Acoustic Stimulation/methods , Adult , Auditory Perception/physiology , Electroencephalography/methods , Evoked Potentials/physiology , Evoked Potentials, Auditory/physiology , Humans , Sound
5.
J Anat ; 241(3): 716-728, 2022 09.
Article in English | MEDLINE | ID: mdl-35488423

ABSTRACT

Caecilians are elongate, limbless and annulated amphibians that, as far as is known, all have an at least partly fossorial lifestyle. It has been suggested that elongate limbless vertebrates show little morphological differentiation throughout the postcranial skeleton. However, relatively few studies have explored the axial skeleton in limbless tetrapods. In this study, we used µCT data and three-dimensional geometric morphometrics to explore regional differences in vertebral shape across a broad range of caecilian species. Our results highlight substantial differences in vertebral shape along the axial skeleton, with anterior vertebrae being short and bulky, whereas posterior vertebrae are more elongated. This study shows that despite being limbless, elongate tetrapods such as caecilians still show regional heterogeneity in the shape of individual vertebrae along the vertebral column. Further studies are needed, however, to understand the possible causes and functional consequences of the observed variation in vertebral shape in caecilians.


Subject(s)
Amphibians , Spine , Amphibians/anatomy & histology , Animals , Spine/anatomy & histology , Spine/diagnostic imaging
6.
Mol Psychiatry ; 26(7): 3430-3443, 2021 07.
Article in English | MEDLINE | ID: mdl-33060818

ABSTRACT

Elevations in peripheral inflammatory markers have been reported in patients with psychosis. Whether this represents an inflammatory process defined by individual or subgroups of markers is unclear. Further, relationships between peripheral inflammatory marker elevations and brain structure, cognition, and clinical features of psychosis remain unclear. We hypothesized that a pattern of plasma inflammatory markers, and an inflammatory subtype established from this pattern, would be elevated across the psychosis spectrum and associated with cognition and brain structural alterations. Clinically stable psychosis probands (Schizophrenia spectrum, n = 79; Psychotic Bipolar disorder, n = 61) and matched healthy controls (HC, n = 60) were assessed for 15 peripheral inflammatory markers, cortical thickness, subcortical volume, cognition, and symptoms. A combination of unsupervised exploratory factor analysis and hierarchical clustering was used to identify inflammation subtypes. Levels of IL6, TNFα, VEGF, and CRP were significantly higher in psychosis probands compared to HCs, and there were marker-specific differences when comparing diagnostic groups. Individual and/or inflammatory marker patterns were associated with neuroimaging, cognition, and symptom measures. A higher inflammation subgroup was defined by elevations in a group of 7 markers in 36% of Probands and 20% of HCs. Probands in the elevated inflammatory marker group performed significantly worse on cognitive measures of visuo-spatial working memory and response inhibition, displayed elevated hippocampal, amygdala, putamen and thalamus volumes, and evidence of gray matter thickening compared to the proband group with low inflammatory marker levels. These findings specify the nature of peripheral inflammatory marker alterations in psychotic disorders and establish clinical, neurocognitive and neuroanatomic associations with increased inflammatory activation in psychosis. The identification of a specific subgroup of patients with inflammatory alteration provides a potential means for targeting treatment with anti-inflammatory medications.


Subject(s)
Bipolar Disorder , Psychotic Disorders , Schizophrenia , Brain/diagnostic imaging , Cognition , Humans , Magnetic Resonance Imaging
7.
J Exp Biol ; 225(12)2022 06 15.
Article in English | MEDLINE | ID: mdl-35662342

ABSTRACT

Caecilians are predominantly burrowing, elongate, limbless amphibians that have been relatively poorly studied. Although it has been suggested that the sturdy and compact skulls of caecilians are an adaptation to their head-first burrowing habits, no clear relationship between skull shape and burrowing performance appears to exist. However, the external forces encountered during burrowing are transmitted by the skull to the vertebral column, and, as such, may impact vertebral shape. Additionally, the muscles that generate the burrowing forces attach onto the vertebral column and consequently may impact vertebral shape that way as well. Here, we explored the relationships between vertebral shape and maximal in vivo push forces in 13 species of caecilian amphibians. Our results show that the shape of the two most anterior vertebrae, as well as the shape of the vertebrae at 90% of the total body length, is not correlated with peak push forces. Conversely, the shape of the third vertebrae, and the vertebrae at 20% and 60% of the total body length, does show a relationship to push forces measured in vivo. Whether these relationships are indirect (external forces constraining shape variation) or direct (muscle forces constraining shape variation) remains unclear and will require quantitative studies of the axial musculature. Importantly, our data suggest that mid-body vertebrae may potentially be used as proxies to infer burrowing capacity in fossil representatives.


Subject(s)
Amphibians , Skull , Amphibians/physiology , Animals , Head , Spine
8.
J Exp Biol ; 225(1)2022 01 01.
Article in English | MEDLINE | ID: mdl-34897477

ABSTRACT

Caecilians are enigmatic limbless amphibians that, with a few exceptions, all have an at least partly burrowing lifestyle. Although it has been suggested that caecilian evolution resulted in sturdy and compact skulls as an adaptation to their head-first burrowing habits, no relationship between skull shape and burrowing performance has been demonstrated to date. However, the unique dual jaw-closing mechanism and the osteological variability of their temporal region suggest a potential relationship between skull shape and feeding mechanics. Here, we explored the relationships between skull shape, head musculature and in vivo bite forces. Although there is a correlation between bite force and external head shape, no relationship between bite force and skull shape could be detected. Whereas our data suggest that muscles are the principal drivers of variation in bite force, the shape of the skull is constrained by factors other than demands for bite force generation. However, a strong covariation between the cranium and mandible exists. Moreover, both cranium and mandible shape covary with jaw muscle architecture. Caecilians show a gradient between species with a long retroarticular process associated with a large and pennate-fibered m. interhyoideus posterior and species with a short process but long and parallel-fibered jaw adductors. Our results demonstrate the complexity of the relationship between form and function of this jaw system. Further studies that focus on factors such as gape distance or jaw velocity will be needed in order to fully understand the evolution of feeding mechanics in caecilians.


Subject(s)
Amphibians , Bite Force , Amphibians/physiology , Animals , Biomechanical Phenomena , Head , Jaw/physiology , Muscle, Skeletal , Skull
9.
Pharm Res ; 39(1): 75-87, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34981317

ABSTRACT

PURPOSE: Polysorbates (PS) are excipients used in the biotech industry to stabilize monoclonal antibody (mAb) protein products. However, PS in drug product formulations can be degraded during storage and lead to particle formation because of the limited solubility of the free fatty acids released through the enzymatic hydrolysis of PS-a process driven by residual host cell proteins, especially lipases, that are co-purified with the drugs. When multiple lipases are present, it is very difficult to know the cause for PS degradation. In this study, we aim to determine the cause of PS degradation from two lipases, lysosomal acid lipase (LAL) and lipoprotein lipase (LPL). METHODS: PS degradation pattern of the drug product was compared with those induced by recombinant lipases. Correlations between the concentration of LPL or LAL and PS20 loss were compared. Specific inhibitors, LAL inhibitor lalistat2 and LPL inhibitor GSK264220A, were used to differentiate their degradation of PS in the drug products. RESULTS: The complete inhibition of PS20 degradation by lalistat2 suggested that LAL, rather than LPL, was responsible for the PS20 degradation. In addition, LAL was more strongly correlated than LPL with the percentage of PS20 degradation. No PS20 degradation was observed for several mAbs containing similar levels of LPL (0.5-1.5 ppm) in the absence of LAL, suggesting that LPL concentrations below 1.5 ppm does not degrade PS20 in drug products. CONCLUSIONS: LAL was determined to be the cause of the PS20 degradation. This study provides a practical strategy to determine the root cause of PS degradation.


Subject(s)
Antibodies, Monoclonal , Polysorbates , Drug Compounding , Solubility , Surface-Active Agents
10.
Biochem Biophys Res Commun ; 579: 62-68, 2021 11 19.
Article in English | MEDLINE | ID: mdl-34587556

ABSTRACT

Urocanic acid (UCA) is an endogenous small molecule that is elevated in skin, blood and brain after sunlight exposure, mainly playing roles in the periphery systems. Few studies have investigated the role of UCA in the central nervous system. In particular, its role in memory consolidation and reconsolidation is still unclear. In the present study, we investigated the effect of intraperitoneal injection of UCA on memory consolidation and reconsolidation in a novel object recognition memory (ORM) task. In the consolidation version of the ORM task, the protocol involved three phases: habituation, sampling and test. UCA injection immediately after the sampling period enhanced ORM memory performance; UCA injection 6 h after sampling did not affect ORM memory performance. In the reconsolidation version of the ORM task, the protocol involved three phases: sampling, reactivation and test. UCA injection immediately after reactivation enhanced ORM memory performance; UCA injection 6 h after reactivation did not affect ORM memory performance; UCA injection 24 h after sampling without reactivation did not affect ORM memory performance. This UCA-enhanced memory performance was not due to its effects on nonspecific responses such as locomotor activity and exploratory behavior. The results suggest that UCA injection enhances consolidation and reconsolidation of an ORM task, which further extends previous research on UCA effects on learning and memory.


Subject(s)
Habituation, Psychophysiologic/drug effects , Learning/drug effects , Memory Consolidation/drug effects , Recognition, Psychology/drug effects , Urocanic Acid/pharmacology , Animals , Behavior, Animal , Brain Mapping , Handling, Psychological , Locomotion , Male , Mice , Mice, Inbred ICR
11.
J Transl Med ; 19(1): 61, 2021 02 09.
Article in English | MEDLINE | ID: mdl-33563287

ABSTRACT

BACKGROUND: The purpose of this study was to investigate the utility of BNP, hsTroponin-I, interleukin-6, sST2, and galectin-3 in predicting the future development of new onset heart failure with preserved ejection fraction (HFpEF) in asymptomatic patients at-risk for HF. METHODS: This is a retrospective analysis of the longitudinal STOP-HF study of thirty patients who developed HFpEF matched to a cohort that did not develop HFpEF (n = 60) over a similar time period. Biomarker candidates were quantified at two time points prior to initial HFpEF diagnosis. RESULTS: HsTroponin-I and BNP at baseline and follow-up were statistically significant predictors of future new onset HFpEF, as was galectin-3 at follow-up and concentration change over time. Interleukin-6 and sST2 were not predictive of future development of new onset HFpEF in this study. Unadjusted biomarker combinations of hsTroponin-I, BNP, and galectin-3 could significantly predict future HFpEF using both baseline (AUC 0.82 [0.73,0.92]) and follow-up data (AUC 0.86 [0.79,0.94]). A relative-risk matrix was developed to categorize the relative-risk of new onset of HFpEF based on biomarker threshold levels. CONCLUSION: We provided evidence for the utility of BNP, hsTroponin-I, and Galectin-3 in the prediction of future HFpEF in asymptomatic event-free populations with cardiovascular disease risk factors.


Subject(s)
Heart Failure , Biomarkers , Cohort Studies , Humans , Natriuretic Peptide, Brain , Prognosis , Retrospective Studies , Stroke Volume
12.
FASEB J ; 34(9): 11997-12008, 2020 09.
Article in English | MEDLINE | ID: mdl-32738093

ABSTRACT

Hematopoietic stem and progenitor cells (HSPCs) have the ability to self-renew and differentiate into various blood cells, thus playing an important role in maintenance of lifelong hematopoiesis. Brahma-related gene 1 (BRG1), which acts as the ATP subunit of mammalian SWI-SNF-related chromatin remodeling complexes, is involved in human acute myeloid leukemia and highly expresses in short-term HSPCs. But its role and regulatory mechanism for HSPC development have not yet been well established. Here, we generated a brg1 knockout zebrafish model using TALEN technology. We found that in brg1-/- embryo, the primitive hematopoiesis remained well, while definitive hematopoiesis formation was significantly impaired. The number of hemogenic endothelial cells was decreased, further affecting definitive hematopoiesis with reduced myeloid and lymphoid cells. During embryogenesis, the nitric oxide (NO) microenvironment in brg1-/- embryo was seriously damaged and the reduction of HSPCs could be partially rescued by a NO donor. Chromatin immunoprecipitation (ChIP) assays showed that BRG1 could bind to the promoter of KLF2 and trigger its transcriptional activity of NO synthase. Our findings show that Brg1 promotes klf2a expression in hemogenic endothelium and highlight a novel mechanism for HSPC formation and maintenance.


Subject(s)
Adaptor Proteins, Signal Transducing/metabolism , Embryo, Nonmammalian/embryology , Hematopoiesis , Hematopoietic Stem Cells/metabolism , Stem Cell Niche , Zebrafish Proteins/metabolism , Zebrafish/embryology , Adaptor Proteins, Signal Transducing/genetics , Animals , Gene Expression Regulation, Developmental , Gene Knockout Techniques , Hematopoietic Stem Cells/cytology , Kruppel-Like Transcription Factors/biosynthesis , Kruppel-Like Transcription Factors/genetics , Nitric Oxide/genetics , Nitric Oxide/metabolism , Response Elements , Transcription, Genetic , Zebrafish/genetics , Zebrafish Proteins/biosynthesis , Zebrafish Proteins/genetics
13.
J Exp Biol ; 224(18)2021 09 15.
Article in English | MEDLINE | ID: mdl-34494653

ABSTRACT

Caecilians are elongate, limbless and annulated amphibians that, with the exception of one aquatic family, all have an at least partly fossorial lifestyle. It has been suggested that caecilian evolution resulted in sturdy and compact skulls with fused bones and tight sutures, as an adaptation to their head-first burrowing habits. However, although their cranial osteology is well described, relationships between form and function remain poorly understood. In the present study, we explored the relationship between cranial shape and in vivo burrowing forces. Using micro-computed tomography (µCT) data, we performed 3D geometric morphometrics to explore whether cranial and mandibular shapes reflected patterns that might be associated with maximal push forces. The results highlight important differences in maximal push forces, with the aquatic Typhlonectes producing a lower force for a given size compared with other species. Despite substantial differences in head morphology across species, no relationship between overall skull shape and push force could be detected. Although a strong phylogenetic signal may partly obscure the results, our conclusions confirm previous studies using biomechanical models and suggest that differences in the degree of fossoriality do not appear to be driving the evolution of head shape.


Subject(s)
Amphibians , Skull , Animals , Biological Evolution , Body Weights and Measures , Phylogeny , X-Ray Microtomography
14.
Exp Cell Res ; 392(1): 112023, 2020 07 01.
Article in English | MEDLINE | ID: mdl-32325079

ABSTRACT

Diabetic retinopathy (DR) is a diabetes-associated complication characterized by irreversible deterioration of the microvessels within the retina, leading subsequently to severe retinal damage and vision loss. Vitamin D (VITD), a steroid hormone, plays multiple physiological functions in cellular homeostasis. Deficiency of VITD has been suggested to be associated with DR. To study the potential protective function of VITD in DR, high-glucose-treated ARPE-19 cells and STZ-induced diabetic mice were used as in vitro and in vivo models. The protective effects of VITD were assessed based on the changes of expression of antioxidant enzymes and cytokines in high-glucose-treated retinal pigment epithelial (RPE) cells and in the retina and RPE of diabetic and VITD-treated diabetic mice. The present study demonstrated that exposure to a high level of glucose caused upregulation of pro-inflammatory cytokines and a decrease in anti-oxidant enzyme expression in both in vitro and in vivo models. VITD treatment increased cell viability, reduced reactive oxygen species (ROS) production and caspase-3/7 activities in high-glucose-treated RPE cells. Our data suggest that VITD can protect the retina and RPE from high-glucose-induced oxidative damage and inflammation.


Subject(s)
Cytoprotection/drug effects , Epithelial Cells/drug effects , Glucose/adverse effects , Retinal Pigment Epithelium/drug effects , Vitamin D/pharmacology , Animals , Cell Line , Cell Survival/drug effects , Diabetes Mellitus, Experimental/chemically induced , Diabetes Mellitus, Experimental/complications , Diabetes Mellitus, Experimental/drug therapy , Diabetes Mellitus, Experimental/pathology , Diabetes Mellitus, Type 1/chemically induced , Diabetes Mellitus, Type 1/complications , Diabetes Mellitus, Type 1/drug therapy , Diabetes Mellitus, Type 1/pathology , Diabetic Retinopathy/pathology , Diabetic Retinopathy/prevention & control , Dose-Response Relationship, Drug , Epithelial Cells/physiology , Glucose/pharmacology , Humans , Mice , Mice, Inbred C57BL , Oxidative Stress/drug effects , Protective Agents/pharmacology , Protective Agents/therapeutic use , Reactive Oxygen Species/metabolism , Retinal Pigment Epithelium/physiology , Streptozocin , Vitamin D/therapeutic use
15.
Molecules ; 26(21)2021 Oct 27.
Article in English | MEDLINE | ID: mdl-34770892

ABSTRACT

When trialkylamines are added to buffered solutions of peptides, unexpected adducts can be formed. These adducts correspond to Schiff base products. The source of the reaction is the unexpected presence of aldehydes in amines. The aldehydes can be detected in a few ways. Most importantly, they can lead to unanticipated results in proteomics experiments. Their undesirable effects can be minimized through the addition of other amines.


Subject(s)
Amines/chemistry , Peptides/chemistry , Aldehydes , Amino Acid Sequence , Hemoglobins/chemistry , Polyamines/chemistry , Proteins/chemistry , Proteolysis , Schiff Bases , Solutions , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
16.
J Proteome Res ; 19(7): 2758-2771, 2020 07 02.
Article in English | MEDLINE | ID: mdl-32496805

ABSTRACT

Multiple ion fragmentation methods involving collision-induced dissociation (CID), higher-energy collisional dissociation (HCD) with regular and very high energy settings, and electron-transfer dissociation with supplementary HCD (EThcD) are implemented to improve the confidence of cross-link identifications. Three different S. cerevisiae proteasome samples cross-linked by diethyl suberthioimidate (DEST) or bis(sulfosuccinimidyl)suberate (BS3) are analyzed. Two approaches are introduced to combine interpretations from the above four methods. Working with cleavable cross-linkers such as DEST, the first approach searches for cross-link diagnostic ions and consistency among the best interpretations derived from all four MS2 spectra associated with each precursor ion. Better agreement leads to a more definitive identification. Compatible with both cleavable and noncleavable cross-linkers such as BS3, the second approach multiplies scoring metrics from a number of fragmentation experiments to derive an overall best match. This significantly increases the scoring gap between the target and decoy matches. The validity of cross-links fragmented by HCD alone and identified by Kojak, MeroX, pLink, and Xi was evaluated using multiple fragmentation data. Possible ways to improve the identification credibility are discussed. Data are available via ProteomeXchange with identifier PXD018310.


Subject(s)
Peptides , Saccharomyces cerevisiae , Algorithms , Cross-Linking Reagents , Ions , Tandem Mass Spectrometry
17.
J Biol Chem ; 294(38): 13953-13963, 2019 09 20.
Article in English | MEDLINE | ID: mdl-31362982

ABSTRACT

Mutations in human prominin 1 (PROM1), encoding a transmembrane glycoprotein localized mainly to plasma membrane protrusions, have been reported to cause retinitis pigmentosa, macular degeneration, and cone-rod dystrophy. Although the structural role of PROM1 in outer-segment (OS) morphogenesis has been demonstrated in Prom1-knockout mouse, the mechanisms underlying these complex disease phenotypes remain unclear. Here, we utilized a zebrafish model to further investigate PROM1's role in the retina. The Prom1 orthologs in zebrafish include prom1a and prom1b, and our results showed that prom1b, rather than prom1a, plays an important role in zebrafish photoreceptors. Loss of prom1b disrupted OS morphogenesis, with rods and cones exhibiting differences in impairment: cones degenerated at an early age, whereas rods remained viable but with an abnormal OS, even at 9 months postfertilization. Immunofluorescence experiments with WT zebrafish revealed that Prph2, an ortholog of the human transmembrane protein peripherin 2 and also associated with OS formation, is localized to the edge of OS and is more highly expressed in the cone OS than in the rod OS. Moreover, we found that Prom1b deletion causes mislocalization of Prph2 and disrupts its oligomerization. We conclude that the variation in Prph2 levels between cones and rods was one of the reasons for the different PROM1 mutation-induced phenotypes of these retinal structures. These findings expand our understanding of the phenotypes caused by PROM1 mutations and provide critical insights into its function.


Subject(s)
AC133 Antigen/metabolism , Photoreceptor Cells/metabolism , Rod Cell Outer Segment/metabolism , AC133 Antigen/genetics , Animals , Cone-Rod Dystrophies/genetics , Disease Models, Animal , HeLa Cells , Humans , Macular Degeneration/metabolism , Membrane Proteins/metabolism , Morphogenesis , Mutation , Peripherins/genetics , Retina/metabolism , Retina/physiology , Retinal Cone Photoreceptor Cells/metabolism , Retinal Degeneration/genetics , Retinal Degeneration/physiopathology , Retinal Rod Photoreceptor Cells/metabolism , Retinitis Pigmentosa/genetics , Sequence Deletion , Zebrafish/metabolism , Zebrafish Proteins/metabolism
18.
Exp Eye Res ; 201: 108291, 2020 12.
Article in English | MEDLINE | ID: mdl-33049273

ABSTRACT

Retinitis pigmentosa (RP) is a collection of heterogenous genetic retinal disorders resulting in cumulative retinal deterioration involving progressive loss of photoreceptors and eventually in total blindness. Oxidative stress plays a central role in this photoreceptor loss. Gypenosides (Gyp) are the main functional component isolated from the climbing vine Gynostemma pentaphyllum and have been shown to defend cells against the effects of oxidative stress and inflammation, providing protection in experimentally-induced optic neuritis. The zebrafish model has been used to investigate a range of human diseases. Previously we reported early retinal degeneration in a mutant zebrafish line carrying a point-nonsense mutation in the retinitis pigmentosa GTPase regulator interacting protein 1 (rpgrip1) gene that is mutated in RP patients. The current study investigated the potential protective effects of Gyp against photoreceptor degeneration in the Rpgrip1 deleted zebrafish. Rpgrip1 mutant zebrafish were treated with 5 µg/ml of Gyp in E3 medium from 6 h post fertilization (hpf) till 1 month post fertilization (mpf). Rpgrip1 mutant zebrafish treated with 5 µg/ml of Gyp showed a significant decrease by 68.41% (p = 0.0002) in photoreceptor cell death compared to that of untreated mutant zebrafish. Expression of antioxidant genes catalase, sod1, sod2, gpx1, gclm, nqo-1 and nrf-2 was significantly decreased in rpgrip1 mutant zebrafish eyes by 61.51%, 77.40%, 60.11%, 81.17%, 72.07%, 78.95% and 85.42% (all p < 0.0001), respectively, when compared to that of wildtype zebrafish; superoxide dismutase and catalase activities, and glutathione levels in rpgrip1 mutant zebrafish eyes were significantly decreased by 87.21%, 21.55% and 96.51% (all p < 0.0001), respectively. There were marked increases in the production of reactive oxygen species (ROS) and malondialdehyde (MDA) by 2738.73% and 510.69% (all p < 0.0001), respectively, in rpgrip1 mutant zebrafish eyes; expression of pro-inflammatory cytokines IL-1ß, IL-6 and TNF-α was also significantly increased by 150.11%, 267.79% and 190.72% (all p < 0.0001), respectively, in rpgrip1 mutant zebrafish eyes, compared to that of wildtype zebrafish. Treatment with Gyp significantly counteracted these effects. This study indicates that Gyp has a potential role in the treatment of RP.


Subject(s)
Oxidative Stress , Photoreceptor Cells, Invertebrate/drug effects , Retina/drug effects , Retinitis Pigmentosa/drug therapy , Animals , Gynostemma , Immunohistochemistry , Photoreceptor Cells, Invertebrate/metabolism , Photoreceptor Cells, Invertebrate/pathology , Plant Extracts/pharmacology , Reactive Oxygen Species/metabolism , Retina/metabolism , Retina/pathology , Retinitis Pigmentosa/metabolism , Retinitis Pigmentosa/pathology , Rhodopsin/metabolism , Zebrafish
19.
Brain Inj ; 34(12): 1674-1684, 2020 10 14.
Article in English | MEDLINE | ID: mdl-33103479

ABSTRACT

BACKGROUND: Most post-concussion eye movement (EM) research involves predominantly male samples. We evaluated pro- (PRO; reflexive shift of visual attention to target) and anti- (ANTI; executive control of visual attention away from target) computer-based saccade task performance among female, collegiate athletes with recent concussion (CON) versus healthy-control athletes (HC). We evaluated the relationship between EM performance and post-concussion outcomes. We hypothesized ANTI performance would differ among CON and HC due to greater executive control demands, and that EM performance (both tasks) would be associated with clinical outcomes in CON. METHODS: 16 CON (assessed 4-10 days post-injury [M = 6.87, SD = 2.15 days]) and 16 age-matched HC athletes were recruited. General linear mixed modeling and Pearson's correlations were used. RESULTS: On ANTI, CON demonstrated higher error rate [F(1,2863) = 12.650, p<.001] and shorter latency on error trials [F(1,469) = 5.976, p=.015] relative to HC. Multiple EM measures were associated with clinical outcomes: PRO duration predicted days to symptom remission (r=.44, p <.05); ANTI error rate was associated with symptom burden on the day of testing (r=.27, p <.05). CONCLUSION: This study demonstrates promising utility of EM measures to detect cognitive control and sensorimotor effects of concussion among female athletes and their use as a prognostic indicators of recovery.


Subject(s)
Athletic Injuries , Brain Concussion , Post-Concussion Syndrome , Athletes , Athletic Injuries/complications , Brain Concussion/complications , Eye Movements , Female , Humans , Male , Neuropsychological Tests
20.
J Emerg Med ; 58(3): 407-412, 2020 Mar.
Article in English | MEDLINE | ID: mdl-31980286

ABSTRACT

BACKGROUND: To our knowledge, no study has assessed the correlation of fraction of inspired oxygen (FiO2) and end-tidal oxygen (EtO2) values obtained from a gas analyzer during the preoxygenation period of rapid sequence intubation (RSI) to predict partial pressure of oxygen (PaO2) among patients requiring intubation in the emergency department (ED). OBJECTIVE: The purpose of this study was to determine whether a simple equation using EtO2 and FiO2 at time of induction could reliably estimate minimal PaO2 in ED patients undergoing RSI. METHODS: We conducted an observational pilot study performed in an adult ED utilizing a gas analyzer to obtain EtO2 and FiO2 values in ED patients undergoing RSI from data collectors blinded to our objective. The Pearson correlation coefficient was calculated between the equation's predicted PaO2 and the PaO2 drawn from an arterial blood gas shortly after intubation. A Bland-Altman plot analysis was performed to identify any additional bias. RESULTS: Seventy-five patients were enrolled. The equation's mean predicted minimal PaO2 and mean PaO2 from an arterial blood gas within 3 min after intubation was 178 mm Hg (95% confidence interval [CI] 145-211 mm Hg) and 209 mm Hg (95% CI 170-258 mm Hg), respectively. The Pearson correlation coefficient between the predicted minimal PaO2 and post-intubation PaO2 demonstrated a strong correlation (r2 = 0.89). The Bland-Altman plot indicated no bias affecting the correlation between the predicted and actual PaO2. CONCLUSIONS: Among ED patients undergoing RSI, the use of a gas analyzer to measure EtO2 and FiO2 can provide a reliable measure of the minimal PaO2 at the time of induction during the RSI phase of preoxygenation.


Subject(s)
Blood Gas Analysis , Oxygen/blood , Rapid Sequence Induction and Intubation , Adult , Emergency Service, Hospital , Humans , Intubation , Pilot Projects
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