There is a pressing need for patient-derived cell models of brain diseases that are relevant and robust enough to produce the large quantities of cells required for molecular and functional analyses. ...We describe here a new cell model based on patient-derived cells from the human olfactory mucosa, the organ of smell, which regenerates throughout life from neural stem cells. Olfactory mucosa biopsies were obtained from healthy controls and patients with either schizophrenia, a neurodevelopmental psychiatric disorder, or Parkinson's disease, a neurodegenerative disease. Biopsies were dissociated and grown as neurospheres in defined medium. Neurosphere-derived cell lines were grown in serum-containing medium as adherent monolayers and stored frozen. By comparing 42 patient and control cell lines we demonstrated significant disease-specific alterations in gene expression, protein expression and cell function, including dysregulated neurodevelopmental pathways in schizophrenia and dysregulated mitochondrial function, oxidative stress and xenobiotic metabolism in Parkinson's disease. The study has identified new candidate genes and cell pathways for future investigation. Fibroblasts from schizophrenia patients did not show these differences. Olfactory neurosphere-derived cells have many advantages over embryonic stem cells and induced pluripotent stem cells as models for brain diseases. They do not require genetic reprogramming and they can be obtained from adults with complex genetic diseases. They will be useful for understanding disease aetiology, for diagnostics and for drug discovery.
Rab GTPases including Rab27a, Rab38 and Rab32 function in melanosome maturation or trafficking in melanocytes. A screen to identify additional Rabs involved in these processes revealed the ...localization of GFP‐Rab17 on recycling endosomes (REs) and melanosomes in melanocytic cells. Rab17 mRNA expression is regulated by microphthalmia transcription factor (MITF), a characteristic of known pigmentation genes. Rab17 siRNA knockdown in melanoma cells quantitatively increased melanosome concentration at the cell periphery. Rab17 knockdown did not inhibit melanosome maturation nor movement, but it caused accumulation of melanin inside cells. Double knockdown of Rab17 and Rab27a indicated that Rab17 acts on melanosomes downstream of Rab27a. Filopodia are known to play a role in melanosome transfer, and in Rab17 knockdown cells filopodia formation was inhibited. Furthermore, we show that stimulation of melanoma cells with α‐melanocyte‐stimulating hormone induces filopodia formation, supporting a role for filopodia in melanosome release. Cell stimulation also caused redistribution of REs to the periphery, and knockdown of additional RE‐associated Rabs 11a and 11b produced a similar accumulation of melanosomes and melanin to that seen after loss of Rab17. Our findings reveal new functions for RE and Rab17 in pigmentation through a distal step in the process of melanosome release via filopodia.
•Novel, agarose gel-based detection methods for base and prime editing detection.•Workflow from transfection through to analysis for base and prime editing.•Base editing of plasmid DNA targets in ...mammalian cells.
Precision chemistry entailing user-directed nucleotide substitutions and template-specified repair can be facilitated by base editing and prime editing, respectively. Recently, the diversification of adenine, cytosine, and prime editor variants obliges a considered, high-throughput evaluation of these tools for optimized, end-point applications. Herein, we outline novel, cost-effective and scalable approaches for the rapid detection of base editing and prime editing outcomes using gel electrophoresis. For base editing, we exploit primer mismatch amplification (SNP genotyping) for the gel-based detection of base editing efficiencies as low as 0.1%. For prime editing, we describe a one-pot reaction combining polymerase chain reaction (PCR) amplification of the target region with restriction digestion (restriction fragment length polymorphism; RFLP). RFLP enables the rapid detection of insertion or deletion events in under 2.5 h from genomic DNA extraction. We show that our method of SNP genotyping is amenable to both endogenous target loci as well as transfected, episomal plasmid targets in BHK-21 cells. Next, we validate the incidence of base and prime editing by describing Sanger sequencing and next-generation sequencing (NGS) workflows for the accurate validation and quantification of on-target editing efficiencies. Our workflow details three different methods for the detection of rare base and prime editing events, enabling a tiered approach from low to high resolution that makes use of gel electrophoresis, Sanger sequencing, and NGS.
Monitoring and modeling aerosol particle life cycle in Southeast Asia (SEA) is challenged by high cloud cover, complex meteorology, and the wide range of aerosol species, sources, and transformations ...found throughout the region. Satellite observations are limited, and there are few in situ observations of aerosol extinction profiles, aerosol properties, and environmental conditions. Therefore, accurate aerosol model outputs are crucial for the region. This work evaluates the Navy Aerosol Analysis and Prediction System Reanalysis (NAAPS-RA) aerosol optical thickness (AOT) and light extinction products using airborne aerosol and meteorological measurements from the Cloud, Aerosol, and Monsoon Processes Philippines Experiment (CAMP2Ex) conducted in 2019 during the SEA southwest monsoon biomass burning season. Modeled AOTs and extinction coefficients are compared to those retrieved with a high spectral resolution lidar (HSRL-2). Agreement between simulated and retrieved AOT (R2= 0.78, relative bias =-5 %, normalized root mean square error (NRMSE) = 48 %) and aerosol extinction coefficients (R2= 0.80, 0.81, and 0.42; relative bias = 3 %, -6 %, and -7 %; NRMSE = 47 %, 53 %, and 118 % for altitudes between 40–500, 500–1500, and >1500 m, respectively) is quite good considering the challenging environment and few opportunities for assimilations of AOT from satellites during the campaign. Modeled relative humidities (RHs) are negatively biased at all altitudes (absolute bias =-5 %, -8 %, and -3 % for altitudes <500 500–1500 and >1500 m, respectively), motivating interest in the role of RH errors in AOT and extinction simulations. Interestingly, NAAPS-RA AOT and extinction agreement with the HSRL-2 does not change significantly (i.e., NRMSE values do not all decrease) when RHs from dropsondes are substituted into the model, yet biases all move in a positive direction. Further exploration suggests changes in modeled extinction are more sensitive to the actual magnitude of both the extinction coefficients and the dropsonde RHs being substituted into the model as opposed to the absolute differences between simulated and measured RHs. Finally, four case studies examine how model errors in RH and the hygroscopic growth parameter, γ, affect simulations of extinction in the mixed layer (ML). We find NAAPS-RA overestimates the hygroscopicity of (i) smoke particles from biomass burning in the Maritime Continent (MC) and (ii) anthropogenic emissions transported from East Asia. This work mainly provides insight into the relationship between errors in modeled RH and simulations of AOT and extinction in a humid and tropical environment influenced by a myriad of meteorological conditions and particle types. These results can be interpreted and addressed by the modeling community as part of the effort to better understand, quantify, and forecast atmospheric conditions in SEA.
Experimental laboratory research has an important role to play in dementia prevention. Mechanisms underlying modifiable risk factors for dementia are promising targets for dementia prevention but are ...difficult to investigate in human populations due to technological constraints and confounds. Therefore, controlled laboratory experiments in models such as transgenic rodents, invertebrates and in vitro cultured cells are increasingly used to investigate dementia risk factors and test strategies which target them to prevent dementia. This review provides an overview of experimental research into 15 established and putative modifiable dementia risk factors: less early‐life education, hearing loss, depression, social isolation, life stress, hypertension, obesity, diabetes, physical inactivity, heavy alcohol use, smoking, air pollution, anesthetic exposure, traumatic brain injury, and disordered sleep. It explores how experimental models have been, and can be, used to address questions about modifiable dementia risk and prevention that cannot readily be addressed in human studies.
Highlights
Modifiable dementia risk factors are promising targets for dementia prevention.
Interrogation of mechanisms underlying dementia risk is difficult in human populations.
Studies using diverse experimental models are revealing modifiable dementia risk mechanisms.
We review experimental research into 15 modifiable dementia risk factors.
Laboratory science can contribute uniquely to dementia prevention.
CRISPR/Cas has opened the prospect of direct gene correction therapy for some inherited retinal diseases. Previous work has demonstrated the utility of adeno-associated virus (AAV) mediated delivery ...to retinal cells in vivo; however, with the expanding repertoire of CRISPR/Cas endonucleases, it is not clear which of these are most efficacious for retinal editing in vivo. We sought to compare CRISPR/Cas endonuclease activity using both single and dual AAV delivery strategies for gene editing in retinal cells. Plasmids of a dual vector system with SpCas9, SaCas9, Cas12a, CjCas9 and a sgRNA targeting YFP, as well as a single vector system with SaCas9/YFP sgRNA were generated and validated in YFP-expressing HEK293A cell by flow cytometry and the T7E1 assay. Paired CRISPR/Cas endonuclease and its best performing sgRNA was then packaged into an AAV2 capsid derivative, AAV7m8, and injected intravitreally into CMV-Cre::Rosa26-YFP mice. SpCas9 and Cas12a achieved better knockout efficiency than SaCas9 and CjCas9. Moreover, no significant difference in YFP gene editing was found between single and dual CRISPR/SaCas9 vector systems. With a marked reduction of YFP-positive retinal cells, AAV7m8 delivered SpCas9 was found to have the highest knockout efficacy among all investigated endonucleases. We demonstrate that the AAV7m8-mediated delivery of CRISPR/SpCas9 construct achieves the most efficient gene modification in neurosensory retinal cells in vivo.
Arsenic is an environmental toxin which increases skin cancer risk for exposed populations worldwide; however the underlying biomolecular mechanism for arsenic-induced carcinogenesis is complex and ...poorly defined. Recent investigations show that histone deacetylase and DNA methyltransferase activity is impaired, and epigenetic patterns of gene regulation are consistently altered in cancers associated with arsenic exposure. Expression of the histone deacetylase SIRT1 is altered in solid tumours and haematological malignancies; however its role in arsenic-induced pathology is unknown. In this study we investigated the effect of arsenic on epigenetic regulation of SIRT1 and its targeting microRNA, miR-34a in primary human keratinocytes.
Acetylation of histone H4 at lysine 16 (H4K16) increased in keratinocytes exposed to 0.5μM arsenite As(III); and this was associated with chromatin remodelling at the miR-34a promoter. Moreover, although SIRT1 protein initially increased in these As(III)-exposed cells, after 24days expression was not significantly different from untreated controls. Extended exposure to low-dose As(III) (0.5μM; >5weeks) compromised the pattern of CpG methylation at SIRT1 and miR-34a gene promoters, and this was associated with altered expression for both genes.
We have found that arsenic alters epigenetic regulation of SIRT1 expression via structural reorganisation of chromatin at the miR-34a gene promoter in the initial 24h of exposure; and over time, through shifts in miR-34a and SIRT1 gene methylation. Taken together, this investigation demonstrates that arsenic produces cumulative disruptions to epigenetic regulation of miR-34a expression, and this is associated with impaired coordination of SIRT1 functional activity.
•Submicromolar arsenic concentrations disrupt SIRT1 activity and expression in human keratinocytes.•Arsenic-induced chromatin remodelling at the miR-34a gene promoter is associated with hyperacetylation of histone H4 (Lys 16).•Continual extended exposure to arsenic reorganises the pattern of SIRT1 and miR-34a promoter methylation.
AIM To determine if exacerbation of pre-existing chronic colitis in Winnie(Muc2 mutant) mice induces colonic dysplasia.METHODS Winnie mice and C57BL6 as a genotype control, were administered 1% w/v ...dextran sulphate sodium(DSS) orally, followed by drinking water alone in weeklong cycles for a total of three cycles. After the third cycle, mice were killed and colonic tissue collected for histological and immunohistochemical evaluation. Inflammation and severity of dysplasia in the colonic mucosa were assessed in H&E sections of the colon. Epithelial cell proliferation was assessed using Ki67 and aberrant β-catenin signalling assessed with enzyme-based immunohistochemistry. Extracted RNA from colonic segments was used for the analysis of gene expression using real-time quantitative PCR. Finally, the distribution of Cxcl5 was visualised using immunohistochemistry.RESULTS Compared to controls, Winnie mice exposed to three cycles of DSS displayed inflammation mostly confined to the distal-mid colon with extensive mucosal hyperplasia and regenerative atypia resembling epithelial dysplasia. Dysplasia-like changes were observed in 100% of Winnie mice exposed to DSS, with 55% of these animals displaying changes similar to high-grade dysplasia, whereas high-grade changes were absent in wild-type mice. Occasional penetration of the muscularis mucosae by atypical crypts was observed in 27% of Winnie mice after DSS. Atypical crypts however displayed no evidence of oncogenic nuclear β-catenin accumulation, regardless of histological severity. Expression of Cav1, Trp53 was differentially regulated in the distal colon of Winnie relative to wild-type mice. Expression of Myc and Ccl5 was increased by DSS treatment in Winnie only. Furthermore, increased Ccl5 expression correlated with increased complexity in abnormal crypts. While no overall difference in Cxcl5 mucosal expression was observed between treatment groups, epithelial Cxcl5 protein appeared to be diminished in the atypical epithelium. CONCLUSION Alterations to the expression of Cav1, Ccl5, Myc and Trp53 in the chronically inflamed Winnie colon may influence the transition to dysplasia.
Summary
Several parallels between stem cell biology and tumour behaviour have been discovered in recent times. Such commonality is apparent in the unlimited capacity for cell division together with ...the lack of a differentiated phenotype in embryonic and adult stem cells, traits shared with tumour cells. Differentiation is a tightly regulated process that is mediated by the actions of multiple transcription factor families. The POU domain‐containing family of transcription factors contains multiple mammalian members divided into six classes, which can be expressed broadly or in a cell‐specific manner, and which are regulators of cell fate decisions of many different lineages. Target gene regulation can occur via a POU factor acting alone, or in combination with other POU proteins, ubiquitous co‐activators or co‐repressors, or other lineage restricted transcription factors. Aberrant levels of POU proteins have been found in several malignancies, including melanoma, connecting the otherwise developmentally restricted gene regulatory functions of POU transcription factors to the critical determinants of malignant transformation. Here, we focus on the role of the BRN2 (POU3F2/N‐Oct‐3) transcription factor in the melanocytic lineage where it may co‐ordinate normal developmental cues that can be re‐activated in melanoma. Recent studies have shown BRN2 to be responsive to MAPK pathway activation and to modulate the levels of MITF so as to suppress the differentiated melanocytic phenotype and to enhance tumour metastasis.
Inadequate knowledge about the complex microphysical and optical processes of the aerosol–cloud system severely restricts our ability to quantify the resultant impact on climate. Contrary to the ...negative radiative forcing (cooling) exerted by aerosols in cloud-free skies over dark surfaces, the absorbing aerosols, when lofted over the clouds, can potentially lead to significant warming of the atmosphere. The sign and magnitude of the aerosol radiative forcing over clouds are determined mainly by the amount of aerosol loading, the absorption capacity of aerosols or single-scattering albedo (SSA), and the brightness of the underlying cloud cover. In satellite-based algorithms that use measurements from passive sensors, the assumption of aerosol SSA is known to be the largest source of uncertainty in quantifying above-cloud aerosol optical depth (ACAOD). In this paper, we introduce a novel synergy algorithm that combines direct airborne measurements of ACAOD and the top-of-atmosphere (TOA) spectral reflectance from Ozone Monitoring Instrument (OMI) and Moderate Resolution Imaging Spectroradiometer (MODIS) sensors of NASA's A-train satellites to retrieve (1) SSA of light-absorbing aerosols lofted over the clouds and (2) aerosol-corrected cloud optical depth (COD). Radiative transfer calculations show a marked sensitivity of the TOA measurements to ACAOD, SSA, and COD, further suggesting that the availability of accurate ACAOD allows retrieval of SSA for above-cloud aerosol scenes using the “color ratio” algorithm developed for satellite sensors carrying ultraviolet (UV) and visible-near-IR (VNIR) wavelength bands. The proposed algorithm takes advantage of airborne measurements of ACAOD acquired from the High Spectral Resolution Lidar-2 (HSRL-2) and Spectrometer for Sky-Scanning, Sun-Tracking Atmospheric Research (4STAR) sun photometer operated during the ORACLES (ObseRvations of Aerosols above CLouds and their intEractionS) field campaign (September 2016, August 2017, and October 2018) over the southeastern Atlantic Ocean and synergizes them with TOA reflectance from OMI and MODIS to derive spectral SSA in the near-UV (354–388 nm) and VNIR (470–860 nm), respectively. When compared against the ORACLES airborne remote sensing and in situ measurements and the inversion dataset of the ground-based Aerosol Robotic Network (AERONET) over land, the retrieved spectral SSAs from the satellites, on average, were found to be within agreement of ∼ 0.01 – the difference well within the uncertainties involved in all these inversion datasets. The retrieved SSA above the clouds at UV–Vis-NIR wavelengths shows a distinct increasing trend from August to October, which is consistent with the ORACLES in situ measurements, AERONET inversions, and previous findings. The sensitivity analysis quantifying theoretical uncertainties in the retrieved SSA shows that errors in the measured ACAOD, aerosol layer height, and the ratio of the imaginary part of the refractive index (spectral dependence) of aerosols by 20 %, 1 km, and 10 %, respectively, produce an error in the retrieved SSA at 388 nm (470 nm) by 0.017 (0.015), 0.008 (0.002), and 0.03 (0.005). The development of the proposed aerosol–cloud algorithm implies a possible synergy of Cloud–Aerosol Lidar with Orthogonal Polarization (CALIOP) and OMI–MODIS passive sensors to deduce a global product of ACAOD and SSA. Furthermore, the presented synergy algorithm assumes implications for future missions, such as the Atmosphere Observing System (AOS) and the Earth Cloud Aerosol and Radiation Explorer (EarthCARE). The availability of the intended global dataset can help constrain climate models with the much-needed observational estimates of the radiative effects of aerosols in cloudy regions and expand our ability to study aerosol effects on clouds.
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