Using the dCas9-KRAB system to repress gene expression in hiPSC-derived NGN2 neurons

We describe a CRISPR inhibition (CRISPRi) protocol to repress endogenous gene expression (e.g., ATP6V1A) in human induced pluripotent stem cell-derived NGN2-induced glutamatergic neurons. CRISPRi enables efficient and precise gene repression of one or multiple target genes via delivering gRNA(s) to direct a dCas9-KRAB fusion protein to the gene(s) of interest. This protocol can also be adapted for gene activation and high-throughput gene manipulation, allowing assessment of the transcriptomic and phenotypic impact of candidate gene(s) associated with neurodevelopment or brain disease. For complete details on the use and execution of this protocol, please refer to Ho et al. (2017) and Wang et al. (2021).

Integration of CRISPR-engineering and hiPSC-based models of psychiatric genomics

Neuropsychiatric disorders are highly heritable polygenic disorders arising from the complex interplay of highly penetrant rare variants and common variants of small effect. There is a large index of comorbidity and shared genetic risk between disorders, reflecting the pleiotropy of individual variants as well as predicted downstream pathway-level convergence. Importantly, the mechanism(s) through which psychiatric disease-associated variants interact to contribute to disease risk remains unknown. Human induced pluripotent stem cell (hiPSC)-based models are increasingly useful for the systematic study of the complex genetics associated with brain diseases, particularly when combined with CRISPR-mediated genomic engineering, which together facilitate isogenic comparisons of defined neuronal cell types. In this review, we discuss the latest CRISPR technologies and consider how they can be successfully applied to the functional characterization of the growing list genetic variants linked to psychiatric disease.

Synergistic effects of common schizophrenia risk variants

The mechanisms by which common risk variants of small effect interact to contribute to complex genetic disorders are unclear. Here, we apply a genetic approach, using isogenic human induced pluripotent stem cells, to evaluate the effects of schizophrenia (SZ)-associated common variants predicted to function as SZ expression quantitative trait loci (eQTLs). By integrating CRISPR-mediated gene editing, activation and repression technologies to study one putative SZ eQTL (FURIN rs4702) and four top-ranked SZ eQTL genes (FURIN, SNAP91, TSNARE1 and CLCN3), our platform resolves pre- and postsynaptic neuronal deficits, recapitulates genotype-dependent gene expression differences and identifies convergence downstream of SZ eQTL gene perturbations. Our observations highlight the cell-type-specific effects of common variants and demonstrate a synergistic effect between SZ eQTL genes that converges on synaptic function. We propose that the links between rare and common variants implicated in psychiatric disease risk constitute a potentially generalizable phenomenon occurring more widely in complex genetic disorders.

Regional-scale assessment of soil salinity in the Red River Valley using multi-year MODIS EVI and NDVI

The ability to inventory and map soil salinity at regional scales remains a significant challenge to scientists concerned with the salinization of agricultural soils throughout the world. Previous attempts to use satellite or aerial imagery to assess soil salinity have found limited success in part because of the inability of methods to isolate the effects of soil salinity on vegetative growth from other factors. This study evaluated the use of Moderate Resolution Imaging Spectroradiometer (MODIS) imagery in conjunction with directed soil sampling to assess and map soil salinity at a regional scale (i.e., 10-10(5) km(2)) in a parsimonious manner. Correlations with three soil salinity ground truth datasets differing in scale were made in Kittson County within the Red River Valley (RRV) of North Dakota and Minnesota, an area where soil salinity assessment is a top priority for the Natural Resource Conservation Service (NRCS). Multi-year MODIS imagery was used to mitigate the influence of temporally dynamic factors such as weather, pests, disease, and management influences. The average of the MODIS enhanced vegetation index (EVI) for a 7-yr period exhibited a strong relationship with soil salinity in all three datasets, and outperformed the normalized difference vegetation index (NDVI). One-third to one-half of the spatial variability in soil salinity could be captured by measuring average MODIS EVI and whether the land qualified for the Conservation Reserve Program (a USDA program that sets aside marginally productive land based on conservation principles). The approach has the practical simplicity to allow broad application in areas where limited resources are available for salinity assessment.

Predictors related to the occurrence of a measles epidemic in the city of São Paulo in 1997

A matched case-control study was performed to identify risk factors for measles during an epidemic that occurred in 1997 in the city of São Paulo, in the Brazilian state of the same name. Measles cases from the city of São Paulo from 1 January 1997 to 15 August 1997 were included in the study. The criteria for case definition were age below 30 years, having received no measles vaccine 5-21 days before the onset of rash, and laboratory confirmation by IgM antibodies detection. From a bank of confirmed measles cases, 130 cases for each of five age ranges (under 1 year, 1-5 years, 6-20 years, 21-24 years, and 25-29 years) were picked at random according to a systematic criterion proportional to the number of cases in seven areas of the city. Data were collected through a home survey, and for each measles case studied two controls matched by age and place of residence were selected. The matched conditional logistic regression analysis for the potential risk factors from the univariate analysis showed that the best predictors for acquiring measles during the epidemic were: lack of measles vaccination, previous contact with a measles-like disease at home or on the job, having been born either outside the state of São Paulo or in a rural area, being employed, and spending time in a semiclosed institution, such as a nursery, day care center, or school. The risk factors were not homogeneous for the different age groups. The data in the present survey suggest that, in addition to lack of vaccination, other risk factors should be considered when planning a measles vaccination strategy for a developing country.