Biology subjects

Spector, M.

Publications and source records attributed to Spector, M..

3 recordsLinked to original sources

bioRxiv2024

Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq

Genome-wide association studies (GWAS) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. We performed capture STARR-sequencing of over 78,000 candidate regions to identify active enhancers in primary human neural progenitor cells (phNPCs). We selected candidate regions by integrating data from NPCs, prefrontal cortex, developmental timepoints, and GWAS. Over 8,000 regions demonstrated enhancer activity in the phNPCs, and we linked these regions to over 2,200 predicted target genes. These genes are involved in neuronal and psychiatric disease-associated pathways, including dopaminergic synapse, axon guidance, and schizophrenia. We functionally validated a subset of these enhancers using mutation STARR-sequencing and CRISPR deletions, demonstrating the effects of genetic variation on enhancer activity and enhancer deletion on gene expression. Overall, we identified thousands of highly active enhancers and functionally validated a subset of these enhancers, improving our understanding of regulatory networks underlying brain function and disease.

neuroscience↗

bioRxiv2023

Variation in the Microbiomes of the Basidiomycete Fungi Scleroderma citrinum (Pers.) and Pisolithus arhizus (Pers.): a tale of two saprotrophs.

In this study we used high throughput DNA sequencing and ICP-MS to compare the microbiome of the common earthball fungus, Scleroderma citrinum (Pers.) to that of its sister taxon in the Sclerodermataceae, Pisolithus arhizus (Scop.). ICP-MS analysis demonstrates that S. citrinum is enriched in silica, sulfur and zinc relative to P. arhizus, while P. arhizus is enriched in arsenic, calcium, cadmium, cobalt, copper, lithium, magnesium, molybdenum, nickel, potassium and vanadium. Statistical analysis of molecular data indicates that the microbiome of P. arhizus is both richer and more diverse than that of S. citrinum, and that the microbiomes are significantly different with that of S. citrinum being enriched in Cyanobacteria represented by the chloroplast of a photosynthetic, cryptoendolithic red alga, Saccharibacteria (TM-7), and Planctomycetes, while that of P. arhizus is enriched in Gemmatimonadetes, Latescibacteria, Elusomicrobia, and Tectomicrobia. Further, the P. arhizus microbiome is enriched in anaerobes relatives to that of S. citrinum, probably reflecting anaerobic zones previously measured in P. arhizus. Together, the data indicate diverse microbiomes comprised of aromatic hydrocarbon-degrading, metal- and radiotolerant bacteria, indicating that these fungi may provide a rich source of novel microbes suitable for bioremediation strategies.

microbiology↗

bioRxiv2019

Marine deforestation leads to widespread loss of ecosystem function

Trophic interactions can result in changes to the abundance and distribution of habitat-forming species that dramatically reduce ecosystem health and functioning. Nowhere may this be as dramatic as in the coastal zone of the Aleutian Archipelago, where overgrazing by herbivorous sea urchins that began in the 1980s resulted in widespread deforestation of the regions kelp forests. Here we show that this deforestation resulted in decreased macroalgal and invertebrate abundance and diversity, increased benthic irradiances, and reduced rates of gross primary production and respiration by the ecosystem. These opposing metabolic processes remain in balance, however, which resulted in little-to-no changes to net ecosystem production. These patterns were consistent across nine islands spanning more than 1000 kilometers of the archipelago. In light of the worldwide declines in kelp forests observed in recent decades, our findings suggest that marine deforestation profoundly affects the health of coastal ecosystems and how they function. Significance statementWidespread marine deforestation results in reduced biodiversity and primary productivity throughout more than 1000 km of the Aleutian Archipelago.

ecology↗