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Science Papers Examine Urine-Based Diagnostic Assays, Sleep Regulation

By analyzing the fragmented cell-free DNA (cfDNA) found in urine, it may be possible to gain diagnostic insights from this degraded genetic material, according to a new study appearing in Science Translational Medicine this week. While cancer-derived cfDNA is present in urine, it is highly fragmented, limiting targeted analysis of genomic alterations. Seeking to overcome this issue, scientists from the Translational Genomics Research Institute used whole-genome sequencing to characterize fragmentation patterns in urine cfDNA. They find a consistent distribution of fragment sizes with a modal size of 80 to 81 base pairs, suggesting nonrandom fragmentation. Further analysis reveals a correlation between cfDNA fragmentation patterns in urine and both chromatin accessibility and gene expression in contributing cells. Using urine samples from cancer patients, the investigators develop a diagnostic framework that uses genome-wide differences in urine cfDNA fragmentation at recurrently protected genomic regions. "Our findings support a stable distribution of cfDNA fragments across the genome in urine and set the stage for future investigation and development of urine-based diagnostic assays," the study's authors conclude.

A study in this week's Science Advances linking a gene associated with neurodevelopmental disorders (NDD) with sleep regulation in fruit flies may help researchers better understand why sleep disruption is so prevalent in NDDs such as ADHD and autism. A team led by researchers from the University of Pennsylvania performed an RNAi screen in fruit flies of human NDD-associated risk genes, identifying the chromatin remodeler ISWI as required for sleep in the adult insect. In addition to disrupting sleep, loss of the gene was also found to impact circadian rhythms, memory, and social behavior in adult fruit flies, but acting in different cells and during distinct developmental times to do so. Notably, expressing human ISWI homologs in the flies rescued all of the phenotypes except sleep disruption. Based on their findings, the investigators suggest that "sleep is a developmentally programmed behavior; sleep abnormalities in NDDs are not simply a by-product of broad cognitive/behavioral deficits but rather emerge from specific developmental anomalies."

The Scan

Alzheimer's Risk Gene Among Women

CNN reports that researchers have found that variants in MGMT contribute to Alzheimer's disease risk among women but not men.

Still Hanging Around

The Guardian writes that persistent pockets of SARS-CoV-2 in the body could contribute to long COVID.

Through a Little Spit

Enteric viruses like norovirus may also be transmitted through saliva, not just the fecal-oral route, according to New Scientist.

Nature Papers Present Method to Detect Full Transcriptome, Viruses Infecting Asgard Archaea, More

In Nature this week: VASA-seq approach to detect full transcriptome, analysis of viruses infecting Asgard archaea, and more.