Agricultural Soil Management Practices Differentially Shape the Bacterial and Fungal Microbiome of Sorghum bicolor.

Soils play important roles in biological productivity. While past work suggests that microbes affect soil health and respond to agricultural practices, it is not well known how soil management shapes crop host microbiomes. To elucidate the impact of management on microbial composition and function in the sorghum microbiome, we performed 16S rRNA gene and ITS2 amplicon sequencing and metatranscriptomics on soil and root samples collected from a site in California's San Joaquin Valley that is under long-term cultivation with 1) standard (ST) or no tilling (NT) and 2) cover-cropping (CC) or leaving the field fallow (NO). Our results revealed that microbial diversity, composition, and function change across tillage and cover type, with a heightened response in fungal communities, versus bacterial. Surprisingly, ST harbored greater microbial alpha diversity than NT, indicating that tillage may open niche spaces for broad colonization. Across management regimes, we observed class-level taxonomic level shifts. Additionally, we found significant functional restructuring across treatments, including enrichment for microbial lipid and carbohydrate transport and metabolism and cell motility with NT. Differences in carbon cycling were also observed, with increased prevalence of glycosyltransferase and glycoside hydrolase carbohydrate active enzyme families with CC. Lastly, treatment significantly influenced arbuscular mycorrhizal fungi, which had the greatest prevalence and activity under ST, suggesting that soil practices mediate known beneficial plant-microbe relationships. Collectively, our results demonstrate how agronomic practices impact critical interactions within the plant microbiome and inform future efforts to configure trait-associated microbiomes in crops.Importance While numerous studies show that farming practices can influence the soil microbiome, there are often conflicting results on how microbial diversity and activity respond to treatment. In addition, there is very little work published on how the corresponding crop plant microbiome is impacted. With bacteria and fungi known to critically affect soil health and plant growth, we concurrently compared how the practices of no and standard tillage, in combination with either cover-cropping or fallow fields, shape soil and plant-associated microbiomes between the two classifications. In determining not only the response to treatment in microbial diversity and composition, but for activity as well, this work demonstrates the significance of agronomic practice in modulating plant-microbe interactions, as well as encourages future work on the mechanisms involved in community assemblages supporting similar crop outcomes.

Author Correction: CasX enzymes comprise a distinct family of RNA-guided genome editors.

In this Article, owing to issues with the first 30 nucleotides of the sgRNA, which run in the opposite direction, corrections have been made to the Protein Data Bank (PDB) accessions in the 'Data availability' section, and this also affects Figs. 3, 4, Extended Data Fig. 6, Supplementary Table 1 and Supplementary Video 1. The original Article has been corrected online. See the accompanying Amendment for further details.

CasX enzymes comprise a distinct family of RNA-guided genome editors.

The RNA-guided CRISPR-associated (Cas) proteins Cas9 and Cas12a provide adaptive immunity against invading nucleic acids, and function as powerful tools for genome editing in a wide range of organisms. Here we reveal the underlying mechanisms of a third, fundamentally distinct RNA-guided genome-editing platform named CRISPR-CasX, which uses unique structures for programmable double-stranded DNA binding and cleavage. Biochemical and in vivo data demonstrate that CasX is active for Escherichia coli and human genome modification. Eight cryo-electron microscopy structures of CasX in different states of assembly with its guide RNA and double-stranded DNA substrates reveal an extensive RNA scaffold and a domain required for DNA unwinding. These data demonstrate how CasX activity arose through convergent evolution to establish an enzyme family that is functionally separate from both Cas9 and Cas12a.

Ventricular tachycardia associated with high-dose chronic loperamide use.

Loperamide is an antidiarrheal medication deemed by the U.S. Food and Drug Administration as safe enough to be sold as an over-the-counter medicine. Unlike other µ-opioid receptor agonists, loperamide acts specifically in the myenteric plexus in the gastrointestinal tract, making the potential for abuse low and reports of toxicity extremely rare. We present a case of a patient previously in good health who developed episodes of cardiac pauses, nonsustained ventricular tachycardia, and eventually runs of sustained ventricular tachycardia with hemodynamic instability. She required cardiopulmonary resuscitation, multiple cardioversions, and placement of a pacemaker. Her medical history was remarkable only for type 2 diabetes and chronic postcholecystectomy diarrhea. Metformin was the only prescription medication she was taking at the time of presentation. However, she reported that she had been taking an entire bottle of Equate brand loperamide (144 mg) daily for ~2 years. Loperamide overdoses associated with ventricular arrhythmias have been reported, but this is the first case to describe a serious ventricular arrhythmia associated with long-term use of a high dose of loperamide. Chronic overtreatment with loperamide may induce life-threatening arrhythmias.

Sea urchin embryos exposed to thalidomide during early cleavage exhibit abnormal morphogenesis later in development.

BACKGROUND: Clinical use of thalidomide has increased drastically, pushing the questions concerning the teratogenic mechanisms of this drug back to the forefront. Progress in understanding the teratogenic mechanisms has been slow, with the lack of non-primate vertebrate animal models susceptible to the classic reduction deformities remaining a concern. Sea urchin embryos have been used as model organisms for developmental studies for the last century. Like vertebrates, they are deuterostomes and share similar developmental and signaling pathways suggesting they may be an effective system for thalidomide studies. Therefore, we tested sea urchin embryos to see if they were sensitive to the effects of thalidomide. METHODS: Sea urchin embryos were obtained using standard spawning and fertilization techniques. Thalidomide dissolved in DMSO was added to embryo cultures either at fertilization or during early cleavage. Samples of the embryos were evaluated during specific development stages. RESULTS: Lytechinus pictus embryos exposed to 400 microM thalidomide at fertilization or within a window during early cleavage (2-6 hours post-fertilization) exhibit significant levels of abnormal embryos (60-82%) at the pluteus stage, compared to controls levels (< or =10%). Strongylocentrotus purpuratus embryos exposed at initial fertilization or during early cleavage (2-6 hours post-fertilization) exhibit similar responses with significant abnormal levels ranging from (55-70%) at pluteus stage. CONCLUSIONS: Both species of sea urchin tested were susceptible to thalidomide-induced teratogenesis during cleavage (4-16 cell stages). This response during cleavage stages warrants further study and indicates that sea urchin embryos may prove to be a useful tool for studying thalidomide effects early in development.