Produce is one of the most popular food commodities. Unfortunately, leafy greens can be a reservoir of transferable antibiotic resistance genes. We found that IncF and IncI plasmids were the most prevalent plasmid types in E. coli isolates from produce. This study highlights the importance of the rare microbiome associated with produce as a source of antibiotic resistance genes that might escape cultivation-independent detection, yet may be transferred to human pathogens or commensals.

Sleep deprivation is a global health problem adversely affecting health as well as causing decrements in learning and performance. Sleep deprivation induces significant changes in gene transcription in many brain regions, with the hippocampus particularly susceptible to acute sleep deprivation. However, less is known about the impacts of sleep deprivation on post-transcriptional gene regulation. To identify the effects of sleep deprivation on the translatome, we took advantage of the RiboTag mouse line to express HA-labeled Rpl22 in CaMKIIα neurons to selectively isolate and sequence mRNA transcripts associated with ribosomes in excitatory neurons. We found 198 differentially expressed genes in the ribosome-associated mRNA subset after sleep deprivation. In comparison with previously published data on gene expression in the hippocampus after sleep deprivation, we found that the subset of genes affected by sleep deprivation was considerably different in the translatome compared with the transcriptome, with only 49 genes regulated similarly. Interestingly, we found 478 genes differentially regulated by sleep deprivation in the transcriptome that were not significantly regulated in the translatome of excitatory neurons. Conversely, there were 149 genes differentially regulated by sleep deprivation in the translatome but not in the whole transcriptome. Pathway analysis revealed differences in the biological functions of genes exclusively regulated in the transcriptome or translatome, with protein deacetylase activity and small GTPase binding regulated in the transcriptome and unfolded protein binding, kinase inhibitor activity, neurotransmitter receptors and circadian rhythms regulated in the translatome. These results indicate that sleep deprivation induces significant changes affecting the pool of actively translated mRNAs.

Transcription by RNA polymerase II (RNAPII) is a dynamic process with frequent variations in the elongation rate. However, the physiological relevance of variations in RNAPII elongation kinetics has remained unclear. Here we show in yeast that a RNAPII mutant that reduces the transcription elongation rate causes widespread changes in alternative polyadenylation (APA). We unveil two mechanisms by which APA affects gene expression in the slow mutant: 3 ′ UTR shortening and gene derepression by premature transcription termination of upstream interfering noncoding RNAs. Strikingly, the genes affected by these mechanisms are enriched for functions involved in phosphate uptake and purine synthesis, processes essential for maintenance of the intracellular nucleotide pool. As nucleotide concentration regulates transcription elongation, our findings argue that RNAPII is a sensor of nucleotide availability and that genes important for nucleotide pool maintenance have adopted regulatory mechanisms responsive to reduced rates of transcription elongation.

The mechanisms underlying memory loss associated with Alzheimer’s disease and related dementias (ADRD) remain unclear, and no effective treatments exist. Fundamental studies have shown that a set of transcriptional regulatory proteins of the nuclear receptor 4a (Nr4a) family serve as molecular switches for long-term memory. Here, we show that Nr4a proteins regulate the transcription of genes encoding chaperones that localize to the endoplasmic reticulum (ER). These chaperones fold and traffic plasticity-related proteins to the cell surface during long-lasting forms of synaptic plasticity and memory. Dysregulation of Nr4a transcription factors and ER chaperones is linked to ADRD, and overexpressing Nr4a1 or the chaperone Hspa5 ameliorates long-term memory deficits in a tau-based mouse model of ADRD, pointing toward innovative therapeutic approaches for treating memory loss. Our findings establish a unique molecular concept underlying long-term memory and provide insights into the mechanistic basis of cognitive deficits in dementia.

25Produce is increasingly recognized as a reservoir of human pathogens and transferable 26 antibiotic resistance genes. This study aimed to explore methods to characterize the 27 transferable resistome of bacteria associated with produce. Mixed salad, arugula, and 28 cilantro purchased from supermarkets were analyzed by means of cultivation-and DNA-29 based methods. Before and after a nonselective enrichment step, tetracycline (tet) 30 resistant Escherichia coli were isolated and plasmids conferring tet resistance were 31 captured by exogenous plasmid isolation. Tet resistant E. coli isolates, transconjugants 32 and total community (TC)-DNA from the microbial fraction detached from leaves or after 33 enrichment were analyzed for the presence of resistance genes, class 1 integrons and 34 various plasmids by real-time PCR and PCR-Southern blot hybridization. Real-time 35 PCR primers were developed for IncI and IncF plasmids. Tet resistant E. coli isolated 36 from arugula and cilantro carried IncF, IncI1, IncN, IncHI1, IncU and IncX1 plasmids. 37 Three isolates from cilantro were positive for IncN plasmids and bla CTX-M-1 . From mixed 38 salad and cilantro, IncF, IncI1, and IncP-1β plasmids were captured exogenously. 39 Importantly, whereas direct detection of IncI and IncF plasmids in TC-DNA failed, these 40 plasmids became detectable in DNA extracted from enrichment cultures. This confirms 41 that cultivation-independent DNA-based methods are not always sufficiently sensitive to 42 detect the transferable resistome in the rare microbiome. In summary, this study 43showed that an impressive diversity of self-transmissible multiple resistance plasmids 44 was detected in bacteria associated with produce that is consumed raw, and exogenous 45 capturing into E. coli suggests that they could transfer to gut bacteria as well. 46 47 48Produce is one of the most popular food commodities. Unfortunately, leafy greens can 49 be a reservoir of transferable antibiotic resistance genes. We found that IncF and IncI 50 plasmids were the most prevalent plasmid types in E. coli isolates from produce. This 51 study highlights the importance of the rare microbiome associated with produce as a 52 source of antibiotic resistance genes that might escape cultivation-independent 53 detection, yet may be transferred to human pathogens or commensals.