De novo gene synthesis by an antiviral reverse transcriptase.

Bacteria defend themselves from viral infection using diverse immune systems, many of which sense and target foreign nucleic acids. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling-circle reverse transcription of a non-coding RNA (ncRNA). Unbiased profiling of RT-associated RNA and DNA ligands in DRT2-expressing cells revealed that reverse transcription generates concatenated cDNA repeats through programmed template jumping on the ncRNA. The presence of phage then triggers second-strand cDNA synthesis, leading to the production of long double-stranded DNA. Remarkably, this DNA product is efficiently transcribed, generating messenger RNAs that encode a stop codon-less, never-ending ORF (neo) whose translation causes potent growth arrest. Phylogenetic analyses and screening of diverse DRT2 homologs further revealed broad conservation of rolling-circle reverse transcription and Neo protein function. Our work highlights an elegant expansion of genome coding potential through RNA-templated gene creation, and challenges conventional paradigms of genetic information encoded along the one-dimensional axis of genomic DNA.

Plain language summary of zanubrutinib or ibrutinib in chronic lymphocytic leukemia that is resistant to treatment or has come back after treatment.

WHAT IS THIS SUMMARY ABOUT?: This is a plain language summary of a research study called ALPINE. The study involved people who had been diagnosed with, and previously treated at least once for, relapsed or refractory chronic lymphocytic leukemia (CLL) or small lymphocytic lymphoma (SLL). Lymphocytes help to find and fight off viruses and infections in the body, but when someone has CLL or SLL, the body creates abnormal lymphocytes, leaving the patient with a weakened immune system and susceptible to illness. In CLL, these lymphocytes are in the bone marrow and bloodstream, whereas for SLL, they are mostly found in the lymph nodes, such as those in the neck. HOW WAS THE RESEARCH DONE?: The ALPINE study was designed to directly compare the cancer-fighting effects and side effects of zanubrutinib and ibrutinib as treatment for patients with relapsed or refractory CLL/SLL. WHAT WERE THE RESULTS?: After 30 months, zanubrutinib was more effective than ibrutinib at reducing and keeping the cancer from coming back. Clinical Trial Registration: NCT03734016 (ClinicalTrials.gov).

Effects of in utero exposure to fluoxetine on the gastrointestinal tract of rat offspring.

Perinatal exposure to selective serotonin reuptake inhibitors (SSRIs) has been shown to disrupt the development of serotonergic signaling pathways in the brain and enteric nervous system. Serotonin (5-hydroxytryptamine; 5-HT) signaling is critical for gastrointestinal homeostasis; changes in 5-HT expression and regulation have been associated with gastrointestinal diseases of motility and inflammation. We tested the hypothesis that perinatal exposure to the SSRI fluoxetine can influence the development of the gastrointestinal tract in exposed offspring. Female nulliparous Wistar rats were given fluoxetine (10 mg/kg) or vehicle control from 2 wk before mating until weaning; small and large intestines of female and male offspring were collected at postnatal days 1, 21 (P1, P21, respectively), and 6 mo of age. In histological preparations, the proportion of serotonergic neurons significantly increased in the colons of both female and male fluoxetine-exposed compared with control offspring at P21, a time point that signifies maximal exposure to fluoxetine. At 6 mo of age, male but not female fluoxetine-exposed offspring had a significant increase in circulating 5-HT, with a significant decrease in transcripts encoding the 5-HT2A receptor and monoamine oxidase as compared with control offspring. Measurement of spatiotemporal mapping of contractile activity of the small and large intestine at 6 mo of age revealed no changes in motility in the small bowel of fluoxetine-exposed offspring but revealed a significant increase in the frequency of colonic contractions in the female fluoxetine-exposed compared with control animals. Susceptibility to inflammation was examined at 6 mo using the dextran sulfate sodium model of acute colitis. In utero exposure to fluoxetine was not found to exacerbate colitis severity. These findings suggest that fluoxetine exposure during fetal and early postnatal development can lead to changes in serotonergic neurons at the peak of exposure with sex-specific changes in 5-HT signaling and colonic motility in adulthood.NEW & NOTEWORTHY There is increasing recognition of the relevance of in utero and early postnatal exposures in the developmental programming of the gastrointestinal tract. Perinatal exposure to selective serotonin reuptake inhibitors and antidepressant medications is of particular relevance as they are commonly prescribed during pregnancy, and serotonergic pathways play key roles during gastrointestinal development and in postnatal homeostasis. Here, we provide a comprehensive evaluation of clinically relevant outcomes of gastrointestinal motility and susceptibility to colitis in fluoxetine-exposed offspring and highlight changes in colonic serotonergic neurons at the peak of perinatal fluoxetine exposure with sex-dependent changes in serotonin signaling and colonic motility in adulthood.

Zanubrutinib or Ibrutinib in Relapsed or Refractory Chronic Lymphocytic Leukemia.

BACKGROUND: In a multinational, phase 3, head-to-head trial, ibrutinib, a Bruton's tyrosine kinase (BTK) inhibitor, was compared with zanubrutinib, a BTK inhibitor with greater specificity, as treatment for relapsed or refractory chronic lymphocytic leukemia (CLL) or small lymphocytic lymphoma (SLL). In prespecified interim analyses, zanubrutinib was superior to ibrutinib with respect to overall response (the primary end point). Data from the final analysis of progression-free survival are now available. METHODS: We randomly assigned, in a 1:1 ratio, patients with relapsed or refractory CLL or SLL who had received at least one previous course of therapy to receive zanubrutinib or ibrutinib until the occurrence of disease progression or unacceptable toxic effects. In this final analysis, progression-free survival (a key secondary end point) was assessed with the use of a hierarchical testing strategy to determine whether zanubrutinib was noninferior to ibrutinib. If noninferiority was established, the superiority of zanubrutinib was assessed and claimed if the two-sided P value was less than 0.05. RESULTS: At a median follow-up of 29.6 months, zanubrutinib was found to be superior to ibrutinib with respect to progression-free survival among 652 patients (hazard ratio for disease progression or death, 0.65; 95% confidence interval, [CI], 0.49 to 0.86; P = 0.002), as assessed by the investigators; the results were similar to those as assessed by an independent-review committee. At 24 months, the investigator-assessed rates of progression-free survival were 78.4% in the zanubrutinib group and 65.9% in the ibrutinib group. Among patients with a 17p deletion, a TP53 mutation, or both, those who received zanubrutinib had longer progression-free survival than those who received ibrutinib (hazard ratio for disease progression or death, 0.53; 95% CI, 0.31 to 0.88); progression-free survival across other major subgroups consistently favored zanubrutinib. The percentage of patients with an overall response was higher in the zanubrutinib group than in the ibrutinib group. The safety profile of zanubrutinib was better than that of ibrutinib, with fewer adverse events leading to treatment discontinuation and fewer cardiac events, including fewer cardiac events leading to treatment discontinuation or death. CONCLUSIONS: In patients with relapsed or refractory CLL or SLL, progression-free survival was significantly longer among patients who received zanubrutinib than among those who received ibrutinib, and zanubrutinib was associated with fewer cardiac adverse events. (Funded by BeiGene; ALPINE ClinicalTrials.gov number, NCT03734016.).

Smoking and fracture risk in men: a meta-analysis of cohort studies, using both frequentist and Bayesian approaches.

Past studies indicate that men are more likely to smoke and be at higher risk of smoking-related conditions than women. Our research aimed, through meta-analysis, to assess the association between smoking and fracture risk in men. The following databases were searched, including MEDLINE, EMBASE, Scopus, PsycINFO, ISI Web of Science, Google Scholar, WorldCat, and Open Grey, for identifying related studies. A random-effects model was used to pool the confounder-adjusted relative risk (R.R.). Frequentist and Bayesian hierarchical random-effects models were used for the analysis. The heterogeneity and publication bias were evaluated in this study. Twenty-seven studies met the inclusion criteria. Overall, smoking is associated with a significantly increased risk of fracture in both the frequentist approach (R.R., 1.37; 95% confidence interval: 1.22, 1.53) and the Bayesian approach (R.R., 1.36; 95% credible interval: 1.22, 1.54). Significant heterogeneity was observed in the meta-analysis (Higgin's I2 = 83%) and Cochran's Q statistic (p < 0.01). A significant association was also observed in multiple pre-specified sensitivity and subgroup analyses. Similar results were observed in the group containing a large sample size (≥ 10,000 participants), and the group has a small sample size (< 10,000 participants); the pooled R.R was 1.23 (95% confidence interval, 1.07-1.41) and 1.56 (95% confidence interval, 1.37-1.78), respectively. With the Bayesian method, the effect size was 1.23 (95% credible interval, 1.05, 1.45) for the large sample size group and 1.57 (95% credible interval, 1.35, 1.82) for the small sample size group. Smoking is associated with a significant increase in fracture risk for men. Thus, smoking cessation would also greatly reduce fracture risk in all smokers, particularly in men.

Nonlinearities between inhibition and T-type calcium channel activity bidirectionally regulate thalamic oscillations.

Absence seizures result from 3 to 5 Hz generalized thalamocortical oscillations that depend on highly regulated inhibitory neurotransmission in the thalamus. Efficient reuptake of the inhibitory neurotransmitter GABA is essential, and reuptake failure worsens human seizures. Here, we show that blocking GABA transporters (GATs) in acute rat brain slices containing key parts of the thalamocortical seizure network modulates epileptiform activity. As expected, we found that blocking either GAT1 or GAT3 prolonged oscillations. However, blocking both GATs unexpectedly suppressed oscillations. Integrating experimental observations into single-neuron and network-level computational models shows how a non-linear dependence of T-type calcium channel gating on GABAB receptor activity regulates network oscillations. Receptor activity that is either too brief or too protracted fails to sufficiently open T-type channels necessary for sustaining oscillations. Only within a narrow range does prolonging GABAB receptor activity promote channel opening and intensify oscillations. These results have implications for therapeutics that modulate inhibition kinetics.

Macaque dorsal premotor cortex exhibits decision-related activity only when specific stimulus-response associations are known.

How deliberation on sensory cues and action selection interact in decision-related brain areas is still not well understood. Here, monkeys reached to one of two targets, whose colors alternated randomly between trials, by discriminating the dominant color of a checkerboard cue composed of different numbers of squares of the two target colors in different trials. In a Targets First task the colored targets appeared first, followed by the checkerboard; in a Checkerboard First task, this order was reversed. After both cues appeared in both tasks, responses of dorsal premotor cortex (PMd) units covaried with action choices, strength of evidence for action choices, and RTs- hallmarks of decision-related activity. However, very few units were modulated by checkerboard color composition or the color of the chosen target, even during the checkerboard deliberation epoch of the Checkerboard First task. These findings implicate PMd in the action-selection but not the perceptual components of the decision-making process in these tasks.

A cross-modal investigation of the neural substrates for ongoing cognition.

What neural mechanisms underlie the seamless flow of our waking consciousness? A necessary albeit insufficient condition for such neural mechanisms is that they should be consistently modulated across time were a segment of the conscious stream to be repeated twice. In this study, we experimentally manipulated the content of a story followed by subjects during functional magnetic resonance imaging (fMRI) independently from the modality of sensory input (as visual text or auditory speech) as well as attentional focus. We then extracted brain activity patterns consistently modulated across subjects by the evolving content of the story regardless of whether it was presented visually or auditorily. Specifically, in one experiment we presented the same story to different subjects via either auditory or visual modality. In a second experiment, we presented two different stories simultaneously, one auditorily, one visually, and manipulated the subjects' attentional focus. This experimental design allowed us to dissociate brain activities underlying modality-specific sensory processing from modality-independent story processing. We uncovered a network of brain regions consistently modulated by the evolving content of a story regardless of the sensory modality used for stimulus input, including the superior temporal sulcus/gyrus (STS/STG), the inferior frontal gyrus (IFG), the posterior cingulate cortex (PCC), the medial frontal cortex (MFC), the temporal pole (TP), and the temporoparietal junction (TPJ). Many of these regions have previously been implicated in semantic processing. Interestingly, different stories elicited similar brain activity patterns, but with subtle differences potentially attributable to varying degrees of emotional valence and self-relevance.

Global selection of saccadic target features by neurons in area v4.

Psychophysical and neurophysiological studies indicate that during the preparation of saccades, visual processing at the target location is facilitated automatically by the deployment of attention. It has been assumed that the neural mechanisms involved in presaccadic shifts of attention are purely spatial in nature. Saccade preparation modulates the visual responses of neurons within extrastriate area V4, where the responses to targets are enhanced and responses to nontargets are suppressed. We tested whether this effect also engages a nonspatial form of modulation. We measured the responses of area V4 neurons to oriented gratings in two monkeys (Macaca mulatta) making delayed saccades to targets distant from the neuronal receptive field (RF). We varied the orientation of both the RF stimulus and the saccadic target. We found that, in addition to the spatial modulation, saccade preparation involves a feature-dependent modulation of V4 neuronal responses. Specifically, we found that the suppression of area V4 responses to nontarget stimuli during the preparation of saccades depends on the features of the saccadic target. Presaccadic suppression was absent when the features of the saccadic target matched the features preferred by individual V4 neurons. This feature-dependent modulation occurred in the absence of any feature-attention task. We show that our observations are consistent with a computational framework in which feature-based effects automatically emerge from saccade-related feedback signals that are spatial in nature.

Brain mechanisms for simple perception and bistable perception.

When faced with ambiguous sensory inputs, subjective perception alternates between the different interpretations in a stochastic manner. Such multistable perception phenomena have intrigued scientists and laymen alike for over a century. Despite rigorous investigations, the underlying mechanisms of multistable perception remain elusive. Recent studies using multivariate pattern analysis revealed that activity patterns in posterior visual areas correlate with fluctuating percepts. However, increasing evidence suggests that vision--and perception at large--is an active inferential process involving hierarchical brain systems. We applied searchlight multivariate pattern analysis to functional magnetic resonance imaging signals across the human brain to decode perceptual content during bistable perception and simple unambiguous perception. Although perceptually reflective activity patterns during simple perception localized predominantly to posterior visual regions, bistable perception involved additionally many higher-order frontoparietal and temporal regions. Moreover, compared with simple perception, both top-down and bottom-up influences were dramatically enhanced during bistable perception. We further studied the intermittent presentation of ambiguous images--a condition that is known to elicit perceptual memory. Compared with continuous presentation, intermittent presentation recruited even more higher-order regions and was accompanied by further strengthened top-down influences but relatively weakened bottom-up influences. Taken together, these results strongly support an active top-down inferential process in perception.