Establishing the anterior-posterior (AP) body axis is a fundamental process during embryogenesis, and the fruit fly, Drosophila melanogaster, provides one of the best-known case studies. But for unknown reasons, different species of flies (Diptera) establish the AP axis through unrelated, structurally distinct anterior determinants. The anterior determinant of Drosophila, Bicoid (Bcd), initiates symmetry-breaking during nuclear cleavage cycles (NCs) when ubiquitous pioneer factors, such as Zelda (Zld), drive zygotic genome activation (ZGA) at the level of chromatin accessibility by nucleosome depletion. While Bcd engages in a concentration-dependent competition with nucleosomes at the loci of a small set of transcription factor (TF) genes that are expressed in the anterior embryo, it remains unknown whether unrelated anterior determinants of other fly species function in the same way and target homologous genes. We have examined the symmetry-breaking mechanism of a moth fly, Clogmia albipunctata, in which a maternally expressed transcript isoform of the pair-rule segmentation gene odd-paired serves as an anterior determinant. We provide a de novo assembly and annotation of the Clogmia genome, report changes in chromatin accessibility during the nuclear cleavage cycles (NCs) of consecutive blastoderm stages, and describe how Clogmia's orthologs of zelda (Cal-zld) and odd-paired (Cal-opa) affect chromatin accessibility and gene expression. We document extensive opening and closing of chromatin regions during cleavage cycles of blastoderm, important roles of Cal-zld in opening chromatin and driving zygotic gene expression, and show that maternal Cal-opa activity initiates zygotic symmetry-breaking along the AP axis by driving chromatin accessibility and expression at Clogmia's homeobrain and sloppy-paired loci. These genes are not known as key targets of Bcd but may serve a more widely conserved role in the initiation of anterior pattern formation, given their early anterior expression and function in head development in insects.

The RNA-binding protein (RBP) LIN28 is a key regulator of temporal cell fates, promoting stem cell identity and suppressing differentiation. It regulates the processing of the let-7 miRNA but additionally binds thousands of mRNAs, suggesting a model of coordinated regulation across many targets. Yet, direct evidence for such a network function is scarce for both LIN28 and other broadly binding RBPs. Here, we show that in Caenorhabditis elegans larvae, loss of LIN28 leaves the levels of most LIN28-bound transcripts unchanged. The only exceptions are the lin-46 mRNA and the let-7 miRNA. Comprehensive genetic analyses identify these two as the functionally essential LIN28 targets: lin-28; lin-46; let-7 triple mutant animals exhibit complete suppression of the lin-28(0) precocious heterochronic phenotypes and recapitulate the retarded lin-46; let-7 double mutant phenotypes. Conversely, simultaneous overexpression of lin-46 and let-7 mimics LIN28 loss. Unexpectedly, LIN28 controls not only cell identity but also the tempo of development, using the same two targets. These findings establish a close functional link between the heterochronic pathway and the clock regulating developmental tempo and demonstrate that an RBP can achieve complex biological outcomes through a small set of targets.

Pathogenic variants in the genes encoding the non-canonical TGFB signaling components TAK1 (MAP3K7), TAB2 and PKA-Cα (PRKACA) cause rare multisystem disorders, which may include congenital heart disease (CHD). To investigate the role of TAK1 signaling in CHD, we performed genetic analysis of CHD patients and discovered an increased burden of rare TAB2 and TAK1 variants in patients with extracardiac abnormalities. To address the mechanism of TAK1 in heart development, we performed experiments in cell and animal models. Zebrafish tak1 and tab2 mutants presented with cardiac and extracardiac developmental defects, and tak1 mutant hearts showed downregulation of genes encoding core cardiac transcription factors, sarcomeric proteins and extracellular matrix proteins. In vitro experiments indicated that TAK1 via TAB2 and PKA-Cα is activated at the primary cilium during cardiomyogenesis; activation at this site is enhanced by TGFB/BMP ligands. Inactivation of TAK1 inhibited ciliary signaling and cardiomyocyte differentiation, and patient-derived TAK1 variants reduced its ciliary localization. In conclusion, our data establish a pivotal role for TAK1 and its upstream regulators at the primary cilium in heart development and syndromic CHD.

How we write scientific papers does not reflect how we do science. Their formal structure infers a pre-ordained linear process rather than reflecting the messy creativity of research. This matters in the AI age because it masks the human in the process.

The dorsal vagal complex (DVC) includes a multi-component brainstem satiety centre which has gained attention as a key target of anti-obesity pharmacotherapies. Our recent studies revealed its circadian timekeeping properties, with molecular and electrophysiological 24 h rhythms persisting independently of the primary hypothalamic clock. However, the factors entraining these brainstem oscillators and the downstream transcriptional targets of the DVC molecular clock remain unclear. Here, using PERIOD2::LUCIFERASE reporter mice and fluorescent in situ hybridisation, we quantitatively demonstrate rhythms in core clock gene expression in the caudal DVC ex vivo and in vivo. We show that the molecular clock is associated with rhythmic expression of numerous neurotransmitter receptor genes in the DVC in vivo, with the phase of both clock and clock-controlled gene expression tightly regulated by meal timing. These findings uncover food-entrained circadian rhythms in the DVC and have important implications for clinical studies targeting brainstem satiety mechanisms.

The temporal, spatial, and cellular diversity of the small intestinal epithelium during the postnatal period, a critical time window that accompanies the transition from placental energy supply to enteral feeding, and the establishment of the enteric microbiota and postnatal immune maturation, has not been systematically investigated. Here, we used laser capture microdissection and bulk RNA-Seq, proteomics, and single cell RNA-Seq to analyze the total, organ site, crypt- and villus-specific intestinal epithelium of specific pathogen-free, germ-free, and Salmonella-infected mice during the postnatal period. We identified key temporal and organ-site specific expression patterns that revealed a weak effect of the microbiota but strong influence of developmental regulators during early life. We also determined age-dependent signaling pathway and transcription factor activity and characterized age- and cell type-specific developmental trajectories revealing a distinct compartmentalized maturation process along the proximal-to-distal length and crypt-villus axis and a discontinuous appearance of goblet/Paneth cell and absorptive enterocyte transcriptional profiles. Finally, we described the cell type-specific response to neonatal enteric infection. Taken together, our findings identify the epithelium as an integral element in the maturation of postnatal mucosal tissues and in the establishment of host-microbe homeostasis.

The cholinergic system shows promise for pain management. Although cholinergic neurons in the ventral pallidum (VP) are involved in neuropathic pain, the anatomical organization and pharmacology of the cholinergic circuit contributing to the processing of acute and chronic pain remain unknown. In the present study, we demonstrate that VP cholinergic neurons in mice received pain signals from and mediated pain modulation by glutamatergic (Glu) neurons in the subthalamic nucleus (STN) in both physiological and neuropathic pain conditions. VP cholinergic neurons were a major source of acetylcholine released in the VP upon pain stimulation, and α4 and α7 were major subunits comprising functional nicotinic acetylcholine receptors (nAChRs) in VP cholinergic, GABAergic, and Glu neurons. In neuropathic pain mouse models, VP cholinergic neurons became hyperactive and released more acetylcholine in the VP, and α4 and α7 nAChRs were differentially modified on VP GABAergic and Glu neurons. These modifications were accompanied by hyperexcitability in VP GABAergic neurons and hypoactivity in VP Glu neurons. Reversal of upregulated α4 nAChRs on VP GABAergic neurons, but not that of downregulated α4 and α7 nAChRs on VP Glu neurons, attenuated the severity of hyperalgesia in neuropathic pain. Therefore, the STNGlu-VPChAT pathway is implicated in neuropathic pain by enhancing VP cholinergic circuits, and α4 nAChRs on VP GABAergic neurons may be potential therapeutic targets for the treatment of neuropathic pain.

grafify online is a free, browser-based app for generating publication-quality graphs and performing statistical tests and post-hoc comparisons. Users can customize plots and explore statistical results without needing R programming experience.

Slow, endogenous brain rhythms in the auditory cortex are hypothesized to track acoustic amplitude modulations during speech comprehension. Temporal predictions from the motor system are thought to enhance this tracking. However, direct evidence for the involvement of endogenous auditory and motor brain rhythms is lacking. Combining magnetoencephalographic recordings with behavioral data, we here show that endogenous peak frequencies of individuals' resting-state theta rhythm in superior temporal gyrus predict speech tracking during comprehension. Importantly, endogenous rates of speech motor areas predicted auditory-cortical speech tracking only in individuals with high auditory-motor synchronization profiles. Higher rates in the supplementary motor area and lower rates in inferior frontal gyrus predicted stronger tracking. These findings provide support for oscillatory accounts of auditory-motor interactions during speech perception. Behaviorally, higher auditory-motor synchronization was related to higher comprehension, with effects of the spontaneous speech motor production rate only in high synchronizers. Working memory capacity predicted speech comprehension performance only in individuals with low auditory-motor synchronization profiles. No significant relationship between the neural data and behavioral readouts was observed. The findings highlight differential speech processing preferences across individuals, with an auditory-motor route related to enhanced comprehension performance.

Human activities are accelerating permafrost thaw and subsequent methane emissions from increased microbial activity, prompting microbiome engineering efforts as an emissions mitigation strategy. We recently demonstrated that catechin amendment could drastically reduce methane emissions (>80%) in peat microcosms by enriching catechin-degrading prokaryotes that outcompeted methanogens for hydrogen. However, viral contributions to such microbiome-level responses remain unexplored and we hypothesized that viral dynamics could help shape the microbiome response as nutrient amendments may alter cellular physiology in ways that could induce lytic viral activity. Here, we performed virus eco-genomics analyses of the previously-studied time-resolved multi-omics data collected from catechin-amended peat microcosms. We conservatively identified 900 putatively lytic viral operational taxonomic units (vOTUs), with 41% predicted to infect active host genomes including the most transcriptionally active vOTUs predicted to infect key catechin-degrading genera (Clostridium and undescribed Bacillota JAGFXR01). Notably, a single JAGFXR01-targeting vOTU dominating the viral response (>40% of community viral transcription; 20-156-fold more abundant than its host), which we interpreted as induction resulting in intense lytic activity that could release catechin degradation intermediates to other community members. Consistent with this, gene expression analysis revealed elevated catechin-intermediate degradation and hydrogenase signals in 34 additional polyphenol-degrading metagenome-assembled genomes. These findings support a model consistent with a viral shunt-like process that extends our previous prokaryote-centric model: viral lysis of fast-growing catechin degraders redistributes phenolic intermediates to diverse phenol-degrading taxa that sustain methane suppression via hydrogen consumption. Beyond carbon cycling importance in this system, elucidating unintended virus-mediated responses to nutrient and prebiotic interventions will enable more predictable and effective microbiome engineering strategies across soil, ocean, and human ecosystems.

Climatic adaptation of plants involves the adjustment of carbon transport to achieve an optimal balance between carbon assimilation and carbon utilization. This study describes a potential molecular mechanism of this adjustment by investigating the climate-dependent regulation of SUCROSE TRANSPORTER 2 (SUC2) in the model plant Arabidopsis thaliana. SUC2 is responsible for loading photosynthetically-produced sucrose into the leaf vascular system. Its protein and mRNA abundance in A. thaliana natural accessions were found to correlate with leaf sucrose export and summer temperature. Exploration of methylome data and epigenome editing experiments suggested that epigenetic marks on SUC2's exon 2 contributed to the climate-dependent expression of SUC2. Two siRNAs were identified as mediators of SUC2 methylations and their respective origins localized to the SUC5 and SUC8 genes. The analysis of plants with reduced or enhanced SUC5 or SUC8 transcriptional activity corroborated the link to SUC2 methylation. Besides illustrating a novel regulatory strategy of carbon export from leaves, our results establish exon methylation mediated by gene-derived siRNAs as yet another potential mechanism for plant adaptation.

Nearly half of Swiss animal researchers have never heard of preregistration. A survey published in PLOS Biology maps their attitudes, barriers, and misconceptions, and identifies what it would take to change minds.

SLC37A4 mediates glucose-6-phosphate transport for glucose homeostasis. Two recent studies in PLOS Biology report its structures and, together with other reports, illuminate the glucose-6-phosphate/phosphate exchange cycle and its inhibition mechanism.