RFX6 regulates human intestinal patterning and function upstream of PDX1.

The gastrointestinal (GI) tract is complex and consists of multiple organs with unique functions. Rare gene variants can cause congenital malformations of the human GI tract, although the molecular basis of these has been poorly studied. We identified a patient with compound-heterozygous variants in RFX6 presenting with duodenal malrotation and atresia, implicating RFX6 in development of the proximal intestine. To identify how mutations in RFX6 impact intestinal patterning and function, we derived induced pluripotent stem cells from this patient to generate human intestinal organoids (HIOs). We identified that the duodenal HIOs and human tissues had mixed regional identity, with gastric and ileal features. CRISPR-mediated correction of RFX6 restored duodenal identity. We then used gain- and loss-of-function and transcriptomic approaches in HIOs and Xenopus embryos to identify that PDX1 is a downstream transcriptional target of RFX6 required for duodenal development. However, RFX6 had additional PDX1-independent transcriptional targets involving multiple components of signaling pathways that are required for establishing early regional identity in the GI tract. In summary, we have identified RFX6 as a key regulator in intestinal patterning that acts by regulating transcriptional and signaling pathways.

Still 'Cool': tobacco industry responds to state-wide menthol ban with synthetic coolants.

INTRODUCTION: In December 2022, California (CA) enforced a voter-approved regulation restricting the retail sale of flavoured tobacco products, including menthol cigarettes. Shortly after, new products emerged on the market containing similar blue and green package colours yet with 'non-menthol' descriptors. Using chemical analyses, we measured the content of menthol and 15 other cooling chemicals in Californian cigarettes with 'non-menthol' descriptors and compared concentrations to similar 'menthol'-labelled counterparts available in New York State (NY). METHODS: A convenience sample of 10 brands and types of cigarettes in CA were purchased based on package colours suggesting a cooling effect and/or 'non-menthol' descriptors. The exact brand and type of cigarettes (with menthol descriptors) were purchased in NY. Cigarettes from CA were compared with equivalent cigarettes from NY on package design and colours, cigarette physical characteristics and the presence of cooling additives. RESULTS: Menthol was not detected in any CA cigarette, except for Maverick-green box type, while its presence was confirmed in most NY counterpart products. A synthetic cooling chemical WS-3 was not detected in any NY cigarettes but was detected in four CA brands and types with implied cooling effect, ranging from 1.24±0.04 to 1.97±0.05 mg/cigarette. CONCLUSION: While manufacturers have removed menthol descriptors from CA packaging and the menthol ingredient from cigarettes, synthetic cooling chemicals detected in several CA brands suggest that cooling sensory effects may still be sustained. Policymakers must consider both the chemical ingredients themselves and sensory effects in future regulatory approaches.

Enteroendocrine Cells Protect the Stem Cell Niche by Regulating Crypt Metabolism in Response to Nutrients.

BACKGROUND & AIMS: The intestinal stem cell niche is exquisitely sensitive to changes in diet, with high-fat diet, caloric restriction, and fasting resulting in altered crypt metabolism and intestinal stem cell function. Unlike cells on the villus, cells in the crypt are not immediately exposed to the dynamically changing contents of the lumen. We hypothesized that enteroendocrine cells (EECs), which sense environmental cues and in response release hormones and metabolites, are essential for relaying the luminal and nutritional status of the animal to cells deep in the crypt. METHODS: We used the tamoxifen-inducible VillinCreERT2 mouse model to deplete EECs (Neurog3fl/fl) from adult intestinal epithelium and we generated human intestinal organoids from wild-type and NEUROGENIN 3 (NEUROG3)-null human pluripotent stem cells. We used indirect calorimetry, 1H-Nuclear Magnetic Resonance (NMR) metabolomics, mitochondrial live imaging, and the Seahorse bioanalyzer (Agilent Technologies) to assess metabolism. Intestinal stem cell activity was measured by proliferation and enteroid-forming capacity. Transcriptional changes were assessed using 10x Genomics single-cell sequencing. RESULTS: Loss of EECs resulted in increased energy expenditure in mice, an abundance of active mitochondria, and a shift of crypt metabolism to fatty acid oxidation. Crypts from mouse and human intestinal organoids lacking EECs displayed increased intestinal stem cell activity and failed to activate phosphorylation of downstream target S6 kinase ribosomal protein, a marker for activity of the master metabolic regulator mammalian target of rapamycin (mTOR). These phenotypes were similar to those observed when control mice were deprived of nutrients. CONCLUSIONS: EECs are essential regulators of crypt metabolism. Depletion of EECs recapitulated a fasting metabolic phenotype despite normal levels of ingested nutrients. These data suggest that EECs are required to relay nutritional information to the stem cell niche and are essential regulators of intestinal metabolism.

Spectral calibration of photon-counting detectors at high photon flux.

BACKGROUND: Calibration of photon-counting detectors (PCDs) is necessary for quantitatively accurate spectral computed tomography (CT), but the calibration process can be complicated by nonlinear flux-dependent physical factors such as pulse pile-up. PURPOSE: This work develops a method for spectral sensitivity calibration of a PCD-based spectral CT system that incorporates nonlinear flux dependence and can thus be employed at high photon flux. METHODS: A calibration model for the spectral response and polynomial flux dependence is proposed, which incorporates prior x-ray source spectrum and PCD models and that has a small set of parameters for adjusting to the spectral CT system of interest. The model parameters are determined by fitting transmission data from a known object of known composition: a step-wedge phantom composed of different thicknesses of aluminum, a bone equivalent, and polymethyl methacrylate (PMMA), a soft-tissue equivalent. This fitting employs Tikhonov regularization, and the regularization strength and the polynomial order for the intensity modeling are determined by bias and variance analysis. The spectral calibration and nonlinear intensity correction is validated on transmission measurements through a third material, Teflon, at different x-ray photon flux levels. RESULTS: The nonlinear intensity dependence is determined to be accurately accounted for with a third-order polynomial. The calibrated spectral CT model accurately predicts Teflon transmission to within 1% for flux levels up to 50% of the detector maximum. CONCLUSIONS: The proposed PCD calibration method enables accurate physical modeling necessary for quantitative imaging in spectral CT. Furthermore, the model applies to high flux settings so that acquisition times will not be limited by restricting the spectral CT system to low flux levels.

Mediator dynamics during heat shock in budding yeast.

The Mediator complex is central to transcription by RNA polymerase II (Pol II) in eukaryotes. In budding yeast (Saccharomyces cerevisiae), Mediator is recruited by activators and associates with core promoter regions, where it facilitates preinitiation complex (PIC) assembly, only transiently before Pol II escape. Interruption of the transcription cycle by inactivation or depletion of Kin28 inhibits Pol II escape and stabilizes this association. However, Mediator occupancy and dynamics have not been examined on a genome-wide scale in yeast grown in nonstandard conditions. Here we investigate Mediator occupancy following heat shock or CdCl2 exposure, with and without depletion of Kin28. We find that Pol II occupancy shows similar dependence on Mediator under normal and heat shock conditions. However, although Mediator association increases at many genes upon Kin28 depletion under standard growth conditions, little or no increase is observed at most genes upon heat shock, indicating a more stable association of Mediator after heat shock. Unexpectedly, Mediator remains associated upstream of the core promoter at genes repressed by heat shock or CdCl2 exposure whether or not Kin28 is depleted, suggesting that Mediator is recruited by activators but is unable to engage PIC components at these repressed targets. This persistent association is strongest at promoters that bind the HMGB family member Hmo1, and is reduced but not eliminated in hmo1Δ yeast. Finally, we show a reduced dependence on PIC components for Mediator occupancy at promoters after heat shock, further supporting altered dynamics or stronger engagement with activators under these conditions.

Climate anomalies and childhood growth in Peru.

Climate change has been linked to poor childhood growth and development through maternal stress, nutritional insults related to lean harvests, and exposure to infectious diseases. Vulnerable populations are often most susceptible to these stressors. This study tested whether susceptibility to linear growth faltering is higher among Peruvian children from indigenous, rural, low-education, and low-income households. High-resolution weather and household survey data from Demographic and Health Survey 1996-2012 were used to explore height-for-age z-scores (HAZ) at each year of life from 0 to 5. Rural, indigenous children at age 0-1 experience a HAZ reduction of 0.35 units associated with prenatal excess rainfall which is also observed at age 4-5. Urban, non-indigenous children at age 4-5 experience a HAZ increase of 0.07 units associated with postnatal excess rainfall, but this advantage is not seen among rural, indigenous children. These findings highlight the need to consider developmental stage and social predictors as key components in public health interventions targeting increased climate change resilience.

Physics of animal health: on the mechano-biology of hoof growth and form.

Global inequalities in economic access and agriculture productivity imply that a large number of developing countries rely on working equids for transport/agriculture/mining. Therefore, the understanding of hoof conditions/shape variations affecting equids' ability to work is still a persistent concern. To bridge this gap, using a multi-scale interdisciplinary approach, we provide a bio-physical model predicting the shape of equids' hooves as a function of physical and biological parameters. In particular, we show (i) where the hoof growth stress originates from, (ii) why the hoof growth rate is one order of magnitude higher than the proliferation rate of epithelial cells and (iii) how the soft-to-hard transformation of the epithelium is possible allowing the hoof to fulfil its function as a weight-bearing element. Finally (iv), we demonstrate that the reason for hoof misshaping is linked to the asymmetrical design of equids' feet (shorter quarters/long toe) together with the inability of the biological growth stress to compensate for such an asymmetry. Consequently, the hoof can adopt a dorsal curvature and become 'dished' overtime, which is a function of the animal's mass and the hoof growth rate. This approach allows us to discuss the potential occurrence of this multifaceted pathology in equids.

Chromatin mediation of a transcriptional memory effect in yeast.

Previous studies have described a transcriptional "memory effect," whereby transcript levels of many Abf1-regulated genes in the budding yeast Saccharomyces cerevisiae are undiminished even after Abf1 has dissociated from its regulatory sites. Here we provide additional support for this effect and investigate its molecular basis. We show that the effect is observed in a distinct abf1 ts mutant from that used in earlier studies, demonstrating that it is robust, and use chromatin immunoprecipitation to show that Abf1 association is decreased similarly from memory effect and transcriptionally responsive genes at the restrictive temperature. We also demonstrate that the association of TATA-binding protein and Pol II decreases after the loss of Abf1 binding for transcriptionally responsive genes but not for memory effect genes. Examination of genome-wide nucleosome occupancy data reveals that although transcriptionally responsive genes exhibit increased nucleosome occupancy in abf1 ts yeast, the promoter regions of memory effect targets show no change in abf1 ts mutants, maintaining an open chromatin conformation even after Abf1 eviction. This contrasting behavior reflects different inherent propensity for nucleosome formation between the two classes, driven by the presence of A/T-rich sequences upstream of the Abf1 site in memory effect gene promoters. These sequence-based differences show conservation in closely related fungi and also correlate with different gene expression noise, suggesting a physiological basis for greater access to "memory effect" promoter regions. Thus, our results establish a conserved mechanism underlying a transcriptional memory effect whereby sequences surrounding Abf1 binding sequences affect local nucleosome occupancy following loss of Abf1 binding. Furthermore, these findings demonstrate that sequence-based differences in the propensity for nucleosome occupancy can influence the transcriptional response of genes to an altered regulatory signal.

Genome-wide association of mediator and RNA polymerase II in wild-type and mediator mutant yeast.

Mediator is a large, multisubunit complex that is required for essentially all mRNA transcription in eukaryotes. In spite of the importance of Mediator, the range of its targets and how it is recruited to these is not well understood. Previous work showed that in Saccharomyces cerevisiae, Mediator contributes to transcriptional activation by two distinct mechanisms, one depending on the tail module triad and favoring SAGA-regulated genes, and the second occurring independently of the tail module and favoring TFIID-regulated genes. Here, we use chromatin immunoprecipitation sequencing (ChIP-seq) to show that dependence on tail module subunits for Mediator recruitment and polymerase II (Pol II) association occurs preferentially at SAGA-regulated over TFIID-regulated genes on a genome-wide scale. We also show that recruitment of tail module subunits to active gene promoters continues genome-wide when Mediator integrity is compromised in med17 temperature-sensitive (ts) yeast, demonstrating the modular nature of the Mediator complex in vivo. In addition, our data indicate that promoters exhibiting strong and stable occupancy by Mediator have a wide range of activity and are enriched for targets of the Tup1-Cyc8 repressor complex. We also identify a number of strong Mediator occupancy peaks that overlap dubious open reading frames (ORFs) and are likely to include previously unrecognized upstream activator sequences.

Mediator, TATA-binding protein, and RNA polymerase II contribute to low histone occupancy at active gene promoters in yeast.

Transcription by RNA polymerase II (Pol II) in eukaryotes requires the Mediator complex, and often involves chromatin remodeling and histone eviction at active promoters. Here we address the role of Mediator in recruitment of the Swi/Snf chromatin remodeling complex and its role, along with components of the preinitiation complex (PIC), in histone eviction at inducible and constitutively active promoters in the budding yeast Saccharomyces cerevisiae. We show that recruitment of the Swi/Snf chromatin remodeling complex to the induced CHA1 promoter, as well as its association with several constitutively active promoters, depends on the Mediator complex but is independent of Mediator at the induced MET2 and MET6 genes. Although transcriptional activation and histone eviction at CHA1 depends on Swi/Snf, Swi/Snf recruitment is not sufficient for histone eviction at the induced CHA1 promoter. Loss of Swi/Snf activity does not affect histone occupancy of several constitutively active promoters; in contrast, higher histone occupancy is seen at these promoters in Mediator and PIC component mutants. We propose that an initial activator-dependent, nucleosome remodeling step allows PIC components to outcompete histones for occupancy of promoter sequences. We also observe reduced promoter association of Mediator and TATA-binding protein in a Pol II (rpb1-1) mutant, indicating mutually cooperative binding of these components of the transcription machinery and indicating that it is the PIC as a whole whose binding results in stable histone eviction.

The mouse frizzy mutation (fr) maps between D7Csu5 and D7Mit165.

We have previously shown that the rat fuzzy and Charles River 'hairless' mutations are defects in the same gene on rat Chr 1, and are likely orthologues of the frizzy mutation (fr) on mouse Chr 7. To test the hypothesis that these variants could result from defects in Fgfr2, we crossed fr/fr mice (from the inbred FS/EiJ strain) with mice that carry a recessive lethal mutation in Fgfr2. Mice inheriting both mutations were phenotypically normal, indicating that fr is not an allele of Fgfr2. To genetically map fr, we crossed these hybrid mice, or F(1) mice made by crossing FS/EiJ with the wild-type C57BL/6J or BALB/cBy strains, back to the FS/EiJ strain. The resulting 546 backcross progeny were typed for linked markers to position fr centromeric of Fgfr2, between D7Csu5 and D7Mit165; an interval that contains only 2.7 Mb and fewer than 70 genes. Further characterization of regional recombinants for sequence-level polymorphisms should allow sufficient refinement of fr's location to facilitate an eventual molecular assignment for this classical mutation.