Trichinella spiralis -induced immunomodulation signatures on gut microbiota and metabolic pathways in mice.

The hygiene hypothesis proposes that decreased exposure to infectious agents in developed countries may contribute to the development of allergic and autoimmune diseases. Trichinella spiralis, a parasitic roundworm, causes trichinellosis, also known as trichinosis, in humans. T. spiralis had many hosts, and almost any mammal could become infected. Adult worms lived in the small intestine, while the larvae lived in muscle cells of the same mammal. T. spiralis was a significant public health threat because it could cause severe illness and even death in humans who eat undercooked or raw meat containing the parasite. The complex interactions between gastrointestinal helminths, gut microbiota, and the host immune system present a challenge for researchers. Two groups of mice were infected with T. spiralis vs uninfected control, and the experiment was conducted over 60 days. The 16S rRNA gene sequences and untargeted LC/MS-based metabolomics of fecal and serum samples, respectively, from different stages of development of the Trichinella spiralis-mouse model, were examined in this study. Gut microbiota alterations and metabolic activity accompanied by parasite-induced immunomodulation were detected. The inflammation parameters of the duodenum (villus/crypt ratio, goblet cell number and size, and histological score) were involved in active inflammation and oxidative metabolite profiles. These profiles included increased biosynthesis of phenylalanine, tyrosine, and tryptophan while decreasing cholesterol metabolism and primary and secondary bile acid biosynthesis. These disrupted metabolisms adapted to infection stress during the enteral and parenteral phases and then return to homeostasis during the encapsulated phase. There was a shift from an abundance of Bacteroides in the parenteral phase to an abundance of probiotic Lactobacillus and Treg-associated-Clostridia in the encapsulated phase. Th2 immune response (IL-4/IL-5/IL-13), lamina propria Treg, and immune hyporesponsiveness metabolic pathways (decreased tropane, piperidine and pyridine alkaloid biosynthesis and biosynthesis of alkaloids derived from ornithine, lysine, and nicotinic acid) were all altered. These findings enhanced our understanding of gut microbiota and metabolic profiles of Trichinella -infected mice, which could be a driving force in parasite-shaping immune system maintenance.

Identification of hypervirulent Klebsiella pneumoniae based on biomarkers and Galleria mellonella infection model.

BACKGROUND: Currently, clinical laboratories lack an effective method to differentiate between classical Klebsiella pneumoniae (cKP) and hypervirulent Klebsiella pneumoniae (hvKP) strains, leading to delays in diagnosing and treating hvKP infections. Previous studies have identified peg-344, iroB, iucA, prmpA, prmpA2, and siderophores (SP) yields greater than 30 µg/ml as reliable markers for distinguishing hvKP from cKp strains. However, these diagnostic tests were conducted on a relatively small study population and lacked sufficient clinical data support. In this study, hvKP strains were identified by biomarker analysis and the Galleria mellonella model. Combined with in vitro and in vivo experiments, the reliability of clinical identification method of hvKP was verified, which provided an experimental basis for timely diagnosis of hvKP infection. RESULTS: According to the clinical data, a total of 108 strains of hvKP were preliminary screened. Among them, 94 strains were further identified using PCR analysis of biomarkers and quantitative determination of SP. The high virulence of hvKP was subsequently confirmed through infection experiments on Galleria mellonella. Additionally, susceptibility testing revealed the identification of 58 carbapenem-resistant hvKP (CR-hvKP) strains and 36 carbapenem-sensitive hvKP (CS-hvKP) strains. By comparing molecular diagnostic indexes, molecular characteristics such as high SP production of CR-hvKP were found. CONCLUSION: The combination of clinical data and molecular diagnostic index analysis effectively enables the identification of hvKP, particularly CR-hvKP. This study provides a scientific basis for accurate clinical identification and timely treatment of hvKP.

Optimization of the hongqu starter preparation process for the manufacturing of red mold rice with high gamma-aminobutyric acid production by solid-state fermentation.

Red mold rice (RMR) generally contains gamma-aminobutyric acid (GABA), which has several physiological functions. Monascus purpureus M162, with a high GABA production of 15.10 mg/g was generated by atmospheric and room temperature plasma mutation. Furthermore, we conducted a response surface methodology to produce a premium hongqu starter. The results revealed that under optimal conditions, that is, a substrate containing brown rice and bran in a brown rice: bran ratio of 9:1 (wt/wt), an inoculation size of 21.50 mL/100 g, a mixing frequency of one time/9 h, and a cultivation time of 7.20 days, the number of active spores, α-amylase activity, and saccharification power activity was 4.15 × 107 spores/g, 155 U/g, and 3260 U/g in the high-quality starter, respectively. These values were 224.32-fold, 139.64%, and 141.74% higher than those obtained with M. purpureus M162 inoculated into steamed indica rice, respectively, and 153.70-fold, 267.24%, and 151.63% higher than those obtained with the parent strain M. purpureus M1, respectively. The premium hongqu starter of M. purpureus M162 was inoculated into steamed indica rice to produce RMR with 15.93 mg/g of GABA. In conclusion, we proposed a novel strategy for functional RMR production with high GABA concentrations by solid-state fermentation with Monascus spp.

Hotair promotes the migration and proliferation in ovarian cancer by miR-222-3p/CDK19 axis.

Previous studies in our laboratory have reported that miR-222-3p was a tumor-suppressive miRNA in OC. This study aims to further understand the regulatory role of miR-222-3p in OC and provide a new mechanism for its prevention and treatment. We first found that miR-222-3p inhibited the migration and proliferation of OC cells. Then, we observed CDK19 was highly expressed in OC and inversely correlated with miR-222-3p. Besides, we observed that miR-222-3p directly binds to the 3'-UTR of CDK19 and inhibits CDK19 translation, thus inhibiting OC cell migration and proliferation in vitro and repressed tumor growth in vivo. We also observed the inhibitory effect of Hotair on miR-222-3p in OC. In addition, Hotair could promote the proliferation and migration of OC cells in vitro and facilitate the growth and metastasis of tumors in vivo. Moreover, Hotair was positively correlated with CDK19 expression. These results suggest Hotair indirectly up-regulates CDK19 through sponging miR-222-3p, which enhances the malignant behavior of OC. This provides a further understanding of the mechanism of the occurrence and development of OC.

Comprehensive network analysis of dysregulated genes revealed MNX1-AS1/hsa-miR-4697-3p/HOXB13 axis in ovarian cancer chemotherapy response.

Poor chemotherapy response is the main obstacle of ovarian cancer (OC) treatment. Platinum-refractory and -resistant patients are associated with a worse outcome than platinum-sensitive and partially sensitive patients, but the comprehensive similarities and differences among them are not yet clear. In this study, we analyzed the data of patients with different chemotherapy response in The Cancer Genome Atlas. We found a minority of altered genes were overlapped in refractory and resistant groups, as did the enriched pathways and Gene Ontology terms. We noticed that the neural signaling and drug metabolism enzymes were more significantly enriched and the protein-protein interaction supported these results. The transcription analysis highlighted PDX1 as the common and central transcription factor in both refractory and resistant groups. The competing endogenous RNA (ceRNA) network shared no common ceRNA pairs, indicating a major difference in noncoding RNA post-transcriptional regulation. In the end, we validated the expression, regulation, binding, and effect on chemotherapy response for selected MNX1-AS1/hsa-miR-4697-3p/HOXB13 in OC cell lines. Our study offered a novel and comprehensive insight into chemotherapy response, and potential targets for improving chemotherapy response in OC.

Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders.

Recent neuroscience studies demonstrate that a deeper understanding of brain function requires a deeper understanding of behavior. Detailed behavioral measurements are now often collected using video cameras, resulting in an increased need for computer vision algorithms that extract useful information from video data. Here we introduce a new video analysis tool that combines the output of supervised pose estimation algorithms (e.g. DeepLabCut) with unsupervised dimensionality reduction methods to produce interpretable, low-dimensional representations of behavioral videos that extract more information than pose estimates alone. We demonstrate this tool by extracting interpretable behavioral features from videos of three different head-fixed mouse preparations, as well as a freely moving mouse in an open field arena, and show how these interpretable features can facilitate downstream behavioral and neural analyses. We also show how the behavioral features produced by our model improve the precision and interpretation of these downstream analyses compared to using the outputs of either fully supervised or fully unsupervised methods alone.

Platelet membrane-camouflaged nanoparticles carry microRNA inhibitor against myocardial ischaemia‒reperfusion injury.

The incidence of myocardial ischaemia‒reperfusion injury (MIRI) is increasing every year, and there is an urgent need to develop new therapeutic approaches. Nrf2 is thought to play a protective role during MIRI and it is regulated by microRNAs (miRNAs). This study focused on PLGA nanoparticles camouflaged by platelet membrane vesicles (PMVs) (i.e., PMVs@PLGA complexes) carrying microRNA inhibitors, which regulate Nrf2 and can play a therapeutic role in the MIRI process. In vitro and in vivo characterization showed that PMVs@PLGA has excellent transfection efficiency, low toxicity and good targeting. MicroRNAs that effectively regulate Nrf2 were identified, and then PMVs@PLGA-miRNA complexes were prepared and used for in vitro and in vivo treatment. PMVs@PLGA-miRNA complexes can effectively target the delivery of inhibitors to cardiomyocytes. Our results suggest that PMVs@PLGA complexes are a novel delivery system and a novel biological approach to the treatment of MIRI.

Brain kernel: A new spatial covariance function for fMRI data.

A key problem in functional magnetic resonance imaging (fMRI) is to estimate spatial activity patterns from noisy high-dimensional signals. Spatial smoothing provides one approach to regularizing such estimates. However, standard smoothing methods ignore the fact that correlations in neural activity may fall off at different rates in different brain areas, or exhibit discontinuities across anatomical or functional boundaries. Moreover, such methods do not exploit the fact that widely separated brain regions may exhibit strong correlations due to bilateral symmetry or the network organization of brain regions. To capture this non-stationary spatial correlation structure, we introduce the brain kernel, a continuous covariance function for whole-brain activity patterns. We define the brain kernel in terms of a continuous nonlinear mapping from 3D brain coordinates to a latent embedding space, parametrized with a Gaussian process (GP). The brain kernel specifies the prior covariance between voxels as a function of the distance between their locations in embedding space. The GP mapping warps the brain nonlinearly so that highly correlated voxels are close together in latent space, and uncorrelated voxels are far apart. We estimate the brain kernel using resting-state fMRI data, and we develop an exact, scalable inference method based on block coordinate descent to overcome the challenges of high dimensionality (10-100K voxels). Finally, we illustrate the brain kernel's usefulness with applications to brain decoding and factor analysis with multiple task-based fMRI datasets.

Transcranial Photobiomodulation (tPBM) With 1,064-nm Laser to Improve Cerebral Metabolism of the Human Brain In Vivo.

BACKGROUND AND OBJECTIVES: In our previous proof-of-principle study, transcranial photobiomodulation (tPBM) with 1,064-nm laser was reported to significantly increase concentration changes of oxygenated hemoglobin (∆[HbO]) and oxidized-state cytochrome c oxidase (∆[oxi-CCO]) in the human brain. This paper further investigated (i) its validity in two different subsets of young human subjects at two study sites over a period of 3 years and (ii) age-related effects of tPBM by comparing sham-controlled increases of ∆[HbO] and ∆[oxi-CCO] between young and older adults. STUDY DESIGN/MATERIALS AND METHODS: We measured sham-controlled ∆[HbO] and ∆[oxi-CCO] using broadband near-infrared spectroscopy (bb-NIRS) in 15 young (26.7 ± 2.7 years of age) and 5 older (68.2 ± 4.8 years of age) healthy normal subjects before, during, and after right-forehead tPBM/sham stimulation with 1,064-nm laser. Student t tests were used to test statistical differences in tPBM-induced ∆[HbO] and ∆[oxi-CCO] (i) between the 15 young subjects and those of 11 reported previously and (ii) between the two age groups measured in this study. RESULTS: Statistical analysis showed that no significant difference existed in ∆[HbO] and ∆[oxi-CCO] during and post tPBM between the two subsets of young subjects at two study sites over a period of 3 years. Furthermore, the two age groups showed statistically identical net increases in sham-controlled ∆[HbO] and ∆[oxi-CCO]. CONCLUSIONS: This study provided strong evidence to validate/confirm our previous findings that tPBM with 1,064-nm laser enables to increase cerebral ∆[HbO] and ∆[oxi-CCO] in the human brain, as measured by bb-NIRS. Overall, it demonstrated the robust reproducibility of tPBM being able to improve cerebral hemodynamics and metabolism of the human brain in vivo in both young and older adults. Lasers Surg. Med. © 2020 The Authors. Lasers in Surgery and Medicine published by Wiley Periodicals, Inc.

uORFs: Important Cis-Regulatory Elements in Plants.

Gene expression is regulated at many levels, including mRNA transcription, translation, and post-translational modification. Compared with transcriptional regulation, mRNA translational control is a more critical step in gene expression and allows for more rapid changes of encoded protein concentrations in cells. Translation is highly regulated by complex interactions between cis-acting elements and trans-acting factors. Initiation is not only the first phase of translation, but also the core of translational regulation, because it limits the rate of protein synthesis. As potent cis-regulatory elements in eukaryotic mRNAs, upstream open reading frames (uORFs) generally inhibit the translation initiation of downstream major ORFs (mORFs) through ribosome stalling. During the past few years, with the development of RNA-seq and ribosome profiling, functional uORFs have been identified and characterized in many organisms. Here, we review uORF identification, uORF classification, and uORF-mediated translation initiation. More importantly, we summarize the translational regulation of uORFs in plant metabolic pathways, morphogenesis, disease resistance, and nutrient absorption, which open up an avenue for precisely modulating the plant growth and development, as well as environmental adaption. Additionally, we also discuss prospective applications of uORFs in plant breeding.

Functions of N6-methyladenosine and its role in cancer.

N6-methyladenosine (m6A) is methylation that occurs in the N6-position of adenosine, which is the most prevalent internal modification on eukaryotic mRNA. Accumulating evidence suggests that m6A modulates gene expression, thereby regulating cellular processes ranging from cell self-renewal, differentiation, invasion and apoptosis. M6A is installed by m6A methyltransferases, removed by m6A demethylases and recognized by reader proteins, which regulate of RNA metabolism including translation, splicing, export, degradation and microRNA processing. Alteration of m6A levels participates in cancer pathogenesis and development via regulating expression of tumor-related genes like BRD4, MYC, SOCS2 and EGFR. In this review, we elaborate on recent advances in research of m6A enzymes. We also highlight the underlying mechanism of m6A in cancer pathogenesis and progression. Finally, we review corresponding potential targets in cancer therapy.

Highly Stretchable, Adaptable, and Durable Strain Sensing Based on a Bioinspired Dynamically Cross-Linked Graphene/Polymer Composite.

Flexible strain sensors can detect physical signals (e.g., temperature, humidity, and flow) by sensing electrical deviation under dynamic deformation, and they have been used in diverse fields such as human motion detection, medical care, speech recognition, and robotics. Existing sensing materials have relatively low adaptability and durability and are not stretchable and flexible enough for complex tasks in motion detection. In this work, a highly flexible self-healing conductive polymer composite consisting of graphene, poly(acrylic acid) and amorphous calcium carbonate is prepared via a biomineralization-inspired process. The polymer composite shows good editability and processability and can be fabricated into stretchable strain sensors of various structures (sandwich structures, fibrous structures, self-supporting structures, etc.). The developed sensors can be attached on different types of surfaces (e.g., flat, cambered) and work well both in air and under water in detecting various biosignals, including crawling, undulatory locomotion, and human body motion.

Lysin cell-binding domain-functionalized magnetic beads for detection of Staphylococcus aureus via inhibition of fluorescence of Amplex Red/hydrogen peroxide assay by intracellular catalase.

Accurate and rapid identification of Staphylococcus aureus (S. aureus) is of great significance for controlling the food poisoning and infectious diseases caused by S. aureus. In this study, a novel strategy that combines lysin cell-binding domain (CBD)-based magnetic separation with fluorescence detection was developed for the specific and sensitive quantification of S. aureus in authentic samples. The S. aureus cells were separated from the sample matrix by lysin CBD-functionalized magnetic beads. Following lysis by lysostaphin, intracellular catalase was released from S. aureus cells and detected by a fluorometric system composed of horseradish peroxidase (HRP), hydrogen peroxide (H2O2), and Amplex Red. S. aureus was quantified via the inhibitory effect of the released intracellular catalase on the fluorometric system since the catalase could decompose the H2O2. Optimized conditions afforded a calibration curve for S. aureus ranging from 1.0 × 102 to 1.0 × 107 CFU mL-1. The detection limit was as low as 78 CFU mL-1 in phosphate-buffered saline (PBS), and the total detection process could be completed in less than 50 min. Other bacteria associated with common food-borne and nosocomial infections negligibly interfered with S. aureus detection, except for Staphylococcus epidermidis, which may have slightly interfered. Moreover, the potential of this proposed method for practical applications has been demonstrated by detection assays of sterilized milk and human serum. Graphical abstract.

The effects of simulated acid rain on internal nutrient cycling and the ratios of Mg, Al, Ca, N, and P in tea plants of a subtropical plantation.

Acid rain alters nutrient cycling in tea plantations. However, the acquisition of Mg and Ca by plants and their nutrient interactions with Al, N, and P in response to acid rain are poorly understood. Experimental treatments simulating acid rain at various acidities (pH 4.5, 3.5, and 2.5) were performed within a red soil tea plantation in China. The available Mg, Al, Ca, N, and P were analyzed in the rhizosphere and bulk soils. Further, these elements were measured in absorptive, transportive, and storative roots in addition to twigs, tea, and mature leaves. Available soil Mg and Ca exhibited negative and positive rhizosphere effects, respectively, but the levels of both decreased due to acid rain treatment. In addition, average Mg and Ca concentrations generally decreased in plant tissues with increasing acidity. In contrast, average Al concentration increased across all plant tissues with increasing acidity treatment. Meanwhile, the ratios of Al/Mg and Al/Ca increased with increasing acidity but that of N/Al decreased in twigs and roots. Lastly, the ratios of N/Al, P/Ca, and N/P were all altered by acid treatment in tea and/or mature leaves. Taken together, these results indicated that elevated acidity increased the internal cycling of Al in plants but decreased Mg and Ca fluxes between soils and roots. Further, the response of interactions among the five measured elements to different acidities varied with tea plant tissue. Our findings may advance our understanding of plant adaptation to increasing soil acidification and atmospheric acid deposition around the world.

Effects of Propofol on Several Membrane Characteristics of Cervical Cancer Cell Lines.

BACKGROUND: Although significant advances have been made toward understanding the molecular mechanisms underlying the effect of propofol on tumor cell metastasis, less is known regarding how cell membrane and cytoskeletal ultrastructure are affected in this process. Here, we investigated the relationship between cell morphology and cell size, which are features mainly defined by the cytoskeleton. METHODS: To confirm the effects of propofol on the migratory ability of human cervical carcinoma cells, cell migration and invasion were examined through scratch wound healing and transwell membrane assays. Furthermore, HeLa cells cultivated with different concentrations of propofol were examined by confocal microscopy and atomic force microscopy (AFM), and the mean optical density and migration ability of these cells were also assessed. In addition, cell membrane morphology was inspected using AFM. RESULTS: The results of the wound healing and transwell membrane assays indicated that propofol decreases the migratory ability of cervical carcinoma cells compared to control cells. A comparative analysis of the test results revealed that short-term (3 h) exposure to propofol induced marked changes in cell membrane microstructure and in the cytoskeleton in a dose-dependent manner. These morphological changes in the cell membrane were accompanied by cytoskeleton (F-actin) derangement. The present findings demonstrate a close relationship between changes in cell membrane ultrastructure and cytoskeletal alterations (F-actin) in propofol-treated HeLa cells. AFM scanning analysis showed that cell membrane ultrastructure was significantly changed, including a clear reduction in membrane roughness. CONCLUSION: The influence of propofol on the HeLa cell cytoskeleton can be directly reflected by changes in cellular morphology, as assessed by AFM. Moreover, the use of AFM is a good method for investigating propofol-mediated changes within cytoskeletal ultrastructure.

MiR-145 promotes TNF-α-induced apoptosis by facilitating the formation of RIP1-FADDcaspase-8 complex in triple-negative breast cancer.

Researches indicate that the dysregulation of microRNA (miRNA) is involved in tumorigenesis. Among such dysregulated miRNAs in cancer, miR-145 is reported to be downregulated in multiple cancers. In this study, we demonstrated the downregulation of miR-145 in triple-negative breast cancer (TNBC) tissues and TNBC cell lines by quantitative reverse-transcription polymerase chain reaction (RT-PCR) analysis. Furthermore, we found that the tumor necrosis factor-alpha (TNF-α)-induced apoptosis was expanded by the transfection of miR-145 in MDA-MB-231 which belongs to the TNBC cell lines. We then indicated that the mechanism by which miR-145 promotes the TNF-α-induced apoptosis is dependent on the formation of RIP1-FADD-caspase-8 complex. The cellular inhibitor of apoptosis (cIAP1), which is the inhibitor of apoptosis protein, was found to be a target of miR-145 in MDA-MB-231 cells. As a result of cIAP1 overexpression, the promotion of miR-145 on TNF-α-induced apoptosis was inhibited in MDA-MB-231 cells. Therefore, our results indicate that miR-145 acts as a tumor suppressor in TNBC, suggesting that the miR-145-cIAP1 axis might be a potential therapeutic target for TNBC.

Mechanical ventilation strategies for intensive care unit patients without acute lung injury or acute respiratory distress syndrome: a systematic review and network meta-analysis.

BACKGROUND: It has been shown that the application of a lung-protective mechanical ventilation strategy can improve the prognosis of patients with acute lung injury (ALI) or acute respiratory distress syndrome (ARDS). However, the optimal mechanical ventilation strategy for intensive care unit (ICU) patients without ALI or ARDS is uncertain. Therefore, we performed a network meta-analysis to identify the optimal mechanical ventilation strategy for these patients. METHODS: We searched the Cochrane Central Register of Controlled Trials (CENTRAL) in the Cochrane Library, EMBASE, MEDLINE, CINAHL, and Web of Science for studies published up to July 2015 in which pulmonary compliance or the partial pressure of arterial oxygen/fraction of inspired oxygen (PaO2/FIO2) ratio was assessed in ICU patients without ALI or ARDS, who received mechanical ventilation via different strategies. The data for study characteristics, methods, and outcomes were extracted. We assessed the studies for eligibility, extracted the data, pooled the data, and used a Bayesian fixed-effects model to combine direct comparisons with indirect evidence. RESULTS: Seventeen randomized controlled trials including a total of 575 patients who received one of six ventilation strategies were included for network meta-analysis. Among ICU patients without ALI or ARDS, strategy C (lower tidal volume (VT) + higher positive end-expiratory pressure (PEEP)) resulted in the highest PaO2/FIO2 ratio; strategy B (higher VT + lower PEEP) was associated with the highest pulmonary compliance; strategy A (lower VT + lower PEEP) was associated with a shorter length of ICU stay; and strategy D (lower VT + zero end-expiratory pressure (ZEEP)) was associated with the lowest PaO2/FiO2 ratio and pulmonary compliance. CONCLUSIONS: For ICU patients without ALI or ARDS, strategy C (lower VT + higher PEEP) was associated with the highest PaO2/FiO2 ratio. Strategy B (higher VT + lower PEEP) was superior to the other strategies in improving pulmonary compliance. Strategy A (lower VT + lower PEEP) was associated with a shorter length of ICU stay, whereas strategy D (lower VT + ZEEP) was associated with the lowest PaO2/FiO2 ratio and pulmonary compliance.

Pioneer Factor Foxa2 Mediates Chromatin Conformation Changes for Activation of Bile Acid Targets of FXR.

BACKGROUND & AIMS: Transcription factors regulate gene expression that orchestrates liver physiology. Many bind at distal enhancers and chromatin looping is required to activate their targets. Chromatin architecture has been linked to essential functions of the liver, including metabolism and sexually dimorphic gene expression. We have previously shown that pioneer factor Foxa2 opens chromatin for binding of nuclear receptors farnesoid X receptor (FXR) and liver X receptor-α during acute ligand activation. FXR is activated by bile acids and deletion of Foxa2 in the liver results in intrahepatic cholestasis. We hypothesized that Foxa2 also enables chromatin conformational changes during ligand activation and performed genome-wide studies to test this hypothesis. METHODS: We performed Foxa2 HiChIP (Hi-C and ChIP) to assess Foxa2-dependent long-range interactions in mouse livers treated with either vehicle control or FXR agonist GW4064. RESULTS: HiChIP contact analysis shows that global chromatin interactions are dramatically increased during FXR activation. Ligand-treated livers exhibit extensive redistribution of topological associated domains and substantial increase in Foxa2-anchored loops, suggesting Foxa2 is involved in dynamic chromatin conformational changes. We demonstrate that chromatin conformation, including genome-wide interactions, topological associated domains, and intrachromosomal and interchromosomal Foxa2-anchored loops, drastically changes on addition of FXR agonist. Additional Foxa2 binding in ligand-activated state leads to formation of Foxa2-anchored loops, leading to distal interactions and activation of gene expression of FXR targets. CONCLUSIONS: Ligand activation of FXR, and likely of related receptors, requires global changes in chromatin architecture. We determine a novel role for Foxa2 in enabling these conformational changes, extending its function in bile acid metabolism.

Multi-Region Markovian Gaussian Process: An Efficient Method to Discover Directional Communications Across Multiple Brain Regions.

Studying the complex interactions between different brain regions is crucial in neuroscience. Various statistical methods have explored the latent communication across multiple brain regions. Two main categories are the Gaussian Process (GP) and Linear Dynamical System (LDS), each with unique strengths. The GP-based approach effectively discovers latent variables with frequency bands and communication directions. Conversely, the LDS-based approach is computationally efficient but lacks powerful expressiveness in latent representation. In this study, we merge both methodologies by creating an LDS mirroring a multi-output GP, termed Multi-Region Markovian Gaussian Process (MRM-GP). Our work establishes a connection between an LDS and a multi-output GP that explicitly models frequencies and phase delays within the latent space of neural recordings. Consequently, the model achieves a linear inference cost over time points and provides an interpretable low-dimensional representation, revealing communication directions across brain regions and separating oscillatory communications into different frequency bands.