CRISPR Comparison Toolkit: Rapid Identification, Visualization, and Analysis of CRISPR Array Diversity.

CRISPR-Cas systems provide immunity against mobile genetic elements (MGEs) through sequence-specific targeting by spacer sequences encoded in CRISPR arrays. Spacers are highly variable between microbial strains and can be acquired rapidly, making them well suited for use in strain typing of closely related organisms. However, no tools are currently available to automate the process of reconstructing strain histories using CRISPR spacers. We therefore developed the CRISPR Comparison Toolkit (CCTK) to enable analyses of array relationships. The CCTK includes tools to identify arrays, analyze relationships between arrays using CRISPRdiff and CRISPRtree, and predict targets of spacers. CRISPRdiff visualizes arrays and highlights the similarities between them. CRISPRtree infers a phylogenetic tree from array relationships and presents a hypothesis of the evolutionary history of the arrays. The CCTK unifies several CRISPR analysis tools into a single command line application, including the first tool to infer phylogenies from array relationships.

Evaluation of bacterial attachment on mineralized collagen scaffolds and addition of manuka honey to increase mesenchymal stem cell osteogenesis.

The design of biomaterials to regenerate bone is likely to increasingly require modifications that reduce bacterial attachment and biofilm formation as infection during wound regeneration can significantly impede tissue repair and typically requires surgical intervention to restart the healing process. Further, much research on infection prevention in bone biomaterials has focused on modeling of non-resorbable metal alloy materials, whereas an expanding direction of bone regeneration has focused on development of bioresorbable materials. This represents a need for the prevention and understanding of infection in resorbable biomaterials. Here, we investigate the ability of a mineralized collagen biomaterial to natively resist infection and examine how the addition of manuka honey, previously identified as an antimicrobial agent, affects gram positive and negative bacterial colonization and mesenchymal stem cell osteogenesis and vasculature formation. We incorporate manuka honey into these scaffolds via either direct fabrication into the scaffold microarchitecture or via soaking the scaffold in a solution of manuka honey after fabrication. Direct incorporation results in a change in the surface characteristics and porosity of mineralized collagen scaffolds. Soaking scaffolds in honey concentrations higher than 10% had significant negative effects on mesenchymal stem cell metabolic activity. Soaking or incorporating 5% honey had no impact on endothelial cell tube formation. Although solutions of 5% honey reduced metabolic activity of mesenchymal stem cells, MSC-seeded scaffolds displayed increased calcium and phosphorous mineral formation, osteoprotegerin release, and alkaline phosphatase activity. Bacteria cultured on mineralized collagen scaffolds demonstrated surfaces covered in bacteria and no method of preventing infection, and using 10 times the minimal inhibitory concentration of antibiotics did not completely kill bacteria within the mineralized collagen scaffolds, indicating bioresorbable scaffold materials may act to shield bacteria from antibiotics. The addition of 5% manuka honey to scaffolds was not sufficient to prevent P. aeruginosa attachment or consistently reduce the activity of methicillin resistant staphylococcus aureus, and concentrations above 7% manuka honey are likely necessary to impact MRSA. Together, our results suggest bioresorbable scaffolds may create an environment conducive to bacterial growth, and potential trade-offs exist for the incorporation of low levels of honey in scaffolds to increase osteogenic potential of osteoprogenitors while high-levels of honey may be sufficient to reduce gram positive or negative bacteria activity but at the cost of reduced osteogenesis.

Prediction of Prophages and Their Host Ranges in Pathogenic and Commensal Neisseria Species.

The genus Neisseria includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. Neisseria species frequently exchange DNA with one another, primarily via transformation and homologous recombination and via multiple types of mobile genetic elements (MGEs). Few Neisseria bacteriophages (phages) have been identified, and their impact on bacterial physiology is poorly understood. Furthermore, little is known about the range of species that Neisseria phages can infect. In this study, we used three virus prediction tools to scan 248 genomes of 21 different Neisseria species and identified 1,302 unique predicted prophages. Using comparative genomics, we found that many predictions are dissimilar from prophages and other MGEs previously described to infect Neisseria species. We also identified similar predicted prophages in genomes of different Neisseria species. Additionally, we examined CRISPR-Cas targeting of each Neisseria genome and predicted prophage. While CRISPR targeting of chromosomal DNA appears to be common among several Neisseria species, we found that 20% of the prophages we predicted are targeted significantly more than the rest of the bacterial genome in which they were identified (i.e., backbone). Furthermore, many predicted prophages are targeted by CRISPR spacers encoded by other species. We then used these results to infer additional host species of known Neisseria prophages and predictions that are highly targeted relative to the backbone. Together, our results suggest that we have identified novel Neisseria prophages, several of which may infect multiple Neisseria species. These findings have important implications for understanding horizontal gene transfer between members of this genus. IMPORTANCE Drug-resistant Neisseria gonorrhoeae is a major threat to human health. Commensal Neisseria species are thought to serve as reservoirs of antibiotic resistance and virulence genes for the pathogenic species N. gonorrhoeae and N. meningitidis. Therefore, it is important to understand both the diversity of mobile genetic elements (MGEs) that can mediate horizontal gene transfer within this genus and the breadth of species these MGEs can infect. In particular, few bacteriophages (phages) are known to infect Neisseria species. In this study, we identified a large number of candidate phages integrated in the genomes of commensal and pathogenic Neisseria species, many of which appear to be novel phages. Importantly, we discovered extensive interspecies targeting of predicted phages by Neisseria CRISPR-Cas systems, which may reflect their movement between different species. Uncovering the diversity and host range of phages is essential for understanding how they influence the evolution of their microbial hosts.

On the global COVID-19 pandemic and China's FDI.

The global COVID-19 pandemic has generated serious challenges for the world economy, including cross-border foreign direct investment (FDI). China's inward FDI (IFDI) and outward FDI (OFDI) are also facing unprecedented risks and challenges. This paper first clarifies the timelines of the pandemic evolving in China, the US, and the rest of the world. It then reflects on China's past development process of IFDI and OFDI, noting the growth of IFDI and highlighting the risks and challenges for OFDI during and after the pandemic. Empirical evidence for the impact of COVID-19 on FDI is set out. Policy recommendations are then made regarding China's latest development strategy using the so-called dual circulation to sustain its economic growth with respect to cross-border FDI.

Place Effects and Chronic Disease Rates in a Rural State: Evidence from a Triangulation of Methods.

High rates of chronic diseases and increasing nutritional polarization between different income groups in the United States are issues of concern to policymakers and public health officials. Spatial differences in access to food are mainly blamed as the cause for these nutritional inequalities. This study first detected hot and cold spots of food providers in West Virginia and then used those places in a quasi-experimental method (entropy balancing) to study the effects of those places on diabetes and obesity rates. We found that although hot spots have lower rates of chronic diseases than non-hot spots and cold spots have higher rates of chronic diseases than non-cold spots-the situation is complicated. With the findings of income induced chronic disease rates in urban areas, where most hot spots are located, there is evidence of another case for "food swamps." However, in cold spots which are located mainly in rural areas, higher rates of chronic diseases are attributed to a combination of access to food providers along with lacking the means (i.e., income for low-income households) to form healthier habits.

From Input to Output: The Lap/c-di-GMP Biofilm Regulatory Circuit.

Biofilms are the dominant bacterial lifestyle. The regulation of the formation and dispersal of bacterial biofilms has been the subject of study in many organisms. Over the last two decades, the mechanisms of Pseudomonas fluorescens biofilm formation and regulation have emerged as among the best understood of any bacterial biofilm system. Biofilm formation by P. fluorescens occurs through the localization of an adhesin, LapA, to the outer membrane via a variant of the classical type I secretion system. The decision between biofilm formation and dispersal is mediated by LapD, a c-di-GMP receptor, and LapG, a periplasmic protease, which together control whether LapA is retained or released from the cell surface. LapA localization is also controlled by a complex network of c-di-GMP-metabolizing enzymes. This review describes the current understanding of LapA-mediated biofilm formation by P. fluorescens and discusses several emerging models for the regulation and function of this adhesin.

MapA, a Second Large RTX Adhesin Conserved across the Pseudomonads, Contributes to Biofilm Formation by Pseudomonas fluorescens.

Mechanisms by which cells attach to a surface and form a biofilm are diverse and differ greatly among organisms. The Gram-negative gammaproteobacterium Pseudomonas fluorescens attaches to a surface through the localization of the large type 1-secreted RTX adhesin LapA to the outer surface of the cell. LapA localization to the cell surface is controlled by the activities of a periplasmic protease, LapG, and an inner membrane-spanning cyclic di-GMP-responsive effector protein, LapD. A previous study identified a second, LapA-like protein encoded in the P. fluorescens Pf0-1 genome: Pfl01_1463. Here, we identified specific growth conditions under which Pfl01_1463, here called MapA (medium adhesion protein A) is a functional adhesin contributing to biofilm formation. This adhesin, like LapA, appears to be secreted through a Lap-related type 1 secretion machinery, and its localization is controlled by LapD and LapG. However, differing roles of LapA and MapA in biofilm formation are achieved, at least in part, through the differences in the sequences of the two adhesins and different distributions of the expression of the lapA and mapA genes within a biofilm. LapA-like proteins are broadly distributed throughout the Proteobacteria, and furthermore, LapA and MapA are well conserved among other Pseudomonas species. Together, our data indicate that the mechanisms by which a cell forms a biofilm and the components of a biofilm matrix can differ depending on growth conditions and the matrix protein(s) expressed.IMPORTANCE Adhesins are critical for the formation and maturation of bacterial biofilms. We identify a second adhesin in P. fluorescens, called MapA, which appears to play a role in biofilm maturation and whose regulation is distinct from the previously reported LapA adhesin, which is critical for biofilm initiation. Analysis of bacterial adhesins shows that LapA-like and MapA-like adhesins are found broadly in pseudomonads and related organisms, indicating that the utilization of different suites of adhesins may be broadly important in the Gammaproteobacteria.

Isotopic systematics of zircon indicate an African affinity for the rocks of southernmost India.

Southern India lies in an area of Gondwana where multiple blocks are juxtaposed along Moho-penetrating structures, the significance of which are not well understood. Adequate geochronological data that can be used to differentiate the various blocks are also lacking. We present a newly acquired SIMS U-Pb, Lu-Hf, O isotopic and trace element geochemical dataset from zircon and garnet from the protoliths of the Nagercoil Block at the very tip of southern India. The data indicate that the magmatic protoliths of the rocks in this block formed at c. 2040 Ma with Lu-Hf, O-isotope and trace element data consistent with formation in a magmatic arc environment. The zircon data from Nagercoil Block are isotopically and temporally distinct from those in all the other blocks in southern India, but remarkably correspond to rocks in East Africa that are exposed on the southern margin of the Tanzania-Bangweulu Block. The new data suggest that the tip of southern India has an African affinity and a major suture zone must lie along its northern margin. All of these blocks were finally brought together during the Ediacaran-Cambrian amalgamation of Gondwana where they underwent high to ultrahigh temperature metamorphism.

A phenomenological exploration of change towards healthier food purchasing behaviour in women from a lower socioeconomic background using a health app.

Food purchasing is dominated by routines and habits that may hamper the use of reflective decision-making and impede change. Disrupting existing behavioural patterns may address this challenge. Individuals from a lower socioeconomic background are more likely to report unhealthier purchasing and targeted initiatives are required. Health apps offer a potential approach although little evidence is available for this specific context. This research examines the individual's experience of changing food purchasing behaviour using an app focusing on women from a lower socioeconomic background. Multiple methods across different time-points explored the individual's experience over an 8-11 week period. An accompanied shop, incorporating think-aloud and researcher observations, was undertaken at baseline, followed by an in-depth interview and questionnaire. A reflective account of the individual's experience was recorded at four weeks and grocery receipts were shared for the duration. At follow-up, an accompanied shop, in-depth interview, and questionnaire were again used. Data were analysed using interpretative phenomenological analysis. The app appeared to disrupt existing behaviour by encouraging a more conscious approach to food purchasing. Self-monitoring, problem solving, and behavioural prompts were expressed as the most effective techniques. Due to the retail environment, self-control was necessary to create and maintain healthier behaviour. Individual higher-order goals appeared to influence behaviour change and the extent to which reflective cognition was employed. The role of retailers in directing behaviour was acknowledged but it appeared that change was still viewed as individual responsibility. In conclusion, apps may facilitate healthier purchasing via specific behaviour change techniques but personal and environmental factors may influence the change process. A range of strategies may be necessary to support sufficient and sustained change.

Dynamic interaction between basin redox and the biogeochemical nitrogen cycle in an unconventional Proterozoic petroleum system.

Precambrian hydrocarbons and their corresponding source rocks are distinctly different from their Phanerozoic counterparts, having been deposited in persistently anoxic environments in ecosystems dominated by bacteria. Here, we show that cyclic enrichment of organic matter in the world's oldest hydrocarbon play (ca. 1.38 Ga), is not associated with flooding surfaces and is unrelated to variations in mineralogy or changes in the relative rate of clastic to biogenic sedimentation-factors typically attributed to organic enrichment in Phanerozoic shales. Instead, the cyclic covariation of total organic carbon, δ15N, δ13C and molybdenum are explained by the feedback between high levels of primary productivity, basin redox and the biogeochemical nitrogen cycle. These factors are important in constraining productivity in the marine biosphere, the development of Precambrian hydrocarbon source rocks, and more generally in understanding oxygenation of the ocean and atmosphere through Earth history; as all are ultimately related to organic carbon burial.

Data analysis of the U-Pb geochronology and Lu-Hf system in zircon and whole-rock Sr, Sm-Nd and Pb isotopic systems for the granitoids of Thailand.

This data article provides zircon U-Pb and Lu-Hf isotopic information along with whole-rock Sm-Nd, Sr and Pb isotopic geochemistry from granitoids in Thailand. The U-Pb ages are described and the classification of crystallisation and inherited ages are explained. The petrography of the granitoid samples is detailed. The data presented in this article are interpreted and discussed in the research article entitled "Probing into Thailand's basement: New insights from U-Pb geochronology, Sr, Sm-Nd, Pb and Lu-Hf isotopic systems from granitoids" (Dew et al., 2018).

Thermochronological insights into reactivation of a continental shear zone in response to Equatorial Atlantic rifting (northern Ghana).

West Africa was subjected to deformation and exhumation in response to Gondwana break-up. The timing and extent of these events are recorded in the thermal history of the margin. This study reports new apatite fission track (AFT) data from Palaeoproterozoic basement along the primary NE-SW structural trend of the Bole-Nangodi shear zone in northwestern Ghana. The results display bimodality in AFT age (populations of ~210-180 Ma and ~115-105 Ma) and length distributions (populations of 12.2 ± 1.6 and 13.1 ± 1.4 µm), supported by differences in apatite chemistry (U concentrations). The bimodal AFT results and associated QTQt thermal history models provide evidence for multiple cooling phases. Late Triassic - Early Jurassic cooling is interpreted to be related with thermal relaxation after the emplacement of the Central Atlantic Magmatic Province (CAMP). Early to middle Cretaceous cooling is thought to be associated with exhumation during the Cretaceous onset of rifting between West Africa and Brazil. Late Cretaceous - Cenozoic cooling can be related with exhumation of the Ivory Coast - Ghana margin and NNW-SSE shortening through western Africa. Furthermore, our data record differential exhumation of the crust with respect to the Bole-Nangodi shear zone, preserving older (CAMP) cooling ages to the south and younger (rifting) cooling ages to the north of the shear zone, respectively. This suggests that the Palaeoproterozoic BN shear zone was reactivated during the Cretaceous as a result of deformation in the Equatorial Atlantic region of Africa.

Ligand-Mediated Biofilm Formation via Enhanced Physical Interaction between a Diguanylate Cyclase and Its Receptor.

The bacterial intracellular second messenger, cyclic dimeric GMP (c-di-GMP), regulates biofilm formation for many bacteria. The binding of c-di-GMP by the inner membrane protein LapD controls biofilm formation, and the LapD receptor is central to a complex network of c-di-GMP-mediated biofilm formation. In this study, we examine how c-di-GMP signaling specificity by a diguanylate cyclase (DGC), GcbC, is achieved via interactions with the LapD receptor and by small ligand sensing via GcbC's calcium channel chemotaxis (CACHE) domain. We provide evidence that biofilm formation is stimulated by the environmentally relevant organic acid citrate (and a related compound, isocitrate) in a GcbC-dependent manner through enhanced GcbC-LapD interaction, which results in increased LapA localization to the cell surface. Furthermore, GcbC shows little ability to synthesize c-di-GMP in isolation. However, when LapD is present, GcbC activity is significantly enhanced (~8-fold), indicating that engaging the LapD receptor stimulates the activity of this DGC; citrate-enhanced GcbC-LapD interaction further stimulates c-di-GMP synthesis. We propose that the I-site of GcbC serves two roles beyond allosteric control of this enzyme: promoting GcbC-LapD interaction and stabilizing the active conformation of GcbC in the GcbC-LapD complex. Finally, given that LapD can interact with a dozen different DGCs of Pseudomonas fluorescens, many of which have ligand-binding domains, the ligand-mediated enhanced signaling via LapD-GcbC interaction described here is likely a conserved mechanism of signaling in this network. Consistent with this idea, we identify a second example of ligand-mediated enhancement of DGC-LapD interaction that promotes biofilm formation.IMPORTANCE In many bacteria, dozens of enzymes produce the dinucleotide signal c-di-GMP; however, it is unclear how undesired cross talk is mitigated in the context of this soluble signal and how c-di-GMP signaling is regulated by environmental inputs. We demonstrate that GcbC, a DGC, shows little ability to synthesize c-di-GMP in the absence of its cognate receptor LapD; GcbC-LapD interaction enhances c-di-GMP synthesis by GcbC, likely mediated by the I-site of GcbC. We further show evidence for a ligand-mediated mechanism of signaling specificity via increased physical interaction of a DGC with its cognate receptor. We envision a scenario wherein a "cloud" of weakly active DGCs can increase their activity by specific interaction with their receptor in response to appropriate environmental signals, concomitantly boosting c-di-GMP production, ligand-specific signaling, and biofilm formation.

A Multimodal Strategy Used by a Large c-di-GMP Network.

The Pseudomonas fluorescens genome encodes more than 50 proteins predicted to be involved in c-di-GMP signaling. Here, we demonstrated that, tested across 188 nutrients, these enzymes and effectors appeared capable of impacting biofilm formation. Transcriptional analysis of network members across ∼50 nutrient conditions indicates that altered gene expression can explain a subset of but not all biofilm formation responses to the nutrients. Additional organization of the network is likely achieved through physical interaction, as determined via probing ∼2,000 interactions by bacterial two-hybrid assays. Our analysis revealed a multimodal regulatory strategy using combinations of ligand-mediated signals, protein-protein interaction, and/or transcriptional regulation to fine-tune c-di-GMP-mediated responses. These results create a profile of a large c-di-GMP network that is used to make important cellular decisions, opening the door to future model building and the ability to engineer this complex circuitry in other bacteria.IMPORTANCE Cyclic diguanylate (c-di-GMP) is a key signaling molecule regulating bacterial biofilm formation, and many microbes have up to dozens of proteins that make, break, or bind this dinucleotide. A major open issue in the field is how signaling specificity is conferred in the unpartitioned space of a bacterial cell. Here, we took a systems approach, using mutational analysis, transcriptional studies, and bacterial two-hybrid analysis to interrogate this network. We found that a majority of enzymes are capable of impacting biofilm formation in a context-dependent manner, and we revealed examples of two or more modes of regulation (i.e., transcriptional control with protein-protein interaction) being utilized to generate an observable impact on biofilm formation.

Can existing mobile apps support healthier food purchasing behaviour? Content analysis of nutrition content, behaviour change theory and user quality integration.

OBJECTIVE: To assess the quality of nutrition content and the integration of user quality components and behaviour change theory relevant to food purchasing behaviour in a sample of existing mobile apps. DESIGN: Descriptive comparative analysis of eleven mobile apps comprising an assessment of their alignment with existing evidence on nutrition, behaviour change and user quality, and their potential ability to support healthier food purchasing behaviour. SETTING: Mobile apps freely available for public use in GoogePlay were assessed and scored according to agreed criteria to assess nutrition content quality and integration of behaviour change theory and user quality components. SUBJECTS: A sample of eleven mobile apps that met predefined inclusion criteria to ensure relevance and good quality. RESULTS: The quality of the nutrition content varied. Improvements to the accuracy and appropriateness of nutrition content are needed to ensure mobile apps support a healthy behaviour change process and are accessible to a wider population. There appears to be a narrow focus towards behaviour change with an overemphasis on behavioural outcomes and a small number of behaviour change techniques, which may limit effectiveness. A significant effort from the user was required to use the mobile apps appropriately which may negatively influence user acceptability and subsequent utilisation. CONCLUSIONS: Existing mobile apps may offer a potentially effective approach to supporting healthier food purchasing behaviour but improvements in mobile app design are required to maximise their potential effectiveness. Engagement of mobile app users and nutrition professionals is recommended to support effective design.

Requirements for Pseudomonas aeruginosa Type I-F CRISPR-Cas Adaptation Determined Using a Biofilm Enrichment Assay.

CRISPR (clustered regularly interspaced short palindromic repeat)-Cas (CRISPR-associated protein) systems are diverse and found in many archaea and bacteria. These systems have mainly been characterized as adaptive immune systems able to protect against invading mobile genetic elements, including viruses. The first step in this protection is acquisition of spacer sequences from the invader DNA and incorporation of those sequences into the CRISPR array, termed CRISPR adaptation. Progress in understanding the mechanisms and requirements of CRISPR adaptation has largely been accomplished using overexpression of cas genes or plasmid loss assays; little work has focused on endogenous CRISPR-acquired immunity from viral predation. Here, we developed a new biofilm-based assay system to enrich for Pseudomonas aeruginosa strains with new spacer acquisition. We used this assay to demonstrate that P. aeruginosa rapidly acquires spacers protective against DMS3vir, an engineered lytic variant of the Mu-like bacteriophage DMS3, through primed CRISPR adaptation from spacers present in the native CRISPR2 array. We found that for the P. aeruginosa type I-F system, the cas1 gene is required for CRISPR adaptation, recG contributes to (but is not required for) primed CRISPR adaptation, recD is dispensable for primed CRISPR adaptation, and finally, the ability of a putative priming spacer to prime can vary considerably depending on the specific sequences of the spacer. IMPORTANCE: Our understanding of CRISPR adaptation has expanded largely through experiments in type I CRISPR systems using plasmid loss assays, mutants of Escherichia coli, or cas1-cas2 overexpression systems, but there has been little focus on studying the adaptation of endogenous systems protecting against a lytic bacteriophage. Here we describe a biofilm system that allows P. aeruginosa to rapidly gain spacers protective against a lytic bacteriophage. This approach has allowed us to probe the requirements for CRISPR adaptation in the endogenous type I-F system of P. aeruginosa Our data suggest that CRISPR-acquired immunity in a biofilm may be one reason that many P. aeruginosa strains maintain a CRISPR-Cas system.

Concern and Helplessness: Citizens' Assessments of Individual and Collective Action on the Provision of Environmental Public Goods in a Coastal City at Risk of Inundation.

Survey data from a representative sample of 1005 households in the UK coastal city of Portsmouth are examined to discern commonalities and contrasts in their assessment of actions to address the related environmental threats of climate change and flooding. The city of Portsmouth is at risk of inundation from rising sea levels and the city has recent experience of flooding. A simple local and global public good framework is used to organize the understanding of reported attitudes and their determinants. The findings show that it is not always the same individuals who express concern about both climate change and flooding. Investigation into perceptions of helplessness in tackling climate change indicates that individuals more often perceived themselves to be helpless in tackling climate but perceived local collective action to be more effective. Individuals considered local collective action to be more effective in tackling climate change. Perceptions of individual helplessness are in turn related to reported concern. Several socioeconomic characteristics of individuals are shown to be useful in explaining the determinants of concern and perceptions of helplessness among respondents. As other cities face climate change-related challenges, the empirical findings, based upon attitudes from an alert urban population, are informative to policy design.

Inhibition of the aryl hydrocarbon receptor prevents Western diet-induced obesity. Model for AHR activation by kynurenine via oxidized-LDL, TLR2/4, TGFß, and IDO1.

Obesity is an increasingly urgent global problem, yet, little is known about its causes and less is known how obesity can be effectively treated. We showed previously that the aryl hydrocarbon receptor (AHR) plays a role in the regulation of body mass in mice fed Western diet. The AHR is a ligand-activated nuclear receptor that regulates genes involved in a number of biological pathways, including xenobiotic metabolism and T cell polarization. This study was an investigation into whether inhibition of the AHR prevents Western diet-based obesity. Male C57Bl/6J mice were fed control and Western diets with and without the AHR antagonist α-naphthoflavone or CH-223191, and a mouse hepatocyte cell line was used to delineate relevant cellular pathways. Studies are presented showing that the AHR antagonists α-naphthoflavone and CH-223191 significantly reduce obesity and adiposity and ameliorates liver steatosis in male C57Bl/6J mice fed a Western diet. Mice deficient in the tryptophan metabolizing enzyme indoleamine 2,3-dioxygenase 1 (IDO1) were also resistant to obesity. Using an AHR-directed, luciferase-expressing mouse hepatocyte cell line, we show that the transforming growth factor ß1 (TGFß1) signaling pathway via PI3K and NF-κB and the toll-like receptor 2/4 (TLR2/4) signaling pathway stimulated by oxidized low-density lipoproteins via NF-κB, each induce luciferase expression; however, TLR2/4 signaling was significantly reduced by inhibition of IDO1. At physiological levels, kynurenine but not kynurenic acid (both tryptophan metabolites and known AHR agonists) activated AHR-directed luciferase expression. We propose a hepatocyte-based model, in which kynurenine production is increased by enhanced IDO1 activity stimulated by TGFß1 and TLR2/4 signaling, via PI3K and NF-κB, to perpetuate a cycle of AHR activation to cause obesity; and inhibition of the AHR, in turn, blocks the cycle's output to prevent obesity. The AHR with its broad ligand binding specificity is a promising candidate for a potentially simple therapeutic approach for the prevention and treatment of obesity and associated complications.

Contribution of Physical Interactions to Signaling Specificity between a Diguanylate Cyclase and Its Effector.

UNLABELLED: Cyclic diguanylate (c-di-GMP) is a bacterial second messenger that controls multiple cellular processes. c-di-GMP networks have up to dozens of diguanylate cyclases (DGCs) that synthesize c-di-GMP along with many c-di-GMP-responsive target proteins that can bind and respond to this signal. For such networks to have order, a mechanism(s) likely exists that allow DGCs to specifically signal their targets, and it has been suggested that physical interactions might provide such specificity. Our results show a DGC from Pseudomonas fluorescens physically interacting with its target protein at a conserved interface, and this interface can be predictive of DGC-target protein interactions. Furthermore, we demonstrate that physical interaction is necessary for the DGC to maximally signal its target. If such "local signaling" is a theme for even a fraction of the DGCs used by bacteria, it becomes possible to posit a model whereby physical interaction allows a DGC to directly signal its target protein, which in turn may help curtail undesired cross talk with other members of the network. IMPORTANCE: An important question in microbiology is how bacteria make decisions using a signaling network made up of proteins that make, break, and bind the second messenger c-di-GMP, which is responsible for controlling many cellular behaviors. Previous work has shown that a given DGC enzyme will signal for specific cellular outputs, despite making the same diffusible molecule as its sibling DGCs in the unpartitioned space of the bacterial cell. Understanding how one DGC differentiates its output from the dozens of other such enzymes in the cell is synonymous with understanding a large component of the bacterial decision-making machinery. We present evidence for a helix on a DGC used to physically associate with its target protein, which is necessary to achieve maximal signaling.