Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease

The presence of advanced fibrosis in nonalcoholic fatty liver disease (NAFLD) is the most important predictor of liver mortality. There are limited data on the diagnostic accuracy of gut microbiota-derived signature for predicting the presence of advanced fibrosis. In this prospective study, we characterized the gut microbiome compositions using whole-genome shotgun sequencing of DNA extracted from stool samples. This study included 86 uniquely well-characterized patients with biopsy-proven NAFLD, of which 72 had mild/moderate (stage 0-2 fibrosis) NAFLD, and 14 had advanced fibrosis (stage 3 or 4 fibrosis). We identified a set of 40 features (p < 0.006), which included 37 bacterial species that were used to construct a Random Forest classifier model to distinguish mild/moderate NAFLD from advanced fibrosis. The model had a robust diagnostic accuracy (AUC 0.936) for detecting advanced fibrosis. This study provides preliminary evidence for a fecal-microbiome-derived metagenomic signature to detect advanced fibrosis in NAFLD.

The yeast cell-cycle network is robustly designed

The interactions between proteins, DNA, and RNA in living cells constitute molecular networks that govern various cellular functions. To investigate the global dynamical properties and stabilities of such networks, we studied the cell-cycle regulatory network of the budding yeast. With the use of a simple dynamical model, it was demonstrated that the cell-cycle network is extremely stable and robust for its function. The biological stationary state, the G1 state, is a global attractor of the dynamics. The biological pathway, the cell-cycle sequence of protein states, is a globally attracting trajectory of the dynamics. These properties are largely preserved with respect to small perturbations to the network. These results suggest that cellular regulatory networks are robustly designed for their functions.

The fecal metabolome as a functional readout of the gut microbiome

The human gut microbiome plays a key role in human health 1 , but 16S characterization lacks quantitative functional annotation 2 . The fecal metabolome provides a functional readout of microbial activity and can be used as an intermediate phenotype mediating host-microbiome interactions 3 . In this comprehensive description of the fecal metabolome, examining 1,116 metabolites from 786 individuals from a population-based twin study (TwinsUK), the fecal metabolome was found to be only modestly influenced by host genetics (heritability (H2) = 17.9%). One replicated locus at the NAT2 gene was associated with fecal metabolic traits. The fecal metabolome largely reflects gut microbial composition, explaining on average 67.7% (±18.8%) of its variance. It is strongly associated with visceral-fat mass, thereby illustrating potential mechanisms underlying the well-established microbial influence on abdominal obesity. Fecal metabolic profiling thus is a novel tool to explore links among microbiome composition, host phenotypes, and heritable complex traits.

Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly women

Omega-3 fatty acids may influence human physiological parameters in part by affecting the gut microbiome. The aim of this study was to investigate the links between omega-3 fatty acids, gut microbiome diversity and composition and faecal metabolomic profiles in middle aged and elderly women. We analysed data from 876 twins with 16S microbiome data and DHA, total omega-3, and other circulating fatty acids. Estimated food intake of omega-3 fatty acids were obtained from food frequency questionnaires. Both total omega-3and DHA serum levels were significantly correlated with microbiome alpha diversity (Shannon index) after adjusting for confounders (DHA Beta(SE) = 0.13(0.04), P = 0.0006 total omega-3: 0.13(0.04), P = 0.001). These associations remained significant after adjusting for dietary fibre intake. We found even stronger associations between DHA and 38 operational taxonomic units (OTUs), the strongest ones being with OTUs from the Lachnospiraceae family (Beta(SE) = 0.13(0.03), P = 8 × 10-7). Some of the associations with gut bacterial OTUs appear to be mediated by the abundance of the faecal metabolite N-carbamylglutamate. Our data indicate a link between omega-3 circulating levels/intake and microbiome composition independent of dietary fibre intake, particularly with bacteria of the Lachnospiraceae family. These data suggest the potential use of omega-3 supplementation to improve the microbiome composition.

Somatic APP gene recombination in Alzheimer's disease and normal neurons

The diversity and complexity of the human brain are widely assumed to be encoded within a constant genome. Somatic gene recombination, which changes germline DNA sequences to increase molecular diversity, could theoretically alter this code but has not been documented in the brain, to our knowledge. Here we describe recombination of the Alzheimer's disease-related gene APP, which encodes amyloid precursor protein, in human neurons, occurring mosaically as thousands of variant 'genomic cDNAs' (gencDNAs). gencDNAs lacked introns and ranged from full-length cDNA copies of expressed, brain-specific RNA splice variants to myriad smaller forms that contained intra-exonic junctions, insertions, deletions, and/or single nucleotide variations. DNA in situ hybridization identified gencDNAs within single neurons that were distinct from wild-type loci and absent from non-neuronal cells. Mechanistic studies supported neuronal 'retro-insertion' of RNA to produce gencDNAs; this process involved transcription, DNA breaks, reverse transcriptase activity, and age. Neurons from individuals with sporadic Alzheimer's disease showed increased gencDNA diversity, including eleven mutations known to be associated with familial Alzheimer's disease that were absent from healthy neurons. Neuronal gene recombination may allow 'recording' of neural activity for selective 'playback' of preferred gene variants whose expression bypasses splicing; this has implications for cellular diversity, learning and memory, plasticity, and diseases of the human brain.

Quantifying the integration of quorum-sensing signals with single-cell resolution

Cell-to-cell communication in bacteria is a process known as quorum sensing that relies on the production, detection, and response to the extracellular accumulation of signaling molecules called autoinducers. Often, bacteria use multiple autoinducers to obtain information about the vicinal cell density. However, how cells integrate and interpret the information contained within multiple autoinducers remains a mystery. Using single-cell fluorescence microscopy, we quantified the signaling responses to and analyzed the integration of multiple autoinducers by the model quorum-sensing bacterium Vibrio harveyi. Our results revealed that signals from two distinct autoinducers, AI-1 and AI-2, are combined strictly additively in a shared phosphorelay pathway, with each autoinducer contributing nearly equally to the total response. We found a coherent response across the population with little cell-to-cell variation, indicating that the entire population of cells can reliably distinguish several distinct conditions of external autoinducer concentration. We speculate that the use of multiple autoinducers allows a growing population of cells to synchronize gene expression during a series of distinct developmental stages.

Although bacteria are unicellular, the individual cells communicate with each other via small diffusible molecules. This communication process, known as quorum sensing, allows groups of bacteria to track the density of the population they are in, synchronize gene expression across the population, and thereby carry out collective activities similar to those of cells in multi-cellular organisms. Many bacterial species use multiple signaling molecules, but it remains a mystery why multiple signals are required and how the information encoded in them is integrated by bacteria. To explore these questions, we studied a model quorum-sensing bacterium Vibrio harveyi. Using single-cell fluorescence microscopy, we quantified quorum-sensing responses and analyzed the mechanism of integration of multiple signals. Surprisingly, we found that information from two distinct signals is combined strictly additively, with precisely equal weight from each signal. Our results revealed a coherent response across the population with little cell-to-cell variation, allowing the entire population of bacterial cells to reliably distinguish multiple environmental states. We argue that multiple signals and multiple response states could be used to distinguish distinct stages in the development of a bacterial community.

How do bacteria integrate multiple cell-to-cell communication signals? Information from two signaling molecules is combined in a strictly additive way with equal weight from each signal.

Negative feedback loops involving small regulatory RNAs precisely control the Vibrio harveyi quorum-sensing response

Quorum-sensing (QS) bacteria assess population density through secretion and detection of molecules called autoinducers (AIs). We identify and characterize two Vibrio harveyi negative feedback loops that facilitate precise transitions between low-cell-density (LCD) and high-cell-density (HCD) states. The QS central regulator LuxO autorepresses its own transcription, and the Qrr small regulatory RNAs (sRNAs) posttranscriptionally repress luxO. Disrupting feedback increases the concentration of AIs required for cells to transit from LCD to HCD QS modes. Thus, the two cooperative negative feedback loops determine the point at which V. harveyi has reached a quorum and control the range of AIs over which the transition occurs. Negative feedback regulation also constrains the range of QS output by preventing sRNA levels from becoming too high and preventing luxO mRNA levels from reaching zero. We suggest that sRNA-mediated feedback regulation is a network design feature that permits fine-tuning of gene regulation and maintenance of homeostasis.

Prebiotic-Induced Anti-tumor Immunity Attenuates Tumor Growth

Growing evidence supports the importance of gut microbiota in the control of tumor growth and response to therapy. Here, we select prebiotics that can enrich bacterial taxa that promote anti-tumor immunity. Addition of the prebiotics inulin or mucin to the diet of C57BL/6 mice induces anti-tumor immune responses and inhibition of BRAF mutant melanoma growth in a subcutaneously implanted syngeneic mouse model. Mucin fails to inhibit tumor growth in germ-free mice, indicating that the gut microbiota is required for the activation of the anti-tumor immune response. Inulin and mucin drive distinct changes in the microbiota, as inulin, but not mucin, limits tumor growth in syngeneic mouse models of colon cancer and NRAS mutant melanoma and enhances the efficacy of a MEK inhibitor against melanoma while delaying the emergence of drug resistance. We highlight the importance of gut microbiota in anti-tumor immunity and the potential therapeutic role for prebiotics in this process.

The coding and noncoding architecture of the Caulobacter crescentus genome

Caulobacter crescentus undergoes an asymmetric cell division controlled by a genetic circuit that cycles in space and time. We provide a universal strategy for defining the coding potential of bacterial genomes by applying ribosome profiling, RNA-seq, global 5′-RACE, and liquid chromatography coupled with tandem mass spectrometry (LC-MS) data to the 4-megabase C. crescentus genome. We mapped transcript units at single base-pair resolution using RNA-seq together with global 5′-RACE. Additionally, using ribosome profiling and LC-MS, we mapped translation start sites and coding regions with near complete coverage. We found most start codons lacked corresponding Shine-Dalgarno sites although ribosomes were observed to pause at internal Shine-Dalgarno sites within the coding DNA sequence (CDS). These data suggest a more prevalent use of the Shine-Dalgarno sequence for ribosome pausing rather than translation initiation in C. crescentus. Overall 19% of the transcribed and translated genomic elements were newly identified or significantly improved by this approach, providing a valuable genomic resource to elucidate the complete C. crescentus genetic circuitry that controls asymmetric cell division.

Caulobacter crescentus is a model system for studying asymmetric cell division, a fundamental process that, through differential gene expression in the two daughter cells, enables the generation of cells with different fates. To explore how the genome directs and maintains asymmetry upon cell division, we performed a coordinated analysis of multiple genomic and proteomic datasets to identify the RNA and protein coding features in the C. crescentus genome. Our integrated analysis identifies many new genetic regulatory elements, adding significant regulatory complexity to the C. crescentus genome. Surprisingly, 75.4% of protein coding genes lack a canonical translation initiation sequence motif (the Shine-Dalgarno site) which hybridizes to the 3′ end of the ribosomal RNA allowing translation initiation. We find Shine-Dalgarno sites primarily inside of genes where they cause translating ribosomes to pause, possibly allowing nascent proteins to correctly fold. With our detailed map of genomic transcription and translation elements, a systems view of the genetic network that controls asymmetric cell division is within reach.

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA

The HLA gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short-read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. Here, we introduce an algorithm, xHLA, that iteratively refines the mapping results at the amino acid level to achieve 99-100% four-digit typing accuracy for both class I and II HLA genes, taking only [Formula: see text]3 min to process a 30× whole-genome BAM file on a desktop computer.

In vitro cellular toxicity predicts Pseudomonas aeruginosa virulence in lung infections

The role of quorum sensing by Pseudomonas aeruginosa in producing cytotoxicity has not been fully investigated. Strains of P. aeruginosa have been characterized as having an invasive or a cytotoxic phenotype (S. M. J. Fleiszig et al., Infect. Immun. 65:579-586, 1997). We noted that the application of a large inoculum of the invasive strain 6294 caused cytotoxicity of cultured epithelial cells. To investigate this dose-related cytotoxicity, we compared the behavior of 6294 to that of another invasive strain, PAO1, and determined whether the cytotoxicity could be related to quorum sensing. Both invasive strains, 6294 and PAO1, appear to have quorum-sensing systems that were operative when large doses of bacteria were applied to cultured lung epithelial cells or instilled into the lungs of animals. Nonetheless, only 6294 was cytotoxic. Cytotoxicity induced by 6294 correlated with increased elastase production. These experiments suggest that there are multiple mechanisms for the induction of cytotoxicity, pathology, and mortality in vivo. However, in vivo cytotoxicity and mortality, but not pathology, could be predicted by quantitative in vitro cellular damage experiments utilizing a range of bacteria-to-cell ratios. It appears that quorum sensing may inversely correlate with virulence in that strains that produced PAI [N-(3-oxododecanoyl) homoserine lactone] also appeared to attract more polymorphonuclear leukocytes in vivo and were possibly eliminated more quickly. In addition, exoproduct production in bacteriological medium in vitro may differ significantly from exoproduct expression from infections in vivo or during cocultivation of bacteria with tissue culture cells.

Organ donation: key factors influencing families' decision-making

AIM

To clarify the decision-making and bereavement needs of family members who had organ donation discussed with them; to provide a rationale for further preparation of professionals involved in this sensitive work.

METHODS

This work used a 3-year longitudinal design. A sample of 49 family members who had donation discussed with them, were recruited. At 3 to 5, 13 to 15, and 18 to 26 months postbereavement, face-to-face interviews and two, self-completed; psychometric measures, the Beck Depression Inventory II and the Grief Experience Inventory, were used with participants who chose to donate. Single interviews were carried out with participants who declined donation. Data were analyzed using a comparative, thematic approach and multivariate statistics, focusing on detection of important similarities and differences between cases.

FINDINGS

Four main categories were identified that illustrated the issues that influenced families' ability to agree or decline donation and their perception of the decision-making process. The categories were concerns about knowledge of the deceased's donation wish, views held by the extended family about donation, giving meaning to the death and events that occurred in the hospital that were perceived as positive or negative. The role of children in the decision-making about organ donation was highlighted. In conclusion, hospital care affected participants' donation decision-making and appeared to impact on subsequent grief. To facilitate decision-making and bereavement that is uncomplicated by questions about brain injury and subsequent death, families needed time to understand the information given, care in the way and context that information was shared and attention to their emotional needs.

Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6

5-methylcytosine (m⁵C) modifications of RNA are ubiquitous in nature and play important roles in many biological processes such as protein translational regulation, RNA processing and stress response. Aberrant expressions of RNA:m⁵C methyltransferases are closely associated with various human diseases including cancers. However, no structural information for RNA-bound RNA:m⁵C methyltransferase was available until now, hindering elucidation of the catalytic mechanism behind RNA:m⁵C methylation. Here, we have solved the structures of NSun6, a human tRNA:m⁵C methyltransferase, in the apo form and in complex with a full-length tRNA substrate. These structures show a non-canonical conformation of the bound tRNA, rendering the base moiety of the target cytosine accessible to the enzyme for methylation. Further biochemical assays reveal the critical, but distinct, roles of two conserved cysteine residues for the RNA:m⁵C methylation. Collectively, for the first time, we have solved the complex structure of a RNA:m5C methyltransferase and addressed the catalytic mechanism of the RNA:m⁵C methyltransferase family, which may allow for structure-based drug design toward RNA:m⁵C methyltransferase–related diseases.

Taxonomic signatures of cause-specific mortality risk in human gut microbiome

The collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases. In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterised due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data. Here, we analyse the long-term association between gut microbiome variation and mortality in a well-phenotyped and representative population cohort from Finland (n = 7211). We report robust taxonomic and functional microbiome signatures related to the Enterobacteriaceae family that are associated with mortality risk during a 15-year follow-up. Our results extend previous cross-sectional studies, and help to establish the basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status.

The development of a method for comparative costing of individual intensive care units. The Intensive Care Working Group on Costing

Intensive care is one of the most costly areas of hospital care. Unfortunately, because of the diversity of case mix, costing intensive care is difficult. Many described costing methods previously are limited by being cumbersome, laborious to apply and expensive. The aim of this study was to develop a method for costing intensive care which can be applied with ease but facilitate meaningful cost comparisons between intensive care units. The method developed was based on cost blocks where the major components were identified and costed in a 'top-down' manner. Using strict definitions, the cost blocks attempted to measure the costs of equipment, estates, nonclinical support services (such as hospital management costs), clinical support services (such as physiotherapy, laboratory services), consumables (such as drugs, fluids and disposables) and staff. The study found that clinical support services, consumables and staff costs accounted for approximately 85% of the total costs.

Ecological-health risks assessment and source apportionment of heavy metals in agricultural soils around a super-sized lead-zinc smelter with a long production history, in China

Smelting activities are considered as the primary cause of heavy metal (HM) accumulation in soils, and the human health around the smelter has been a great concern worldwide. In this study, a total of 242 agricultural soil samples were collected around a large scale Pb/Zn smelter in China, and eight HMs (As, Cd, Cr, Cu, Hg, Ni, Pb and Zn) were analyzed to assess HMs status, ecological -health risks, and identify source. Monte Carlo simulation was utilized to evaluate the probabilistic health risks, and positive matrix factorization (PMF) was employed to identify sources. The results revealed the average contents of five heavy metals (Cd 5.28 mg/kg, Pb 203.36 mg/kg, Hg 0.39 mg/kg, Zn 293.45 mg/kg, Cu 37.14 mg/kg) are higher than their background values in Hunan province. Cd had the highest mean pollution index (PI) of 41.8 and the greatest average ecological risk index (E_r) of 1256.34, indicating that Cd was the primary enriched pollutant and had a higher ecological risk than other HMs. The mean hazard index (HI) through exposure to eight HMs was 2.95E-01 and 9.74E-01 for adults and children, respectively, with 35.94% of HI values for children exceeding the risk threshold of 1. Moreover, the mean total cancer risks (TCR) were 2.75E-05 and 2.37E-04 for adults and children, respectively, with 75.48% of TCR values for children exceeding the guideline value of 1E-04. In addition, the positive matrix factorization results showed smelting activities, natural sources, agricultural activities and atmospheric deposition were the three sources in soils, with the contribution rate of 48.62%, 22.35%, and 29.03%, respectively. The uncertainty analysis of the PMF indicated that the three-factor solution is reliable. This work will provide scientific reference for the comprehensive prevention of soil HM pollution adjacent to the large smelter.

Chloroform Cometabolism by Butane-Grown CF8, Pseudomonas butanovora, and Mycobacterium vaccae JOB5 and Methane-Grown Methylosinus trichosporium OB3b

Chloroform (CF) degradation by a butane-grown enrichment culture, CF8, was compared to that by butane-grown Pseudomonas butanovora and Mycobacterium vaccae JOB5 and to that by a known CF degrader, Methylosinus trichosporium OB3b. All three butane-grown bacteria were able to degrade CF at rates comparable to that of M. trichosporium. CF degradation by all four bacteria required O(inf2). Butane inhibited CF degradation by the butane-grown bacteria, suggesting that butane monooxygenase is responsible for CF degradation. P. butanovora required exogenous reductant to degrade CF, while CF8 and M. vaccae utilized endogenous reductants. Prolonged incubation with CF resulted in decreased CF degradation. CF8 and P. butanovora were more sensitive to CF than either M. trichosporium or M. vaccae. CF degradation by all three butane-grown bacteria was inactivated by acetylene, which is a mechanism-based inhibitor for several monooxygenases. Butane protected all three butane-grown bacteria from inactivation by acetylene, which indicates that the same monooxygenase is responsible for both CF and butane oxidation. CF8 and P. butanovora were able to degrade other chlorinated hydrocarbons, including trichloroethylene, 1,2-cis-dichloroethylene, and vinyl chloride. In addition, CF8 degraded 1,1,2-trichloroethane. The results indicate the potential of butane-grown bacteria for chlorinated hydrocarbon transformation.

Long-term storage and safe retrieval of DNA from microorganisms for molecular analysis using FTA matrix cards

We assessed the potential use of Whatman FTA paper as a device for archiving and long-term storage of bacterial cell suspensions of over 400 bacterial strains representing 61 genera, the molecular applications of immobilised DNA on FTA paper, and tested its microbial inactivation properties. The FTA paper extracted bacterial DNA is of sufficiently high quality to successfully carryout the molecular detection of several key genes including 16S rRNA, esp (Enterococcus surface protein), Bft (Bacteroides fragilis enterotoxin) and por (porin protein) by PCR and for DNA fingerprinting by random amplified polymorphic DNA-PCR (RAPD-PCR). To test the long-term stability of the FTA immobilised DNA, 100 of the 400 archived bacterial samples were randomly selected following 3 years of storage at ambient temperature and PCR amplification was used to monitor its success. All of the 100 samples were successfully amplified using the 16S rDNA gene as a target and confirmed by DNA sequencing. Furthermore, the DNA was eluted into solution from the FTA cards using a new alkaline elution procedure for evaluation by real-time PCR-based assays. The viability of cells retained on the FTA cards varied among broad groups of bacteria. For the more fragile gram-negative species, no viable cells were retained even at high cell densities of between 10(7) and 10(8) colony forming units (cfu) ml(-1), and for the most robust species such as spore-formers and acid-fast bacteria, complete inactivation was achieved at cell densities ranging between 10(1) and 10(4) cfu ml(-1). The inactivation of bacterial cells on FTA cards suggest that this is a safe medium for the storage and transport of bacterial nucleic acids.

Returning to school after heart or heart-lung transplantation: how well do children adjust?

BACKGROUND

Up to 40% of children and adolescents with chronic illness experience school-related problems, including learning difficulties and problems in social adjustment and peer relationships. Despite the life-threatening nature of heart and heart-lung transplantation and the severity of illness, which results in the necessity for surgery, there is little information on the school performance of children after transplantation.

METHODS

Eighty-one children and adolescents were assessed with regard to their academic attainments and behavior at school at regular intervals after heart (n=47) or heart-lung (n=34) transplantation and comparisons made with a group of healthy children.

RESULTS

Cognitive ability and performance on academic attainments were within the normal range and did not change significantly as a function of time since transplant. However, performance was at a significantly lower level than that of the healthy children. Although the prevalence of behavior problems was only 8% at 6 months posttransplant, at 3 years, it had increased to 29% and, at 5 years, it was still 27%. Children with an initial diagnosis of congenital heart disease had more academic and behavioral difficulties than those with either cardiomyopathy or cystic fibrosis.

CONCLUSIONS

A significant number of children who had undergone successful transplantation experienced difficulties at school. Contrary to expectations, educational problems were more prevalent in the medium term, rather than short term, after transplant. Initial diagnosis was a salient factor in posttransplant psychological functioning at school. Early intervention and close liaison with schools is indicated to reduce psychological morbidity and enhance adaptation within the school environment.

Structural basis for itraconazole-mediated NPC1 inhibition

Niemann-Pick C1 (NPC1), a lysosomal protein of 13 transmembrane helices (TMs) and three lumenal domains, exports low-density-lipoprotein (LDL)-derived cholesterol from lysosomes. TMs 3–7 of NPC1 comprise the Sterol-Sensing Domain (SSD). Previous studies suggest that mutation of the NPC1-SSD or the addition of the anti-fungal drug itraconazole abolishes NPC1 activity in cells. However, the itraconazole binding site and the mechanism of NPC1-mediated cholesterol transport remain unknown. Here, we report a cryo-EM structure of human NPC1 bound to itraconazole, which reveals how this binding site in the center of NPC1 blocks a putative lumenal tunnel linked to the SSD. Functional assays confirm that blocking this tunnel abolishes NPC1-mediated cholesterol egress. Intriguingly, the palmitate anchor of Hedgehog occupies a similar site in the homologous tunnel of Patched, suggesting a conserved mechanism for sterol transport in this family of proteins and establishing a central function of their SSDs.

Niemann-Pick C1 (NPC1) exports low-density-lipoprotein (LDL)-derived cholesterol from lysosomes and comporses a Sterol-Sensing Domain (SSD). Here authors report a cryo-EM structure of human NPC1 bound to itraconazole which reveals how this binding site in the center of NPC1 blocks a putative lumenal tunnel linked to the SSD.

Sterols in an intramolecular channel of Smoothened mediate Hedgehog signaling

Smoothened (SMO), a class Frizzled G protein-coupled receptor (class F GPCR), transduces the Hedgehog signal across the cell membrane. Sterols can bind to its extracellular cysteine-rich domain (CRD) and to several sites in the seven transmembrane helices (7-TMs) of SMO. However, the mechanism by which sterols regulate SMO via multiple sites is unknown. Here we determined the structures of SMO-Gi complexes bound to the synthetic SMO agonist (SAG) and to 24(S),25-epoxycholesterol (24(S),25-EC). A novel sterol-binding site in the extracellular extension of TM6 was revealed to connect other sites in 7-TMs and CRD, forming an intramolecular sterol channel from the middle side of 7-TMs to CRD. Additional structures of two gain-of-function variants, SMOD384R and SMOG111C/I496C, showed that blocking the channel at its midpoints allows sterols to occupy the binding sites in 7-TMs, thereby activating SMO. These data indicate that sterol transport through the core of SMO is a major regulator of SMO-mediated signaling.

Measurement of the copy number of the master quorum-sensing regulator of a bacterial cell

Quorum-sensing is the mechanism by which bacteria communicate and synchronize group behaviors. Quantitative information on parameters such as the copy number of particular quorum-sensing proteins should contribute strongly to understanding how the quorum-sensing network functions. Here, we show that the copy number of the master regulator protein LuxR in Vibrio harveyi can be determined in vivo by exploiting small-number fluctuations of the protein distribution when cells undergo division. When a cell divides, both its volume and LuxR protein copy number, N, are partitioned with slight asymmetries. We measured the distribution functions describing the partitioning of the protein fluorescence and the cell volume. The fluorescence distribution is found to narrow systematically as the LuxR population increases, whereas the volume partitioning is unchanged. Analyzing these changes statistically, we determined that N = 80-135 dimers at low cell density and 575 dimers at high cell density. In addition, we measured the static distribution of LuxR over a large (3000) clonal population. Combining the static and time-lapse experiments, we determine the magnitude of the Fano factor of the distribution. This technique has broad applicability as a general in vivo technique for measuring protein copy number and burst size.

Enhanced transverse migration of bacteria by chemotaxis in a porous T-sensor

Subsurface bioremediation is often hindered by the inability to achieve good mixing between injected bacteria and residual contaminants. Chemotaxis, which is the ability of bacteria to migrate preferentially toward higher concentrations of certain chemical attractants, could potentially increase bacterial transport into the contaminated zone. To observe and quantify this chemotactic enhancement to bacterial dispersion transverse to groundwater flow, a microfluidic device--a porous T-sensor-was created. It allowed two streams of equal flow rate to enter side-by-side into a porous channel; the transverse mixing of the two streams was controlled primarily by dispersion. When a suspension of the chemotactic bacteria Escherichia coli HCB1 and a solution of chemical attractant alpha-methylaspartate were injected as the two incoming streams, enhanced bacterial migration into the attractant stream was observed relative to a control experiment with dispersion alone. Chemotaxis was observed under lower flow rates comparable to natural groundwaterflow. The chemotactic response was greater than that predicted by an advection-dispersion equation model using a chemotactic coefficient derived under quiescent experimental conditions, which suggests that flow in porous media may further enhance transverse migration for chemotactic bacteria. This study provided direct evidence of the significance of bacterial chemotactic transverse migration at groundwater flow rates.