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Recent studies of animal metabolism have revealed large numbers of novel metabolites that are involved in all aspects of organismal biology, but it is unclear to what extent metabolomes differ between sexes. Here, using untargeted comparative metabolomics for the analysis of wildtype animals and a series of germline mutants, we show that C. elegans hermaphrodites and males exhibit pervasive metabolomic differences. Several hundred small molecules are produced exclusively or in much larger amounts in one sex, including a host of previously unreported metabolites that incorporate building blocks from nucleoside, carbohydrate, lipid, and amino acid metabolism. A subset of male-enriched metabolites is specifically associated with the presence of a male germline, whereas enrichment of other compounds requires a male soma. Further, we show that one of the male germline-dependent metabolites, an unusual dipeptide incorporating N,N-dimethyltryptophan, accelerates the last stage of larval development in hermaphrodites. Our results serve as a foundation for mechanistic studies of how the genetic sex of soma and germline shape the C. elegans metabolome and provides a blueprint for the discovery of sex-dependent metabolites in other animals.

Untargeted metabolomics via high-resolution mass spectrometry can reveal more than 100,000 molecular features in a single sample, many of which may represent unidentified metabolites, posing significant challenges to data analysis. We here introduce Metaboseek, an open-source analysis platform designed for untargeted comparative metabolomics and demonstrate its utility by uncovering biosynthetic functions of a conserved fat metabolism pathway, α-oxidation, using C. elegans as a model. Metaboseek integrates modules for molecular feature detection, statistics, molecular formula prediction, and fragmentation analysis, which uncovers more than 200 previously uncharacterized α-oxidation-dependent metabolites in an untargeted comparison of wildtype and α-oxidation-defective hacl-1 mutants. The identified metabolites support the predicted enzymatic function of HACL-1 and reveal that α-oxidation participates in metabolism of endogenous β-methyl-branched fatty acids and food-derived cyclopropane lipids. Our results showcase compound discovery and feature annotation at scale via untargeted comparative metabolomics applied to a conserved primary metabolic pathway and suggest a model for the metabolism of cyclopropane lipids.

Excreted small-molecule signals can bias developmental trajectories and physiology in diverse animal species. However, the chemical identity of these signals remains largely obscure. Here we report identification of an unusual N-acylated glutamine derivative, nacq#1, that accelerates reproductive development and shortens lifespan in Caenorhabditis elegans. Produced predominantly by C. elegans males, nacq#1 hastens onset of sexual maturity in hermaphrodites by promoting exit from the larval dauer diapause and by accelerating late larval development. Even at picomolar concentrations, nacq#1 shortens hermaphrodite lifespan, suggesting a trade-off between reproductive investment and longevity. Acceleration of development by nacq#1 requires chemosensation and is dependent on three homologs of vertebrate steroid hormone receptors. Unlike ascaroside pheromones, which are restricted to nematodes, fatty acylated amino acid derivatives similar to nacq#1 have been reported from humans and invertebrates, suggesting that related compounds may serve signaling functions throughout metazoa.

Many bacterivorous and parasitic nematodes secrete signaling molecules called ascarosides that play a central role regulating their behavior and development. Combining stable-isotope labeling and mass spectrometry-based comparative metabolomics, here we show that ascarosides are taken up from the environment and metabolized by a wide range of phyla, including plants, fungi, bacteria, and mammals, as well as nematodes. In most tested eukaryotes and some bacteria, ascarosides are metabolized into derivatives with shortened fatty acid side chains, analogous to ascaroside biosynthesis in nematodes. In plants and C. elegans, labeled ascarosides were additionally integrated into larger, modular metabolites, and use of different ascaroside stereoisomers revealed the stereospecificity of their biosynthesis. The finding that nematodes extensively metabolize ascarosides taken up from the environment suggests that pheromone editing may play a role in conspecific and interspecific interactions. Moreover, our results indicate that plants, animals, and microorganisms may interact with associated nematodes via manipulation of ascaroside signaling.

We describe a mathematical model for the aggregation of starved first-stage C elegans larvae (L1s). We propose that starved L1s produce and respond chemotactically to two labile diffusible chemical signals, a short-range attractant and a longer range repellent. This model takes the mathematical form of three coupled partial differential equations, one that describes the movement of the worms and one for each of the chemical signals. Numerical solution of these equations produced a pattern of aggregates that resembled that of worm aggregates observed in experiments. We also describe the identification of a sensory receptor gene, srh–2, whose expression is induced under conditions that promote L1 aggregation. Worms whose srh–2 gene has been knocked out form irregularly shaped aggregates. Our model suggests this phenotype may be explained by the mutant worms slowing their movement more quickly than the wild type.Author summaryAmong the most complex of animal behaviors are collective behaviors, in which animals interact with each other so as to produce large-scale organization. Starved first-stage larvae of the nematode Caenorhabditis elegans exhibit such a behavior: they come together to form aggregates of several hundred worms. How and why they do this are unknown. To address these questions, we developed a mathematical model of starved L1 aggregation. This model reproduced the main features of the behavior.

Few nucleoside-derived natural products have been identified from animals, despite the ubiquity of nucleosides in living organisms. Here, we use a combination of synthesis and the emerging electron microscopy technique microcrystal electron diffraction to determine the structures of several N3-(β-glucopyranosyl)uric acid derivatives in Caenorhabditis elegans. These noncanonical gluconucleosides further integrate an ascaroside moiety, for which we present a shortened synthetic route. The production of a phosphorylated gluconucleoside is influenced by evolutionarily conserved insulin signaling.

Few nucleoside-derived natural products have been identified from animals, despite the ubiquity of nucleosides in living organisms. Here, we use a combination of synthesis and the emerging electron microscopy technique microcrystal electron diffraction to determine the structures of several N(3)-(β-glucopyranosyl)uric acid derivatives in Caenorhabditis elegans. These noncanonical gluconucleosides further integrate an ascaroside moiety, for which we present a shortened synthetic route. The production of a phosphorylated gluconucleoside is influenced by evolutionarily conserved insulin signaling.

We attempt to explain the aggregation behavior of starved C. elegans L1s (Artyukhin et al., 2015) by a variation of the Keller-Segel chemotaxis model (1970). Each worm releases a diffusible, unstable attractant. The worms chemotax towards the attractant. By using a continuous density function to approximate the spatial distribution of worms, behavior may be described by a nonlinear system of partial differential equations. To determine whether such a model can account for C. elegans L1 behavior, we solve this PDE system numerically. In the original Keller-Segel model, density is unbounded, leading to unrealistic results. We modified the model in such a way as to limit the maximum density. We also developed numerical methods designed to work well near equilibrium. With these changes our model can reproduce some but not all aspects of the behavior.

We describe a mathematical model for the aggregation of starved first-stage C elegans larvae (L1s). We propose that starved L1s produce and respond chemotactically to two labile diffusible chemical signals, a short-range attractant and a longer range repellent. This model takes the mathematical form of three coupled partial differential equations, one that describes the movement of the worms and one for each of the chemical signals. Numerical solution of these equations produced a pattern of aggregates that resembled that of worm aggregates observed in experiments. We also describe the identification of a sensory receptor gene, srh–2, whose expression is induced under conditions that promote L1 aggregation. Worms whose srh–2 gene has been knocked out form irregularly shaped aggregates. Our model suggests this phenotype may be explained by the mutant worms slowing their movement more quickly than the wild type., Author summary Among the most complex of animal behaviors are collective behaviors, in which animals interact with each other so as to produce large-scale organization. Starved first-stage larvae of the nematode Caenorhabditis elegans exhibit such a behavior: they come together to form aggregates of several hundred worms. How and why they do this are unknown. To address these questions, we developed a mathematical model of starved L1 aggregation. This model reproduced the main features of the behavior.

One Sentence SummaryHPLC-MS metabolite profiling of maize seedlings, in combination with genome-wide association studies, identifies numerous quantitative trait loci that influence the accumulation of foliar metabolites.AbstractCultivated maize (Zea mays) retains much of the genetic and metabolic diversity of its wild ancestors. Non-targeted HPLC-MS metabolomics using a diverse panel of 264 maize inbred lines identified a bimodal distribution in the prevalence of foliar metabolites. Although 15% of the detected mass features were present in >90% of the inbred lines, the majority were found in

Peroxisomal β-oxidation (pβo) is a highly conserved fat metabolism pathway involved in the biosynthesis of diverse signaling molecules in animals and plants. In Caenorhabditis elegans, pβo is required for the biosynthesis of the ascarosides, signaling molecules that control development, lifespan, and behavior in this model organism. Via comparative mass spectrometric analysis of pβo mutants and wildtype, we show that pβo in C. elegans and the satellite model P. pacificus contributes to life stage-specific biosynthesis of several hundred previously unknown metabolites. The pβo-dependent portion of the metabolome is unexpectedly diverse, e.g., intersecting with nucleoside and neurotransmitter metabolism. Cell type-specific restoration of pβo in pβo-defective mutants further revealed that pβo-dependent submetabolomes differ between tissues. These results suggest that interactions of fat, nucleoside, and other primary metabolism pathways can generate structural diversity reminiscent of that arising from combinatorial strategies in microbial natural product biosynthesis.

Summary In the nematodes Caenorhabditis elegans and Pristionchus pacificus, a modular library of small molecules control behavior, lifespan, and development. However, little is known about the final steps of their biosynthesis, in which diverse building blocks from primary metabolism are attached to glycosides of the dideoxysugar ascarylose, the ascarosides. We combine metabolomic analysis of natural isolates of P. pacificus with genome-wide association mapping to identify a putative carboxylesterase, Ppa-uar-1, that is required for attachment of a pyrimidine-derived moiety in the biosynthesis of ubas#1, a major dauer pheromone component. Comparative metabolomic analysis of wild-type and Ppa-uar-1 mutants showed that Ppa-uar-1 is required specifically for the biosynthesis of ubas#1 and related metabolites. Heterologous expression of Ppa-UAR-1 in C. elegans yielded a non-endogenous ascaroside, whose structure confirmed that Ppa-uar-1 is involved in modification of a specific position in ascarosides. Our study demonstrates the utility of natural variation-based approaches for uncovering biosynthetic pathways.

The nematode Caenorhabditis elegans uses simple building blocks from primary metabolism and a strategy of modular assembly to build a great diversity of signaling molecules, the ascarosides, which function as a chemical language in this model organism. In the ascarosides, the dideoxysugar ascarylose serves as a scaffold to which diverse moieties from lipid, amino acid, neurotransmitter, and nucleoside metabolism are attached. However, the mechanisms that underlie the highly specific assembly of ascarosides are not understood. We show that the acyl-CoA synthetase ACS-7, which localizes to lysosome-related organelles, is specifically required for the attachment of different building blocks to the 4′-position of ascr#9. We further show that mutants lacking lysosome-related organelles are defective in the production of all 4′-modified ascarosides, thus identifying the waste disposal system of the cell as a hotspot for ascaroside biosynthesis.

Small-molecule signaling in nematode dauer formation has emerged as a major model to study chemical communication in development and evolution. Developmental arrest as nonfeeding and stress-resistant dauer larvae represents the major survival and dispersal strategy. Detailed studies in Caenorhabditis elegans and Pristionchus pacificus revealed that small-molecule communication changes rapidly in evolution resulting in extreme structural diversity of small-molecule compounds. In C. elegans, a blend of ascarosides constitutes the dauer pheromone, whereas the P. pacificus dauer pheromone includes additional paratosides and integrates building blocks from diverse primary metabolic pathways. Despite this complexity of small-molecule structures and functions, little is known about the biosynthesis of small molecules in nematodes outside C. elegans. Here, we show that the genes encoding enzymes of the peroxisomal β-oxidation pathway involved in small-molecule biosynthesis evolve rapidly, including gene duplications and domain switching. The thiolase daf-22, the most downstream factor in C. elegans peroxisomal β-oxidation, has duplicated in P. pacificus, resulting in Ppa-daf-22.1, which still contains the sterol-carrier-protein (SCP) domain that was lost in C. elegans daf-22, and Ppa-daf-22.2. Using the CRISPR/Cas9 system, we induced mutations in both P. pacificus daf-22 genes and identified an unexpected complexity of functional conservation and divergence. Under well-fed conditions, ascaroside biosynthesis proceeds exclusively via Ppa-daf-22.1. In contrast, starvation conditions induce Ppa-daf-22.2 activity, resulting in the production of a specific subset of ascarosides. Gene expression studies indicate a reciprocal up-regulation of both Ppa-daf-22 genes, which is, however, independent of starvation. Thus, our study reveals an unexpected functional complexity of dauer development and evolution.

We report a hybrid bionanoelectronic transistor that has a local ATP-powered protein gate. ATP-dependent activity of a membrane ion pump, Na(+)/K(+)-ATPase, embedded in a lipid membrane covering the carbon nanotube, modulates the transistor output current by up to 40%. The ion pump gates the device by shifting the pH of the water layer between the lipid bilayer and nanotube surface. This transistor is a versatile bionanoelectronic platform that can incorporate other membrane proteins.

Rapid progress in materials science and electrical engineering has led to the development of miniature electronic platforms that have devices and components as small as the main components of live cells. These developments open up an exciting possibility of building integrated systems in which electronic and biological components function side-by-side. However, to realize this vision of bionanoelectronics, researchers need to overcome a number of challenges ranging from materials incompatibility to drastically different operation modes. Fortunately, recent developments in biosensing, and device-level and tissue-level integration with nanomaterials have started to address these challenges.

Molecular force spectroscopy experiments probe the stochastic kinetics of individual intermolecular bond rupture under external loading. While there are numerous examples describing rupture kinetics under fast-loading, far from equilibrium conditions, bond rupture at slow loading rates near equilibrium conditions is seldom explored. We use an analytical and numerical approach to show that rupture forces in this qualitatively different regime reach an equilibrium plateau value that is a function of the probe stiffness and the free energy difference between the bound and dissociated state of the bond. Chemical force microscopy measurements of the interaction between a small number of well-defined COOH functional groups confirm these predictions and show the expected scaling of the force plateau values with the square root of the probe stiffness. Finally, we discuss the implications of these results for the interpretation of force spectroscopy experiments.

Pancreatic ductal adenocarcinoma (PDA) is the fourth leading cause of cancer-related deaths in the United States, and is projected to be second by 2025. It has the worst survival rate among all major cancers. Two pressing needs for extending life expectancy of affected individuals are the development of new approaches to identify improved therapeutics, addressed herein, and the identification of early markers. PDA advances through a complex series of intercellular and physiological interactions that drive cancer progression in response to organ stress, organ failure, malnutrition, and infiltrating immune and stromal cells. Candidate drugs identified in organ culture or cell-based screens must be validated in preclinical models such as KIC (p48Cre;LSL-KrasG12D;Cdkn2af/f) mice, a genetically engineered model of PDA in which large aggressive tumors develop by 4 weeks of age. We report a rapid, systematic and robust in vivo screen for effective drug combinations to treat Kras-dependent PDA. Kras mutations occur early in tumor progression in over 90% of human PDA cases. Protein kinase and G-protein coupled receptor (GPCR) signaling activates Kras. Regulators of G-protein signaling (RGS) proteins are coincidence detectors that can be induced by multiple inputs to feedback-regulate GPCR signaling. We crossed Rgs16::GFP bacterial artificial chromosome (BAC) transgenic mice with KIC mice and show that the Rgs16::GFP transgene is a KrasG12D-dependent marker of all stages of PDA, and increases proportionally to tumor burden in KIC mice. RNA sequencing (RNA-Seq) analysis of cultured primary PDA cells reveals characteristics of embryonic progenitors of pancreatic ducts and endocrine cells, and extraordinarily high expression of the receptor tyrosine kinase Axl, an emerging cancer drug target. In proof-of-principle drug screens, we find that weanling KIC mice with PDA treated for 2 weeks with gemcitabine (with or without Abraxane) plus inhibitors of Axl signaling (warfarin and BGB324) have fewer tumor initiation sites and reduced tumor size compared with the standard-of-care treatment. Rgs16::GFP is therefore an in vivo reporter of PDA progression and sensitivity to new chemotherapeutic drug regimens such as Axl-targeted agents. This screening strategy can potentially be applied to identify improved therapeutics for other cancers., Editor's choice - Drug Discovery Collection: The study describes a rapid in vivo screen for novel strategies to treat pancreatic ductal adenocarcinoma (PDA).

We describe a new type of collective behavior in C. elegans nematodes, aggregation of starved L1 larvae. Shortly after hatching in the absence of food, L1 larvae arrest their development and disperse in search for food. In contrast, after two or more days without food, the worms change their behavior—they start to aggregate. The aggregation requires a small amount of ethanol or acetate in the environment. In the case of ethanol, it has to be metabolized, which requires functional alcohol dehydrogenase sodh-1. The resulting acetate is used in de novo fatty acid synthesis and some of the newly made fatty acids are then derivatized to glycerophosphoethanolamides and released into the surrounding medium. We examined several other Caenorhabditis species and found an apparent correlation between propensity of starved L1s to aggregate and density dependence of their survival in starvation. Aggregation locally concentrates worms and may help the larvae to survive long starvation. This work demonstrates how presence of ethanol or acetate, relatively abundant small molecules in the environment, induces collective behavior in C. elegans associated with different survival strategies.

Neuropeptides are essential for the regulation of appetite. Here we show that neuropeptides could regulate feeding in mutants that lack neurotransmission from the motor neurons that stimulate feeding muscles. We identified nlp-24 by an RNAi screen of 115 neuropeptide genes, testing whether they affected growth. NLP-24 peptides have a conserved YGGXX sequence, similar to mammalian opioid neuropeptides. In addition, morphine and naloxone respectively stimulated and inhibited feeding in starved worms, but not in worms lacking NPR-17, which encodes a protein with sequence similarity to opioid receptors. Opioid agonists activated heterologously expressed NPR-17, as did at least one NLP-24 peptide. Worms lacking the ASI neurons, which express npr-17, did not response to naloxone. Thus, we suggest that Caenorhabditis elegans has an endogenous opioid system that acts through NPR-17, and that opioids regulate feeding via ASI neurons. Together, these results suggest C. elegans may be the first genetically tractable invertebrate opioid model. DOI: http://dx.doi.org/10.7554/eLife.06683.001, eLife digest When and how much an animal eats is controlled by a complex web of signals that are produced by the animal's body and brain. Molecules called opioid neuropeptides are among these signals, and act to control eating in mammals by binding to receptors in the brain and body. These receptors can also bind to similar molecules called opiates (such as morphine); opiates are amongst the oldest drugs used by humans and have diverse effects ranging from pain relief to addiction. While the activities of opiates and opioid neuropeptides have been studied in mammals, relatively little is known about opioid signaling in simpler animals. The mechanisms behind many biological processes have been investigated using a worm called C. elegans as a model system because it has a simple body plan and its genes can be altered easily. The feeding behavior of C. elegans is no exception. This worm feeds by contracting and relaxing its pharyngeal muscle to move food into its gut. When the worms sense that food is available, this ‘pharyngeal pumping’ is regulated by one type of nerve cell. Slow pharyngeal pumping also continues in starved worms when food is not available, possibly to encourage them to eat new potential sources of food. However, this slow pumping does not require the same type of nerve cell. Cheong et al. hypothesized that the slow pumping in starved worms might depend on neuropeptide signaling instead, and have now tested this idea using engineered worms that made lower levels of a number of these molecules. The experiments uncovered a molecule called NLP-24 that promotes the slow pharyngeal pumping. This molecule is similar to opioid neuropeptides found in mammals. Worms that made less NLP-24 than normal grew more slowly; this suggests that they had problems feeding. Moreover, the levels of NLP-24 were found to increase in normal worms soon after they were deprived of food. Further experiments revealed the identity of the receptor for this molecule, which is also similar to mammalian opioid receptors. The discovery that opioid signaling is involved in C. elegans' feeding behavior may well, in future, also help to identify new molecular players involved in opioid signaling. Further studies might also help the search for ways to reduce the problematic side-effects that limit the usefulness of opiate drugs as medicines. DOI: http://dx.doi.org/10.7554/eLife.06683.002

We report gas and water flow measurements through microfabricated membranes in which aligned carbon nanotubes with diameters of less than 2 nanometers serve as pores. The measured gas flow exceeds predictions of the Knudsen diffusion model by more than an order of magnitude. The measured water flow exceeds values calculated from continuum hydrodynamics models by more than three orders of magnitude and is comparable to flow rates extrapolated from molecular dynamics simulations. The gas and water permeabilities of these nanotube-based membranes are several orders of magnitude higher than those of commercial polycarbonate membranes, despite having pore sizes an order of magnitude smaller. These membranes enable fundamental studies of mass transport in confined environments, as well as more energy-efficient nanoscale filtration.

Because of their wide occurrence, specific functions, and properties, solid-supported phospholipid bilayers are often incorporated in biosensors. The stability of these bilayers in aqueous environments is of utmost importance in sensing. By using surface plasmon resonance, we obtained experimental results for corrosive effects of chemicals on bilayers of 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) supported on self-assembled monolayers of thiol on gold. The POPC supported bilayers were treated with aqueous solutions of three surfactants, which were anionic (sodium dodecyl sulfate, SDS), cationic (cetyltrimethylammonium bromide, CTAB), and nonionic (Triton X-100), as well as an alcohol (propanol-2), a strong acid (HCl), and a base (NaOH). For all of the surfactants studied, complete corrosion of the bilayer (i.e., complete bilayer removal) occurred at surfactant concentrations near the critical micelle concentration (cmc). However, onset of bilayer solubilization is observed at surfactant concentrations...

Using sodium dodecyl sulfate (SDS) as a surfactant and poly(diallyldimethylammonium chloride) (PDDA) as a polyelectrolyte, we formed a surfactant−polymer complex on a model surface of a positively charged 2-aminoethanethiol (cysteamine) self-assembled monolayer on gold. The complex formation is achieved by first SDS adsorption on cysteamine and subsequent adsorption of PDDA on the preformed SDS layer. Successful deposition of the PDDA layer on SDS without noticeable surfactant desorption shows that the complex formation is a fast process. The presence of SDS−PDDA complex on a cysteamine-modified gold substrate was observed by surface plasmon resonance (SPR) and Fourier transformed infrared spectroscopy. The thicknesses obtained from the SPR data were 1.5 nm for SDS and 1.1 nm for PDDA. Concentrations of SDS and PDDA in the parent solutions necessary to yield the complex upon adsorption were determined.

The functional repertoire of a network is determined by its topology. Ma et al. (2009) analyze enzyme networks with three nodes and take a reverse-engineering approach to ask how many core network topologies can establish perfect adaptation, the ability to reset after perturbation. Surprisingly, the answer is just two.

Availability of food is often a limiting factor in nature. Periods of food abundance are followed by times of famine, often in unpredictable patterns. Reliable information about the environment is a critical ingredient of successful survival strategy. One way to improve accuracy is to integrate information communicated by other organisms. To test whether such exchange of information may play a role in determining starvation survival strategies, we studied starvation of L1 larvae in C. elegans and other Caenorhabditis species. We found that some species in genus Caenorhabditis, including C. elegans, survive longer when starved at higher densities, while for others survival is independent of the density. The density effect is mediated by chemical signal(s) that worms release during starvation. This starvation survival signal is independent of ascarosides, a class of small molecules widely used in chemical communication of C. elegans and other nematodes.

The ascarosides, small-molecule signals derived from combinatorial assembly of primary metabolism-derived building blocks, play a central role in Caenorhabditis elegans biology and regulate many aspects of development and behavior in this model organism as well as in other nematodes. Using HPLCMS/ MS-based targeted metabolomics, we identified novel ascarosides incorporating a side chain derived from succinylation of the neurotransmitter octopamine. These compounds, named osas#2, osas#9, and osas#10, are produced predominantly by L1 larvae, where they serve as part of a dispersal signal, whereas these ascarosides are largely absent from the metabolomes of other life stages. Investigating the biogenesis of these octopamine- derived ascarosides, we found that succinylation represents a previously unrecognized pathway of biogenic amine metabolism. At physiological concentrations, the neurotransmitters serotonin, dopamine, and octopamine are converted to a large extent into the corresponding succinates, in addition to the previously described acetates. Chemically, bimodal deactivation of biogenic amines via acetylation and succinylation parallels posttranslational modification of proteins via acetylation and succinylation of L-lysine. Our results reveal a small-molecule connection between neurotransmitter signaling and interorganismal regulation of behavior and suggest that ascaroside biosynthesis is based in part on co-option of degradative biochemical pathways.

Neutrophil polarity relies on local, mutual inhibition to segregate incompatible signaling circuits to the leading and trailing edges. Mutual inhibition alone should lead to cells having strong fronts and weak backs or vice versa. However, analysis of cell-to-cell variation in human neutrophils revealed that back polarity remains consistent despite changes in front strength. How is this buffering achieved? Pharmacological perturbations and mathematical modeling revealed a functional role for microtubules in buffering back polarity by mediating positive, long-range crosstalk from front to back; loss of microtubules inhibits buffering and results in anticorrelation between front and back signaling. Furthermore, a systematic, computational search of network topologies found that a long-range, positive front-to-back link is necessary for back buffering. Our studies suggest a design principle that can be employed by polarity networks: short-range mutual inhibition establishes distinct signaling regions, after which directed long-range activation insulates one region from variations in the other. © 2013 The Authors.

In an attempt to develop an alternative method to extract DNA from complex samples with much improved sensitivity and efficiency, here we report a proof-of-concept work for a new DNA extraction method using DNA methyltransferase (Mtase) and "click" chemistry. According to our preliminary data, the method has improved the current methods by (i) employing a DNA-specific enzyme, TaqI DNA Mtase, for improved selectivity, and by (ii) capturing the DNA through covalent bond to the functionalized surface, enabling a broad range of treatments yielding the final sample DNA with minimal loss and higher purity such that it will be highly compatible with downstream analyses. By employing Mtase, a highly DNA specific and efficient enzyme, and click chemistry, we demonstrated that as little as 0.1 fg of λ-DNA (close to copy number 1) was captured on silica (Si)-based beads by forming a covalent bond between an azide group on the surface and the propargyl moiety on the DNA. This method holds promise in versatile applications where extraction of minute amounts of DNA plays critical roles such as basic and applied molecular biology research, bioforensic and biosecurity sciences, and state-of-the-art detection methods.

Biological molecules perform a sophisticated array of transport and signaling functions that rival anything that the modern electronics industry can create. Incorporating such building blocks into nanoelectronic devices could enable new generations of electronic circuits that use biomimetics to perform complicated tasks. Such types of circuits could ultimately blur the interface between living biological organisms and synthetic structures. Our laboratory has recently developed a versatile and flexible platform for integrating ion channels and pumps into single-walled carbon nanotube (SWNT) and silicon nanowire (SiNW) transistor devices, in which membrane proteins are embedded in a lipid bilayer shell covering the nanotube or nanowire component. In this chapter, we provide details for the fabrication of these devices and outline procedures for incorporating biological molecules into them. In addition, we also provide several examples of the use of these devices to couple biological transport to electronic signaling.

Biological molecules perform a sophisticated array of transport and signaling functions that rival anything that the modern electronics industry can create. Incorporating such building blocks into nanoelectronic devices could enable new generations of electronic circuits that use biomimetics to perform complicated tasks. Such types of circuits could ultimately blur the interface between living biological organisms and synthetic structures. Our laboratory has recently developed a versatile and flexible platform for integrating ion channels and pumps into single-walled carbon nanotube (SWNT) and silicon nanowire (SiNW) transistor devices, in which membrane proteins are embedded in a lipid bilayer shell covering the nanotube or nanowire component. In this chapter, we provide details for the fabrication of these devices and outline procedures for incorporating biological molecules into them. In addition, we also provide several examples of the use of these devices to couple biological transport to electronic signaling.

We report a versatile biofunctional subwavelength photonic device platform for real-time detection of biological molecules. Our devices contain lipid bilayer membranes fused onto metal oxide nanowire waveguides stretched across polymeric flow channels. The lipid bilayers incorporating target receptors are submersed in the propagating evanescent field of the optical cavity. We show that the lipid bilayers in our devices are continuous, have very high mobile fraction, and are resistant to fouling. We also demonstrate that our platform allows rapid membrane exchange. Finally, we use this device to detect the hybridization of specific DNA target sequences in solution to complementary probe DNA strands anchored to the lipid bilayer. This evanescent wave sensing architecture holds great potential for portable, all-optical detection systems.

Curved lipid membranes are ubiquitous in living systems and play an important role in many biological processes. To understand how curvature and lipid composition affect membrane formation and fluidity, we have assembled and studied mixed 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) supported lipid bilayers on amorphous silicon nanowires grown around carbon nanotube cores with controlled wire diameters ranging from 20 to 200 nm. We found that lipid vesicles fused onto nanowire substrates and formed continuous bilayers for all DOPC-DOPE mixtures tested (with the DOPE content of up to 30%). Our measurements demonstrate that nanowire-supported bilayers are mobile, exhibit fast recovery after photobleaching, and have a low concentration of defects. Lipid diffusion coefficients in these high-curvature tubular membranes are comparable to the values reported for flat supported bilayers and increase slightly with decreasing nanowire diameter. A free space diffusion model adequately describes the effect of bilayer curvature on the lipid mobility for nanowire substrates with diameters greater than 50 nm, but shows significant deviations from the experimental values for smaller diameter nanowires.

Carbon nanotubes1 display a consummate blend of materials properties that affect applications ranging from nanoelectronic circuits2 and biosensors3 to field emitters4 and membranes5. These applications use the non-covalent interactions between the nanotubes and chemical functionalities6, often involving a few molecules at a time. Despite their wide use, we still lack a fundamental understanding and molecular-level control of these interactions. We have used chemical force microscopy7 to measure the strength of the interactions of single chemical functional groups with the sidewalls of vapour-grown individual single-walled carbon nanotubes. Surprisingly, the interaction strength does not follow conventional trends of increasing polarity or hydrophobicity, and instead reflects the complex electronic interactions between the nanotube and the functional group. Ab initio calculations confirm the observed trends and predict binding force distributions for a single molecular contact that match the experimental results. Our analysis also reveals the important role of molecular linkage dynamics in determining interaction strength at the single functional group level.

Ultra-low density polymers, metals, and ceramic nanofoams are valued for their high strength-to-weight ratio, high surface area and insulating properties ascribed to their structural geometry. We obtain the labrynthine internal structure of a tantalum oxide nanofoam by X-ray diffractive imaging. Finite element analysis from the structure reveals mechanical properties consistent with bulk samples and with a diffusion limited cluster aggregation model, while excess mass on the nodes discounts the dangling fragments hypothesis of percolation theory., Comment: 8 pages, 5 figures, 30 references

Carbon nanotube transistors are a promising platform for the next generation of nonoptical biosensors. However, the exact nature of the biomolecule interactions with nanotubes in these devices remains unknown, creating one of the major obstacles to their practical use. We assembled alternating layers of oppositely charged polyelectrolytes on the carbon nanotube transistors to mimic gating of these devices by charged molecules. The devices showed reproducible oscillations of the transistor threshold voltage depending on the polarity of the outer polymer layer in the multilayer film. This behavior shows excellent agreement with the predictions of a simple electrostatic model. Finally, we demonstrate that complex interactions of adsorbed species with the device substrate and the surrounding electrolyte can produce significant and sometimes unexpected effects on the device characteristics.

We have studied layer-by-layer polyelectrolyte self-assembly on pristine individual single-wall carbon nanotubes as a function of solution ionic strength. We report the existence of an ionic strength threshold for the deposition, below which the majority of nanotubes remain uncoated. Once the ionic strength reaches the threshold value, the majority of the individual nanotubes become coated with polyelectrolytes. Our results indicate that the self-assembly process likely involves wrapping of polymer chains around nanotubes and that the polymer chain's ability to bend in order to accommodate the nanotube curvature is one of the critical parameters controlling layer-by-layer electrostatic self-assembly on these one-dimensional templates.

Use of biological machines and environments in novel bioinorganic nanostructures is critical for development of new types of biosensors, bio-NEMS devices, and functional materials. Lipid bilayers that mimic a cell membrane have already played an important role in such applications. We present supported lipid bilayers that spontaneously assemble in a continuous nanoshell around a template of a carbon nanotube wrapped with hydrophilic polymer cushion layers. We demonstrate that such 1-D lipid membranes are fluid and can heal defects, even over repeated damage-recovery cycles. A simple diffusion model can describe mobility of lipid molecules in these 1-D nanoshells. These structures could lead to the development of new classes of biosensors and bioelectronic devices.

Carbon nanotubes have been featured prominently in the nanotechnology research for some time, yet robust strategies for noncovalent chemical modification of the nanotube surface are still missing. Such strategies are essential for the creation of functional device architectures. Here, we present a new general procedure for carbon nanotube modification based on polyelectrolyte layer-by-layer assembly. We have built multilayer structures around individual carbon nanotube bridges by first modifying the nanotube surface with a pyrene derivative followed by layer-by-layer deposition of polyelectrolyte macroions on the nanotube. Transmission electron microscopy and scanning confocal fluorescence microscopy images confirm the formation of nanometer-thick amorphous polymer nanoshells around the nanotubes. These multilayer polyelectrolyte shells on individual carbon nanotubes introduce nearly unlimited opportunities for the incorporation of various functionalities into nanotube devices, which, in turn, opens up the possibility of building more complex multicomponent structures.

Suspended carbon nanotube devices represent a promising platform for future bio-electronic applications. Suspended carbon nanotube transistors have been previously fabricated in air; however all previous attempts to bring them into liquid failed. We analyse forces acting on the suspended nanotube devices during immersion into liquids and during device operation and show that surface tension forces acting on the suspended nanotubes during transfer into the liquid phase are responsible for the nanotube damage. We have developed a new strategy that circumvents these limitations by coating suspended nanotubes with a rigid inorganic shell in the gas phase. The coating reinforces the nanotubes and allows them to survive transfer through the interface. Subsequent removal of the coating in the solution phase restores pristine suspended nanotubes. We demonstrate that devices fabricated using this technique preserve their original electrical characteristics.

Biological molecules perform sophisticated functions in living systems with complexity often far exceeding most of man-made devices and objects. Direct integration of biological components with electronic circuits could drastically increase their efficiency, complexity, and capabilities and result in novel sensing and signaling architectures. Yet, one of the obstacles for this vision of a bionanoelectronic circuit is the absence of a versatile interface that facilitates communication between biomolecules and electronic materials. We have been building platforms that integrates membrane proteins with one-dimensional inorganic materials such as carbon nanotubes and silicon nanowires. In our devices, a nanotube of nanowire is covered by a lipid bilayer that serves both as a universal membrane protein matrix and an insulating shield. I will discuss the fabrication and properties of these “shielded” nanowires and of their use in bionanoelectronic devices that incorporate working membrane proteins in an electronic circuit.