Browse
Submit Data
Databases
API
Help

Dataset Information

5 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A curious formulation robot enables the discovery of a novel protocell behavior.

ABSTRACT: We describe a chemical robotic assistant equipped with a curiosity algorithm (CA) that can efficiently explore the states a complex chemical system can exhibit. The CA-robot is designed to explore formulations in an open-ended way with no explicit optimization target. By applying the CA-robot to the study of self-propelling multicomponent oil-in-water protocell droplets, we are able to observe an order of magnitude more variety in droplet behaviors than possible with a random parameter search and given the same budget. We demonstrate that the CA-robot enabled the observation of a sudden and highly specific response of droplets to slight temperature changes. Six modes of self-propelled droplet motion were identified and classified using a time-temperature phase diagram and probed using a variety of techniques including NMR. This work illustrates how CAs can make better use of a limited experimental budget and significantly increase the rate of unpredictable observations, leading to new discoveries with potential applications in formulation chemistry.

SUBMITTER: Grizou J

PROVIDER: S-EPMC6994213 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Robot Gaze Behavior Affects Honesty in Human-Robot Interaction.

Project description:As the use of humanoid robots proliferates, an increasing amount of people may find themselves face-to-"face" with a robot in everyday life. Although there is a plethora of information available on facial social cues and how we interpret them in the field of human-human social interaction, we cannot assume that these findings flawlessly transfer to human-robot interaction. Therefore, more research on facial cues in human-robot interaction is required. This study investigated deception in human-robot interaction context, focusing on the effect that eye contact with a robot has on honesty toward this robot. In an iterative task, participants could assist a humanoid robot by providing it with correct information, or potentially secure a reward for themselves by providing it with incorrect information. Results show that participants are increasingly honest after the robot establishes eye contact with them, but only if this is in response to deceptive behavior. Behavior is not influenced by the establishment of eye contact if the participant is actively engaging in honest behavior. These findings support the notion that humanoid robots can be perceived as, and treated like, social agents, since the herein described effect mirrors one present in human-human social interaction.

| S-EPMC8144295 | biostudies-literature

Zymophore identification enables the discovery of novel phenylalanine ammonia lyase enzymes.

Project description:The suite of biological catalysts found in Nature has the potential to contribute immensely to scientific advancements, ranging from industrial biotechnology to innovations in bioenergy and medical intervention. The endeavour to obtain a catalyst of choice is, however, wrought with challenges. Herein we report the design of a structure-based annotation system for the identification of functionally similar enzymes from diverse sequence backgrounds. Focusing on an enzymatic activity with demonstrated synthetic and therapeutic relevance, five new phenylalanine ammonia lyase (PAL) enzymes were discovered and characterised with respect to their potential applications. The variation and novelty of various desirable traits seen in these previously uncharacterised enzymes demonstrates the importance of effective sequence annotation in unlocking the potential diversity that Nature provides in the search for tailored biological tools. This new method has commercial relevance as a strategy for assaying the 'evolvability' of certain enzyme features, thus streamlining and informing protein engineering efforts.

| S-EPMC5651878 | biostudies-literature

Curious kinetic behavior in silica polymorphs solves seifertite puzzle in shocked meteorite.

Project description:The presence of seifertite, one of the high-pressure polymorphs of silica, in achondritic shocked meteorites has been problematic because this phase is thermodynamically stable at more than ~100 GPa, unrealistically high-pressure conditions for the shock events in the early solar system. We conducted in situ x-ray diffraction measurements at high pressure and temperatures, and found that it metastably appears down to ~11 GPa owing to the clear difference in kinetics between the metastable seifertite and stable stishovite formations. The temperature-insensitive but time-sensitive kinetics for the formation of seifertite uniquely constrains that the critical shock duration and size of the impactor on differentiated parental bodies are at least ~0.01 s and ~50 to 100 m, respectively, from the presence of seifertite.

| S-EPMC4640644 | biostudies-literature

Discovery of a Novel Multi-Strains Probiotic Formulation with Improved Efficacy toward Intestinal Inflammation.

Project description:Dysbiosis is commonly detected in patients with inflammatory bowel disease (IBD), supporting the concept that a dysregulated immune reaction to bacterial antigens has a pathogenic role in the development of intestinal inflammation. In the present study, we have investigated the beneficial effects of a novel probiotic formulation assembled by combining four probiotics (Streptococcus thermophilus, Lactobacillus casei, Bifidobacterium breve) with Bacillus subtilis, a Gram-positive bacterium, with extensive bio-applications. Mice rendered colitic by administration of TNBS or DSS were administered with Bacillus subtilis alone, Vivomixx® or the novel Five strains formulation. Vivomixx® attenuated the severity of inflammation and reduced the development of signs and symptoms of colitis in both models. Adding Bacillus subtilis to Vivomixx® improved the beneficial effects of the bacterial therapy. The novel Five strains formulation was as effective as Vivomixx® in reducing the development of signs and symptoms of colitis and reduced the expression of pro-inflammatory mediators including Il-6 and Tnf-α while increased the expression of Il-10 mRNA and the number of Treg. In summary, we have shown that a novel Five strains probiotics formulation exerts beneficial effects on two chemical models of colitis, establishing Bacillus subtilis as a probiotic in rodent models of inflammation.

| S-EPMC7400193 | biostudies-literature

Optimizing the Rigid or Compliant Behavior of a Novel Parallel-Actuated Architecture for Exoskeleton Robot Applications.

Project description:The purpose of this work is to optimize the rigid or compliant behavior of a new type of parallel-actuated robot architecture developed for exoskeleton robot applications. This is done in an effort to provide those that utilize the architecture with the means to maximize, minimize, or simply adjust its stiffness property so as to optimize it for particular tasks, such as augmented lifting or impact absorption. This research even provides the means to produce non-homogeneous stiffness properties for applications that may require non-homogeneous dynamic behavior. In this work, the new architecture is demonstrated in the form of a shoulder exoskeleton. An analytical stiffness model for the shoulder exoskeleton is created and validated experimentally. The model is then used, along with a method of bounded nonlinear multi-objective optimization to configure the parallel substructures for desired rigidity, compliance or nonhomogeneous stiffness behavior. The stiffness model and its optimization can be applied beyond the shoulder to any embodiment of the new parallel architecture, including hip, wrist and ankle robot applications. In order to exemplify this, we present the rigidity optimization for a theoretical hip exoskeleton.

| S-EPMC7941672 | biostudies-literature

Chemical communication in spatially organized protocell colonies and protocell/living cell micro-arrays.

Project description:Micro-arrays of discrete or hemifused giant unilamellar lipid vesicles (GUVs) with controllable spatial geometries, lattice dimensions, trapped occupancies and compositions are prepared by acoustic standing wave patterning, and employed as platforms to implement chemical signaling in GUV colonies and protocell/living cell consortia. The methodology offers an alternative approach to GUV micro-array fabrication and provides new opportunities in protocell research and bottom-up synthetic biology.

| S-EPMC6991169 | biostudies-literature

Colony-like Protocell Superstructures.

Project description:We report the formation, growth, and dynamics of model protocell superstructures on solid surfaces, resembling single cell colonies. These structures, consisting of several layers of lipidic compartments enveloped in a dome-shaped outer lipid bilayer, emerged as a result of spontaneous shape transformation of lipid agglomerates deposited on thin film aluminum surfaces. Collective protocell structures were observed to be mechanically more stable compared to isolated spherical compartments. We show that the model colonies encapsulate DNA and accommodate nonenzymatic, strand displacement DNA reactions. The membrane envelope is able to disassemble and expose individual daughter protocells, which can migrate and attach via nanotethers to distant surface locations, while maintaining their encapsulated contents. Some colonies feature "exocompartments", which spontaneously extend out of the enveloping bilayer, internalize DNA, and merge again with the superstructure. A continuum elastohydrodynamic theory that we developed suggests that a plausible driving force behind subcompartment formation is attractive van der Waals (vdW) interactions between the membrane and surface. The balance between membrane bending and vdW interactions yields a critical length scale of 236 nm, above which the membrane invaginations can form subcompartments. The findings support our hypotheses that in extension of the "lipid world hypothesis", protocells may have existed in the form of colonies, potentially benefiting from the increased mechanical stability provided by a superstructure.

| S-EPMC9979656 | biostudies-literature

Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples.

Project description:Metagenomics and single-cell genomics have enabled genome discovery from unknown branches of life. However, extracting novel genomes from complex mixtures of metagenomic data can still be challenging and represents an ill-posed problem which is generally approached with ad hoc methods. Here we present a microfluidic-based mini-metagenomic method which offers a statistically rigorous approach to extract novel microbial genomes while preserving single-cell resolution. We used this approach to analyze two hot spring samples from Yellowstone National Park and extracted 29 new genomes, including three deeply branching lineages. The single-cell resolution enabled accurate quantification of genome function and abundance, down to 1% in relative abundance. Our analyses of genome level SNP distributions also revealed low to moderate environmental selection. The scale, resolution, and statistical power of microfluidic-based mini-metagenomics make it a powerful tool to dissect the genomic structure of microbial communities while effectively preserving the fundamental unit of biology, the single cell.

| S-EPMC5498146 | biostudies-literature

Optimization of recombinant expression enables discovery of novel cytochrome P450 activity in rice diterpenoid biosynthesis.

Project description:The oxygenation reactions catalyzed by cytochromes P450 (CYPs) play critical roles in plant natural products biosynthesis. At the same time, CYPs are one of most challenging enzymes to functionally characterize due to the difficulty of recombinantly expressing these membrane-associated monooxygenases. In the course of investigating rice diterpenoid biosynthesis, we have developed a synthetic biology approach for functional expression of relevant CYPs in Escherichia coli. In certain cases, activity was observed for only one of two closely related paralogs although it seems clear that related reactions are required for production of the known diterpenoids. Here, we report that optimization of the recombinant expression system enabled characterization of not only these previously recalcitrant CYPs, but also discovery of additional activity relevant to rice diterpenoid biosynthesis. Of particular interest, CYP701A8 was found to catalyze 3β-hydroxylation of syn-pimaradiene, which is presumably relevant to momilactone biosynthesis, while CYP71Z6 & 7 were found to catalyze multiple reactions, with CYP71Z6 catalyzing the production of 2α,3α-dihydroxy-ent-isokaurene via 2α-hydroxy-ent-isokaurene, and CYP71Z7 catalyzing the production of 3α-hydroxy-ent-cassadien-2-one via 2α-hydroxy-ent-cassadiene and ent-cassadien-2-one, which may be relevant to oryzadione and phytocassane biosynthesis, respectively.

| S-EPMC4546517 | biostudies-literature

Deep learning model enables the discovery of a novel immunotherapeutic agent regulating the kynurenine pathway.

Project description:Kynurenine (Kyn) is a key inducer of an immunosuppressive tumor microenvironment (TME). Although indoleamine 2,3-dioxygenase (IDO)-selective inhibitors have been developed to suppress the Kyn pathway, the results were not satisfactory due to the presence of various opposing mechanisms. Here, we employed an orally administered novel Kyn pathway regulator to overcome the limitation of anti-tumor immune response. We identified a novel core structure that inhibited both IDO and TDO. An orally available lead compound, STB-C017 (designated hereafter as STB), effectively inhibited the enzymatic and cellular activity of IDO and TDO in vitro. Moreover, it potently suppressed Kyn levels in both the plasma and tumor in vivo. STB monotherapy increased the infiltration of CD8+ T cells into TME. In addition, STB reprogrammed the TME with widespread changes in immune-mediated gene signatures. Notably, STB-based combination immunotherapy elicited the most potent anti-tumor efficacy through concurrent treatment with immune checkpoint inhibitors, leading to complete tumor regression and long-term overall survival. Our study demonstrated that a novel Kyn pathway regulator derived using deep learning technology can activate T cell immunity and potentiate immune checkpoint blockade by overcoming an immunosuppressive TME.

| S-EPMC8632076 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data