Comparison of the Strengths and Weaknesses of Machine Learning Algorithms and Feature Selection on KEGG Database Microbial Gene Pathway Annotation and Its Effects on Reconstructed Network Topology.

The development of tools for the annotation of genes from newly sequenced species has not evolved much from homologous alignment to prior annotated species. While the quality of gene annotations continues to decline as we sequence and assemble more evolutionary distant gut microbiome species, machine learning presents a high quality alternative to traditional techniques. In this study, we investigate the relative performance of common classical and nonclassical machine learning algorithms in the problem of gene annotation using human microbiome-associated species genes from the KEGG database. The majority of the ensemble, clustering, and deep learning algorithms that we investigated showed higher prediction accuracy than CD-Hit in predicting partial KEGG function. Motif-based, machine-learning methods of annotation in new species were faster and had higher precision-recall than methods of homologous alignment or orthologous gene clustering. Gradient boosted ensemble methods and neural networks also predicted higher connectivity in reconstructed KEGG pathways, finding twice as many new pathway interactions than blast alignment. The use of motif-based, machine-learning algorithms in annotation software will allow researchers to develop powerful tools to interact with bacterial microbiomes in ways previously unachievable through homologous sequence alignment alone.

Spray-On Colorimetric Sensors for Distinguishing the Presence of Lead Ions.

Sprayable stimuli-responsive material coatings represent a new class of detection system which can be quickly implemented to transform a surface into a color-responsive sensor. In this work, we describe a dipicolylamine-terminated diacetylene-containing amphiphile formulation for spray coating on to a simple paper substrate to yield disposable test strips that can be used to detect the presence of lead ions in solution. We find the response to be very selective to only lead ions and that the sensitivity can be modulated by altering the UV curing time after spraying. Sensitive detection to at least 0.1 mM revealed a clear color change from a blue to red phase. This represents the first demonstration of a spray-on sensor system capable of detection of lead ions in solution.

Implementation of an Experiential Service-Learning Course in Biomedical Engineering Design for Undergraduate Students.

The unique characteristics of the training needed for today's biomedical engineers can represent a challenge in curriculum design. Practical experiential learning for biomedical engineering undergraduates is important to prevent under-developed professional skills. In this teaching tips article, we provide an example of how to incorporate experiential learning into the biomedical engineering curriculum to address the need for undergraduates to gain the desired skillsets to serve as the next generation of leaders in engineering, medicine, and business all through the lens of civic engagement. Here we outline our implementation of a recently developed service-learning course for our sophomore students that allows introduction of biomedical engineering discipline-specific design process early on in their undergraduate studies. Student teams work to design, build, and test novel devices to solve the unmet need of community partners, and in doing so, the course prepares students in developing technologies that not only address public health needs but that are also embraced by the community. This course in team-based design can help train students in analyzing real world problems for needs-based biomedical engineering through projects identified by interaction with community partners. Providing specifics of how this course was implemented as well as our reflection on student learning, we offer an analysis of the areas of success, a discussion of how interactions with community partners benefits the student professional skills development, and considerations regarding implementation. Here we highlight the ability of this course to exercise students' social awareness in the design of technologies to improve society by addressing the genuine needs of community partners.

Supramolecular Peptide Nanofiber/PLGA Nanocomposites for Enhancing Pulmonary Drug Delivery.

Effective drug delivery to pulmonary sites will benefit from the design and synthesis of novel drug delivery systems that can overcome various tissue and cellular barriers. Cell penetrating peptides (CPPs) have shown promise for intracellular delivery of various imaging probes and therapeutics. Although CPPs improve delivery efficacy to a certain extent, they still lack the scope of engineering to improve the payload capacity and protect the payload from the physiological environment in drug delivery applications. Inspired by recent advances of CPPs and CPP-functionalized nanoparticles, in this work, we demonstrate a novel nanocomposite consisting of fiber-forming supramolecular CPPs that are coated onto polylactic-glycolic acid (PLGA) nanoparticles to enhance pulmonary drug delivery. These nanocomposites show a threefold higher intracellular delivery of nanoparticles in various cells including primary lung epithelial cells, macrophages, and a 10-fold increase in endothelial cells compared to naked PLGA nanoparticles or a twofold increase compared to nanoparticles modified with traditional monomeric CPPs. Cell uptake studies suggest that nanocomposites likely enter cells through mixed macropinocytosis and passive energy-independent mechanisms, which is followed by endosomal escape within 24 h. Nanocomposites also showed potent mucus permeation. More importantly, freeze-drying and nebulizing formulated nanocomposite powder did not affect their physiochemical and biological activity, which further highlights the translative potential for use as a stable drug carrier for pulmonary drug delivery. We expect nanocomposites based on peptide nanofibers, and PLGA nanoparticles can be custom designed to encapsulate and deliver a wide range of therapeutics including nucleic acids, proteins, and small-molecule drugs when employed in inhalable systems to treat various pulmonary diseases.

Peptide Linked Diacetylene Amphiphiles for Detection of Epitope Specific Antibodies.

Antibodies produced in response to adaptive immunity provide a receptor with multiple sites for binding to a distinct epitope of an antigen. Determining antibody levels to specific antigens has important clinical applications in assessing immune status or deficiency, monitoring infectious or autoimmune diseases, and diagnosing allergies. Leveraging that a specific antibody will bind to a distinct small peptide epitope without requiring the entire antigen to be present, we demonstrate in this work a proof-of-concept assay to detect the presence of an antibody by using peptide epitopes linked to an amphiphile to generate a vesicle-based sensing system. By affording multiple copies of the epitope site on the vesicle, we revealed that the vesicles visibly aggregate in response to an antibody specific for that epitope due to multivalent binding provided by the antibody. We also uncovered the role of peptide surface density in providing accessible epitopes on the vesicles for antibody binding. In summary, using a peptide derived from the coat protein of human influenza virus directly linked to a diacetylene-containing amphiphile afforded peptide-laden vesicles that proved capable of detecting the presence of antibodies specific for human influenza hemagglutinin.

Introduction of Plasmid to the Murine Gut via Consumption of an Escherichia coli Carrier and Examining the Impact of Bacterial Dosing and Antibiotics on Persistence.

Purpose: We examine the impacts of dosing strategies of plasmids on bacterial communities in the murine gut by measuring the quantity of plasmids in mouse feces. Methods: We fed mice carrier bacteria, E. coli, that contain plasmids with both a reporter gene and an antibiotic resistant gene. We varied the quantity of the plasmid-carrying bacteria and the length of time the mice consumed the bacteria. We also pretreated the gut with broad-spectrum antibiotics and used continuous antibiotic treatment to investigate selection pressure. We collected bacteria from fecal pellets to quantify the number of plasmid-carrying bacteria via plate assay. Results: Dosing regimens with plasmid-carrying bacteria resulted in a significantly increased duration of persistence of the plasmid within the gut when supplemented continuously with kanamycin during as well as after completion of bacterial dosing. The carrier bacteria concentration influenced the short-term abundance of carrier bacteria. Conclusion: We evaluated the persistence of plasmid-carrying bacteria in the murine gut over time using varying dosage strategies. In future work, we will study how bacterial diversity in the gut impacts the degree of plasmid transfer and the prevalence of plasmid-carrying bacteria over time. Lay Summary: Observing how plasmids persist within the gut can help us understand how newly introduced genes, including antibiotic resistance, are transmitted within the gut microbiome. In our experiments, mice were given bacteria containing a genetically engineered plasmid and were examined for the persistence of the plasmid in the gut. We found long-term persistence of the plasmid in the gut when administering antibiotics during and following dosing of the mice with bacteria carrying the plasmid. The use of higher concentrations of carrier bacteria influenced the short-term abundance of the plasmid-carrying bacteria in the gut. Description of Future Works: Building on evidence from these initial studies that persistence of plasmids within the gut can be regulated by the dosage strategy, we will explore future studies and models of gene uptake in the context of spatial and taxonomic control and further determine if dosing strategies alter the compositional diversity of the gut microbiome.

Engineering Escherichia coli for Conversion of Dietary Isoflavones in the Gut.

Introducing metabolic pathways to the gut is important to tailor the biochemical components ultimately absorbed by the host. Given identical diets, hosts possessing different consortia of gut bacteria can exhibit distinct health outcomes regulated by metabolic capabilities of the gut microbiota. The disparate competency of the population to metabolize isoflavones, such as dietary daidzein, has shown health benefits for those individuals possessing gut bacteria capable of producing equol from daidzein-rich diets. To begin addressing health inequalities due to gut metabolic pathway deficiencies, we developed a probiotic that allows metabolism of isoflavones to provide a gut phenotype paralleling that of natural equol producers. Toward this goal, we engineered Escherichia coli to produce the enzymes necessary for conversion of daidzein to equol, and as demonstrated in a murine model, these bacteria enabled elevated serum equol levels to dietary daidzein, thus serving as a starting point for more sophisticated systems.

Self-Assembled Peptide-Labeled Probes for Agglutination-Based Sensing.

The use of polydiacetylene (PDA) vesicles in sensing systems are wide-spread due to the interesting optical properties of this stimuli-responsive material; however, agglutination based sensing with PDA have been relatively underutilized. To demonstrate the means for rapidly generating an agglutination probe based on peptide-displaying polydiacetylene vesicles, we implement here the use of a biotin mimetic peptide functionalized to a diacetylene amphiphile for proof-of-concept detection of a multivalent target, specifically streptavidin. Tuning of the vesicle composition revealed a distinct limit in the surface density of peptide amphiphile that could be displayed for this particular peptide sequence. A wide operational detection range was demonstrated, and the result also revealed an effective agglutination response of the PDA-based probe to streptavidin suggesting possible use of future formulations in profiling other multivalent targets.

Corrigendum: Notch Intracellular Domain Plasmid Delivery via Poly(Lactic-Co-Glycolic Acid) Nanoparticles to Upregulate Notch Pathway Molecules.

[This corrects the article DOI: 10.3389/fcvm.2021.707897.].

Notch Intracellular Domain Plasmid Delivery via Poly(Lactic-Co-Glycolic Acid) Nanoparticles to Upregulate Notch Pathway Molecules.

Notch signaling is a highly conserved signaling system that is required for embryonic development and regeneration of organs. When the signal is lost, maldevelopment occurs and leads to a lethal state. Delivering exogenous genetic materials encoding Notch into cells can reestablish downstream signaling and rescue cellular functions. In this study, we utilized the negatively charged and FDA approved polymer poly(lactic-co-glycolic acid) to encapsulate Notch Intracellular Domain-containing plasmid in nanoparticles. We show that primary human umbilical vein endothelial cells (HUVECs) readily uptake the nanoparticles with and without specific antibody targets. We demonstrated that our nanoparticles are non-toxic, stable over time, and compatible with blood. We further demonstrated that HUVECs could be successfully transfected with these nanoparticles in static and dynamic environments. Lastly, we elucidated that these nanoparticles could upregulate the downstream genes of Notch signaling, indicating that the payload was viable and successfully altered the genetic downstream effects.

Engineering a reporter cell line to mimic the high oligomannose presenting surface immunoglobulin of follicular lymphoma B cells.

Subtypes of B cell non-Hodgkin's lymphomas, including follicular lymphomas, have shown a unique high oligomannose presentation on their immunoglobulins that will interact with natural receptors of the innate immunity, reportedly causing stimulation and proliferation. From deep sequencing of the variable heavy and light chain sequences of follicular lymphoma involved tissue sections, we identified the consensus variable sequences possessing glycosylation sites at the complementarity determining region. Using this information, we developed a cell line, referred to here as BZ, which displays the consensus variable segments as part of a surface antibody (IgM) and confirmed its presentation of high oligomannose on the heavy chain both in vitro and in vivo. An mCherry expressing variant provided a reporter cell line displaying the high oligomannose surface biomarker while affording clear fluorescent signals for FACS screening as well as for fluorescent in vivo imaging of ectopic xenograft tumors. In developing this reporter cell line that displays the biomarker glycan of follicular lymphoma, we provide a tool that may be used for future screening and validation of receptive moieties for selectively binding high oligomannose for development of targeted diagnostics or therapeutics to such B cell malignancies that display this unique glycan.

Modifying Polydiacetylene Vesicle Compositions to Reduce Non-Specific Interactions.

Polydiacetylene (PDA) vesicles provide useful stimuli-responsive behavior as well as by the modular structure afford a means for the design of sensing and delivery systems with tunable target specificity. To reduce inherent non-specific interaction with either anionic or cationic formulations of polydiacetylene vesicles, we explored the use of various lengths of poly(ethylene glycol) (PEG) amphiphiles for integration and polymerization within PDA vesicles. Our results established that as little as 1% of polyethylene glycol amphiphile integration into anionic vesicles was sufficient to significantly reduce non-specific association with mammalian cells. Similarly integrating a low percent of PEG amphiphile content within cationic vesicles could also significantly reduce non-specific cell association, and moreover reduced cytotoxicity. These results may be prove useful in augmenting PDA vesicles formulations for reduced non-specific interaction which is of particularly interest to enhancing selectivity in vesicles designed with integrated targeting moieties for sensing and drug delivery applications.

Tuning the Surface Charge of Self-Assembled Polydiacetylene Vesicles to Control Aggregation and Cell Binding.

Polydiacetylene vesicles of various compositions were assembled using a two-part mixture of 10,12-pentacosadiynoic acid (PCDA) and ethylenedioxy-bis-ethylamine (EDEA)-labeled PCDA in order to control surface charge and stability within a desired pH range. Investigation of the interaction of the vesicles with mammalian cells as a function of surface charge was carried out and identified a clear correlation in cell-vesicle association and corresponding cell death for vesicles with positive surface charge. The binding behavior of the vesicles was found to be tunable by regulating the proportion of anionic PCDA relative to cationic PCDA-EDEA content within vesicles as to control the surface charge as a function of pH. Association of vesicles with cells thus depended on the corresponding charge of the vesicles and cell surface. The prospect of this work may serve as a step toward future vesicle designs to allow triggered uptake of vesicles locally within low pH tumor microenvironments.

A Peptide-Lectin Fusion Strategy for Developing a Glycan Probe for Use in Various Assay Formats.

While nucleic acid and protein analysis approaches continue to see significant breakthroughs, analytical strategies for glycan determination have by comparison seen slower technological advances. Here we provide a strategy for glycan probe development using an engineered lectin fusion that can be incorporated into various common pathology lab assay formats including Western blot and agglutination assays. In this proof of concept, we use the natural lectin, Pseudomonas fluorescens agglutinin (PFA), capable of binding core Man alpha(1-3)-Man alpha(1-6)-Man units, where this lectin has previously been shown to bind to the glycans presented by the gp120 coat protein of (HIV) Human Immunodeficiency Virus. In our strategy, we engineered the lectin to possess a fusion of the biotin mimetic tag equence of amino acids V-S-H-P-Q-A-P-F. With the glycan receptive PFA directly linked to the biotin mimic, we could facilitate a probe for various standard clinical assay formats by virtue of coupling to streptavidin-HRP (horseradish peroxidase) or streptavidin beads for Western blot and agglutination assays respectively. We found the PFA fusion retained low nanomolar affinity for gp120 by ELISA (Enzyme Linked Immunosorbent Assay) and microscale thermophoresis. This probe engineering strategy proved effective in the relevant assay formats that may now allow detection for the presence of glycans containing the core Man alpha(1-3)-Man alpha(1-6)-Man units recognized by PFA.

IR-783 Labeling of a Peptide Receptor for 'Turn-On' Fluorescence Based Sensing.

In this study, we examine a means for developing near-IR fluorescent sensors through streamlined, site-specific coupling with peptide-based receptors. As the penultimate step of solid-phase synthesis of a peptide-based receptor, we show a simple means of labeling the N' terminus with the near IR fluorophore IR-783 to afford a viable fluorescent sensor after cleavage from the resin. The proof-of-concept probe utilized a biotin mimetic peptide sequence as the receptive moiety. Here we revealed a "turn-on" fluorescence enhancement upon binding of the biotin mimetic probe to its intended streptavidin target. Not all peptide-receptive moieties tested were able to generate such an enhancement upon target binding, and as such, the rationale for the observed fluorescence response properties is discussed.

Silica formation with nanofiber morphology via helical display of the silaffin R5 peptide on a filamentous bacteriophage.

Biological systems often generate unique and useful structures, which can have industrial relevance either as direct components or as an inspiration for biomimetic materials. For fabrication of nanoscale silica structures, we explored the use of the silaffin R5 peptide from Cylindrotheca fusiformis expressed on the surface of the fd bacteriophage. By utilizing the biomineralizing peptide component displayed on the bacteriophage surface, we found that low concentrations (0.09 mg/mL of the R5 bacteriophage, below the concentration range used in other studies) could be used to create silica nanofibers. An additional benefit of this approach is the ability of our R5-displaying phage to form silica materials without the need for supplementary components, such as aminopropyl triethoxysilane, that are typically used in such processes. Because this method for silica formation can occur under mild conditions when implementing our R5 displaying phage system, we may provide a relatively simple, economical, and environmentally friendly process for creating silica nanomaterials.

Ultraviolet Patterned Calixarene-Derived Supramolecular Gels and Films with Spatially Resolved Mechanical and Fluorescent Properties.

Supramolecular assemblies have in the past been considered mechanically weak and in most cases unable to withstand their own weight. Calixarene-derived networks can, however, provide robust supramolecular gels. Incorporating a photoreactive stilbene moiety, we show that the aggregation state of the material can be tuned by heating and UV exposure in order to control the mechanical as well as the fluorescent properties. Regulating the extent of heating to control the proportion of H-aggregates and J-aggregates and further cross-linking of H-aggregates by control over UV exposure allows for adjustable photopatterning of the fluorescence as well as the material stiffness in the range from ∼100 to 450 kPa. We expect this straightforward supramolecular system will be suitable for advanced prototyping in applications where modulus and shape are important design criteria.

Progression in the Fountain Pen Approach: From 2D Writing to 3D Free-Form Micro/Nanofabrication.

The fountain pen approach, as a means for transferring materials to substrates, has shown numerous incarnations in recent years for creating 2D micro/nanopatterns and even generating 3D free-form nanostructures using a variety of material "inks". While the idea of filled reservoirs used to deliver material to a substrate via a capillary remains unchanged since antiquity, the advent of precise micromanipulation systems and functional material "inks" allows the extension of this mechanism to more high-tech applications. Herein, the recent growth in meniscus guided fountain pen approaches for benchtop micro/nanofabrication, which has occurred in the last decade, is discussed. Particular attention is given to the theory, equipment, and experimentation encompassing this unique direct writing approach. A detailed exploration of the diverse ink systems and functional device applications borne from this strategy is put forth to reveal its rapid expansion to a broad range of scientific and engineering disciplines. As such, this informative review is provided for researchers considering adoption of this recent advancement of a familiar technology.

Luminescent Probe Based Techniques for Hypoxia Imaging.

Hypoxia is a condition of tissue environments wherein a lower than normal level of oxygen is available, and it serves as the root cause and indicator of various diseases. Detection of hypoxia in tumors is imperative for furthering our understanding of the pathological effects and the development of proper treatments, as it is well established that hypoxic tumors are able to impede the cancer treatment process by being resistant to many therapies. It is important therefore to be able to detect hypoxia in tissues and tumors through in vivo imaging methods. A growing area for detection of hypoxia in vivo is the use of fluorescent/luminescent probes which has accelerated in recent years. The continued quest for improvements in selectivity and sensitivity has inspired researchers to pursue new strategies for fluorescence/luminescent probe design. This review will discuss various luminescent probes based on small molecules, dyes, macromolecules, and nanoparticles for sensitive and specific detection of oxygen levels directly or by indirect mechanisms such as the presence of enzymes or related factors that arise in a hypoxic environment. Following the particular mechanism of detection, each probe has specific structural and photophysical properties which permit its selectivity and sensitivity. These probes show promise in terms of low toxicity and high specificity among other merits discussed, and in providing new dimensions for hypoxia detection, these works contribute to future potential methods for clinical diagnosis of hypoxic tissues and tumors.