A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening.

Mass spectrometry (MS) enables detection of different chemical species with a very high specificity; however, it can be limited by its throughput. Integrating MS with microfluidics has a tremendous potential to improve throughput and accelerate biochemical research. In this work, we introduce Drop-NIMS, a combination of a passive droplet loading microfluidic device and a matrix-free MS laser desorption ionization technique called nanostructure-initiator mass spectrometry (NIMS). This platform combines different droplets at random to generate a combinatorial library of enzymatic reactions that are deposited directly on the NIMS surface without requiring additional sample handling. The enzyme reaction products are then detected with MS. Drop-NIMS was used to rapidly screen enzymatic reactions containing low (on the order of nL) volumes of glycoside reactants and glycoside hydrolase enzymes per reaction. MS "barcodes" (small compounds with unique masses) were added to the droplets to identify different combinations of substrates and enzymes created by the device. We assigned xylanase activities to several putative glycoside hydrolases, making them relevant to food and biofuel industrial applications. Overall, Drop-NIMS is simple to fabricate, assemble, and operate and it has potential to be used with many other small molecule metabolites.

Optically induced electrothermal microfluidic tweezers in bio-relevant media.

Non-contact micro-manipulation tools have enabled invasion-free studies of fragile synthetic particles and biological cells. Rapid electrokinetic patterning (REP) traps target particles/cells, suspended in an electrolyte, on an electrode surface. This entrapment is electrokinetic in nature and thus depends strongly on the suspension medium's properties. REP has been well characterized for manipulating synthetic particles suspended in low concentration salt solutions (~ 2 mS/m). However, it is not studied as extensively for manipulating biological cells, which introduces an additional level of complexity due to their limited viability in hypotonic media. In this work, we discuss challenges posed by isotonic electrolytes and suggest solutions to enable REP manipulation in bio-relevant media. Various formulations of isotonic media (salt and sugar-based) are tested for their compatibility with REP. REP manipulation is observed in low concentration salt-based media such as 0.1× phosphate buffered saline (PBS) when the device electrodes are passivated with a dielectric layer. We also show manipulation of murine pancreatic cancer cells suspended in a sugar-based (8.5% w/v sucrose and 0.3% w/v dextrose) isotonic medium. The ability to trap mammalian cells and deposit them in custom patterns enables high-impact applications such as determining their biomechanical properties and 3D bioprinting for tissue scaffolding.

Time-resolved particle image velocimetry analysis and computational modeling of transient optically induced electrothermal micro vortex.

Trapping, sorting, transportation, and manipulation of synthetic microparticles and biological cells enable investigations in their behavior and properties. Microfluidic techniques like rapid electrokinetic patterning (REP) provide a non-invasive means to probe into the nature of these micro and nanoparticles. The opto-electrically induced nature of a REP micro vortex allows tuning of the trap characteristics in real-time. In this work, we studied the effects of transient optical heating on the induced electrothermal vortex using micro-particle image velocimetry (µ-PIV) and computational modeling. A near infra-red (980 nm) laser beam was focused on a colloidal suspension of 1 µm polystyrene beads sandwiched between two parallel-plate electrodes. The electrodes were subjected to an AC current. The laser spot was scanned back-and-forth in a line, at different frequencies, to create the transient vortex. This phenomenon was also studied with a computational model made using COMSOL Multiphysics. We visualize fluid flow in custom-shaped REP traps by superposing multiple axisymmetric (spot) vortices and discuss the limitations of using superposition in dynamically changing traps.

Biofunctionalization of Silver Nanoparticles With Lactonase Leads to Altered Antimicrobial and Cytotoxic Properties.

Background: N-acylated homoserine lactone lactonase which cleave the Acyl homoserine lactone molecules produced by biofilm-forming pathogens and silver nano-particles (AgNPs), are known for their antibacterial effect against several Gram-positive and Gram-negative bacteria. In this study, AgNPs were coated with N-acylated homoserine lactonase protein (AgNPs-AiiA) isolated from Bacillus sp. ZA12. Results: The AgNPs-AiiA complex was characterized by UV-visible spectra, Dynamic light Scattering, Fourier transform infrared spectroscopy (FTIR), and Field Emission Scanning Electron Microscope (Fe-SEM). The synthesized nano-particles were found to be spherical in shape and had an approximate size of 22.4 nm. Treatment with AiiA coated AgNPs showed a significant reduction in exopolysaccharide production, metabolic activity, cell surface hydrophobicity of bacterial cells, and anti-biofilm activity against multidrug-resistant K. pneumoniae as compared to treatment with AiiA protein and neat AgNPs. AgNPs-AiiA complex exhibited potent antibiofilm activity at sub-optimal concentration of 14.4 µg/mL without being harmful to the macrophages and to the various tissues including kidney, liver, spleen and lungs of BALB/c mice upon intra-venous administration. Conclusion: It is concluded that at a concentration of 14.4 µg/mL, AgNPs coated with AiiA kill bacteria without harming the host tissue and provides a suitable template to design novel anti-biofilm drug to circumvent the issue of drug resistance.

Parallels among natural and synthetically modified quorum-quenching strategies as convoy to future therapy.

Quorum sensing (QS) refers to chemical signalling between micro-organisms and defines a social concord among them. Once a threshold of signal is accumulated, certain virulent traits are regulated within bacteria in response to the surrounding environment. These virulence traits are known to contribute in the pathogenicity of bacterial diseases. To prevent the activation of virulence factors, QS is inhibited in different ways through a strategy known as quorum quenching. Various types of quorum-quenching strategies have already been used and characterized, as discussed in this review. The phenomenon of quorum quenching has long been considered as an alternative therapy to circumvent the ill-effects of the overuse of antibiotics. Considering the need to compare and evaluate various strategies, selected quorum-quenching paradigms are detailed along with their pros and cons in this review. A rationale has been drawn between naturally evolved quorum-quenching strategies and synthetically modified approaches adopted to abrogate QS.

Sphingosine Induces Apoptosis and Down-regulation of MYCN in PAX3-FOXO1-positive Alveolar Rhabdomyosarcoma Cells Irrespective of TP53 Mutation.

BACKGROUND/AIM: Rhabdomyosarcoma is the most common type of pediatric soft-tissue sarcoma. Among the subsets of this disease, alveolar rhabdomyosarcoma (ARMS) expressing paired box 3 (PAX3) and forkhead box O1 (PAX3-FOXO1) fusion oncoprotein has the worst prognosis. The goal of this study was to investigate the chemotherapeutic effects of sphingosine on PAX3-FOXO1-positive ARMS cells [tumor protein p53 (TP53)-mutated RH30 and TP53 wild-type RH18 cells]. MATERIALS AND METHODS: The proliferation, cell death, apoptosis, cell cycle, and MYCN proto-oncogene (MYCN) expression of RH30 and RH18 cells were determined. RESULTS: Sphingosine inhibited the growth and caused cell death in a dose-dependent manner in both cell lines. Sphingosine triggered cell death by inducing apoptosis without affecting the cell cycle. MYCN expression was down-regulated within 2 and 4 h of sphingosine treatment in both RH30 and RH18 cells. CONCLUSION: Sphingosine exerts antiproliferative and pro-apoptotic effects via MYCN down-regulation independently of TP53 mutation status in PAX3-FOXO1-positive ARMS cells.

Marginal zone B cells regulate antigen-specific T cell responses during infection.

Marginal zone B cells (MZB) participate in the early immune response to several pathogens. In this study, we show that in µMT mice infected with Leishmania donovani, CD8 T cells displayed a greater cytotoxic potential and generated more effector memory cells compared with infected wild type mice. The frequency of parasite-specific, IFN-γ(+) CD4 T cells was also increased in µMT mice. B cells were able to capture parasites, which was associated with upregulation of surface IgM and MyD88-dependent IL-10 production. Moreover, MZB presented parasite Ags to CD4 T cells in vitro. Depletion of MZB also enhanced T cell responses and led to a decrease in the parasite burden but did not alter the generation of effector memory T cells. Thus, MZB appear to suppress protective T cell responses during the early stages of L. donovani infection.

Lab-on-a-chip devices as an emerging platform for stem cell biology.

The advent of stem cell based therapies has brought regenerative medicine into an increased focus as a part of the modern medicine practice, with a potential to treat a myriad of intractable diseases in the future. Stem cells reside in a complex microenvironment presenting them with a multitude of potential cues that are chemical, physical, and mechanical in nature. Conventional techniques used for experiments involving stem cells can only poorly mimic the physiological context, and suffer from imprecise spatial and temporal control, low throughput, lack of scalability and reproducibility, and poor representation of the mechanical and physical cell microenvironment. Novel lab-on-a-chip platforms, on the other hand, can much better mimic the complexity of in vivo tissue milieu and provide a greater control of the parameter variation in a high throughput and scalable manner. This capability may be especially important for understanding the biology and cementing the clinical potential of stem cell based therapies. Here we review microfabrication- and microfluidics-based approaches to investigating the complex biology of stem cell responses to changes in the local microenvironment. In particular, we categorize each method based on the types of controlled inputs it can have on stem cells, including soluble biochemical factors, extracellular matrix interactions, homotypic and heterotypic cell-cell signaling, physical cues (e.g. oxygen tension, pH, temperature), and mechanical forces (e.g. shear, topography, rigidity). Finally, we outline the methods to perform large scale observations of stem cell phenotypes and high-throughput screening of cellular responses to a combination of stimuli, and many new emerging technologies that are becoming available specifically for stem cell applications.

Synergistic effect of HIF-1alpha gene therapy and HIF-1-activated bone marrow-derived angiogenic cells in a mouse model of limb ischemia.

Ischemia induces the production of angiogenic cytokines and the homing of bone-marrow-derived angiogenic cells (BMDACs), but these adaptive responses become impaired with aging because of reduced expression of hypoxia-inducible factor (HIF)-1alpha. In this study, we analyzed the effect of augmenting HIF-1alpha levels in ischemic limb by intramuscular injection of AdCA5, an adenovirus encoding a constitutively active form of HIF-1alpha, and intravenous administration of BMDACs that were cultured in the presence of the prolyl-4-hydroxylase inhibitor dimethyloxalylglycine (DMOG) to induce HIF-1 expression. The combined therapy increased perfusion, motor function, and limb salvage in old mice subjected to femoral artery ligation. Homing of BMDACs to the ischemic limb was dramatically enhanced by intramuscular AdCA5 administration. DMOG treatment of BMDACs increased cell surface expression of beta(2) integrins, which mediated increased adherence of BMDACs to endothelial cells. The effect of DMOG was abolished by coadministration of the HIF-1 inhibitor digoxin or by preincubation with a beta(2) integrin-blocking antibody. Transduction of BMDACs with lentivirus LvCA5 induced effects similar to DMOG treatment. Thus, HIF-1alpha gene therapy increases homing of BMDACs to ischemic muscle, whereas HIF-1 induction in BMDACs enhances their adhesion to vascular endothelium, leading to synergistic effects of combined therapy on tissue perfusion.

Mechanosensitivity of fibroblast cell shape and movement to anisotropic substratum topography gradients.

In this report, we describe using ultraviolet (UV)-assisted capillary force lithography (CFL) to create a model substratum of anisotropic micro- and nanotopographic pattern arrays with variable local density for the analysis of cell-substratum interactions. A single cell adhesion substratum with the constant ridge width (1 microm), and depth (400 nm) and variable groove widths (1-9.1 microm) allowed us to characterize the dependence of cellular responses, including cell shape, orientation, and migration, on the anisotropy and local density of the variable micro- and nanotopographic pattern. We found that fibroblasts adhering to the denser pattern areas aligned and elongated more strongly along the direction of ridges, vs. those on the sparser areas, exhibiting a biphasic dependence of the migration speed on the pattern density. In addition, cells responded to local variations in topography by altering morphology and migrating along the direction of grooves biased by the direction of pattern orientation (short term) and pattern density (long term), suggesting that single cells can sense the topography gradient. Molecular dynamic live cell imaging and immunocytochemical analysis of focal adhesions and actin cytoskeleton suggest that variable substratum topography can result in distinct types of cytoskeleton reorganization. We also demonstrate that fibroblasts cultured as monolayers on the same substratum retain most of the properties displayed by single cells. This result, in addition to demonstrating a more sophisticated method to study aspects of wound healing processes, strongly suggests that even in the presence of adhesive cell-cell interactions, the cues provided by the underlying substratum topography continue to exercise substantial influence on cell behavior. The described experimental platform might not only further our understanding of biomechanical regulation of cell-matrix interactions, but also contribute to bioengineering of devices with the optimally structured design of cell-material interface.

Physical transfer of membrane and cytoplasmic components as a general mechanism of cell-cell communication.

Recent evidence from different research areas has revealed a novel mechanism of cell-cell communication by spontaneous intercellular transfer of cellular components (ICT). Here we studied this phenomenon by co-culturing different cells that contain distinct levels of proteins or markers for the plasma membrane or cytoplasm. We found that a variety of transmembrane proteins are transferable between multiple cell types. Membrane lipids also show a high efficiency of intercellular transfer. Size-dependent cytoplasmic transfer allows exchange of cytoplasmic macromolecules up to 40 kDa between somatic cells, and up to 2000 kDa between uncommitted human precursor cells and human umbilical vein endothelial cells. Protein transfer, lipid transfer and cytoplasmic component transfer can occur simultaneously and all require direct cell-cell contact. Analyses of the properties of ICT, together with a close examination of cell-cell interactions, suggest that the spontaneous ICT of different cellular components might have a common underlying process: transient local membrane fusions formed when neighboring cells undergo close cell-cell contact.

A method for probabilistic mapping between protein structure and function taxonomies through cross training.

BACKGROUND: Prediction of function of proteins on the basis of structure and vice versa is a partially solved problem, largely in the domain of biophysics and biochemistry. This underlies the need of computational and bioinformatics approach to solve the problem. Large and organized latent knowledge on protein classification exists in the form of independently created protein classification databases. By creating probabilistic maps between classes of structural classification databases (e.g. SCOP) and classes of functional classification databases (e.g. PROSITE), structure and function of proteins could be probabilistically related. RESULTS: We demonstrate that PROSITE and SCOP have significant semantic overlap, in spite of independent classification schemes. By training classifiers of SCOP using classes of PROSITE as attributes and vice versa, accuracy of Support Vector Machine classifiers for both SCOP and PROSITE was improved. Novel attributes, 2-D elastic profiles and Blocks were used to improve time complexity and accuracy. Many relationships were extracted between classes of SCOP and PROSITE using decision trees. CONCLUSION: We demonstrate that presented approach can discover new probabilistic relationships between classes of different taxonomies and render a more accurate classification. Extensive mappings between existing protein classification databases can be created to link the large amount of organized data. Probabilistic maps were created between classes of SCOP and PROSITE allowing predictions of structure using function, and vice versa. In our experiments, we also found that functions are indeed more strongly related to structure than are structure to functions.

Detailed protein sequence alignment based on Spectral Similarity Score (SSS).

BACKGROUND: The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary protein sequences. However, character based similarity cannot provide insight into the structural aspects of a protein. We present a method based on spectral similarity to compare subsequences of amino acids that behave similarly but are not aligned well by considering amino acids as mere characters. This approach finds a similarity score between sequences based on any given attribute, like hydrophobicity of amino acids, on the basis of spectral information after partial conversion to the frequency domain. RESULTS: Distance matrices of various branches of the human kinome, that is the full complement of human kinases, were developed that matched the phylogenetic tree of the human kinome establishing the efficacy of the global alignment of the algorithm. PKCd and PKCe kinases share close biological properties and structural similarities but do not give high scores with character based alignments. Detailed comparison established close similarities between subsequences that do not have any significant character identity. We compared their known 3D structures to establish that the algorithm is able to pick subsequences that are not considered similar by character based matching algorithms but share structural similarities. Similarly many subsequences with low character identity were picked between xyna-theau and xyna-clotm F/10 xylanases. Comparison of 3D structures of the subsequences confirmed the claim of similarity in structure. CONCLUSION: An algorithm is developed which is inspired by successful application of spectral similarity applied to music sequences. The method captures subsequences that do not align by traditional character based alignment tools but give rise to similar secondary and tertiary structures. The Spectral Similarity Score (SSS) is an extension to the conventional similarity methods and results indicate that it holds a strong potential for analysis of various biological sequences and structural variations in proteins.