Integration of micro nano and bio technologies with layer -by -layer self -assembly

In the past decade, layer-by-layer (LbL) nanoassembly has been used as a tool for immobilization and surface modification of materials with applications in biology and physical sciences. Often, in such applications, LbL assembly is integrated with various techniques to form functional surface coatings and immobilized matrices. In this work, integration of LbL with microfabrication and microfluidics, and tissue engineering are explored. In an effort to integrate microfabrication with LbL nanoassembly, microchannels were fabricated using soft-lithography and the surface of these channels was used for the immobilization of materials using LbL and laminar flow patterning. Synthesis of poly(dimethyldiallyl ammonium chloride)/poly(styrene sulfonate) and poly(dimethyldiallyl ammonium chloride)/bovine serum albumin microstrips is demonstrated with the laminar flow microfluidic reactor. Resulting micropatterns are 8-10 μm wide, separated with few micron gaps. The width of these microstrips as well as their position in the microchannel is controlled by varying the flow rate, time of interaction and concentration of the individual components, which is verified by numerical simulation. Spatially resolved pH sensitivity was observed by modifying the surface of the channel with a pH sensitive dye. In order to investigate the integration of LbL assembly with tissue engineering, glass substrates were coated with nanoparticle/polyelectrolyte layers, and two different cell types were used to test the applicability of these coatings for the surface modification of medical implants. Titanium dioxide (TiO 2), silicon dioxide, halloysite and montmorillonite nanoparticles were assembled with oppositely charged polyelectrolytes. In-vitro cytotoxicity tests of the nanoparticle substrates on human dermal firbroblasts (HDFs) showed that the nanoparticle surfaces do not have toxic effects on the cells. HDFs retained their phenotype on the nanoparticle coatings, by synthesizing type-I collagen. These cells also showed active proliferation on the nanoparticle substrates. Cells attached on TiO2 substrates showed faster rate of spreading compared with the other types of nanoparticle coatings. Mesenchymal stem cells (MSCs) were used as a second cell type to support and elaborate on the results obtained with the HDFs. Increasing surface roughness was observed with increasing number of layers of TiO2. Tests with a higher number of layers of TiO2, showed an increased attachment, proliferation and faster spreading of the MSCs on a larger number of layers of TiO2

R.KpnI, an HNH superfamily REase, exhibits differential discrimination at non-canonical sequences in the presence of Ca2+ and Mg2+

KpnI REase recognizes palindromic sequence, GGTAC↓C, and forms complex in the absence of divalent metal ions, but requires the ions for DNA cleavage. Unlike most other REases, R.KpnI shows promiscuous DNA cleavage in the presence of Mg2+. Surprisingly, Ca2+ suppresses the Mg2+-mediated promiscuous activity and induces high fidelity cleavage. To further analyze these unique features of the enzyme, we have carried out DNA binding and kinetic analysis. The metal ions which exhibit disparate pattern of DNA cleavage have no role in DNA recognition. The enzyme binds to both canonical and non-canonical DNA with comparable affinity irrespective of the metal ions used. Further, Ca2+-imparted exquisite specificity of the enzyme is at the level of DNA cleavage and not at the binding step. With the canonical oligonucleotides, the cleavage rate of the enzyme was comparable for both Mg2+- and Mn2+-mediated reactions and was about three times slower with Ca2+. The enzyme discriminates non-canonical sequences poorly from the canonical sequence in Mg2+-mediated reactions unlike any other Type II REases, accounting for the promiscuous behavior. R.KpnI, thus displays properties akin to that of typical Type II REases and also endonucleases with degenerate specificity in its DNA recognition and cleavage properties

Multimodal Cotranslational Interactions Direct Assembly of the Human Multi-tRNA Synthetase Complex

Amino acid ligation to cognate transfer RNAs (tRNAs) is catalyzed by aminoacyl-tRNA synthetases (aaRSs)-essential interpreters of the genetic code during translation. Mammalian cells harbor 20 cytoplasmic aaRSs, out of which 9 (in 8 proteins), with 3 non-aaRS proteins, AIMPs 1 to 3, form the similar to 1.25-MDa multi-tRNA synthetase complex (MSC). The function of MSC remains uncertain, as does its mechanism of assembly. Constituents of multiprotein complexes encounter obstacles during assembly, including inappropriate interactions, topological constraints, premature degradation of unassembled subunits, and suboptimal stoichiometry. To facilitate orderly and efficient complex formation, some complexes are assembled cotranslationally by a mechanism in which a fully formed, mature protein binds a nascent partner as it emerges from the translating ribosome. Here, we show out of the 121 possible interaction events between the 11 MSC constituents, 15 are cotranslational. AIMPs are involved in the majority of these cotranslational interactions, suggesting they are not only critical for MSC structure but also for assembly. Unexpectedly, several cotranslational events involve more than the usual dyad of interacting proteins. We show two modes of cotranslational interaction, namely a multisite mechanism in which two or more mature proteins bind the same nascent peptide at distinct sites and a second piggy-back mechanism in which a mature protein carries a second fully formed protein and binds to a single site on an emerging peptide. Multimodal mechanisms of cotranslational interaction offer a diversity of pathways for ordered, piecewise assembly of small subcomplexes into larger heteromultimeric complexes such as the mammalian MSC

Increasing cleavage specificity and activity of restriction endonuclease KpnI

Restriction enzyme KpnI is a HNH superfamily endonuclease requiring divalent metal ions for DNA cleavage but not for binding. The active site of KpnI can accommodate metal ions of different atomic radii for DNA cleavage. Although Mg2+ ion higher than 500 μM mediates promiscuous activity, Ca2+ suppresses the promiscuity and induces high cleavage fidelity. Here, we report that a conservative mutation of the metal-coordinating residue D148 to Glu results in the elimination of the Ca2+-mediated cleavage but imparting high cleavage fidelity with Mg2+. High cleavage fidelity of the mutant D148E is achieved through better discrimination of the target site at the binding and cleavage steps. Biochemical experiments and molecular dynamics simulations suggest that the mutation inhibits Ca2+-mediated cleavage activity by altering the geometry of the Ca2+-bound HNH active site. Although the D148E mutant reduces the specific activity of the enzyme, we identified a suppressor mutation that increases the turnover rate to restore the specific activity of the high fidelity mutant to the wild-type level. Our results show that active site plasticity in coordinating different metal ions is related to KpnI promiscuous activity, and tinkering the metal ion coordination is a plausible way to reduce promiscuous activity of metalloenzymes

The Zinc-binding Domain of Mammalian prolyl-tRNA synthetase is Indispensable for Catalytic Activity and Organism Viability

Aminoacyl-tRNA synthetases (AARS) participate in decoding the genome by catalyzing conjugation of amino acids to their cognate tRNAs. During evolution, biochemical and environmental conditions markedly influenced the sequence and structure of the 20 AARSs, revealing adaptations dictating canonical and orthogonal activities. Here, we investigate the function of the appended Zn2+-binding domain (ZBD) in the bifunctional AARS, glutamyl-prolyl-tRNA synthetase (GluProRS). We developed GluProRS mutant mice by CRISPR-Cas9 with a deletion of 29 C-terminal amino acids, including two of four Zn2+-coordinating cysteines. Homozygous ZBD mutant mice die before embryonic day 12.5, but heterozygous mice are healthy. ZBD disruption profoundly reduces GluProRS canonical function by dual mechanisms: it induces rapid proteasomal degradation of the protein and inhibits ProRS aminoacylation activity, likely by suboptimal positioning of ATP in the spatially adjacent catalytic domain. Collectively, our studies reveal the ZBD as a critical determinant of ProRS activity and GluProRS stability in vitro and in vivo

EPRS is a critical mTORC1-S6K1 effector that influences adiposity in mice

Metabolic pathways that contribute to adiposity and ageing are activated by the mammalian target of rapamycin complex 1 (mTORC1) and p70 ribosomal protein S6 kinase 1 (S6K1) axis. However, known mTORC1-S6K1 targets do not account for observed loss-of-function phenotypes, suggesting that there are additional downstream effectors of this pathway. Here we identify glutamyl-prolyl-tRNA synthetase (EPRS) as an mTORC1-S6K1 target that contributes to adiposity and ageing. Phosphorylation of EPRS at Ser999 by mTORC1-S6K1 induces its release from the aminoacyl tRNA multisynthetase complex, which is required for execution of noncanonical functions of EPRS beyond protein synthesis. To investigate the physiological function of EPRS phosphorylation, we generated Eprs knock-in mice bearing phospho-deficient Ser999-to-Ala (S999A) and phospho-mimetic (S999D) mutations. Homozygous S999A mice exhibited low body weight, reduced adipose tissue mass, and increased lifespan, similar to S6K1-deficient mice and mice with adipocyte-specific deficiency of raptor, an mTORC1 constituent. Substitution of the EprsS999D allele in S6K1-deficient mice normalized body mass and adiposity, indicating that EPRS phosphorylation mediates S6K1-dependent metabolic responses. In adipocytes, insulin stimulated S6K1-dependent EPRS phosphorylation and release from the multisynthetase complex. Interaction screening revealed that phospho-EPRS binds SLC27A1 (that is, fatty acid transport protein 1, FATP1), inducing its translocation to the plasma membrane and long-chain fatty acid uptake. Thus, EPRS and FATP1 are terminal mTORC1-S6K1 axis effectors that are critical for metabolic phenotypes

Effect of laser treatment on the attachment and viability of mesenchymal stem cell responses on shape memory NiTi alloy

The objectives of this study were to investigate the effect of laser-induced surface features on the morphology, attachment and viability of mesenchymal stem cells (MSCs) at different periods of time, and to evaluate the biocompatibility of different zones: laser-melted zone (MZ), heat-affected zone (HAZ) and base metal (BM) in laser-treated NiTi alloy. The surface morphology and composition were studied by scanning electron microscope (SEM) and X-ray photoemission spectroscopy (XPS), respectively. The cell morphology was examined by SEM while the cell counting and viability measurements were done by hemocytometer and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) colorimetric assay. The results indicated that the laser-induced surface features, such as surface roughening, presence of anisotropic dendritic pattern and complete surface Ni oxidation were beneficial to improve the biocompatibility of NiTi as evidenced by the highest cell attachment (4 days of culture) and viability (7 days of culture) found in the MZ. The biocompatibility of the MZ was the best, followed by the BM with the HAZ being the worst. The defective and porous oxide layer as well as the coarse grained structure might attribute to the inferior cell attachment (4 days of culture) and viability (7 days of culture) on the HAZ compared with the BM which has similar surface morphology. © 2014 Elsevier B.V

In vitro mesenchymal stem cell response to a CO2 laser modified polymeric material

With an ageing world population it is becoming significantly apparent that there is a need to produce implants and platforms to manipulate stem cell growth on a pharmaceutical scale. This is needed to meet the socio-economic demands of many countries worldwide. This paper details one of the first ever studies in to the manipulation of stem cell growth on CO2 laser surface treated nylon 6,6 highlighting its potential as an inexpensive platform to manipulate stem cell growth on a pharmaceutical scale. Through CO2 laser surface treatment discrete changes to the surfaces were made. That is, the surface roughness of the nylon 6,6 was increased by up to 4.3 µm, the contact angle was modulated by up to 5° and the surface oxygen content increased by up to 1 atom%. Following mesenchymal stem cell growth on the laser treated samples, it was identified that CO2 laser surface treatment gave rise to an enhanced response with an increase in viable cell count of up to 60,000 cells/ml when compared to the as-received sample. The effect of surface parameters modified by the CO2 laser surface treatment on the mesenchymal stem cell response is also discussed along with potential trends that could be identified to govern the mesenchymal stem cell response

Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota

Campylobacter fetus is a venereal pathogen of cattle and sheep, and an opportunistic human pathogen. It is often assumed that C. fetus infection occurs in humans as a zoonosis through food chain transmission. Here we show that mammalian C. fetus consists of distinct evolutionary lineages, primarily associated with either human or bovine hosts. We use whole-genome phylogenetics on 182 strains from 17 countries to provide evidence that C. fetus may have originated in humans around 10,500 years ago and may have "jumped" into cattle during the livestock domestication period. We detect C. fetus genomes in 8% of healthy human fecal metagenomes, where the human-associated lineages are the dominant type (78%). Thus, our work suggests that C. fetus is an unappreciated human intestinal pathobiont likely spread by human to human transmission. This genome-based evolutionary framework will facilitate C. fetus epidemiology research and the development of improved molecular diagnostics and prevention schemes for this neglected pathogen

Comparative molecular markers\u27 based analyses of cotton (Gossypium L.) lines

This study focuses on AFLP based molecular marker analyses of the breeding lines developed from two cotton species, i.e., Upland cotton (Gossypium hirsutum), well known for its high yields and Pima cotton ( Gossypium barbadense), known for its exceptional fiber fineness. This study used an aneuploid, CS-B17 breeding line of Upland cotton produced by deleting chromosome 17 of G. hirsutum variety TM-1 and replacing it with 3-79 variety of Pima cotton for combining their diverse adaptability and superior fiber quality, respectively. This study also used 47 Recombinant Inbred Lines (RILs) that were developed by crossing CS-B17 with TM-1 and also two commercial Pima cotton varieties, DP-393 and PHY-370 WR, known to have good fiber quality. AFLP System Analysis Kit from Li-Cor including fluorescent dye IRD-700 and IRD-800 labeled primers designed for EcoRI adapters was used in this study. One hundred and twenty eight primer combinations were used and 14 AFLP primer pairs were found suitable for producing polymorphic markers when using IRDye 700 labeled primers for cotton samples. Similarly, 17 IRDye 800 labeled AFLP primer pairs were found usable for these cotton lines. Saga™ Generation 2- AFLP® Analysis Software Version 3.1 (Li-Cor) mediated confirmed gel images were used to prepare the report on comparative presence or absence of AFLP markers among 47 RILs, TM-1, 3-79, CS-B17 as well as two commercial varieties DP-393 and PHY-370 WR. Sixteen markers produced by each AFLP IRDye 700 and 800 labeled primers were used to enrich 3-79 chromosome 17 in TM-1 genetic background. Eight IRDye 700 labeled primers and five IRDye 800 labeled primers were used for producing AFLP markers to compare 47 CS-B17 RILs with fine fiber cotton varieties DP-393 and PHY-370 WR and three markers were found common among them