Cell-targeted regulation of gene expression through synthetic RNA devices

The ability to interface with and program cellular function remains a challenging research frontier in biotechnology. Although the emerging field of synthetic biology has recently generated a variety of gene-regulatory strategies based on synthetic RNA molecules, few strategies exist through which to control such regulatory effects in response to specific exogenous or endogenous molecular signals. Here, we present the development of an engineered RNA-based device platform to detect and act on endogenous protein signals, linking these signals to the regulation of genes and thus cellular function.

We describe efforts to develop an RNA-based device framework for regulating endogenous genes in human cells. Previously developed RNA control devices have demonstrated programmable ligand-responsive genetic regulation in diverse cell types, and we attempted to adapt this class of cis-acting control elements to function in trans. We divided the device into two strands that reconstitute activity upon hybridization. Device function was optimized using an in vivo model system, and we found that device sequence is not as flexible as previously reported. After verifying the in vitro activity of our optimized design, we attempted to establish gene regulation in a human cell line using additional elements to direct device stability, structure, and localization. The significant limitations of our platform prevented endogenous gene regulation.

We next describe the development of a protein-responsive RNA-based regulatory platform. Employing various design strategies, we demonstrated functional devices that both up- and downregulate gene expression in response to a heterologous protein in a human cell line. The activity of our platform exceeded that of a similar, small-molecule-responsive platform. We demonstrated the ability of our devices to respond to both cytoplasmic- and nuclear-localized protein, providing insight into the mechanism of action and distinguishing our platform from previously described devices with more restrictive ligand localization requirements. Finally, we demonstrated the versatility of our device platform by developing a regulatory device that responds to an endogenous signaling protein.

The foundational tool we present here possesses unique advantages over previously described RNA-based gene-regulatory platforms. This genetically encoded technology may find future applications in the development of more effective diagnostic tools and targeted molecular therapy strategies.

Avaliação da resposta imune de neonatos não infectados pelo HIV-1 nascidos de gestantes soropositivas

A síndrome da imunodeficiência adquirida (AIDS), causada pelo vírus da imunodeficiência humana (HIV), é uma das mais destrutivas epidemias do mundo, e a infecção pelo HIV em mulheres jovens vem aumentando rapidamente nos dias atuais. Esse fato tem um impacto importante na transmissão vertical do vírus. Apesar da grande maioria dos casos de aids pediátrica em todo mundo resultar da transmissão vertical, aproximadamente dois terços das crianças expostas ao HIV durante a vida fetal não são infectadas pelo vírus. Muitos trabalhos sugerem que durante a gestação doenças infecciosas maternas podem ter consequências complexas para o desenvolvimento do feto, e poucos trabalhos têm explorado o impacto da exposição ao HIV sobre a responsividade imunológica de crianças não infectadas a diferentes estímulos, particularmente na era das drogas antirretrovirais. Portanto, esse trabalho teve como objetivo avaliar eventos imunes em neonatos não-infectados expostos ao HIV-1 nascidos de gestantes que controlam (G1) ou não (G2) a carga viral plasmática, usando neonatos não expostos como controle. Para tanto, sangue do cordão umbilical de cada neonato foi coletado, plasma e células mononucleares foram separados e a linfoproliferação e o perfil de citocinas foram avaliados. Os resultados demonstraram que a linfoproliferação in vitro induzido por ativadores policlonais foi maior nos neonatos do G2. Entretanto, nenhuma cultura de célula respondeu a um conjunto de peptídeos sintéticos do envelope do HIV-1. A dosagem de citocinas no plasma e nos sobrenadantes das culturas ativadas policlonalmente demonstrou que, enquanto a IL-4 e IL-10 foram as citocinas dominantes produzidas nos grupos G1 e controle, a secreção de IFN-γ, IL-1, Il-6, IL-17 e TNF-α foi significativamente superior nos neonatos G2. Níveis sistêmicos de IL-10 observados dentre os neonatos G1 foram maiores naqueles nascidos de mães tratadas com drogas inibidoras da transcriptase reversa do vírus. Por outro lado, níveis superiores de citocinas inflamatórias foram observados dentre estes nascidos de gestantes tratadas com terapia antirretroviral de alta eficácia. Em resumo, nossos resultados indicam uma responsividade imune alterada em neonatos expostos in utero ao HIV-1 e reforça o papel do tratamento materno anti-viral com drogas menos potentes em atenuar tais distúrbios.

Produção de IL-1β, IL-6 e IL-8 por fibroblastos estimulados por cimentos endodônticos e submetidos à terapia laser de baixa potência

O sucesso do tratamento endodôntico depende da cuidadosa realização de todas as suas fases, terminando com uma obturação tridimensional que alcance todo o sistema de canais radiculares. Desta forma, os materiais obturadores, ou as substâncias liberadas, entrarão em contato com os tecidos perirradiculares, o que poderá influenciar a resposta inflamatória e o processo de reparo. A terapia laser de baixa potência (TLBP) tem sido estudada quanto à sua ação anti-inflamatória, favorecendo o reparo. O objetivo deste estudo foi investigar a produção das citocinas IL-1β, IL-6 e IL-8 por fibroblastos de gengiva humana (linhagem FMM1) como resposta à presença dos extratos dos cimentos endodônticos AH Plus, MTA Fillapex e EndoSequence BC Sealer, bem como a eficácia da TLBP, neste modelo. Para isto, extratos destes cimentos, recém-manipulados e após 24 h do endurecimento, foram preparados em meio de cultura DMEM fresco, conforme as normas ISO 10993-12. Inicialmente, a citotoxicidade dos cimentos foi avaliada, após a interação das células com a diluição seriada destes extratos (1:1 a 1:16), por meio do ensaio MTT. Para a análise da produção de citocinas, 106 células por poço foram cultivadas em placas de cultura de 24 poços, para a interação com os extratos dos cimentos, na diluição 1:4. Estabeleceram-se os grupos não irradiado e irradiado. No grupo irradiado, as culturas celulares receberam duas irradiações do laser InGaAlP (660 nm, 30 mW, 5 J/cm2 e área do feixe de 0,028 cm2), com intervalo de 12 h. O grupo não irradiado foi submetido às mesmas condições ambientais que o irradiado. Os sobrenadantes das culturas foram coletados, centrifugados, aliquotados e armazenados congelados, para a posterior análise pelo ensaio de ELISA. Todos os dados obtidos (médias erro padrão) foram tratados estatisticamente por ANOVA one-way, complementado pelo teste de Tuckey e ANOVA two-way, com correção de Bonferroni (p< 0,05). A citotoxicidade dos cimentos AH Plus e EndoSequence BC Sealer revelou-se tempo/concentração-dependente, enquanto a do MTA Fillapex mostrou-se concentração-dependente. Os cimentos endodônticos induziram a produção das citocinas IL-1β, IL-6 e IL-8 pelos fibroblastos, sem diferença significativa com os controles (p> 0,05). Somente o LPS de E. coli induziu a secreção de IL-8, com diferença estatística (p< 0,05). A TLBP não foi capaz de modular a produção das citocinas em questão, significativamente.

THE POSSIBLE INVOLVEMENT OF TISSUE-TYPE PLASMINOGEN-ACTIVATOR IN LUTEOLYSIS OF RHESUS-MONKEY

Changes of plasminogen activators (PA) during different stages of development of the corpus luteum, and their possible physiological role in luteolysis were studied in rhesus monkeys. It was demonstrated for the first time that monkey corpus luteal cells not only produce PA, but that the function of the corpus luteum is also closely related to the activity of this enzyme system. Generally, the life span for a corpus luteum in monkey is approximately 14-16 days, its demise beginning thereafter. In the present study, we found that urokinase in the corpus luteum is higher on day 5 and day 10 after human chorionic gonadotrophin injection, while the tissue type (t) PA is mainly produced on day 13 when luteolysis may take place. Progesterone production remained high on day 5 and day 10 and decreased dramatically from day 13, indicating the important role of tPA but not urokinase (u) PA in suppressing luteal function. When purified tPA (but not uPA) monoclonal antibody was added to luteal cell culture to neutralize endogenously produced tPA activity, progesterone production in the cells was increased significantly. Interestingly, prolactin alone was capable of increasing PA production by luteal cells; prolactin together with luteinizing hormone, however, had a synergistic luteotrophic effect.

Serum-free culture of rhesus monkey embryonic stem cells

Previous studies have shown that the maintenance and proliferation of undifferentiated rhesus monkey embryonic stem (rES) cells requires medium supplemented with fetal bovine serum (FBS). Due to the uncharacterized composition and variation in serum nature, the present study aimed to replace the serum-containing medium with a serum-free medium in the rES cell culture. The results showed that after the initial 48-h culture in the routinely used serum-containing medium, rES cells can grow and proliferate for a prolonged period in the serum-free medium composed of DMEM supplemented with a cocktail of BSA, IGF-1, TGF-alpha, bFGF, aFGF, estradiol, and progesterone. rES cells cultured in the serum-free medium maintained high level of alkaline phosphatase activity and OCT4 level. There was no indication of differentiation as judged by the marker gene expression of all three embryonic germ layers and trophoblast. In addition, serum-free culture would not affect the passage capacity and differentiation potential of rES cells. This work will facilitate the future study of induced differentiation of rES cells and other applications.

An improved microtiter assay for evaluating anti-HIV-I neutralizing antibodies from sera or plasma

Background: The anti-HIV-1 neutralizing antibody assay is widely used in AIDS vaccine research and other experimental and clinical studies. The vital dye staining method applied in the detection of anti-HIV-1 neutralizing antibody has been used in many laboratories. However, the unknown factor(s) in sera or plasma affected cell growth and caused protection when the tested sera or plasma was continuously maintained in cell culture. In addition, the poor solubility of neutral red in medium (such as RPMI-1640) also limited the use of this assay. Methods: In this study, human T cell line C8166 was used as host cells, and 3-(4,5-Dimethyl-2-thiazolyl)- 2,5-diphenyl-2H-tetrazolium bromide (MTT) instead of neutral red was used as vital dye. In order to avoid the effect of the unknown factor( s), the tested sera or plasma was removed by a washout procedure after initial 3 - 6 h culture in the assay. Result: This new assay eliminated the effect of the tested sera or plasma on cell growth, improved the reliability of detection of anti-HIV-1 neutralizing antibody, and showed excellent agreement with the p24 antigen method. Conclusion: The results suggest that the improved assay is relatively simple, highly duplicable, cost-effective, and well reliable for evaluating anti-HIV-1 neutralizing antibodies from sera or plasma.

In vitro osteoblast response to ferritic stainless steel fiber networks for magneto-active layers on implants

The use of a porous coating on prosthetic components to encourage bone ingrowth is an important way of improving uncemented implant fixation. Enhanced fixation may be achieved by the use of porous magneto-active layers on the surface of prosthetic implants, which would deform elastically on application of a magnetic field, generating internal stresses within the in-growing bone. This approach requires a ferromagnetic material able to support osteoblast attachment, proliferation, differentiation, and mineralization. In this study, the human osteoblast responses to ferromagnetic 444 stainless steel networks were considered alongside those to nonmagnetic 316L (medical grade) stainless steel networks. While both networks had similar porosities, 444 networks were made from coarser fibers, resulting in larger inter-fiber spaces. The networks were analyzed for cell morphology, distribution, proliferation, and differentiation, extracellular matrix production and the formation of mineralized nodules. Cell culture was performed in both the presence of osteogenic supplements, to encourage cell differentiation, and in their absence. It was found that fiber size affected osteoblast morphology, cytoskeleton organization and proliferation at the early stages of culture. The larger inter-fiber spaces in the 444 networks resulted in better spatial distribution of the extracellular matrix. The addition of osteogenic supplements enhanced cell differentiation and reduced cell proliferation thereby preventing the differences in proliferation observed in the absence of osteogenic supplements. The results demonstrated that 444 networks elicited favorable responses from human osteoblasts, and thus show potential for use as magnetically active porous coatings for advanced bone implant applications. © 2012 Wiley Periodicals, Inc.

Embryonic and genetic manipulation in fish

Fishes, the biggest and most diverse community in vertebrates are good experimental models for studies of cell and developmental biology by many favorable characteristics. Nuclear transplantation in fish has been thoroughly studied in China since 1960s. Fish nuclei of embryonic cells from different genera were transplanted into enucleated eggs generating nucleo-cytoplasmic hybrids of adults. Most importantly, nuclei of cultured goldfish kidney cells had been reprogrammed in enucleated eggs to support embryogenesis and ontogenesis of a fertile fish. This was the first case of cloned fish with somatic cells. Based on the technique of microinjection, recombinant MThGH gene has been transferred into fish eggs and the first batch of transgenic fish were produced in 1984. The behavior of foreign gene was characterized and the onset of the foreign gene replication occurred between the blastula to gastrula stages and random integration mainly occurred at later stages of embryogenesis. This eventually led to the transgenic mosaicism. The MThGH-transferred common carp enhanced growth rate by 2-4 times in the founder juveniles and doubled the body weight in the adults. The transgenic common carp were more efficient in utilizing dietary protein than the controls. An "all-fish" gene construct CAgcGH has been made by splicing the common carp beta-actin gene (CA) promoter onto the grass carp growth hormone gene (gcGH) coding sequence. The CAgcGH-transferred Yellow River Carp have also shown significantly fast-growth trait. Combination of techniques of fish cell culture, gene transformation with cultured cells and nuclear transplantation should be able to generate homogeneous strain of valuable transgenic fish to fulfil human requirement in 21(st) century.

Primmorphs from archaeocytes-dominant cell population of the sponge Hymeniacidon perleve: Improved cell proliferation and spiculogenesis

Marine sponges (Porifera) possess an extraordinary diversity of bioactive metabolites for new drug discovery and development. In vitro cultivation of sponge cells in a bioreactor system is very attractive for the sustainable production of sponge-derived bioactive metabolites; however, it is still a challenging task. The recent establishment of sponge primmorphs, multicellular aggregates from dissociated mixed-cell population (MCP), has been widely acknowledged to hold great promise for cultivation in vitro. Here we present a new method to establish an in vitro sponge primmorph culture from archaeocyte-dominant cell population (ADCP) enriched by a Ficoll gradient, rather than a mixed-cell population (MCP). Our rationale is based upon the totipotency (the ability of a cell to differentiate into other cell types) of archaeocyte cells and the different biological functions of various sponge cell types. A sponge, Hymeniacidon perleve collected from the China Yellow Sea was used as a model system for this investigation. Distinct dynamics of primmorph formation were observed while significant increases in DNA synthesis, cell proliferation (up to threefold), and cell growth (up to fourfold) were achieved. Furthermore, a time-dependent spiculogenesis was clearly demonstrated in our longterm culture, indicating high metabolic activity of primmorphs from the ADCP. This new method represents an important step forward to advance sponge cell culture in vitro that may lead to commercial exploitation of sponge-derived drugs. (C) 2003 Wiley Periodicals, Inc.

Towards manipulation of post-biosynthetic events in secondary metabolism of plant cell cultures

Plant cell cultures have been suggested as a feasible technology for the production of a myriad of plant-derived metabolites. However, commercial application of plant cell culture has met limited success with only a handful of metabolites produced at the pilot- and commercial-scales. To improve the production of secondary metabolites in plant cell cultures, efforts have been devoted predominantly to the optimization of biosynthetic pathways by both process and genetic engineering approaches. Given that secondary metabolism includes-the synthesis. metabolism and catabolism of endogenous compounds by the specialized proteins, this review intends to draw attention to the manipulation and optimization of post-biosynthetic events that follow the formation of core metabolite structures in biosynthetic pathways. These post-biosynthetic events-the chemical and enzymatic modifications, transport, storage/secretion and catabolism/degradation have been largely unexplored in the past. Potential areas are identified where further research is needed to answer fundamental questions that have implications for advanced bioprocess design. Anthocyanin production by plant cell cultures is used as a case study for this discussion, as it presents a good example of compounds for which there are extensive research publications but still no commercial bioprocess. It is perceived that research on post-biosynthetic processes may lead to future opportunities for significant advances in commercial plant cell cultures. (C) 2002 Elsevier Science Inc. All rights reserved.

Layer-by-layer assembly of viral capsid for cell adhesion

Cowpea mosaic virus (CPMV)-based thin films are biologically active for cell culture. Using layer-by-layer assembly of CPMV and poly(diallyldimethylammonium chloride), quantitatively scalable biomolecular surfaces were constructed, which were well characterized using quartz crystal microbalance, UV-vis and atomic force microscopy. The surface coverage of CPMV nanoparticles depended on the adsorption time and pH of the virus solution, with a greater amount of CPMV adsorption occurring near its isoelectric point. It was found that the adhesion and proliferation of NIH-3T3 fibroblasts can be controlled by the coverage of viral particles using this multilayer technique.

Primary culture and characteristic morphologies of medulla terminalis neurons in the eyestalks of Chinese shrimp, Fenneropenaeus chinensis

A method for culturing medulla terminalis (MT) neurons in the eyestalk of Chinese shrimp, Fenneropenaeus chinensis, was first established. The neurons showed immediate outgrowth in the culture medium supplemented with glutamine, glucose and antibiotics. The cells grew for about 2-7 days and then sustained for a week or more. At least six types of neurons were distinguished on the basis of size and form of soma and outgrowth pattern of cells. (C) 2003 Elsevier Science B.V. All rights reserved.

Exploitation of Ebola Virus VP35 Protein to identify new drugs counteracting its type I IFN antagonism

Ebolaviruses (EBOVs) are among the most virulent and deadly pathogens ever known, causing fulminant haemorrhagic fevers in humans and non-human primates. The 2014 outbreak of Ebola virus disease (EVD) in West Africa has claimed more lives than all previous EVD outbreaks combined. The EBOV high mortality rates have been related to the virus-induced impairment of the host innate immunity reaction due to two virus-coded proteins, VP24 and VP35. EBOV VP35 is a multifunctional protein, it is essential for viral replication as a component of the viral RNA polymerase and it also participates in nucleocapsid assembly. Early during EBOV infection, alpha-beta interferon (IFN-α/β) production would be triggered upon recognition of viral dsRNA products by cytoplasmic retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs). However, this recognition is efficiently prevented by the double-stranded RNA (dsRNA) binding activity of the EBOV VP35 protein, which hides RLRs binding sites on the dsRNA phosphate backbone as well the 5’-triphosphate (5’-ppp) dsRNA ends to RIG-I recognition. In addition to dsRNA binding and sequestration, EBOV VP35 inhibits IFN-α/β production preventing the activation of the IFN regulatory factor 3 (IRF-3) by direct interaction with cellular proteins. Previous studies demonstrated that single amino acid changes in the VP35 dsRNA binding domain reduce EBOV virulence, indicating that VP35 is an attractive target for antiviral drugs development. Within this context, here we report the establishment of a novel method to characterize the EBOV VP35 inhibitory function of the dsRNA-dependent RIG-I-mediated IFN-β signaling pathway in a BLS2 cell culture setting. In such system, a plasmid containing the promoter region of IFN-β gene linked with a luciferase reporter gene was transfected, together with a EBOV VP35 mammalian expression plasmid, into the IFN-sensitive A549 cell line, and the IFN-induction was stimulated through dsRNA transfection. Through alanine scanning mutational studies with biochemical, cellular and computational methods we highlighted the importance of some VP35 residues involved in dsRNA end-capping binding, such as R312, K282 and R322, that may serve as target for the development of small-molecule inhibitors against EBOV. Furthermore, we identified a synthetic compound that increased IFN-induction only under antiviral response stimulation and subverted VP35 inhibition, proving to be very attractive for the development of an antiviral drug. In conclusion, our results provide the establishment of a new assay as a straightforward tool for the screening of antiviral compounds that target i) dsRNA-VP35 or cellular protein-VP35 interaction and ii) dsRNA-dependent RIG-I-mediated IFN signaling pathway, in order to potentiate the IFN response against VP35 inhibition, setting the bases for further drug development.

Continuous non-destructive monitoring of cell health using impedance based interdigitated electrode structured sensors

This article examines some preliminary tests which were performed in order to evaluate the best electrode configuration (width and spacing) for cell culture analyses. Biochips packaged with indium tin oxide (ITO) interdigitated electrodes (IDEs) were used to perform impedance measurements on A549 cells cultured on the surface of the biochip. Several tests were carried out using a 10 mM solution of Sodium Chloride (NaCl), cell medium and the cell culture itself to characterize some of the configurations already fabricated in the facilities at Tyndall National Institute.

Assessment of the immunomodulatory effects of raw/farm milk and probiotic bacteria

The overall aims of this study were to investigate the differences between raw/farm milk and pasteurised milk with respect to potential immune modifying effects following consumption and investigate the bacterial composition of raw milk compared to pasteurised milk. Furthermore, in this thesis, panels of potential probiotic bacteria from the Bifidobacterium and Lactobacillus genera were investigated. The overall bacterial composition of raw milk was compared with pasteurised milk using samples obtained from commercial milk producers around Ireland using next generation sequencing technology (454 pyrosequencing). Here the presence of previously unrecognised and diverse bacterial populations in unpasteurised cow’s milk was identified. Futhermore the bacterial content of pasteurised milk was found to be more diverse than previously thought. The global response of the adenocarcinoma cell line HT-29 to raw milk and pasteurised milk exposures were also characterised using whole genome microarray technology. Over one thousand differentially expressed genes were identified which were found to be involved in a plethora of cellular functions. Interestingly a reduction in immune related activity (e.g. Major histocompatability complex class II signalling and T and B cell proliferation) was identified in cells exposed to pasteurised milk compared with raw milk exposures. Further studies comparing human cell response to raw versus pasteurised milk was performed using peripheral blood mononuclear cells (PBMC) from healthy donors. A reduction in CD14 was identified following raw milk exposures compared with pasteurised milk and the pattern of cytokine production may indicate that gram positive bacteria in the raw milk were contributing to the differences in the cellular response to raw versus pasteurised milk. Panels of potentially probiotic bacteria (comprising of lactobacilli and bifidobacteria) were further assessed for immunomodulatory capabilities using cell culture based models. Gene expression and cytokine production were used to evaluate stimulated and unstimulated (LPS) cellular responses as well as interaction mechanisms