Magnetically propelled chained nanocomposites for biologically relevant media exploration.

Elongated nanostructures to be remotely and magnetically propelled in biologically relevant media, have gained attention as offering themselves as effective tools or carriers in theragnostics applications. However, the magnetic actuation associated remains challenging due to the lack of mechanical information in the media of interest, taking into account biophysical or biomedical purposes. In this study, we detail the magnetic actuation of magnetically propelled chained nanocomposites considering their dynamics, in which their velocity can be modulated in terms of the viscosity of the medium considered, given a magnetic field gradient. Simpler cases of distilled water, a water/glycerol mixture and a fluid made of cell extracts (imitating the cytosol of cells) of known viscosity are the basis experiments for the study of more complex media inside HeLa cells, murine NIH-3T3 fibroblasts and zebrafish larvae, offering the mechanical information required. The experimental results indicate that the magnetically propelled performance of the chained nanostructures can be precisely controlled in potentially changing scenarios, where drug and heat delivery, magnetic separation, or microfluidic technologies are demanded, using a magnetic field gradient and providing good estimations of the dynamical parameters involved.

Red Blood Cells Protein Profile Is Modified in Breast Cancer Patients.

Metastasis is the primary cause of death for most breast cancer (BC) patients who succumb to the disease. During the hematogenous dissemination, circulating tumor cells interact with different blood components. Thus, there are microenvironmental and systemic processes contributing to cancer regulation. We have recently published that red blood cells (RBCs) that accompany circulating tumor cells have prognostic value in metastatic BC patients. RBC alterations are related to several diseases. Although the principal known role is gas transport, it has been recently assigned additional functions as regulatory cells on circulation. Hence, to explore their potential contribution to tumor progression, we characterized the proteomic composition of RBCs from 53 BC patients from stages I to III and IV, compared with 33 cancer-free controls. In this work, we observed that RBCs from BC patients showed a different proteomic profile compared to cancer-free controls and between different tumor stages. The differential proteins were mainly related to extracellular components, proteasome, and metabolism. Embryonic hemoglobins, not expected in adults' RBCs, were detected in BC patients. Besides, lysosome-associated membrane glycoprotein 2 emerge as a new RBCs marker with diagnostic and prognostic potential for metastatic BC patients. Seemingly, RBCs are acquiring modifications in their proteomic composition that probably represents the systemic cancer disease, conditioned by the tumor microenvironment.

Manganese Ferrite Nanoparticles Encapsulated into Vitamin E/Sphingomyelin Nanoemulsions as Contrast Agents for High-Sensitive Magnetic Resonance Imaging.

Magnetic resonance imaging (MRI) is one of the most powerful non-invasive imaging modalities used in clinics due to its great spatial resolution and excellent soft-tissue contrast, though still less sensitive than other techniques such as the nuclear imaging modalities. This lack of sensitivity can be improved with the use of contrast agents based on nanomaterials. In recent years, researchers have focused on the development of magnetic nanoparticles, given their role as enhancers of the contrast signal based on the magnetic resonance. Manganese ferrite nanoparticles stand out, given their high magnetic susceptibility and magnetic soft nature. Herein, 10 nm MnFe2 O4 nanoparticles, functionalized with the natural antioxidant vitamin E (VitE-MFO) are encapsulated into simple, biodegradable and non-toxic nanoemulsions (NEs), by a reproducible one-step method obtaining stable 150 nm-sized magnetic nanoemulsions (VitE-MFO-NEs). After encapsulation, the superparamagnetic properties of VitE-MFO are maintained and MR imaging studies reveal an extremely high transverse relaxivity for VitE-MFO-NEs (652.9 × 10-3  m-1  s-1 ), twofold higher than VitE-MFO value. Moreover, VitE-MFO-NEs show great in vivo biocompatibility and good signal in in vivo and ex vivo MRI, which indicates their great potential for biomedical imaging enhancing the negative MR contrast and significantly improving the sensitivity of MRI.

Methodology for the Isolation and Analysis of CTCs.

The majority of deaths related to breast cancer are caused by metastasis. Understanding the process of metastasis is key to achieve a reduction on breast cancer mortality. Currently, liquid biopsies are gaining attention in this regard. Circulating tumor cells (CTCs), an important component of liquid biopsies, are cells shed from primary tumor that disseminate to blood circulation being responsible of distal metastasis. Hence, the study CTCs is a promising alternative to monitor the progress of metastasis disease and can be used for early diagnosis of cancers as well as for earlier assessment of cancer recurrence and therapy efficacy. Despite their clinical interest, CTC analysis is not recommended by oncology guidelines so far. The main reason is that there is no gold standard technology for CTCs isolation and most of the current technologies are not yet validated for clinical use. In this chapter we will focus on the most relevant technologies for CTC isolation based on their properties and depending on whether it is a positive or negative selection. We also describe each technology based on its potential use and its relevance in breast cancer. The chapter also contains a future perspective including the challenges and requirements of CTC detection.

A pathogenesis-related 10 protein catalyzes the final step in thebaine biosynthesis.

The ultimate step in the formation of thebaine, a pentacyclic opiate alkaloid readily converted to the narcotic analgesics codeine and morphine in the opium poppy, has long been presumed to be a spontaneous reaction. We have detected and purified a novel enzyme from opium poppy latex that is capable of the efficient formation of thebaine from (7S)-salutaridinol 7-O-acetate at the expense of labile hydroxylated byproducts, which are preferentially produced by spontaneous allylic elimination. Remarkably, thebaine synthase (THS), a member of the pathogenesis-related 10 protein (PR10) superfamily, is encoded within a novel gene cluster in the opium poppy genome that also includes genes encoding the four biosynthetic enzymes immediately upstream. THS is a missing component that is crucial to the development of fermentation-based opiate production and dramatically improves thebaine yield in engineered yeast.

Lignocellulose-derived thin stillage composition and efficient biological treatment with a high-rate hybrid anaerobic bioreactor system.

BACKGROUND: This study aims to chemically characterize thin stillage derived from lignocellulosic biomass distillation residues in terms of organic strength, nutrient, and mineral content. The feasibility of performing anaerobic digestion on these stillages at mesophilic (40 °C) and thermophilic (55 °C) temperatures to produce methane was demonstrated. The microbial communities involved were further characterized. RESULTS: Energy and sugar cane stillage have a high chemical oxygen demand (COD of 43 and 30 g/L, respectively) and low pH (pH 4.3). Furthermore, the acetate concentration in sugar cane stillage was high (45 mM) but was not detected in energy cane stillage. There was also a high amount of lactate in both types of stillage (35-37 mM). The amount of sugars was 200 times higher in energy cane stillage compared to sugar cane stillage. Although there was a high concentration of sulfate (18 and 23 mM in sugar and energy cane stillage, respectively), both thin stillages were efficiently digested anaerobically with high COD removal under mesophilic and thermophilic temperature conditions and with an organic loading rate of 15-21 g COD/L/d. The methane production rate was 0.2 L/g COD, with a methane percentage of 60 and 64, and 92 and 94 % soluble COD removed, respectively, by the mesophilic and thermophilic reactors. Although both treatment processes were equally efficient, there were different microbial communities involved possibly arising from the differences in the composition of energy cane and sugar cane stillage. There was more acetic acid in sugar cane stillage which may have promoted the occurrence of aceticlastic methanogens to perform a direct conversion of acetate to methane in reactors treating sugar cane stillage. CONCLUSIONS: Results showed that thin stillage contains easily degradable compounds suitable for anaerobic digestion and that hybrid reactors can efficiently convert thin stillage to methane under mesophilic and thermophilic conditions. Furthermore, we found that optimal conditions for biological treatment of thin stillage were similar for both mesophilic and thermophilic reactors. Bar-coded pyrosequencing of the 16S rRNA gene identified different microbial communities in mesophilic and thermophilic reactors and these differences in the microbial communities could be linked to the composition of the thin stillage.

Does size matter? Separations on guard columns for fast sample analysis applied to bioenergy research.

BACKGROUND: Increasing sample throughput is needed when large numbers of samples have to be processed. In chromatography, one strategy is to reduce column length for decreased analysis time. Therefore, the feasibility of analyzing samples simply on a guard column was explored using refractive index and ultraviolet detection. Results from the guard columns were compared to the analyses using the standard 300 mm Aminex HPX-87H column which is widely applied to the analysis of samples from many biotechnology- and bioenergy-related experiments such as biomass conversions or fermentations. RESULTS: The 50 mm Rezex RFQ Fast Acid H(+) guard column was able to separate the most common fermentation products (ethanol, acetone, iso- and n-butanol) and promising precursors (furfural and 5-hydroxymethylfurfural) of biofuels and value-added chemicals. Compound profiles in fermentation samples were analyzed with similar accuracy compared to results using the 300 mm column. However, separation of glucose and xylose was not achieved. Nevertheless, it was possible to monitor the consumption of one of the two sugars during fermentation if the other one was absent or remained constant over the course of the experiment. If correct peak integration and interference subtraction was applied, concentration profiles from enzymatic digestibility experiments and even more complex samples (e.g. acetone-butanol-ethanol (ABE) fermentation) were reliably obtained. With the 50 mm guard column, samples were analyzed up to ten-times faster compared to the 300 mm column. A further decrease in analysis time was achieved by using the 30 mm Micro Guard Cation H guard column. This column is especially suitable for the rapid analysis of compounds with long elution times on the standard 300 mm column, such as biofuel-related alcohols (e.g., n-butanol, n-hexanol) and furan- and tetrahydrofuran-type molecules. CONCLUSION: Applied to a suitable set of samples, separations on a guard column can give rapid and sufficiently accurate information on compound changes over the course of an experiment. Therefore, it is an inexpensive and ideal tool for processing a large amount of samples, such as in screening or discovery experiments, where detecting relative changes is often sufficient to identify promising candidates for further analysis.

Fungi isolated from Miscanthus and sugarcane: biomass conversion, fungal enzymes, and hydrolysis of plant cell wall polymers.

BACKGROUND: Biofuel use is one of many means of addressing global change caused by anthropogenic release of fossil fuel carbon dioxide into Earth's atmosphere. To make a meaningful reduction in fossil fuel use, bioethanol must be produced from the entire plant rather than only its starch or sugars. Enzymes produced by fungi constitute a significant percentage of the cost of bioethanol production from non-starch (i.e., lignocellulosic) components of energy crops and agricultural residues. We, and others, have reasoned that fungi that naturally deconstruct plant walls may provide the best enzymes for bioconversion of energy crops. RESULTS: Previously, we have reported on the isolation of 106 fungi from decaying leaves of Miscanthus and sugarcane (Appl Environ Microbiol 77:5490-504, 2011). Here, we thoroughly analyze 30 of these fungi including those most often found on decaying leaves and stems of these plants, as well as four fungi chosen because they are well-studied for their plant cell wall deconstructing enzymes, for wood decay, or for genetic regulation of plant cell wall deconstruction. We extend our analysis to assess not only their ability over an 8-week period to bioconvert Miscanthus cell walls but also their ability to secrete total protein, to secrete enzymes with the activities of xylanases, exocellulases, endocellulases, and beta-glucosidases, and to remove specific parts of Miscanthus cell walls, that is, glucan, xylan, arabinan, and lignin. CONCLUSION: This study of fungi that bioconvert energy crops is significant because 30 fungi were studied, because the fungi were isolated from decaying energy grasses, because enzyme activity and removal of plant cell wall components were recorded in addition to biomass conversion, and because the study period was 2 months. Each of these factors make our study the most thorough to date, and we discovered fungi that are significantly superior on all counts to the most widely used, industrial bioconversion fungus, Trichoderma reesei. Many of the best fungi that we found are in taxonomic groups that have not been exploited for industrial bioconversion and the cultures are available from the Centraalbureau voor Schimmelcultures in Utrecht, Netherlands, for all to use.

Analytical method for the determination of organic acids in dilute acid pretreated biomass hydrolysate by liquid chromatography-time-of-flight mass spectrometry.

BACKGROUND: For the development of lignocellulosic biofuels a common strategy to release hemicellulosic sugars and enhance the enzymatic digestibility of cellulose is the heat pretreatment of biomass with dilute acid. During this process, fermentation inhibitors such as 5-hydroxymethylfurfural, furfural, phenolics, and organic acids are formed and released into the so-called hydrolysate. The phenolic inhibitors have been studied fairly extensively, but fewer studies have focused on the analysis of the organic acids profile. For this purpose, a simple and fast liquid chromatography/mass spectrometry (LC/MS) method for the analysis of organic acids in the hydrolysate has been developed using an ion exchange column based on a polystyrene-divinylbenzene polymer frequently used in biofuel research. The application of the LC/MS method to a hydrolysate from Miscanthus has been evaluated. RESULTS: The presented LC/MS method involving only simple sample preparation (filtration and dilution) and external calibration for the analysis of 24 organic acids present in dilute acid pretreated biomass hydrolysate is fast (12 min) and reasonably sensitive despite the small injection volume of 2 µL used. The lower limit of quantification ranged from 0.2 µg/mL to 2.9 µg/mL and the limit of detection from 0.03 µg/mL to 0.7 µg/mL. Analyte recoveries obtained from a spiked hydrolysate were in the range of 70 to 130% of the theoretical yield, except for glyoxylic acid, malic acid, and malonic acid, which showed a higher response due to signal enhancement. Relative standard deviations for the organic acids ranged from 0.4 to 9.2% (average 3.6%) for the intra-day experiment and from 2.1 to 22.8% (average 8.9%) for the inter-day (three-day) experiment. CONCLUSION: We have shown that the analysis of the profile of 24 organic acids present in biomass hydrolysate can be achieved by a simple LC/MS method applying external calibration and minimal sample preparation. The organic acids eluted within only 12 min by isocratic elution, enabling high sample throughput. Repeatability (precision and accuracy) and recovery were sufficiently accurate for most of the organic acids tested, making the method suitable for their fast determination in hydrolysate. We envision that this method can be further expanded to a larger number of organic acids, including phenolic acids such as p-coumaric acid and ferulic acid and other molecules depending on the researchers' needs.

Rapid determination of cellulose.

The cellulose analysis results of four feedstocks and Avicel obtained by a one-step/two-step hydrolysis method were compared to the conventional cellulose assay according to Updegraff. Slightly lower cellulose levels were observed for Avicel (97%), corn stover (97%), poplar (96%), and Miscanthus (94%) but for pine the amounts were almost identical (101%). Despite these differences, the one-step/two-step method can be seen as a true alternative to the more labor-intensive Updegraff method.

Synergy effects of magnetic silica nanostructures for drug delivery applications.

This article presents a capable strategy of using hybrid nanostructures to improve the magnetic-based performance jointly with the internalization process into cells, for drug delivery applications. The promising combination stems from the concept of magnetic silica nanostructures, referring to magnetic nanoparticles of transition metal ferrites, coated with a silica (or hydroxyapatite) shell or included in a hollow silica nanostructure, such that they can offer a proper and controlled drug delivery. The synergy effects are brought on considering several characteristics; the magnetic properties of the transition metal ferrites as aggregates, the increased biocompatibility, the reduced toxicity, the porosity, the suitable chemical functionalization of silica and different effects such as local heating based on hyperthermia or other triggering effects for a time-space controlled drug delivery.

Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates.

The efficient production of biofuels from cellulosic feedstocks will require the efficient fermentation of the sugars in hydrolyzed plant material. Unfortunately, plant hydrolysates also contain many compounds that inhibit microbial growth and fermentation. We used DNA-barcoded mutant libraries to identify genes that are important for hydrolysate tolerance in both Zymomonas mobilis (44 genes) and Saccharomyces cerevisiae (99 genes). Overexpression of a Z. mobilis tolerance gene of unknown function (ZMO1875) improved its specific ethanol productivity 2.4-fold in the presence of miscanthus hydrolysate. However, a mixture of 37 hydrolysate-derived inhibitors was not sufficient to explain the fitness profile of plant hydrolysate. To deconstruct the fitness profile of hydrolysate, we profiled the 37 inhibitors against a library of Z. mobilis mutants and we modeled fitness in hydrolysate as a mixture of fitness in its components. By examining outliers in this model, we identified methylglyoxal as a previously unknown component of hydrolysate. Our work provides a general strategy to dissect how microbes respond to a complex chemical stress and should enable further engineering of hydrolysate tolerance.

Assessment of DNA complexation onto polyelectrolyte-coated magnetic silica nanoparticles.

The polyelectrolyte-DNA complexation method to form magnetoplexes using silica-coated iron oxide magnetic nanoparticles as inorganic substrates is an attractive and promising process in view of the potential applications including magnetofection, DNA extraction and purification, and directed assembly of nanostructures. Herein, we present a systematic physico-chemical study that provides clear evidence of the type of interactions established, reflects the importance of the DNA length, the nanoparticle size and the ionic strength, and permits the identification of the parameters controlling both the stability and the type of magnetoplexes formed. This information can be used to develop targeted systems with properties optimized for the various proposed applications of magnetoplexes.

Characterization of Miscanthus giganteus lignin isolated by ethanol organosolv process under reflux condition.

Miscanthus giganteus lignin was extracted by an organosolv process under reflux conditions (4 h) with varying concentrations of ethanol (65%, 75%, 85%, 95%) and 0.2 M hydrochloric acid as catalyst. The resulting lignin was extensively characterized by size exclusion chromatography (SEC), Fourier-transform infrared spectroscopy (FTIR), gas chromatography-mass spectrometry (GC/MS), two-dimensional nuclear magnetic resonance spectroscopy (2D-NMR), and chemical analysis (residual sugars, Klason lignin, ash). The predominant linkage units present were ß-O-4' (82-84%), resinol (6-7%), and phenylcoumaran (10-11%). The 65% ethanol solvent system gave the lowest lignin yield (14% of starting biomass) compared to 29-32% of the other systems. Increasing ethanol concentration resulted in decreasing carbohydrate content of the lignins (3.6-1.1%), a higher solubility in tetrahydrofuran (THF), a slight reduction of the molecular weight (M(w) 2.72-2.25 KDa), an increasing α-ethoxylation, and an increase in ethoxylated phenylpropenoic compounds (p-coumaric and ferulic acid), but the S/G ratio of the monolignols (0.63, GC/MS) and Klason lignin content (86-88%) were unaffected. An extraction method for these ethyl-esterified phenylpropenoids and smaller molecular weight lignin compounds was developed. The effect of reaction time (2, 4, and 8 h) was investigated for the 95% ethanol solvent system. Besides increased lignin yield (13-43%), a slight increase in M(w) (2.21-2.38 kDa) and S/G ratio (0.53-0.68, GC-MS) was observed. Consecutive extractions suggested that these changes were not from lignin modifications (e.g., condensations) but rather from extraction of lignin of different composition. The results were compared to similar solvent systems with 95% acetone and 95% dioxane.

Magnetic silica nanoparticle cellular uptake and cytotoxicity regulated by electrostatic polyelectrolytes-DNA loading at their surface.

Magnetic silica nanoparticles show great promise for drug delivery. The major advantages correspond to their magnetic nature and ease of biofunctionalization, which favors their ability to interact with cells and tissues. We have prepared magnetic silica nanoparticles with DNA fragments attached on their previously polyelectrolyte-primed surface. The remarkable feature of these materials is the compromise between the positive charges of the polyelectrolytes and the negative charges of the DNA. This dual-agent formulation dramatically changes the overall cytotoxicity and chemical degradation of the nanoparticles, revealing the key role that surface functionalization plays in regulating the mechanisms involved.

Amorphous tunable-size Co-B magnetic nanoparticles from the cobalt-catalyzed NaBH4 hydrolysis.

The cobalt-catalyzed hydrolysis of sodium borohydride (NaBH(4)) has become an attractive process in view of the possibilities of using the hydride for hydrogen storage material and also for the production of amorphous and tunable-size magnetic nanoparticles. This process in which the metallic catalyst transforms into a Co- and B-based magnetic by-product when in contact with NaBH(4) has been modified in order to control the mechanism of formation, tune the final size and study the particular magnetic behavior of the Co-B alloy nanoparticles provided.

G protein-coupled receptor mediated trimethylamine sensing.

A new approach for the detection of trimethylamine (TMA) using a recombinant cell line of Xenopus laevis melanophores was developed. The cells were genetically modified to express the mouse trace amine-associated receptor 5 (mTAAR5), a G protein-coupled receptor from the mouse olfactory epithelium, which conferred high sensitivity to TMA. Cellular responses to TMA were analyzed by two different techniques, either by absorbance measurements using a microplate reader or by cellular imaging via an inverted microscope. A focused chemical screen allowed the discovery of additional, previously unknown stimuli of mTAAR5. The developed cell-based sensor demonstrated no sensitivity to trimethylamine N-oxide (TMAO), making it suitable for a straightforward evaluation of TMA levels in fish tissue extracts. For the detection of TMA vapor, the cells were covered with agarose, which allowed for intact cell viability for at least 6h in air. The developed gas measurement platform was able to detect TMA from 1 to 100 ppm within 35 min.

Addressing variability in a Xenopus laevis melanophore cell line.

Xenopus laevis melanophores can be used in high-throughput screens for guanine nucleotide binding protein coupled receptor ligands and have potential as biosensors. Inherent in this immortal cell line is a substantial variability, which macroscopic evaluations disregard. Here we demonstrate a systematic way to incorporate this natural variability in the evaluations. Clusters of similar cells from a sparsely seeded cell culture are examined by imaging changes in cell appearance, pigment motility, and cumulative displacements. The time evolution of the image intensity distributions of clusters upon a pigment-dispersing stimulus is used as a signature of the cell clusters, and their behaviors are classified by multivariate analysis. Conventional image subtraction procedures are used to highlight cumulative and transitory changes in the pigment dynamics, enabling characterization of multiple aspects of the cell response from a single experiment. Additionally, a simple way to accomplish standard optical density changes at the single-cell group level is shown. The present results also provide evidence that natural cell variability arising from a cell culture can enrich the diversity of responses from pigment-containing cells assays and underscore that in conventional macroscopic evaluations these aspects are overlooked and can lead to spurious results.