Characterization of agarophytic seaweeds from the biorefinery context

The major seaweed components such as natural colorants (R-phycoerythrin (R-PE), R-phycocyanin (R-PC)), minerals, proteins, lipids, cellulose and agar which are of considerable commercial value were estimated in 15 different agarophytic seaweeds. R-PE and R-PC contents ranged from 138.33 ± 17.67 to 1039.43 ± 27.65 μg/g and 50.26 ± 6.63 to 818.2 ± 48 μg/g on fresh weight (fw) basis, respectively. Appreciable amounts of both macro-minerals (K, Na, Ca, Mg) and micro-minerals (Fe, Zn, Se, Mn) were estimated. The total lipid and protein contents were 0.65 ± 0.06% to 1.53 ± 0.07% and 4.75 ± 0.5% to 19.31 ± 3.5% on dry weight (dw) basis respectively while cellulose and agar contents varied from 3.7 ± 0.13% to 12.20 ± 0.45% and 9.17 ± 0.62% to 25.23 ± 0.50% dw, respectively. The overall finding of this study enable the selection and value addition of agarophytic feedstock for biorefinery.

A fresh liver agar substrate for rearing small numbers of forensically important blow flies (Diptera: Calliphoridae)

Forensically important calliphorids can be reared on a mixture of beef liver and agar. Small pieces of meat, especially fresh or frozen beef liver, will desiccate in 2-6 h, but this simple-to-make feeding substrate remains moist for at least 12 h at 25 and 30 degrees C without desiccation, even in small (5 g) amounts. We determined the survivorship of small numbers of Chrysomya megacephala (F.) (first-instar larvae to adult eclosion) raised on 5 g of liver agar and fresh beef liver. We found that all larvae raised on 5 g of liver died due to desiccation, but survivorship on 5 g of liver agar was equivalent to that on larger (50 g) pieces of either liver agar or beef liver.

Comparison of M.I.C.E. and Etest with CLSI agar dilution for antimicrobial susceptibility testing against oxacillin-resistant Staphylococcus spp

Objective

The main objective of this study was to comparatively evaluate the performance of M.I.C.E. and Etest methodologies to that of agar dilution for determining the antimicrobial susceptibility profile of oxacillin-resistant Staphylococcus spp.

Methods

A total of 100 oxacillin-resistant Staphylococcus spp. isolates were collected from hospitalized patients at a teaching hospital. Antimicrobial susceptibility testing for vancomycin, teicoplanin and linezolid was performed using the reference CLSI agar dilution method (2009), Etest and M.I.C.E. methodologies. The MIC values were interpreted according to CLSI susceptibility breakpoints and compared by regression analysis.

Results

In general, the essential agreement (±1-log₂) between M.I.C.E. and CLSI agar dilution was 93.0%, 84.0% and 77.0% for linezolid, teicoplanin and vancomycin, respectively. Essential agreement rates between M.I.C.E. and Etest were excellent (>90.0%) for all antibiotics tested. Both strips (M.I.C.E. and Etest) yielded two very major errors for linezolid. Unacceptable minor rates were observed for teicoplanin against CoNS and for vancomycin against S. aureus.

Conclusions

According to our results, linezolid and teicoplanin MICs against all staphylococci and S. aureus, respectively, were more accurately predicted by M.I.C.E. strips. However, the Etest showed better performance than M.I.C.E. for predicting vancomycin MICs against all staphylococci. Thus, microbiologists must be aware of the different performance of commercially available gradient strips against staphylococci.

Inactivation mechanisms of pathogenic bacteria in several matrixes during the composting process in a composting toilet

This study aimed to compare the inactivation rate and the mechanisms of pathogenic bacteria in three matrixes (sawdust, rice husk and charcoal) during the composting process. The inactivation rate was evaluated with Escherichia coli strain and the damaged parts and/or functions were evaluated with three different media. Normalized inactivation rate constant in three media and from three matrixes had no significant difference in each process (pure, 1 month and 2 months). The value in rice husk was relatively increased during 2 months but there was no significant difference. The inactivation rate constants of Tryptic Soy Agar (TSA) and Compact Dry E. coli/Coliform in pure sawdust and rice husk were relatively lower than that of Desoxycholate Agar, but increased in 2 months. This indicated that damaging part was changed from outer membrane to enzymes and metabolisms during the 2-month composting process. In the case of charcoal, only the TSA value in apure matrix was relatively lower than that of others, but it increased in 2 months. This indicated that damaging part was changed from outer membrane and enzyme to metabolisms during the composting process. Composting matrix and composting process did not significantly affect inactivation rate of pathogenic bacteria during the process but affected the damaging part of the bacteria.

Conventional and microwave pyrolysis of a macroalgae waste from the Agar-Agar industry. Prospects for bio-fuel production

A comparative study of the pyrolysis of a macroalgae industrial solid waste (algae meal) in an electrical conventional furnace and in a microwave furnace has been carried out. It was found that the chars obtained from both pyrolyses are similar and show good properties for performing as a solid bio-fuel and as a precursor of activated carbon. Bio-oils from conventional pyrolysis have a greater number of phenolic, pyrrole and alkane compounds whereas benzene and pyridine compounds are more predominant in microwave pyrolysis with a major presence of light compounds. The bio-gas fraction from microwave pyrolysis presents a much higher syngas content (H2+CO), and a lower CO2 and CH4 proportion than that obtained by conventional pyrolysis. Yields are similar for both treatments with a slightly higher gas yield in the case of microwave pyrolysis due to the fact that microwave heating favors heterogeneous reactions between the gases and the char.

Traditional methods for isolation of Listeria monocytogenes

Conventional methods for the detection of Listeria monocytogenes in foods and environmental samples relies on selective pre-enrichment, enrichment, and plating. This is followed by confirmation of suspected colonies by testing a limited number of biochemical markers.

Shear wave pulse compression for dynamic elastography using phase-sensitive optical coherence tomography

Assessing the biomechanical properties of soft tissue provides clinically valuable information to supplement conventional structural imaging. In the previous studies, we introduced a dynamic elastography technique based on phase-sensitive optical coherence tomography (PhS-OCT) to characterize submillimetric structures such as skin layers or ocular tissues. Here, we propose to implement a pulse compression technique for shear wave elastography. We performed shear wave pulse compression in tissue-mimicking phantoms. Using a mechanical actuator to generate broadband frequency-modulated vibrations (1 to 5 kHz), induced displacements were detected at an equivalent frame rate of 47 kHz using a PhS-OCT. The recorded signal was digitally compressed to a broadband pulse. Stiffness maps were then reconstructed from spatially localized estimates of the local shear wave speed. We demonstrate that a simple pulse compression scheme can increase shear wave detection signal-to-noise ratio (>12  dB gain) and reduce artifacts in reconstructing stiffness maps of heterogeneous media.

Agar gel immunodiffusion assay to detect antibodies to Type A influenza virus

The agar gel immunodiffusion (AGID) test is used to detect antibodies to Type A influenza group-specific antigens, i.e., the ribonucleoprotein (RNP) and matrix (M) proteins. Therefore, this test will detect antibodies to all influenza A virus subtypes. AGID is commonly used to screen poultry flocks for avian influenza virus infection. The AGID is a simple and economical serological test. All serological testing has its advantages and disadvantages which should be considered before choosing the optimal test for the laboratory needs. Each laboratory must evaluate the laboratory's resources, the volume of testing, the goal of testing, how the test results are used and what types of samples are being tested in order to select the optimal test.

Agar-encapsulated adsorbent based on leaf of platanus sp. to adsorb cadmium ion in water

A low cost and environmentally friendly adsorbent was developed based on leaf of platanus sp. to adsorb cadmium ion in water. The adsorbent was modified with citric acid and then also encapsulated in agar for easy separation after the adsorption process. Parameters such as adsorbent dose, stirring time, solution pH and modification of the adsorbent with citric acid were investigated in a batch experiment in order to determine the optimum condition for Cd (II) adsorption. Based on the Langmuir isotherm adsorption model, the adsorption capacity of cadmium ion for raw adsorbent, modified adsorbent with citric acid and encapsulated adsorbent were 3.69, 15.31 and 6.89 mg/g, respectively. The high adsorption capacity after treatment with citric acid may be due to the increase in carboxylic content of the adsorbent surface and also the increase of surface area and pore volume of the adsorbent. With this high adsorption capacity for cadmium ion and an abundance of raw materials, this bio-adsorbent could be considered as a low cost adsorbent in the near future.

Fast depth-sensitive fluorescence measurements in turbid media using cone shell configuration

Depth-sensitive fluorescence spectroscopy in a two-layered epithelial tissue phantom was demonstrated using a cone shell configuration implemented by an axicon lens and a fiber assembly including five rings of collection fibers. Each collection fiber ring was located at a different radial distance away from the center, for which fluorescence measurements from all rings showed a larger range of sensitivities to the top and bottom layers compared to the previously reported cone shell configuration. Furthermore, multiple fluorescence spectra corresponding to a range of successive targeted depths can be obtained simultaneously, which shortened data acquisition dramatically and eliminated the mechanical moving components required for depth-sensitive optical measurements in the previous setup. This new setup therefore would be preferred in a clinical setting.

MRI phantoms - are there alternatives to agar?

The suitability of different gelling agents as MRI phantoms was evaluated in terms of homogeneity, gel stability and reproducibility. Time and effort for preparation were also taken into account. The relaxation times of various gel compositions were estimated. Carbomer-980 and Carbopol-974P were determined to be promising novel phantom materials. These gelling agents are readily available, inexpensive and easy to handle given that thermal treatment is not required. Furthermore, the viscoelasticity of their polymer network is pH-dependent. With such characteristics, it was even possible to embed sensitive objects and retrieve them after testing. This was demonstrated with a fiber phantom for Diffusion Weighted MRI applications. Since Carbomer-980 and Carbopol-974P are non-hazardous, they are also suitable for multimodal setups (e.g., MRI as well as ultrasonic imaging).

Development of blood-yolk-polymyxin B-trimethoprim agar for the enumeration of Bacillus cereus in various foods

Blood-yolk-polymyxin B-trimethoprim agar (BYPTA) was developed by the addition of egg yolk, laked horse blood, sodium pyruvate, polymyxin B, and trimethoprim, and compared with mannitol-yolk-polymyxin B agar (MYPA) for the isolation and enumeration of Bacillus cereus (B. cereus) in pure culture and various food samples. In pure culture, there was no statistical difference (p>0.05) between the recoverability and sensitivity of MYPA and BYPTA, whereas BYPTA exhibited higher specificity (p<0.05). To evaluate BYPTA agar with food samples, B. cereus was experimentally spiked into six types of foods, triangle kimbab, sandwich, misugaru, Saengsik, red pepper powder, and soybean paste. No statistical difference was observed in recoverability (p>0.05) between MYPA and BYPTA in all tested foods, whereas BYPTA exhibited higher selectivity than MYPA, especially in foods with high background microflora, such as Saengsik, red pepper powder, and soybean paste. The newly developed selective medium BYPTA could be a useful enumeration tool to assess the level of B. cereus in foods, particularly with high background microflora.

Ultrasound effect used as external stimulus for viscosity change of aqueous carrageenans

Ultrasound (US) serves as a stimulus to change shear viscosity of aqueous polysaccharides of ι-carrageenan, κ-carrageenan and, agar. The US effect was compared in their aqueous solutions at 60 °C for the US frequency of 23, 45, and 83 kHz. Under the US condition with 50 W at 45 kHz, the shear viscosity of each aqueous solution was decreased significantly. Subsequently, when the US was stopped, the shear viscosity returned back to the original value. In addition, the US showed different effects of the US frequency over the viscosity change in the three kinds of polysaccharides. When the US frequency was changed, the US effects were less at 83 kHz and 28 kHz for the shear viscosity change. In addition, as NaCl was present in the aqueous solution, the viscosity change decreased by the US exposure. These results suggest that the US effect on the viscosity reduction was influenced by the condition of polymer coil conformation, which was expanded or shrank by electrostatic repulsion of the SO3(-) groups. FT-IR analysis supported that the hydrogen bonds of carrageenans were broken during the US exposure. Using Fourier self-deconvolution for the FT-IR spectra without and with US exposure suggests that the US influenced the hydrogen bonds of water and the OH group of polysaccharides.

Genome-wide quantitative identification of DNA differentially methylated sites in Arabidopsis seedlings growing at different water potential

Background

In eukaryotes, the combinatorial usage of cis-regulatory elements enables the assembly of composite genetic switches to integrate multifarious, convergent signals within a single promoter. Plants as sessile organisms, incapable of seeking for optimal conditions, rely on the use of this resource to adapt to changing environments. Emerging evidence suggests that the transcriptional responses of plants to stress are associated with epigenetic processes that govern chromatin accessibility. However, the extent at which specific chromatin modifications contribute to gene regulation has not been assessed.

Methodology/Principal Findings

In the present work, we combined methyl-sensitive-cut counting and RNA-seq to follow the transcriptional and epigenetic response of plants to simulated drought. Comprehensive genome wide evidence supports the notion that the methylome is widely reactive to water potential. The predominant changes in methylomes were loci in the promoters of genes encoding for proteins suited to cope with the environmental challenge.

Conclusion/Significance

These selective changes in the methylome with corresponding changes in gene transcription suggest drought sets in motion an instructive mechanism guiding epigenetic machinery toward specific effectors genes.

Characterizing an agar/gelatin phantom for image guided dosing and feedback control of high-intensity focused ultrasound

The temperature dependence of an agar/gelatin phantom was evaluated. The purpose was to predict the material property response to high-intensity focused ultrasound (HIFU) for developing ultrasound guided dosing and targeting feedback. Changes in attenuation, sound speed, shear modulus and thermal properties with temperature were examined from 20°C to 70°C for 3 weeks post-manufacture. The attenuation decreased with temperature by a power factor of 0.15. Thermal conductivity, diffusivity and specific heat all increased linearly with temperature for a total change of approximately 16%, 10% and 6%, respectively. Sound speed had a parabolic dependence on temperature similar to that of water. Initially, the shear modulus irreversibly declined with even a slight increase in temperature. Over time, the gel maintained its room temperature shear modulus with moderate heating. A stable phantom was achieved within 2 weeks post-manufacture that possessed quasi-reversible material properties up to nearly 55°C.

Downregulation of TRAF2 mediates NIK-induced pancreatic cancer cell proliferation and tumorigenicity

BACKGROUND

Increased levels of NF-κB are hallmarks of pancreatic ductal adenocarcinoma (PDAC) and both classical and alternative NF-κB activation pathways have been implicated.

METHODOLOGY/PRINCIPAL FINDINGS

Here we show that activation of the alternative pathway is a source for the high basal NF-κB activity in PDAC cell lines. Increased activity of the p52/RelB NF-κB complex is mediated through stabilization and activation of NF-κB-inducing kinase (NIK). We identify proteasomal downregulation of TNF receptor-associated factor 2 (TRAF2) as a mechanism by which levels of active NIK are increased in PDAC cell lines. Such upregulation of NIK expression and activity levels relays to increased proliferation and anchorage-independent growth, but not migration or survival of PDAC cells.

CONCLUSIONS/SIGNIFICANCE

Rapid growth is one characteristic of pancreatic cancer. Our data indicates that the TRAF2/NIK/NF-κB2 pathway regulates PDAC cell tumorigenicity and could be a valuable target for therapy of this cancer.

Microalgal immobilization methods

In this review, methods for the most common microalgal immobilization procedures are gathered and described. Passive (due to natural adherence of cells to surfaces) and active immobilization methods should be distinguished. Among active immobilization methods, calcium alginate entrapment is the most widely used method if living cells are intended to be immobilized, due to the chemical, optical, and mechanical characteristics of this substance. Immobilization in synthetic foams, immobilization in agar and carrageenan as well as immobilization in silica-based matrix or filters are also discussed and described. Finally, some considerations on the use of flocculation for microalgae are mentioned.

Whole cell entrapment techniques

Microbial whole cells are efficient, ecological, and low-cost catalysts that have been successfully applied in the pharmaceutical, environmental, and alimentary industries, among others. Microorganism immobilization is a good way to carry out the bioprocess under preparative conditions. The main advantages of this methodology lie in their high operational stability, easy upstream separation and bioprocess scale-up feasibility. Cell entrapment is the most widely used technique for whole cell immobilization. This technique-in which the cells are included within a rigid network-is porous enough to allow the diffusion of substrates and products, protects the selected microorganism from the reaction medium, and has high immobilization efficiency (100 % in most cases).

Slicing softly with shear

A soft solid is more easily sliced using a combination of normal and shearing deformations rather than diced by squeezing down on it normally with the same knife. To explain why this is so, we experimentally probe the slicing and dicing of a soft agar gel with a wire, and complement this with theory and numerical simulations of cutting of a highly deformable solid. We find that purely normal deformations lead to global deformations of the soft solid, so that the blade has to penetrate deeply into the sample, well beyond the linear regime, to reach the relatively large critical stress to nucleate fracture. In contrast, a slicing motion leads to fracture nucleation with minimal deformation of the bulk and thus a much lower barrier. This transition between global and local deformations in soft solids as a function of the angle of shear explains the mechanics of the paper cut and design of guillotine blades.

Investigating the effectiveness of economically sustainable carrier material complexes for marine oil remediation

The application of bioremediation to marine oil spills is limited due to dilution of either nutrients or hydrocarbonoclastic organisms. This study investigated the effectiveness of three unique natural carrier materials (mussel shells, coir peat and mussel shell/agar complex) which allowed nutrients, hydrocarbonoclastic organisms and oil to be in contact, facilitating remediation. TPH analysis after 30 d showed that mussel shells exhibited the greatest capacity to degrade oil with a 55% reduction (123.3 mg l(-1) from 276 mg l(-1)) followed by mussel shell/agar complex (49%) and coir peat (36%). Both the mussel shells and mussel shell/agar complex carriers were significantly different to the control (P=0.008 and P=0.002, respectively). DGGE based cluster analysis of the seawater microbial community showed groupings based on time rather than carriers. This study demonstrated that inexpensive, accessible waste materials used as carriers of hydrocarbonoclastic bacteria led to significant degradation of hydrocarbon contaminants in seawater.

Thin-film sparse boundary array design for passive acoustic mapping during ultrasound therapy

A new 2-D hydrophone array for ultrasound therapy monitoring is presented, along with a novel algorithm for passive acoustic mapping using a sparse weighted aperture. The array is constructed using existing polyvinylidene fluoride (PVDF) ultrasound sensor technology, and is utilized for its broadband characteristics and its high receive sensitivity. For most 2-D arrays, high-resolution imagery is desired, which requires a large aperture at the cost of a large number of elements. The proposed array's geometry is sparse, with elements only on the boundary of the rectangular aperture. The missing information from the interior is filled in using linear imaging techniques. After receiving acoustic emissions during ultrasound therapy, this algorithm applies an apodization to the sparse aperture to limit side lobes and then reconstructs acoustic activity with high spatiotemporal resolution. Experiments show verification of the theoretical point spread function, and cavitation maps in agar phantoms correspond closely to predicted areas, showing the validity of the array and methodology.

Simple screening method to identify toxic/non-toxic ionic liquids: agar diffusion test adaptation

A wide range of ionic liquids (ILs), containing a diverse set of cations, anions and alkyl chain lengths, was screened for their antimicrobial activity toward four microorganisms, Escherichia coli CCT-0355, Staphylococcus aureus ATCC-6533, Fusarium sp. LM03 and Candida albicans ATCC-76645. For that purpose an adaptation of the Agar Diffusion test was validated and successfully applied as a rapid screen method to identify toxic ILs, avoiding the use of more complex and expensive techniques. The effects of the cation alkyl chain length were studied, being observed both the "alkyl side chain" effect (increase in antimicrobial activity with the elongation of the alkyl chain) and "cut-off" effect (beyond a given chain length, the toxicity cannot be increased any further). Imidazolium-based ILs have in general, negative effects on the growth of these microorganisms dependent on the anion and alkyl chain length (growth inhibition halo from 1.98±0.04 mm for [C(2)mim]Cl to 39.53±0.81 mm for [C(10)mim]Cl). On the opposite, the phosphonium-based ILs do not seem to have negative effects for the longest alkyl chains (growth inhibition halos between 0.00±0.00 and 7.30±0.42 mm). It was also observed that the alkyl chain, cation family, and anion moiety all have significant effects on the antimicrobial activity these effects being well correlated with the lipophilicity of the ILs tested. The results also show that the microorganisms responses to the diverse ILs tested are dependent on their morphologic differences.

Campylobacter jejuni type VI secretion system: roles in adaptation to deoxycholic acid, host cell adherence, invasion, and in vivo colonization

The recently identified type VI secretion system (T6SS) of proteobacteria has been shown to promote pathogenicity, competitive advantage over competing microorganisms, and adaptation to environmental perturbation. By detailed phenotypic characterization of loss-of-function mutants, in silico, in vitro and in vivo analyses, we provide evidence that the enteric pathogen, Campylobacter jejuni, possesses a functional T6SS and that the secretion system exerts pleiotropic effects on two crucial processes--survival in a bile salt, deoxycholic acid (DCA), and host cell adherence and invasion. The expression of T6SS during initial exposure to the upper range of physiological levels of DCA (0.075%-0.2%) was detrimental to C. jejuni proliferation, whereas down-regulation or inactivation of T6SS enabled C. jejuni to resist this effect. The C. jejuni multidrug efflux transporter gene, cmeA, was significantly up-regulated during the initial exposure to DCA in the wild type C. jejuni relative to the T6SS-deficient strains, suggesting that inhibition of proliferation is the consequence of T6SS-mediated DCA influx. A sequential modulation of the efflux transporter activity and the T6SS represents, in part, an adaptive mechanism for C. jejuni to overcome this inhibitory effect, thereby ensuring its survival. C. jejuni T6SS plays important roles in host cell adhesion and invasion as T6SS inactivation resulted in a reduction of adherence to and invasion of in vitro cell lines, while over-expression of a hemolysin co-regulated protein, which encodes a secreted T6SS component, greatly enhanced these processes. When inoculated into B6.129P2-IL-10(tm1Cgn) mice, the T6SS-deficient C. jejuni strains did not effectively establish persistent colonization, indicating that T6SS contributes to colonization in vivo. Taken together, our data demonstrate the importance of bacterial T6SS in host cell adhesion, invasion, colonization and, for the first time to our knowledge, adaptation to DCA, providing new insights into the role of T6SS in C. jejuni pathogenesis.

Trace amounts of furan-2-carboxylic acids determine the quality of solid agar plates for bacterial culture

Background

Many investigators have recognised that a significant proportion of environmental bacteria exist in a viable but non-culturable state on agar plates, and some researchers have also noticed that some of such bacteria clearly recover their growth on matrices other than agar. However, the reason why agar is unsuitable for the growth of some bacteria has not been addressed.

Methodology/Principal Findings

According to the guide of a bioassay for swarming inhibition, we identified 5-hydroxymethylfuran-2-carboxylic acid (5-HMFA) and furan-2-carboxylic acid (FA) as factors that inhibit bacterial swarming and likely inhibit extracellular polysaccharide production on agar. The furan-2-carboxylic acids 5-HMFA and FA effectively inhibited the swarming and swimming of several environmental bacteria at concentrations of 1.8 and 2.3 µg L⁻¹ (13 and 21 nmol L⁻¹), respectively, which are equivalent to the concentrations of these compounds in 0.3% agar. On Luria-Bertani (LB) plates containing 1.0% agar that had been previously washed with MeOH, a mixture of 5-HMFA and FA in amounts equivalent to their original concentrations in the unwashed agar repressed the swarming of Escherichia coli K12 strain W3110, a representative swarming bacterium.

Conclusions/Significance

Agar that contains trace amounts of 5-HMFA and FA inhibits the proliferation of some slow-growing or difficult-to-culture bacteria on the plates, but it is useful for single colony isolation due to the ease of identification of swarmable bacteria as the non-swarmed colonies.