Mechanical properties of β-HMX

Background: For a full understanding of the mechanical properties of a material, it is essential to understand the defect structures and associated properties and microhardness indentation is a technique that can aid this understanding. Results: The Vickers hardness on (010), {011} and {110} faces lay in the range of 304-363 MPa. The Knoop Hardnesses on the same faces lay in the range 314-482 MPa. From etching of three indented surfaces, the preferred slip planes have been identified as (001) and (101). For a dislocation glide, the most likely configuration for dislocation movement on the (001) planes is (001) [100] (|b| = 0.65 nm) and for the (101) plane as (101) 101~(|b| = 1.084 nm) although (101) [010] (|b| = 1.105 nm) is possible. Tensile testing showed that at a stress value of 2.3 MPa primary twinning occurred and grew with increasing stress. When the stress was relaxed, the twins decreased in size, but did not disappear. The twinning shear strain was calculated to be 0.353 for the (101) twin plane. Conclusions: HMX is considered to be brittle, compared to other secondary explosives. Comparing HMX with a range of organic solids, the values for hardness numbers are similar to those of other brittle systems. Under the conditions developed beneath a pyramidal indenter, dislocation slip plays a major part in accommodating the local deformation stresses. © 2015 Gallagher et al.; licensee Springer

Effects of L1-ORF2 fragments on green fluorescent protein gene expression

The retrotransposon known as long interspersed nuclear element-1 (L1) is 6 kb long, although most L1s in mammalian and other eukaryotic cells are truncated. L1 contains two open reading frames, ORF1 and ORF2, that code for an RNA-binding protein and a protein with endonuclease and reverse transcriptase activities, respectively. In this work, we examined the effects of full length L1-ORF2 and ORF2 fragments on green fluorescent protein gene (GFP) expression when inserted into the pEGFP-C1 vector downstream of GFP. All of the ORF2 fragments in sense orientation inhibited GFP expression more than when in antisense orientation, which suggests that small ORF2 fragments contribute to the distinct inhibitory effects of this ORF on gene expression. These results provide the first evidence that different 280-bp fragments have distinct effects on the termination of gene transcription, and that when inserted in the antisense direction, fragment 280-9 (the 3' end fragment of ORF2) induces premature termination of transcription that is consistent with the effect of ORF2

Effect of Ultrasonic-Assisted Blanching on Size Variation, Heat Transfer, and Quality Parameters of Mushrooms

The main aim of this work was to assess the influence of the application of power ultrasound during blanching of mushrooms (60 90 °C) on the shrinkage, heat transfer, and quality parameters. Kinetics of mushroom shrinkage was modeled and coupled to a heat transfer model for conventional (CB) and ultrasonic-assisted blanching (UB). Cooking value and the integrated residual enzymatic activity were obtained through predicted temperatures and related to the hardness and color variations of mushrooms, respectively. The application of ultrasound led to an increase of shrinkage and heat transfer rates, being this increase more intense at low process temperatures. Consequently, processing time was decreased (30.7 46.0 %) and a reduction in hardness (25.2 40.8 %) and lightness (13.8 16.8 %) losses were obtained. The best retention of hardness was obtained by the UB at 60 °C, while to maintain the lightness it was the CB and UB at 90 °C. For enhancing both quality parameters simultaneously, a combined treatment (CT), which consisted of a CB 0.5 min at 90 °C and then an UB 19.9min at 60 °C, was designed. In this manner, compared with the conventional treatment at 60 °C, reductions of 39.1, 27.2, and 65.5 % for the process time, hardness and lightness losses were achieved, respectively. These results suggest that the CT could be considered as an interesting alternative to CB in order to reduce the processing time and improve the overall quality of blanched mushrooms.The authors acknowledge the financial support of Consejo Nacional de Investigaciones Cientificas y Tecnicas and Universidad Nacional de La Plata from Argentina, Erasmus Mundus Action 2-Strand 1 and EuroTango II Researcher Training Program and Ministerio de Economia y Competitividad (SPAIN) and the FEDER (project DPI2012-37466-CO3-03).Lespinard, A.; Bon Corbín, J.; Cárcel Carrión, JA.; Benedito Fort, JJ.; Mascheroni, RH. (2015). Effect of Ultrasonic-Assisted Blanching on Size Variation, Heat Transfer, and Quality Parameters of Mushrooms. Food and Bioprocess Technology. 8(1):41-53. https://doi.org/10.1007/s11947-014-1373-zS415381Aguirre, L., Frias, J. M., Barry-Ryan, C., & Grogan, H. (2009). Modelling browning and brown spotting of mushrooms (Agaricus bisporus) stored in controlled environmental conditions using image analysis. Journal of Food Engineering, 91, 280–286.Anantheswaran, R. C., Sastry, S. K., Beelman, R. B., Okereke, A., & Konanayakam, M. (1986). Effect of processing on yield, color, and texture of canned mushrooms. Journal of Food Science, 51(5), 1197–1200.Biekman, E. S. A., Kroese-Hoedeman, H. I., & Schijvens, E. P. H. M. (1996). Loss of solutes during blanching of mushrooms (Agaricus bisporus) as a result of shrinkage and extraction. Journal of Food Engineering, 28(2), 139–152.Biekman, E. S. A., van Remmen, H. H. J., Kroese-Hoedeman, H. I., Ogink, J. J. M., & Schijvens, E. P. H. M. (1997). Effect of shrinkage on the temperature increase in evacuated mushrooms (Agaricus bisporus) during blanching. Journal of Food Engineering, 33(1–2), 87–99.Brennan, M., Le Port, G., & Gormley, R. (2000). Post-harvest treatment with citric acid or hydrogen peroxide to extend the shelf life of fresh sliced mushrooms. Lebensmittel Wissenschaft und Technologie, 33, 285–289.Cárcel, J. A., Benedito, J., Rosselló, C., & Mulet, A. (2007). Influence of ultrasound intensity on mass transfer in apple immersed in a sucrose solution. Journal of Food Engineering, 78, 472–479.Cárcel, J. A., Benedito, J., Bon, J., & Mulet, A. (2007). High intensity ultrasound effects on meat brining. Meat Science, 76, 611–619.Cárcel, J. A., García-Pérez, J. V., Benedito, J., & Mulet, A. (2011). Food process innovation through new technologies: Use of ultrasound. Journal of Food Engineering, 110, 200–207.Cheng, X., Zhang, M., & Adhikari, B. (2013). The inactivation kinetics of polyphenol oxidase in mushroom (Agaricus bisporus) during thermal and thermosonic treatmemts. Ultrasonics Sonochemistry, 20, 674–679.Cliffe-Byrnes, V., & O’Beirne, D. (2007). Effects of gas atmosphere and temperature on the respiration rates of whole and sliced mushrooms (Agaricus bisporus): implications for film permeability in modified atmosphere packages. Journal of Food Science, 72, 197–204.Coskuner, Y., & Ozdemir, Y. (1997). Effects of canning processes on the elements content of cultivated mushrooms (Agaricus bisporus). Food Chemistry, 60(4), 559–562.Cruz, R. M. S., Vieira, M. C., Fonseca, S. C., & Silva, C. L. M. (2011). Impact of thermal blanching and thermosonication treatments on watercress (Nasturtium officinale) quality: thermosonication process optimisation and microstructure evaluation. Food and Bioprocess Technology, 4(7), 1197–1204.De Gennaro, L., Cavella, S., Romano, R., & Masi, P. (1999). The use of ultrasound in food technology I: inactivation of peroxidase by thermosonication. Journal of Food Engineering, 39, 401–407.De la Fuente, S., Riera, E., Acosta, V. M., Blanco, A., & Gallego-Juárez, J. A. (2006). Food drying process by power ultrasound. Ultrasonics, 44, 523–527.Delgado, A. E., Zheng, L., & Sun, D. W. (2009). Influence of ultrasound on freezing rate of immersion-frozen apples. Food and Bioprocess Technology, 2, 263–270.Devece, C., Rodríguez-López, J. N., Fenoll, J. T., Catalá, J. M., De los Reyes, E., & García-Cánovas, F. (1999). Enzyme inactivation analysis for industrial blanching applications: comparison of microwave, conventional, and combination heat treatments on mushroom polyphenoloxidase activity. Journal of Agricultural and Food Chemistry, 47(11), 4506–4511.Fernandes, F. A. N., & Rodrigues, S. (2007). Ultrasound as pre-treatment for drying of fruits: dehydration of banana. Journal of Food Engineering, 82, 261–267.Gabaldón-Leyva, C. A., Quintero-Ramos, A., Barnard, J., Balandrán-Quintana, R. R., Talamás-Abbud, R., & Jiménez-Castro, J. (2007). Effect of ultrasound on the mass transfer and physical changes in brine bell pepper at different temperatures. Journal of Food Engineering, 81, 374–379.Gallego-Juárez, J. A., Riera, E., De la Fuente, S., Rodríguez-Corral, G., Acosta-Aparicio, V. M., & Blanco, A. (2007). Application of high-power ultrasound for dehydration of vegetables: processes and devices. Drying Technology, 25, 1893–1901.Gamboa-Santos, J., Montilla, A., Soria, A. C., & Villamiel, M. (2012). Effects of conventional and ultrasound blanching on enzyme inactivation and carbohydrate content of carrots. European Food Research and Technology, 234, 1071–1079.García-Pérez, J. V., Cárcel, J. A., De la Fuente, S., & Riera, E. (2006). Ultrasonic drying of foodstuff in a fluidized bed. Parametric study. Ultrasonics, 44, 539–543.García-Pérez, J. V., Cárcel, J. A., Riera, E., Rosselló, C., & Mulet, A. (2012). Intensification of low-temperature drying by using ultrasound. Drying Technology, 30, 1199–1208.Gonzáles-Fandos, E., Giménez, M., Olarte, C., Sanz, S., & Simón, A. (2000). Effect of packaging conditions on the growth of microorganisms and the quality characteristics of fresh mushrooms (Agaricus bisporus) stored at inadequate temperatures. Journal of Applied Microbiology, 89, 624–632.Gormley, T. R. (1975). Chill storage of mushrooms. Journal of the Science of Food and Agriculture, 26, 401–411.Gouzi, H., Depagne, C., & Coradin, T. (2012). Kinetics and thermodynamics of thermal inactivation of polyfenol oxidase in an aqueous extract from Agaricus bisporus. Journal of Agricultural and Food Chemistry, 60, 500–506.Holdsworth, S. D. (1997). Thermal processing of packaged foods. London: Chapman Hall.Horžić, D., Jambrak, A. R., Belščak-Cvitanović, A., Komes, D., & Lelas, V. (2012). Comparison of conventional and ultrasound assisted extraction techniques of yellow tea and bioactive composition of obtained extracts. Food and Bioprocess Technology, 5, 2858–2870.Jambrak, A. R., Mason, T. J., Paniwnyk, L., & Lelas, V. (2007a). Ultrasonic effect on pH, electric conductivity, and tissue surface of button mushrooms, brussels sprouts and cauliflower. Czech Journal of Food Science, 25, 90–99.Jambrak, A. R., Mason, T. J., Paniwnyk, L., & Lelas, V. (2007b). Accelerated drying of button mushrooms, Brussels sprouts and cauliflower by applying power ultrasound and its rehydration properties. Journal of Food Engineering, 81, 88–97.Jasinski, E. M., Stemberger, B., Walsh, R., & Kilara, A. (1984). Ultra structural studies of raw and processed tissue of the major cultivated mushroom, Agaricus bisporus. Food Microstructure, 3, 191–196.Jolivet, S., Arpin, N., Wicher, H. J., & Pellon, G. (1998). Agaricus bisporus browning: a review. Mycological Research, 102, 1459–1483.Konanayakam, M., & Sastry, S. K. (1988). Kinetics of shrinkage of mushroom during blanching. Journal of Food Science, 53(5), 1406–1411.Kotwaliwale, N., Bakane, P., & Verma, A. (2007). Changes in textural and optical properties of oyster mushroom during hot air drying. Journal of Food Engineering, 78(4), 1207–1211.Leadley C. & Williams A. (2002). Power ultrasound—current and potential applications for food processing, Review No 32, Campden and Chorleywood Food Research Association.Lespinard, A. R., Goñi, S. M., Salgado, P. R., & Mascheroni, R. H. (2009). Experimental determination and modeling of size variation, heat transfer and quality indexes during mushroom blanching. Journal of Food Engineering, 92, 8–17.Lima, M., & Sastry, S. K. (1990). Influence of fluid rheological properties and particle location on ultrasound-assisted heat transfer between liquid and particles. Journal of Food Science, 55(4), 1112–1115.López, P., & Burgos, J. (1995). Peroxidase stability and reactivation after heat treatment and manothermosonication. Journal of Food Science, 60(3), 551–553.López, P., Sala, F. J., Fuente, J. L., Cardon, S., Raso, J., & Burgos, J. (1994). Inactivation of peroxidase lipoxigenase and phenol oxidase by manothermosonication. Journal of Agricultural and Food Chemistry, 42(2), 253–256.Mansfield, T. (1962). High temperature-short time sterilization. Proceedings First International Congress on Food Science and Technology, 4, 311–316.Mason T. J. (1998). Power ultrasound in food processing—the way forward. In M. J. W. Povey & T. J. Mason (Eds.), Ultrasound in Food Processing (pp 103–126). Blackie Academic & Professional, London.McArdle F. J. & Curwen D. (1962). Some factors influencing shrinkage of canned mushrooms. Mushroom Science, 5, 547–557.McArdle, F. J., Kuhn, G. D., & Beelman, R. B. (1974). Influence of vacuum soaking on yield and quality of canned mushrooms. Journal of Food Science, 39, 1026–1028.Mohapatra, D., Bira, Z. M., Kerry, J. P., Frías, J. M., & Rodrigues, F. A. (2010). Postharvest hardness and color evolution of White button mushrooms (Agaricus bisporus). Journal of Food Science, 75(3), 146–152.Ohlsson, T. (1980). Temperature dependence of sensory quality changes during thermal processing. Journal of Food Science, 45(4), 836–847.Ortuño, C., Martínez-Pastor, M., Mulet, A., & Benedito, J. (2013). Application of high power ultrasound in the supercritical carbon dioxide inactivation of Saccharomyces cerevisiae. Food Research International, 51, 474–481.Peralta-Jimenez, L., & Cañizares-Macías, M. P. (2012). Ultrasound-assisted method for extraction of theobromine and caffeine from cacao seeds and chocolate products. Food and Bioprocess Technology, 6, 3522–3529.Rodríguez-López, J. N., Fenoll, N. G., Tudela, J., Devece, C., Sánchez-Hernández, D., De los Reyes, D., et al. (1999). Thermal inactivation of mushroom polyphenoloxidase employing 2450 MHz microwave radiation. Journal of Agricultural Food Chemistry, 47, 3028–3035.Sala, F., Burgos, J., Condon, S., Lopez, P., & Raso, J. (1995). Effect of heat and ultrasound on microorganisms and enzymes. In G. W. Gould (Ed.), New methods of food preservation (1st ed., pp. 176–204). Glasgow: Blackie Academic and professional.Sanjuán, N., Hernando, I., Lluch, M. A., & Mullet, A. (2005). Effects of low temperature blanching on texture, microstructure and rehydration capacity of carrots. Journal of the Science of Food and Agriculture, 85, 2071–2076.Santos, M. V., & Lespinard, A. R. (2011). Numerical simulation of mushrooms during freezing using the FEM and an enthalpy—Kirchhoff formulation. Heat and Mass Transfer, 47, 1671–1683.Sastry, S. K., Beelman, R. B., & Speroni, J. J. (1985). A three-dimensional finite element model for thermally induced changes in foods: application to degradation of agaritine in canned mushrooms. Journal of Food Science, 50(5), 1293–1299.Sastry, S. K., Shen, G. Q., & Blaisdel, J. L. (1989). Effect of ultrasonic vibration on fluid-to-particule convective heat transfer coefficients. Journal of Food Science, 54(1), 229–230.Sensoy, I., & Sastry, S. K. (2004). Ohmic blanching of mushrooms. Journal of Food Process Engineering, 27(1), 1–15.Sheen, S., & Hayakawa, K. (1991). Finite difference simulation for heat conduction with phase change in an irregular food domain with volumetric change. International Journal of Heat and Mass Transfer, 34(6), 1337–1346.Simal, S., Benedito, J., Sanchez, E. S., & Rossello, C. (1998). Use of ultrasound to increase mass transport rates during osmotic dehydration. Journal of Food Engineering, 36, 323–336.Siró, I., Vén, C., Balla, C., Jónás, G., Zeke, I., & Friedrich, L. (2009). Application of an ultrasonic assisted curing technique for improving the diffusion of sodium chloride in porcine meat. Journal of Food Engineering, 91, 353–362.Soria, A. C., & Villamiel, M. (2010). Effect of ultrasound on the technological properties and bioactivity in foods: a review. Trends in Food Science and Technology, 21, 323–331.Verlinden, B. E., Yuksel, D., Baheri, M., De Baerdemaeker, J., & Van Dijk, C. (2000). Low temperature blanching effect on the changes in mechanical properties during subsequent cooking of three potato cultivars. International Journal of Food Science and Technology, 35, 331–340.Wu, C. M., Wu, J. L.-P., Chen, C.-C., & Chou, C.-C. (1981). Flavor recovery from mushroom blanching water. In G. Charalambous & G. Inglett (Eds.), The quality of foods and beverages: chemistry and technology, vol. 1. New York: Academic Press.Zivanovic, S., & Buescher, R. (2004). Changes in mushroom texture and cell wall composition affected by thermal processing. Journal of Food Science, 69, 44–48

Dynamic Changes in the MicroRNA Expression Profile Reveal Multiple Regulatory Mechanisms in the Spinal Nerve Ligation Model of Neuropathic Pain

Neuropathic pain resulting from nerve lesions or dysfunction represents one of the most challenging neurological diseases to treat. A better understanding of the molecular mechanisms responsible for causing these maladaptive responses can help develop novel therapeutic strategies and biomarkers for neuropathic pain. We performed a miRNA expression profiling study of dorsal root ganglion (DRG) tissue from rats four weeks post spinal nerve ligation (SNL), a model of neuropathic pain. TaqMan low density arrays identified 63 miRNAs whose level of expression was significantly altered following SNL surgery. Of these, 59 were downregulated and the ipsilateral L4 DRG, not the injured L5 DRG, showed the most significant downregulation suggesting that miRNA changes in the uninjured afferents may underlie the development and maintenance of neuropathic pain. TargetScan was used to predict mRNA targets for these miRNAs and it was found that the transcripts with multiple predicted target sites belong to neurologically important pathways. By employing different bioinformatic approaches we identified neurite remodeling as a significantly regulated biological pathway, and some of these predictions were confirmed by siRNA knockdown for genes that regulate neurite growth in differentiated Neuro2A cells. In vitro validation for predicted target sites in the 3′-UTR of voltage-gated sodium channel Scn11a, alpha 2/delta1 subunit of voltage-dependent Ca-channel, and purinergic receptor P2rx ligand-gated ion channel 4 using luciferase reporter assays showed that identified miRNAs modulated gene expression significantly. Our results suggest the potential for miRNAs to play a direct role in neuropathic pain

RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes

<p>Abstract</p> <p>Background -</p> <p>The availability of multiple whole genome sequences has facilitated <it>in silico </it>identification of fixed and polymorphic transposable elements (TE). Whereas polymorphic loci serve as makers for phylogenetic and forensic analysis, fixed species-specific transposon insertions, when compared to orthologous loci in other closely related species, may give insights into their evolutionary significance. Besides, TE insertions are not isolated events and are frequently associated with subtle sequence changes concurrent with insertion or post insertion. These include duplication of target site, 3' and 5' flank transduction, deletion of the target locus, 5' truncation or partial deletion and inversion of the transposon, and post insertion changes like inter or intra element recombination, disruption etc. Although such changes have been studied independently, no automated platform to identify differential transposon insertions and the associated array of sequence changes in genomes of the same or closely related species is available till date. To this end, we have designed RISCI - 'Repeat Induced Sequence Changes Identifier' - a comprehensive, comparative genomics-based, <it>in silico </it>subtractive hybridization pipeline to identify differential transposon insertions and associated sequence changes using specific alignment signatures, which may then be examined for their downstream effects.</p> <p>Results -</p> <p>We showcase the utility of RISCI by comparing full length and truncated L1HS and AluYa5 retrotransposons in the reference human genome with the chimpanzee genome and the alternate human assemblies (Celera and HuRef). Comparison of the reference human genome with alternate human assemblies using RISCI predicts 14 novel polymorphisms in full length L1HS, 24 in truncated L1HS and 140 novel polymorphisms in AluYa5 insertions, besides several insertion and post insertion changes. We present comparison with two previous studies to show that RISCI predictions are broadly in agreement with earlier reports. We also demonstrate its versatility by comparing various strains of <it>Mycobacterium tuberculosis </it>for IS 6100 insertion polymorphism.</p> <p>Conclusions -</p> <p>RISCI combines comparative genomics with subtractive hybridization, inferring changes only when exclusive to one of the two genomes being compared. The pipeline is generic and may be applied to most transposons and to any two or more genomes sharing high sequence similarity. Such comparisons, when performed on a larger scale, may pull out a few critical events, which may have seeded the divergence between the two species under comparison.</p

Excessive activation of the TLR9/TGF-β1/PDGF-B pathway in the peripheral blood of patients with systemic lupus erythematosus

Abstract Background Our aim is to study the existence of the TLR9/TGF-β1/PDGF-B pathway in healthy humans and patients with systemic lupus erythematosus (SLE), and to explore its possible involvement in the pathogenesis of lupus nephritis (LN). Methods Protein levels of the cytokines were detected by ELISA. mRNA levels of the cytokines were analyzed by real-time PCR. MTT assay was used to test the proliferation of mesangial cells under different treatments. Results Compared to healthy controls (N Control = 56), levels of Toll-like receptor (TLR)9, transforming growth factor (TGF)-β1, and platelet-derived growth factor B (PDGF-B) were increased significantly in the peripheral blood of SLE patients (N SLE = 112). Significant correlations between the levels of TLR9, TGF-β1, and PDGF-B were observed in both healthy controls and SLE patients. The levels of TGF-β1 and PDGF-B were greatly enhanced by TLR9 activation in primary cell cultures. The proliferation of mesangial cells induced by the plasma of SLE patients was significantly higher than that induced by healthy controls; PDGF-B was involved in this process. The protein levels of PDGF-B homodimer correlated with the levels of urine protein in SLE patients with LN (N LN =38). Conclusions The TLR9/TGF-β1/PDGF-B pathway exists in humans and can be excessively activated in SLE patients. High levels of PDGF-B may result in overproliferation of mesangial cells in the kidney that are involved in the development of glomerulonephritis and LN. Further studies are necessary to identify TLR9, TGF-β1, and PDGF-B as new therapeutic targets to prevent the development of glomerulonephritis and LN