Neuroscience goes on a chip

Advances in microelectronics, microfluidics, polymers and microfabrication have enabled the creation of disposable lab-on-a-chips (LOCs) as the new tools for neuroscience research. The LOCs have been applied for a wide range of neurobiology studies, including cellular and molecular biochemical experimentations, morphological observations and electrophysiological investigations. The integration of miniaturised components leads to analytical instrumentations with unprecedented automation, speed of analysis, and flexibility. These features make LOCs capable enough to replace their bulky and expensive bench-top counterparts. LOCs can be useful for genomic, proteomic, epigenomic, peptidomic, connectomic and electrophysiological studies and also as effective tools for reductionist neuroscientists. Moreover, they can be applied at higher level studies such as developmental neurobiology and behavioural investigations. This work provides an in-depth review of LOC platforms for neuroscience research. First, we review the essential bench-top neuroscience instrumentation as per their functions and features. Next, we present LOC counterparts for those bench-top instrumentations. Finally, we offer perspectives on persistent challenges and our perception of opportunities based on LOC instrumentations in neuroscience research.     

Calcium efflux of plasma membrane vesicles exposed to ELF magnetic fields-test of a nuclear magnetic resonance interaction model

The question whether very weak, low frequency magnetic fields can affect biological matter is still under debate. The theoretical possibility of such an interaction is often questioned and the site of interaction in the cell is unknown. In the present study, the influence of extremely weak 60 Hz magnetic fields on the transport of Ca²⁺ was studied in a biological system consisting of highly purified plasma membrane vesicles. We tested a newly proposed quantum mechanical model postulates that polarization of hydrogen nuclei can elicit a biological effect. Vesicles were exposed for half an hour at 32 °C and the calcium efflux was studied using radioactive ⁴⁵Ca²⁺ as a tracer. A static magnetic field of 26 µT and time‐varying magnetic fields with a frequency of 60 Hz and amplitudes between 0.6 and 6.3 µT were used. The predictions of the model, proposed by Lednev, that at a frequency of 60 Hz the biological effect under investigation would significantly be altered at the amplitudes of 1.3 and 3.9 µT could not be confirmed. Bioelectromagnetics 33:535–542, 2012. © 2012 Wiley Periodicals, Inc.     

Dioxouranium complexes as ligand. Synthesis and characterization of sandwich-type polyoxometalates [X2W18(UO2)2{(H2O)3M}2O68] (X = As and P) (M = Co, Cu, Mn, Ni and Zn)

The title complexes are synthesized by the reaction of an unusual ligand of [K₂P₂W₁₈(UO₂)₂O₆₈]¹²⁻ (1) and [KAs₂W₁₈(UO₂)₂O₆₈]¹³⁻ (2) with divalent metal ions of Co^II, Cu^II, Mn^II, Ni^II and Zn^II in 1:2 mole ratio and are characterized by elemental analysis, IR, ³¹P NMR, UV-Vis spectroscopy, TGA, and single crystal structure analysis. Crystals of [P₂W₁₈(UO₂)₂{(H₂O)₃Co}₂O₆₈]¹⁰⁻ (1a) and [As₂W₁₈(UO₂)₂{(H₂O)₃Cu}₂O₆₈]¹⁰⁻ (2b) are orthorhombic space group Cmca. Both 1a and 2b have structures in which two [M(H₂O)₃] (M = Co^II, Cu^II) and two UO₂ groups are sandwiched between two symmetry equivalent (XW₉) (X = P, As) units in a virtual C_i symmetry. In solution, 1a and [P₂W₁₈(UO₂)₂{(H₂O)₃Zn}₂O₆₈]¹⁰⁻ (1d) give two-line P NMR spectra that are consistent with a C_s symmetry structures so, are not consistent with the solid-state structures. The sodium salts of them give one-line P NMR spectra and are consistent with the C_i symmetry of solid-state structures. The uranium atoms have pentagonal-bipyramidal coordination, achieved by three equatorial bonds to the one XW₉ and two bonds to the other. The M atoms have octahedral or square pyramidal coordination, but only one bond to the one XW₉ and one bond to the other.     

Ethnic and Geographic Differentiation of Helicobacter pylori within Iran

The bacterium Helicobacter pylori colonizes the human stomach, with individual infections persisting for decades. The spread of the bacterium has been shown to reflect both ancient and recent human migrations. We have sequenced housekeeping genes from H. pylori isolated from 147 Iranians with well-characterized geographical and ethnic origins sampled throughout Iran and compared them with sequences from strains from other locations. H. pylori from Iran are similar to others isolated from Western Eurasia and can be placed in the previously described HpEurope population. Despite the location of Iran at the crossroads of Eurasia, we found no evidence that the region been a major source of ancestry for strains across the continent. On a smaller scale, we found genetic affinities between the H. pylori isolated from particular Iranian populations and strains from Turks, Uzbeks, Palestinians and Israelis, reflecting documented historical contacts over the past two thousand years.     

Proteomic signature of human embryonic stem cells

Human embryonic stem cells (hESC) represent a population of undifferentiated pluripotent cells with both self-renewal and multilineage differentiation characteristics. Proteomics provides a powerful approach for studying the characteristics of hESC and discovering molecular markers. We have analyzed proteome profiles of three hESC lines using 2-DE and MALDI TOF-TOF. Out of 844 spots analyzed with MALDI TOF-TOF, 685 proteins were identified of which 60 proteins were classified as the most abundant proteins on 2-D gels. A large number of proteins particularly high abundant ones were identified as chaperones, heat shock proteins, ubiquitin/proteasome, and oxidative stress responsive proteins underscoring the ability of these cells to resist oxidative stress and increase the life span. Several proteins involved in cell proliferation and differentiation were also among the highly expressed proteins. Although overall expression pattern of three hESC were similar, 54 spots changed quantitatively and 14 spots changed qualitatively among the hESC cell lines. Most of these proteins were identified as proteins involved in cell growth, metabolism and signal transduction, which may affect the self-renewal and pluripotency. To our knowledge, this study represents the first proteomic dataset for hESC and provides a better insight into the biology of hESC. Proteome maps of hESC are accessible at http://www.RoyanProteomics.ir.     

Arabidopsis AtGSTF2 is regulated by ethylene and auxin, and encodes a glutathione S-transferase that interacts with flavonoids

Expression of the Arabidopsis glutathione S-transferase (GST) gene AtGSTF2 is induced by several stimuli, but the function of this GST remains unknown. We demonstrate that AtGSTF2 expression is also induced by glutathione, paraquat, copper, and naphthalene acetic acid (NAA) via a mechanism independent of ethylene perception, as determined by analysis of the ethylene-insensitive etr1 mutant. Deletion analyses identified two promoter regions important for regulation of AtGSTF2 expression in response to several of these inducers. Previous studies have suggested that AtGSTF2 interacts with indole-3-acetic acid (IAA) and the auxin transport inhibitor 1-N-naphthylphthalamic acid (NPA). We show that recombinant AtGSTF2 directly binds IAA, NPA, and the artificial auxin NAA. As NPA may act as an endogenous flavonoid regulator of auxin transport, competition between NPA and flavonoids for binding to AtGSTF2 was examined. Both quercetin and kaempferol competed with NPA for AtGSTF2 binding, indicating that all three compounds bind AtGSTF2 at the same site. In transgenic Arabidopsis seedlings, AtGSTF2::GUS expression occurred at the root-shoot transition zone and was induced in this region, as well as at the root distal elongation zone, after treatment with IAA. In wild-type seedlings, AtGSTF2 is localized near the plasma membrane of cells in the root-shoot transition zone. However, both AtGSTF2::GUS expression and localization of AtGSTF2 protein were disrupted in flavonoid-deficient tt4 seedlings. Our results indicate that AtGSTF2 is involved not only in stress responses but also in development under normal growth conditions.     

Expression of senescence-enhanced genes in response to oxidative stress

Expression of the LSC54 gene, encoding a metallothionein protein, has been shown previously to increase during leaf senescence and cell death. Evidence is presented in this paper to indicate that the extent of LSC54 expression is related to levels of oxidative stress in the tissues. Treatment of Arabidopsis cotyledon and leaf tissues with the catalase inhibitor, 3-amino-1,2,4-triazole, or with silver nitrate result in the enhanced expression of LSC54. Combined treatments with quenchers of reactive oxygen species (ROS), such as ascorbate, tiron and benzoic acid indicated that this induced expression was due to increased levels of ROS. The expression of many other senescence-enhanced genes was also found to be inducible by the increase in ROS. Treatment of plant tissue with 3-amino-1,2,4-triazole, followed by silver nitrate, resulted in protection from the severe damage caused by the silver nitrate treatment and reduced expression of many of the genes examined. However, one gene, encoding a lipid hydroperoxide-dependent glutathione peroxidase, showed increased expression in the protected tissue, which may indicate a role for this enzyme in the protection of plant tissue from oxidative stress. ROS-enhanced expression of at least one of the genes investigated required the presence of the salicylic acid signalling pathway, which was not required for the expression of LSC54.     

Non-linear heteroscedastic regression model for determination of methotrexate in human plasma by high-performance liquid chromatography

Generalized least squares regression with variance function estimation was used to derive the calibration function for measurement of methotrexate plasma concentration and its results were compared with weighted least squares regression by usual weight factors and also with that of ordinary least squares method. In the calibration curve range of 0.05 to 100 microM, both heteroscedasticity and non-linearity were present therefore ordinary least squares linear regression methods could result in large errors in the calculation of methotrexate concentration. Generalized least squares regression with variance function estimation worked better than both the weighted regression with the usual weight factors and ordinary least squares regression and gave better estimates for methotrexate concentration.     

H1 histones from mammalian testes : The widespread occurrence of H1t

H1t is a testis-specific H1 histone variant recently isolated from the rat [13]. We have now identified H1t in testicular extracts from mice, rabbits, hamsters, bulls, and boars, thus establishing its widespread presence in animals. H1t from all species could be differentiated from standard somatic H1 forms by a variety of criteria. It was poorly extracted by 5% trichloroacetic acid (TCA), migrated more rapidly than standard H1 forms during electrophoresis in the presence of sodium dodecyl sulfate (SDS), and eluted more slowly than standard H1 species during chromatography over cross-linked polyacrylamide beads (Bio-Gel P100). Using an improved purification procedure, H1t was isolated from two new species, mouse and rabbit. In these species as with the rat, H1t is readily identified by its low lysine (ca 19 mol%) and high arginine (6–7 mol%) content as compared with that of standard somatic H1 forms (ca 25% lysine and 3% arginine).