Analysis of fern spore banks from the soil of three vegetation types in the central region of Mexico

The vertical structure of fern spore banks was studied in a xerophilous shrubland, montane rain forest, and pine-oak forest in Hidalgo, Mexico, using the emergence method. Soil samples were collected in April 1999 at depths of 0-10, 10-20, and 20-30 cm. Viable spores decreased significantly with depth in all vegetation types, and the highest number of prothallia and sporophytes was found in the uppermost layer. The montane rain forest and the xerophilous shrubland had the largest and the richest banks, respectively. Twenty-three fern taxa were registered in the aboveground vegetation, 12 in the soil banks, and 43.5% were in both. Aboveground and in the soil bank, the xerophilous shrubland, the montane rain forest, and the pine-oak forest had, 17 and 7, 1 and 6, and 7 and 3 taxa, respectively. These were distributed differentially in relation to depth. The S?rensen index indicated a similarity of 61.5% between the xerophilous shrubland and the montane rain forest, and the Czeckanovsky index indicated 19.75%. The presence of viable spores in the soil of all vegetation types confirmed the existence of natural spore banks. Long-distance dispersal was an important factor determining the specific composition of the xerophilous shrubland and the pine-oak forest.     

Analysis of sequence determinants of F1Fo-ATP synthase in the N-terminal region of alpha subunit for binding of delta subunit

The stator in F(1)F(o)-ATP synthase resists strain generated by rotor torque. In Escherichia coli, the b(2)delta subunit complex comprises the stator, bound to subunit a in F(o) and to the alpha(3)beta(3) hexagon of F(1). Previous work has shown that N-terminal residues of alpha subunit are involved in binding delta. A synthetic peptide consisting of the first 22 residues of alpha (alphaN1-22) binds specifically to isolated wild-type delta subunit with 1:1 stoichiometry and high affinity, accounting for a major portion of the binding energy between delta and F(1). Residues alpha6-18 are predicted by secondary structure algorithms and helical wheels to be alpha-helical and amphipathic, and a potential helix capping box occurs at residues alpha3-8. We introduced truncations, deletions, and mutations into alphaN1-22 peptide and examined their effects on binding to the delta subunit. The deletions and mutations were introduced also into the N-terminal region of the uncA (alpha subunit) gene to determine effects on cell growth in vivo and membrane ATP synthase activity in vitro. Effects seen in the peptides were well correlated with those seen in the uncA gene. The results show that, with the possible exception of residues close to the initial Met, all of the alphaN1-22 sequence is required for binding of delta to alpha. Within this sequence, an amphipathic helix seems important. Hydrophobic residues on the predicted nonpolar surface are important for delta binding, namely alphaIle-8, alphaLeu-11, alphaIle-12, alphaIle-16, and alphaPhe-19. Several or all of these residues probably make direct interaction with helices 1 and 5 of delta. The potential capping box sequence per se appeared less important. Impairment of alpha/delta binding brings about functional impairment due to reduced level of assembly of ATP synthase in cells.     

Nanofabricated biomimetic structures for smart targeting and drug delivery

We present a new approach to hybrid artificial cells (AC) designed for specific targeting and active drug delivery by combining an impermeable non-biological scaffold with an artificial bilayer lipid membrane (BLM) that supports the functioning bio-molecules required to provide AC functionality. We report on the fabrication of the scaffold using nanotechnology, as well as on loading of the scaffold and the functionalization of the AC. The results presented here are a first step towards the development of a biomimetic AC using nanotechnology.     

Quantitative analysis of both protein expression and serine / threonine post-translational modifications through stable isotope labeling with dithiothreitol

While phosphorylation and O-GlcNAc (cytoplasmic and nuclear glycosylation) are linked to normal and pathological changes in cell states, these post-translational modifications have been difficult to analyze in proteomic studies. We describe advances in beta-elimination / Michael addition-based approaches which allow for mass spectrometry-based identification and comparative quantification of O-phosphate or O-GlcNAc-modified peptides, as well as cysteine-containing peptides for expression analysis. The method (BEMAD) involves differential isotopic labeling through Michael addition with normal dithiothreitol (DTT) (d0) or deuterated DTT (d6), and enrichment of these peptides by thiol chromatography. BEMAD was comparable to isotope-coded affinity tags (ICAT; a commercially available differential isotopic quantification technique) in protein expression analysis, but also provided the identity and relative amounts of both O-phosphorylation and O-GlcNAc modification sites. Specificity of O-phosphate vs. O-GlcNAc mapping is achieved through coupling enzymatic dephosphorylation or O-GlcNAc hydrolysis with differential isotopic labeling. Blocking of cysteine labeling by prior oxidation of a cytosolic lysate from mouse brain allowed specific targeting of serine / threonine post-translational modifications as demonstrated through identification of 21 phosphorylation sites (5 previously reported) in a single mass spectrometry analysis. These results demonstate BEMAD is suitable for large-scale quantitative analysis of both protein expression and serine / threonine post-translational modifications.     

Opsonization with C1q and mannose-binding lectin targets apoptotic cells to dendritic cells

Deficiencies of early components of the classical complement pathway, particularly C1q, are strongly associated with susceptibility to systemic lupus erythematosus. Recent data link this predisposal to autoimmunity to an inappropriate clearance of apoptotic cells, which could lead to a loss of self-tolerance. In the present study, we demonstrate that opsonization of apoptotic cells with C1q and mannose-binding lectin allows and facilitates their uptake not only by macrophages but also by human immature dendritic cells (DCs). Both C1q and mannose-binding lectin enhance the uptake of apoptotic cells by DCs in a dose-dependent way. The uptake of C1q-opsonized apoptotic cells, but not nonopsonized apoptotic cells, by DCs stimulated the production of IL-6, IL-10, and TNF-alpha, without an effect on IL-12p70. We conclude that these recognition molecules of the complement system do not sequester apoptotic cells from DCs, but rather promote their uptake by immature DCs. Therefore, we propose that early complement components support safe clearance of cellular debris by facilitating phagocytosis and possibly by immunomodulatory mechanisms, thus preventing autoimmunity.     

Synthesis of the measles virus nucleoprotein in yeast Pichia pastoris and Saccharomyces cerevisiae

The development of a simple, efficient and cost-effective system for generation of measles virus nucleoprotein might help to upgrade reagents for measles serology. The gene encoding measles nucleoprotein was successfully expressed in two different yeast genera, Pichia pastoris and Saccharomyces cerevisiae, respectively. Both yeast genera synthesized a high level of nucleoprotein, up to 29 and 18% of total cell protein, in P. pastoris and S. cerevisiae, respectively. This protein is one of most abundantly expressed in yeast. After purification nucleocapsid-like particles (NLPs) derived from both yeast genera appeared to be similar to those detected in mammalian cells infected with measles virus. A spontaneous assembly of nucleoprotein into nucleocapsid-like particles in the absence of the viral leader RNA or viral proteins has been shown. Compartmentalisation of recombinant protein into large compact inclusions in the cytoplasm of yeast S. cerevisiae by green fluorescence protein (GFP) fusion has been demonstrated. Sera from measles patients reacted with the recombinant protein expressed in both yeast genera and a simple diagnostic assay to detect measles IgM could be designed on this basis.     

Why complexity and entropy matter: information, posttranslational modifications, and assay fidelity

Computationally aided protein identification of mass spectrometry (MS) data has been a challenge for the proteomic community since the field's inception. As the community attempts to address challenges such as computational site assignment of posttranslational modifications (PTMs), selective reaction monitoring data analysis, and the transition of proteomic assays to the clinic a robust framework with defined metrics is essential. The frameworks used for protein identification are currently score based, not hypothesis driven nor deterministic, resulting in a gradation from poor to good but without the ability to recognize when a given tandem MS spectrum has insufficient information in the context of the proteome to be identified. Means of computing deterministic and pseudodeterministic assays have been proposed by both us and others [Sherman, J., McKay, M.J., Ashman, K., Molloy, M.P., Unique ion signature mass spectrometry, a deterministic method to assign peptide identity. Mol. Cell. Proteomics 2009, 8, 2051-2062; Kiyonami, R., Schoen, A., Prakash, A., Peterman, S., et al., Increased selectivity, analytical precision, and through-put in targeted proteomics. Mol. Cell. Proteomics 2011, 10, M110.002931]. We believe it is crucial to incorporate the complexity of the proteome into the design of the experiment/data analysis upstream and that by doing so proteomic data analysis will become more robust. The seminal paper by Claude Shannon published in 1948 provides the robust mathematical framework now called Information Theory, to achieve this goal. Information Theory defines appropriate metrics for information and complexity as well as means to account for interference, all of which is directly applicable to peptide identification. We attempt to encourage the adoption of Information Theory as a means to ensure that appropriate metrics are used to measure the uncertainty in a peptide identification with or without PTM site assignment.     

Comparison of central versus peripheral delivery of pregabalin in neuropathic pain states

Background

Although pregabalin therapy is beneficial for neuropathic pain (NeP) by targeting the CaV??₂??-1 subunit, its site of action is uncertain. Direct targeting of the central nervous system may be beneficial for the avoidance of systemic side effects.

Results

We used intranasal, intrathecal, and near-nerve chamber forms of delivery of varying concentrations of pregabalin or saline delivered over 14 days in rat models of experimental diabetic peripheral neuropathy and spinal nerve ligation. As well, radiolabelled pregabalin was administered to determine localization with different deliveries. We evaluated tactile allodynia and thermal hyperalgesia at multiple time points, and then analyzed harvested nervous system tissues for molecular and immunohistochemical changes in CaV??₂??-1 protein expression. Both intrathecal and intranasal pregabalin administration at high concentrations relieved NeP behaviors, while near-nerve pregabalin delivery had no effect. NeP was associated with upregulation of CACNA2D1 mRNA and CaV??₂??-1 protein within peripheral nerve, dorsal root ganglia (DRG), and dorsal spinal cord, but not brain. Pregabalin's effect was limited to suppression of CaV??₂??-1 protein (but not CACNA2D1 mRNA) expression at the spinal dorsal horn in neuropathic pain states. Dorsal root ligation prevented CaV??₂??-1 protein trafficking anterograde from the dorsal root ganglia to the dorsal horn after neuropathic pain initiation.

Conclusions

Either intranasal or intrathecal pregabalin relieves neuropathic pain behaviours, perhaps due to pregabalin's effect upon anterograde CaV??₂??-1 protein trafficking from the DRG to the dorsal horn. Intranasal delivery of agents such as pregabalin may be an attractive alternative to systemic therapy for management of neuropathic pain states.     

Cytosolic manganese superoxide dismutase genes from the white shrimp Litopenaeus vannamei are differentially expressed in response to lipopolysaccharides, white spot virus and during ontogeny

Manganese superoxide dismutase (MnSOD) is an antioxidant enzyme usually located in mitochondria. There are only a few examples of cytosolic MnSOD (cMnSOD). In the shrimp Litopenaeus vannamei, we have previously characterized three cMnSOD cDNAs and their differential tissue-specific expression. To obtain insights about their genomic organization, we characterized the three corresponding cMnSOD genes, named them cMnsod1, cMnsod2, and cMnsod3 and studied their specific expression during ontogeny, response to lipopolysaccharides (LPS) and white spot virus infection (WSSV) in hemocytes from shrimp. The first two genes contain five introns flanked by canonical 5'-GT-AG-3' intron splice-site junctions, while the third one is intron-less. We analyzed 995 nucleotides upstream cMnsod2, but no classical promoter sequences were found. The deduced products of the three cMnSOD genes differ in two amino acids and there are four silent changes. cMnsod3 expression is modulated by WSSV and cMnsod2 by LPS. cMnsod2 is expressed from eggs to post larval stage during ontogeny. This is the first report of crustacean cMnSOD multigenes that are differently induced during the defense response and ontogeny.