Zinc Extraction potential of two common crop plants,Nicotiana tabacum and Zea mays

White spruce [Picea glauca (Moench) Voss] seedlings were inoculated with Hebeloma crustuliniforme and treated with 25 mM NaCl to examine the effects of salinized soil and mycorrhizae on root hydraulic conductance and growth. Mycorrhizal seedlings had significantly greater shoot and root dry weights, number of lateral branches and chlorophyll content than non-mycorrhizal seedlings. Salt treatment reduced seedling growth in both non-mycorrhizal and mycorrhizal seedlings. However, needles of salt-treated mycorrhizal seedlings had several-fold higher needle chlorophyll content than that in non-mycorrhizal seedlings treated with salt. Mycorrhizae increased N and P concentrations in seedlings. Na levels in shoots and roots of salt-treated mycorrhizal seedlings were significantly lower and root hydraulic conductance was several-fold higher than in non-mycorrhizal seedlings. A reduction of about 50% in root hydraulic conductance of mycorrhizal seedlings was observed after removal of the fungal hyphal sheath. Transpiration and root respiration rates were reduced by salt treatments in both groups of seedlings compared with the controls, however, both transpiration and respiration rates of salt-treated mycorrhizal seedlings were as high as those in the non-mycorrhizal seedlings that had not been subjected to salt treatment. The reduction of shoot Na uptake while increasing N and P absorption and maintaining high transpiration rates and root hydraulic conductance may be important resistance mechanisms in ectomycorrhizal plants growing in salinized soil.     

Amine-reactive Neutron-encoded Labels for Highly Plexed Proteomic Quantitation

We describe a novel amine-reactive chemical label that exploits differential neutron-binding energy between ¹³C and ¹⁵N isotopes. These neutron-encoded (NeuCode) chemical labels enable up to 12-plex MS1-based protein quantification. Each structurally identical, but isotopically unique, tag is encoded with a 12.6-mDa mass difference—relative to its nearest neighbor—so that peptides bearing these NeuCode signatures do not increase spectral complexity and are detected only upon analysis with very high mass-resolving powers. We demonstrate that the method provides quantitative performance that is comparable to both metabolic labeling and isobaric tagging while combining the benefits of both strategies. Finally, we employ the tags to characterize the proteome of Saccharomyces cerevisiae during the diauxic shift, a metabolic transition from fermentation to aerobic respiration.Proteome quantification is an increasingly essential component of modern biology and translational medicine (1, 2). Whether targeted or global, stable isotope incorporation with mass spectrometry (MS) analysis is a core technique for protein abundance measurements. There are numerous approaches that can be used to introduce stable isotopes into peptides, the most frequently used being stable isotope labeling with amino acids in cell culture (SILAC)¹ and isobaric tagging (tandem mass tags or isobaric tags for relative and absolute quantitation) (3–7). Both of these methods incorporate heavy isotopes to increase mass by at least 1 Da. SILAC is the quantification gold standard for global proteomic analysis. However, the SILAC approach is not easily adapted for tissue sample analysis; SILAC mouse labeling, for example, requires feeding mice a specialized diet for multiple generations (8). Tissue samples can be analyzed if they are mixed with SILAC cell-culture-based labeled standards, but this strategy does not permit multiplexing (9). Isobaric labels, in contrast, are conjugated to the primary amines of peptides following proteolytic digestion and thus have the advantage of being completely compatible with samples from virtually any source (10, 11). That said, isobaric tagging suffers from dynamic range suppression caused by co-isolation of precursor peptides (12). Multiple studies have revealed that this problem greatly erodes quantitative accuracy—for example, 10-fold changes often are detected as much smaller ∼4-fold changes (13, 14). Here we propose a new approach to protein quantification, one that achieves tissue-compatible 4-plexed MS1-based quantification without increasing spectral complexity.Recently, we described the use of mass defects to expand SILAC quantification from 3-plex to 12-plex and beyond (i.e., NeuCode SILAC) (15). NeuCode SILAC exploits the subtle mass differences that exist in atoms as a result of the varying energies of nuclear binding in common stable isotopes (e.g., carbon, nitrogen, hydrogen, and oxygen) by using the extremely high resolving power of modern Fourier transform mass spectrometer systems (16, 17). For example, the multiplexing capability of tandem mass tagging was increased from 6 to 8 by incorporating a difference in mass of 6.3 mDa in specific reporter ions by swapping ¹⁴N for a ¹⁵N atom while concomitantly switching a ¹³C with a ¹²C atom (18, 19). This method requires only 30,000 resolving power to resolve the reporter ions, but it still suffers from the interference problem described above. Repetition of this process, within the context of an analyte molecule, can generate several chemically identical isotopologues that, when analyzed under normal MS analysis conditions (resolving power R) are indistinguishable (i.e., produce one m/z peak). Analysis of these NeuCode m/z peaks with high resolving power (480,000), however, often reveals distinct m/z peaks whose abundances can be extracted and used to determine analyte quantity across the sundry conditions. This strategy permits very high levels of MS1-based multiplexing (>10), which has several advantages. First, MS1 scans across the entire analyte elution profile can be averaged to increase quantitative accuracy and precision. Second, a tandem mass spectrum is not necessary for quantification. Mann and colleagues showed that once a peptide is identified via tandem MS analysis, it can be confidently identified in other runs with only the exact mass and elution profile matching (20). Third, MS1-based quantification does not suffer from the pervasive problem of precursor interference that cripples the quantitative accuracy of the isobaric tagging strategies (13).The NeuCode SILAC approach, however, relies on the use of amino acid isotopologues and still requires metabolic incorporation. Chemical labeling strategies for proteome quantification can be convenient and, for certain systems, are requisite. We reasoned that our NeuCode strategy could be extended to create novel chemical reagents for proteome quantification. We describe here the design, synthesis, and use of 12-plex NeuCode amine reactive labels for global proteome quantification.     

NLRP10 enhances Shigella-induced pro-inflammatory responses

Members of the NLR family evolved as intracellular sensors for bacterial and viral infection. However, our knowledge on the implication of most of the human NLR proteins in innate immune responses still remains fragmentary. Here we characterized the role of human NLRP10 in bacterial infection. Our data revealed that NLRP10 is a cytoplasmic localized protein that positively contributes to innate immune responses induced by the invasive bacterial pathogen Shigella flexneri. SiRNA-mediated knock-down studies showed that NLRP10 contributes to pro-inflammatory cytokine release triggered by Shigella in epithelial cells and primary dermal fibroblasts, by influencing p38 and NF-κB activation. This effect is dependent on the ATPase activity of NLRP10 and its PYD domain. Mechanistically, NLRP10 interacts with NOD1, a NLR that is pivotally involved in sensing of invasive microbes, and both proteins are recruited to the bacterial entry point at the plasma membrane. Moreover, NLRP10 physically interacts with downstream components of the NOD1 signalling pathway, such as RIP2, TAK1 and NEMO. Taken together, our data revealed a novel role of NLRP10 in innate immune responses towards bacterial infection and suggest that NLRP10 functions as a scaffold for the formation of the NOD1-Nodosome.     

Production of ethanol from corn stover hemicellulose hydrolyzate using <Emphasis Type="Italic">Pichia stipitis</Emphasis>

Hemicellulose liquid hydrolyzate from dilute acid pretreated corn stover was fermented to ethanol using Pichia stipitis CBS 6054. The fermentation rate increased with aeration but the pH also increased due to consumption of acetic acid by Pichia stipitis. Hemicellulose hydrolyzate containing 34 g/L xylose, 8 g/L glucose, 8 g/L Acetic acid, 0.73 g/L furfural, and 1 g/L hydroxymethyl furfural was fermented to 15 g/L ethanol in 72 h. The yield in all the hemicellulose hydrolyzates was 0.37–0.44 g ethanol/g (glucose + xylose). Nondetoxified hemicellulose hydrolyzate from dilute acid pretreated corn stover was fermented to ethanol with high yields, and this has the potential to improve the economics of the biomass to ethanol process.     

Uptake and metabolism of radioactively labeled sphingomyelin in cultured skin fibroblasts from controls and patients with Niemann-Pick disease and other lysosomal storage diseases

The metabolism of [stearoyl-1-14C]- and [choline-methyl-14C]sphingomyelin, [stearoyl-1-14C]ceramide-1-phospho-N,N-dimethylethanolamine (demethylsphingomyelin) and [choline-methyl-14C]phosphatidylcholine was measured 1, 3 and 5 days after uptake from the media of cultured skin fibroblasts. This was done to measure the relative contributions of lysosomal sphingomyelinase and plasma membrane phosphocholine transferase on the metabolism of sphingomyelin, a component of all cell membranes. By using cell lines from controls and from patients with Niemann-Pick disease and other lysosomal storage diseases, it was concluded that a significant portion (10-15%) of the observed degradation of sphingomyelin is due to exchange of the phosphocholine moiety producing phosphatidylcholine. Although cell lines from type A and B Niemann-Pick disease have only 0-2% of lysosomal sphingomyelinase activity measured in vitro, three cell lines from type B Niemann-Pick disease could metabolize 54.4% of the labeled sphingomyelin by day 3 while cell lines from type A Niemann-Pick disease could only metabolize 18.5% by day 3. This compares to 86.7% metabolized in control cells by day 3. Cells from one patient with juvenile Niemann-Pick disease and one with type D Niemann-Pick disease metabolized sphingomyelin normally while cells from two other patients with juvenile or type C Niemann-Pick disease could only metabolize 58.2% by day 3. Cells from patients with I-cell disease and 'lactosylceramidosis' also demonstrated decreased metabolism of sphingomyelin (55.1 and 54.9% by day 3, respectively). Cells from the patient with Farber disease accumulated [14C]stearic acid-labeled ceramide produced from [14C]sphingomyelin. Studies with choline-labeled sphingomyelin and phosphatidylcholine demonstrated that phosphocholine exchange takes place in either direction in the cells, and this is normal in Niemann-Pick disease. Studies in cells from patients with all clinical types of sphingomyelinase deficiency have led to new methods for diagnosis and prognosis and to a better understanding of sphingomyelin metabolism.     

Efficient feeding profile optimization for recombinant protein production using physiological information

A multivariate study was performed aiming at the optimization of a recombinant rhamnose inducible E. coli induction system with alkaline phosphatase as target product. The effects of typical factors with impact on post- as well as pre-induction feeding rates were investigated with respect to the space–time yield of the target product. The goal was increased understanding as well as quantitative characterization of these factors with respect to their physiological impact on the model system. The optical density (OD) at which the culture was induced had a strong positive effect on the space–time yield. Pre-induction growth rate (k) had a second-order effect, while induction feed rate drop (J), a factor defining the linear post-induction feed rate, was interacting with (k). However, explanation of the observed effects to acquire more understanding regarding their effect on cell metabolism was not straight forward. Hence, the original process parameters were transformed into physiological more meaningful parameters and served as the basis for a multivariate data analysis. The observed variance with respect to observed volumetric activity was fully explained by the specific substrate uptake rate (q _s) and induction OD, merging the process parameters pre-induction growth rate (k) and feed rate drop (J) into the physiological parameter specific substrate uptake rate (q _s). After transformation of the response volumetric activity (U/ml) into the biomass specific activity (U/g_biomass), the observed variance was fully explained solely by the specific substrate uptake rate (q _s). Due to physiological multivariate data analysis, the interpretation of the results was facilitated and factors were reduced. On the basis of the obtained results, it was concluded that the physiological parameter q _s rather than process parameters (k, J, induction OD) should be used for process optimization with respect to the feeding profile.     

Basic calcium phosphate crystals stimulate the endocytotic activity of cells--inhibition by anti-calcification agents

Pathological calcifications are associated with many medical conditions including diabetes, breast cancer, and crystals-associated osteoarthritis. The deposition of calcium-containing crystals on cells induces detrimental cellular effects and speeds up the progression of associated diseases. We carried out the present study to test the hypotheses that calcium-containing crystals may stimulate the influx of other molecules existing in the extracellular fluid disturbing normal molecular signaling and that anti-calcification agent will inhibit such endocytotic process. We found that basic calcium phosphate (BCP) crystals greatly stimulated the endocytotic activity of cells by rendering the cells more permeable and that the anti-calcification agent phosphocitrate and several others inhibited the crystals-mediated endocytosis. This is the first study reporting that the endocytotic activity of cells is affected by BCP crystals and that such endocytotic activity can be inhibited by anti-calcification agents. Since calcium-containing crystals are associated with many human diseases and in many circumstances are associated with apoptotic bodies, extracellular and matrix vesicles where DNA fragments, small peptides, and minerals are released into extracellular space, the findings reported here are important for our understanding of the complex biological effects and the potential pathological role of calcium-containing crystals in crystals-associated diseases, and for the development of disease modifying agents as well.     

Structure of the human blood platelet membrane glycoprotein Ib alpha gene

The gene for human platelet glycoprotein Ib alpha-chain has been cloned from a genomic cosmid library using a partial cDNA clone as probe. 3530 bp were sequenced including the entire transcribed part, as well as additional 5' and 3' regions. A single intron was found 6 bp upstream of the ATG initiation codon. An exceptionally long exon was identical to the recently published cDNA sequence (1). The 5' upstream promoter region is atypical for eukaryotic genes with only a weak homology to the characteristic promoter consensus sequences. The 3' region contains two repetitive Alu elements, belonging to distinct subfamilies, connected by an oligo(dA) linker.     

Relationship between the two immunologically distinguishable forms of glucocerebrosidase in tissue extracts

Extracts of human spleen contain two immunologically distinguishable forms of glucocerebrosidase: form I is precipitable by polyclonal or monoclonal anti-(placental glucocerebrosidase) antibodies, whereas form II is not [Aerts, J. M. F. G., Donker-Koopman, W. E., Van der Vliet, M. F. K., Jonsson, L. M. V., Ginns, E. I., Murray, G. J., Barranger, J. A., Tager, J. M. & Schram, A. W. (1985) Eur. J. Biochem. 150, 565-574]. The proportion of form II glucocerebrosidase was high in extracts of spleen, liver and kidney and low in extracts of brain, placenta and fibroblasts. Furthermore, the proportion of form II enzyme was higher in a detergent-free aqueous extract of spleen than in a Triton X-100 extract of total spleen or splenic membranes. When form II glucocerebrosidase in a splenic extract was separated from form I enzyme by immunoaffinity chromatography and stored at 4 degrees C, a gradual conversion to form I enzyme occurred. The conversion was almost immediate if 30% (v/v) ethylene glycol was present. In the denatured state both forms of glucocerebrosidase reacted with anti-(placental glucocerebrosidase) antibodies. Form I glucocerebrosidase was stimulated by sodium taurocholate or sphingolipid-activator protein 2 (SAP-2), whereas form II enzyme exhibited maximal activity in the absence of the effectors. The pH activity profile of form II glucocerebrosidase was almost identical to that of form I enzyme in the presence of SAP-2. In the native state, form I glucocerebrosidase had a molecular mass of 60 kDa whereas that of form II glucocerebrosidase was about 200 kDa. After gel-permeation high-performance liquid chromatography of splenic extracts, the fractions with form II glucocerebrosidase contained material cross-reacting with both anti-(placental glucocerebrosidase) and anti-(SAP-2) antibodies. Preincubation of form I glucocerebrosidase with SAP-2 at pH 4.5 led to masking of the epitope on glucocerebrosidase reacting with monoclonal anti-(placental glucocerebrosidase) antibody 2C7. Furthermore, preincubation of form I glucocerebrosidase with monoclonal antibody 2C7 prevented activation of the enzyme by SAP-2. We propose that form I glucocerebrosidase is a monomeric form of the enzyme, whereas form II glucocerebrosidase is a high-Mr complex of the enzyme in association with sphingolipid-activator protein 2.