Effects of enzymatically digested microsome fractions on red-light-enhanced pelletability of pea phytochrome in vitro in the presence of calcium ion

The 130,000 ?g supernatant of Sephadex G-50 filtrate and a 78,000?g microsomal fraction were prepared separately from homogenatesof etiolated pea (Pisum sativum L. cv. Alaska) shoots. The pelletabilityof phytochrome increased ca. 10-fold by exposure of the filtrateto red light and mixing the filtrate with the microsomal fractionin the dark at ca. 0?C. The increase of pelletable phytochromewas inhibited by 84% when the microsomal fraction digested withtrypsin was used. Phospholipase C (Clostridium welchii) digestionof the microsome inhibited no more than 13% of the pelletability.Although phospholipase A₂ (Crotalus terrificus terrificus) digestioninhibited 43% of the pelletability, addition of defatted albuminduring the enzymatic digestion completely restored the levelof the pelletability. The decrease of RNA content of the microsomalfractions by ribonuclease A digestion did not result in a proportionalinhibition of the pelletability. These results indicate thatproteinaceous component in the microsomal fraction is essentialfor phytochrome pelletability in vitro, that RNA and polar headsof phospholipids are unlikely to be the partner for the binding,and that products of phospholipase A₂ digestion inhibit thepelletability partially. (Received September 12, 1979; )     

Use of flow cytometry in oenology to analyse yeasts

Flow cytometry is a rapid method with many microbiological applications. This technique can be used to obtain counts of viable yeasts in 30 min, whereas a 48 h incubation is necessary with plate counts. This rapid method was tested for its suitability to analyse wine yeasts in a multicentre study in our three laboratories. The study compares measurements obtained by flow cytometry and the usual method, in order to test the reliability of the new method. The results obtained were very similar in terms of both the micro-organisms detected and the precision of measurements.     

Induction of cytokines and nitric oxide in murine macrophages stimulated with enzymatically digested lactobacillus strains

Based on observations that lactic acid bacteria have the ability to activate macrophages, we assessed the potential effects of eight different Lactobacillus strains treated with gastrointestinal enzymes on the production of nitric oxide and various cytokines in macrophages. RAW 264.7 murine macrophage cells were cultured with either precipitates or supernatants of Lactobacillus strains digested with pepsin followed by pancreatin. The increased production of nitric oxide and interleukin (IL)-1beta, IL-6, IL-12 and tumour necrosis factor (TNF)-alpha were observed when cultured with precipitates, and this effect was largely strain-dependent. In contrast, the exposure of RAW 264.7 cells to supernatants produced weaker or nearly undetectable effects in comparison to the effects of exposure to precipitates. The induction of nitric oxide appeared to be unaffected. These results demonstrate that nitric oxide and cytokines were effectively induced when the bacterial precipitate was treated with macrophages. The results of the present study also indicate that Lactobacillus strains treated with digestive enzymes are capable of stimulating the production of nitric oxide and cytokines in macrophages, which may modulate the gastrointestinal immune function of the host when it is given as a feed additive.     

Sensitivity of Candida albicans to negative air ion streams

Negative air ions (NAIs) are known to kill C. albicans; however, their precise mechanism of action is uncertain. Elucidation of this has been hampered by a lack of reproducibility between results obtained by different investigators. The aim of this study was to determine the influence of variation in experimental parameters on the sensitivity of C. albicans to negative air ions and the role of ozone in this process. Ten strains of C. albicans were exposed to NAIs generated at different emitter distances, exposure times, relative humidities and under aerobic and oxygen-free conditions. In further experiments, ozone levels were measured under the same conditions. The effect of NAIs on C. albicans growth was assessed by measuring the area of the zone of inhibition generated around the electrode of the ionizer. There was a significant reduction in area of zone of inhibition with increasing emitter distance (P < 0.05), relative humidity (P < 0.05) or under oxygen-free conditions (P < 0.05). Increases in exposure time resulted in a significant increase in growth inhibition (P < 0.05). Ozone levels increased with increasing exposure times (P < 0.01) but were significantly reduced as emitter distance increased (P < 0.01). When utilized in a nonventilated room, levels of ozone produced did not exceed recognized safety limits. These results (a) demonstrate the importance of careful control of experimental parameters if reproducibility of studies involving NAIs is to be achieved, and (b) highlight the possible role of ozone in the microbicidal effects of NAIs.     

Use of Gaussian-type functions for flux-based dose calculations in carbon ion therapy

Radiation and Environmental Biophysics - In radiation therapy, it is very important to ensure that the radiation dose is correctly delivered to the patient. This is achieved by obtaining...     

Use of monoclonal antibodies to analyse the expression of a multi-tubulin family

We have used a panel of monoclonal antibodies in a study of the expression of multiple tubulins in Physarum polycephalum. Three anti-beta-tubulin monoclonal antibodies, DM1B, DM3B3 and KMX-1 all reacted with the beta 1-tubulin isotypes expressed in both myxamoebae and plasmodia. However, these antibodies showed a spectrum of reduced reactivity with the plasmodial beta 2-tubulin isotype - the competence of recognition of this isotype was graded DM1B greater than KMX-1 greater than DM3B3. The anti-alpha-tubulin monoclonal antibody, YOL 1/34 defined the full complement of Physarum alpha-tubulin isotypes, whilst the anti-alpha-tubulin monoclonal antibody, KMP-1 showed a remarkably high degree of isotype specificity. KMP-1 recognises all of the myxamoebal alpha 1-tubulin isotypes but only recognises 3 out of the 4 alpha 1-tubulin isotypes expressed in the plasmodium (which normally focus in the same 2D gel spot). KMP-1 does not recognise the plasmodial specific alpha 2-tubulin isotype. This monoclonal antibody reveals a new level of complexity amongst the tubulin isotypes expressed in Physarum and suggests that monoclonal antibodies are valuable probes for individual members of multi-tubulin families.     

Comparative study of gamma-ray and high-energy carbon ion irradiation on negative gravitaxis inEuglena gracilisZ

The effects of ⁶⁰Co gamma-ray and 290 MeV/amu carbon ion irradiation on negative gravitaxis was studied in the photosynthetic flagellate Euglena gracilis strain Z in a dose-response dependent manner. Cells were exposed to the doses (0-200 Gy for water). The negative gravitaxis was quantified by the r-value observed in a recently developed biomonitoring system. The present results demonstrate the inhibitory effects of gamma-rays and 290 MeV/amu carbon ions on negative gravitaxis of the Euglena gracilis strain Z. The 290 MeV/amu carbon ions had a greater impact at a low dose (<40 Gy) than the ⁶⁰Co gamma-rays.     

Use of fluorescent protein to analyse recombination at three loci in Neurospora crassa

We have inserted a histone H1-GFP fusion gene adjacent to three loci on different chromosomes of Neurospora crassa and made mating pairs in which a wild type version of GFP is crossed to one with a mutation in the 5' end of GFP. The loci are his-3, am and his-5, chosen because recombination mechanisms appear to differ between his-3 and am, and because crossing over adjacent to his-5, like his-3, is regulated by rec-2. At his-3, the frequencies of crossing over between GFP and the centromere and of conversion of 5'GFP to GFP(+) are comparable to those obtained by classical recombination assays, as is the effect of rec-2 on these frequencies, suggesting that our system does not alter the process of recombination. At each locus we have obtained sufficient data, on both gene conversion and crossing over, to be able to assess the effect of deletion of any gene involved in recombination. In addition, crosses between a GFP(+) strain and one with normal sequence at all three loci have been used to measure the interval to the centromere and to show that GFP experiences gene conversion with this system. Since any gene expressed in meiosis is silenced in Neurospora if hemizygous, any of our GFP(+) strains can be used as a quick screen to determine if a gene deleted by the Neurospora Genome Project is involved in crossing over or gene conversion.     

A relative quantitative positive/negative ion switching method for untargeted lipidomics via high resolution LC-MS/MS from any biological source

Introduction

Advances in high-resolution mass spectrometry have created renewed interest for studying global lipid biochemistry in disease and biological systems.

Objectives

Here, we present an untargeted 30 min. LC-MS/MS platform that utilizes positive/negative polarity switching to perform unbiased data dependent acquisitions (DDA) via higher energy collisional dissociation (HCD) fragmentation to profile more than 1000–1500 lipid ions mainly from methyl-tert-butyl ether (MTBE) or chloroform:methanol extractions.

Methods

The platform uses C₁₈ reversed-phase chromatography coupled to a hybrid QExactive Plus/HF Orbitrap mass spectrometer and the entire procedure takes?~10 h from lipid extraction to identification/quantification for a data set containing 12 samples (~4 h for a single sample). Lipids are identified by both accurate precursor ion mass and fragmentation features and quantified using LipidSearch and Elements software.

Results

Using this approach, we are able to profile intact lipid ions from up to 18 different main lipid classes and 66 subclasses. We show several studies from different biological sources, including cultured cancer cells, resected tissues from mice such as lung and breast tumors and biological fluids such as plasma and urine.

Conclusions

Using mouse embryonic fibroblasts, we showed that TSC2^?/? KD significantly abrogates lipid biosynthesis and that rapamycin can rescue triglyceride (TG) lipids and we show that SREBP^?/? shuts down lipid biosynthesis significantly via mTORC1 signaling pathways. We show that in mouse EGFR driven lung tumors, a large number of TGs and phosphatidylmethanol (PMe) lipids are elevated while some phospholipids (PLs) show some of the largest decrease in lipid levels from ~?2000 identified lipid ions. In addition, we identified more than 1500 unique lipid species from human blood plasma.

     

Use of 3-D computer modelling and kinetic studies to analyse grapefruit pyrophosphate-dependent phosphofructokinase

The glycolytic reaction of grapefruit PPi-dependent phosphofructokinase (PFP) depends on the presence of Fru-2,6-P₂ (K_a=6.7 nM). This molecule was further demonstrated in grapefruit juice sac cells. Citrate, -ketoglutarate and isocitrate competitively inhibited the binding of Fru-2,6-P₂ to PFP. The affinity for Fru-6-P (K_m=159 μM) and PPi (K_m=33 μM) were not affected by the addition of these molecules. In the gluconeogenic reaction, the presence of Fru-2,6-P₂ did not affect the K_m of Fru-1,6-P₂ (61 μM) in contrast to orange fruit PFP. These results led to the building of a computer model of PFP, based on the known structure of Bacillus stearothermophilus ATP-dependent phosphofructokinase (ATP-PFK). The results show that catalysis of Fru-6-P in the chain is most unlikely, due to amino-acid substitutions and that Fru-2,6-P₂ can bind between the and β subunits.     

Use of the collagen I-deficient Mov13 mouse mutant to analyse epithelial-mesenchymal tissue interaction

The collagen I-deficient mouse mutant (Mov13 — an embryonic recessive lethal) was used to investigate the function of this major constituent of the extracellular matrix (ECM) in organ development. All epithelial-mesenchymal organs tested as explants (lung, kidney, pancreas, salivary glands, skin) developed normally and, in particular, showed typical branching morphogenesis in the absence of collagen I. It is concluded that the ECM of these organs can organize for proper developmental function in the absence of the major interstitial collagen, but a possible morphogenetic function of other fibrillar collagens (types III and V) cannot be excluded. The only insufficiencies in the mutant were seen in the cornea where deposition and organization of the collagenous stroma was highly inadequate; but even there, development and migration of cells proceeded normally. In summary, the results indicate that ‘cellular’ development in epithelial-mesenchymal organs (including growth, morphogenesis, and differentiation) does not depend on collagen I.     

Use of an adsorbed chiral selector in capillary LC-MS

Lasalocid was utilized as a chiral selector adsorbed on porous graphitic carbon. Important parameters were identified for the use of the chiral selector in capillary liquid chromatography combined with MS detection. The influence on both retention and enantioselectivity as well as mass spectrometric performance was studied at lasalocid concentrations of up to 12 mg/l (20 microM). Moreover, the stability of retention factors and enantioselectivities was also evaluated at low selector concentration of 1 mg/l (2 microM). The results show that in order to optimize the MS performance the selector concentration should be kept at low microM. The chromatographic performance at reduced selector concentration (1 mg/l = 2 microM) was studied over a 10-day period, showing satisfactory enantioselectivity and stable performance concerning enantioselectivity and retention.     

Secondary ion mass spectrometry for sulfoglycolipids: application of negative ion detection

A series of underivatized sulfoglycolipids (SM4g, lyso-SM4g, SM4s, SM3, SM2, SB2, and SB1a) from various tissues were analyzed by both positive (POS-SI-MS) and negative (NEG-SI-MS) secondary ion mass spectrometry. By POS-SI-MS were detected the molecular ions of sulfoglycolipids in the form with sodium or potassium together with some fragment ions useful for the carbohydrate sequence determination. The analysis of monosulfogangliotriaosyl- or monosulfogangliotetraosylceramide and bis-sulfoglycolipid was difficult due to noise in the high mass region. On the other hand, NEG-SI-MS of sulfoglycolipids gave more intense signals from molecular ion of (M-H)- for monosulfoglycolipids and [M-H+Na)-H)- for bis-sulfoglycolipid. Many fragment ions useful for the elucidation of the carbohydrate sequences were also obtained with significant intensities. The fragmentation was assessed to occur at the glycosidic linkages to form ions of the oligosaccharides with or without ceramide. These ions were useful for sugar sequencing and also for distinguishing the differences in the position of the sulfate group. The intensities of saccharide ions without sulfate were lower than those with sulfates. In the case of SB2 and SB1a, containing 2 mol of sulfate ester groups, the molecular ion was detected as [M-H+Na)-H)-. Also, fragment ions with 2 mol of sulfate were detected as the sodium-additive form. It was concluded that NEG-SI-MS is a very useful technique for the structural elucidation of higher sulfoglycolipids.     

High sensitivity LC-MS profiling of antibody-drug conjugates with difluoroacetic acid ion pairing

ABSTRACT

Reversed-phase liquid chromatography (RPLC) separations of proteins using optical detection generally use trifluoroacetic acid (TFA) because it is a strong, hydrophobic acid and a very effective ion-pairing agent for minimizing chromatographic secondary interactions. Conversely and in order to avoid ion suppression, analyses entailing mass spectrometry (MS) detection is often performed with a weaker ion-pairing modifier, like formic acid (FA), but resolution quality may be reduced. To gain both the chromatographic advantages of TFA and the enhanced MS sensitivity of FA, we explored the use of an alternative acid, difluoroacetic acid (DFA). This acid modifier is less acidic and less hydrophobic than TFA and is believed to advantageously affect the surface tension of electrospray droplets. Thus, it is possible to increase MS sensitivity threefold by replacing TFA with DFA. Moreover, we have observed DFA ion pairing to concomitantly produce higher chromatographic resolution than FA and even TFA. For this reason, we prepared and used MS-quality DFA in place of FA and TFA in separations involving IdeS digested, reduced NIST mAb and a proprietary antibody-drug conjugate (ADC), aiming to increase sensitivity, resolution and protein recovery. The resulting method using DFA was qualified and applied to two other ADCs and gave heightened sensitivity, resolution and protein recovery versus analyses using TFA. This new method, based on a purified, trace metal free DFA, can potentially become a state-of-the-art liquid chromatography-MS technique for the deep characterization of ADCs.     

Comparison of cytokine and nitric oxide induction in murine macrophages between whole cell and enzymatically digested Bifidobacterium sp. obtained from monogastric animals

The principal objective of this study was to compare the effects of whole and hydrolyzed cells (bifidobacteria) treated with gastrointestinal digestive enzymes on the activation of cloned macrophages. Seven different strains of Bifidobacterium obtained from swine, chickens, and rats, were digested with pepsin followed by pancreatin and the precipitate (insoluble fraction) and supernatant (soluble fraction) obtained via centrifugation. The RAW 264.7 murine macrophages were incubated with either whole cells, the precipitate, or supernatant at various concentrations. Pronounced increases in the levels of nitric oxide (NO), interleukin (IL)-1beta, IL-6, IL-12, and tumor necrosis factor (TNF)-alpha were observed in the whole cells and precipitates, but these effects were less profound in the supernatants. The precipitates also evidenced a slight, but significant, inductive activity for NO and all tested cytokines, with the exception of TNF-alpha in the macrophage model as compared with the whole cells. By way of contrast, TNF-alpha production when cultured with whole cells (100 ng/ml) resulted in marked increases as compared with what was observed with the precipitates. The results of this study indicated, for the first time, that digested Bifidobacterium sp. can induce the production of NO and several cytokines in RAW 264.7 murine macrophage cells. In the current study, it was demonstrated that Bifidobacterium strains treated with digestive enzymes, as compared with whole cells, are capable of stimulating the induction of macrophage mediators, which reflects that they may be able to modulate the gastrointestinal immune functions of the host.     

Modelling the long-term response to positive and negative priming of soil organic carbon by black carbon

Observed increases in the mineralization rate of labile organic carbon (LOC) in the presence of black carbon (BC) have led to speculation that corresponding decreases in non-pyrogenic (i.e. non-BC) soil organic carbon (npSOC) could significantly reduce or negate the C sequestration benefit of BC in soils. Here we show that the potential effect of an increased LOC decomposition rate on long-term npSOC stocks is negligible, even when using assumptions that would favour large losses, potentially causing no more than 3–4 % loss of npSOC over 100 years if 50 % of above-ground crop residues were converted to BC annually. Conversely, if the BC-stimulated enhanced stabilization of npSOC that has been observed in laboratory trials is extrapolated to the long-term, it would greatly increase soil carbon stocks by 30–60 %. Annual additions of BC derived from crop residues would increase total SOC (including both BC and npSOC) by an amount five times greater than the potential increase from enhanced stabilization and an order of magnitude greater than losses of npSOC caused by annual removals of biomass to provide BC feedstock.     

Rapid analysis of tryptically digested cerebrospinal fluid using capillary electrophoresis-electrospray ionization-Fourier transform ion cyclotron resonance-mass spectrometry

Mass spectrometry has in recent years been established as the method of choice for protein identification and characterization in proteomics. Capillary electrophoresis (CE) is a fast and efficient method for the separation of peptides and proteins. The on-line combination of CE with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry (MS) has been shown to be a powerful tool in the analysis of complex mixtures of proteins. This paper presents the first results from a proteomic analysis of human cerebrospinal fluid proteins by tryptic digestion and CE-FTICR-MS, where 30 proteins could be identified on a 95% confidence level with mass measurement errors less than 5 ppm.     

Use of growth-attachment correlation plots to analyse human melanoma cell dependency on 2-oxocarboxylates and serum

Modulation of the population-dependent growth of the human melanoma line MM96 by serum and a series of 2-oxocarboxylates was analysed by a method offering several useful features. Initial cell attachment was measured by the use of cells prelabelled with [14C] thymidine (C) while the size of the replicating cell population on any particular day was monitored by [3H] thymidine (H) incorporation for that particular 24 hr. The 3H incorporation was normalized for the initial cell attachment as the 3H/14C ratio (H/C), which was found to be little affected by artifacts of precursor equilibration. The method allows large numbers of replicate samples so that quantitation of dose-response relationships is simple and statistically robust, and simultaneous monitoring of cell attachment and growth within the same sample is routine. Not only cell growth, but also attachment to the culture vessel surface was found to be increased by higher seeded population densities, by increasing serum concentration and by pyruvate supplementation. Further investigation of the pyruvate effect showed that all nine of the soluble 2-oxocarboxylates tested were effective for both parameters, with little difference between them which was attributable to molecular structure. Quantitative studies of the potentiation of growth and attachment by increasing cell density or a range of concentrations of 2-oxocarboxylates led to the finding that increments in the growth parameter (H/C) were directly proportional to increments in attachment (C). Such a relationship would be unexpected in ordinary logarithmically-growing cultures. The observation is consistent with the hypothesis that increases in initial cell attachment, whether induced by 2 oxocarboxylates or higher inoculation densities, lead to conditioning of the medium by cell factors which stimulate growth and are produced in amounts proportional to the attached cell numbers. Pyruvate, when present with higher serum concentrations, stimulated growth above the levels accounted for by concomitant increases in cell attachment. Serum also appears to have other potentiating factors in addition to those attributable to its content of 2-oxocarboxylates. Differences in the response to 2-oxocarboxylates of human melanoma cells and human diploid fibroblasts were noted, and suggest that the present observations may be due to unique properties of the melanoma cell.