Determination of complex type free, non-conjugated oligosaccharide glucose unit values in tomato xylem sap for early detection of nutrient deficiency.

Although knowledge on glycan biosynthesis and processing is continuously maturing, there are still a limited number of studies that examine biological functions of N-glycan structures in plants, which remain virtually unknown. Here, the statistical correlation between nutrient (nitrogen) deficiency symptoms of crops and changes in 8-aminopyrene-1,3,6-trisulfonic acid (APTS)-labeled complex type free oligosaccharides is reported. While deficiency symptoms are predicted by multispectral images and Kjeldahl digestion, APTS-labeled complex type free oligosaccharides are identified by their glucose unit (GU) values in tomato xylem sap, using capillary electrophoresis with laser induced fluorescence detection (CE-LIF). Given the limited number of structures obtained from plants, archived in the literature, in the future, it is intended to create an open access database of promising indicators, namely, glycan structures that are presumably responsible for the nutrient deficiency caused stress in plants (http://glycoplants.org).

Increased Cd2+ biosorption capability of Aspergillus nidulans elicited by crpA deletion.

The P-type ATPase CrpA is an important Cu2+ /Cd2+ pump in the Aspergilli, significantly contributing to the heavy metal stress tolerance of these ascomycetous fungi. As expected, the deletion of crpA resulted in Cu2+ /Cd2+ -sensitive phenotypes in Aspergillus nidulans on stress agar plates inoculated with conidia. Nevertheless, paradoxical growth stimulations were observed with the ΔcrpA strain in both standard Cu2+ stress agar plate experiments and cellophane colony harvest (CCH) cultures, when exposed to Cd2+ . These observations reflect efficient compensatory mechanisms for the loss of CrpA operating under these experimental conditions. It is remarkable that the ΔcrpA strain showed a 2.7 times higher Cd biosorption capacity in CCH cultures, which may facilitate the development of new, fungal biomass-based bioremediation technologies to extract harmful Cd2+ ions from the environment. The nullification of crpA also significantly changed the spatial distribution of Cu and Cd in CCH cultures, as demonstrated by the combined particle-induced X-ray emission and scanning transmission ion microscopy technique. Most important, the centers of gravity for Cu and Cd accumulations of the ΔcrpA colonies shifted toward the older regions as compared with wild-type surface cultures.

Effect of the elapsed time between sampling and formalin fixation on the N-glycosylation profile of mouse tissue specimens.

Formalin-fixed, paraffin-embedded (FFPE) samples are generally used for histology-study, however, they also possess important molecular diagnostics information. While it has been reported that the N-glycan moieties of glycoproteins is not affected by the FFPE process, no information is available about the effect of the elapsed time between sampling and fixation on the resulting N-glycosylation profile. In this study, lung, brain, heart, spleen, liver, kidney, and intestine mouse tissue specimens were used for N-glycan profiling analysis and the elapsed sampling time effect was investigated with the lung tissue. N-glycan extraction from the tissue samples was performed by glycoprotein retrieval from the FFPE specimens using radioimmunoprecipitation assay (RIPA) buffer followed PNGase F digestion. The released oligosaccharides were fluorophore labeled and analyzed by capillary electrophoresis-laser induced fluorescent detection (CE-LIF). N-glycosylation profiles of freshly collected lung-tissue samples (zero time point), as well as 1 and 2 h after sampling were compared by carbohydrate profiling and exoglycosidase treatment based deep glycomic analysis. It was found that up to two hours of room temperature storage of tissue specimens apparently did not cause changes in the N-glycosylation profiles of complex carbohydrates, but resulted in considerable decrease in the amount of linear glucose oligomers and high mannose type glycans present in the samples.

Authors' Reply to the Commentary in the journal of Electrophoresis regarding "The effect of simulated space radiation on the N-glycosylation of human immunoglobulin G1" by J.J. Bevelacqua and S.M.J. Mortazavi.

By reading the commentary of Bevelacqua and Mortazavi regarding our recently published paper titled as "The effect of simulated space radiation on the N-glycosylation of human immunoglobulin G1"[1], we are afraid that some of the important messaging aspects of our paper might not have been articulated adequately to be fully understandable for a wider audience, i.e., not separation scientists. First, we should clarify that complete space radiation description was not the goal of this paper. In this short communication we only intended to show the effect of simulated space radiation on the conserved N-glycosylation of IgG1 molecules with the goal to understand if they could be utilized as disease biomarkers during longer space missions, similar to that as they are currently used here on Earth, e.g. for autoimmune disease or aging markers. Therefore, no discussion was given about any biological effects either as our study only investigated the qualitative effects of proton irradiation on the N-linked carbohydrate decomposition of IgG type 1 molecules with the intent of suggesting them to be used as biomarkers during deep space travel. Radioadaptation was never an issue in our study for the reasons mentioned above.

The effect of simulated space radiation on the N-glycosylation of human immunoglobulin G1.

On a roundtrip to Mars, astronauts are expectedly exposed to an approximate amount of radiation that exceeds the lifetime limits on Earth. This elevated radiation dose is mainly due to Galactic Cosmic Rays and Solar Particle Events. Specific patterns of the N-glycosylation of human Igs have already been associated with various ailments such as autoimmune diseases, malignant transformation, chronic inflammation, and ageing. The focus of our work was to investigate the effect of low-energy proton irradiation on the IgG N-glycosylation profile with the goal if disease associated changes could be detected during space travel and not altered by space radiation. Two ionization sources were used during the experiments, a Van de Graaff generator for the irradiation of solidified hIgG samples in vacuum, and a Tandetron accelerator to irradiate hIgG samples in aqueous solution form. Structural carbohydrate analysis was accomplished by CE with laser induced fluorescent detection to determine the effects of simulated space radiation on N-glycosylation of hIgG1 samples. Our results revealed that even several thousand times higher radiation doses that of astronauts can suffer during long duration missions beyond the shielding environment of Low Earth Orbit, no changes were observed in hIgG1 N-glycosylation. Consequently, changes in N-linked carbohydrate profile of IgG1 can be used as molecular diagnostic tools in space.

Molecular glycopathology by capillary electrophoresis: Analysis of the N-glycome of formalin-fixed paraffin-embedded mouse tissue samples.

Capillary electrophoresis with laser-induced fluorescence (CE-LIF) detection was used to analyze endoglycosidase released and fluorophore-labeled N-glycans from formalin-fixed paraffin-embedded (FFPE) mouse tissue samples of lung, brain, heart, spleen, liver, kidney and intestine. The FFPE samples were first deparaffinized followed by solubilization and glycoprotein retrieval. PNGase F mediated release of the N-linked oligosaccharides was followed by labeling with aminopyrene trisulfonate. After CE-LIF glycoprofiling of the FFPE mouse tissues, the N-glycan pool of the lung specimen was subject to further investigation by exoglycosidase array based carbohydrate sequencing. Structural assignment of the oligosaccharides was accomplished by the help of the GUcal software and the associated database, based on the mobility shifts after treatments with the corresponding exoglycosidase reaction mixtures. Sixteen major N-linked carbohydrate structures were sequenced from the mouse lung FFPE tissue glycome and identified, as high mannose (3) neutral biantennary (3) sialylated monoantennary (1) and sialylated bianennary (9) oligosaccharides. Two of these latter ones also possessed alpha(1-3) linked galactose residues.

N-Glycosylation analysis of formalin fixed paraffin embedded samples by capillary electrophoresis.

In this study, N-linked glycans from intact, formalin treated and formalin fixed paraffin embedded (FFPE) standard glycoproteins, human serum and mouse tumor tissue samples were investigated in respect to their susceptibility for formaldehyde treatment mediated changes. FFPE samples were first deparaffinized, followed by solubilization in radioimmunoprecipitation assay buffer and treated with PNGase F for N-glycan release. The released glycans were labeled with a charged fluorophore and analyzed by capillary electrophoresis with laser induced fluorescent detection. No significant alterations were found in the N-glycome profile at any of the investigated complexation levels (i.e., glycoprotein, serum and tissue samples) of the study. These results suggest that FFPE samples can be readily used for global N-glycome analysis holding the promise to find novel carbohydrate biomarkers in prospective and retrospective studies. Exoglycosidase based carbohydrate sequencing was also applied to reveal some basic structural information about the N-linked carbohydrates of the mouse tumor tissue samples.

Glycan microarrays: new angles and new strategies.

Carbohydrate microarrays, comprising hundreds to thousands of different glycan structures on solid surfaces in a spatially discrete pattern, are sensitive and versatile tools for the analysis of glycosylation changes in complex biological samples. Glycoarrays are also suitable for monitoring multiple molecular interactions with biomolecules where sugars are involved, offering a large variety of bioassay options. In this paper we review the most important glycan microarray types currently used with their main applications, and discuss some of the future challenges the technology faces.

Species- and Metal-Specific Responses of the Ionome of Three Duckweed Species under Chromate and Nickel Treatments.

In this study, growth and ionomic responses of three duckweed species were analyzed, namely Lemna minor, Landoltia punctata, and Spirodela polyrhiza, were exposed for short-term periods to hexavalent chromium or nickel under laboratory conditions. It was found that different duckweed species had distinct ionomic patterns that can change considerably due to metal treatments. The results also show that, because of the stress-induced increase in leaf mass-to-area ratio, the studied species showed different order of metal uptake efficiency if plant area was used as unit of reference instead of the traditional dry weight-based approach. Furthermore, this study revealed that µXRF is applicable in mapping elemental distributions in duckweed fronds. By using this method, we found that within-frond and within-colony compartmentation of metallic ions were strongly metal- and in part species-specific. Analysis of duckweed ionomics is a valuable approach in exploring factors that affect bioaccumulation of trace pollutants by these plants. Apart from remediating industrial effluents, this aspect will gain relevance in food and feed safety when duckweed biomass is produced for nutritional purposes.

Hidden behind the mask: An authentication study on the Aztec mask of the Museum of Ethnography, Budapest, Hungary.

Turquoise covered mosaic objects - especially masks - were attractive components of treasures transported to Europe from Mexico after the fall of the Aztec Empire in the 1500s. According to our present knowledge, the mosaic masks were manufactured for ritual purpose. The main material of mosaics, the turquoise was a high-prestige semi-precious stone among Mexican native people. During the 20th century, such objects derived both from illegal treasure hunting and documented archaeological excavations. The aim of our research was the authentication of a turquoise covered Aztec wooden mask, which presumably originates from the Tehuacán Valley, Mexico and exchanged by the Museum of Ethnography, Budapest, in 1973. The detailed and complex analytical investigation of the mask is a curiosity. To reveal the origin of the object, UV photographs were taken, the wooden base was subjected to biological studies and C-14 dating, the organic glue fixing the tesserae and the inorganic mosaic tesserae were investigated by non-destructive chemical, FT-IR and Raman spectroscopic methods. Our investigations determined that the mask of the Museum of Ethnography was made of an alder species of tree and its age is AD 1492-1653. The light-coloured covering mosaic lamellae were identified as alabaster and claystone. Comparing the turquoise tesserae cover with reference materials, their chemical composition has been clearly differentiated from most of the well-known turquoise sources of the US Southwest. Based on our results, the Aztec mask of the Museum of Ethnography proved to be an original piece of art from the 15th-17th century.

N-glycosylation of blood coagulation factor XIII subunit B and its functional consequence.

BACKGROUND: The protective/inhibitory B subunits of coagulation factor XIII (FXIII-B) is a ~80 kDa glycoprotein containing two N-glycosylation sites. Neither the structure nor the functional role of the glycans on FXIII-B has been explored. OBJECTIVE: To reveal the glycan structures linked to FXIII-B, to design a method for deglycosylating the native protein, to find out if deglycosylation influences the dimeric structure of FXIII-B and its clearance from the circulation. METHODS: Asparagine-linked carbohydrates were released from human FXIIII-B by PNGase F digestion. The released N-linked oligosaccharides were fluorophore labeled and analyzed by capillary electrophoresis. Structural identification utilized glycan database search and exoglycosidase digestion based sequencing. The structure of deglycosylated FXIII-B was investigated by gel filtration. The clearance of deglycosylated and native FXIII-B from plasma was compared in FXIII-B knock out mice. RESULTS: PNGase F completely removed N-glycans from the denatured protein. Deglycosylation of the native protein was achieved by repeated digestion at elevated PNGase F concentration. The total N-glycan profile of FXIII-B featured nine individual structures; three were fucosylated and each structure contained at least one sialic acid. Deglycosylation did not change the native dimeric structure of FXIII-B, but accelerated its clearance from the circulation of FXIII-B knock out mice. CONCLUSION: Characterization of the glycan moieties attached to FXIII-B is reported for the first time. Complete deglycosylation of the native protein was achieved by a deglycosylation workflow. The associated glycan structure is not required for FXIII-B dimer formation, but it very likely prolongs the half-life of FXIII-B in the plasma.

Biomedical analysis of formalin-fixed, paraffin-embedded tissue samples: The Holy Grail for molecular diagnostics.

More than a century ago in 1893, a revolutionary idea about fixing biological tissue specimens was introduced by Ferdinand Blum, a German physician. Since then, a plethora of fixation methods have been investigated and used. Formalin fixation with paraffin embedment became the most widely used types of fixation and preservation method, due to its proper architectural conservation of tissue structures and cellular shape. The huge collection of formalin-fixed, paraffin-embedded (FFPE) sample archives worldwide holds a large amount of unearthed information about diseases that could be the Holy Grail in contemporary biomarker research utilizing analytical omics based molecular diagnostics. The aim of this review is to critically evaluate the omics options for FFPE tissue sample analysis in the molecular diagnostics field.