Comparison of the methods for profiling glycoprotein glycans--HUPO Human Disease Glycomics/Proteome Initiative multi-institutional study

Mass spectrometry (MS) of glycoproteins is an emerging field in proteomics, poised to meet the technical demand for elucidation of the structural complexity and functions of the oligosaccharide components of molecules. Considering the divergence of the mass spectrometric methods employed for oligosaccharide analysis in recent publications, it is necessary to establish technical standards and demonstrate capabilities. In the present study of the Human Proteome Organisation (HUPO) Human Disease Glycomics/Proteome Initiative (HGPI), the same samples of transferrin and immunoglobulin-G were analyzed for N-linked oligosaccharides and their relative abundances in 20 laboratories, and the chromatographic and mass spectrometric analysis results were evaluated. In general, matrix-assisted laser desorption/ionization (MALDI) time-of-flight MS of permethylated oligosaccharide mixtures carried out in six laboratories yielded good quantitation, and the results can be correlated to those of chromatography of reductive amination derivatives. For underivatized oligosaccharide alditols, graphitized carbon-liquid chromatography (LC)/electrospray ionization (ESI) MS detecting deprotonated molecules in the negative ion mode provided acceptable quantitation. The variance of the results among these three methods was small. Detailed analyses of tryptic glycopeptides employing either nano LC/ESI MS/MS or MALDI MS demonstrated excellent capability to determine site-specific or subclass-specific glycan profiles in these samples. Taking into account the variety of MS technologies and options for distinct protocols used in this study, the results of this multi-institutional study indicate that MS-based analysis appears as the efficient method for identification and quantitation of oligosaccharides in glycomic studies and endorse the power of MS for glycopeptide characterization with high sensitivity in proteomic programs.     

Depression‐like symptoms of withdrawal in a genetic mouse model of binge methamphetamine intake

Binge methamphetamine (MA) users have higher MA consumption, relapse rates and depression‐like symptoms during early periods of withdrawal, compared with non‐binge users. The impact of varying durations of MA abstinence on depression‐like symptoms and on subsequent MA intake was examined in mice genetically prone to binge‐level MA consumption. Binge‐level MA intake was induced using a multiple‐bottle choice procedure in which mice were offered one water drinking tube and three tubes containing increasing concentrations of MA in water, or four water tubes (control group). In two studies, depression‐like symptoms were measured using a tail‐suspension test and a subsequent forced‐swim test, after forced abstinence of 6 and 30 hours from a 28‐day course of chronic MA intake. An additional study measured the same depression‐like symptoms, as well as MA intake, after prolonged abstinence of 1 and 2 weeks. MA high drinking mice and one of their progenitor strains DBA/2J escalated their MA intake with increasing MA concentration; however, MA high drinking mice consumed almost twice as much MA as DBA/2J mice. Depression‐like symptoms were significantly higher early after MA access was withdrawn, compared to levels in drug‐naïve controls, with more robust effects of MA withdrawal observed in MA high drinking than DBA/2J mice. When depression‐like symptoms were examined after 1 or 2 weeks of forced abstinence in MA high drinking mice, depression‐like symptoms dissipated, and subsequent MA intake was high. The MA high drinking genetic mouse model has strong face validity for human binge MA use and behavioral sequelae associated with abstinence.     

The effect of methyl jasmonate on enzyme activities in wheat genotypes infected by the crown and root rot pathogen <Emphasis Type="Italic">Fusarium culmorum</Emphasis>

The hemibiotrophic pathogen Fusarium culmorum (Fc) causes crown and root rot (CRR) in wheat. In this study, MeJA treatment was done 6 h after pathogen inoculation (hai) to focus the physiological and biochemical responses in root tissue of the susceptible wheat cv Falat, partially resistant cv Pishtaz and the tolerant cv Sumai3 at the beginning of the necrotrophic stage. The results indicate that treatment with MeJA at 6 hai significantly delayed the necrotic progress in cv Falat, whereas no significant difference was seen in other cultivars. The activities of pathogen responsive defense-related enzymes (SOD, CAT, POX, PPO, LOX and PAL), total phenols and callose contents were higher in Sumai3, while treatment with MeJA significantly increased these enzymes activities and total phenols content in Falat, signifying the most sensitive cultivar which had a weak reaction to the pathogen but a strong response to MeJA treatment. Additionally, MeJA treatment decreased the level of H₂O₂ and MDA contents particularly in cv Falat. This is the first work reporting the regulation of defense-related enzymes by MeJA treatment at particular time point of 6 hai suggests the possible role of JA in regulating basal resistance in CRR pathogen–wheat interaction. Taken together, our data add new insights into the mechanism of wheat defense including enzymatic events controlling wheat protection against Fc infection.     

Colonization and Biodegradation of Photo-Oxidized Low-Density Polyethylene (LDPE) by New Strains of Aspergillus sp. and Lysinibacillus sp.

The primary objective of this study was the isolation of low-density polyethylene (LDPE)-degrading microorganisms. Soil samples were obtained from an aged municipal landfill in Tehran, Iran, and enrichment culture procedures were performed using LDPE films and powder. Screening steps were conducted using linear paraffin, liquid ethylene oligomer, and LDPE powder as the sole source of carbon. Two landfill-source isolates, identified as Lysinibacillus xylanilyticus XDB9 (T) strain S7-10F and Aspergillus niger strain F1-16S, were selected as super strains. Photo-oxidation (25 days under ultraviolet [UV] irradiation) was used as a pretreatment of the LDPE samples without pro-oxidant additives. The PE biodegradation process was performed for 56 days in a liquid mineral medium using UV-irradiated pure LDPE films without pro-oxidant additives in the presence of the bacterial isolate, the fungal isolate, and the mixture of the two isolates. The process was monitored by measuring the fungal biomass, the bacterial growth, and the pH of the medium. During the process, the fungal biomass and the bacterial growth increased, and the pH of the medium decreased, which suggests the utilization of the preoxidized PE by the selected isolates as the sole source of carbon. Carbonyl and double bond indices exhibited the highest amount of decrement and increment, respectively, in the presence of the fungal isolate, and the lowest indices were obtained from the treatment of a mixture of both fungal and bacterial isolates. Fourier transform infrared (FT-IR), x-ray diffraction (XRD), and scanning electron microscopy (SEM) analyses showed that the selected isolates modified and colonized preoxidized pure LDPE films without pro-oxidant additives.     

Circulating NOD1 Activators and Hematopoietic NOD1 Contribute to Metabolic Inflammation and Insulin Resistance

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A mathematical model for histamine synthesis,release, and control in varicosities

Background

Histamine (HA), a small molecule that is synthesized from the amino acid histidine, plays an important role in the immune system where it is associated with allergies, inflammation, and T-cell regulation. In the brain, histamine is stored in mast cells and other non-neuronal cells and also acts as a neurotransmitter. The histamine neuron cell bodies are in the tuberomammillary (TM) nucleus of the hypothalamus and these neurons send projections throughout the central nervous system (CNS), in particular to the cerebral cortex, amygdala, basal ganglia, hippocampus, thalamus, retina, and spinal cord. HA neurons make few synapses, but release HA from the cell bodies and from varicosities when the neurons fire. Thus the HA neural system seems to modulate and control the HA concentration in projection regions. It is known that high HA levels in the extracellular space inhibit serotonin release, so HA may play a role in the etiology of depression.

Results

We compare model predictions to classical physiological experiments on HA half-life, the concentration of brain HA after histidine loading, and brain HA after histidine is dramatically increased or decreased in the diet. The model predictions are also consistent with in vivo experiments in which extracellular HA is measured, using Fast Scan Cyclic Voltammetry, in the premammillary nucleus (PM) after a 2 s antidromic stimulation of the TM, both without and in the presence of the H ₃ autoreceptor antagonist thioperamide. We show that the model predicts well the temporal behavior of HA in the extracellular space over 30 s in both experiments.

Conclusions

Our ability to measure in vivo histamine dynamics in the extracellular space after stimulation presents a real opportunity to understand brain function and control. The observed extracellular dynamics depends on synthesis, storage, neuronal firing, release, reuptake, glial cells, and control by autoreceptors, as well as the behavioral state of the animal (for example, depression) or the presence of neuroinflammation. In this complicated situation, the mathematical model will be useful for interpreting data and conducting in silico experiments to understand causal mechanisms. And, better understanding can suggest new therapeutic drug targets.

     

Fabrication of Au/Fe3O4/RGO based aptasensor for measurement of miRNA‐128, a biomarker for acute lymphoblastic leukemia (ALL)

Due to their high sensitivity, simplicity, portability, self‐contained, and low cost, the development of electrochemical biosensors is a beneficial way to diagnose and anticipate many types of cancers. An electrochemical nanocomposite‐based aptasensor is fabricated for the determination of miRNA‐128 concentration as the acute lymphoblastic leukemia (ALL) biomarker for the first time. The aptamer chains were immobilized on the surface of the glassy carbon electrode (GCE) through gold nanoparticles/magnetite/reduced graphene oxide (AuNPs/Fe₃O₄/RGO). Fast Fourier transform infrared (FTIR), X‐ray diffraction (XRD), vibrating sample magnetometer (VSM), and transmission electron microscopy (TEM) were used to characterize synthesized nanomaterials. Cyclic voltammetry (CV), square wave voltammetry (SWV), and electrochemical impedance spectroscopy (EIS) were used to characterize the modified GCE in both label‐free and labeled methods. The results indicate that the modified working electrode has high selectivity and for miRNA‐128 over other biomolecules. The hexacyanoferrate redox system typically operated at around 0.3 V (vs. Ag/AgCl), and the methylene blue redox system ran at about 0 V, were used as an electrochemical probe. The detection limit and linear detection range for hexacyanoferrate and methylene blue are 0.05346 fM, 0.1–0.9 fM, and 0.005483 fM, 0.01–0.09 fM, respectively. The stability and diffusion control analyses were performed as well. In both label‐free and labeled methods, the modified electron showed high selectivity for miRNA‐128. The use of methylene blue as a safer redox mediator caused miRNA‐128 to be detected with greater accuracy at low potentials in PBS media. The findings also show the substantial improvement in detection limit and linearity by using reduced graphene oxide‐magnetite‐gold nanoparticles that can be verified by comparing with previous studies on the detection of other miRNAs.     

Exploring the possible mitoprotective and neuroprotective potency of thymoquinone,betanin, and vitamin D against cytarabine-induced mitochondrial impairment and neurotoxicity in rats' brain

It has been suggested that cytarabine (Ara-C) induces toxicity via mitochondrial dysfunction and oxidative stress. Therefore, we hypothesized that mitochondrial protective agents and antioxidants can reduce cytarabine-induced neurotoxicity. For this purpose, 48 male Wistar rats were assigned into eight equal groups include control group, Ara-C (70 mg/kg, i.p.) group, Ara-C plus betanin (25 mg/kg, i.p.) group, Ara-C plus vitamin D (500 U/kg, i.p.) group, Ara-C plus thymoquinone (0.5 mg/kg, i.p.) group, betanin group, vitamin group, and thymoquinone group. The activity of acetylcholinesterase (AChE), and butyrylcholinesterase (BChE), the concentrations of antioxidants (reduced glutathione and oxidized glutathione), oxidative stress (malondialdehyde) biomarkers, mitochondrial toxicity parameters as well as histopathological alteration in brain tissues were measured. Our results demonstrated that Ara-C exposure significantly declines the brain enzymes activity (AChE and BChE), levels of antioxidant biomarkers (GSH), and mitochondrial functions, but markedly elevate the levels of oxidative stress biomarkers (MDA) and mitochondrial toxicity. Almost all of the previously mentioned parameters (especially mitochondrial toxicity) were retrieved by betanin, vitamin D, and thymoquinone compared to Ara-C group. These findings conclusively indicate that betanin, vitamin D, and thymoquinone administration provide adequate protection against Ara-C-induced neurotoxicity through modulations of oxidative, antioxidant activities, and mitochondrial protective (mitoprotective) effects.     

Fine needle aspiration of subcutaneous masses caused by Aspergillus: a report of 2 cases

BACKGROUND: Fine needle aspiration biopsy is a well-established method for dijfrrentiation of infective from neoplastic lesions. Varions infective agents, such as mycobacteria, leishmaniasis and microfaria can be diagnosed from aspirates, but there are few case reports on fungal infections in aspirates. Cytologic diagnosis of Aspergillus has occasionally occurred on sputum, pulmonary samples, vaginal secretions, endometrial washings and maxillary sinus specimens. One case of hepatic and subcutaneous masses was diagnosed as Aspergillus by fine needle aspiration and confirmed by culture and histology. CASES: Two cases of subcutaneous aspergillosis were diagnosed by fine needle aspiration and confirmed by culture and histology. CONCLUSION: Fine needle aspiration cytology is a rapid, sensitive and important method of diagnosing Aspergillus and provides a rapid diagnosis, which may be life saving in an immunocompromised patient.