Biases and complex patterns in the residues flanking protein N-glycosylation sites

N-Glycosylation, the most common and most versatile protein modification reaction, occurs at the beta-amide of the aspargine of the Asn-Xaa-Ser/Thr sequon. For reasons that are unclear, not all such sequons are glycosylated. To find patterns that affect glycosylation, we examined the amino acid residues from the 20th preceding the sequon to the 20th residue following it, using bioinformatics tools. A clean data set of annotated, experimentally verified, glycosylated and nonglycosylated sequons derived from 617 well-defined nonredundant N- and N-,O-glycoproteins listed in SWISS-PROT (June 2002) was used. NXS and NXT sequons were analyzed separately. Although no overt patterns were found to explain sequon occupancy or nonoccupancy, trends for over- or underrepresentation of certain amino acids at particular positions were statistically significant and different in NXS and NXT sequons. In extension of earlier reports, none of the 80 Asn-Pro-Ser/Thr found were glycosylated, and a markedly low level of glycosylation was seen in sequons with Pro at the position following the Ser/Thr. In addition, a general observation was made that the considerable number of glycosylated sequons in the C-terminal 10 residues of glycoproteins suggests that N-glycosylation in these cases may be posttranslational and not cotranslational, as widely accepted.     

Accumulation of label from radioactive precursors into dry matter by wheat endosperm cultured in vitro

The capacity of in vitro cultured common wheat ( Triticum aestivum L.) endosperms to incorporate starch and protein precursors was investigated. Isolated 2–3 week-old endosperms were cultured up to 2 weeks in a liquid medium containing labelled (¹⁴C)-sucrose and (³H)-glutamine. Cultured endosperms were separated into ethanolsoluble, starch and protein fractions and the incorporation of the label into each of these fractions was assessed at different times after commencement of culture. The same medium was introduced through the peduncle into normally-developing grains, which were then similarly analyzed. Accumulation of both ¹⁴C and ³H in the ethanol-soluble fraction occurred, at a decreasing rate, only during the first 3 days, and then ceased. The accumulated label in the starch fraction, which originated mainly as ¹⁴C sucrose, proceeded at a relatively constant rate for one week and reached only about 1/5 of the expected in vivo starch production. Incorporation of both isotopes into the protein fraction reflected similar utilization of sucrose and glutamine from the medium (molar base), decreasing in rate with time. Culturing beyond one week produced deteriorated endosperms. Compared to cultured endosperms, normally-developing grains incorporated proportionally less precursors into the ethanol-soluble and more into the insoluble fraction. It is suggested that the reduced starch and protein synthesis in cultured grains stems from impaired capacity of the biosynthetic machinery rather than from low availability of precursors.     

Inappropriate expression of IgD from a transgene inhibits the function of antigen-specific memory B cells

IgD expression has been shown to be downmodulated upon mitogenic or antigenic activation of B cells. To investigate whether this decrease is of functional significance we studied a mouse strain that expresses transgenic IgD on all B cells. The rearranged gene encoding the heavy chain of this IgD requires endogenous gene rearrangement before it can be expressed; therefore, normal B cell development is not affected. As a result, both transgenic IgD and endogenous IgM and IgD are expressed on all peripheral B cells. We show that the presence of extraneous IgD does not affect normal B cell activation by polyclonal stimulators, nor does it affect the primary IgM or IgG responses to TI or TD antigens. However, the secondary memory response is significantly diminished. The decrease is not attributable to a defective generation of memory B cells; instead the activation of memory cells appears to be compromised. Since the depressed response can be overcome by prior aggregation of the transgenic IgD with allotype-specific anti-IgD antibodies, it appears that persistence of the transgenic IgD on memory cells may influence their ability to be activated. Thus, the decrease in IgD expression on normal B cells after activation may be necessary for optimal activation of memory cells.     

RAGE expression in human T cells: a link between environmental factors and adaptive immune responses

The Receptor for Advanced Glycation Endproducts (RAGE) is a scavenger ligand that binds glycated endproducts as well as molecules released during cell death such as S100b and HMGB1. RAGE is expressed on antigen presenting cells where it may participate in activation of innate immune responses but its role in adaptive human immune responses has not been described. We have found that RAGE is expressed intracellularly in human T cells following TCR activation but constitutively on T cells from patients with diabetes. The levels of RAGE on T cells from patients with diabetes are not related to the level of glucose control. It co-localizes to the endosomes. Its expression increases in activated T cells from healthy control subjects but bystander cells also express RAGE after stimulation of the antigen specific T cells. RAGE ligands enhance RAGE expression. In patients with T1D, the level of RAGE expression decreases with T cell activation. RAGE+ T cells express higher levels of IL-17A, CD107a, and IL-5 than RAGE- cells from the same individual with T1D. Our studies have identified the expression of RAGE on adaptive immune cells and a role for this receptor and its ligands in modulating human immune responses.     

Contribution of β-globin cluster polymorphisms to raise fetal hemoglobin levels in normal adults

Hereditary persistence of fetal hemoglobin (HPFH) is a group of genetically heterogeneous conditions characterized by continued expression of fetal hemoglobin (HbF) in adulthood. HPFH may be due not only to point mutations or large deletions in different regions of the cluster β globin, but also to variations in several polymorphic sequences in this cluster. The objective of this work was to evaluate effects of polymorphic markers within cluster β globin on HbF expression. For the purpose, we have explored in this first study of Tunisian HPFH four polymorphic regions of β globin cluster in 68 healthy adults (34 subjects with high levels of HbF and 34 with normal HbF levels). Our results showed that the increase of HbF levels is associated with the −158 Gγ C → T polymorphism, the TG₁₈CG₂CACG, TC TG₉AG TG₂CG₂ and TG₁₁CG₄ configurations in the second intron of Gγ gene and the −540 β (AT)₆T₉ and (AT)₇T₈ repeated sequences. Among the 34 subjects with raised levels of HbF, approximately 97% carried one or more of these six markers. This study suggests that there is a significant association between certain polymorphic configurations of the β globin cluster and the increase of HbF levels in healthy individuals.     

Analysis of δ-globin gene alleles in Tunisians: description of three new delta-thalassemia mutations

Molecular Biology Reports - Thalassemia is one of the most prevalent worldwide autosomal recessive disorders characterized by a great molecular and clinical expression heterogeneity. Alpha and...     

Biostimulation potential of biochar for remediating the crude oil contaminated soil and plant growth

Crude oil contamination is a serious environmental threat to soil and plants growing in it. Biochar has the potential of biostimulation for remediation of crude oil-contaminated soil. Therefore, the current research was designed to analyze the bio-stimulatory impact of biochar for remediating the crude oil contaminated soil (10%, and 15%), and growth of maize under glasshouse conditions. Biochar was produced by pyrolysis of Australian pines at 350 °C. Soil incubations were done for 20 days. The results of soil analysis showed that the crude oil degradation efficiency of biochar was 34%. The soil enzymatic activities had shown 38.5% increase in fluorescein diacetate (FDA) hydrolysis and 55.6% increase in dehydrogenase activity in soil incubated with biochar in comparison to control. The soil microbial diversity was improved to 41% in biochar treated soil with respect to untreated one, while microbial respiration rate had shown a 33.67% increase in soil incubated with biochar with respect to control under oil stress. Gas Chromatography Mass spectrometry (GC-MS) analysis had shown the high content of low molecular weight hydrocarbons (C₉-C₁₃) in the soil incubated with biochar in comparison to untreated soil. Biochar showed a significant increase in fresh and dry biomass (25%, 14.61%), leaf area (10%), total chlorophyll (11%), water potential (21.6%), osmotic potential (21%), and membrane stability index (12.7%). Moreover, biochar treatment showed a higher increase in the contents of proline (29%), total amino acids (18%), soluble sugars (30.4%), and antioxidant enzymes like superoxide dismutase (16.5%), catalase (11%), and peroxidase (12%). Overall, the results of the present study suggest the bio-stimulating potential of biochar for degradation of hydrocarbons in crude oil contaminated soil and their growth-stimulating effects on maize.     

Two Medicinal Plants (Alkanna trichophila and Convolvulus galaticus) from Turkey: Chemical Characterization and Biological Perspectives

The aim of the present study was to quantify selected phenolic compounds, determine antioxidant activity and enzyme inhibitory effects of the aerial parts of Alkanna trichophylla Hub.-Mor. (A. trichophylla) and Convolvulus galaticus Rost.ex Choisy (C. galaticus) extracts prepared by homogenizer-assisted extraction (HAE), maceration (MAC) and infusion techniques. This is the first time such study has been designed to validate the phytochemical composition and bioactivity of these plants. Multivariate analysis was conducted on collected data. Rutin and caffeoylquinic acid derivatives were the most significant compounds in A. trichophylla and C. galaticus, respectively. The highest antioxidant activity of A. trichophylla was mostly exhibited by HAE/methanolic extracts as determined by DPPH, ABTS, FRAP (51.39, 112.70 and 145.73 mg TE/g, respectively) and phosphomolybdenum (2.05 mmol TE/g) assays. However, significant antioxidant activities varied within the extracts of C. galaticus. HAE/methanolic extract of A. trichophylla significantly depressed AChE (2.70 mg GALAE/g), BChE (5.53 mg GALAE/g) and tyrosinase (26.34 mg KAE/g) activities and that of C. galaticus inhibited AChE (2.04 mg GALAE/g), tyrosinase (31.25 mg KAE/g) and α-amylase (0.53 mmol ACAE/g) activities significantly. We concluded that HAE was the most efficient extraction technique as high yield of compounds and promising bioactivities were recorded from extracts prepared. Multivariate analysis showed that types of solvents influenced recovery of compounds and biological activities. This research study can be used as one methodological starting point for further investigation on these plants as all results are clearly promising and open the door to further research challenges such as cytotoxicity evaluation, molecular docking analysis, and more screening of pharmacological actions.