DNA sequence recognition by an isopropyl substituted thiazole polyamide

We have used DNA footprinting and fluorescence melting experiments to study the sequence-specific binding of a novel minor groove binding ligand (thiazotropsin A), containing an isopropyl substituted thiazole polyamide, to DNA. In one fragment, which contains every tetranucleotide sequence, sub-micromolar concentrations of the ligand generate a single footprint at the sequence ACTAGT. This sequence preference is confirmed in melting experiments with fluorescently labelled oligonucleotides. Experiments with DNA fragments that contain variants of this sequence suggest that the ligand also binds, with slightly lower affinity, to sequences of the type XCYRGZ, where X is any base except C, and Z is any base except G.     

The role of calcium,NF-κB and NFAT in the regulation of CXCL8 and IL-6 expression in Jurkat T-cells

T-cells play an important role in host immunity against invading pathogens. Determining the underlying regulatory mechanisms will provide a better understanding of T-cell-derived immune responses. In this study, we have shown the differential regulation of IL-6 and CXCL8 by NF-κB and NFAT in Jurkat T-cells, in response to PMA, heat killed Escherichia coli and calcium. CXCL8 was closely associated with the activation pattern of NFAT, while IL-6 expression was associated with NF-κB. Furthermore, increasing the intracellular Ca²⁺ concentration by calcium ionophore treatment of the cells resulted in NFAT induction without affecting the NF-κB activity. Interestingly, NF-κB activation by heat killed E. coli, as well as CXCL8 and IL-6 expression was significantly suppressed following addition of the calcium ionophore. This indicates that calcium plays an important role in regulating protein trafficking and T-cell signalling, and the subsequent inflammatory gene expression infers an involvement of NFAT in CXCL8 regulation.Understanding these regulatory patterns provide clarification of conditions that involve altered intracellular signalling leading to T-cell-derived cytokine expression.     

Modifications of antioxidant activity and protein composition of bean leaf due to <Emphasis Type="Italic">Bean yellow mosaic virus</Emphasis> infection and salicylic acid treatments

The antioxidant status as well as protein composition of faba bean leaves infected with Bean yellow mosaic virus (BYMV) and the effect of salicylic acid application was examined in this paper. Some modifications in the antioxidant status were observed by changing some antioxidant enzymes activities and contents of antioxidant metabolites. BYMV-infected leaves revealed POD, CAT, APX and SOD induced activities while SA treatments could inhibit POD, CAT activities but induced SOD activity. The enzyme activities seemed to be SA concentration dependant. Higher H₂O₂ and MDA concentrations were recorded in virus-infected leaves than those of the corresponding controls while treatment with SA followed by virus inoculation caused lowering of MDA concentration and reducing the damage due to lipid peroxidation. Moreover, because of virus infection and/or SA treatments, an increase in the amounts of phenolics and flavonoids was noticed. As compared to the control, BYMV infection or SA application caused pronounced increase in the antioxidant activity of leaf extracts detected by DPPH assay, indicating an increase in the amounts of antioxidant compounds occurred. To test the protein composition, the contents of each protein fractions (soluble, insoluble and total) were analyzed and the change in protein patterns was visualized using SDS-PAGE. The BYMV-infected bean leaves had protein contents higher than the control indicating accumulation of pathogenesis-related proteins. Moreover, spraying SA with or without virus inoculation could accumulate soluble, insoluble and total proteins and the pattern of increase was in accordance with SA concentration. Alterations in protein patterns were observed in faba bean leaves (Vicia faba cv Giza 461) in response to BYMV infection and SA treatments. Because of BYMV infection and SA treatments, the protein profiles showed new bands in comparison to the control. Some polypeptides were highly accumulated in treatments of SA followed by virus inoculation. Changing antioxidant status and accumulation of some antioxidant metabolites as well as the pronounced alterations in the protein composition indicate a kind of plant response against pathogen invasion and in case of SA treatment it is considered a way by which a defence response was initiated and/or activated.     

Optimising sporulation and virulence in Drechslera avenacea

Studies were conducted on agar media to optimise sporulation of Drechslera avenacea, a fungal pathogen being evaluated as a biological control agent for Avena species (wild oats). Conidium production was affected by nutrition, pH, temperature and light conditions. Of the agar media tested, Czapek Dox agar (CZA) and half-strength oatmeal agar (½OMA) were the only media where sporulation occurred at all temperatures tested under a 12-h light:12-h dark photoperiod (L/D). The optimum temperature for conidium production was 20°C on ½OMA, whereas there was no optimum temperature on CZA. Under a 12-h near-ultraviolet (NUV):12-h dark photoperiod (NUV/D), similar numbers of conidia were produced on CZA at 6.66, 14.56, and 22.78 W m^?2, whereas on ½OMA conidium production was the highest at 14.56 W m^?2. When NUV/D and L/D conditions were compared, similar numbers of conidia where produced on CZA, whereas ½OMA conidium production was superior under the NUV/D photoperiod. Considerable variation in sporulation and degree of virulence of D. avenacea was detected among isolates from different geographic areas. The most virulent conidia were obtained on ½OMA at 20°C incubated under continuous illumination NUV light. Therefore, the most suitable conditions for conidium production of D. avenacea were growth for 1 week on ½OMA at 20°C under continuous NUV at an intensity of 14.56 W m^?2. Under these conditions, 1.1×10⁵ conidia mL^?1 were produced which is the highest sporulation yet reported for any Drechslera spp., which are traditionally poor sporulators.     

Screening of certain barley lines for resistance to root rot disease caused by Fusarium graminearum

This investigation was conducted in 2005/2006 and 2006/2007 to test 235 barley lines plus two varieties Giza 127 and Giza 128 for resistance and susceptibility to Fusarium graminearum. All screened barley lines showed varied significant degrees of infestation to root rot pathogen. A screening system is described for identifying barley lines which are effective in controlling resistant or susceptible lines. By detecting small but consistent differences in root rot severity, the bioassay proved effective in large-scale screening for partial resistance: already 335 barley lines and two varieties have been screened. We found five groups (7.12%), 22 barley lines and both varieties are resistant (R) (8.31%); 28 barley lines are moderately resistant (MR) (19.29%); 65 barley lines are moderately susceptible (MS) (27.89%); 94 barley lines are susceptible (S) and (37.39%) 126 barley lines are highly susceptible (HS). The high degree of precision makes this an invaluable tool in the understanding of pathogen aggressiveness, host specialisation and parasitic fitness. Disease scale was strongly negative and had moderate correlation with germination (?0.309?? and ?0.649??) under normal and disease treatment. The correlation between yield and normal and disease treatment during two seasons was strong and negative (?0.834?? and ?0.847??, respectively were detected).     

Laser tweezers as a biophotonic tool to investigate the efficacy of living sickle red blood cells in response to optical deformation

A laser tweezer technique based on single and/or dual-laser beams is proposed as a biophotonic tool to trap single cells and investigate their biophysical and biomechanical characteristics. Optical deformability and changes in size and cellular morphology of living and nonliving cells can be measured using the proposed technique. Representative results of red blood cell (RBC) optical deformability of 20 homozygous patients with sickle cell disease, including follow-up patients after treating with hydroxyurea (HU) for at least 3 months and 20 healthy control groups, are presented and compared. Shape recovery of deformed RBCs and relaxation time are recorded for each RBC. Results showed that healthy blood and patients treated with HU demonstrate significantly higher optical deformability and degree of optical elongation with morphological change of RBCs than untreated patients. Moreover, the healthy control group and patients treated with HU exhibited faster relaxation time for RBCs than untreated patients. A trapping power that reaches 180 mW caused no observable photo-damage at a wavelength 1064 nm.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12551-021-00790-0.     

Genome-wide analysis of the emerging infection with Mycobacterium avium subspecies paratuberculosis in the Arabian camels (Camelus dromedarius)

Mycobacterium avium subspecies paratuberculosis (M. ap) is the causative agent of paratuberculosis or Johne's disease (JD) in herbivores with potential involvement in cases of Crohn's disease in humans. JD is spread worldwide and is economically important for both beef and dairy industries. Generally, pathogenic ovine strains (M. ap-S) are mainly found in sheep while bovine strains (M. ap-C) infect other ruminants (e.g. cattle, goat, deer), as well as sheep. In an effort to characterize this emerging infection in dromedary/Arabian camels, we successfully cultured M. ap from several samples collected from infected camels suffering from chronic, intermittent diarrhea suggestive of JD. Gene-based typing of isolates indicated that all isolates belong to sheep lineage of strains of M. ap (M. ap-S), suggesting a putative transmission from infected sheep herds. Screening sheep and goat herds associated with camels identified the circulation of this type in sheep but not goats. The current genome-wide analysis recognizes these camel isolates as a sub-lineage of the sheep strain with a significant number of single nucleotide polymorphisms (SNPs) between sheep and camel isolates (～1000 SNPs). Such polymorphism could represent geographical differences among isolates or host adaptation of M. ap during camel infection. To our knowledge, this is the first attempt to examine the genomic basis of this emerging infection in camels with implications on the evolution of this important pathogen. The sequenced genomes of M. ap isolates from camels will further assist our efforts to understand JD pathogenesis and the dynamic of disease transmission across animal species.     

RANTES gene polymorphisms (-403G>A and -28C>G) associated with hepatitis B virus infection in a Saudi population

Besides the host immune response, genetic and environmental factors play crucial roles in the manifestation of hepatitis B virus (HBV) infection. "Regulated on activation normal T-cell expressed and secreted" factor (RANTES) plays a vital role in CD4(+), CD8(+) T-lymphocyte and dendritic cell activation and proliferation in inflammation. Single nucleotide polymorphisms (SNPs) in the RANTES gene are associated with several viral and non-viral diseases. Association studies have invariably indicated a lack of association between RANTES gene SNPs and HBV infection in ethnic populations, even though RANTES gene SNPs exhibit distinct ethnic distributions. Despite the high prevalence of HBV infections in Saudi Arabia, no studies have been made concerning a possible relationship between RANTES gene polymorphisms and susceptibility to and progression of HBV infection. We examined -403G>A and -28C>G RANTES gene variants in 473 healthy controls and 484 HBV patients in ethnic Saudi populations. Significant differences were found in the genotype and allele distributions of the SNPs between the controls and the HBV patients. Both SNPs were significantly linked to viral clearance in these subjects. Our data demonstrate for the first time in a Saudi population, a relationship between the RANTES gene polymorphisms and the clinical course of HBV infection and underscore the importance of evaluating the genetic background of the affected individual to determine how it may affect disease progression.