<Emphasis Type="Italic">In silico</Emphasis> characterization and Molecular modeling of double-strand break repair protein <Emphasis Type="Italic">MRE11</Emphasis> from <Emphasis Type="Italic">Phoenix dactylifera</Emphasis> v deglet nour

Background

DNA double-strand breaks (DSBs) are highly cytotoxic and mutagenic. MRE11 plays an essential role in repairing DNA by cleaving broken ends through its 3′ to 5′ exonuclease and single-stranded DNA endonuclease activities.

Methods

The present study aimed to in silico characterization and molecular modeling of MRE11 from Phoenix dactylifera L cv deglet nour (DnMRE11) by various bioinformatic approaches. To identify DnMRE11 cDNA, assembled contigs from our cDNA libraries were analysed using the Blast2GO2.8 program.

Results

The DnMRE11 protein length was 726 amino acids. The results of HUMMER show that DnMRE11 is formed by three domains: the N-terminal core domain containing the nuclease and capping domains, the C-terminal half containing the DNA binding and coiled coil region. The structure of DnMRE11 is predicted using the Swiss-Model server, which contains the nuclease and capping domains. The obtained model was verified with the structure validation programs such as ProSA and QMEAN servers for reliability. Ligand binding studies using COACH indicated the interaction of DnMRE11 protein with two Mn²⁺ ions and dAMP. The ConSurf server predicted that residues of the active site and Nbs binding site have high conservation scores between plant species.

Conclusions

A model structure of DnMRE11 was constructed and validated with various bioinformatics programs which suggested the predicted model to be satisfactory. Further validation studies were conducted by COACH analysis for active site ligand prediction, and revealed the presence of six ligands binding sites and two ligands (2 Mn²⁺ and dAMP).

     

Contrasted resistance of stone-dwelling Geodermatophilaceae species to stresses known to give rise to reactive oxygen species

Stones in arid environments are inhabited by actinobacteria of the family Geodermatophilaceae like the genera Blastococcus and Modestobacter frequently isolated from altered calcarenites. Their habitat requires adaptation to light-induced and other stresses that generate reactive oxygen species. Here, we show that representative members of the species Blastococcus saxobsidens, Geodermatophilus obscurus, and Modestobacter multiseptatus are differentially adapted to stresses associated with arid environments. Whereas B.?saxobsidens was found to be sensitive to gamma radiation (D(10) =?900 Gy; 10% survival at 900 Gy), M.?multiseptatus was moderately (D(10) =?6000 Gy) and G.?obscurus was highly tolerant (D(10) =?9000 Gy). A difference in resistance to high-frequency (λ value?=?254?nm) UV was shown by B.?saxobsidens, M.?multiseptatus, and G.?obscurus, being sensitive, tolerant, and highly tolerant (D(10) of 6, 900, and >?3500?kJ?m(-2) , respectively). Tolerance to desiccation, mitomycin C and hydrogen peroxide correlated with the ionizing radiation and UV resistance profiles of the three species and were correlated with the pigments synthesized. Resistance to heavy metals/metalloids did not follow the same pattern, with resistance to Ag(2+) and Pb(2+) being similar for B.?saxobsidens, M.?multiseptatus, and G.?obscurus, whereas resistance to AsO4 3-, Cr(2+) , or Cu(2+) was greater for B.?saxobsidens than for the other two species. The stress resistance profiles of M.?multiseptatus and B.?saxobsidens were reflected in different calcarenite colonization patterns. While M.?multiseptatus was predominantly isolated from the first two millimeters of stone surface, B.?saxobsidens was predominantly isolated from the deeper part of the stone where it is better protected from sun irradiation, suggesting that the response to light- and desiccation-induced oxidative stress is an important driver for niche colonization in the stone biotope.     

Production of biosurfactant on crude date syrup under saline conditions by entrapped cells of Natrialba sp. strain E21, an extremely halophilic bacterium isolated from a solar saltern (Ain Salah, Algeria)

A bacterial strain E21 was isolated from a sample of water collected in the salt lake located close to Ain Salah, Algeria. The analysis of 16S rRNA gene sequence had indicated that the strain had 93 % sequence similarity with the genus Natrialba sp. strain E21 (GenBank, FR750525.1) and was considered extremely halophilic. Production of biosurfactant by the strain E21 with free and entrapped cells was investigated using soluble starch in the saline conditions. Biosurfactant synthesis was followed by measuring the surface tension and emulsifying index 9 days under optimal conditions (40 °C, pH 7). Some diffusional limitations in alginate and agar beads affected the kinetics of biosurfactant production when compared to that obtained with free cells culture. The minimum values of surface tension were 27 and 30 mN m^?1 achieved after 9 days with free and immobilized cells, respectively, while the corresponding maximum E24 values were 65.3 and 62.3 %, respectively. The re-use of bacterial cells along with the limited cell losses provided by the immobilized system might lead to significant reduction of the biosurfactant production cost.     

Subtelomeric Microduplications in Three Sisters with Moderate Mental Retardation

Copy number changes of subtelomeric regions are a common cause of mental retardation, occurring in approximately 5% of mentally retarded patients. New molecular techniques allow the identification of subtelomeric microduplications. We report a Tunisian family of three sisters with moderate mental retardation, facial dysmorphism, cardiopathy, and bilateral clinodactyly of the third and fourth toes, explored by MLPA, showing the same associated microduplications, 15q and Xq, without a concurrent deletion.     

Influence of stress factors on growth and pigment production in three Dunaliella species cultivated outdoors in flat-plate photobioreactors

Abstract

Growth and production of carotenoid in three Dunaliella species (Dunaliella salina (Dunal) Teodoresco, Dunaliella bardawil Ben-Amotz & Avron and Dunaliella sp.) were investigated using flat-plate photobioreactors in outdoor conditions with two optical paths (3?cm and 5?cm). The experiment was conducted in duplicate and lasted four weeks during which light intensity, temperature, pH and optical density were checked daily. The pigment production (total carotenoid and chlorophyll a) was monitored every two days. To induce an additional stress besides temperature and light intensity, two different salt concentrations were used, i.e. 6% and 8% NaCl. The highest growth in all treatment groups was noticed for Dunaliella sp. followed by D. bardawil and D. salina. D. salina produced a higher content of carotenoid concentrations corresponding to 5?cm/8% and 5?cm/6% groups; 779.102?±?0.434?μg.mL^?1 and 694.326?±?0.098?μg.mL^?1 were registered at the end of the experiment. The same species had also greater content of β-carotene.     

Factors Associated With Insulin Pump Discontinuation in Adults With Diabetes: A Time-to-Invent Analysis and Prediction Model

ObjectiveInsulin pump discontinuation has mostly been studied in children and adolescents living with diabetes. We aimed to assess the rate of insulin pump continuation in a population of adult patients with diabetes, at 18 months after initiation; determine the factors associated with pump discontinuation; and develop a simple prediction model.MethodsThis single-center, retrospective study included all adult patients with type 1 diabetes or type 2 diabetes who started insulin pump treatment between January 2015 and June 2018. The exclusion criteria were pregnancy, short-term pregnancy plans, and insulin pump discontinuation within the previous 6 months. The probability of insulin pump continuation after 18 months was estimated using the Kaplan-Meier method. Factors associated with insulin pump discontinuation were studied using a Cox regression model, and an exponential model was built for prediction purposes.ResultsThe study included 315 patients. The mean age was 41 years, the mean duration of diabetes was 16 years, 50% were men, 74% had type 1 diabetes, and the mean hemoglobin A1c level was 9.1% (76 mmol/mol). After 18 months, the rate of insulin pump continuation was 0.80 (95% Confidence Interval (CI), 0.76-0.85). By multivariate analysis, the occurrence of severe hypoglycemia in the previous year was associated with insulin pump discontinuation (hazard ratio, 2.42; 95% CI, 1.30-4.51), while other factors did not reach statistical significance.ConclusionInsulin pump discontinuation occurred in 20% of patients at 18 months after initiation and was mainly associated with a recent history of severe hypoglycemia. The type of diabetes and glycemic control at baseline were not associated with treatment discontinuation.     

IgG Western Blot for Confirmatory Diagnosis of Equivocal Cases of Toxoplasmosis by EIA-IgG and Fluorescent Antibody Test

The performance values of available techniques used in serodiagnosis of toxoplasmosis are satisfactory but they raise problems of equivocal and discordant results for very low IgG titers. Recently marketed, LDBio-Toxo II IgG Western blot (IB) showed an excellent correlation with the dye test. We estimated the proportion of equivocal and discordant results between the enzyme immunoassay Platelia Toxo IgG (EIA-IgG) and fluorescent antibody test (FAT) and assessed the usefulness of the IB as a confirmatory test. Out of 2,136 sera collected from pregnant women, 1,644 (77.0%) tested unequivocally positive and 407 (19.0%) were negative in both EIA-IgG and FAT. The remaining 85 (4%) sera showed equivocal or discordant results. Among them, 73 (85.9%) were positive and 12 (14.1%) were negative in IB. Forty-one (89.1%) equivocal sera in EIA-IgG and 46 (86.8%) equivocal sera in FAT were positive in IB. Reducing the cut-off values of both screening techniques improved significantly their sensitivity in detecting very low IgG titers at the expense of their specificity. In conclusion, equivocal results in routine-used techniques and their discordance in determination of the immune status in pregnancy women were not uncommon. IB test appeard to be highly useful in these situations as a confirmatory technique.