Complete mitochondrial genome and draft chloroplastic genome of Haslea ostrearia (Simonsen 1974)

The first completed, circular mitochondrial genome and the first draft, linear chloroplastic genome of the blue diatom Haslea ostrearia (Simonsen 1974, Naviculaceae, Bacillariophyceae) were assembled from Illumina and PacBio sequencing. The mitochondrial genome was composed of 38,696 bases and contained 64 genes, including 31 protein-coding genes (CDS), 2 ribosomal RNA (rRNA) genes and 23 transfer RNA (tRNA) genes. For the chloroplast, the genome was composed of 130,200 bases with 169 genes (131 CDS, 6 rRNA genes, 31 tRNA genes, and 1 transfer messenger RNA gene). Phylogenetic trees, using the maximum-likehood method and partial genes currently available for Haslea ostrearia and other diatom species, suggested the proximity of all the Haslea ostrearia strains/isolates and the possibility of using these genomes as future references.

Association between CX3CR1 rs3732378 polymorphism and neovascular age-related macular degeneration in a sample of Algerian population

Neovascular age-related macular degeneration (nAMD) is a progressive ocular disease, responsible for central visual loss and blindness in elderly population. Increase data demonstrate that genetic factors play an important role in pathogenesis process of this disease. The aim of this study is to investigate the association between rs3732378 polymorphism in CX3CR1 gene and nAMD in a sample of Algerian patients. This case-control study consisted of 72 patients with nAMD and 124 control subjects. DNA of participants was extracted using salting out method. Genotyping was carried out using the TaqMan real-time polymerase chain reaction method. Statistical analysis was performed by SPSS.21.0. The prevalence of the risk genotype AA was higher in the nAMD group than in control group (OR=5.02, 95% CI=1.44-17.4, P=0.011). In our sample of Algerian patients, the rs3732378 polymorphism is associated with nAMD. This result may support the role of CX3CR1 gene in the pathogenesis of nAMD.

Characterization of polymorphisms in CFI and ARMS genes and their association with exudative age-related macular degeneration in Algerian patients

Increasing evidence shows that polymorphisms in CFI and ARMS2 genes can influence exudative age-related macular degeneration (nAMD) risk. The aim of this study was to assess the role of CFI rs10033900 and ARMS2 rs3750846 polymorphisms in susceptibility to nAMD for the first time in the Algerian population. A total of one hundred twenty four controls and seventy two nAMD cases were included in the present study. Genomic DNA was extracted from venous blood leukocytes. CFI rs10033900 and ARMS2 rs3750846 variants were determined by using the real‑time polymerase chain reaction method. Differences in allele and genotype distribution between the cases and controls were tested with adjustment for age by logistic regression analysis. A stratification of case and control groups by age (<65 or ≥65) and by gender (male and female) was also performed. Statistical analyses were done using SPSS21.0. No statistically significant association was observed between CFI rs10033900 and ARMS2 rs3750846 polymorphisms and nAMD risk (p>0.05 for all comparisons). Stratification by age and gender did not show any significant association between these two polymorphisms and nAMD in a sample of the Algerian population. In our study, CFI rs10033900 and ARMS2 rs3750846 polymorphisms did not predispose alone to nAMD in our population. This study is a contribution to the enrichment of the bank data concerning the CFI and ARMS2 genes, reporting, for the first time, the allelic and genotypic frequencies of these genes polymorphisms characterizing the Algerian population.

What Was Old Is New Again: The Pennate Diatom Haslea ostrearia (Gaillon) Simonsen in the Multi-Omic Age

The marine pennate diatom Haslea ostrearia has long been known for its characteristic blue pigment marennine, which is responsible for the greening of invertebrate gills, a natural phenomenon of great importance for the oyster industry. For two centuries, this taxon was considered unique; however, the recent description of a new blue Haslea species revealed unsuspected biodiversity. Marennine-like pigments are natural blue dyes that display various biological activities—e.g., antibacterial, antioxidant and antiproliferative—with a great potential for applications in the food, feed, cosmetic and health industries. Regarding fundamental prospects, researchers use model organisms as standards to study cellular and physiological processes in other organisms, and there is a growing and crucial need for more, new and unconventional model organisms to better correspond to the diversity of the tree of life. The present work, thus, advocates for establishing H. ostrearia as a new model organism by presenting its pros and cons—i.e., the interesting aspects of this peculiar diatom (representative of benthic-epiphytic phytoplankton, with original behavior and chemodiversity, controlled sexual reproduction, fundamental and applied-oriented importance, reference genome, and transcriptome will soon be available); it will also present the difficulties encountered before this becomes a reality as it is for other diatom models (the genetics of the species in its infancy, the transformation feasibility to be explored, the routine methods needed to cryopreserve strains of interest).

Association of IL4 rs2070874, FoxP3 rs3761548 Polymorphisms with Keratoconus in Algeria

Purpose

The aim of this case–control study was to determine the impact of environmental factors on the predisposition to develop keratoconus in a sample of Western Algerian population. Subsequently, we were interested in the implication of two single nucleotide polymorphisms (SNPs) IL4 rs2070874 and FOXP3 rs3761548, previously described as contributing to the occurrence of allergy, in the development of keratoconus.

Methods

The study included 70 unrelated KC cases and 70 controls originating from Western Algeria. DNA genotyping was done using predesigned probe-based allelic discrimination TaqManⓇ assays. Allele and genotype frequencies were compared between the cases and controls by Chi-square test and odds ratios with 95% confidence intervals.

Results

A significant association between risk factors such as family history, atopy, eye rubbing, and the development of keratoconus was found in our sample. Smoking would provide a protective effect against the pathology. No statistically significant differences were found in the allele and genotype frequencies between cases and controls neither for IL4 rs2070874 nor for FOXP3 rs3761548.

Conclusion

Our study provides, for the first time, a clear demonstration of the absence of association of the allergy-associated IL4 and FOXP3 polymorphisms with KC in a sample from Western Algerian population.

In Silico Study of Correlation between Missense Variations of F8 Gene and Inhibitor Formation in Severe Hemophilia A

Objective:

Deleterious substitutions of the F8 gene are responsible for causing hemophilia A, which is an inherited bleeding disorder resulting from reduced or absent activity of the coagulant protein factor VIII (FVIII). The most important complication in treatment is inhibitor development toward therapeutic factor VIII. In this study, we aimed to analyze the effects of deleterious substitutions in the F8 gene upon protein structure and function.

Materials and Methods:

All tests were conducted by computational methods from the CHAMP (CDC Hemophilia A Mutation Project) database. We performed an in silico analysis of deleterious variations using five software programs, Sift, PolyPhen-2, Align-GVGD, KD4v, and MutationTaster, in order to analyze the correlation between variation and the disease. We also studied the correlation between these variations and inhibitor formation.

Results:

Our analysis showed that these in silico tools are coherent and that there are more variations in the A than the C domains. Moreover, we noticed that there are more deleterious variations than neutral variations in each of the A and C domains. We also found that 13.51% of the patients suffered from a severe form of hemophilia A and that carriers of missense variations developed inhibitors. Also, for the first time, we determined that variation nature is not associated with inhibitor formation. Furthermore, this analysis showed that the risk of developing inhibitors increases when the variation causes a change of amino acid class.

Conclusion:

This study will help to correctly associate variations with inhibitor development and aid in early characterization of novel variants.

Association of the HLA-B27 antigen and the CTLA4 gene CT60/rs3087243 polymorphism with ankylosing spondylitis in Algerian population: A case-control study

Ankylosing spondylitis (AS) is a complex inflammatory disease that represents a major health problem both in Algeria and worldwide. Several lines of evidence support that genetic risk factors play a role in AS etiology and the CTLA4 gene has attracted a considerable attention. In this study, we were interested in evaluating the HLA-B27 frequency and in exploring the CTLA4 gene in a sample of the North African population. The dataset of the current study is composed of 81 patients with AS and 123 healthy controls. All samples were genotyped by TaqMan^® allelic discrimination assay. The genetic risk of the HLA-B27 specificity and the CTLA4/CT60 polymorphism were assessed by odds ratios (OR) with 95% confidence intervals (CI). High spondylitis risk was detected for HLA-B27 allele (OR= 14.62, p = 10^-6 ) in addition to a significant association of the CT60*G allele (OR= 1.89, p = .002). After gender and age stratifications, the association of the CT60*G allele was still significant in females sample (OR= 2.10, p = .001) and when age up to 30 years (OR = 2.21, p = .008). Interestingly, the CT60*G allele revealed an increased spondylitis risk in the B27 negative group (OR= 2.81, p = .006). The present work showed in West Algerian population that the HLA-B27 antigen and the variation in the CTLA4 3'UTR region played an important role in the ankylosing spondylitis susceptibility. The heterogeneity of this disease is deduced by genetic difference found between B27+ and B27- groups.

Assessment of Clinical Practices for Crushing Medication in Geriatric Units

OBJECTIVES

To assess the modification of the form of medication and evaluate staff observance of good clinical practices.

DESIGN

One-day assessment of clinical practices.

SETTING

17 geriatrics units in the 3 Teaching Hospitals of Paris-Sud (APHP), France.

PARTICIPANTS

Elderly in-patients with difficulties swallowing capsules and tablets.

MEASUREMENTS

Assessment of target-patient prescriptions and direct observation of nurses' medical rounds.

RESULTS

155/526 in-patients (29.5%) were unable to swallow tablets or capsules: 98 (40.3%) in long-term care, 46 patients (23.8%) in the rehabilitation unit and 11 (12.2%) in the acute care unit (p = .005). In thirty-nine (27.3%) of the 143 prescriptions studied all tablets were safe to crush and all capsules were safe to open. In 104 cases, at least one medication could not be safely modified, including 26 cases (18.2%) in which none of the prescribed drugs were safe to crush or open. In 48.2% of the 110 medications that were crushed, crushing was forbidden, and presented a potential threat in 12.7% of cases or a reduced efficacy in 8.2% of cases. Crushing methods were rarely appropriate: no specific protective equipment was used (81.8%), crushing equipment was shared between patients without cleaning (95.1%), medications were spilled or lost (69.9%). The method of administration was appropriate (water, jellified water) in 25% of the cases, questionable (soup, coffee, compote, juice, cream) in 55% of the cases and unacceptable (laxative) in 21% of the cases.

CONCLUSION

Management of drug prescriptions in patients with swallowing difficulties is not optimal, and may even have iatrogenic effects. In this study, 12.7% of the modifications of the drug form could have been harmful. Doctors, pharmacists and nurses need to reevaluate their practices.

Impact of MTHFR rs1801133, MTHFR rs1801131 and ABCB1 rs1045642 polymorphisms with increased susceptibility of rheumatoid arthritis in the West Algerian population: A case-control study

Rheumatoid arthritis (RA) is an autoimmune disease that results in a chronic systemic inflammation. A few genetic epidemiologic studies found a potential association between genetic polymorphisms C677T (rs1801133) and A1298C (rs1801131) of methylenetatrahydrofolate reductase (MTHFR) gene and C3435T (rs1045642) of ATP-Binding cassette (ABCB1) gene and the increased risk for RA. The aim of this case-control study was to determine the relationship between these polymorphisms and RA susceptibility in West Algerian population. The dataset of the current study is composed of 110 RA patients and 101 healthy controls. All samples were genotyped for theses polymorphisms by TaqMan® allelic discrimination assay. Data were compared between cases and controls by the calculation of the odds ratio (OR) with a confidence interval at 95%. After age and RA erosion-stratified analyzes, no differences in genotypes or alleles frequencies distribution were found for MTHFR C677T (rs1801133) and ABCB1 C3435T (rs1045642) polymorphisms between RA cases and controls. However, the MTHFR A1298C (rs1801131) polymorphism presented a significant distribution in RA with age ≥ 40 (Genotypic data: p=0.007, OR=13.53[1.44-63.31], Allelic data: p=0.001, OR=2.39[1.39-4.1]), and in RA erosive form (Genotypic data: p=0.002, OR=6.92[1.68-30.23], Allelic data: p=0.0001, OR=2.43[1.54-3.85]).These results were confirmed after the Bonferroni correction. In this study we have showed, for the first time in the West Algerian population, that the MTHFR A1298C (rs1801131) polymorphism can be associated with rheumatoid arthritis.

Association of PTPN22 (rs2476601) and STAT4 (rs7574865) polymorphisms with Rheumatoid Arthritis in the Western Algerian population

AIM

The aim of the present study was to replicate the association of five risk gene polymorphisms (PTPN22-rs2476601, STAT4-rs7574865, 6q23-rs6927172, IRF5-rs2004640 and TRAF1/C5-rs10818488) with RA in a specific population of the Western Algeria.

MATERIAL AND METHODS

The study group comprised 110 patients with RA and 197 ethnically matched healthy control subjects. All polymorphisms were genotyped using predesigned TaqMan® assays. Allele and genotype frequencies in patients and control subjects were compared by chi-square test and odds ratios with 95% confidence intervals. Correction for multiple testing was carried out using the Bonferroni adjustment.

RESULTS

Statistically significant associations with RA were detected. The strongest signal was obtained for PTPN22-rs2476601 with an allelic Pvalue 3.32 x 10(-11) (OR = 9.83, 95% CI [4.28 - 22.56]). A second significant association was obtained with STAT4-rs7574865 (allelic Pvalue = 4 x 10(-3); OR = 1.75, 95% CI [1.16 - 2.63]). The third SNP, 6q23-rs6927172, showed a significant result of association with RA, but missed our criteria for significance at allelic level after Bonferroni's correction (allelic Pvalue = 0.027; OR = 0.64, 95% CI [0.42 - 0.97]). Finally, IRF5-rs2004640 and TRAF1/C5-rs10818488 showed a significant association only at genotypic level (Pvalues: 3 x 10(-4) and 2.9 x 10(-3) respectively) but did not reach statistical significance when comparing allele frequencies (Pvalues: 0.96 and 0.21 respectively).

CONCLUSIONS

From this initial study, we can conclude that PTPN22-rs2476601 and STAT4-rs7574865 polymorphisms are clearly associated with the risk of RA in the Western Algerian population.

Relationship between SNPs and expression level for candidate genes in rheumatoid arthritis

OBJECTIVES

The study of polymorphisms of genes differentially expressed may lead to the identification of putative causal genetic variants in multifactorial diseases such as rheumatoid arthritis (RA). Based on preceding transcriptomic results, we genotyped 10 single nucleotide polymorphisms (SNPs) belonging to six genes (S100A8, RNASE2, PGLYRP1, RUNX3, IL2RB, and LY96) showing the highest fold change (> 1.9) when level of expression was compared between RA patients and controls. These SNPs were then analysed to evaluate their role in RA.

METHOD

The relationship between gene expression and genotypes of SNPs was first investigated by Kruskal-Wallis and Mann-Whitney tests in RA patients and controls. The genetic association of these SNPs with RA were then analysed using family-based association tests in trio families.

RESULTS

We found that RNASE2 gene expression was related to rs2013109 genotypes in 14 RA patients (p = 0.030). The association study in a discovery sample of 200 French trio families revealed a significant association with RA for one SNP, PGLYRP1-rs2041992 (p = 0.019); this association was stronger in trios where RA patients carried the HLA-DRB1 shared epitope (SE) (p = 0.003). However, this association was not found in a replication sample of 240 European trio families (p = 0.6).

CONCLUSIONS

Family-based association tests did not reveal an association between RA and any SNP of the candidate genes tested. However, RNASE2 gene expression was differentially expressed in RA patients considering a sequence polymorphism. This result led us to highlight the potential disease-specific regulation for this candidate gene in RA.

No association between XRCC3 Thr241Met and XPD Lys751Gln polymorphisms and the risk of colorectal cancer in West Algerian population: a case-control study

Colorectal cancer (CRC) is a complex and multifactorial disease, in which genetic and environmental factors both seem to play a part. Many epidemiological studies have explored the association between genetic polymorphisms of X-ray repair cross-complementing group 3 (XRCC3) (Thr241Met) and Xeroderma pigmentosum group D (XPD) lysine to glutamine at codon 751 (Lys751Gln) and risk of CRC in various populations; however, the results are controversial. We conducted this case-control study in a West Algerian population to assess the potential role of this genetic polymorphism on the risk of CRC in this population. Genomic DNA was extracted from blood samples collected from 129 sporadic CRC patients and 148 normal controls. The polymorphisms were determined by pyrosequencing technique. The distribution of XRCC3 Thr241Met and XPD Lys751Gln genotypes among controls did not differ significantly from those predicted by the Hardy-Weinberg distribution (p > 0.05). There were no significant differences in the genotypes distribution and allele frequencies between CRC patients and controls. A significant association was found between the combined heterozygous of XRCC3 and homozygous variant of XPD gene and CRC. This is the first study on DNA repair genetic polymorphisms in West Algerian population, and it suggests that the XRCC3 Thr241Met and XPD Lys751Gln polymorphisms may not be associated with the CRC risk in this population.

First molecular analysis of F8 gene in algeria: identification of two novel mutations

The aim of this study was to detect the genetic alterations in the Factor 8 gene in 26 patients from Western Algeria. We detected the presence of "intron 22 inversion" with long-range polymerase chain reaction (PCR). Negative patients for this inversion were analyzed for "intron 1 inversion" using multiplex PCR. Patients who were negative for both inversions were analyzed using a direct sequencing. Deleterious effects of novel mutations on protein were assayed with bioinformatics tools. Causing mutations were identified in 85.71% of the families, including 11 "intron 22 inversion," 1 "intron 1 inversion," and 6 different point mutations (2 nonsense, 1 splice site, and 3 missense mutations). Among these mutations, c.2189G > A (p.Cys711Tyr) and c.5219+1G>T are novel. This is the first study that reports spectrum of mutations in the Factor 8 gene in the Western Algerian population. Knowledge of these mutations is important for genetic counseling and medical care of affected families.

[Prophylactic prescription of low-molecular-weight heparin in the non-surgical setting: impact of recommendations]

OBJECTIVE

Low-molecular-weight heparins (LMWH) had official approval for use for venous thromboembolism prophylaxis only for surgery patients when this survey was conducted, but were nevertheless often used in non-surgery patients. We conducted this "before and after" survey from May 1998 to April 1999 to assess the impact of the recommendations implemented in the beginning of 1999.

METHODS

Data on the use of LMWH were collected on three different days within a three week interval in all non-surgery departments at the Tenon hospital before distribution of expert recommendations early in 1999. Published in La Presse Médicale in January 2000, these recommendations issued from an external panel of 43 experts who were contacted to establish a consensus opinion using the Delphi method. Data were again collected on three different days after implementation of the recommendations. Implementation was based on a patient-specific prescription order form requested by the hospital pharmacy for delivery to the department.

RESULTS

Data were collected for 121 prescriptions prior to the recommendations and for 158 after. Sex-ratio, mean age and percentage of LMWH prescriptions did not differ significantly between the two periods. There was a lower number of non-appropriate prescriptions after implementation of the recommendations from 54.5% to 35.4% (p = 0.01) with better conformity for recommendation A (high-risk patients) (36% versus 43%, NS) and for recommendation B (= 2 risk situations or = 1 risk situation and = 2 aggravating factors) (10% versus 22%, p = 0.01). Better conformity of LMWH prescriptions in oncology and radiotherapy departments partially explained this general improvement, but the difference remained significant when excluding these two departments (p = 0.04).

CONCLUSION

This study shows that physician compliance with recognized expert recommendations can improve their implementation. This procedure is now in general use in the Tenon hospital.