Mitochondrial DNA and Alzheimer’s disease: a first case–control study of the Tunisian population

Molecular Biology Reports - Alzheimer’s disease (AD) is the most common neurodegenerative disorder in humans and presents a major health problem throughout the world. The etiology of AD is...     

NGF and P75NTR Gene Expression Is Associated with the Hepatic Fibrosis Stage Due to Viral and Non-Viral Causes

This study evaluated the relative mRNA expression levels of nerve growth factor (NGF) and the p75 neurothrophin receptor (p75^NTR) in different histological stages of human liver disease. Fifty-one liver biopsy specimens obtained from patients with hepatitis B virus (n = 6), hepatitis C virus (n = 28), and non-viral hepatitis – (n = 9) and standard histological liver (n = 8) as controls (CT) were subjected to qPCR and histopathological exams. Our data revealed a significant difference in the NGF expression levels between the three patient groups and the Control group. p75^NTR expression levels in the HCV and NVH groups were higher than those observed in the HBV and Control groups. In cases of liver cirrhosis, higher p75^NTR mRNA expression was observed, whereas NGF was expressed at higher levels in patients with hepatic fibrosis. NGF expression was lower in the F1 liver fibrosis stage, and p75^NTR receptor expression continuously and proportionately increased compared to the increase in the degree of fibrosis and was significantly higher in livers in fibrosis stages 3 and 4. The hepatic levels of NGF and p75^NTR were decreased and increased, respectively, relative to the stage of inflammatory activity. A positive correlation between p75^NTR and NGF gene expression was observed in livers with mild to moderate fibrosis, though not in cases of severe fibrosis and cirrhosis.

Conclusion

Our results demonstrate that the course of chronic liver disease can be regulated by NGF and p75^NTR, which function by decreasing or inhibiting hepatocyte regeneration and proliferation.     

Content of Fatty Acids and Phenolics in Coratina Olive Oil from Tunisia: Influence of Irrigation and Ripening

The quality indices and chemical composition of Coratina olive oil produced in the northern region of Tunisia were evaluated, to determine the effect of three different irrigation regimes of the trees on the olive oils. The olives were sampled at two different stages of maturity, the oils were extracted, and standard methods were used to analyze the composition and quality of the oils. The fatty‐acid contents and quality parameters were only slightly affected by the irrigation regime. The contents of palmitic, oleic, and linoleic acids were above 12, 72, and 8%, respectively, for the second harvest, regardless of the irrigation level of the olive trees. Parameters such as the α‐tocopherol content and the phenolic profile were found to be significantly affected by the harvesting time; however, inconsistent changes were observed for the irrigation regimes, especially for the oil of the second harvest. It was shown that the irrigation conditions of the olive trees as well as the harvesting time of the fruits gave rise to a diverse range of olive oils in Tunisia.     

An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data

Next-generation sequencing (NGS) approaches rapidly produce millions to billions of short reads, which allow pathogen detection and discovery in human clinical, animal and environmental samples. A major limitation of sequence homology-based identification for highly divergent microorganisms is the short length of reads generated by most highly parallel sequencing technologies. Short reads require a high level of sequence similarities to annotated genes to confidently predict gene function or homology. Such recognition of highly divergent homologues can be improved by reference-free (de novo) assembly of short overlapping sequence reads into larger contigs. We describe an ensemble strategy that integrates the sequential use of various de Bruijn graph and overlap-layout-consensus assemblers with a novel partitioned sub-assembly approach. We also proposed new quality metrics that are suitable for evaluating metagenome de novo assembly. We demonstrate that this new ensemble strategy tested using in silico spike-in, clinical and environmental NGS datasets achieved significantly better contigs than current approaches.     

Testicular oxidative damage and role of combined antioxidant supplementation in experimental diabetic rats

The present study was designated to assess oxidative damage and its effect on germ cell apoptosis in testes of streptozotocin (STZ)-induced diabetic rats. The role of antioxidant supplementation with a mixture of vitamins E and C and alpha lipoic acid for protection against such damage was also evaluated. Forty-five adult male rats were randomly divided into three groups: group I, control, non-diabetic rats; group II, STZ-induced, untreated diabetic rats; group III, STZ-induced diabetic rats supplemented with a mixture of vitamins E and C and alpha lipoic acid. Glycated hemoglobin (HbA_1C), glucose, and insulin levels were estimated in blood samples. Malondialdehyde (MDA), the activities of the enzymes superoxide dismutase (SOD), glutathione peroxidase (GPx), and caspase-3 in addition to testosterone (T) level were all determined in testicular tissues. Histopathological studies using H&E stain, as well as, immunohistochemical detection of apoptosis using (TUNEL) method were also performed. Blood glucose and HbA_1c were significantly increased while insulin was significantly decreased in STZ-induced diabetic rats as compared with controls. In rat testicular tissues, MDA, and caspase-3 activity were significantly elevated while SOD and GPx enzymatic activities as well as T level were significantly decreased in diabetic rats as compared with control group. Antioxidant supplementation to diabetic rats restored the testicular enzymatic activities of SOD and GPx to almost control levels, in addition, MDA and caspase-3 activity decrease while T increase significantly as compared with untreated diabetic group. Prominent reduction of germ cell apoptosis was found in diabetic rats supplemented with antioxidants. An important role of testicular oxidative damage and germ cell apoptosis in diabetes-induced infertility could be suggested, treatment with antioxidants has a protective effect by restoring SOD and GPx antioxidant enzymatic activity.     

Morphology, developmental ultrastructure and ultracytochemistry of staminal hairs in Bulbine inflata (Asphodelaceae) in relation to function

Results of light and electron microscopy and preliminary ultracytochemical studies of the staminal hairs of Bulbine inflata at different stages of development are reported here. The staminal filaments are covered with yellow, unicellular, linear, erecto-patent hairs. These staminal hairs arise directly as single cell outgrowths from epidermal cells of the filament. The surface of each hair is patterned with helical wall thickenings in an anticlockwise direction. This wall is covered by a thick folded cuticle, and formed of a loosely fibrillar cellulose layer. The hair cell possesses a cytoplasm rich in organelles. Especially ribosomes are abundant. Plastids contain large starch grains and peripheral lipid droplets. The smooth endoplasmic reticulum cisternae (SER) encircle the plastids and mitochondria; it is extended in the cytoplasm along the hair length. These hairs have functions in flower pollination attracting pollinators visually, secreting specific substances, providing increased surface area, protecting the filaments and being involved in their movement and vibration.     

Pre-existing diabetes mellitus and adverse pregnancy outcomes

ABSTRACT: BACKGROUND: Pregnancies complicated by pre-existing diabetes mellitus (PDM) are associated with a high rate of adverse outcomes, including an increased miscarriage rate, preterm delivery, preeclampsia, perinatal mortality and congenital malformations; compared to the background population. The objectives of this study are to determine the prevalence of PDM and to investigate the maternal and the neonatal outcomes of women with PDM. METHODS: This is a retrospective cohort study for women who delivered in King Khalid University Hospital (KKUH) during the period of January 1st to the 31st of December 2008. The pregnancy outcomes of the women with PDM were compared to the outcomes of all non-diabetic women who delivered during the same study period. RESULTS: A total of 3157 deliveries met the inclusion criteria. Out of the study population 116 (3.7%) women had PDM. There were 66 (57%) women with T1DM and 50 (43%) women with T2DM. Compared to non-diabetic women those with PGMD were significantly older, of higher parity, and they had more previous miscarriages. Women with PDM were more likely to be delivered by emergency cesarean section (C/S), OR 2.67, 95% confidence intervals (CI) (1.63-4.32), P < 0.001, or elective C/S, OR 6.73, 95% CI (3.99-11.31), P < 0.001. The neonates of the mothers with PDM were significantly heavier, P < 0.001; and more frequently macrosomic; OR 3.97, 95% CI (2.03-7.65), P = 0.002. They more frequently have APGAR scores <7 in 5 minutes, OR 2.61, 95% CI (0.89-7.05), P 0.057 and more likely to be delivered at <37 gestation weeks, OR 2.24, 95% CI (1.37- 3.67), P 0.003. The stillbirth rate was 2.6 times more among the women with PDM group; however the difference did not reach statistical significance, P 0.084. CONCLUSION: PDM is associated with increased risk for C/S delivery, macrosomia, stillbirth, preterm delivery and low APGAR scores at 5 min.     

Molecular identification of a novel inulinolytic fungus isolated from and grown on tubers of Helianthus tuberosus and statistical screening of medium components

Of 24 fungi belonging to more than five genera isolated from tubers of rotten Helianthus tuberosus, 11-inulinolytic active isolates were able to develop halo zones around their fungal colonies, indicating inulinase activity. Alternaria, Aspergillus, Fusarium, Pencillium and Trichoderma were the most common inulinolytic genera, representing more than 90?% of the total positive inulinolytic fungi. Aspergillus tamarii and Pencillium citrinum quantitatively recorded better growth (5.5 and 4.7?mg?ml^?1) and inulinase production (21.53 and 20.15?U?ml^?1) in submerged culture. The enzyme preparation showed also invertase activity. Aspergillus tamarii, as the most potent producer of inulinase, was identified using the Inter Transcribed Spacer marker. The sequence comparisons showed that our molecularly identified strain (GU295949) is related more closely to A. tamarii strains of the gene bank. Statistical screening using the fractional factorial Plackett-Burman design with 12 run was applied for screening ten variables, the low levels of pH (4.8), inoculum size (10³ spore?g^?1), NH₄NO₃ (1.0?mg?g^?1) and MgSO₄ (0.12?mg?g^?1), were the most significant variables on A. tamarii inulinase production. The high inulinase/invertase ratio (1.841?C4.293) classified the enzyme preparation as inulinases, which can be used efficiently in production of fructose syrup from tubers of H. tuberosus.     

Computational design, construction, and characterization of a set of specificity determining residues in protein-protein interactions

Proteins interact with different partners to perform different functions and it is important to elucidate the determinants of partner specificity in protein complex formation. Although methods for detecting specificity determining positions have been developed previously, direct experimental evidence for these amino acid residues is scarce, and the lack of information has prevented further computational studies. In this article, we constructed a dataset that is likely to exhibit specificity in protein complex formation, based on available crystal structures and several intuitive ideas about interaction profiles and functional subclasses. We then defined a “structure‐based specificity determining position (sbSDP)” as a set of equivalent residues in a protein family showing a large variation in their interaction energy with different partners. We investigated sequence and structural features of sbSDPs and demonstrated that their amino acid propensities significantly differed from those of other interacting residues and that the importance of many of these residues for determining specificity had been verified experimentally. Proteins 2012;. © 2012 Wiley Periodicals, Inc.