Expression levels of the tetratricopeptide repeat protein gene ttc39b covary with carotenoid-based skin colour in cichlid fish

Carotenoid pigments play a major role in animal body colouration, generating strong interest in the genes involved in the metabolic processes that lead from their dietary uptake to their storage in the integument. Here, we used RNA sequencing (RNA-Seq) to test for differentially expressed genes in a taxonomically replicated design using three pairs of related cichlid fish taxa from the genera Tropheus and Aulonocara. Within each pair, taxa differed in terms of red and yellow body colouration, and high‐performance liquid chromatography (HPLC) analyses of skin extracts revealed different carotenoid profiles and concentrations across the studied taxa. Five genes were differentially expressed in all three yellow–red skin contrasts (dhrsx, nlrc3, tcaf2, urah and ttc39b), but only the tetratricopeptide repeat protein-coding gene ttc39b, whose gene product is linked to mammalian lipid metabolism, was consistently expressed more highly in the red skin samples. The RNA-Seq results were confirmed by quantitative PCR. We propose ttc39b as a compelling candidate gene for variation in animal carotenoid colouration. Since differential expression of ttc39b was correlated with the presence/absence of yellow carotenoids in a previous study, we suggest that ttc39b is more likely associated with the concentration of total carotenoids than with the metabolic formation of red carotenoids.     

Cell communication with the neural plate is required for induction of neural markers by BMP inhibition: evidence for homeogenetic induction and implications for Xenopus animal cap and chick explant assays

In Xenopus, the animal cap is very sensitive to BMP antagonists, which result in neuralization. In chick, however, only cells at the border of the neural plate can be neuralized by BMP inhibition. Here we compare the two systems. BMP antagonists can induce neural plate border markers in both ventral Xenopus epidermis and non-neural chick epiblast. However, BMP antagonism can only neuralize ectodermal cells when the BMP-inhibited cells form a continuous trail connecting them to the neural plate or its border, suggesting that homeogenetic neuralizing factors can only travel between BMP-inhibited cells. Xenopus animal cap explants contain cells fated to contribute to the neural plate border and even to the anterior neural plate, explaining why they are so easily neuralized by BMP-inhibition. Furthermore, chick explants isolated from embryonic epiblast behave like Xenopus animal caps and express border markers. We propose that the animal cap assay in Xenopus and explant assays in the chick are unsuitable for studying instructive signals in neural induction.     

A comparison between osteogenic differentiation of human unrestricted somatic stem cells and mesenchymal stem cells from bone marrow and adipose tissue

To evaluate the potential of three stem cells for cell therapy and tissue engineering applications, the biological behavior and osteogenic capacity of the newly introduced cord-blood-derived, unrestricted somatic stem cells (USSC) were compared with those of mesenchymal stem cells isolated from bone marrow (BM-MSC) and adipose tissue (AT-MSC). There was no significant difference between the rates of proliferation of the three stem cells. During osteogenic differentiation, alkaline phosphatase (ALP) activity peaked on day 7 in USSC compared to BM-MSC which showed the maximum value of ALP activity on day 14. However, BM-MSC had the highest ALP activity and mineralization during osteogenic induction. In addition, AT-MSC showed the lowest capacity for mineralization during differentiation and had the lowest ALP activity on days 7 and 14. Although AT-MSC expressed higher levels of collagen type I, osteonectin and BMP-2 in undifferentiated state, but these genes were expressed higher in BM-MSC during differentiation. BM-MSC also expressed higher levels of ALP, osteocalcin and Runx2 during induction. Taking together, BM-MSC showed the highest capacity for osteogenic differentiation and hold promising potential for bone tissue engineering and cell therapy applications.     

The cyanobacterial UV-absorbing pigment scytonemin displays radical-scavenging activity

Scytonemin is a 544-Da hydrophobic pigment that can absorb UV-A radiation. It is present in cyanobacterial sheaths and is thought to function as a UV protectant. In this study, scytonemin was purified from the terrestrial cyanobacterium Nostoc commune, and its radical-scavenging activity was characterized. The purified scytonemin quenched an organic radical in vitro and accounted for up to 10% of the total activity of an ethanol extract of N. commune. These results suggest that the extracellular UV-absorbing pigment scytonemin has multiple roles, functioning as a UV sunscreen and an antioxidant relevant to anhydrobiosis in N. commune.     

Quantifying the effects of root reinforcement of Persian Ironwood (Parrotia persica) on slope stability; a case study: Hillslope of Hyrcanian forests,northern Iran

Forest vegetation is known to enhance the stability of slopes by reinforcing soil and increasing its shear resistance through root system. The effects of root reinforcement depend on the morphological characteristics of the root system, the tensile strength of single roots, and the spatial distribution of the roots in soil. In the present study the results of research carried out in order to evaluate the biotechnical characteristics of the root system of Persian Ironwood (Parrotia persica), in northern Iran are presented. Profile trenching method was used to obtain root area ratio (RAR) values for uphill and downhill sides of the individual trees. For each species, single root specimens were sampled and tested for their tensile strength. It was found that root density generally decreases with depth according to an exponential law. Maximum RAR values were located within the first 0.1 m, with maximum rooting depth at about 0.65 m. RAR values ranged from 0.001% at lower depths to 1.39% near the surface, at upper 0.1 m depth. Significant differences of RAR values, rooting depth and root cohesion between uphill and downhill were observed, however, the differences were not significant for number of roots (ANCOVA). Downhill profiles had higher RAR values, rooting depth and root cohesion. In general, root tensile strength tends to decrease with diameter according to a power law, as observed by other researchers. Downhill roots were significantly stronger in tensile strength than uphill ones. Inter-species variation of tensile strength in downhill roots was also observed. The resulting data were used to evaluate the reinforcing effects in terms of increased shear strength of the soil, using Wu/Waldron Model. The root reinforcement provided by Persian Ironwood is about 46.0 kPa in the upper layers and 0.3 kPa in the deeper horizons. The results of Spearman test revealed a significant correlation between RAR and c_r and that best followed by a power law. The results presented in this paper contribute to expanding the knowledge on biotechnical characteristics of Persian Ironwood on slope reinforcement.     

Network of three specific microRNAs influence type 2 diabetes through inducing insulin resistance in muscle cell lines

Insulin resistance has been implicated as one of the best predictors for type 2 diabetes. Growing evidence propose the involvement of microRNAs (miRNAs) as short regulatory molecules in modulating and inducing resistance. In this regard, we have investigated the role of three selected miRNAs in insulin resistance development (miR-135, miR-202, and miR-214), via assessing glucose uptake levels in C2C12 and L6 muscle cell lines. Interestingly, miRNA-transfected cells demonstrated a significantly different glucose uptake compared to the positive control cells. In addition, we evaluated the expression levels of three putative miRNA target genes (Rho-associated coiled-coil containing protein kinase 1, serine/threonine kinase 2, and vesicle-associated membrane protein 2) in transfected cells, recruiting luciferase assay. Our results indicated the targeting and downregulation of Rho-associated coiled-coil containing protein kinase 1 and serine/threonine kinase 2 genes in all miR-transfected cell lines ( P ≤ 0.05), but not for vesicle-associated membrane protein 2. MiRNA upregulation led to the poor stimulation of glucose uptake through insulin and developed insulin-resistant phenotype in both muscle cell lines. Our study showed the role of three miRNAs in the induction of insulin resistance in cell lines and making them prone to type 2 diabetes development.     

Identification and characterization of inulinases by bioinformatics analysis of bacterial glycoside hydrolases family 32 (GH32)

The glycoside hydrolase family contains enzymes that break the glycosidic bonds of carbohydrates by hydrolysis. Inulinase is one of the most important industrial enzymes in the family of Glycoside Hydrolases 32 (GH32). In this study, to identify and classify bacterial inulinases initially, 16,002 protein sequences belonging to the GH32 family were obtained using various databases. The inulin-effective enzymes (endoinulinase and exoinulinase) were identified. Eight endoinulinases (EC 3.2.1.7) and 4318 exoinulinases (EC 3.2.1.80) were found. Then, the localization of endoinulinase and exoinulinase enzymes in the cell was predicted. Among them, two extracellular endoinulinases and 1232 extracellular exoinulinases were found. The biochemical properties of 363 enzymes of the genus Arthrobacter, Bacillus, and Streptomyces (most abundant) showed that exoinulinases have an acid isoelectric point up to the neutral range due to their amino acid length. That is, the smaller the protein (336 aa), the more acidic the pI (4.39), and the larger the protein (1207 aa), the pI is in the neutral range (8.84). Also, a negative gravitational index indicates the hydrophilicity of exoinulinases. Finally, considering the biochemical properties affecting protein stability and post-translational changes studies, one enzyme for endoinulinase and 40 enzymes with desirable characteristics were selected to identify their enzyme production sources. To screen and isolate enzyme-containing strains, now with the expansion of databases and the development of bioinformatics tools, it is possible to classify, review and analyze a lot of data related to different enzyme-producing strains. Although, in laboratory studies, a maximum of 20 to 30 strains can be examined. Therefore, when more strains are examined, finally, strains with more stable and efficient enzymes were selected and introduced for laboratory activities. The findings of this study can help researchers to select the appropriate gene source from introduced strains for cloning and expression heterologous inulinase, or to extract native inulinase from introduced strains.