Application of molecular dynamics simulations to design a dual-purpose oligopeptide linker sequence for fusion proteins

Proteins are often monitored by combining a fluorescent polypeptide tag with the target protein. However, due to the high molecular weight and immunogenicity of such tags, they are not suitable choices for combining with fusion proteins such as immunotoxins. In this study, we designed a polypeptide sequence with a dual role (it acts as both a linker and a fluorescent probe) to use with fusion proteins. Two common fluorescent tag sequences based on tetracysteine were compared to a commonly used rigid linker as well as our proposed dual-purpose sequence. Computational investigations showed that the dual-purpose sequence was structurally stable and may be a good choice to use as both a linker and a fluorescence marker between two moieties in a fusion protein.     

Genomic characterization of some Iranian children with idiopathic mental retardation using array comparative genomic hybridization

BACKGROUND:

Mental retardation (MR) has a prevalence of 1-3% and genetic causes are present in more than 50% of patients. Chromosomal abnormalities are one of the most common genetic causes of MR and are responsible for 4-28% of mental retardation. However, the smallest loss or gain of material visible by standard cytogenetic is about 4 Mb and for smaller abnormalities, molecular cytogenetic techniques such as array comparative genomic hybridization (array CGH) should be used. It has been shown that 15-25% of idiopathic MR (IMR) has submicroscopic rearrangements detectable by array CGH. In this project, the genomic abnormalities were investigated in 32 MR patients using this technique.

MATERIALS AND METHODS:

Patients with IMR with dysmorphism were investigated in this study. Karyotype analysis, fragile X and metabolic tests were first carried out on the patients. The copy number variation was then assessed in a total of 32 patients with normal results for the mentioned tests using whole genome oligo array CGH. Multiple ligation probe amplification was carried out as a confirmation test.

RESULTS:

In total, 19% of the patients showed genomic abnormalities. This is reduced to 12.5% once the two patients with abnormal karyotypes (upon re-evaluation) are removed.

CONCLUSION:

The array CGH technique increased the detection rate of genomic imbalances in our patients by 12.5%. It is an accurate and reliable method for the determination of genomic imbalances in patients with IMR and dysmorphism.     

Alirocumab inhibits atherosclerosis,improves the plaque morphology,and enhances the effects of a statin

Proprotein convertase subtilisin/kexin type 9 (PCSK9) inhibition is a potential novel strategy for treatment of CVD. Alirocumab is a fully human PCSK9 monoclonal antibody in phase 3 clinical development. We evaluated the antiatherogenic potential of alirocumab in APOE*3Leiden.CETP mice. Mice received a Western-type diet and were treated with alirocumab (3 or 10 mg/kg, weekly subcutaneous dosing) alone and in combination with atorvastatin (3.6 mg/kg/d) for 18 weeks. Alirocumab alone dose-dependently decreased total cholesterol (−37%; −46%, P < 0.001) and TGs (−36%; −39%, P < 0.001) and further decreased cholesterol in combination with atorvastatin (−48%; −58%, P < 0.001). Alirocumab increased hepatic LDL receptor protein levels but did not affect hepatic cholesterol and TG content. Fecal output of bile acids and neutral sterols was not changed. Alirocumab dose-dependently decreased atherosclerotic lesion size (−71%; −88%, P < 0.001) and severity and enhanced these effects when added to atorvastatin (−89%; −98%, P < 0.001). Alirocumab reduced monocyte recruitment and improved the lesion composition by increasing the smooth muscle cell and collagen content and decreasing the macrophage and necrotic core content. Alirocumab dose-dependently decreases plasma lipids and, as a result, atherosclerosis development, and it enhances the beneficial effects of atorvastatin in APOE*3Leiden.CETP mice. In addition, alirocumab improves plaque morphology.     

Enhanced reconstruction of rat calvarial defects achieved by plasma-treated electrospun scaffolds and induced pluripotent stem cells

Tissue engineering with a combination of stem cells and nanofibrous scaffolds has attracted interest with regard to bone regeneration applications. In the present study, human induced pluripotent stem cells (iPSCs) were cultured on polymeric nanofibrous polyethersulfone (PES) with and without plasma treatment. The capacity of PES and plasma-treated PES (Plasma-PES) scaffolds to support the proliferation and osteogenic differentiation of iPSCs was investigated by MTT assay and for common osteogenic markers such as alkaline phosphatase activity, calcium mineral deposition and bone-related genes. Plasma-PES scaffolds with or without iPSCs were subsequently used to evaluate bone regeneration of critical-size defects in the rat by digital mammography, multislice spiral-computed tomography imaging and histological analysis. The results of in vitro analysis showed that plasma treatment significantly enhanced iPSC proliferation and osteogenesis. After 8 weeks of iPSC-loaded Plasma-PES implantation, no mortality or complication was observed in animals or at the site of surgery. Imaging analysis revealed more extensive bone reconstruction in rats receiving nanofibers compared with untreated control groups. Moreover, Plasma-PES seeded with iPSCs induced the highest regeneration of bone defects among all groups. These findings were confirmed by histological staining. Affective osseointegration was observed in implanted scaffolds. Thus, plasma-treated nanofibrous scaffolds are suitable tissue-engineered matrices for supporting the proliferation and osteogenic differentiation of iPSCs and might also be appropriate for the reconstruction of bone defects.     

Small molecule of sphingosine as a rescue of dopaminergic cells: A cell therapy approach in neurodegenerative diseases therapeutics

Multiple sclerosis (MS) patients should take medication such as fingolimod (FTY-720) for a long time, hence pharmaceutical effects on other neural cells such as dopaminergic cells are important. Dopaminergic cell line, BE(2)-M17, was treated by FTY-720 and then cell viability and genes involve in neurosurvival were investigated. It was disclosed that FTY-720 significantly stimulates Bcl2 overexpression. Whereas, it decreased intracellular reactive oxygen species production and cell membrane damage of dopaminergic cells. The increase in Bcl2/Bax ratio increased the cell metabolic activity and decreased propidium iodide-positive cells. Besides, FTY-720 induced the overexpression of CACNA1C, nNOS gene, and nitric oxide production. However, FTY-720 induced GABARA1 overexpression and eventually it could overcame to the cytotoxic effect of intracellular calcium. This cascade led to tyrosine hydroxylase and BDNF genes overexpression whereas FTY-720 did not change GDNF concentration in BE(2)-M17 cells. Concluding, it might be said that taking FTY-720 in MS patients did not induce adverse effect on dopaminergic cells.     

Plant growth promoting activity of an auxin and siderophore producing isolate of <Emphasis Type="Italic">Streptomyces</Emphasis> under saline soil conditions

A biocontrol Streptomyces isolate (C) was tested for its plant growth promoting qualities under saline conditions. Exposure to elevated osmotic strengths up to 300 mM NaCl increased dry weight and cfu/ml significantly. The isolate C produced indolyl-3-acetic acid (IAA) into the medium in the amount of 2.4 μg/ml. The amount of auxin increased after adding salt and reached to 4.7 μg/ml in 300 mM NaCl. Biosynthesis of siderophore was detectable and increased in presence of NaCl. Streptomyces isolate C showed good solubilization of tricalcium phosphate in culture medium with 92 mg/l. Solubilization decreased in presence of NaCl. Soil treatment with isolate C increased the growth and development of wheat plant in normal and saline conditions. In this treatment there were significant increases in germination rate, percentage and uniformity, shoot length and dry weight compared to the control. Applying the bacterial inocula increased the concentration of N, P, Fe and Mn in wheat shoots grown in normal and saline soil, but had non-significant effect on other micro and macronutrients concentrations. Results of this study show that Streptomyces isolate C has potential to be utilized as biofertilizer in saline soils.     

The Autism Related Protein Contactin-Associated Protein-Like 2 (CNTNAP2) Stabilizes New Spines: An In Vivo Mouse Study

The establishment and maintenance of neuronal circuits depends on tight regulation of synaptic contacts. We hypothesized that CNTNAP2, a protein associated with autism, would play a key role in this process. Indeed, we found that new dendritic spines in mice lacking CNTNAP2 were formed at normal rates, but failed to stabilize. Notably, rates of spine elimination were unaltered, suggesting a specific role for CNTNAP2 in stabilizing new synaptic circuitry.     

Intraspecific interactions in a high‐density leopard population

Although less studied than interspecific interactions, interactions among members of the same species can influence space use and temporal activity. Using techniques commonly applied to the analysis of interspecific interactions—multispecies occupancy modeling and the analysis of temporal activity patterns—we studied intraspecific interactions within a high‐density population of Persian leopards (Panthera pardus saxicolor) in Tandoureh National Park, northeastern Iran. Using camera‐trap data, we investigated spatiotemporal interactions between male leopards, lone female leopards, and families (cubs/females with cubs). While we hypothesized that male and female leopards would display different temporal activity patterns, we did not predict spatial avoidance between these groups. We also predicted that leopard families would exhibit spatiotemporal avoidance from male leopards due to the risk of infanticide. Contrary to our expectations, we did not find any evidence for spatial or temporal avoidance between leopard families and adult male leopards. Male and lone female leopards exhibited positive pairwise co‐occurrence, consistent with reports of high overlap between male and female leopard home ranges. While a high level of overlap in temporal activity patterns was found between males/lone females and males/families, there was evidence for variation in the proportion of time each leopard group was active in particular periods of the diel cycle. Male leopards showed cathemeral activity, while lone females and families were more active during daylight hours. The application of these techniques to interactions within a species has improved understanding of the ecology and behavior of this endangered solitary carnivore.     

Analysis of Genome-scale Expression Network in Four Major Bacterial Residents of Cystic Fibrosis Lung

In polymicrobial communities where several species co-exist in a certain niche and consequently the possibility of interactions among species is very high, gene expression data sources can give better insights in to underlying adaptation mechanisms assumed by bacteria. Furthermore, several possible synergistic or antagonistic interactions among species can be investigated through gene expression comparisons. Lung is one of the habitats harboring several distinct pathogens during severe pulmonary disorders such as chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF). Expression data analysis of these lung residents can help to gain a better understanding on how these species interact with each other within the host cells. The first part of this paper deals with introducing available data sources for the major bacteria responsible for causing lung diseases and their genomic relations. In the second part, the main focus is on the studies concerning gene expression analyses of these species.     

Specific and behaviorally consequential astrocyte Gq GPCR signaling attenuation in vivo with iβARK

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