ROTS: reproducible RNA-seq biomarker detector—prognostic markers for clear cell renal cell cancer

Recent comprehensive assessments of RNA-seq technology support its utility in quantifying gene expression in various samples. The next step of rigorously quantifying differences between sample groups, however, still lacks well-defined best practices. Although a number of advanced statistical methods have been developed, several studies demonstrate that their performance depends strongly on the data under analysis, which compromises practical utility in real biomedical studies. As a solution, we propose to use a data-adaptive procedure that selects an optimal statistic capable of maximizing reproducibility of detections. After demonstrating its improved sensitivity and specificity in a controlled spike-in study, the utility of the procedure is confirmed in a real biomedical study by identifying prognostic markers for clear cell renal cell carcinoma (ccRCC). In addition to identifying several genes previously associated with ccRCC prognosis, several potential new biomarkers among genes regulating cell growth, metabolism and solute transport were detected.     

He–Ne Laser Enhances Seed Germination and Salt Acclimation in Salvia officinalis Seedlings in a Manner Dependent on Phytochrome and H2O2

Protoplasma - In the current study the role of H2O2 in He–Ne laser-induced effects on seed germination and post-germinative performance of Salvia officinalis seedlings was assessed under both...     

Tumour induction in BALB/c mice for imaging studies: An improved protocol

Dealing with nude mice, which lack thymus and therefore are sensitive to unsterile conditions, needs special care and laboratory conditions. For preclinical studies, especially tumour imaging purposes, in which therapeutic properties of drugs or therapeutic compounds are not studied, mice with normal immune system can be a favourable alternative if they carry tumours of interest. In the current study, we introduce an optimized protocol for induction of human tumours in BALB/c mice for preclinical studies. Immune system of BALB/c mice was suppressed by administration of cyclosporine A (CsA), ketoconazole and cyclophosphamide. The tumours of MDA-MB-231, A-431 and U-87-MG human cancer cells were induced by subcutaneous injection of the cells to the immunosuppressed mice. Tumour size was calculated weekly. Histopathological and metastatic analyses were performed using haematoxylin and eosin staining. The combination of the three drugs was found to suppress immune system and decrease the numbers of white blood cells, including lymphocytes. At the eighth week, tumours with a dimension of approximately 1400 mm³ developed. Large atypical nuclei with scant cytoplasm were found to exist using histopathological analysis. No metastasis was observed in the tumour-bearing mice. A combination of CsA, ketoconazole and cyclophosphamide can be used to suppress the immune system in BALB/c mice and induce tumours with significant size.     

Ginkgo biloba attenuated hepatotoxicity induced by combined exposure to cadmium and fluoride via modulating the redox imbalance,Bax/Bcl-2 and NF-kB signaling pathways in male rats

Molecular Biology Reports - Aim of this study was to investigate the efficacy of Ginkgo Biloba (G.B) hydro-ethanolic extract against hepatotoxicity induced by combined exposure to cadmium (Cd) and...     

Experimental tracking and numerical mapping of novel coronavirus micro-droplet deposition through nasal inhalation in the human respiratory system

Biomechanics and Modeling in Mechanobiology - It is essential to study the viral droplet’s uptake in the human respiratory system to better control, prevent, and treat diseases....     

RAPD-based evaluation of genetic diversity among populations of the Iranian endemic species Rhabdosciadium aucheri Boiss. (Apiaceae)

Molecular Biology Reports - Rhabosciadium aucheri is an Iranian endemic herbaceous species that grows in the west, center, and south regions of Iran. In the present study, genetic variation of 70...     

Detecting the Dominant T and B Epitopes of Klebsiella pneumoniae Ferric Enterobactin Protein (FepA) and Introducing a Single Epitopic Peptide as Vaccine Candidate

International Journal of Peptide Research and Therapeutics - Klebsiella pneumoniae causes various human infections. Ferric enterobactin protein (FepA) is a conserved protein of K. pneumoniae with...     

Recent advances of dendrimer in targeted delivery of drugs and genes to stem cells as cellular vehicles

Stem cells can be used to repair dysfunctional and injured (or cancerous) tissues by delivering therapeutics. However, in comparison with other cells, it is harder to transfect drugs or genes into stem cells. Dendrimers have been considered as efficient vectors to deliver both genes and drugs to stem cells due to their unique properties including adjustable molecular weight and size, low toxicity, high loading capacity, and having multiple peripheral chemical agents which can be functionalized to improve deliverance efficiency. In this review, we discuss dendrimer-mediated drug and gene delivery to stem cells as cellular vehicles and the role of this strategy in treating a variety of disorders via regenerative medicine approaches.     

Predicting efficiency of different chemical extraction methods in risk assessment of trace metals in sediment of the Persian Gulf

Different chemical methods have been developed to evaluate the bioavailable fraction of the trace metals. Due to the lack of a universal method for analysis of the bioavailable metal fractions, due to the differences in sediment characteristics, it is necessary to validate an appropriate chemical method for assessing the available fraction of trace metals. For this propose, in this study, different chemical extraction methods including extraction with HCl and desorption test as a single reagent leaching test as well as geochemical fractions method have been evaluated. Bushehr coastal sediments in the Persian Gulf coasts have been selected for this purpose. To validate the efficacy of these methods, a gastropod species (Trochus erithreus), as a bioindicator, has been selected and monitored for trace metals of Fe²⁺, Pb²⁺, Cu²⁺, Zn²⁺, Mn²⁺, and Ni²⁺. According to the one-way ANOVA results, all partial extraction methods for all the trace metals (except for Mn²⁺) showed no significant variation, but linear correlation coefficients were between the results of the selective chemical extraction methods and concentrations of trace metals in organism tissues. It offered that selective extraction with HCl can be used as a simple method for measuring the bioavailable fraction of the metals in the sediments.