The Effect of Continued Training with Crocin on Apoptosis Markers in Liver Tissue of High Fat Diet Induced Diabetic Rats

Diabetes mellitus (DM) disease can affect process of apoptosis by increasing oxidative stress, nevertheless exercise and crocin can improve apoptosis; therefore present study aimed to investigate the effect of continued training with crocin on apoptosis markers in liver tissue of diabetic rats. In this experimental study 32 diabetic rats based on fasting glucose divided into four groups of eight rats including: 1) sham, 2) training, 3) crocin, and 4) training with crocin also for investigate the effect of DM induction on apoptosis markers, eight healthy rats assigned in healthy control group. During eight weeks groups 2 and 4 ran 60 minutes on treadmill with intensity of 50–55% maximum speed for three sessions per week and groups 3 and 4 received 25 mg/kg/day crocin peritoneally. Shapiro–Wilk, one-way ANOVA with Tukey’s post-hot tests were used for statistical analysis of data (P ≤ 0.05). DM induction significantly increased Bcl-2 as well as decreased Bax and P52 (P ≤ 0.05) nevertheless training and training with crocin significantly decreased Bcl-2 and increased Bax and P53 (P ≤ 0.05); crocin significantly decreased Bcl-2 and increased P53 (P ≤ 0.05) and training with crocin had higher effect on increase of Bax and P53 compare to training (P ≤ 0.05) also increase of Bax compare to crocin. Although training and crocin alone can improve apoptotic markers in diabetic rats, nevertheless training simultaneously with crocin have better effects than training alone.     

Three-dimensional electrospun gelatin scaffold coseeded with embryonic stem cells and sertoli cells: A promising substrate for in vitro coculture system

In this study, we present an electrospun gelatin (EG) scaffold to mimic the extracellular matrix of the testis. The EG scaffold was synthesized by electrospinning and crosslinked with glutaraldehyde vapor to decrease its water solubility and degradation rate. The scanning electron microscope micrographs showed the homogenous morphology of randomly aligned gelatin fibers. The average diameter of gelatin fibers before and after crosslinking was approximately 180 and 220 nm, respectively. Modulus, tensile strength, and elongation at break values were as 161.8 ± 24.4 MPa, 4.21 ± 0.54 MPa, and 7.06 ± 2.12 MPa, respectively. The crosslinked EG showed 75.2% ± 4.5% weight loss after 14 days with no changes in the pH value of degradation solution. Cytobiocompatibility of the EG for sertoli cells and embryonic stem cells (ESCs) was determined in vitro. Sertoli cells were isolated from mouse testis and characterized by immunostaining and flow cytometry. The effects of EG on proliferation and attachment of both sertoli cells and ESCs were examined. The EG scaffolds exhibited no cytotoxicity for sertoli and ESCs. Both sertoli and ESCs were well attached and grown on EG. Coculture of sertoli and ESCs on EG showed better ESCs adhesion compared with ESCs alone. Our findings indicate the potential of EG as a substrate for proliferation, adhesion, and coculture of sertoli and ESCs and may be considered as a promising engineered microenvironment for in vitro coculture system with the aim of guiding stem cells differentiation toward sperm-producing cells.     

Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states

Background

The dynamics of epigenomic marks in their relevant chromatin states regulate distinct gene expression patterns, biological functions and phenotypic variations in biological processes. The availability of high-throughput epigenomic data generated by next-generation sequencing technologies allows a data-driven approach to evaluate the similarities and differences of diverse tissue and cell types in terms of epigenomic features. While ChromImpute has allowed for the imputation of large-scale epigenomic information to yield more robust data to capture meaningful relationships between biological samples, widely used methods such as hierarchical clustering and correlation analysis cannot adequately utilize epigenomic data to accurately reveal the distinction and grouping of different tissue and cell types.

Methods

We utilize a three-step testing procedure–ANOVA, t test and overlap test to identify tissue/cell-type- associated enhancers and promoters and to calculate a newly defined Epigenomic Overlap Measure (EPOM). EPOM results in a clear correspondence map of biological samples from different tissue and cell types through comparison of epigenomic marks evaluated in their relevant chromatin states.

Results

Correspondence maps by EPOM show strong capability in distinguishing and grouping different tissue and cell types and reveal biologically meaningful similarities between Heart and Muscle, Blood & T-cell and HSC & B-cell, Brain and Neurosphere, etc. The gene ontology enrichment analysis both supports and explains the discoveries made by EPOM and suggests that the associated enhancers and promoters demonstrate distinguishable functions across tissue and cell types. Moreover, the tissue/cell-type-associated enhancers and promoters show enrichment in the disease-related SNPs that are also associated with the corresponding tissue or cell types. This agreement suggests the potential of identifying causal genetic variants relevant to cell-type-specific diseases from our identified associated enhancers and promoters.

Conclusions

The proposed EPOM measure demonstrates superior capability in grouping and finding a clear correspondence map of biological samples from different tissue and cell types. The identified associated enhancers and promoters provide a comprehensive catalog to study distinct biological processes and disease variants in different tissue and cell types. Our results also find that the associated promoters exhibit more cell-type-specific functions than the associated enhancers do, suggesting that the non-associated promoters have more housekeeping functions than the non-associated enhancers.

     

OptCAM: An ultra‐fast all‐optical architecture for DNA variant discovery

Nowadays, the accelerated expansion of genetic data challenges speed of current DNA sequence alignment algorithms due to their electrical implementations. Essential needs of an efficient and accurate method for DNA variant discovery demand new approaches for parallel processing in real time. Fortunately, photonics, as an emerging technology in data computing, proposes optical correlation as a fast similarity measurement algorithm; while complexity of existing local alignment algorithms severely limits their applicability. Hence, in this paper, employing optical correlation for global alignment, we present an optical processing approach for local DNA sequence alignment to benefit both high‐speed processing and operational parallelism, inherently exist in optics. The proposed method, named as OptCAM, utilizes amplitude and wavelength of the optical signals, to accurately locate mutations through three main procedures. Furthermore, an all‐optical implementation of the OptCAM method is proposed consisting of three units, corresponding to the three OptCAM procedures. Performing considerably fast processes by passing optical signals through high‐throughput photonic devices, OptCAM avoids various limitations of electrical implementations. Accuracy and efficiency of the OptCAM method and its optical implementation are validated through numerical simulation by a gold standard simulation benchmark. The results indicate the proposed method is significantly faster than its electrical counterparts, in both single node and grid computation.      

Circular RNA-associated ceRNA network involved in HIF-1 signalling in triple-negative breast cancer: circ_0047303 as a potential key regulator

The aggressive and highly metastatic nature of triple-negative breast cancer (TNBC) causes patients to suffer from the poor outcome. HIF-1 signalling pathway is a prominent pathway that contributes to angiogenesis and metastasis progression in tumours. On the contrary, the undeniable importance of circular RNAs (circRNAs) as multifunctional non-coding RNAs (ncRNAs) has been identified in breast cancer. These ncRNAs owing to their high stability and specificity have been becoming a hotspot in cancer researches. circRNAs act as competing endogenous RNAs (ceRNAs) and compete with mRNAs for shared miRNAs, thus modulate gene expression. Since the most dysregulated biological functions in TNBC are associated with cellular invasion, understanding the molecular pathogenesis of these processes is a crucial step towards the development of new treatment approaches. The purpose of this study is to undermine the circRNA-associated ceRNA network involved in HIF-1 signalling in TNBC using an integrative bioinformatics approach. In the next step, the novel circ_0047303-mediated ceRNA regulatory axes have been extracted and validated across TNBC samples. We show that circ_0047303 has the highest degree in the circRNA-associated ceRNA network and shows a significant up-expression in TNBC. Moreover, our results suggest that circ_0047303 could mediate the upregulation of key angiogenesis-related genes, including HIF-1, EIF4E2 and VEGFA in TNBC through sponging the tumour-suppressive miRNAs. The circ_0047303 could be a promising molecular biomarker and/or therapeutic target for TNBC.     

Transfection efficiency and cytotoxicity of polyethyleneimine-coated magnetic iron oxide nanoparticles in rooster sperm cells

Since the morphology of the rooster spermatozoa is different to other animal spermatozoa, the aim of the current study was to investigate the transfection efficiency and cytotoxicity of polyethyleneimine (PEI) coated magnetic iron oxide nanoparticles (MION) on these cells. Liposome/nucleic acid (NA) complexes and PEI-coated MION linked to the labeled oligonucleotides were used. Viability and percentage of exogenous nucleic acid uptake of spermatozoa were measured by flow cytometry analyses. The results showed a significant increase in exogenous nucleic acid uptake by rooster spermatozoa (P < 0.001) when treated with MION-NA complexes in comparison to liposome/NA. There were no significant differences between efficiency of lipid-based transfection agent and MION (P > 0.05) during short incubation period. MION with or without magnetic field, did not show significant cytotoxicity while the lipid-based transfection agent significantly decreased (P < 0.05) the viability of rooster spermatozoa. Results of this study showed that magnetofection and lipofection were both effective methods which increased exogenous nucleic acid uptake by rooster spermatozoa. However, the magnetofection method was more successful in maintaining the cell's survival than lipofection method.     

Gain-Assisted Propagation and Angular Response of Surface Plasmon Resonance in Nonlinear Kretschmann Configuration

The present study investigates the optical characteristics and angular response of gain-assisted surface plasmon resonance incorporating a nonlinear Kretschmann configuration. Nonlinear susceptibility of two-level atoms is used to describe the gain and nonlinear characteristics of amplifying medium. The structure is investigated and compared in both linear and nonlinear regimes. Our theory presents surface plasmon polaritons (SPPs) amplification accounting for saturation of linear gain by nonlinear losses. Reflectivity curve of the Kretschamnn configuration, attenuation constant, propagation length, and magnetic field intensity of plasmonic wave at the interface provide direct proofs of saturated gain induced by nonlinear absorption loss. Linear analysis predicts enhanced total reflection (ETR) in the presence of gain while in nonlinear regime, no ETR phenomenon occurs due to nonlinear loss absorption. Our analysis verifies that in the presence of nonlinear absorption loss, a saturation tendency of propagation length and plasmonic intensity is inevitable which is coincident with the practical observations.     

Prevention is better than cure: Persian Gulf biodiversity vulnerability to the impacts of desalination plants

Due to extremely high rates of evaporation and low precipitation in the Persian Gulf, discharges from desalination plants (DPs) can lead to ecological stresses by increasing water temperatures, salinities, and heavy metal concentrations, as well as decreasing dissolved oxygen levels. We discuss the potential ecological impacts of DPs on marine organisms and propose mitigating measures to reduce the problems induced by DPs discharges. The daily capacity of DPs in the Persian Gulf exceeds 11 million m³ per day, which is approximately half of global daily freshwater production; multistage flash distillation (MSF) is the dominant desalination process. Results from field and laboratory studies indicate that there are potentially serious and chronic threats to marine communities following exposure to DP discharges, especially within the zoobenthos, echinodermata, seagrasses, and coral reefs. DP discharges can lead to decreases in sensitive species, plankton abundance, hard substrate epifauna, and growth rates of seagrasses. However, the broad applicability of any one of these impacts is currently hard to scale because of the limited number of studies that have been conducted to assess the ecological impacts of DP discharge on Persian Gulf organisms. Even so, available data suggest that appropriately sited, designed, and operated DPs combined with current developments in impingement and entrainment reduction technology can mitigate many of the negative environmental impacts of DPs.