PPARgamma dependent PEX11beta counteracts the suppressive role of SIRT1 on neural differentiation of HESCs.

The membrane peroxisomal proteins PEX11, play a crucial role in peroxisome proliferation by regulating elongation, membrane constriction, and fission of pre-existing peroxisomes. In this study, we evaluated the function of PEX11B gene in neural differentiation of human embryonic stem cell (hESC) by inducing shRNAi-mediated knockdown of PEX11B expression. Our results demonstrate that loss of PEX11B expression led to a significant decrease in the expression of peroxisomal-related genes including ACOX1, PMP70, PEX1, and PEX7, as well as neural tube-like structures and neuronal markers. Inhibition of SIRT1 using pharmacological agents counteracted the effects of PEX11B knockdown, resulting in a relative increase in PEX11B expression and an increase in differentiated neural tube-like structures. However, the neuroprotective effects of SIRT1 were eliminated by PPAR inhibition, indicating that PPARÉ£ may mediate the interaction between PEX11B and SIRT1. Our findings suggest that both SIRT1 and PPARÉ£ have neuroprotective effects, and also this study provides the first indication for a potential interaction between PEX11B, SIRT1, and PPARÉ£ during hESC neural differentiation.

Transcriptional drug repositioning and cheminformatics approach for differentiation therapy of leukaemia cells.

Differentiation therapy is attracting increasing interest in cancer as it can be more specific than conventional chemotherapy approaches, and it has offered new treatment options for some cancer types, such as treating acute promyelocytic leukaemia (APL) by retinoic acid. However, there is a pressing need to identify additional molecules which act in this way, both in leukaemia and other cancer types. In this work, we hence developed a novel transcriptional drug repositioning approach, based on both bioinformatics and cheminformatics components, that enables selecting such compounds in a more informed manner. We have validated the approach for leukaemia cells, and retrospectively retinoic acid was successfully identified using our method. Prospectively, the anti-parasitic compound fenbendazole was tested in leukaemia cells, and we were able to show that it can induce the differentiation of leukaemia cells to granulocytes in low concentrations of 0.1 µM and within as short a time period as 3 days. This work hence provides a systematic and validated approach for identifying small molecules for differentiation therapy in cancer.

Upregulation of miR-9 and miR-193b over human Th17 cell differentiation.

BACKGROUND: Th17 cells are a newly discovered subset of CD4+ T cells known as key participants in various immune responses and inflammatory conditions including autoimmune diseases. Mi(cro)RNAs are a family of non-coding RNAs that regulate numerous critical immune functions. Immuno-miRNAs modulate cell biological processes in T cells, such as differentiation and function of Th17 cells. The aim of the present study is to investigate the expression of miR-9-5p, miR-193b-3p, and autoimmunity-related genes during human Th17 cells differentiation. METHODS: Human naïve CD4+ T cells were purified from peripheral blood mononuclear cells (PBMCs) by magnetic cell sorting system (MACS) and their purity was checked by flow-cytometric analysis. Naïve CD4+ T cells were cultured under Th17-polarizing condition for 6 days. IL- 17 secretion was determined by means of enzyme-linked immunosorbent assay (ELISA). Next, the expression levels of miRNAs and putative targets genes were assessed by qRT-PCR at different time points of differentiation. RESULTS: Our result showed dramatic downregulation of TCF7, MAP3K1, ENTPD1, and NT5E genes during human Th17 differentiation. Polarization also had a significant inducible effect on the expression of miR-9 and miR-193b over differentiation of human Th17 cells. According to our results, miR-9-5p and miR-193b-3p may contribute to Th17 differentiation probably by inhibiting the expression of negative regulators of Th17 differentiation. CONCLUSION: This study confirmed deregulation of TCF7, MAP3K1, ENTPD1, and NT5E genes in Th17 differentiation process and introduced miR-9 and miR-193b as Th17 cell-associated miRNAs, making them good candidates for further investigations.

Full small molecule conversion of human fibroblasts to neuroectodermal cells via a cocktail of Dorsomorphin and Trichostatin A.

A revolutionary new approach to produce efficient cells is to induce transdifferentiation to make it conventional in therapeutic strategies. In this paper, we describe a brief cocktail of small molecules including Dorsomorphin (DSM) and Trichostatin A (TSA) to produce safe neuroectodermal cells as a resource to produce various types of nervous system cells for a safe cytotherapy. Furthermore, in order to optimize this strategy, we implemented a cocktail of neurotrophic factors to enhance the viability of the cell. This modification was accompanied by pretreatment of the culture dishes with a combination of poly-l-ornithine and laminin and fibronectin. In order to decrease the length of protocol and transdifferentiation variation concomitantly, TSA was utilized as an epigenetic modulator. Finally, this improved protocol mediated neuroectodermal conversion of human fibroblasts within 12 days with an average efficiency of 24%, promising a fast strategy to produce neuroectodermal cells applicable for therapeutic purposes in neural damages. Here we induce neural cells by a cocktail consists of two small molecules of DSM and TSA. Our protocol is a 12 day protocol with the efficiency of 24% which is a more efficient one in comparison to previous protocols inducing neural cells. Consequently, our protocol shortens the path of in vitro and preclinical studies in the field of neural conversion and neuroregeneration.

A deformable template method for describing and averaging the anatomical variation of the human nasal cavity.

BACKGROUND: Understanding airflow through human airways is of importance in drug delivery and development of assisted breathing methods. In this work, we focus on development of a new method to obtain an averaged upper airway geometry from computed tomography (CT) scans of many individuals. This geometry can be used for air flow simulation. We examine the geometry resulting from a data set consisting of 26 airway scans. The methods used to achieve this include nasal cavity segmentation and a deformable template matching procedure. METHODS: The method uses CT scans of the nasal cavity of individuals to obtain a segmented mesh, and coronal cross-sections of this segmented mesh are taken. The cross-sections are processed to extract the nasal cavity, and then thinned ('skeletonized') representations of the airways are computed. A reference template is then deformed such that it lies on this thinned representation. The average of these deformations is used to obtain the average geometry. Our procedure tolerates a wider variety of nasal cavity geometries than earlier methods. RESULTS: To assess the averaging method, key landmark points on each of the input scans as well as the output average geometry are located and compared with one another, showing good agreement. In addition, the cross-sectional area (CSA) profile of the nasal cavities of the input scans and average geometry are also computed, showing that the CSA of the average model falls within the variation of the population. CONCLUSIONS: The use of a deformable template method for aligning and averaging the nasal cavity provides an improved, detailed geometry that is unavailable without using deformation.

Nurr1 and PPARγ protect PC12 cells against MPP(+) toxicity: involvement of selective genes, anti-inflammatory, ROS generation, and antimitochondrial impairment.

Parkinson's disease (PD) can degenerate dopaminergic (DA) neurons in midbrain, substantia-nigra pars compacta. Alleviation of its symptoms and protection of normal neurons against degeneration are the main aspects of researches to establish novel therapeutic strategies. PPARγ as a member of PPARs have shown neuroprotection in a number of neurodegenerative disorders such as Alzheimer's disease and PD. Nuclear receptor related 1 protein (Nurr1) is, respectively, member of NR4A family and has received great attentions as potential target for development, maintenance, and survival of DA neurons. Based on neuroprotective effects of PPARγ and dual role of Nurr1 in anti-inflammatory pathways and development of DA neurons, we hypothesize that PPARγ and Nurr1 agonists alone and in combined form can be targets for neuroprotective therapeutic development for PD in vitro model. 1-Methyl-4-phenylpyridinium (MPP(+)) induced neurotoxicity in PC12 cells as an in vitro model for PD studies. Treatment/cotreatment with PPARγ and Nurr1 agonists 24 h prior to MPP(+) induction enhanced the viability of PC12 cell. The viability of PC12 cells was determined by MTS test. Mitochondrial membrane potential (MMP) and intracellular reactive oxygen species (ROS) were detected by flow cytometry. In addition, the relative expression of four genes including TH (the marker of DA neurons), Ephrin A1, Nurr1, and Ferritin light chain were assessed by RT-qPCR. In the MPP(+)-pretreated PC12 cells, PPARγ and Nurr1 agonists and their combined form resulted in a decrease in the cell death rate. Moreover, production of intracellular ROS and MMP modulated by MPP(+) was decreased by PPARγ and Nurr1 agonists' treatment alone and in the combined form.

Zinc finger protein 521 overexpression increased transcript levels of Fndc5 in mouse embryonic stem cells.

Zinc finger protein 521 is highly expressed in brain, neural stem cells and early progenitors of the human hematopoietic cells. Zfp521 triggers the cascade of neurogenesis in mouse embryonic stem cells through inducing expression of the early neuroectodermal genes Sox1, Sox3 and Pax6. Fndc5, a precursor of Irisin has inducing effects on the expression level of brain derived neurotrophic factor in hippocampus. Therefore, it is most likely that Fndc5 may play an important role in neural differentiation. To exhibit whether the expression of this protein is under regulation with Zfp521, we overexpressed Zfp521 in a stable transformants of mESCs expressing EGFP under control of Fndc5 promoter. Increased expression of Zfp521 enhanced transcription levels of both EGFP and endogenous Fndc5. This result was confirmed by overexpression the aforementioned vectors in HEK cells and indicated that Zfp521 functions upstream of Fndc5 expression. It is most likely that Zfp521 may act through the binding to its response element on Fndc5 core promoter. Therefore it is concluding that an enhanced expression of Fndc5 in neural progenitor cells is stimulated by Zfp521 overexpression in these cells.

A ground state of PPARγ activity and expression is required for appropriate neural differentiation of hESCs.

BACKGROUND: Several evidences indicate stimulation of peroxisome proliferator activated receptor γ (PPARg), promotes neuronal differentiation. This study was conducted to testify the prominence of PPARγ during neural differentiation of human embryonic stem cells (hESCs). METHODS: PPARγ expression level was assessed during neural differentiation of hESCs. Meanwhile, the level of endogenous miRNAs, which could be engaged in regulation of PPARγ expression, was measured. Next, natural and synthetic components of PPARγ agonists and antagonist were implemented on neural progenitor formation during neural differentiation of hESCs. RESULTS: Data showed an increasing wave of PPARγ expression level when human neural progenitors (NPs) were formed upon retinoic acid treatment. Interestingly, there was no significant difference in the amount of PPARγ proteins during the differentiation of hESCs that is inconsistent with what we observed for RNA level. Our results indicated that miRNAs are not involved in the regulation of PPARγ expression, while proteasome-mediated degradation may to some degree be involved in this process. Among numerous treatments, PPARγ inactivation during NPs formation significantly decreased expression of NP markers. CONCLUSIONS: We conclude that a ground state of PPARγ activity is required for NP formation of hESCs during early neural differentiation. However, high expression and activity of PPARγ could not enhance the required neural differentiation, whereas the PPARγ inactivation could negatively influence NP formation from hESCs by antagonist.

Fndc5 overexpression facilitated neural differentiation of mouse embryonic stem cells.

Fndc5 has been recently recognized as a myokine which could be cleaved and secreted into blood stream. It is termed as irisin with an important role in thermogenesis and energy homeostasis. Increased expression of Fndc5 has been reported upon retinoic acid treatment during neural differentiation and its knockdown decreased neural differentiation and neurite outgrowth. This study tries to evaluate the effect of Fndc5 overexpression on rate of neural differentiation in mouse. (Thus, transduced cell line of mouse embryonic stem cell with ability to express Fndc5 under Doxycycline treatment was established. Subsequently, the effect of overexpression of Fndc5 on different stages of neural differentiation was studied). Our study showed an increase enhancement in neuronal precursor markers and mature neuron markers upon overexpression of Fndc5, concluding that Fndc5 facilitates neural differentiation. This effect might be related to increased expression of BDNF following overexpression of Fndc5. Our findings are consistent with recent studies reporting a similar role for Fndc5 in proliferation of neural cells and increase in the expression of neurotrophins like BDNF.

Enhanced expression of FNDC5 in human embryonic stem cell-derived neural cells along with relevant embryonic neural tissues.

Availability of human embryonic stem cells (hESCs) has enhanced the capability of basic and clinical research in the context of human neural differentiation. Derivation of neural progenitor (NP) cells from hESCs facilitates the process of human embryonic development through the generation of neuronal subtypes. We have recently indicated that fibronectin type III domain containing 5 protein (FNDC5) expression is required for appropriate neural differentiation of mouse embryonic stem cells (mESCs). Bioinformatics analyses have shown the presence of three isoforms for human FNDC5 mRNA. To differentiate which isoform of FNDC5 is involved in the process of human neural differentiation, we have used hESCs as an in vitro model for neural differentiation by retinoic acid (RA) induction. The hESC line, Royan H5, was differentiated into a neural lineage in defined adherent culture treated by RA and basic fibroblast growth factor (bFGF). We collected all cell types that included hESCs, rosette structures, and neural cells in an attempt to assess the expression of FNDC5 isoforms. There was a contiguous increase in all three FNDC5 isoforms during the neural differentiation process. Furthermore, the highest level of expression of the isoforms was significantly observed in neural cells compared to hESCs and the rosette structures known as neural precursor cells (NPCs). High expression levels of FNDC5 in human fetal brain and spinal cord tissues have suggested the involvement of this gene in neural tube development. Additional research is necessary to determine the major function of FDNC5 in this process.

C86Y: as a destructive homozygous mutation deteriorating Pex7p function causing rhizomelic chondrodysplasia punctata type I.

Rhizomelic Chondrodysplasia Punctata (RCDP) type 1 is a peroxisomal biogenesis disorder with a genetic abnormality in PEX7 gene. In the present study, mutational analysis was performed on two Iranian RCDP patients with distinct clinical phonotype. Mutation detection was carried out by sequencing of RT-PCR product consisting the whole length of PEX7 cDNA. Sequence data revealed the same missense homozygous mutation of G to A at nucleotide 257 in exon3 of PEX7 coding sequence in both patients. Moreover, genomic analysis of the PEX7 gene confirmed the RT-PCR data. This mutation caused one amino acid residue substitution of Cys to Tyr at codon 86 located on WD1 repeat domain region of Pex7p, which severely affected the functionality of PEX7 protein. Back-transfection of vector encoding mutant Pex7p did not restore the normal peroxisomal function in RCDP patient's fibroblast cells dissimilar to the native type of PEX7.

Improving active contour methods for tracking endothelial cells by the removal of low-confidence edge segments.

Previously we developed an active contour method for segmenting and tracking cells in phase-contrast microscopy images. Our method is capable of fine-grained segmentation on noisy image sequences. In this paper, we improve the active contour segmentation model to provide better accuracy, by selectively identifying areas of the contour with low confidence and removing them. The method is applied to HMEC-1 cells (human microvascular endothelial cells). The segmentation provided by the method is quantitavely compared with manually-drawn contours, showing close fit and capability to 'lock' on to cell boundaries for hundreds of frames.

3-D Modeling of nitric oxide emission and vasodilation induced by CA3 hippocampal neurons.

The modeling of the spread, diffusion, and decay of chemicals in the brain is a complex problem that is made difficult by the fact that the structures that produce chemicals (synapses etc.) may be very small in comparison to their radii of chemical influence. In this article, we concentrate on modeling a simple instance of this problem; that of a proficiently diffusing molecule that may cause changes in smooth muscle contractions over relatively large areas. An optimized diffusion system was developed to study the diffusion of neuronal nitric oxide. Our diffusion system allows us to model the spread of nitric oxide from all areas of neurons, including the soma and dendritic processes. In addition, our system allows us to model tiny diffusing structures without sacrificing large-scale granularity. To study the effect of NO-producing neurons on vasodilation, we simulate systems of 1 and 2 neurons. We show that it is possible for nitric oxide emitted from neurons to be involved in regulating blood flow.

Isolation and characterization of ACC deaminase-producing fluorescent pseudomonads, to alleviate salinity stress on canola (Brassica napus L.) growth.

Salinity stress is of great importance in arid and semi-arid areas of the world due to its impact in reducing crop yield. Under salinity stress, the amount of 1-aminocyclopropane-1-carboxylate (ACC), a precursor for ethylene production in plants, increases. Here, we conducted research under the hypothesis that isolated ACC deaminase-producing Pseudomonas fluorescens and Pseudomonas putida can alleviate the stressful effects of salinity on canola (Brassica napus L.) growth. The experiments were conducted in the Soil and Water Research Institute, Tehran, Iran. Seven experimental stages were conducted to isolate and characterize ACC deaminase-producing Pseudomonas fluorescens strains and to determine factors enhancing their growth and, consequently, their effects on the germination of canola seeds. Under salinity stress, in 14% of the isolates, ACC deaminase activity was observed, indicating that they were able to utilize ACC as the sole N-source. Bacterial strains differed in their ability to synthesize auxin and hydrogen cyanide compounds, as well as in their ACC deaminase activity. Under salinity stress, the rate of germinating seeds inoculated with the strains of ACC deaminase-producing Pseudomonas fluorescens and Pseudomonas putida, and seedling growth was significantly higher. These results indicate the significance of soil biological activities, including the activities of plant growth-promoting bacteria, in the alleviation of soil stresses such as salinity on plant growth.