Computational identification of MicroRNAs and their transcript target[s] in field mustard [Brassica rapa L.]

Background: Micro RNAs [miRNAs] are a pivotal part of non-protein-coding endogenous small RNA molecules that regulate the genes involved in plant growth and development, and respond to biotic and abiotic environmental stresses posttranscriptionally

Objective: In the present study, we report the results of a systemic search for identification of new miRNAs in B. rapa using homology-based ESTs [Expressed Sequence Tags] analysis and considering a series of filtration criteria

Materials and Methods: Plant mature miRNA sequences were searched in non-protein coding ESTs registered in NCBI EST database. Zuker RNA folding algorithm was used to generate the secondary structures of the ESTs. Potential sequences were candidate as miRNA genes and characterized evolutionarily only and if only they fit some described criteria. Also, the web tool psRNATarget was applied to predict candidate B. rapa miRNA targets

Results: In this study, 10 novel miRNAs from B. rapa belonging to 6 miRNA families were identified using EST-based homology analysis by considering a series of filtration criteria. All potent miRNAs appropriate fold back structure. Several potential targets with known/unknown functions for these novel miRNAs were identified. The target genes mainly encode transcription factors, enzymes, DNA binding proteins, disease resistance proteins, carrier proteins and other biological processes

Conclusions: MicroRNA having diverse functions in plant species growth, development and evolution by posttranscriptionally regulating the levels of specific transcriptome so by effecting on their translation products. Research in miRNA led to the identification of many miRNAs and their regulating genes from diverse plant species

Variability of the cyclin-dependent kinase 2 flexibility without significant change in the initial conformation of the protein or its environment; a computational study

Background: Protein flexibility, which has been referred as a dynamic behavior has various roles in proteins' functions. Furthermore, for some developed tools in bioinformatics, such as protein-protein docking software, considering the protein flexibility, causes a higher degree of accuracy. Through undertaking the present work, we have accomplished the quantification plus analysis of the variations in the human Cyclin Dependent Kinase 2 [hCDK2] protein flexibility without affecting a significant change in its initial environment or the protein per se

Objectives: The main goal of the present research was to calculate variations in the flexibility for each residue of the hCDK2, analysis of their flexibility variations through clustering, and to investigate the functional aspects of the residues with high flexibility variations

Materials and Methods: Using Gromacs package [version 4.5.4], three independent molecular dynamics [MD] simulations of the hCDK2 protein [PDB ID: 1HCL] was accomplished with no significant changes in their initial environments, structures, or conformations, followed by Root Mean Square Fluctuations [RMSF] calculation of these MD trajectories. The amount of variations in these three curves of RMSF was calculated using two formulas

Results: More than 50% of the variation in the flexibility [the distance between the maximum and the minimum amount of the RMSF] was found at the region of Val-154. As well, there are other major flexibility fluctuations in other residues. These residues were mostly positioned in the vicinity of the functional residues. The subsequent works were done, as followed by clustering all hCDK2 residues into four groups considering the amount of their variability with respect to flexibility and their position in the RMSF curves

Conclusions: This work has introduced a new class of flexibility aspect of the proteins' residues. It could also help designing and engineering proteins, with introducing a new dynamic aspect of hCDK2, and accordingly, for the other similar globular proteins. In addition, it could provide a better computational calculation of the protein flexibility, which is, especially important in the comparative studies of the proteins' flexibility

Caffeic Acid Phenethyl Ester Increases Radiosensitivity of Estrogen Receptor-Positive and -Negative Breast Cancer Cells by Prolonging Radiation-Induced DNA Damage / 한국유방암학회지

PURPOSE: Breast cancer is an important cause of death among women. The development of radioresistance in breast cancer leads to recurrence after radiotherapy. Caffeic acid phenethyl ester (CAPE), a polyphenolic compound of honeybee propolis, is known to have anticancer properties. In this study, we examined whether CAPE enhanced the radiation sensitivity of MDA-MB-231 (estrogen receptor-negative) and T47D (estrogen receptor-positive) cell lines. METHODS: The cytotoxic effect of CAPE on MDA-MB-231 and T47D breast cancer cells was evaluated by performing an 3-(4,5-dimethylthiazol-2-yl)-2,5 diphenyltetrazolium bromide (MTT) assay. To assess clonogenic ability, MDA-MB-231 and T47D cells were treated with CAPE (1 µM) for 72 hours before irradiation, and then, a colony assay was performed. A comet assay was used to determine the number of DNA strand breaks at four different times. RESULTS: CAPE decreased the viability of both cell lines in a dose- and time-dependent manner. In the clonogenic assay, pretreatment of cells with CAPE before irradiation significantly reduced the surviving fraction of MDA-MB-231 cells at doses of 6 and 8 Gy. A reduction in the surviving fraction of T47D cells was observed relative to MDA-MB-231 at lower doses of radiation. Additionally, CAPE maintained radiation-induced DNA damage in T47D cells for a longer period than in MDA-MB-231 cells. CONCLUSION: Our results indicate that CAPE impairs DNA damage repair immediately after irradiation. The induction of radiosensitivity by CAPE in radioresistant breast cancer cells may be caused by prolonged DNA damage.

Comparative analysis of prostate cancer gene regulatory networks via hub type variation

Prostate cancer is one of the most widespread cancers in men and is fundamentally a genetic disease. Identifying regulators in cancer using novel systems biology approaches will potentially lead to new insight into this disease. It was sought to address this by inferring gene regulatory networks [GRNs]. Moreover, dynamical analysis of GRNs can explain how regulators change among different conditions, such as cancer subtypes. In our approach, independent gene regulatory networks from each prostate state were reconstructed using one of the current state-of-art reverse engineering approaches. Next, crucial genes involved in this cancer were highlighted by analyzing each network individually and also in comparison with each other. In this paper, a novel network-based approach was introduced to find critical transcription factors involved in prostate cancer. The results led to detection of 38 essential transcription factors based on hub type variation. Additionally, experimental evidence was found for 29 of them as well as 9 new transcription factors. The results showed that dynamical analysis of biological networks may provide useful information to gain better understanding of the cell

Analysis of candidate genes has proposed the role of y chromosome in human prostate cancer

Prostate cancer, a serious genetic disease, has known as the first widespread cancer in men, but the molecular changes required for the cancer progression has not fully understood. Availability of high-throughput gene expression data has led to the development of various computational methods, for identification of the critical genes, have involved in the cancer. In this paper, we have shown the construction of co-expression networks, which have been using Y-chromosome genes, provided an alternative strategy for detecting of new candidate, might involve in prostate cancer. In our approach, we have constructed independent co-expression networks from normal and cancerous stages have been using a reverse engineering approach. Then we have highlighted crucial Y chromosome genes involved in the prostate cancer, by analyzing networks, based on party and date hubs. Our results have led to the detection of 19 critical genes, related to prostate cancer, which 12 of them have previously shown to be involved in this cancer. Also, essential Y chromosome genes have searched based on reconstruction of sub-networks which have led to the identification of 4 experimentally established as well as 4 new Y chromosome genes might be linked putatively to prostate cancer. Correct inference of master genes, which mediate molecular, has changed during cancer progression would be one of the major challenges in cancer genomics. In this paper, we have shown the role of Y chromosome genes in finding of the prostate cancer susceptibility genes. Application of our approach to the prostate cancer has led to the establishment of the previous knowledge about this cancer as well as prediction of other new genes

Protein-protein interaction networks [PPI] and complex diseases

The physical interaction of proteins which lead to compiling them into large densely connected networks is a noticeable subject to investigation. Protein interaction networks are useful because of making basic scientific abstraction and improving biological and biomedical applications. Based on principle roles of proteins in biological function, their interactions determine molecular and cellular mechanisms, which control healthy and diseased states in organisms. Therefore, such networks facilitate the understanding of pathogenic [and physiologic] mechanisms that trigger the onset and progression of diseases. Consequently, this knowledge can be translated into effective diagnostic and therapeutic strategies. Furthermore, the results of several studies have proved that the structure and dynamics of protein networks are disturbed in complex diseases such as cancer and autoimmune disorders. Based on such relationship, a novel paradigm is suggested in order to confirm that the protein interaction networks can be the target of therapy for treatment of complex multi-genic diseases rather than individual molecules with disrespect the network

Apoptotic and necrotic effects of pectic acid on rat pituitary GH3/B6 tumor cells

Pectin is composed of complex polysaccharides that can inhibit cancer metastasis and proliferation with no evidence of toxicity. In the present study, the apoptotic and necrotic effects of pectic acid [PA] on the rat pituitary GH3/B6 tumor cells has been investigated. GH3/B6 cells were cultured in the Ham's F12 medium enriched with 15% horse serum and 2.5% fetal bovine serum for 3 days. Then, they were treated by various amounts of PA in different periods [6, 24 and 48 hours]. Bromocriptine was used as positive control and the cell viability was detected by MTT test. The nuclear morphology of cells was explored by florescent stains including acridine orange [AO]/ethidium bromide [EB]. In addition, percentages of apoptotic and necrotic cells were studied with triphosphate nick-end labeling [TUNEL] assay, cell cycle analysis and propidium iodide [PI] staining. Long-term incubation with PA results in increased cell death and DNA damage as detected by MTT assay and AO/EB staining. TUNEL assay showed that PA [100 micro g/ml to 1 mg/ml] could induce apoptosis in a dose-dependent manner, while higher concentrations of PA [2.5 and 5 mg/ml] induced necrosis which was confirmed by PI staining. Furthermore, cell cycle analysis indicated that PA induced sub G1 events, and DNA fragmentation was also correlated with the number of the apoptotic cells. It can be concluded that PA is responsible for apoptosis in the rat pituitary tumor cells. Therefore, one may suggest that this group of polysaccharides can be used in treatment of pituitary tumors

effect of hyperthremia on the differentiation of leukemic cell lines

Treatment of human promonocytic leukemic cell line U937 with mild hyperthermia in the temperature range of 40-43°C resulted in differentiation of these cells into monocyte/macrophage-like cells in a heat dose and time dependent manner. This process was accompanied by marked morphological, functional and proliferational changes. U937 cells which normally grow in supension in the logarithmic phase of growth showed marked inhibition in proliferation after treatment with heat in comparison with controls, without significant decrease in cell viability. The clonogenicity of these cells in semisolid agar cultures was also reduced upon heat treatment. Heat treatment increased the fraction of cells which could reduce nitro blue tetrazolium [NET] and phagocytize latex particles. These data demonstrate that heat treatment can induce differentiation of U937 cells into monocytes/macrophages and thus have possible applications in treatment of leukemia. Temperatures higher than 43°C or exposures of longer than 30 minutes at such high temperatures resulted in cytotoxic effects

Chromosomal proteins in pulmonary alveolar macrophages

In this study the nature of chromosomal proteins, histones and nonhistone in resident alveolar macrophages was investigated in comparison to peritoneal neutrophils and calf thymus proteins. Cells were obtained by lavaging the lung and after purity determination they were subjected to fractional extraction procedures. Proteins were then analyzed on SDS polyacrylamide gels and densitometric scans were obtained. The results show that in macrophages, the pattern of histone and nonhistone proteins were similar to thymus proteins, two distinct and specific proteins Hi[°] and HMG14b and also a protein with a molecular weight of l2kd [Hx] were present. These data suggest a different chromatin protein pattern in pulmonary alveolar macrophages

Sequestration of leukocytes by the isolated perfused rat lung

The sequestration of rat leukocytes and bone marrow cells by the lung vasculature was studied using an isolated perfused rat lung preparation. The passage of latex particles of 7.6 .microm in diameter and non-hematopoietic cells through the lung blood vessels was also studied. Leukocytes and bone marrow cells were reversibly sequestered from circulation, whereas, latex particles and non-hematopoietic cells were removed irreversibly. Continuous circulation of leukocytes or bone marrow cells results in a steady- state at which circulating cells and the lung reach some kind of equilibrium with no net cell removal by the lung. Further cell removal or release can occur by changing the circulating cell concentration. Removal of Ca + + and Mg + + from circulating medium decreased the sequestration of leukocytes by the lung. Complement activation is not involved in this process, since whole blood as well as serum free suspension of leukocytes, bone marrow cells or peritoneal cavity neutrophils showed similar patterns of sequestration. The results indicate that cell sequestration by the isolated perfused lung is a physiological process which can be considered as a suitable model of the in-vivo sequestration of blood leukocytes by the vascular system of the body. The pattern and the rate of sequestration depends on the cell type, cell concentration in circulation, and chemical factors in circulating medium. The results provide new information about the mechanisms which might be responsible for the sequestration of leukocytes by the lung vasculature in the absence of complement activation