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To investigate the impact of conformational properties of genetic material of living cells on radiation-induced DNA damage, single strand breaks (SSB), double strand breaks (DSB) and some microdosimetric quantities of A, B and Z-DNA conformations caused by 60Co gamma rays, have been calculated. Based on a previous B-DNA geometrical model, models of A and Z forms have been developed. Simple 34 base pairs segments of each model repeated in high number and secondary electron spectrum of 60Co gamma rays have been simulated in a volume of a typical animal cell nucleus. All simulations in this study have been performed by using the Geant4 (GEometry ANd Tracking 4)-DNA extension of the Geant4 toolkit. The results showed that, B-DNA has the lowest yield of simple strand breaks with 2.23×10−10 Gy−1 Da−1 and 1.0×10−11 Gy−1 Da−1 for the SSB and DSB damage yield, respectively. The A-DNA has the highest SSB yield with 3.59×10−10 Gy−1 Da−1 and the Z-DNA has the highest DSB yields with 1.8×10−11 Gy−1 Da−1. It has been concluded that there is a direct correlation between the hit probability, mean specific imparted energy and SSB yield in each model of DNA. Moreover, there is a direct correlation between the DSB yield and both the mean lineal energy and topological characteristics of each model. [ABSTRACT FROM AUTHOR]

The purpose of this work was to study the response that is invoked by hyperthermia in the production of Granulocyte-Macrophage colony-stimulating factor (GM-CSF) by the lung. Rats were heated regionally at chest area by a RF generator operating at 27.397MHz for 1h at various temperatures and then allowed to recover or repair in various periods of time after heat application. Lung tissue from these animals was then removed and cultured for the production of GMCSF. GM-CSF was assayed by the production of colonies in the semi-solid agar cultures of bone marrow cells. Immediately after heat treatment hyperthermia had no significant effect on the production of GM-CSF by the lung. A delayed effect was observed about 3.5h after heat treatment. This effect consisted of a temperature dependent decrease in GM-CSF production. The damage was recoverable and required 1-50 days of post heat treatment time for animals to reach normal level of GM-CSF production. The results suggest that in-vivo application of hyperthermia invokes temporary reduction in GM-CSF production by the lung, which has not been reported previously. [ABSTRACT FROM AUTHOR]

The effect of prior heat treatment on the ability of bone marrow cells to form long-term bone marrow culture has been studied. Bone marrow cells were heated for various times in the temperature range of 39-43 C and then cultured in the modified Dexter type suspension culture. At weekly intervals, the behaviour of the cultures in terms of stroma formation and confluency, cellular viability, and myelopoiesis were evaluated. The results show that there was a dose-dependent decrease in the number of viable cells in the non-adherent fraction of the cultures. Cytological analysis of these cells showed a strong shift towards macrophage population in the successive weeks of the cultures and also as a function of heat dose delivered to these cultures. The stroma formation was delayed or inhibited as a function of the heat dose. The number of granulocyte-macrophage colony forming cells (CFU-GM) in both adherent and non-adherent fraction of the cultures were decreased substantially after hyperthermia treatment. At 41 C and higher temperatures, the CFU-GM were severely diminished in both fractions. The dose response experiments showed that the decrease in the number of CFU-GM was dependent on the heat dose. The results suggest that CFU-GM is an extremely sensitive target in the hyperthermia treatment of bone marrow cells and heat-treated bone marrow cells lose their ability to maintain long-term cultures. [ABSTRACT FROM AUTHOR]

Abstract Background Pattern discovery in DNA sequences is one of the most fundamental problems in molecular biology with important applications in finding regulatory signals and transcription factor binding sites. An important task in this problem is to search (or predict) known binding sites in a new DNA sequence. For this reason, all subsequences of the given DNA sequence are scored based on an scoring function and the prediction is done by selecting the best score. By assuming no dependency between binding site base positions, most of the available tools for known binding site prediction are designed. Recently Tomovic and Oakeley investigated the statistical basis for either a claim of dependence or independence, to determine whether such a claim is generally true, and they presented a scoring function for binding site prediction based on the dependency between binding site base positions. Our primary objective is to investigate the scoring functions which can be used in known binding site prediction based on the assumption of dependency or independency in binding site base positions. Results We propose a new scoring function based on the dependency between all positions in biding site base positions. This scoring function uses joint information content and mutual information as a measure of dependency between positions in transcription factor binding site. Our method for modeling dependencies is simply an extension of position independency methods. We evaluate our new scoring function on the real data sets extracted from JASPAR and TRANSFAC data bases, and compare the obtained results with two other well known scoring functions. Conclusion The results demonstrate that the new approach improves known binding site discovery and show that the joint information content and mutual information provide a better and more general criterion to investigate the relationships between positions in the TFBS. Our scoring function is formulated by simple mathematical calculations. By implementing our method on several biological data sets, it can be induced that this method performs better than methods that do not consider dependencies.

The age-old discipline of plant therapy has gained renewed importance through the utilization of plants for the synthesis of metal nanoparticles. However, toxicity testing and characterization of the recently synthesized nanomaterials are essential to evaluating their appropriate application. Citrullus colocynthis is a medicinal plant with several health benefits. Herein, we used its ethanolic pulp extract (PE) to manufacture gold nanoparticles (PE-AuNPs). Various approaches were employed to assess the MTT 50 and NR 50 values of PE and PE-AuNPs at different concentrations in the human hepatocarcinoma cell line (HepG2). The study aimed to assess the genotoxic effects and in vivo toxicity of PE and PE-AuNPs at MTT 50 dosages. The quasi-spherical, cubic/triangular prisms, and nail-looking particles exhibited no antioxidant properties. They had an absorbance peak between 540 and 560 nm, diameters of less than 20 nm, hydrodynamic diameters of 177.9 nm, and a negative surface charge (-10.3 mV). The significant role of plant phytochemicals in the formation of metal nanoparticles is confirmed by the diminished antioxidant capacity of extract residues following PE-AuNP synthesis. PE-AuNPs exhibited in vivo and cytotoxic effects at relatively lower concentrations compared to PE. In contrast to PE, PE-AuNPs exhibited lower genotoxic at MTT 50 dosages. Despite having MTT 50 values of approximately 1.95 ± 0.06 and 0.89 ± 0.03 mg/ml, PE and PE-AuNPs can still be considered biocompatible. Nonetheless, our results suggest that the characteristics of recently produced nanoparticles can differ from those of the matching plant. Further investigation can provide a better understanding of the possible therapeutic and pharmacological impacts of PE-AuNPs., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Theta burst stimulation (TBS) is a form of repetitive transcranial magnetic stimulation (rTMS) with unknown underlying mechanisms and highly variable responses across subjects. To investigate these issues, we developed a simple computational model. Our model consisted of two neurons linked by an excitatory synapse that incorporates two mechanisms: short-term plasticity (STP) and spike-timing-dependent plasticity (STDP). We applied a variable-amplitude current through I-clamp with a TBS time pattern to the pre- and post-synaptic neurons, simulating synaptic plasticity. We analyzed the results and provided an explanation for the effects of TBS, as well as the variability of responses to it. Our findings suggest that the interplay of STP and STDP mechanisms determines the direction of plasticity, which selectively affects synapses in extended neurons and underlies functional effects. Our model describes how the timing, number, and intensity of pulses delivered to neurons during rTMS contribute to induced plasticity. This not only successfully explains the different effects of intermittent TBS (iTBS) and continuous TBS (cTBS), but also predicts the results of other protocols such as 10 Hz rTMS. We propose that the variability in responses to TBS can be attributed to the variable span of neuronal thresholds across individuals and sessions. Our model suggests a biologically plausible mechanism for the diverse responses to TBS protocols and aligns with experimental data on iTBS and cTBS outcomes. This model could potentially aid in improving TBS and rTMS protocols and customizing treatments for patients, brain areas, and brain disorders., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Background: The global need for wireless technologies is growing rapidly. So, we have been exposed to a new type of environmental pollution: radiofrequency radiation (RFR). Recent studies have shown that RFR can cause not only direct effects but also indirect or non-targeted effects such as the bystander effect (BE). In this study, we investigated the BE induced by RFR in the present of gold nanoparticles (GNP). Moreover, we studied the expression of cyclooxygenase-2 (COX-2)., Methods: Non-toxic dose of 15-nm GNP was used to treat the Chinese Hamster Ovary (CHO) cells. After 48 h of incubation, cells were exposed to 900 MHz GSM RFR for 24 h. Then we collected the cell culture medium of these cells (conditioned culture medium, CCM) and transferred it to new cells (bystander cells). Cell deaths, DNA breaks, oxidative stress and COX-2 expression were analyzed in all groups., Results: The results showed that RFR increased metabolic death in cells treated with GNP. Inversely, the colony formation ability was reduced in bystander cells and RFR exposed cells either in the presence or absence of GNP. Also, the level of reactive oxygen species (ROS) in GNP treated cells showed a significant reduction compared to those of untreated cells. However, RFR-induced DNA breaks and the frequencies of micronuclei (MN) were not significantly affected by GNP. The expression of COX-2 mRNA increased in RFR GNP treated cells, but the difference was not significant., Conclusion: Our results for the first time indicated that RFR induce indirect effects in the presence of GNP. However, the molecular mediators of these effects differ from those in the absence of GNP. Also, to our knowledge, this is the first study to show that COX-2 is not involved in the bystander effect induced by 900 MHz RFR., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Studying the bioeffects of electric fields have been the subject of ongoing research which led to promising therapeutic effect, particularly in cancer treatment. Here, we investigated the impact of low-intensity, intermediate-frequency alternating electric fields on the differentiation of human myeloid leukemia cell line U937. The results showed a near twofold increase in differentiation of U937 cells treated for 24 h by alternating 600 kHz, 150 V/m electric fields, in comparison to their control groups. This measure was evaluated by latex bead phagocytosis assay, nitro blue tetrazolium test, and cell cycle analysis which revealed a significant shift in the number of cells from G 2 +M to G 0 +G 1 phases. The simulation result for the intracellular field intensity showed around 50% attenuation with respect to the applied external field for our setup which ruled out masking of the applied field by the internal electric noise of the cell. Based on previous studies we postulate a possible calcium-related effect for the observed differentiation, yet the exact underlying mechanism requires further investigation. Finally, our results may offer a potential therapeutic method for leukemia in the future., (© 2023 Bioelectromagnetics Society.)

Our study aimed to investigate the effects of ultrasound on the fibrillation kinetics of HEWL (hen egg white lysozyme) and its physicochemical properties. Ultrasound, a mechanical wave, can induce conformational changes in proteins. To achieve this, we developed an ultrasound exposure system and used various biophysical techniques, including ThT fluorescence spectroscopy, ATR-FTIR, Far-UV CD spectrophotometry, Fluorescence microscopy, UV-spectroscopy, and seeding experiments. Our results revealed that higher frequencies significantly accelerated the fibrillation of lysozyme by unfolding the native protein and promoting the fibrillation process, thereby reducing the lag time. We observed a change in the secondary structure of the sonicated protein change to the β-structure, but there was no difference in the T m of native and sonicated proteins. Furthermore, we found that higher ultrasound frequencies had a greater seeding effect. We propose that the effect of frequency can be explained by the impact of the Reynolds number, and for the Megahertz frequency range, we are almost at the transition regime of turbulence. Our results suggest that laminar flows may not induce any significant change in the fibrillation kinetics, while turbulent flows may affect the process., Competing Interests: Declaration of competing interest The authors report that they have no conflict of interest., (Copyright © 2023. Published by Elsevier B.V.)

Background: Recent achievements in cancer therapy are the use of alternating electrical fields at intermediate frequencies (100-300 kHz) and low intensities (1-3 V/cm), which specifically target cell proliferation while affecting different cellular activities depending on the frequency used., Methods: In this article, we examine the effect of electric fields on spherical suspended cells and propose the combination of Daunorubicin, a chemotherapy agent widely used in the treatment of acute myeloid leukemia, with electric field exposure. U937 cells were subjected to an electric field with a frequency of 200 kHz and an intensity of 0.75 V/cm, or to a combination of Daunorubicin and electric field exposure, resulting in a significant reduction in cell proliferation. Furthermore, the application of an electric field to U937 cells increased Daunorubicin uptake., Results: Apoptosis and DNA damage were induced by the electric field or in conjunction with Daunorubicin. Notably, normal cells exposed to an electric field did not show significant damage, indicating a selective effect on dividing cancer cells (U937). Moreover, the electric field affects the U937 cell line either alone or in combination with Daunorubicin. This effect may be due to increased membrane permeability., Conclusions: Our findings suggest that the use of electric fields at intermediate frequencies and low intensities, either alone or in combination with Daunorubicin, has potential as a selective anti-cancer therapy for dividing cancer cells, particularly in the treatment of acute myeloid leukemia. Further research is needed to fully understand the underlying mechanisms and to optimize the use of this therapy., (© 2023. BioMed Central Ltd., part of Springer Nature.)

The efficacy of human recombinant insulin can be affected by its aggregation. Effects of acetylation were observed on insulin structure, stability, and aggregation at 37 and 50 °C and pH of 5.0 and 7.4 with the use of spectroscopy, circular dichroism (CD), dynamic light scattering (DLS), and atomic force microscopy (AFM). Raman and FTIR results were indicative of structural changes in AC-INS, and CD analyses showed a slight increase in β-sheet content in AC-INS. Melting temperature (T m ) measurements indicated an overall more stable structure and spectroscopic assessment showed a more compact one. Formation of amorphous aggregates was followed over time and kinetics parameters showed a longer nucleation phase (higher t* amount) and lower aggregates amount (lower A lim ) for acetylated insulin (AC-INS) compared to native (N-INS) in all tested conditions. The results of amyloid-specific probes approved the formation of amorphous aggregates. Size particle and microscopic analysis suggested that AC-INS was less prone to form aggregates, which were smaller if formed. In conclusion, this study has demonstrated that controlled acetylation of insulin may lead to its higher stability and lower propensity toward amorphous aggregation and has provided insight into the result of this type of post-translational protein modification., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The use of hydrogel dressings has become increasingly popular as a scaffold for skin tissue engineering. Herein, we have developed an innovative wound dressing using chitosan, fibrinogen, nisin, and EDTA as an effective antibacterial scaffold for wound treatment. The structural and functional characteristics of the hydrogel, including morphology, mechanical strength, drug encapsulation and release, swelling behaviors, blood coagulation, cytotoxicity, and antibacterial activity, were studied. Spectroscopic studies indicated that the attachment of chitosan to fibrinogen is associated with minimal change in its secondary structure; subsequently, at higher temperatures, it is expected to preserve fibrinogen's conformational stability. Mechanical and blood coagulation analyses indicated that the incorporation of fibrinogen into the hydrogel resulted in accelerated clotting and enhanced mechanical properties. Our cell studies showed biocompatibility and non-toxicity of the hydrogel along with the promotion of cell migration. In addition, the prepared hydrogel indicated an antibacterial behavior against both Gram-positive and Gram-negative bacteria. Interestingly, the in vivo data revealed enhanced tissue regeneration and recovery within 17 days in the studied animals. Taken together, the results obtained from in vitro and histological assessments indicate that this innovatively designed hydrogel shows good potential as a candidate for wound healing., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Among the different breast cancer subsets, triple-negative breast cancer (TNBC) has the worst prognosis and limited options for targeted therapies. Immunotherapies are emerging as novel treatment opportunities for TNBC. However, the surging immune response elicited by immunotherapies to eradicate cancer cells can select resistant cancer cells, which may result in immune escape and tumor evolution and progression. Alternatively, maintaining the equilibrium phase of the immune response may be advantageous for keeping a long-term immune response in the presence of a small-size residual tumor. Myeloid-derived suppressor cells (MDSCs) are activated, expanded, and recruited to the tumor microenvironment by tumor-derived signals and can shape a pro-tumorigenic micro-environment by suppressing the innate and adaptive anti-tumor immune responses. We recently proposed a model describing immune-mediated breast cancer dormancy instigated by a vaccine consisting of dormant, immunogenic breast cancer cells derived from the murine 4T1 TNBC-like cell line. Strikingly, these 4T1-derived dormant cells recruited fewer MDSCs compared to aggressive 4T1 cells. Recent experimental studies demonstrated that inactivating MDSCs has a profound impact on reconstituting immune surveillance against the tumor. Here, we developed a deterministic mathematical model for simulating MDSCs depletion from mice bearing aggressive 4T1 tumors resulting in immunomodulation. Our computational simulations indicate that a vaccination strategy with a small number of tumor cells in combination with MDSC depletion can elicit an effective immune response suppressing the growth of a subsequent challenge with aggressive tumor cells, resulting in sustained tumor dormancy. The results predict a novel therapeutic opportunity based on the induction of effective anti-tumor immunity and tumor dormancy., (© 2023. The Author(s).)

Considering the central role of oxidative stress in the onset and progress of Parkinson's diseases (PD), search for compounds with antioxidant properties has attracted a growing body of attention. Here, we compare the neuroprotective effect of bulk and nano forms of the polyphenolic fraction of propolis (PFP) against rotenone-induced cellular and animal models of PD. Mass spectrometric analysis of PFP confirmed the presence of multiple polyphenols including kaempferol, naringenin, coumaric acid, vanillic acid, and ferulic acid. In vitro cellular experiments indicate the improved efficiency of the nano form, compared to the bulk form, of PFP in attenuating rotenone-induced cytotoxicity characterized by a decrease in cell viability, release of lactate dehydrogenase, increased ROS generation, depolarization of the mitochondrial membrane, decreased antioxidant enzyme activity, and apoptosis induction. In vivo experiments revealed that while no significant neuroprotection was observed relating to the bulk form, PFP nanosheets were very effective in protecting animals, as evidenced by the improved behavioral and neurochemical parameters, including decreased lipid peroxidation, increased GSH content, and antioxidant enzyme activity enhancement. We suggest that improved neuroprotective effects of PFP nanosheets may be attributed to their increased water solubility and enrichment with oxygen-containing functional groups (such as OH and COOH), leading to increased antioxidant activity of these compounds.

Cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed cell death protein 1 (PD-1), two clinically relevant targets for the immunotherapy of cancer, are negative regulators of T-cell activation and migration. Optimizing the therapeutic response to CTLA-4 and PD-1 blockade calls for a more comprehensive insight into the coordinated function of these immune regulators. Mathematical modeling can be used to elucidate nonlinear tumor-immune interactions and highlight the underlying mechanisms to tackle the problem. Here, we investigated and statistically characterized the dynamics of T-cell migration as a measure of the functional response to these pathways. We used a previously developed three-dimensional organotypic culture of patient-derived tumor spheroids treated with anti-CTLA-4 and anti-PD-1 antibodies for this purpose. Experiment-based dynamical modeling revealed the delayed kinetics of PD-1 activation, which originates from the distinct characteristics of PD-1 and CTLA-4 regulation, and followed through with the modification of their contributions to immune modulation. The simulation results show good agreement with the tumor cell reduction and active immune cell count in each experiment. Our findings demonstrate that while PD-1 activation provokes a more exhaustive intracellular cascade within a mature tumor environment, the time-delayed kinetics of PD-1 activation outweighs its preeminence at the individual cell level and consequently confers a functional dominance to the CTLA-4 checkpoint. The proposed model explains the distinct immunostimulatory pattern of PD-1 and CTLA-4 blockade based on mechanisms involved in the regulation of their expression and may be useful for planning effective treatment schemes targeting PD-1 and CTLA-4 functions.

Extremely low-frequency electromagnetic field (ELF-EMF) induces biological effects on different cells through various signaling pathways. To study the impact of the ELF-EMF on living cells under an optimal physiological condition, we have designed and constructed a novel system that eliminates several limitations of other ELF-EMF systems. Apoptosis and cell number were assessed by flow cytometry and the Trypan Blue dye exclusion method, respectively. In vitro cell survival was evaluated by colony formation assay. The distribution of cells in the cell cycle, intracellular ROS level, and autophagy were analyzed by flow cytometer. Suspended cells differentiation was assessed by phagocytosis of latex particles and NBT reduction assay. Our results showed that response to the exposure to ELF-EMF is specific and depends on the biological state of the cell. For DU145, HUVEC, and K562 cell lines the optimum results were obtained at the frequency of 0.01 Hz, while for MDA-MB-231, the optimum response was obtained at 1 Hz. Long-term exposure to ELF-EMF in adherent cells effectively inhibited proliferation by arresting the cell population at the cell cycle G2/M phase and increased intracellular ROS level, leading to morphological changes and cell death. The K562 cells exposed to the ELF-EMF differentiate via induction of autophagy and decreasing the cell number. Our novel ELF-EMF instrument could change morphological and cell behaviors, including proliferation, differentiation, and cell death., (© 2022. The Author(s).)

By growing the electrical power networks and electronic devices, electromagnetic fields (EMF) have become an inseparable part of the modern world. Considering the inevitable exposure to a various range of EMFs, especially at extremely low frequencies (ELF-EMF), investigating the biological effects of ELF-EMFs on biological systems became a global issue. The possible adverse consequences of these exposures were studied, along with their potential therapeutic capabilities. Also, their biological impacts in combination with other chemical and physical agents, specifically ionizing radiation (IR), as a co-carcinogen or as adjuvant therapy in combination with radiotherapy were explored. Here, we review the results of several in-vitro and in-vivo studies and discuss some proposed possible mechanisms of ELF-EMFs' actions in combination with IR. The results of these experiments could be fruitful to develop more precise safety standards for environmental ELF-EMFs exposures. Furthermore, it could evaluate the therapeutic capacities of ELF-EMFs alone or as an improver of radiotherapy., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Wound healing is a complex process and rapid healing necessitates a proper micro-environment. Therefore, design and fabrication of an efficacious wound dressing is an impressive innovation in the field of wound healing. The fabricated wound dressing in this scenario was designed using a combination of the appropriate coagulating and anti-bacterial materials like fibrinogen (as coagulating agent), nisin (as anti-bacterial agent), ethylenediaminetetraacetic acid (as anti-bacterial agent), and alginate (as wound healing agent). Biophysical characterization showed that the interaction of fibrinogen and alginate was associated with minor changes in the secondary structure of the protein. Conformational studies showed that the protein was structurally stable at 42 °C, is the maximum temperature of the infected wound. The properties of the hydrogel such as swelling, mechanical resistance, nisin release, antibacterial activity, cytotoxicity, gel porosity, and blood coagulation were assessed. The results showed a slow release for the nisin during 48 h. Antibacterial studies showed an inhibitory effect on the growth of Gram-negative and Gram-positive bacteria. The hydrogel was also capable to absorb a considerable amount of water and provide oxygenation as well as incorporation of the drug into its structure due to its sufficient porosity. Scanning electron microscopy showed pore sizes of about 14-198 µm in the hydrogel. Cell viability studies indicated high biocompatibility of the hydrogel. Blood coagulation test also confirmed the effectiveness of the synthesized hydrogel in accelerating the process of blood clot formation. In vivo studies showed higher rates of wound healing, re-epithelialization, and collagen deposition. According to the findings from in vitro as well as in vivo studies, the designed hydrogel can be considered as a novel attractive wound dressing after further prerequisite assessments., (© 2022. The Author(s).)

Background and Objective: Optogenetics has opened new insights into biomedical research with the ability to manipulate and control cellular activity using light in combination with genetically engineered photosensitive proteins. By stimulating with light, this method provides high spatiotemporal and high specificity resolution, which is in contrast to conventional pharmacological or electrical stimulation. Optogenetics was initially introduced to control neural activities but was gradually extended to other biomedical fields., Study Design: In this paper, firstly, we summarize the current optogenetic tools stimulated by different light sources, including lasers, light-emitting diodes, and laser diodes. Second, we outline the variety of biomedical applications of optogenetics not only for neuronal circuits but also for various kinds of cells and tissues from cardiomyocytes to ganglion cells. Furthermore, we highlight the potential of this technique for treating neurological disorders, cardiac arrhythmia, visual impairment, hearing loss, and urinary bladder diseases as well as clarify the mechanisms underlying cancer progression and control of stem cell differentiation., Conclusion: We sought to summarize the various types of promising applications of optogenetics to treat a broad spectrum of disorders. It is conceivable to expect that optogenetics profits a growing number of patients suffering from a range of different diseases in the near future., (© 2021 Wiley Periodicals LLC.)

Early detection of colorectal cancer (CRC) increases the chances of survival and reduces the therapeutic problems and costs of treatment. Since molecular biomarkers can help us diagnose colorectal cancer early, we need to identify novel gene for predicting the early stages of tumorigenesis. Here, we integrated five independent CRC gene expression datasets derived from expression profiling by array comparing CRC with normal samples in: GSE21510, GSE4107, GSE25071, GSE15781 dataset, and GSE8671 dataset, including 64 samples from 32 patients comparing 32 colonic normal mucosa with 32 colorectal adenoma. To detect genes that expressed differentially in experimental circumstances of these datasets, we used web tool of GEO2R to compare groups of samples in the GEO data series. Furthermore, we constructed the protein-protein interactions network by STRING database for mostly downregulated genes and the expression of their members in PPI network were studied into five datasets separately. Also, the level of expression of selected biomarker genes in different stages of CRC compared to normal was studied. Our data revealed 17 common downregulated genes (average fold change (FC) in five tests ≥6) in CRC in comparison with normal (Test 1 to Test 4) and in adenoma compared with normal (Test 5). Studying of gene expression of PPI network members of these downregulated genes led to identifying of CLCA1, SELENBP1, CWC25, ACOT11, GUCY2C and ALDH1A1 as suppressor genes and PTGS2, PROCR, MOCS3 and NFS1 as oncogenes which respectively downregulated and upregulated in CRC. Since decreasing of gene expression was seen in CRC comparing with normal and due to no different expression seen for these 10 genes in adenoma, they, especially CLCA1 and SELENBP1, could be considered as biomarkers for early detection of CRC. Before using these signature genes in the clinic; however, further validations are required., Competing Interests: None., (AJCR Copyright © 2022.)

Radiation therapy is common in the current procedures of cancer treatment, but in many cases, radiation resistance of cancerous tissue limits efficacy in clinical applications. Therefore, the use of radiosensitizers has been introduced as an effective strategy to increase the efficiency of radiotherapy. Butein (2', 3, 4, 4'-Tetrahydroxychalcone), a polyphenolic compound of flavonoids family, presents anti-cancer properties and inhibits the signaling pathways associated with radiation resistance. Therefore, we hypothesized that butein in combination with radiation may increase radiosensitivity. To evaluate the radiosensitizing effect of butein, we used MKN-45 cell line and performed several assays such as MTT, soft-agar colony formation, apoptosis, cell cycle, and comet assays. Based on obtained results, butein significantly enhanced radiosensitivity of MKN-45 cells. Butein treatment abrogated the radiation-induced G2/M cell cycle arrest, increased DNA damage, enhanced apoptosis, and reduced colony-forming ability of irradiated cells. This study on MKN-45 cells demonstrates that combination of butein with radiotherapy increases its radiosensitivity by abrogating the radiation-induced G2/M blockage, impairing DNA repair, and enhancing apoptotic and reproductive cell death. Therefore, we suggest butein as a candidate for combination with radiation therapy to decrease dose of radiation delivered to the patients and its corresponding side effects., Competing Interests: Declaration of competing interest The authors report that they have no conflict of interest., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Background: Genetic heterogeneity of a cancer tumor that develops during clonal evolution is one of the reasons for cancer treatment failure, by increasing the chance of drug resistance. Clones are cell populations with different genotypes, resulting from differences in somatic mutations that occur and accumulate during cancer development. An appropriate approach for identifying clones is determining the variant allele frequency of mutations that occurred in the tumor. Although bulk sequencing data can be used to provide that information, the frequencies are not informative enough for identifying different clones with the same prevalence and their evolutionary relationships. On the other hand, single-cell sequencing data provides valuable information about branching events in the evolution of a cancerous tumor. However, the temporal order of mutations may be determined with ambiguities using only single-cell data, while variant allele frequencies from bulk sequencing data can provide beneficial information for inferring the temporal order of mutations with fewer ambiguities., Result: In this study, a new method called Conifer (ClONal tree Inference For hEterogeneity of tumoR) is proposed which combines aggregated variant allele frequency from bulk sequencing data with branching event information from single-cell sequencing data to more accurately identify clones and their evolutionary relationships. It is proven that the accuracy of clone identification and clonal tree inference is increased by using Conifer compared to other existing methods on various sets of simulated data. In addition, it is discussed that the evolutionary tree provided by Conifer on real cancer data sets is highly consistent with information in both bulk and single-cell data., Conclusions: In this study, we have provided an accurate and robust method to identify clones of tumor heterogeneity and their evolutionary history by combining single-cell and bulk sequencing data., (© 2021. The Author(s).)

Introduction: Non-clinical cardiovascular drug safety assessment is the main step in the progress of new pharmaceutical products. Cardiac drug safety testing focuses on a delayed rectifier potassium channel block and QT interval prolongation, whereas optogenetics is a powerful technology for modulating the electrophysiological properties of excitable cells. Methods: For this purpose, the blue light-gated ion channel, channelrhodopsin-2 (ChR2), has been introduced into isolated primary neonatal cardiomyocytes via a lentiviral vector. After being subjected to optical stimulation, transmembrane potential and intracellular calcium were assessed. Results: Here, we generated cardiomyocytes expressing ChR2 (light-sensitive protein), that upon optical stimulation, the cardiomyocytes depolarized result from alterations of membrane voltage and intracellular calcium. Conclusion: This cell model was easily adapted to a cell culture system in a laboratory, making this method very attractive for therapeutic research on cardiac optogenetics., (Copyright © 2021 J Lasers Med Sci.)

Triple-negative breast cancer (TNBC) is a molecular subtype of breast malignancy with a poor clinical prognosis. There is growing evidence that some chemotherapeutic agents induce an adaptive anti-tumor immune response. This reaction has been proposed to maintain the equilibrium phase of the immunoediting process and to control tumor growth by immunological cancer dormancy. We recently reported a model of immunological breast cancer dormancy based on the murine 4T1 TNBC model. Treatment of 4T1 cells in vitro with high-dose chemotherapy activated the type I interferon (type I IFN) signaling pathway, causing a switch from immunosuppressive to cytotoxic T lymphocyte-dependent immune response in vivo, resulting in sustained dormancy. Here, we developed a deterministic mathematical model based on the assumption that two cell subpopulations exist within the treated tumor: one population with high type I IFN signaling and immunogenicity and lower growth rate; the other population with low type I IFN signaling and immunogenicity and higher growth rate. The model reproduced cancer dormancy, elimination, and immune-escape in agreement with our previously reported experimental data. It predicted that the injection of dormant tumor cells with active type I IFN signaling results in complete growth control of the aggressive parental cancer cells injected at a later time point, but also of an already established aggressive tumor. Taken together, our results indicate that a dormant cell population can suppress the growth of an aggressive counterpart by eliciting a cytotoxic T lymphocyte-dependent immune response.

The emergence of phenotypic diversity in a population of cells and their arrangement in space and time is one of the most fascinating features of living systems. In fact, understanding multicellularity is unthinkable without explaining the proximate and the ultimate causes of cell differentiation in time and space. Simpler forms of cell differentiation can be found in unicellular organisms, such as bacterial biofilm, where reversible cell differentiation results in phenotypically diverse populations. In this manuscript, we attempt to start with the simple case of reversible nongenetic phenotypic to construct a model of differentiation and pattern formation. Our model, which we refer to as noise-driven differentiation (NDD) model, is an attempt to consider the prevalence of noise in biological systems, alongside what is known about genetic switches and signaling, to create a simple model which generates spatiotemporal patterns from bottom-up. Our simulations indicate that the presence of noise in cells can lead to reversible differentiation and the addition of signaling can create spatiotemporal pattern., Competing Interests: The authors have declared that no competing interests exist.

Background: Patterns on proteins and genomic sequences are vastly analyzed, extracted and collected in databases. Although protein patterns originate from genomic coding regions, very few works have directly or indirectly dealt with coding region patterns induced from protein patterns. Results: In this paper, we have defined a new genomic pattern structure suitable for representing induced patterns from proteins. The provided pattern structure, which is called "Consecutive Positions Scoring Matrix (CPSSM)", is a replacement for protein patterns and profiles in the genomic context. CPSSMs can be identified, discovered, and searched in genomes. Then, we have presented a novel pattern matching algorithm between the defined genomic pattern and genomic sequences based on dynamic programming. In addition, we have modified the provided algorithm to support intronic gaps and huge sequences. We have implemented and tested the provided algorithm on real data. The results on Saccharomyces cerevisiae's genome show 132% more true positives and no false negatives and the results on human genome show no false negatives and 10 times as many true positives as those in previous works. Conclusion: CPSSM and provided methods could be used for open reading frame detection and gene finding. The application is available with source codes to run and download at http://app.foroughmand.ir/cpssm/.

Mesoporous silica nanoparticles (MSNs) have ideal characteristics as next generation of controlled drug delivery systems. In this study, a MSN-based nanocarrier was fabricated and gold nanoparticle (GNP)-biotin conjugates were successfully grafted onto the pore outlets of the prepared MSN. This bioconjugate served as a capping agent with a peptide-cleavable linker sensitive to matrix metalloproteinases (MMPs), which are overexpressed extracellular proteolytic enzymes in cancerous tissue. The prepared nanocarriers were fully characterised by scanning electron microscopy (SEM), transmission electron microscopy (TEM), nitrogen adsorption/desorption, Fourier transform infra-red spectroscopy (FTIR), dynamic light scattering (DLS) and thermo gravimetric analysis (TGA). In vitro release studies showed efficient capping of MSNs with gold gate and controlled release of Doxorubicin (DOX) in the presence of matrix metalloproteinase-2 (MMP-2) and acidic pH values. High DOX-loading capacity (21%) and encapsulation efficiency (95.5%) were achieved using fluorescence technique. DOX-loaded nanocarriers showed high cytocompatibility and could efficiently induce cell death and apoptosis in the MMP-2 overexpressed cell lines. Moreover, Haemolysis, platelet activation and inflammatory responses assessment approved excellent hemocompatibility and minimal side effects by encapsulation of DOX in MSNs carrier.

Cardiac optogenetics is an emergent research area and refers to the delivery of light-activated proteins to excitable heart tissue and the subsequent use of light for controlling the electrical function with high spatial and temporal resolution. Channelrhodopsin-2 (ChR2) is a light-sensitive ion channel with the chromophore, all trans retinal, derived from vitamin A (all-trans-retinol; retinol). In this study, we explored whether exogenous vitamin A can be a limiting factor in the light responsiveness of cardiomyocytes-expressing ChR2. We showed that in cardiomyocytes virally transduced with ChR2 (H134R)-enhanced yellow fluorescent protein, vitamin A supplements lower than 10 μM significantly increased ChR2 expression. Adding 1 μM vitamin A changed light-induced transmembrane potential difference significantly, whereas 5 μM dramatically induced membrane depolarization and triggered intracellular calcium elevation. We concluded that vitamin A supplementation can modulate the efficiency of ChR2 and provide a complementary strategy for improving the performance of optogenetic tools., (© 2019 International Union of Biochemistry and Molecular Biology.)