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BackgroundA growing body of preclinical studies report that preconceptional experiences can have a profound and long-lasting impact on adult offspring behavior and physiology. However, less is known about paternal drug exposure and its effects on reward sensitivity in the next generation.MethodsAdult male rats self-administered morphine for 65 days; controls received saline. Sires were bred to drug-naïve dams to produce first-generation (F1) offspring. Morphine, cocaine, and nicotine self-administration were measured in adult F1 progeny. Molecular correlates of addiction-like behaviors were measured in reward-related brain regions of drug naïve F1 offspring.ResultsMale, but not female offspring produced by morphine-exposed sires exhibited dose-dependent increased morphine self-administration and increased motivation to earn morphine infusions under a progressive ratio schedule of reinforcement. This phenotype was drug-specific as self-administration of cocaine, nicotine, and sucrose were not altered by paternal morphine history. The male offspring of morphine-exposed sires also had increased expression of mu-opioid receptors in the ventral tegmental area but not in the nucleus accumbens.ConclusionsPaternal morphine exposure increased morphine addiction-like behavioral vulnerability in male but not female progeny. This phenotype is likely driven by long-lasting neural adaptations within the reward neural brain pathways.

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Increasing concerns about the emergence of antibiotic-resistant bacteria have drawn much attention for research efforts to introduce new types of antibacterial compounds among scientists. In the present report, 24 bacterial strains isolated from the coastal areas of the Persian Gulf in Iran were investigated in order to assess their potentials to produce antibacterial metabolites. Among these, the crude extract from the isolate REB264 showed promising inhibition activity on the growth of two pathogenic bacteria, Pseudomonas aeruginosa and Staphylococcus aureus. Molecular identification via sequencing of the amplified 16S rDNA gene of the strain REB264 revealed that the bacterium belonging to the genus Bacillus and was tentatively named Bacillus sp. REB264, while the sequence was deposited in GenBank database, NCBI. Optimization of the carbon and nitrogen sources of the strain REB264 culture media determined that 743 mg/l active extract was achieved when using 1% glycerol and 0.5% yeast extract as carbon and nitrogen sources, respectively. Crude extract purification to obtain the antibacterial metabolite was performed in three steps using fractionation in organic and aqueous solvents, silica gel 60 column chromatography and LH-20 gel filtration with the yield of 80%. The purified compound exhibited inhibitory effect on P. aeruginosa growth at minimum inhibitory concentration (MIC) of 15 µg/ml, while lacking antibacterial effect on S. aureus. The P. aeruginosa growth inhibitor 264 (PAGI264) compound was further purified using reversed-phase high-performance liquid chromatography (C18-HPLC) up to 95% and the structural analysis by FTIR and H1-NMR confirmed that PAGI264 is composed of alcoholic, carbonyl and phenolic functional groups. Moreover, MS data in positive mode showed that the molecular weight of the compound is 761.74 Da. Lack of toxicity to MCF-7 cell line up to 500 µg/ml and lack of the hemolytic effect on red blood cells showed that the present natural product, PAGI264, has capability to use as a lead or drug in the future.

Background Iranian traditional medicine, also known as Persian Medicine, is a holistic school of medicine with a long prolific history. It describes numerous concepts and the relationships between them. However, no unified language system has been proposed for the concepts of this medicine up to the present time. Considering the extensive terminology in the numerous textbooks written by the scholars over centuries, comprehending the totality of concepts is obviously a very challenging task. To resolve this issue, overcome the obstacles, and code the concepts in a reusable manner, constructing an ontology of the concepts of Iranian traditional medicine seems a necessity. Construction and content Makhzan al-Advieh, an encyclopedia of materia medica compiled by Mohammad Hossein Aghili Khorasani, was selected as the resource to create an ontology of the concepts used to describe medicinal substances. The steps followed to accomplish this task included (1) compiling the list of classes via examination of textbooks, and text mining the resource followed by manual review to ensure comprehensiveness of extracted terms; (2) arranging the classes in a taxonomy; (3) determining object and data properties; (4) specifying annotation properties including ID, labels (English and Persian), alternative terms, and definitions (English and Persian); (5) ontology evaluation. The ontology was created using Protégé with adherence to the principles of ontology development provided by the Open Biological and Biomedical Ontology (OBO) foundry. Utility and discussion The ontology was finalized with inclusion of 3521 classes, 15 properties, and 20,903 axioms in the Iranian traditional medicine General Ontology (IrGO) database, freely available at http://ir-go.net/. An indented list and an interactive graph view using WebVOWL were used to visualize the ontology. All classes were linked to their instances in UNaProd database to create a knowledge base of ITM materia medica. Conclusion We constructed an ontology-based knowledge base of ITM concepts in the domain of materia medica to help offer a shared and common understanding of this concept, enable reuse of the knowledge, and make the assumptions explicit. This ontology will aid Persian medicine practitioners in clinical decision-making to select drugs. Extending IrGO will bridge the gap between traditional and conventional schools of medicine, helping guide future research in the process of drug discovery.

An improved one-pot three-component reaction of carbonyl compounds (dimedon, 4-hydroxy coumarin and 1,3-cyclohexadion) with malononitrile and aryl aldehydes in aqueous media (H2O:EtOH) as a solvent with short reaction time for the synthesis of benzo[b]pyran and 3,4- dihydropyrano[c]chromane derivatives by using nanostructured coumarin-based cobalt complex as an efficient heterogeneous catalyst. The salient features of this new protocol include simple procedure, high yields, easy isolation of products without need to column chromatography and short reaction times. Also, the nanocatalyst was recovered by adding EtOH and reused five times without significant loss of its catalytic activity. Biological impact assessments of the complex were conducted by DNA cleavage ability assay and eukaryotic cell toxicity measurement. Although the complex showed single-strand DNA breakage under oxidative conditions, its high polar nature revealed a marked decrease in cell toxicity data due to the restriction on cell entry.

Aim: This study was designed to perform network analysis of Alzheimers҆ disease and diabetes and to find their correlation with each other and other diseases/pathways. Background: Alzheimer’s disease (AD) as a neurodegenerative disease and diabetes as a metabolic disease are two major health problems in the recent years. The recent studies have reported their correlation and same spreading pathways of these two diseases together, but details of this relation are not well known yet at molecular level.. Methods: In thermal proteome profiling (TPP) technique, after treatment of the extracted proteins by heat and drug concentration, the resulting proteins were analyzed by mass spectrometry. Enrichment analysis of these proteins led to development of AD and diabetes. First, corresponding genes for each disease were extracted from DisGeNET database and then, protein-protein interaction network was constructed for each of them using the search tool for retrieval of interacting genes and proteins (STRING). After analyzing these networks, hub-bottleneck nodes of networks were evaluated. Also, common nodes between two networks were extracted and used for further analysis. Results: High correlation was found between AD and diabetes based on the existence of 40 common genes. Results of analyses revealed 14 genes in AD and 12 genes in diabetes as hub-bottleneck 7 of which were common including caspase 3 (CASP3), insulin-like growth factor 1 (IGF1), catalase (CAT), tumor necrosis factor (TNF), leptin (LEP), vascular endothelial growth factor A (VEGFA), and interleukin 6 ( IL-6). Conclusion: Our results revealed a direct correlation between AD and diabetes and also a correlation between these two diseases and non-alcoholic fatty liver disease (NAFLD), suggesting that a small change in each of these three diseases can lead to development of any other diseases in the patients. Also, the enrichments exhibited the existence of common pathways between AD, diabetes, NAFLD, and male infertility.

Parental history of opioid exposure is seldom considered when prescribing opioids for pain relief. To explore whether parental opioid exposure may affect sensitivity to morphine in offspring, we developed a “rat pain scale” with high-speed imaging, machine learning, and mathematical modeling in a multigenerational model of paternal morphine self-administration. We find that the most commonly used tool to measure mechanical sensitivity in rodents, the von Frey hair, is not painful in rats during baseline conditions. We also find that male progeny of morphine-treated sires had no baseline changes in mechanical pain sensitivity but were more sensitive to the pain-relieving effects of morphine. Using RNA sequencing across pain-relevant brain regions, we identify gene expression changes within the regulator of G protein signaling family of proteins that may underlie this multigenerational phenotype. Together, this rat pain scale revealed that paternal opioid exposure increases sensitivity to morphine’s pain-relieving effects in male offspring.

Early life adversity can alter reproductive development in humans, changing the timing of pubertal onset and sexual activity. One common form of early adversity is limited access to resources. This adversity can be modeled in rats using the limited bedding/nesting model (LBN), in which dams and pups are placed in a low resource environment from pups' postnatal days 2-9. Our laboratory previously found that adult male rats raised in LBN conditions have elevated levels of plasma estradiol compared to control males. In females, LBN had no effect on plasma hormone levels, pubertal timing, or estrous cycle duration. Estradiol mediates male reproductive behaviors. Thus, here we compared reproductive behaviors in adult males exposed to LBN vs. control housing. LBN males acquired the suite of reproductive behaviors (mounts, intromissions, and ejaculations) more quickly than their control counterparts over 3 weeks of testing. However, there was no effect of LBN in males on puberty onset or masculinization of certain brain regions, suggesting LBN effects on estradiol and reproductive behaviors manifest after puberty. In male and female rats, we next used RNA sequencing to characterize LBN-induced transcriptional changes in the medial preoptic area (mPOA), which underlies male reproductive behaviors. LBN produced sex-specific alterations in gene expression, with many transcripts showing changes in opposite directions. Numerous transcripts altered by LBN in males are regulated by estradiol, linking hormonal changes to molecular changes in the mPOA. Pathway analysis revealed that LBN induced changes in neurosignaling and immune signaling in males and females, respectively. Collectively, these studies reveal novel neurobiological mechanisms by which early life adversity can alter reproductive strategies.

The metal organic framework (MOF) member, MIL-100(Fe), is considered as attractive drug nanocarrier that may be due to the great porosity, colloidal stability, and biocompatibility. In the present study, the new electrochemical synthesis procedure was presented for MIL-100(Fe) building block, and secondly, folic acid (FA) was introduced to the structure for assessing its potential targeted ability to be entrapped by folic acid-positive breast cancer cells, MCF-7. Several techniques such as SEM, XRD, and FT-IR were used to characterize synthesized nanostructures. Both MIL-100(Fe) and MIL-100(Fe)/FA nanoparticles were between 50 to 200 nm with a slightly positive net charge with an area of 1350 and 831.84 m2/g, respectively. The prodigiosin (PG) is selected as a model drug for MIL-100(Fe) and MIL-100(Fe)/FA-targeted delivery owing to its natural fluorescence and cancer cell selectiveness. The loading capacity of both nanocarrier was around 40% with 93-97% loading efficacy. Moreover, the pH-sensitive prodigiosin release rate of MIL-100(Fe)@PG and MIL-100(Fe)/FA@PG showed that 69 to 73% of the drug was released after 24 hours in an acidic environment with around 20% unwanted leakage. The anticancer potential MIL-100(Fe)/FA cells showed the improvement of selective index (SI) from 3.21 to 12.48 which means that folic acid acts as an effective ligand. The study of cells treated with fluorescence microscopy and flow cytometry analysis reveals the dependence of the receptor on the nanoparticle through endocytosis. Considering the effects of nanoparticles on healthy cells, MIL-100(Fe) and MIL-100(Fe)/FA nanoparticles can be introduced as targeted drug delivery systems for smart targeting breast cancer cells with minimal side effects.

Analysis of networks of digestive disorder and their relationship with Covid-19 based on systems biology methods, evaluation similarity, and usefulness of networks to give a new treatment approach.Digestive disorders are typically complex diseases associated with high treatment costs. They are related to the immune system and inflammation. With the outbreak of Covid-19, this disease was shown to have signs like diarrhea. Some signs of Covid-19 are similar to those of digestive disorders, like IBD and diarrhea. Both of them are accompanied by inflammation and induce disorders in the digestive system.DisGeNET and STRING databases were sources of disease genes and constructing networks and were used to construct the network of digestive diseases and Covid-19. Three plugins of Cytoscape software, namely ClusterONE, ClueGO, and CluePedia, were used to analyze cluster networks and enrichment pathways. To describe the interaction of proteins, information from KEGG pathway and Reactome was used.According to the results, IBD, gastritis, and diarrhea have common pathways. The CXCL8, IL-6, IL-1β, TNF-α, TLR4, and MBL2 molecules were identified as inflammatory molecules in all networks.It seems that detecting genes and pathways can be useful in applying new approaches for treating these diseases.

Background The current study was aimed at evaluating the role of the N-SH2 domain of SHP-2 as a partner protein in the expression of a toxic peptide, laterosporulin (LTS). We also investigated its effects on the formation of the disulfide bond and functional folding of the peptide in vitro. The N-SH2-LTS protein was expressed as a His-tagged fusion protein, capable of undergoing enzymatic cleavage. Results Based on the data presented herein, the total yield of the folded fusion protein from inclusion bodies was found to be about 105 mg/l, demonstrating a high-level of heterologous expression. After enzymatic cleavage, 1.5 mg of the folded recombinant laterosporulin was obtained from each 10 mg of the fusion protein. The purity of the recombinant laterosporulin was analyzed by RP-HPLC, to yield peptides with suitable purity (85%). Conclusions Our findings indicated the advantages of using the N-SH2 domain of SHP-2 as a rapid and easy approach not only in producing easy target proteins but also in its function as a chaperone. N-SH2 domain of SHP-2 can influence on the purification of laterosporulin at reasonable yield and in a cost-effective fashion. The N-SH2 domain of SHP-2 as a protein chaperone may be potentially favorable to produce other proteins with disulfide bonds.

Incubation of craving is a well-documented phenomenon referring to the intensification of drug craving over extended abstinence. The neural adaptations that occur during forced abstinence following chronic drug taking have been a topic of intense study. However, little is known about the transcriptomic changes occurring throughout this window of time. To define gene expression changes associated with morphine consumption and extended abstinence, male and female rats underwent 10 days of morphine self-administration. Separate drug-naive rats self-administered sucrose in order to compare opioid-induced changes from those associated with natural, non-drug rewards. After one or 30 days of forced abstinence, rats were tested for craving, or nucleus accumbens shell tissue was dissected for RNA sequencing. Morphine consumption was predictive of drug seeking after extended (30 days) but not brief (1 day) abstinence in both sexes. Extended abstinence was also associated with robust sex- and reinforcer-specific changes in gene expression, suggesting sex differences underlying incubation of morphine and sucrose seeking respectively. Importantly, these changes in gene expression occurred without re-exposure to drug-paired cues, indicating that chronic morphine causes long-lasting changes in gene expression that prime the system for increased craving. These findings lay the groundwork for identifying specific therapeutic targets for curbing opioid craving without impacting the natural reward system in males and females.

Background Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy associated with a poor prognosis. High-throughput disease-related-gene expression data provide valuable information on gene interaction, which consequently lead to deeper insight about pathogenesis. The co-expression analysis is a common approach that is used to investigate gene interaction. However, such an approach solely is inadequate to reveal the complexity of the gene interaction. The three-way interaction model is known as a novel approach applied to decode the complex relationship between genes. Methods In the current study, the liquid association method was used to capture the statistically significant triplets involved in the PDAC pathogenesis. Subsequently, gene set enrichment and gene regulatory network analyses were performed to trace the biological relevance of the statistically significant triplets. Results The results of the current study suggest that “response to estradiol” and “Regulation of T-cell proliferation” are two critical biological processes that may be associated with the PDAC pathogenesis. Additionally, we introduced six switch genes, namely Lamc2, Klk1, Nqo1, Aox1, Tspan1, and Cxcl12, which might be involved in PDAC triggering. Conclusion In the current study, for the first time, the critical genes and pathways involved in the PDAC pathogenesis were investigated using the three-way interaction approach. As a result, two critical biological processes, as well as six potential biomarkers, were suggested that might be involved in the PDAC triggering. Surprisingly, strong evidence for the biological relevance of our results can be found in the literature.

The search for disease-related targets and studying drug-protein and protein-protein interactions are central issues that would accelerate the clinical approval of a drug. Also, by developing an accurate method in this regard, time and resource consumption will significantly decrease. The low efficiency of some drugs in humans is a grave issue leading to a low rate of FDA approval after spending billions of dollars and decades of research. Several strategies and methods have been expanded to fill this gap, such as drug affinity responsive target stability (DARTS), stability of proteins from rates of oxidation (SPROX), cellular thermal shift assay (CETSA), and finally, thermal proteome profiling (TPP). The TPP is based on the combination of CETSA and quantitative mass spectrometry. Among recently introduced proteomics technologies, TPP demonstrates the ability to offer detailed proteomic profiles for the large-scale analysis of protein-ligand interactions, including endogenous ligands and proteins like cofactors and metabolites. TPP facilitates the identification of the markers governing drug efficacy and toxicity and provides an unbiased measure for estimating the rate of drug-target engagement. At a glance at TPP steps, after protein extraction, the molecule is exposed to different temperatures and drug concentrations. After discarding solubilized and stabilized proteins, the protein’s identity is investigated by mass spectrometry analysis. As a result of the protein’s structural stabilization after binding to its substrate, TTP helps to accurately identify target proteins with high throughput. In this study, we aimed to introduce the basics of this method and review most recent studies on this technique.

Experiencing some early life adversity can have an "inoculating" effect that promotes resilience in adulthood. However, the mechanisms underlying stress inoculation are unknown, and animal models are lacking. Here we used the limited bedding and nesting (LBN) model of adversity to evaluate stress inoculation of addiction-related phenotypes. In LBN, pups from postnatal days 2 to 9 and their dams were exposed to a low-resource environment. In adulthood, they were tested for addiction-like phenotypes and compared to rats raised in standard housing conditions. High levels of impulsivity are associated with substance abuse, but in males, LBN reduced impulsive choice compared to controls. LBN males also self-administered less morphine and had a lower breakpoint on a progressive ratio reinforcement schedule than controls. These effects of LBN on addiction-related behaviors were not found in females. Because the nucleus accumbens (NAc) mediates these behaviors, we tested whether LBN altered NAc physiology in drug-naive and morphine-exposed rats. LBN reduced the frequency of spontaneous excitatory postsynaptic currents in males, but a similar effect was not observed in females. Only in males did LBN prevent a morphine-induced increase in the AMPA/NMDA ratio. RNA sequencing was performed to delineate the molecular signature in the NAc associated with LBN-derived phenotypes. LBN produced sex-specific changes in transcription, including in genes related to glutamate transmission. Collectively, these studies reveal that LBN causes a male-specific stress inoculation effect against addiction-related phenotypes. Identifying factors that promote resilience to addiction may reveal novel treatment options for patients.

Celecoxib, or Celebrex, a nonsteroidal anti-inflammatory drug, is one of the most common medicines for treating inflammatory diseases. Recently, it has been shown that celecoxib is associated with implications in complex diseases, such as Alzheimer disease and cancer as well as with cardiovascular risk assessment and toxicity, suggesting that celecoxib may affect multiple unknown targets. In this project, we detected targets of celecoxib within the nervous system using a label-free thermal proteome profiling method. First, proteins of the rat hippocampus were treated with multiple drug concentrations and temperatures. Next, we separated the soluble proteins from the denatured and sedimented total protein load by ultracentrifugation. Subsequently, the soluble proteins were analyzed by nano-liquid chromatography tandem mass spectrometry to determine the identity of the celecoxib-targeted proteins based on structural changes by thermal stability variation of targeted proteins toward higher solubility in the higher temperatures. In the analysis of the soluble protein extract at 67°C, 44 proteins were uniquely detected in drug-treated samples out of all 478 identified proteins at this temperature. Ras-associated binding protein 4a, 1 out of these 44 proteins, has previously been reported as one of the celecoxib off targets in the rat central nervous system. Furthermore, we provide more molecular details through biomedical enrichment analysis to explore the potential role of all detected proteins in the biologic systems. We show that the determined proteins play a role in the signaling pathways related to neurodegenerative disease-and cancer pathways. Finally, we fill out molecular supporting evidence for using celecoxib toward the drug-repurposing approach by exploring drug targets. SIGNIFICANCE STATEMENT: This study determined 44 off-target proteins of celecoxib, a nonsteroidal anti-inflammatory and one of the most common medicines for treating inflammatory diseases. It shows that these proteins play a role in the signaling pathways related to neurodegenerative disease and cancer pathways. Finally, the study provides molecular supporting evidence for using celecoxib toward the drug-repurposing approach by exploring drug targets.

Phthalates are widely used in polymer science and have potential toxicity related to their chemical structures. However, lots of evidence indicate that phthalate derivatives are undoubtedly produced as secondary metabolites by organisms, including plants, animals, and microorganisms. In the present study, Bacillus velezensis strain RP137 was cultured under optimized conditions. Its biomass was extracted with ethyl acetate with one fraction showing cytotoxic properties. A pure compound was isolated from the active fraction using combined silica gel and LH20 size exclusion column chromatography. Structural evaluation including FT-IR, 1H NMR, 13C NMR, HR-MS and CHN analysis identified the purified compound as di(2-ethylhexyl)phthalate (DEHP) with the formula C24H38O4 and the molecular weight of 389.29 Da. The microorganism-derived (stereospecific) DEHP was strongly reduced the proliferation and induced cytotoxic effects on various eukaryotic cell lines in compare to the synthetic racemic mixture of the compound when assessed by MTT assay. Furthermore, crystal violet assay and morphological changes confirmed the cytotoxic effect of DEHP. Interestingly, non-malignant SV40-immortalized fibroblast cells were less affected by the purified DEHP. Further evaluation on the antibacterial activity of DEHP documented no effect toward Gram-positive (S. aureus) and Gram-negative (E. coli and P. aeruginosa) pathogens even at a high concentration of 100 μM. In conclusion, existence of DEHP as byproduct of microorganism's metabolism can seriously be considered as a warning to human health.

Due to the rapid emergence of multi-resistant bacterial strains in recent decades, the commercially available effective antibiotics are becoming increasingly limited. On the other hand, widespread antimicrobial peptides (AMPs) such as the lantibiotic nisin has been used worldwide for more than 40 years without the appearance of significant bacterial resistance. Lantibiotics are ribosomally synthesized antimicrobials generated by posttranslational modifications. Their biotechnological production is of particular interest to redesign natural scaffolds improving their pharmaceutical properties, which has great potential for therapeutic use in human medicine and other areas. However, conventional protein engineering methods are limited to 20 canonical amino acids prescribed by the genetic code. Therefore, the expansion of the genetic code as the most advanced approach in Synthetic Biology allows the addition of new amino acid building blocks (non-canonical amino acids, ncAAs) during protein translation. We now have solid proof-of-principle evidence that bioexpression with these novel building blocks enabled lantibiotics with chemical properties transcending those produced by natural evolution. The unique scaffolds with novel structural and functional properties are the result of this bioengineering. Here we will critically examine and evaluate the use of the expanded genetic code and its alternatives in lantibiotics research over the last 7 years. We anticipate that Synthetic Biology, using engineered lantibiotics and even more complex scaffolds will be a promising tool to address an urgent problem of antibiotic resistance, especially in a class of multi-drug resistant microbes known as superbugs.

Celecoxib is one of the most common medicines for treating inflammatory diseases. Recently, it has been shown that celecoxib is associated with implications in complex diseases such as Alzheimer’s disease and cancer, as well as with cardiovascular risk assessment and toxicity, suggesting that celecoxib may affect multiple unknown targets. In this project, we detected targets of celecoxib within the nervous system using a label-free TPP (Thermal Proteome Profiling) method. First, proteins of the rat hippocampus were treated with multiple drug concentrations and temperatures. Next, we separated the soluble proteins from the denatured and sedimented total protein load by ultracentrifugation. Subsequently, the soluble proteins were analyzed by nano-liquid chromatography-mass spectrometry to determine the identity of the celecoxib targeted proteins based on structural changes by thermal stability variation of targeted proteins towards higher solubility in the higher temperatures. In the analysis of the soluble protein extract at 67 centigrade, 44 proteins were uniquely detected in drug-treated samples out of all 478 identified proteins at this temperature. Rab4a, one out of these 44 proteins, has previously been reported as one of the celecoxib off-targets in the rat CNS. Furthermore, we provide more molecular details through biomedical enrichment analysis to explore the potential role of all detected proteins in the biological systems. We show that the determined proteins play a role in the signaling pathways related to neurodegenerative disease - and cancer pathways. Finally, we fill out molecular supporting evidence for using celecoxib towards the drug repurposing approach by exploring drug targets. Significance Statement In this study, we determined forty-four off-target proteins of celecoxib, a non-steroidal anti-inflammatory, and one of the most common medicines for treating inflammatory diseases. We showed that these proteins play a role in the signaling pathways related to neurodegenerative disease and cancer pathways. Finally, we provided molecular supporting evidence for using celecoxib towards the drug repurposing approach by exploring drug targets.

Studying relationships among gene-product expression profiles is a common approach in systems biology. Many studies have generalized this subject to different levels of the central dogma information flow and assumed correlation of transcript and protein expression levels. All these efforts have updated the signaling network models and expanded the current signaling databases, which include interactions among the gene-products extracted based on either the literature or direct and indirect experiments. In fact, due to unavailability or high-cost of the experiments, most of the studies do not look for the direct interactions (gene-protein or protein-protein) and some of them are contradictory. In addition, it is now a standard practice to undertake enrichment analysis on biological annotations especially in omics research to make claims about the potentially implicated biological pathways in disease. Specifically, upon identifying differentially expressed genes, molecular mechanistic insights are proposed based on statistically enriched biological processes for disease etiology and drug discovery. However, it remains to be demonstrated that expression data may be used as a reliable source to infer causal relationships among gene pairs. In this study, using four common and comprehensive databases i.e. GEO, GDSC, KEGG, and OmniPath, we extracted all relevant gene expression data and all relationships among directly linked gene pairs in order to evaluate the rate of coherency or sign consistency. We illustrated that the signaling network was not more consistent or coherent with the measured expression profile compare to random relationships. Finally, we provided the pieces of evidence and concluded that gene-product expression data, especially at the transcript level, are not reliable or at least insufficient to infer biological relationships among genes and in turn describe cellular behavior.

Background. Iranian traditional medicine (ITM) is a holistic medical system that uses a wide range of medicinal substances to treat disease. Reorganization and standardization of the data on ITM concepts is a necessity for optimal use of this rich source. In an initial step towards this goal, we created a database of ITM materia medica. Main Body. Primarily based on Makhzan al-Advieh, which is the most recent encyclopedia of materia medica in ITM with the largest number of monographs, a database of natural medicinal substances was created using both text mining methods and manual editing. UNaProd, a Universal Natural Product database for materia medica of ITM, is currently host to 2696 monographs, from herbal to animal to mineral compounds in 16 diverse attributes such as origin and scientific name. Currently, systems biology, and more precisely systems medicine and pharmacology, can be an aid in providing rationalizations for many traditional medicines and elucidating a great deal of knowledge they can offer to guide future research in medicine. Conclusions. A database of materia medica is a stepping stone in creating a systems pharmacology platform of ITM that encompasses the relationships between the drugs, their targets, and diseases. UNaProd is hyperlinked to IrGO and CMAUP databases for Mizaj and molecular features, respectively, and it is freely available at http://jafarilab.com/unaprod/.

In the present work, biosurfactant production of the bacterial strain Stenotrophomonas sp. IE-93 was surveyed and quantified through four conventional screening methods. The biosurfactant produced by the strain IE-93 could reduce the surface tension to 24 mN m−1 and showed 100% emulsification activity when equal volume of n-hexane and fermentation medium was applied. Effects of culture conditions on productivity of the strain revealed that olive oil and ammonium sulfate were the best carbon and nitrogen sources, respectively. The crude produced biosurfactant showed a good stability during exposure to high temperatures (up to 120 °C), high salinity (up to 20% NaCl) and a wide range of pHs (2.0–12.0). Purification of the biosurfactant was performed using ethyl acetate, and crude extract was separated on silica gel column chromatography. The chemical characterization of the purified biosurfactant by FTIR spectroscopy revealed that it has a lipopeptide nature. Moreover, ultraviolet mutation of Stenotrophomonas sp. IE-93 yielded a stable mutant that produced over 1.7-fold more of the biosurfactant than the parent strain. Overall, the results suggest that Stenotrophomonas sp. IE-93 could be suitable candidate to use in various industrial processes needing emulsifier, especially in oil industry which needs a stable surfactant in high temperature and salinity conditions.

Production of the optically pure enantiomers has attracted much attention for both agrochemicals and drugs due to their more target-specific feature and fewer side effects than racemic mixtures. In the case of ibuprofen, an anti-inflammatory drug, the (S)-(+)-form is remarkably active than (R)-(−)-enantiomer. Lipolytic enzymes were considered as excellent biocatalysts for enantiomeric resolution of ibuprofen. In this study, the gene encoding a thermo-halophile putative esterase/lipase/thioesterase, briefly named ELT, from Rhodothermus marinus DSM 4252 was cloned and overexpressed in Escherichia coli. Reusability of the enzyme was provided by the immobilization onto biocompatible supports of SiO2 and chitosan coated Fe3O4-nanoparticles (CS-MNPs). Immobilized enzymes were recovered from the reaction mixture and employed to catalyze at least ten reactions with a residual activity above 80%. The storage stability increased from 45% for the free enzyme to 75 and 92% for ELT-SiO2 and ELT-MNPs, respectively, after 14 days incubation at 25 °C. Kinetic studies showed that the ELT-SiO2 had higher substrate affinity and turnover number in comparison to the free enzyme. ELT-SiO2 and ELT-MNPs showed enantioselective potential towards hydrolysis of ibuprofen ethyl ester with the conversion percent of 44 and 42% and the product enantiomeric excess of 40 and 43, respectively. The present reusable biocatalyst can be considered to obtain enantiopure ibuprofen with invaluable impact in pharmaceutical industry.

In the food industry, biocatalysts provide ecofriendly procedures to accomplish biochemical reactions with high specificity in moderate conditions. In this regard, enzymes are welcomed as process aids in food processing. Microbial lipases, especially of extremophiles, are one of the most useful enzymes for biotechnology and food industry. Accordingly, thermo-halophile GDSL lipase-encoding gene from Rhodothermus marinus, RD , was cloned and expressed in Escherichia coli . The enzyme revealed the highest hydrolytic activity (1055.3 Umg −1 ) towards p -nitrophenyl butyrate (C4) at 70 °C/pH 8.5 and retained 78.6% of its initial activity after 60 min incubation at this temperature. The enzyme was recovered by covalent immobilization on chitosan coated Fe 3 O 4 -nanoparticles (CS-MNPs) and the potential to synthesize aroma ester methyl acetate in n -hexane was investigated. The reaction yields were 22% and 67% for free and immobilized enzyme, respectively. This study provides a time-saving, economic, biocompatible and a renewable catalyst to synthesize natural flavor compounds. This biocatalyst has excellent potential in food industry and can be applied for lipid processing or to improve the aroma of foods. In addition to exhibiting good stability in high temperatures and organic solvents, RD lipase from Rhodothermus marinus can also be considered as an excellent candidate in organic synthesis in harsh industry conditions.

Background Expression patterns between males and females vary in every adult tissue, even in organs with no conspicuous dimorphisms such as the heart. While studies of male and female differences have traditionally focused on the influence of sex hormones, these do not account for all the differences at the molecular and epigenetic levels. We previously reported that a substantial number of genes were differentially expressed in male and female mouse embryonic stem (ES) cells and revealed dose-dependent enhancer activity in response to Prdm14, a key pluripotency factor expressed more highly in female ES cells. In this work, we investigated the role of Prdm14 in establishing sex-specific gene expression networks. We surveyed the sex-specific landscape in early embryogenesis with special reference to cardiac development. We generated sex-specific co-expression networks from mouse ES cells, examined the presence of sex-specific chromatin domains, and analyzed previously published datasets from different developmental time points to characterize how sex-biased gene expression waxes and wanes to evaluate whether sex-biased networks are detectable throughout heart development. Results We performed ChIP-seq on male and female mouse ES cells to determine differences in chromatin status. Our study reveals sex-biased histone modifications, underscoring the potential for the sex chromosome complement to prime the genome differently in early development with consequences for later expression biases. Upon differentiation of ES cells to cardiac precursors, we found sex-biased expression of key transcription and epigenetic factors, some of which persisted from the undifferentiated state. Using network analyses, we also found that Prdm14 plays a prominent role in regulating a subset of dimorphic expression patterns. To determine whether sex-biased expression is present throughout cardiogenesis, we re-analyzed data from two published studies that sampled the transcriptomes of mouse hearts from 8.5 days post-coitum embryos to neonates and adults. We found sex-biased expression at every stage in heart development, and interestingly, identified a subset of genes that exhibit the same bias across multiple cardiogenic stages. Conclusions Overall, our results support the existence of sexually dimorphic gene expression profiles and regulatory networks at every stage of cardiac development, some of which may be established in early embryogenesis and epigenetically perpetuated. Electronic supplementary material The online version of this article (10.1186/s13293-019-0259-1) contains supplementary material, which is available to authorized users.

We report the synthesis of some novel β-lactam hybrids of 2-mercaptobenzothiazole and benzoquinoline. These compounds were synthesized by a [2 + 2]-cycloaddition reaction of imines 8a-d and ketenes derived from substituted acetic acids. The reaction was totally diastereoselective leading exclusively to the formation of cis-β-lactams 10a-m. All products were obtained in good to excellent yields and their structures were established based on IR, 1H NMR, 13C NMR spectral data and elemental analysis. Schiff bases 8a-d and β-lactam hybrids 10a-m were evaluated for antimicrobial activities against six bacterial species. The minimum inhibitory concentration (MIC) values indicate that two of the β-lactams, 10k and 10m, have good activities against the two Gram-negative bacteria, E. coli and P. aeruginosa, while three of the Schiff bases, 8a-c, are active against P. aeruginosa and the Gram-positive pathogen S. aureus. The molecular and cellular basis for these observed antibacterial properties are not determined. Moreover, the five most active compounds showed acceptably low cytotoxicity (less than 25% cell growth inhibition after 72 h of incubation) against the MCF-7 cell line, and below 10% in vitro hemolytic activity at 50 and 200 µM concentrations. These results suggest a need for further inquiry into the reason for why these compounds are bioactive, and as to what their full biological activities and antibiotic potential may be. The cis stereochemistry of β-lactam 10a was confirmed by X-ray crystallographic studies.

In the present work, we investigated the prodiginine family as secondary metabolite members. Bacterial strain S2B, with the ability to produce red pigment, was isolated from the Sarcheshmeh copper mine in Iran. 16S rDNA gene sequencing revealed that the strain was placed in the Serratia genus. Pigment production was optimized using low-cost culture medium and the effects of various physicochemical factors were studied via statistical approaches. Purification of the produced pigment by silica gel column chromatography showed a strong red pigment fraction and a weaker orange band. Mass spectrometry, FT-IR spectroscopy and (1)H NMR analysis revealed that the red pigment was prodigiosin and the orange band was a prodigiosin-like analog, with molecular weights of 323 and 317 Da, respectively. Genotoxicity and cytotoxicity studies confirmed their membership in the prodiginine family. Analysis of the production pattern of the pigments in the presence of different concentrations of ammonium salts revealed the role of sulfate as an important factor in regulation of the pigment biosynthesis pathway. Overall, the data showed that regulation of the pigment biosynthesis pathway in Serratia sp. strain S2B was affected by inorganic micronutrients, particularly the sulfate ions.

Some new water soluble complexes [N,N'-bis{5-[(triphenyl phosphonium chloride)-methyl]salicylidine}-3,4-diaminopyridine] M(ii), which are formulated as nano-[Zn(5-CH2PPh3-3,4-salpyr)](ClO4)2 (), [Zn(5-CH2PPh3-3,4-salpyr)](ClO4)2 (), nano-[Ni(5-CH2PPh3-3,4-salpyr)](ClO4)2 (), [Ni(5-CH2PPh3-3,4-salpyr)](ClO4)2 (), and [N,N'-bis{5-[(triphenyl phosphonium chloride)-methyl]salicylidine}-2,3-diaminopyridine]Ni(ii) [Ni(5-CH2PPh3-2,3-salpyr)](ClO4)2 () have been isolated and characterized by elemental analysis, FT-IR, (1)H NMR, (13)C NMR, (31)P NMR, and UV-vis spectroscopy. The morphology and size of the nano complexes were determined using FE-SEM and TEM. In vitro DNA binding studies were investigated by UV-vis absorption spectroscopy, viscosity measurements, CD spectroscopy, cyclic voltammetry, emission spectra and gel electrophoresis, which suggest that the metal complexes act as efficient DNA binders. The absorption spectroscopy of the compounds with DNA reveals that the DNA binding affinity (Kb) has this order: > > > > > Ligand. The metal complexes show DNA binding stronger than the ligand, which is expected due to the nature of the metal. The nano complexes display DNA binding stronger than the other complexes which is related to the effect of size on binding affinity and the Ni(ii) complexes reveal DNA binding stronger than the corresponding Zn(ii) analogues, which is expected due to their z* effect and geometry. The prominent double strand DNA cleavage abilities of compound are observed in the absence of H2O2 with efficiencies of more than 50% even at 70 μM complex concentration. Surprisingly, Zn(ii) complexes (compounds & ) exhibit a higher cytotoxicity (IC50: 7.3 & 10.9 μM at 24 h; IC50: 4.6 & 8.7 μM at 48 h) against human hepatoma (HepG2) and HeLa cell lines than the Ni(ii) complexes (compounds , & ) and 5-fluorouracil as control in spite of their inability to cleave DNA. Finally, DNA binding interactions were performed by docking studies. Density functional theory (DFT) studies were performed using the GAUSSIAN 03 program. The DFT method with B3LYP functional, LANL2DZ basis set for metal centers and 6-311g* for other atoms was used. The synthesized compounds and DNA were simulated by molecular docking to explore more details of the ligands conformation and their orientations in the active site of the receptor.

Based on the importance of central metal complexes to interact with DNA, in this research focused on synthesis of some new water soluble Mn(II) complexes 1-4 which modified substituted in ligand at the same position with N, Me, H, and Cl. These complexes were isolated and characterized by elemental analyses, FT-IR, electrospray ionization mass spectrometry (ESI-MS) and UV-vis spectroscopy. DNA binding studies had been studied by using circular dichroism (CD) spectroscopy, UV-vis absorption spectroscopy, cyclic voltammetry (CV), viscosity measurements, emission spectroscopy and gel electrophoresis which proposed the metal buildings go about as effective DNA binders were studied in the presence of Fish-DNA (FS-DNA) which showed the highest binding affinity to DNA with hydrophobic and electron donating substituent. Cell toxicity assays against two human leukemia (Jurkat) and breast cancer (MCF-7) cell lines showed that the complex 3 exhibited a remarkable effects equal to a famous anticancer drug, cisplatin that high cytotoxic activity strongly depend on the hydrophobic substituted ligand. In the theoretical part, density functional theory (DFT) was performed to optimize the geometry of complexes through IR and UV spectra of the complexes that ligand substitution did not affect the geometry and theoretical IR and UV spectra showed good resemblance to the experimental data. The docking studies calculated the lowest-energy between complexes and DNA with the minor grooves mode.

Aim: Analysis reconstruction networks from two diseases, NAFLD and Alzheimer`s diseases and their relationship based on systems biology methods. Background: NAFLD and Alzheimer`s diseases are two complex diseases, with progressive prevalence and high cost for countries. There are some reports on relation and same spreading pathways of these two diseases. In addition, they have some similar risk factors, exclusively lifestyle such as feeding, exercises and so on. Therefore, systems biology approach can help to discover their relationship. Methods: DisGeNET and STRING databases were sources of disease genes and constructing networks. Three plugins of Cytoscape software, including ClusterONE, ClueGO and CluePedia, were used to analyze and cluster networks and enrichment of pathways. An R package used to define best centrality method. Finally, based on degree and Betweenness, hubs and bottleneck nodes were defined. Results: Common genes between NAFLD and Alzheimer`s disease were 190 genes that used construct a network with STRING database. The resulting network contained 182 nodes and 2591 edges and comprises from four clusters. Enrichment of these clusters separately lead to carbohydrate metabolism, long chain fatty acid and regulation of JAK-STAT and IL-17 signaling pathways, respectively. Also seven genes selected as hub-bottleneck include: IL6, AKT1, TP53, TNF, JUN, VEGFA and PPARG. Enrichment of these proteins and their first neighbors in network by OMIM database lead to diabetes and obesity as ancestors of NAFLD and AD. Conclusion: Systems biology methods, specifically PPI networks, can be useful for analyzing complicated related diseases. Finding Hub and bottleneck proteins should be the goal of drug designing and introducing disease markers.

Alzheimer’s disease (AD) is a complex neurodegenerative disease with various deleterious perturbations in regulatory pathways of various brain regions. Thus, it would be critical to understanding the role of different regions of the brain in initiation and progression of AD, However, owing to complex and multifactorial nature of this disease, the molecular mechanism of AD has yet to be fully elucidated. To confront with this challenge, we launched a meta-analytical study of current transcriptomics data in four different regions of the brain in AD (Entorhinal, Hippocampus, Temporal and Frontal) with systems analysis of identifying involved signaling and metabolic pathways. We found different regulatory patterns in Entorhinal and Hippocampus regions to be associated with progression of AD. We also identified shared versus unique biological pathways and critical proteins among different brain regions. ACACB, GAPDH, ACLY, and EGFR were the most important proteins in Entorhinal, Frontal, Hippocampus and Temporal regions, respectively. Moreover, eight proteins including CDK5, ATP5G1, DNM1, GNG3, AP2M1, ALDOA, GPI, and TPI1 were differentially expressed in all four brain regions, among which, CDK5 and ATP5G1 were enriched in KEGG Alzheimer’s disease pathway as well.

Ionic liquids (ILs) are considered as green alternatives to organic solvents in various enzymatic biotechnological processes. A wide variety of hydrophilic and hydrophobic ionic liquids have been synthesized in order to investigate their effects on both enzyme activity and stability. In most cases, hydrophobic ILs such as those containing PF6⿿ anion have shown better performances in enzymatic reactions. In the present work, the effect of alkyl chain length of [CnMIM][Br] (n = 2, 4, 6, 12) on hydrolytic activity of Thermoanaerobacter thermohydrosulfuricus lipase (TTL), as a model enzyme, was evaluated and compared with [C4MIM][PF6] as a hydrophobic ionic liquid. Moreover, effect of hydrophilic ILs on the activity and thermal stability of TTL in different concentrations of ionic liquids was studied. The results showed that TTL had the highest lipase activity in the presence of 0.3 M [C2MIM][Br], 1 M [C4MIM][Br] and 0.3 M [C6MIM][Br]. However, no significant effect was revealed in the presence of [C12MIM][Br]. A comparison between the effects of [C4MIM][PF6] and [C4MIM][Br] on the TTL thermostability at 85 °C and 90 °C revealed that the hydrophobic anion PF6⿿ provided a good stabilizing effect for TTL; although the influence of hydrophilic functions is also promising. According to the findings, it could be concluded that the TTL and probably similar enzymes can be used for several biotransformation reactions by tuning the hydrophilic ionic liquids concentrations as solvents.

Highly diastereoselective synthesis of some novel benzothiazole-substituted beta-lactam hybrids was achieved starting from (benzo[d]thiazol-2-yl)phenol as an available precursor. This is the first time (benzo[d]thiazol-2-yl)phenoxyacetic acid has been used as ketene source in synthesizing monocyclic 2-azetidinones. These compounds were evaluated for their antimicrobial activities against a large panel of Gram-positive and Gram-negative bacterial strains and moderate activities were encountered. Antimalarial data revealed that adding methoxyphenyl or ethoxyphenyl group on the beta-lactam ring makes compounds that are more potent. Moreover, hemolytic activity and mammalian cell toxicity survey of the compounds showed their potential as a medicine. (C) 2017 Elsevier Masson SAS. All rights reserved.

Background: Pectinases are pectin degrading class of enzymes including polygalacturonase (PG), polymethyl galacturonase (PMG), pectate lyase (PEL), and pectin esterase (PE) that are commonly used in processes involving the degradation of plant materials, such as speeding up the extraction of fruit juices. Objectives: A highly methylated pectin degrading bacterium from soil covered with fruit waste was isolated and its extracellular pectinase as a novel polymethyl galacturonase was characterized. Materials and Methods: Pectin-degrading microorganism screening was performed using agar plates containing pectin as the sole carbon source. The biochemical studies were used to characterize the enzyme. Results: Bacterium with greater PMG activity was a Bacillus sp. based on 16S rDNA sequence analysis and named as a Bacillus sp. strain BR1390. Two steps column chromatography showed a dimeric protein with apparent molecular masses of 104 and 56 kDa, evident by gel filtration and SDS-PAGE. Substrate specificity analysis using various polygalacturonic acid compounds revealed its polymethyl galacturonase (PMG, EC 3.2.1.-) activity. Biochemical studies represent the thermophilic characteristics and reasonable pH stability of the polymethyl galacturonase when using pectin as substrate. The PMG activity significantly enhanced in the presence of most divalent cations such as Ca2+ and Mg2+, but Hg2+ and Fe3+ served as strong inhibitor. Conclusions: Overall, regarding to have suitable activity in acidic conditions and high operational stability of the purified pectinase, the introduced PMG can be an ideal functional substitute for applications in the fruit juice industry, especially in citrus fruits extraction and clarification.