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Sus scrofa or pig was domesticated thousands of years ago. Through various indigenous breeds, different phenotypes were produced such as Chinese inbred miniature minipig or Wuzhishan pig (WZSP), which is broadly used in the life and medical sciences. The whole genome of WZSP was sequenced in 2012. Through a bioinformatics study of pig carbonic anhydrase (CA) sequences, we detected some β- and γ-class CAs among the WZSP CAs annotated in databases, while β- or γ-CAs had not previously been described in vertebrates. This finding urged us to analyze the quality of whole genome sequence of WZSP for the possible bacterial contamination. In this study, we used bioinformatics methods and web tools such as UniProt, European Bioinformatics Institute, National Center for Biotechnology Information, Ensembl Genome Browser, Ensembl Bacteria, RSCB PDB and Pseudomonas Genome Database. Our analysis defined that pig has 12 classical α-CAs and 3 CA-related proteins. Meanwhile, it was approved that the detected CAs in WZSP are categorized in the β- and γ-CA families, which belong to Pseudomonas spp. and Acinetobacter spp. The protein structure study revealed that the identified β-CA sequence from WZSP belongs to Pseudomonas aeruginosa with PDB ID: 5JJ8, and the identified γ-CA sequence from WZSP belongs to P. aeruginosa with PDB ID: 3PMO. Bioinformatics and computational methods accompanied with bacterial-specific markers, such as 16S rRNA and β- and γ-class CA sequences, can be used to identify bacterial contamination in mammalian DNA samples. [ABSTRACT FROM AUTHOR]

Genomic islands (GIs) are a type of mobile genetic element (MGE) that are present in bacterial chromosomes. They consist of a cluster of genes that produce proteins that contribute to a variety of functions, including, but not limited to, the regulation of cell metabolism, antimicrobial resistance, pathogenicity, virulence, and resistance to heavy metals. The genes carried in MGEs can be used as a trait reservoir in times of adversity. Transfer of genes using MGEs, occurring outside reproduction, is called horizontal gene transfer (HGT). Previous data have shown that numerous HGT events have occurred through endosymbiosis between prokaryotes and eukaryotes. β-Carbonic anhydrase (β-CA) enzymes play a critical role in the biochemical pathways of many prokaryotes and eukaryotes. We previously suggested the horizontal transfer of β-CA genes from plasmids of some prokaryotic endosymbionts to their protozoan hosts. In this study, we set out to identify β-CA genes that might have been transferred between prokaryotic and protist species through HGT in GIs. Therefore, we investigated prokaryotic chromosomes containing β-CA-encoding GIs and utilized multiple bioinformatics tools to reveal the distinct movements of β-CA genes among a wide variety of organisms. Our results identify the presence of β-CA genes in GIs of several medically and industrially relevant bacterial species, and phylogenetic analyses reveal multiple cases of likely horizontal transfer of β-CA genes from GIs of ancestral prokaryotes to protists. [ABSTRACT FROM AUTHOR]

Background: A parasitic roundworm, Ascaris lumbricoides, is the causative agent of ascariasis, with approximately 760 million cases around the world. Helminthic infections occur with a high prevalence mostly in tropical and developing xcountries. Therefore, design of affordable broad-spectrum anti-helminthic agents against a variety of pathogens, including not only A. lumbricoides but also hookworms and whipworms, is desirable. Beta carbonic anhydrases (β-CAs) are considered promising targets of novel anthelminthics because these enzymes are present in various parasites, while completely absent in vertebrates. Methods: In this study, we identified an A. lumbricoides β-CA (AIBCA) protein from protein sequence data using bioinformatics tools. We used computational biology resources and methods (including InterPro, CATH/Gene3D, KEGG, and METACYC) to analyze AlBCA and define potential roles of this enzyme in biological pathways. The AlBCA gene was cloned into pFastBac1, and recombinant AIBCA was produced in sf-9 insect cells. Kinetics of AlBCA were analyzed by a stopped-flow method. Results: Multiple sequence alignment revealed that AIBCA contains the two sequence motifs, CXDXR and HXXC, typical for β-CAs. Recombinant AIBCA showed significant CA catalytic activity with kcat of 6.0 × 105 s-1 and kcat/KM of 4.3 × 107 M-1 s-1. The classical CA inhibitor, acetazolamide, showed an inhibition constant of 84.1 nM. Computational modeling suggests that the molecular architecture of AIBCA is highly similar to several other known β-CA structures. Functional predictions suggest that AIBCA might play a role in bicarbonate-mediated metabolic pathways, such as gluconeogenesis and removal of metabolically produced cyanate. Conclusions: These results open new avenues to further investigate the precise functions of β-CAs in parasites and suggest that novel β-CA specific inhibitors should be developed and tested against helminthic diseases. [ABSTRACT FROM AUTHOR]

The present study was carried out to investigate the effect of γ-irradiation at two irradiation doses of 10 and 25 kGy, on the antibacterial activities of cumin essential oils (E.Os) in vitro and in vivo systems. For this purpose, the cumin seeds were irradiated with Co60 source (0, 10 and 25 kGy) and subjected to Clevenger extraction to obtain E.Os. In vitro antibacterial activities of cumin E.Os was determined on Gram-negative and Gram-positive bacterial strains including E. coli, P. aeroginosa, B. cereus and S. aureus using agar well diffusion method, disk diffusion method and, MIC and MBC determinations. In vivo antibacterial activity was performed on polymicrobial infection induced by cecal ligation and puncture (CLP) in rat through blood colony forming units (CFUs) determination. The results showed that CLP operation caused a marked increase in bacterial load of blood which was reduced in rats treated with fresh and irradiated cumin oils. In vitro results also showed the sensitivity of all tested bacterial strains against the fresh and irradiated cumin E.Os. These data may suggest that cumin E.O has potential antibacterial activity both in vivo and in vitro systems. Also, γ-irradiation to cumin seeds at 10 and 25 kGy has no significant effects on the antibacterial properties of cumin E.Os. [ABSTRACT FROM AUTHOR]

Background: The genomes of many insect and parasite species contain beta carbonic anhydrase (β-CA) protein coding sequences. The lack of β-CA proteins in mammals makes them interesting target proteins for inhibition in treatment of some infectious diseases and pests. Many insects and parasites represent important pests for agriculture and cause enormous economic damage worldwide. Meanwhile, pollution of the environment by old pesticides, emergence of strains resistant to them, and their off-target effects are major challenges for agriculture and society. Methods: In this study, we analyzed a multiple sequence alignment of 31 β-CAs from insects, some parasites, and selected plant species relevant to agriculture and livestock husbandry. Using bioinformatics tools a phylogenetic tree was generated and the subcellular localizations and antigenic sites of each protein were predicted. Structural models for β-CAs of Ancylostoma caninum, Ascaris suum, Trichinella spiralis, and Entamoeba histolytica, were built using Pisum sativum and Mycobacterium tuberculosis β-CAs as templates. Results: Six β-CAs of insects and parasites and six β-CAs of plants are predicted to be mitochondrial and chloroplastic, respectively, and thus may be involved in important metabolic functions. All 31 sequences showed the presence of the highly conserved β-CA active site sequence motifs, CXDXR and HXXC (C: cysteine, D: aspartic acid, R: arginine, H: histidine, X: any residue). We discovered that these two motifs are more antigenic than others. Homology models suggested that these motifs are mostly buried and thus not well accessible for recognition by antibodies. Conclusions: The predicted mitochondrial localization of several β-CAs and hidden antigenic epitopes within the protein molecule, suggest that they may not be considered major targets for vaccines. Instead, they are promising candidate enzymes for small-molecule inhibitors which can easily penetrate the cell membrane. Based on current knowledge, we conclude that β-CAs are potential targets for development of small molecule pesticides or anti-parasitic agents with minimal side effects on vertebrates. [ABSTRACT FROM AUTHOR]

With the increase in CO2 emissions worldwide and its dire effects, there is a need to reduce CO2 concentrations in the atmosphere. Alpha-carbonic anhydrases (α-CAs) have been identified as suitable sequestration agents. This study reports the sequence and structural analysis of 15 α-CAs from bacteria, originating from hydrothermal vent systems. Structural analysis of the multimers enabled the identification of hotspot and interface residues. Molecular dynamics simulations of the homo-multimers were performed at 300 K, 363 K, 393 K and 423 K to unearth potentially thermostable α-CAs. Average betweenness centrality (BC) calculations confirmed the relevance of some hotspot and interface residues. The key residues responsible for dimer thermostability were identified by comparing fluctuating interfaces with stable ones, and were part of conserved motifs. Crucial long-lived hydrogen bond networks were observed around residues with high BC values. Dynamic cross correlation fortified the relevance of oligomerization of these proteins, thus the importance of simulating them in their multimeric forms. A consensus of the simulation analyses used in this study suggested high thermostability for the α-CA from Nitratiruptor tergarcus. Overall, our novel findings enhance the potential of biotechnology applications through the discovery of alternative thermostable CO2 sequestration agents and their potential protein design. [ABSTRACT FROM AUTHOR]

Schistosoma mansoni is an intestinal parasite with one β-class carbonic anhydrase, SmaBCA. We report the sequence enhancing, production, catalytic activity, and inhibition results of the recombinant SmaBCA. It showed significant catalytic activity on CO2 hydration in vitro with kcat 1.38 × 105 s−1 and kcat/Km 2.33 × 107 M−1 s−1. Several sulphonamide inhibitors, from which many are clinically used, showed submicromolar or nanomolar inhibitory effects on SmaBCA. The most efficient inhibitor with a KI of 43.8 nM was 4-(2-amino-pyrimidine-4-yl)-benzenesulfonamide. Other effective inhibitors with KIs in the range of 79.4–95.9 nM were benzolamide, brinzolamide, topiramate, dorzolamide, saccharin, epacadostat, celecoxib, and famotidine. The other tested compounds showed at least micromolar range inhibition against SmaBCA. Our results introduce SmaBCA as a novel target for drug development against schistosomiasis, a highly prevalent parasitic disease. [ABSTRACT FROM AUTHOR]

Alveolar soft part sarcoma (ASPS) is a highly aggressive rare soft tissue sarcoma (STS) with poor prognosis especially in the metastatic form. ASPS is resistant to standard chemotherapy. Although, early diagnosis and surgical resection of operable tumor could lead to improved patient survival but novel treatment options are needed for advanced (metastatic) ASPS. This malignancy exhibits highly angiogenic behavior which reflects hyper-activation and over expression of angiogenic factors. Understanding the molecular events in this type of sarcoma is important in finding novel molecular based targeted therapies. We aim to review molecular aspects of ASPS growth and treatment. [ABSTRACT FROM AUTHOR]

Regulfatory T cells (Tregs) and myeloid‐derived suppressor cells (MDSCs) are common immunosuppressive cells in the tumor microenvironment. These cells, through various mechanisms, inhibit antitumor immune responses and impede effective therapies. Therefore, designing an efficient protocol for inducing immune surveillance in tumors is highly recommended. Recently, nanoliposomes have provided broad‐spectrum and state‐of‐the‐art vehicles to deliver antigens or immune system compartments in immunotherapies. It has been shown that different lipids in the structure of liposomes and various liposomal formulations can affect immune responses in the tumor microenvironment. This study was aimed to evaluate the effects of four different liposomal formulations on MDSCs and Tregs in C26 tumor‐bearing mice. To this end, after preparing liposomes, they were injected into tumor‐inoculated mice and analyzed MDSC and Treg population and functions in spleen and tumor tissues. Results showed that 1,2‐dioleoyl‐3‐trimethylammonium propane (DOTAP)‐containing liposomes reduced MDSC population and activity in the spleen, but not tumor, compared with other groups significantly (p < 0.05 and p < 0.01, respectively). Moreover, DOTAP‐containing liposomes reduced the expression of S100A8 and arginase‐1 genes in splenic MDSCs (p < 0.05). In conclusion, we provided evidence that DOTAP‐containing liposomes contributed to stimulating immune responses and provided a situation to inhibit immunosuppression in the tumor microenvironment. [ABSTRACT FROM AUTHOR]

We report the production and biochemical characterization of an α-carbonic anhydrase (LrhCA) from gram-positive probiotic bacteria Lactobacillus rhamnosus GG. CAs form a family of metalloenzymes that catalyze hydration of CO2/interconversion between CO2 and water to bicarbonate ions and protons. They are divided into eight independent gene families (α, β, γ, δ, ζ, η, θ, and ι). Interestingly, many pathogens have been identified with only β- and/or γ-CAs, which can be targeted with CA-specific inhibitors (CAIs) acting as anti-pathogen drugs. Since it is important to study the potential off-target effects of CAIs for both the human body and its commensal bacteria, we took L. rhamnosus GG as our study subject. To date, only a single α-CA has been identified in L. rhamnosus GG, which was successfully produced and biochemically characterized. LrhCA showed moderate catalytic activity with the following kinetic parameters: kcat of 9.86 × 105 s−1 and kcat/KM of 1.41 × 107 s−1 M−1. Moderate inhibition was established with 11 of the 39 studied sulfonamides. The best inhibitors were 5-((4-aminophenyl)sulfonamido)-1,3,4-thiadiazole-2-sulfonamide, 4-(2-hydroxymethyl-4-nitrophenyl-sulfonamidoethyl)-benzenesulfonamide, and benzolamide with Ki values of 319 nM, 378 nM, and 387 nM, respectively. The other compounds showed weaker inhibitory effects. The Ki of acetazolamide, a classical CAI, was 733 nM. In vitro experiments with acetazolamide showed that it had no significant effect on cell growth in L. rhamnosus GG culture. Several sulfonamides, including acetazolamide, are in use as clinical drugs, making their inhibition data highly relevant to avoid any adverse off-target effects towards the human body and its probiotic organisms. Key points: • The α-carbonic anhydrase from Lactobacillus rhamnosus GG (LrhCA) is 24.3 kDa. • LrhCA has significant catalytic activity with a kcat of 9.9 × 105 s-1. • Acetazolamide resulted in a marginal inhibitory effect on cell growth. [ABSTRACT FROM AUTHOR]

Background: Niemann-Pick disease type C (NPC) is a rare lysosomal neurovisceral storage disease caused by mutations in the NPC 1 (95%) or NPC2 (5%) genes. The products of NPC1 and NPC2 genes play considerable roles in glycolipid and cholesterol trafficking, which could consequently lead to NPC disease with variable phenotypes displaying a broad spectrum of symptoms. Materials: In the present study 35 Iranian NPC unrelated patients were enrolled. These patients were first analysed by the Filipin Staining test of cholesterol deposits in cells for NPC diagnostics. Genomic DNA was extracted from the samples of peripheral blood leukocytes in EDTA following the manufacturer's protocol. All exon–intron boundaries and coding exons of the NPC1gene were amplified by polymerase chain reaction (PCR) using appropriate sets of primers. Thereafter, the products of PCR were sequenced and analysed using the NCBI database (https://blast.ncbi.nlm.nih.gov/Blast.cgi). The variants were reviewed by some databases including the Human Gene Mutation Database (HGMD) (http://www.hgmd.cf.ac.uk/ac/index.php) and ClinVar (https://www.ncbi.nlm.nih.gov/clinvar (. Moreover, all the variants were manually classified in terms of the American College of Medical Genetics and Genomics (ACMG) guideline. Results: The sequence analysis revealed 20 different variations, 10 of which are new, including one nonsense mutation (c.406C > T); three small deletions, (c.3126delC, c.2920_2923delCCTG, and c.2037delG); and six likely pathogenic missense mutations, (c.542C > A, c.1970G > A, c.1993C > G, c.2821 T > C, c.2872C > G, and c.3632 T > A). Finally, the pathogenicity of these new variants was determined using the ACMG guidelines. Conclusion: The present study aimed to facilitate the prenatal diagnosis of NPC patients in the future. In this regard, we identified 10 novel mutations, and verified that the majority of them occurred in six NPC1 exons (5, 8, 9, 13, 19, and 21), that should be considered with a high priority for Iranian patients' cost-effective evaluation. [ABSTRACT FROM AUTHOR]

This study aimed to detect the presence of Acanthamoeba spp. in different water resources of Zahedan, southeast of Iran, and also systematically reviewed all publications regarding Acanthamoeba in Iran (2005-2018). Fifty water samples were collected from different water resources in Zahedan. The positive samples were identified morphologically and subjected to polymerase chain reaction (PCR) using fragments of 18S rRNA. In the systematic review, data collection using particular terms was carried out using the following electronic databases including Science Direct, ISI Web of Science, MEDLINE, EBSCO, Scopus, and Google Scholar. A total of 17 (34%) samples were positive for Acanthamoeba spp., and nucleotide sequencing indicated that 15 samples (88.23%) belonged to the T4 genotype and the rest belonged to the T5 genotype. A total of 39 studies reported genotyping of Acanthamoeba spp. from various geographical areas of Iran and revealed that T4 (35 studies), T5 (19 studies), T3 (11 studies), T11 (8 studies), and T2 (6 studies) genotypes were the most prevalent in Iran. The T4 genotype of Acanthamoeba is a prevalent free-living amoeba and widely distributed not only in Zahedan but also in other provinces of Iran. Phylogenetic analysis reveals that A. castellanii and A. griffini predominantly colocalize with the T4 genotype. [ABSTRACT FROM AUTHOR]

• Doxorubicin and Sildenafil citrate were co-loaded in nanostructured lipid carriers. • Arginyl-glycyl-aspartic acid containing nanoparticles promote uptake of drugs. • Sildenafil citrate causes higher accumulation of Doxorubicin into cells. • Sildenafil citrate reduces expression of ABCC1 and Nrf2 in cancerous cells. Resistance to anticancer agents is considered as the main cause of chemotherapy failure. This study is aimed to prepare and optimize [Doxorubicin (Dox) + Sildenafil citrate (SC)]-coloaded Arginyl-glycyl-aspartic acid (RGD)-containing nanostructured lipid carriers (NLC-RGD) to overcome multidrug resistance limitation and improve cancer treatments. Consequently, [DOX + SC]-coloaded NLC-RGD were fabricated by homogenization method and characterized by several techniques. Then, cytotoxicity, cellular uptake, apoptosis, and expression level of some multi-drug resistance related genes were evaluated in [DOX + SC]-coloaded NLC-RGD treated cells. As results, particles with nano-size, narrow size distribution and suitable encapsulation efficiency (∼56% for DOX and ∼81% for SC) were prepared. Our Results also demonstrated that co-delivery of DOX and SC by NLC-RGD promotes uptake and accumulation of drugs by integrin mediated endocytosis and possible ABC transporter inhibition. Cytotoxicity and apoptosis experiments revealed that co-delivery of DOX and SC by NLC-RGD is more effective approach for induction of apoptosis in comparison to individual treatment and delivery. Gene expression experiments revealed that SC reduces expression of ABCC1 and Nrf2. These findings indicated that NLC-RGD can be considered as an appropriate delivery system for co-delivery of DOX and SC to overcome DOX resistance to improve treatment efficacy in cancer. [ABSTRACT FROM AUTHOR]

Immune response elicited by therapeutic proteins is an important safety and efficacy issue for regulatory agencies, drug manufacturers, clinicians, and patients. Administration of therapeutic proteins can potentially induce the production of anti-drug antibodies or cell-mediated immune responses. At first, it was speculated that the immunogenicity is related to the non-human origin of these proteins. Later on, it was confirmed that the human proteins may also show immunogenicity. In this review article, we will focus on a number of factors, which play crucial roles in the human protein immunogenicity. These factors are related to the patient's status (or intrinsic properties) and molecular characteristics of the therapeutic protein's (or extrinsic properties). Furthermore, we will discuss available in silico, in vitro, and in vivo methods for the prediction of sequences, which may generate an immune response following parenteral administration of these proteins. In summary, nowadays, it is possible for drug manufacturers to evaluate the risk of immunogenicity of therapeutic proteins and implement a management plan to overcome the problems prior to proceeding to human clinical trials. [ABSTRACT FROM AUTHOR]

There are several human viruses with known potential for causing cancers including, Hepatitis B virus, Hepatitis C virus, Epstein-Barr virus, Kaposi's sarcoma herpesvirus, Human T-cell lymphotropic virus, Human papillomavirus, and Merkel cell polyomavirus. Cancer is the second leading cause of death that affects humans worldwide, especially in developing countries. Surgery, chemotherapy, and radiotherapy can cure about 60% of humans with cancer but recurrent and metastatic diseases remain a major reason for death. In recent years, understanding the molecular characteristics of cancer cells has led to the improvement of therapeutic strategies using novel emerging therapies. Oncolytic viruses with the potential of lysing cancer cells defined the field of oncolytic virology, hence becoming a biotechnology tool rather than just a cause of disease. This study mainly focused on targeting cell proliferation and death pathways in human tumor-inducing viruses by developing innovative therapies for cancer patients based on the natural oncolytic properties of reovirus. To kill tumor cells efficiently and reduce the chance of recurrence both the direct ability of reovirus infection to lyse the tumor cells and the stimulation of a potent host immune response are applied. Hence, bioengineered stem cells can be used as smart carriers to improve the efficacy of oncolytic reovirus and safety profiles. [Display omitted] [ABSTRACT FROM AUTHOR]

Hydroxyapatite nanorods were synthesized with a new strategy by mixing hydrogen (15%) and argon (85%) gas injected into hydrothermal autoclave. Calcium nitrate tetrahydrate and diammonium hydrogen phosphate solutions were used as precursors. These materials were mixed together to maintain Ca/P ratio of 1.67. The final solution pH was adjusted with ammonia solution and transferred to the autoclave for hydrothermal process. The temperature and pH were set to 180 o C and 11 respectively. Powder synthesis was carried out once without gas injection, which was 10 h. The powders synthesized at 5, 10, and 15 h by injecting the gas mixture. The synthesized powders were characterized with Fourier transform infrared spectroscopy, Field emission scanning electron microscopy, X-ray diffraction, High-resolution transmission electron microscopy, and Raman spectroscopy. The results showed that use of injected gas increased crystallinity and crystallite size. Also, the use of gas injection has increased the hardness and elastic modulus. Unlabelled Image • The crystallinity of the hydroxyapatite nanorods was increased. • Dimensions of the synthesized powders are in the nanometric range. • Gas injection caused the growth rate to increase in all directions. • Gas injection increased the elastic modulus and hardness of consolidated samples. [ABSTRACT FROM AUTHOR]