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IntroductionPlant protection products (PPPs) such as pesticides and herbicides are experiencing increased use worldwide. In the context of PPP authorization and registration, water exposure assessments (drinking water and aquatic exposure) use numerical modeling to simulate relevant hydrological processes and exposure pathways. A common practice for estimating PPP leaching to groundwater, PPP loading onto surface water via tile drainage, or PPP transport via runoff utilizes multiple one-dimensional models, each representing a separate exposure pathway. Separate analysis of individual exposure pathways can result in disparate assumptions being made that represent relative worst-case scenarios for each pathway, rather than an integrated reasonable worst-case scenario for all pathways.MethodsThe interplay between PPP degradation, leaching to groundwater, transport in tile drainage, and runoff is well-suited for simulation using an integrated surface–subsurface hydrologic and chemical fate and transport model. This study presents functionality added to HydroGeoSphere (HGS), a three-dimensional, fully integrated, surface–subsurface hydrologic model. HGS was verified against other recognized models: PRZM, HYDRUS, PEARL, PELMO, and MACRO. Added features include automatic irrigation, non-linear adsorption, temperature and soil water content-dependent degradation, and solute uptake by plant roots.Results and DiscussionHGS results for leaching of PPP mass to groundwater showed the highest correlation, lowest error, and lowest bias relative to PEARL model results. Simulation of macropore flow to tile drains in HGS produced an intermittent tile drain flow in summer that resulted in generally lower peak effluent concentrations compared to the MACRO model. Simulation of runoff in HGS produced a higher total runoff compared to the PRZM model, attributed to lower evapotranspiration in HGS. Use of the integrated HGS model resulted in a greater agreement in water balance components relative to using multiple models to simulate individual hydrologic pathways.

Statment of the Problem: Podoplanin can indicate the lymphangiogenesis. On the other hand, lymphangiogenesis affects the biological behavior of lesions. The clinical behavior of odontogenic keratocysts (OKC) and dentigerous cysts (DC) is different.Purpose: This study aimed to evaluate the immunohistochemical expression of podoplanin and to investigate lymphangiogenesis in OKCs as compared to DCs.Materials and Method: In this experimental laboratory study, sixty paraffined blocks, including 30 OKC and 30 DC samples, were examined in this study, all of which were histopathologically non-inflamed. To evaluate lymphangiogenesis, the immunohistochemi­cal reaction of D2-40 was evaluated via cytoplasmic and membrane staining of lymphatic endothelial cells. The expression of podoplanin in the epithelial cells of two cyst groups was also examined. To analyze the collected data and compare the results between the two groups of cysts, independent samples t-test, Mann-Whitney U test, and Chi-square test were performed in SPSS version 22. The significance level was set at 0.05.Results: The mean lymph node count and podoplanin expression were significantly higher in the OKC epithelium as compared to DC (P

Objective: While most of the evidence in CTO interventions emerge from Western and Japanese studies, few data have been published up today from the Middle East. Objective of this study was to evaluate technical success rates and clinical outcomes of an Iranian population undergoing CTO PCI in a tertiary referral hospital. Moreover, we sought to evaluate the efficacy of our CTO teaching program. Methods: This is a retrospective single-center cohort study including 790 patients who underwent CTO PCI performed by operators with different volumes of CTOs PCI performed per year. According to PCI result, all patients have been divided into successful (n = 555, 70.3 %) and unsuccessful (n = 235, 29.7 %) groups. Study endpoints were Major Adverse Cardiovascular Events and Health Status Improvement evaluated using the Seattle Angina Questionnaire at one year. Results: A global success rate of 70 % for antegrade and 80 % for retrograde approach was shown despite the lack of some CTO-dedicated devices. During the enrollment period, the success rate increased significantly among operators with a lower number of CTO procedures per year. One-year MACE rate was similar in both successful and unsuccessful groups (13.5 % in successful and 10.6 % in unsuccessful group, p = 0.173). One year patients’ health status improved significantly only in successful group. Conclusions: No significant differences of in-hospital and one-year MACE were found between the successful and unsuccessful groups. Angina symptoms and quality of life significantly improved after successful CTO PCI. The RAIAN registry confirmed the importance of operator expertise for CTO PCI success.

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 Background Coronavirus disease 2019 was spread worldwide, as a pandemic, from December 2019. Venous thromboembolism events can inflict patients with coronavirus disease 2019 during the hospitalization or convalescent period. Therefore, monitoring of these patients, in terms of venous thromboembolism events signs and symptoms, and timely management of antithrombotic agents are of great importance. Case report A 45-year-old Iranian man, who is the first author of this case report, was infected by severe acute respiratory syndrome coronavirus 2 and displayed the typical signs and symptoms of coronavirus disease 2019. Although reverse transcription polymerase chain reaction for coronavirus disease 2019, and specific immunoglobulin M and immunoglobulin G against severe acute respiratory syndrome coronavirus 2, were negative at first, chest computed tomography scan showed the characteristic pattern of lung involvement of a coronavirus disease 2019 infection including bilateral and multilobar ground-glass opacities. At that time, there were no signs or symptoms of deep-vein thrombosis or pulmonary thromboembolism, so these were not investigated. About 30 hours after hospital discharge, the patient presented back to the hospital with acute-onset chest pain. We instantly tested his blood for D-dimer, and sent him to take a Doppler sonography of his lower legs and a chest computed tomography angiography in search of pulmonary thromboembolism and deep-vein thrombosis. Although we could confirm pulmonary thromboembolism with computed tomography angiography in our patient, there were no signs or symptoms of venous thromboembolism in his lower legs, and color Doppler sonography of lower limbs was normal. So, the patient was treated with rivaroxaban as an antithrombotic agent. After some days, he was discharged in good condition. About 1 month later, he was referred to our hospital because of left lower limb edema. Although he was under antithrombotic therapy, color Doppler sonography of lower limbs revealed acute deep-vein thrombosis of the left leg. Hence, we decided to shift antithrombotic therapy from rivaroxaban to warfarin, as it is more potent than rivaroxaban in recurrent venous thromboembolism and when taking new oral anticoagulants. Unlike rivaroxaban, which needs no blood test to monitor its efficacy but has a warning for signs and symptoms of bleeding, warfarin therapy must be monitored carefully by regular blood tests for prothrombin time and international normalized ratio to maintain them in the therapeutic range. The patient was informed about the bleeding cautions, and required regular check of prothrombin time and international normalized ratio to maintain them in the proper and advised range of treatment (international normalized ratio therapeutic range 2–3). Conclusion In the case of unexpected recurrent venous thromboembolism in coronavirus disease 2019, especially when patients are taking rivaroxaban or other new oral anticoagulants, such drugs should be substituted by warfarin, with routine follow-up, to maintain the value of prothrombin time and international normalized ratio within the therapeutic range.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is potentially pathogenic and causes severe symptoms; in addition to respiratory syndromes, patients might experience other severe conditions such as digestive complications and liver complications injury. The abnormality in the liver is manifested by hepatobiliary dysfunction and enzymatic elevation, which is associated with morbidity and mortality. The direct cytopathic effect, immune dysfunction, cytokine storm, and adverse effects of therapeutic regimens have a crucial role in the severity of liver injury. According to aging and immune system alterations, cytokine patterns may also change in the elderly. Moreover, hyperproduction of cytokines in the inflammatory response to SARS-CoV-2 can lead to multi-organ dysfunction. The mortality rate in elderly patients, particularly those with other comorbidities, is also higher than in adults. Although the pathogenic effect of SARS-CoV-2 on the liver has been widely studied, the impact of age and immune-mediated responses at different ages remain unclear. This review discusses the association between immune system responses in coronavirus disease 2019 (COVID-19) patients of different ages and liver injury, focusing on cytokine alterations.

Abstract Background Malaria is a significant parasitic infection, and human infection is mediated by mosquito (Anopheles) biting and subsequent transmission of protozoa (Plasmodium) to the blood. Carbonic anhydrases (CAs) are known to be highly expressed in the midgut and ectoperitrophic space of Anopheles gambiae. Transmembrane CAs (tmCAs) in Plasmodium may be potential vaccine candidates for the control and prevention of malaria. Methods In this study, two groups of transmembrane CAs, including α-CAs and one group of η-CAs were analysed by immunoinformatics and computational biology methods, such as predictions on transmembrane localization of CAs from Plasmodium spp., affinity and stability of different HLA classes, antigenicity of tmCA peptides, epitope and proteasomal cleavage of Plasmodium tmCAs, accessibility of Plasmodium tmCAs MHC-ligands, allergenicity of Plasmodium tmCAs, disulfide-bond of Plasmodium tmCAs, B cell epitopes of Plasmodium tmCAs, and Cell type-specific expression of Plasmodium CAs. Results Two groups of α-CAs and one group of η-CAs in Plasmodium spp. were identified to contain tmCA sequences, having high affinity towards MHCs, high stability, and strong antigenicity. All putative tmCAs were predicted to contain sequences for proteasomal cleavage in antigen presenting cells (APCs). Conclusions The predicted results revealed that tmCAs from Plasmodium spp. can be potential targets for vaccination against malaria.

Abstract 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.

Since recent research indicates that the addition of graphene increases the mechanical and biological properties of calcium phosphates simultaneously, graphene oxide (GO) was used in this research to enhance the properties of brushite cement. The main objective of this study is to investigate the mechanism of nucleation and growth of brushite crystals on GO sheets. Calcium nitrate tetrahydrate and diammonium hydrogenphosphate were used as calcium and phosphate precursors. The brushite chemical precipitation method on graphene sheets was used in this study and computer-assisted modeling was used to understand the process. The results of this study showed that the hybrid powders contained brushite and GO. Brushite crystals were grown after nucleation in proportion to the three main planes containing (020), (121¯), and (141). The final particles were plate shaped. The results of setting time tests showed that increasing the GO% decreases the setting time and this trend continues with an increasing amount of GO. The results of the mechanical evaluation showed that increasing the GO by up to 2% increased the mechanical properties and more than that decreased the mechanical properties. Resumen: Estudios recientes muestran una mejora de las propiedades mecánicas y biológicas de los fosfatos de calcio con la adición de grafeno. En este trabajo, el óxido de grafeno (GO) se propone para mejorar las propiedades de cementos de composición brushita. El principal objetivo es estudiar el mecanismo de nucleación de cristales de brushita sobre láminas de grafeno. Como precursores de calcio y fosfato se han usado nitrato cálcico tetrahidratado e hidrogenofosfato amónico. Para comprender el proceso se ha usado el método de precipitación química de la brushita sobre láminas de grafeno, y la modelización asistida por ordenador. Los resultados mostraron que el producto de síntesis consistía en un polvo híbrido que contenía brushita y GO. Los cristales de brushita crecieron, tras su nucleación, a lo largo de los planos principales (020), (121¯) y (141). Las partículas resultantes tienen morfología de plaquetas. Las medidas de los tiempos de endurecimiento mostraron que el aumento en GO disminuye el tiempo de endurecimiento. En cuanto al estudio de las propiedades mecánicas reveló que el incremento en GO, hasta del 2%, mejora las propiedades mecánicas para disminuir una vez se excede dicha cantidad.

Carbonic anhydrases (CAs) are metalloenzymes that can help organisms survive in hydrothermal vents by hydrating carbon dioxide (CO2). In this study, we focus on alpha (α), beta (β), and gamma (γ) CAs, which are present in the thermophilic microbiome of marine hydrothermal vents. The coding genes of these enzymes can be transferred between hydrothermal-vent organisms via horizontal gene transfer (HGT), which is an important tool in natural biodiversity. We performed big data mining and bioinformatics studies on α-, β-, and γ-CA coding genes from the thermophilic microbiome of marine hydrothermal vents. The results showed a reasonable association between thermostable α-, β-, and γ-CAs in the microbial population of the hydrothermal vents. This relationship could be due to HGT. We found evidence of HGT of α- and β-CAs between Cycloclasticus sp., a symbiont of Bathymodiolus heckerae, and an endosymbiont of Riftia pachyptila via Integrons. Conversely, HGT of β-CA genes from the endosymbiont Tevnia jerichonana to the endosymbiont Riftia pachyptila was detected. In addition, Hydrogenovibrio crunogenus SP-41 contains a β-CA gene on genomic islands (GIs). This gene can be transferred by HGT to Hydrogenovibrio sp. MA2-6, a methanotrophic endosymbiont of Bathymodiolus azoricus, and a methanotrophic endosymbiont of Bathymodiolus puteoserpentis. The endosymbiont of R. pachyptila has a γ-CA gene in the genome. If α- and β-CA coding genes have been derived from other microorganisms, such as endosymbionts of T. jerichonana and Cycloclasticus sp. as the endosymbiont of B. heckerae, through HGT, the theory of the necessity of thermostable CA enzymes for survival in the extreme ecosystem of hydrothermal vents is suggested and helps the conservation of microbiome natural diversity in hydrothermal vents. These harsh ecosystems, with their integral players, such as HGT and endosymbionts, significantly impact the enrichment of life on Earth and the carbon cycle in the ocean.

Background: Canine babesiosis is one of the mainly worldwide-distributed tick-borne haemoprotozoan parasitic dis­eases in dogs. Methods: A total of 43 blood samples were randomly collected from naturally infected dogs in seven villages from different geographical areas of Meshkin Shahr, Ardabil Province, Iran. The presence of Babesia species detected with standard methods including parasitological and gene sequencing techniques targeting the 18S rRNA gene. Results: Our results revealed that four dogs 9.3% (4/43) including one female and three male dogs were infected with Babesia. All four Babesia-infected dogs were confirmed B. canis by the molecular-based method. Sequence alignments comparison of the B. canis genotypes A and B, it was revealed that all B. canis isolates belonged to genotype B. Conclusion: This study provides essential data for subsequently define the critical importance of the molecular studies in management and prevention of the canine babesiosis in Iran.

Abstract Objective This study describes the occurrence of a silent mutation in the RNA binding domain of nucleocapsid phosphoprotein (N protein) coding gene from SARS-CoV-2 that may consequence to a missense mutation by onset of another single nucleotide mutation. Results In the DNA sequence isolated from severe acute respiratory syndrome (SARS-CoV-2) in Iran, a coding sequence for the RNA binding domain of N protein was detected. The comparison of Chinese and Iranian DNA sequences displayed that a thymine (T) was mutated to cytosine (C), so “TTG” from China was changed to “CTG” in Iran. Both DNA sequences from Iran and China have been encoded for leucine. In addition, the second T in “CTG” in the DNA or uracil (U) in “CUG” in the RNA sequences from Iran can be mutated to another C by a missense mutation resulting from thymine DNA glycosylase (TDG) of human and base excision repair mechanism to produce “CCG” encoding for proline, which consequently may increase the affinity of the RNA binding domain of N protein to viral RNA and improve the transcription rate, pathogenicity, evasion from human immunity system, spreading in the human body, and risk of human-to-human transmission rate of SARS-CoV-2.

In this study, a solvothermal method at the temperature of 180 °C for 4 h was used for the synthesis of hydroxyapatite-reduced graphene oxide (HA-rGO) nanopowders by employing the nitrogen gas injection. To synthesize the powders, a solvent containing dimethylformamide, anhydrous ethanol, diethylene glycol, and water was used (1:1:1:2, respectively). Calcium nitrate tetrahydrate and diammonium hydrogenphosphate were used as calcium and phosphate precursors, respectively. The synthesized powders were consolidated by a high-frequency induction heat sintering method. The powders and sintered samples were then evaluated using X-ray diffraction, Raman spectroscopy, high-resolution transmission electron microscopy, Vickers indentation technique, and biocompatibility assay. The findings of this study showed that the final powders synthesized by the solvothermal method had calcium to phosphate ratio of about 1.67. The high frequency induction heat sintering method was suitable for consolidating these powders and exhibited a higher relative density than other methods. The mechanical properties of the nanocomposite were higher than those of pure HA. In biological experiments the difference of HA effect in comparison with the nanocomposite was not significant and both were biocompatible.

Abstract In this study, the effect of the argon, nitrogen, and hydrogen gases on the final properties of the reduced graphene oxide- hydroxyapatite nanocomposites synthesized by gas injected hydrothermal method was investigated. Four samples were synthesized, which in the first sample the pressure was controlled by volume change at a constant concentration. In subsequent samples, the pressure inside the autoclave was adjusted by the injecting gases. The initial pressure of the injected gases was 10 bar and the final pressure considered was 25 bar. The synthesized powders were consolidated at 950 °C and 2 MPa by spark plasma sintering method. The final samples were subjected to Vickers indentation analysis. The findings of this study indicate that the injection of argon, hydrogen, and nitrogen gases improved the mechanical properties of the nanocomposites. Injection of gases increased the crystallinity and particle size of hydroxyapatite, and this increase was greater for nitrogen gas than for others. Injection of these gases increased the rate of graphene oxide reduction and in this case the effect of nitrogen gas was greater than the others.

Abstract Background The fucose-mannose ligand (FML) of Leishmania infantum is a complex glycoprotein which does not elicit adequate immunogenicity in humans. In recent years, adjuvant compounds derived from plants have been used for improving the immunogenicity of vaccines. Glycyrrhizin (GL) is a natural triterpenoid saponin that has known immunomodulatory activities. In the present study, we investigated the effects of co-treatment with FML and GL on the production of cytokines and nitric oxide (NO) by macrophages, in vitro. Methods Lipopolysaccharide (LPS) stimulated murine peritoneal macrophages were treated with FML (5 μg/ml) of L. infantum and various concentrations of GL (1 μg/ml, 10 μg/ml and 20 μg/ml). After 48 h of treatment, cell culture supernatants were recovered and the levels of TNF-α, IL-10, IL-12p70 and IP-10 were measured by sandwich ELISA and NO concentration by Griess reaction. Results Our results indicate that the treatment of activated macrophages with FML plus GL leads to enhanced production of NO, TNF-α and IL-12p70, and reduction of IL-10 levels in comparison with FML treatment alone. Conclusions Therefore, we concluded that GL can improve the immunostimulatory effect of FML on macrophages and leads to their polarization towards an M1-like phenotype.

Abstract Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 19 (COVID-19) that was emerged as a new member of coronaviruses since December 2019 in Wuhan, China and then after was spread in all continentals. Since SARS-CoV-2 has shown about 77.5% similarity to SARS-CoV, the transcriptome and immunological regulations of SARS-CoV-2 was expected to have high percentage of overlap with SARS-CoV. Results In this study, we applied the single cell transcriptomics data of human bronchial epithelial cells (2B4 cell line) infected with SARS-CoV, which was annotated in the Expression Atlas database to expand this data to COVID-19. In addition, we employed system biology methods including gene ontology (GO) and Reactome pathway analyses to define functional genes and pathways in the infected cells with SARS-CoV. The transcriptomics analysis on the Expression Atlas database revealed that most genes from infected 2B4 cell line with SARS-CoV were downregulated leading to immune system hyperactivation, induction of signaling pathways, and consequently a cytokine storm. In addition, GO:0016192 (vesicle-mediated transport), GO:0006886 (intracellular protein transport), and GO:0006888 (ER to Golgi vesicle-mediated transport) were shown as top three GOs in the ontology network of infected cells with SARS-CoV. Meanwhile, R-HAS-6807070 (phosphatase and tensin homolog or PTEN regulation) showed the highest association with other Reactome pathways in the network of infected cells with SARS-CoV. PTEN plays a critical role in the activation of dendritic cells, B- and T-cells, and secretion of proinflammatory cytokines, which cooperates with downregulated genes in the promotion of cytokine storm in the COVID-19 patients. Conclusions Based on the high similarity percentage of the transcriptome of SARS-CoV with SARS-CoV-2, the data of immunological regulations, signaling pathways, and proinflammatory cytokines in SARS-CoV infection can be expanded to COVID-19 to have a valid platform for future pharmaceutical and vaccine studies.

Abstract Background Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appears with common symptoms including fever, dry cough, and fatigue, as well as some less common sysmptoms such as loss of taste and smell, diarrhea, skin rashes and discoloration of fingers. COVID-19 patients may also suffer from serious symptoms including shortness of breathing, chest pressure and pain, as well as loss of daily routine habits, pointing out to a sever reduction in the quality of life. COVID-19 has afftected almost all countries, however, the United States contains the highest number of infection (> 1,595,000 cases) and deaths cases (> 95,000 deaths) in the world until May 21, 2020. Finding an influential treatment strategy against COVID-19 can be facilitated through better understanding of the virus pathogenesis and consequently interrupting the biochemical pathways that the virus may play role in human body as the current reservoir of the virus. Results In this study, we combined system biology and bioinformatic approaches to define the role of coexpression of angiotensin-converting enzyme 2 (ACE2), neprilysin or membrane metallo-endopeptidase (MME), and carbonic anhydrases (CAs) and their association in the pathogenesis of SARS-CoV-2. The results revealed that ACE2 as the cellular attachment site of SARS-CoV-2, neprilysin, and CAs have a great contribution together in the renin angiotensin system (RAS) and consequently in pathogenesis of SARS-CoV-2 in the vital organs such as respiratory, renal, and blood circulation systems. Any disorder in neprilysin, ACE2, and CAs can lead to increase of CO2 concentration in blood and respiratory acidosis, induction of pulmonary edema and heart and renal failures. Conclusions Due to the presence of ACE2-Neprilysin-CA complex in most of vital organs and as a receptor of COVID-19, it is expected that most organs are affected by SARS-CoV-2 such as inflammation and fibrosis of lungs, which may conversely affect their vital functions, temporary or permanently, sometimes leading to death. Therefore, ACE2-Neprilysin-CA complex could be the key factor of pathogenesis of SARS-CoV-2 and may provide us useful information to find better provocative and therapeutic strategies against COVID-19.

Abstract Background The inaccuracy of DNA sequence data is becoming a serious problem, as the amount of molecular data is multiplying rapidly and expectations are high for big data to revolutionize life sciences and health care. In this study, we investigated the accuracy of DNA sequence data from commonly used databases using carbonic anhydrase (CA) gene sequences as generic targets. CAs are ancient metalloenzymes that are present in all unicellular and multicellular living organisms. Among the eight distinct families of CAs, including α, β, γ, δ, ζ, η, θ, and ι, only α-CAs have been reported in vertebrates. Results By an in silico analysis performed on the NCBI and Ensembl databases, we identified several β- and γ-CA sequences in vertebrates, including Homo sapiens, Mus musculus, Felis catus, Lipotes vexillifer, Pantholops hodgsonii, Hippocampus comes, Hucho hucho, Oncorhynchus tshawytscha, Xenopus tropicalis, and Rhinolophus sinicus. Polymerase chain reaction (PCR) analysis of genomic DNA persistently failed to amplify positive β- or γ- CA gene sequences when Mus musculus and Felis catus DNA samples were used as templates. Further BLAST homology searches of the database-derived “vertebrate” β- and γ-CA sequences revealed that the identified sequences were presumably derived from gut microbiota, environmental microbiomes, or grassland ecosystems. Conclusions Our results highlight the need for more accurate and fast curation systems for DNA databases. The mined data must be carefully reconciled with our best knowledge of sequences to improve the accuracy of DNA data for publication.

Abstract Background Coronavirus disease 2019 (COVID-19) is an emerging zoonotic viral infection, which was started in Wuhan, China, in December 2019 and transmitted to other countries worldwide as a pandemic outbreak. Iran is one of the top ranked countries in the tables of COVID-19-infected and -mortality cases that make the Iranian patients as the potential targets for diversity of studies including epidemiology, biomedical, biodata, and viral proteins computational modelling studies. Results In this study, we applied bioinformatic biodata mining methods to detect CDS and protein sequences of ORF1ab polyprotein of SARS-CoV-2 isolated from oronasopharynx of an Iranian patient. Then through the computational modelling and antigenicity prediction approaches, the identified polyprotein sequence was analyzed. The results revealed that the identified ORF1ab polyprotein belongs to a part of nonstructural protein 1 (nsp1) with the high antigenicity residues in a glycine-proline or hydrophobic amino acid rich domain. Conclusions The results revealed that nsp1 as a virulence factor and crucial agent in spreading of the COVID-19 among the society can be a potential target for the future epidemiology, drug, and vaccine studies.

We report the biochemical and structural characterisation of a beta-carbonic anhydrase (β-CA) from Trichomonas vaginalis, a unicellular parasite responsible for one of the world’s leading sexually transmitted infections, trichomoniasis. CAs are ubiquitous metalloenzymes belonging to eight evolutionarily divergent groups (α, β, γ, δ, ζ, η, θ, and ι); humans express only α-CAs, whereas many clinically significant pathogens express only β- and/or γ-CAs. For this reason, the latter two groups of CAs are promising biomedical targets for novel antiinfective agents. The β-CA from T. vaginalis (TvaCA1) was recombinantly produced and biochemically characterised. The crystal structure was determined, revealing the canonical dimeric fold of β-CAs and the main features of the enzyme active site. The comparison with the active site of human CA enzymes revealed significant differences that can be exploited for the design of inhibitors selective for the protozoan enzyme with respect to the human ones.

Introduction: Clinical registries are a targeted way of data collection aimed at finding a solution to a specific clinical inquiry. The present report introduces the Rajaie Cardiovascular, Medical and Research Center percutaneous coronary intervention (RHC-PCI) Registry. The primary objectives of the RHC-PCI Registry consist of monitoring different complex PCI procedures and their mutual impact on interventional cardiology programs. Methods: RHC is a large and well-known cardiovascular tertiary center in Iran. The RHC-PCI Registry was first launched in 2015, since which time it has collected >5000 parameters regarding the baseline, clinical, and procedural characteristics of various PCI procedures. Noncomplex coronary interventions, bifurcation stenting, left main interventions, chronic total occlusion (CTO) PCI, and bypass graft interventions comprise the major categories gathered by the RHC-PCI Registry. The main registry outcomes are comprised in-hospital mortality, major adverse cardiovascular events, vascular access site complications, and 6-month all-cause mortality. Results: In this primary report, we elaborate on the principal infrastructure of the RHC-PCI Registry and present a synopsis of the registry scope. During the first 40 months of the registry, 11,005 patients underwent PCI. The acute coronary syndrome was reported in 5043 (45.8%) patients. Bifurcation stenting, left main interventions, CTO PCI, and bypass graft interventions were performed in 1679 (15.2%), 236 (2.1%), 946 (8.5%), and 764 (6.9%) patients, respectively. The preferred access site was the femoral artery (n = 6614, 60%), and drug-eluting stents were deployed in 9230 (83.8%) patients. In-hospital mortality in the total registry data was reported in 104 (0.9%) patients. Conclusions: This report introduces the RHC-PCI Registry, its primary objectives, infrastructure, and preliminary results (the 3-year outcome).

The synthesis of nanocomposites containing hydroxyapatite and graphene sheets has received much attention recently. Therefore, strategies that improve their properties will be useful. The aim of this study was to investigate the effect of diethylene glycol on the characteristics of hydroxyapatite-reduced graphene oxide powders synthesized by a hydrothermal method (180 ​°C, 5 ​h) and the nanocomposites obtained by spark plasma sintering (950 ​°C, 50 ​MPa). Graphene oxide, calcium nitrate tetrahydrate and diammonium hydrogenphosphate were used as precursors. The characterization methods included electron microscopy, X-ray diffraction, Raman spectroscopy, and indentation technique. Obtained results have shown that the presence of diethylene glycol reduced the average size of hydroxyapatite crystallites from 27 to 16 nm, reduced the particle size distribution, and increased the graphene oxide reduction rate. The presence of diethylene glycol during the synthesis process increased the elastic modulus (from 116.4 ​± ​4.9 to 125 ​± ​3.8 ​GPa), hardness (from 4.08 ​± ​0.7 to 6.32 ​± ​0.4 ​GPa), and fracture toughness (from 1.66 ​± ​0.7 to 1.87 ​± ​0.9 ​MPa ​m0.5) of the composite.

Parvalbumins are the most important fish allergens, which are heat-stable, classified in the family of calcium-binding EF-hand proteins, and contain one magnesium binding site. The functional connection between calcium and parvalbumin gives fish the high-speed swimming ability because of high concentration of Ca2+-binding parvalbumin in fish white muscles. Although parvalbumins are widely studied and conceivably play crucial roles in the physiology and swimming pattern of fishes, still no report is available about their presence in microbes, such as pathogenic fungal species. We detected a DNA sequence in the genome of Trichophyton violaceum and used in silico and polymerase chain reaction (PCR) technique with a designed pair of primers to identify it as parvalbumin-coding gene.

Background: Dirofilariasis is a globally distributed arthropod-borne parasitic disease of mainly canids and felids. We evaluated to extend the knowledge of morpho-molecular characteristics and outer ultrastructure of Dirofilaria immitis isolated from Northwest of Iran. Methods: Overall, 67 filarial worms including 41 females and 26 males parasites were collected from the cardiovascular system of the 43 stray dogs in Meshkinshar, Ardebil Province, Northwest of Iran in 2017, and subjected to light and scanning electron microscopy (SEM) as well as carmine alum staining for morpho-molecular and identification. Molecular methods were used for confirmation of morphological findings by sequencing of Cytochrome c oxidase subunit I (cox1) gene. Results: The partial DNA sequencing of cox1 gene of adult parasites showed considerable homology and close proximity to the previously isolated from Kerman and Meshkinshahr, Iran. The lowest genetic variation and the highest intra-species variability was found in D. immitis and Dirofilaria repens, respectively. No similarity was identified between D. immitis nucleotide sequence and Wolbachia species as its endosymbiont bacteria. Conclusion: The SEM technique is an excellent tool for differential recognition of the parasite surface morphology and molecular techniques could differentiate and identify Dirofilaria spp.

Aim: This study was designed to evaluate the network productions and research collaborations on toxoplasmosis worldwide. Materials and Methods: A bibliometric research was carried out using the Web of Science (WOS) database. The analysis unit was the original research articles about toxoplasmosis published between 2000 and 2016 (17 years). Results: Totally, 6,550 articles about toxoplasmosis were indexed in the WOS with the following information: (A) 18,410 researchers played a role in drafting the articles; (B) 33 different countries have contributed in the toxoplasmosis studies; (C) the USA was ranked at the first place with 2,162 publications about toxoplasmosis; and (D) "Dubey JP" was compiled and participated in 401 articles from the USA, as the highest number and main core of publications in the toxoplasmosis network. Conclusion: The main focus of the toxoplasmosis research activities in the world was article production in the indexed journals in WOS. Hence, it is necessary to strengthen the collaboration networks to improve the quality of articles. Furthermore, the priority would be the identification of institutions with a higher number of research article productions in WOS, to perform toxoplasmosis collaborative original researches according to the strategic roadmap and scientific plan of each country.

Many research studies have been conducted on the liberation of locked minerals using a crusher and comparing this device with the other devices. This paper reviews the liberation of middle coal by different methods of crushing force. In the Tabas coal washing plant, particles of 0.5-50 mm size are processed through the heavy media method (using 3 Tri-flo separators) and particles of 0-0.5 mm size are processed using the flotation method (using 6 column flotation cells). A Tri-flo separator with a diameter of 700 mm and the capacity of 120 tons per hour is used for the cleaning of 6-50 mm raw coal particles. The study was conducted using a laboratory jaw crusher and a cage mill with a specific comminution ratio, both crushing forces were analyzed with the same distribution and mechanism of production of fines. In this study, grading and washability characteristics of a representative sample of middle product were reviewed and the dimensions of the ash were measured for each section. Intermediate product crushing using a laboratory jaw crusher and an industrial cage mill were conducted at up to 5 mm size and 50 percent of final speed. The amount of coal released after each section grading was determined by a sinking and floating test for size +0.5 mm and release analysis and ash testing for smaller dimensions of -0.5, these tests were conducted for each section product dimension. The results indicated that utilizing a cage mill is more effective than a laboratory jaw crusher, resulting in 11-percent more yield with 12 ash. The rate of fines produced through the laboratory jaw crusher is less than the industrial cage mill.

Background: Carotid artery stenosis is one of the main causes of ischemic stroke in Iranian population. Carotid artery stenting (CAS) is a method with for treating carotid artery disease, in order to prevent stroke. Dispersion of the embolus is a significant risk for carotid angioplasty which can be prevented by using protective devices. But studies have shown that the use of these protective devices is not safe and can have side effects such as vascular spasm and dissection. Method: 36 patients who underwent unprotected carotid artery angioplasty from April 2018 to August 2019 in Shahid Madani hospital retrospectively entered this study. Hospital records were studied for data collection. Patients were followed by phone interviews. Major adverse cardiovascular and cerebral events (MACCE) was defined as a composite of the occurrence of stroke, MI, bleeding, and all-cause mortality in the long term. Mean duration of our follow-up was 6 months. Results: During in-hospital course, an 82 years old woman with a history of CVA, hypertension, diabetes and a significant stenosis in her contralateral ICA, had an episode of stroke which was fatal. Also, there was a 46 years old woman without any risk factors, who had developed intracranial hemorrhage (ICH). 22 patients were followed. No MI, stroke, or death occurred in any of the patients. There were only 2 cases of bleeding. Conclusion: Carotid artery stenting without protection may be is a safe method of carotid revascularization. Further prospective studies and clinical trials are needed.

Abstract 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 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 Background Despite the high prevalence of parasitic infections, and their impact on global health and economy, the number of drugs available to treat them is extremely limited. As a result, the potential consequences of large-scale resistance to any existing drugs are a major concern. A number of recent investigations have focused on the effects of potential chemical inhibitors on bacterial and fungal carbonic anhydrases. Among the five classes of carbonic anhydrases (alpha, beta, gamma, delta and zeta), beta carbonic anhydrases have been reported in most species of bacteria, yeasts, algae, plants, and particular invertebrates (nematodes and insects). To date, there has been a lack of knowledge on the expression and molecular structure of beta carbonic anhydrases in metazoan (nematodes and arthropods) and protozoan species. Methods Here, the identification of novel beta carbonic anhydrases was based on the presence of the highly-conserved amino acid sequence patterns of the active site. A phylogenetic tree was constructed based on codon-aligned DNA sequences. Subcellular localization prediction for each identified invertebrate beta carbonic anhydrase was performed using the TargetP webserver. Results We verified a total of 75 beta carbonic anhydrase sequences in metazoan and protozoan species by proteome-wide searches and multiple sequence alignment. Of these, 52 were novel, and contained highly conserved amino acid residues, which are inferred to form the active site in beta carbonic anhydrases. Mitochondrial targeting peptide analysis revealed that 31 enzymes are predicted with mitochondrial localization; one was predicted to be a secretory enzyme, and the other 43 were predicted to have other undefined cellular localizations. Conclusions These investigations identified 75 beta carbonic anhydrases in metazoan and protozoan species, and among them there were 52 novel sequences that were not previously annotated as beta carbonic anhydrases. Our results will not only change the current information in proteomics and genomics databases, but will also suggest novel targets for drugs against parasites.

Several cytochrome P450 (CYP) enzymes catalyze the C4-hydroxylation of retinoic acid (RA), a potent inducer of cell differentiation and an agent in the treatment of several diseases. Here, we have characterized CYP2C22, a member of the rat CYP2C family with homology to human CYP2C8 and CYP2C9. CYP2C22 was expressed nearly exclusively in hepatocytes, where it was one of the more abundant mRNAs transcripts. In H-4-II-E rat hepatoma cells, CYP2C22 mRNA was upregulated by all-trans (at)-RA, and Am580, a nonmetabolizable analog of at-RA. In comparison, in primary human hepatocytes, at-RA increased CYP2C9 but not CYP2C8 mRNA. Analysis of the CYP2C22 promoter region revealed a RA response element (5 ′ -GGTTCA-(n)5-AGGTCA-3 ′) in the distal flanking region, which bound the nuclear hormone receptors RAR and RXR and which was required for transcriptional activation response of this promoter to RA in CYP2C22-luciferase-transfected RA-treated HepG2 cells. The cDNA-expressed CYP2C22 protein metabolized [3H]at-RA to more polar metabolites. While long-chain polyunsaturated fatty acids competed, 9-cis-RA was a stronger competitor. Our studies demonstrate that CYP2C22 is a high-abundance, retinoid-inducible, hepatic P450 with the potential to metabolize at-RA, providing additional insight into the role of the CYP2C gene family in retinoid homeostasis.

Vitamin A (VA) is stored in tissues predominantly as retinyl esters (REs), which provide substrate for the production of bioactive retinoids. Retinoic acid (RA), a principal metabolite, has been shown to induce postnatal lung development. To better understand lung RE storage, we compared VA (given as retinyl palmitate), RA, and a nutrient-metabolite combination, VARA, given orally on postnatal days 5–7, for their ability to increase lung RE in neonatal rats. VARA increased lung RE significantly [∼14, 2.4, 2.1, and

Lecithin:retinol acyltransferase (LRAT), present in microsomes, catalyzes the transfer of the sn-1 fatty acid of phosphatidylcholine to retinol bound to a cellular retinol-binding protein. In the present study we have cloned mouse and rat liver LRAT cDNA and tested the hypothesis that LRAT mRNA, like LRAT activity, is regulated physiologically in a liver-specific manner. The nucleotide sequences of mouse and rat liver LRAT cDNA each encode a 231-amino acid protein with 94% similarity between these species, and approximately 80% similarity to a cDNA for LRAT from human retinal pigment epithelium. Expression of rat LRAT cDNA in HEK293T cells resulted in functional retinol esterification and storage. RNA from several rat tissues hybridized with liver LRAT cDNA. However, LRAT mRNA was virtually absent from the liver of vitamin A-deficient animals, while being unaffected in intestine and testis. LRAT mRNA was rapidly induced by retinoic acid (RA) in liver of vitamin A-deficient mice and rats (P < 0.01). LRAT mRNA and enzymatic activity were well correlated in the same livers of rats treated with exogenous RA (r = 0.895, P < 0.0001), and in a dietary study that encompassed a broad range of vitamin A exposure (r = 0.799, P < 0.0001). Liver total retinol of

Background: Appropriate treatment methods lead to a reduced rate of mortality and morbidity, and an improved quality of life, in patients with multi-vessel coronary artery disease. Objectives: In this study, we compared short and long-term outcomes of coronary artery bypass grafting (CABG) versus medical therapy in patients 80 years of age and older with multi-vessel coronary artery disease (MVCAD). Patients and Methods: In this retrospective study, 50 octogenarian patients with MVCAD who underwent CABG were compared with 50 patients in the same condition who were treated with medical therapy during the same time. The primary objective was to compare mortality and morbidity rates, as well as other factors such as the occurrence of chest pain, deterioration of the NYHA functional class, and re-hospitalization, between the two groups. The comparison was made using medical records from the five years post-treatment. Results: After five years, the overall mortality rate included 11 patients (22%) in the CABG group versus 18 patients (36%) in the medical therapy group; this difference was not significant between the two groups (P = 0.186). Regarding short-term outcomes, in the CABG group, cardiogenic shock occurred in 9 patients (18%), renal failure in 13 patients (26%), pulmonary complications in 9 patients (18%) and neurologic complications in 3 patients (6%); in the medical therapy group, these same complications occurred, respectively, in 6 patients (12%), 7 patients (14%), 10 patients (20%) and 1 patient (2%). In addition to these factors, freedom from chest pain and improvement in the functional class among the CABG group was significantly higher than among the medical therapy group (P =

Introduction: Some Azotobacter species can produce melanin. Melanin protects against UV. The purpose of this study was to isolate Azotobacter with the power of producing melanin and optimize its production and the effect of its combination with titanium oxide nanoparticles on the protection against ultraviolet light (UV). Materials & Methods: Overall, 200 soil samples from different parts of Qom, Iran, were cultured on Ashby's mannitol agar medium using Bio-test method. The effect of optimization of conditions such as pH, temperature, glucose source, amino acid sources, and aeration on the amount of melanin production was assessed. Afterwards, melanin was extracted, conjugated with titanium nanosilicate compound, and then the effect of each of the compounds on Escherichia coli was examined under the influence of UV based on time. Findings: Melanin-producing Azotobacter vinelandii species were isolated. The optimum pH was determined about 7.5. Glucose at different concentrations (1-6%) reduced the production of the product. Methionine amino acid had an inhibitory effect, while tyrosine amino acid increased the production rate. Tryptophan amino acid at 0.1-0.7% also increased the production rate, while cysteine and phenylalanine did not change the production rate. The combination of titanium oxide with melanin showed a significant protective effect against Escherichia coli bacterium under the influence of UV. Discussion & Conclusions: Native isolates of Azotobacter isolated from agricultural soil with the power of producing melanin can be used as a source for its use in the industry.