Identification of functional cis-regulatory elements by sequential enrichment from a randomized synthetic DNA library

BACKGROUND: The identification of endogenous cis-regulatory DNA elements (CREs) responsive to endogenous and environmental cues is important for studying gene regulation and for biotechnological applications but is labor and time intensive. Alternatively, by taking a synthetic biology approach small specific DNA binding sites tailored to the needs of the scientist can be generated and rapidly identified. RESULTS: Here we report a novel approach to identify stimulus-responsive synthetic CREs (SynCREs) from an unbiased random synthetic element (SynE) library. Functional SynCREs were isolated by screening the SynE libray for elements mediating transcriptional activity in plant protoplasts. Responsive elements were chromatin immunoprecipitated by targeting the active Ser-5 phosphorylated RNA polymerase II CTD (Pol II ChIP). Using sequential enrichment, deep sequencing and a bioinformatics pipeline, candidate responsive SynCREs were identified within a pool of constitutively active DNA elements and further validated. These included bonafide biotic/abiotic stress-responsive motifs along with novel SynCREs. We tested several SynCREs in Arabidopsis and confirmed their response to biotic stimuli. CONCLUSIONS: Successful isolation of synthetic stress-responsive elements from our screen illustrates the power of the described methodology. This approach can be applied to any transfectable eukaryotic system since it exploits a universal feature of the eukaryotic Pol II

The study of harmful and beneficial drug interactions in intensive care, Kerman, Iran

Since multidrug therapy is common in the intensive care unit (ICU), the risk of drug interactions is high. This study aimed to examine the prevalence of drug interactions and risk factors in patients who were admitted to ICUs. In a crosssectional study, the medication flow sheet of 101 patients was investigated in terms of the number and the type of drug interactions. The Drug Interaction Facts reference text book (2010 edition) was used to determine the type and the number of drug interactions. In total, 609 potential drug interactions were found. The mean number of drug interactions per patient was 6.1 (SD=5.6). Of all observed drug interactions, 66.9 were classified as harmful and 33.1 beneficial. In terms of the nature of interactions, delayed, moderate, and possible were the most common types. The most frequent harmful interaction was between phenytoin and omeprazole (63 occasions). Critically ill patients are at a higher risk of drug interactions. Although 33.1 of the drug interactions were considered beneficial, medical teams should be awarethat even beneficial interactions can have undesirable side-effects in the critically ill. © The Intensive Care Society 2013

Sport injuries of karate during training: An epidemiologic study in Iran

Background: Karate is a public sport that has athletes in various age ranges and abundant active sport clubs in Iran. The pattern of injury in this sport in Iranian athletes seems diferent from other countries. Objectives: This study was performed with the purpose of considering the incidence and type of injury of karate athletes aged below 30 years from Tehran, Iran clubs. Materials and Methods: In a cross-sectional study, 10 karate clubs were selected in Tehran. Clubs were selected based on a cluster method from 5 diferent geographical regions of Tehran. All injuries were collected based on athletes� or clubs� weekly report with a designed questionnaire. The injuries were classifed according to: low, medium and severe injury. Collected data was analyzed with SPSS software version 17. Results: 620 athletes were studied totally and incidence rate of injury per athletes was 16.1 and 20.2 per 100 athletes. Ninety percent of than 70 kg and lower sport experience (P � 0.05). The commonest locations for injury were head and neck followed by trunk, lower and injuries were during bout practice, 6 during ftness and 4 during kata. The rate of injury was more common in athletes with weight less upper limb, respectively. Just 2 cases needed surgical intervention and no one led to decreased level of consciousness. The most common type of injury was contusion, bruise and superfcial scratch (64). Conclusions: Severe injury was uncommon in this study and similar to other Iranian studies head and neck had the most injuries. Athletes with lower experience and lower weight were associated with higher injuries. © 2015, Sports Medicine Research Center

Loss of CLN7 results in depletion of soluble lysosomal proteins and impaired mTOR reactivation

Defects in the MFSD8 gene encoding the lysosomal membrane protein CLN7 lead to CLN7 disease, a neurodegenerative lysosomal storage disorder belonging to the group of neuronal ceroid lipofuscinoses (NCLs). Here we have performed a SILAC-based quantitative analysis of the lysosomal proteome using Cln7-deficient mouse embryonic fibroblasts (MEFs) from a Cln7 knockout (ko) mouse model. From 3335 different proteins identified, we detected 56 soluble lysosomal proteins and 29 highly abundant lysosomal membrane proteins. Quantification revealed that the amounts of 12 different soluble lysosomal proteins were significantly reduced in Cln7 ko MEFs compared with wild type controls. One of the most significantly depleted lysosomal proteins was Cln5 protein that underlies another distinct NCL disorder. Expression analyses showed that the mRNA expression, biosynthesis, intracellular sorting and proteolytic processing of Cln5 were not affected, whereas the depletion of mature Cln5 protein was due to increased proteolytic degradation by cysteine proteases in Cln7 ko lysosomes. Considering the similar phenotypes of CLN5 and CLN7 patients, our data suggest that depletion of CLN5 may play an important part in the pathogenesis of CLN7 disease. In addition, we found a defect in the ability of Cln7 ko MEFs to adapt to starvation conditions as shown by impaired mammalian target of rapamycin complex 1 reactivation, reduced autolysosome tubulation and increased perinuclear accumulation of autolysosomes compared to controls. In summary, depletion of multiple soluble lysosomal proteins suggest a critical role of CLN7 for lysosomal function, which may contribute to the pathogenesis and progression of CLN7 disease

A Comparison between Recombinant Activated Factor VII (Aryoseven) and Novoseven in Patients with Congenital Factor VII Deficiency

In order to establish the efficacy and biosimilar nature of AryoSeven to NovoSeven in the treatment of congenital factor VII (FVII) deficiency, patients received either agent at 30 1/4g/kg, intravenously per week for 4 weeks, in a randomized fashion. The primary aim was to compare FVII:coagulation activity (FVII:C), 20 minutes after recombinant activated FVII (rFVIIa) injection, in the 2 groups. A secondary measure was self-reported bleeding. The median interquartile baseline range of the plasma level of activated FVII (FVIIa) activity in the 2 groups was 1.6 (1.1-14.0) IU/dL and 5.0 (1.1-25.5) IU/dL. All patients achieved levels of FVIIa (FVII:C) >30 IU/dL, 20 minutes after the injection of rFVIIa. Bleeding was similar between the 2 groups, with a comparable decrease in severity and frequency compared to the last month prior to treatment. AryoSeven is similar to NovoSeven in increasing postinjection FVIIa activity as well as in clinical safety and efficacy. © The Author(s) 2014

Evaluation of suspicious appearing microcalcification groups on mammogram: Comparing BI-RADS 5th edition descriptors with the BI-RADS 4th edition and pathologic association

Background: Groups of microcalcifications are the most frequent recognized features of ductal carcinoma on mammograms. However, heterogeneity (in size, morphology and density) and number of microcalcification groups as well as presence of accompanied soft-tissue density are not included in breast imaging reporting and data system (BI-RADS) descriptors. Objectives: The study purposes to determine the malignancy risk of microcalcification groups regarding these characteristics and also compare the 4th and 5th versions of BI-RADS. Patients and Methods: In a cross sectional study, 88 patients with microcalcification groups (age range, 26-80 years; mean, 53.4 years) who had undergone mammographically guided biopsy between March 2013 and March 2015 were evaluated. The overall number of microcalcification groups in each patient, number of deposits within each group, group location and heterogeneity in size, density and morphology were assessed and subsequently BI-RADS descriptors for 4th and 5th editions were recorded separately. Finally, correlation with histopathology was performed. Results: Overall, positive predictive value (PPV) of suspicious microcalcifications was 22.4. PPVs of morphology descriptors were as follows: amorphous, 7.9; coarse heterogeneous, 17.8; fine pleomorphic, 63.2; fine linear/fine linear branching, 100; (P < 0.001). Heterogenicity in size existed in 81 cases (92), in density in 69 cases (86.4) and in morphology in 86 cases (97.7). Additionally, microcalcification groups that were accompanied with soft-tissue density had a higher percentage of malignancy (67.5 vs. 54.5) but with no significant difference (P = 0.2). According to BI-RADS 4th edition, the risk of malignancy was 49.1, 66.7 and 88.1 in 4b, 4c and 5, respectively. These figures were 30, 82.9, and 100 for BI-RADS 5th version, respectively. The area under the receiver (AUC) of 4th and 5th versions of BI-RADS was 0.76 and 0.74 (both P values < 0.001, 95 confidence intervals = 0.66-0.87 and 0.63-0.85 respectively). P value for comparison was insignificant. Conclusion: The risk of malignancy increased with the heterogeneity of microcalcifications, especially in the groups with heterogeneity in density, however with no statistically significant difference. BI-RADS 5th edition could predict the likelihood of malignancy as well as 4th version. © 2018, Iranian Journal of Radiology

Evaluation of suspicious appearing microcalcification groups on mammogram: Comparing BI-RADS 5th edition descriptors with the BI-RADS 4th edition and pathologic association

Background: Groups of microcalcifications are the most frequent recognized features of ductal carcinoma on mammograms. However, heterogeneity (in size, morphology and density) and number of microcalcification groups as well as presence of accompanied soft-tissue density are not included in breast imaging reporting and data system (BI-RADS) descriptors. Objectives: The study purposes to determine the malignancy risk of microcalcification groups regarding these characteristics and also compare the 4th and 5th versions of BI-RADS. Patients and Methods: In a cross sectional study, 88 patients with microcalcification groups (age range, 26-80 years; mean, 53.4 years) who had undergone mammographically guided biopsy between March 2013 and March 2015 were evaluated. The overall number of microcalcification groups in each patient, number of deposits within each group, group location and heterogeneity in size, density and morphology were assessed and subsequently BI-RADS descriptors for 4th and 5th editions were recorded separately. Finally, correlation with histopathology was performed. Results: Overall, positive predictive value (PPV) of suspicious microcalcifications was 22.4. PPVs of morphology descriptors were as follows: amorphous, 7.9; coarse heterogeneous, 17.8; fine pleomorphic, 63.2; fine linear/fine linear branching, 100; (P < 0.001). Heterogenicity in size existed in 81 cases (92), in density in 69 cases (86.4) and in morphology in 86 cases (97.7). Additionally, microcalcification groups that were accompanied with soft-tissue density had a higher percentage of malignancy (67.5 vs. 54.5) but with no significant difference (P = 0.2). According to BI-RADS 4th edition, the risk of malignancy was 49.1, 66.7 and 88.1 in 4b, 4c and 5, respectively. These figures were 30, 82.9, and 100 for BI-RADS 5th version, respectively. The area under the receiver (AUC) of 4th and 5th versions of BI-RADS was 0.76 and 0.74 (both P values < 0.001, 95 confidence intervals = 0.66-0.87 and 0.63-0.85 respectively). P value for comparison was insignificant. Conclusion: The risk of malignancy increased with the heterogeneity of microcalcifications, especially in the groups with heterogeneity in density, however with no statistically significant difference. BI-RADS 5th edition could predict the likelihood of malignancy as well as 4th version. © 2018, Iranian Journal of Radiology

Risk factors of developing critical conditions in Iranian patients with COVID-19

COVID-19 due to novel Coronavirus was first reported in Wuhan, China. Nowadays, the Islamic Republic of Iran stands among countries with high COVID-19 prevalence and high burden of disease. Since the medical resources are limited, we aimed to identify the risk factors for patients developing critical conditions. This can help to improve resource management and treatment outcomes. In this retrospective study, we included 12,677 patients who were from 26 hospitals, supervised by Tehran University of Medical Sciences with signs and symptoms of COVID-19, until April 12. University integrated IT system was adopted to collect the data. We performed Logistic regression to evaluate the association between death in COVID-19 positive patients and other variables. Cough, respiratory distress and fever were the most common symptoms in our patients, respectively. Cancer, chronic lung diseases and chronic neurologic diseases were the strongest risk factors for death in COVID-19 patients. © 202

Barley Ror1 encodes a class XI myosin required for mlo-based broad-spectrum resistance to the fungal powdery mildew pathogen

Loss-of-function alleles of plant MLO genes confer broad-spectrum resistance to powdery mildews in many eudicot and monocot species. Although barley (Hordeum vulgare) mlo mutants have been used in agriculture for more than 40 years, understanding of the molecular principles underlying this type of disease resistance remains fragmentary. Forward genetic screens in barley have revealed mutations in two Required for mlo resistance (Ror) genes that partially impair immunity conferred by mlo mutants. While Ror2 encodes a soluble N-ethylmaleimide-sensitive factor-attached protein receptor (SNARE), the identity of Ror1, located at the pericentromeric region of barley chromosome 1H, remained elusive. We report the identification of Ror1 based on combined barley genomic sequence information and transcriptomic data from ror1 mutant plants. Ror1 encodes the barley class XI myosin Myo11A (HORVU.MOREX.r3.1HG0046420). Single amino acid substitutions of this myosin, deduced from non-functional ror1 mutant alleles, map to the nucleotide-binding region and the interface between the relay-helix and the converter domain of the motor protein. Ror1 myosin accumulates transiently in the course of powdery mildew infection. Functional fluorophore-labeled Ror1 variants associate with mobile intracellular compartments that partially colocalize with peroxisomes. Single-cell expression of the Ror1 tail region causes a dominant-negative effect that phenocopies ror1 loss-of-function mutants. We define a myosin motor for the establishment of mlo-mediated resistance, suggesting that motor protein-driven intracellular transport processes are critical for extracellular immunity, possibly through the targeted transfer of antifungal and/or cell wall cargoes to pathogen contact sites

Fluorescent mannosides serve as acceptor substrates for glycosyltransferase and sugar-1-phosphate transferase activities in <i>Euglena gracilis</i> membranes

Synthetic hexynyl α-D-mannopyranoside and its α-1,6-linked disaccharide counterpart were fluorescently labelled through CuAAC click chemistry with 3-azido-7-hydroxycoumarin. The resulting triazolyl-coumarin adducts, which were amenable to analysis by TLC, HPLC and mass spectrometry, proved to be acceptor substrates for α-1,6-ManT activities in mycobacterial membranes, as well as α- and β-GalT activities in trypanosomal membranes, benchmarking the potential of the fluorescent acceptor approach against earlier radiochemical assays. Following on to explore the glycobiology of the benign protozoan alga Euglena gracilis, α-1,3- and α-1,2-ManT activities were detected in membrane preparations, along with GlcT, Glc-P-T and GlcNAc-P-T activities. These studies serve to demonstrate the potential of readily accessible fluorescent glycans as substrates for exploring carbohydrate active enzymes