MicroRNA profiling in dogs undergoing induced ischemic heart infarction: An experimental study.

Background and Aim: MicroRNAs (miRNAs) play an important role in various biological functions. According to many studies, miRNA expression is tissue-specific, strongly controlled throughout embryogenesis, and over- or under-expressed in numerous disorders, including cardiovascular pathologies. This study aimed to screen, characterize, and profile many induced biomarkers (miRNAs) in dog serum before and after experimentally inducing a regional myocardial infarction (MI) by occluding the coronary arteries under general anesthesia. Materials and Methods: A preclinical experimental animal study recruited 12 healthy canine dogs. The selected canine dogs were anesthetized with 1 mg/kg xylazine and 15 mg/kg ketamine before undergoing femoral arterial catheterization under fluoroscopic supervision. Commercial assay kits were used to purify total RNA and miRNA before the occlusion and 2 h after the occlusion according to the manufacturer's guidelines, and the samples were stored in RNase/DNase-free water at -80°C. Data were analyzed by GraphPad Prism 5.0 software (GraphPad Prism, San Diego, CA) SPSS, and GenEx software (www.multid.se) or (REST V3). Results: Among 325 transcribed genes, 20 were identified in 2 h. After MI, 14 biomarkers were negative, indicating downregulation, and 6 (3-F08, 3-B10, 4-A11, 1-A06, 2-E01, 3-F10) were positive, indicating upregulation. Polymerase chain reaction assay results showed a normalized fold-change in gene expression in the test sample. Fold values >1 represented a biologically significant change. Conclusion: Profiling of miRNAs before and after MI in a dog model revealed upregulation of six previously unidentified biomarkers (3-F08, 3-B10, 4-A11, 1-A06, 2-E01, and 3-F10), indicating various miRNA regulatory patterns.

Potential linear B-cells epitope change to a helix structure in the spike of Omicron 21L or BA.2 predicts increased SARS-CoV-2 antibodies evasion.

The world health organization has announced that SARS-CoV-2 Omicron variant (B.1.1.529), including the three versions; 21K (BA.1), 21L (BA.2) and 21M (BA.3) as a variant of concern (VOC) on November 2022. In this study, we used the specialized computational platforms to predict the stability and flexibility of the spike protein of Omicron. The aim of this study was to investigate the expected effect of Omicron spike mutations on its physiochemical properties. Findings of this study revealed 16 stabilizing mutations that might explain a newly gained environmental stability. We expect the new mutations to play a crucial role in changing the physiochemical properties of epitopes of the spike protein. The notable finding of SuerPose work was the potential linear B-cells epitope G252 → S255 that has been changed in the spike protein of the Omicron 21L to a helix structure which might confer an escape from human monoclonal antibodies.

Dynamics prediction of emerging notable spike protein mutations in SARS-CoV-2 implies a need for updated vaccines.

The spike protein of SARS-CoV-2 plays a crucial role in binding with the human cell surface, which causes its pathogenicity. This study aimed to predict molecular dynamics change of emerging variants in the spike protein. In this study, several structural biology tools, such as SuperPose, were utilized to study spike protein structures' thermodynamics, superimposition, and the spike protein disulphide bonds. This questions the current vaccines efficacies that were based on the Nextstrain clade 19A that first documented in Wuhan and lacks any variants. The prediction results of this study have exhibited the stabilizing role of the globally dominant variant, the D614G; clade 20A, and other variants in addition to their role in increasing the flexibility of the spike protein of the virus. The SuperPose findings have revealed a conformational change impact of D614G in allowing the polybasic Furin cleavage site (682RRAR↓S686) to be closer to the receptor-binding domain (RBD) and hence more exposed to cleavage. The presence of D614G in any clade or subclade, such as 20A, B.1.1.7 (20I/501Y.V1) or Alpha, B.1.351 (20H/501Y.V2) or Beta, P.1 (20J/501Y.V3) or Gamma, B.1.617.2 (21A/478K.V1) or Delta, has increased its stability and flexibility and unified the superimposition among all clades which might impact the virus ability to escape the antibodies neutralization by changing the antigenicity drift of the protein three-dimensional (3D) structure from the wild type clade 19A; this is in agreement with previous study. In conclusion, a new design for the current vaccines to include at least the mutation D614G is immediately needed.

Characterizing and Profiling microRNAs in Dogs Undergoing Induced Ischemic Brain Stroke After Middle Cerebral Artery Occlusion Under Fluoroscopic Guidance.

PURPOSE: Ischemic stroke of the brain is still considered one of the most common causes of disability and death in developed and developing countries in human beings despite advances in medicine and technology. This study was conducted to characterize and profile tens of induced biomarkers (microRNAs) after experimentally inducing regional ischemic stroke of the brain by occluding the middle cerebral artery under fluoroscopic guidance using an autologous blood clot. PATIENT AND METHODS: A total of six healthy dogs were recruited for this study. The microRNAs were profiled in the blood and urine before and after occluding the middle cerebral artery using genetic techniques. RESULTS: The very highly expressed genes were comprised within cluster A, followed by cluster D in both 24 and 48-hour brain samples. Clusters B and C revealed down-regulated genes, while miRNAs remained up-regulated in the 24-hour samples merely in cluster F. Upregulated genes at 48 hours of reperfusion were included in cluster E. On the other hand, changes were observed after a day on the cluster G genes. Exclusive upregulation was notified after 2 days due to the changes in mIR-138. The normalized gene expression in the test sample is witnessed through Fold-Change, which divides the control sample's normalized gene expression. Moreover, fold-change has emerged as a significant approach for representing fold-regulation. CONCLUSION: The microRNAs expression in blood and urine may have a potential role in the diagnosis, prognosis, and assessment of therapy associated with cerebral artery occlusion under fluoroscopic guidance.

Mutational sensitivity of D614G in spike protein of SARS-CoV-2 in Jordan.

BACKGROUND: Spike protein is the surface glycoprotein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) necessary for the entry of the virus via the transmembrane receptors of the human respiratory cells causing COVID-19 disease. AIM: Here, we aimed to predict the three-dimensional monomer structure of spike protein of SARS-CoV-2 from 20 Jordanian nasopharyngeal samples and to determine the percentage of single amino acid variants (SAV) in the spike protein of SARS-CoV-2. METHODS: The output of the Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) found four single amino acid variants in the spike gene. RESULTS: The first variant represented by 5% of samples that showed tyrosine deletion at Y144 located in the N terminal domain. The second and the dominant variant, represented by 62%, showed aspartate a coil amino acid substitution to glycine an extracellular amino acid at D614G located in the spike recognition binding site. The third variant, represented by 5%, showed aspartate substitution to tyrosine at D1139Y, and the fourth variant, represented by 5% glycine substitution to serine at G1167S. CONCLUSION: Our results have shown low mutational sensitivity in all variants except to D614G the one with the most likely neutral mutational sensitivity that all variants might not explicitly affect the function of spike glycoprotein. However, D614G might change the viral conformational plasticity and hence a potential viral fitness gain but one must be cautious about drawing any concrete conclusions about the severity of symptoms and viral transmission from genomic data only. GENERAL SIGNIFICANCE: Studying mutations such as D614G in deep is essential to control the pandemic in terms of immune systems, antibodies, or even vaccines.

miRNA target prediction might explain the reduced transmission of SARS-CoV-2 in Jordan, Middle East.

MicroRNAs (miRNAs) are non-coding RNAs that control many functions within the human cells by controlling protein levels through binding to messenger RNA (mRNA) translation process or mRNA abundance. Many pieces of evidence show that miRNAs affect the viral RNA replication and pathogenesis through direct binding to the RNA virus to mediate changes in the host transcriptome. Many previous studies have been studying the interaction between human cells' miRNA and viral RNA to predict many targets along the viral genome. In this work, via the miRDB database, we determined the target scores of predicted human miRNA to bind with the ss-RNA of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) in general and its spike gene in specific. Our predicted miRNA targets of the ss-RNA of SARS-CoV-2 might destabilize the ss-RNA translation of SARS-CoV-2 that has been established by more than 80% of asymptomatic infected cases in Jordan due to host miRNA interactions. In respiratory epithelial cells, the high prediction scoring for miRNAs covers the RNA from 5' to 3' that explains successful antiviral defenses against ss-RNA of SARS-CoV-2 and might lead to new nucleotide deletion mechanisms. The exciting findings here that the nucleotide substitution 1841A > G at the viral genomic RNA level, which is an amino acid substation D614G at the spike protein level showed a change in the predicted miRNA sequence from hsa-miR-4793-5p to hsa-miR-3620-3p with an increase in the target score from 91 to 92.

Novel mutations in the SMPD1 gene in Jordanian children with Acid sphingomyelinase deficiency (Niemann-Pick types A and B).

Acid sphingomyelinase (ASM) deficiency (ASMD) is a spectrum that includes Niemann-Pick disease (NPD) types A (NPD A) and B (NPD B). ASMD is characterized by intracellular accumulation of unesterified cholesterol and gangliosides within the endosomal-lysosomal system. It is caused by different mutations in SMPD1 gene that result in reduction or complete absence of acid sphingomyelinase activity in the cells. Herein, four unrelated consanguineous families with two NPD A and three NPD B patients were assessed for their genotypes via sequencing of the SMPD1 gene and their acid sphingomyelinase enzymatic activity. Among the eight identified mutations, three were novel and reported for the first time in Jordanian families (c.120_131delGCTGGCGCTGGC or c.132_143delGCTGGCGCTGGC, c.1758T > G, and c.1344T > A). All the patients displayed ASM activity lower than 1.3 µmol/l/h (P < 0.001). Genotyping and enzymatic assessment might play a significant role in disease identification in people at risk to facilitate genetic counseling in the future.

Identification and Characterization of BTD Gene Mutations in Jordanian Children with Biotinidase Deficiency.

Biotinidase deficiency is an autosomal recessive metabolic disorder whose diagnosis currently depends on clinical symptoms and a biotinidase enzyme assay. This study aimed to investigate the mutational status and enzymatic activity of biotinidase deficiency in seven unrelated Jordanian families including 10 patients and 17 healthy family members. Amplified DNA was analyzed by the automated Sanger sequencing method, and the enzymatic assay was performed using a colorimetric assessment. Biotinidase level was significantly lower (p < 0.001) in BTD children compare to their non-affected family members. Genetic sequencing revealed six different mutations in Jordanian patients. One mutation was novel and located in exon 4, which could be a prevalent mutation for biotinidase deficiency in the Jordanian population. Identification of these common mutations and combing the enzymatic activity with genotypic data will help clinicians with regard to better genetic counseling and management through implementing prevention programs in the future.

Analysis of Zn, Cd, As, Cu, Pb, and Fe in snails as bioindicators and soil samples near traffic road by ICP-OES.

Snails are used as biological indicators of the environment pollution for heavy metals. Living snail samples were collected from different sites at the city of Irbid-Jordan and classified according to their morphological features including Helix pelasga, Eobania vermiculata, Xeropicta derbentina, Oychilus, Xerocrassa seetzenii, Xerocrassa simulata, and Pila. Zn, Cd, As, Cu, Pb, and Fe levels were measured by inductively coupled plasma-optical emission spectroscopy. Results indicated that metal concentrations in all snail shell samples were with an average and range for Zn 22.4 (6.5-105.5) µg g(-1), Cd 7.8 (0.4-48.1) µg g(-1), As 25.9 (0.7-248.5) µg g(-1), Cu 15.1 (1.6-69.0) µg g(-1), Pb 0.4 (0.2-1.7) µg g(-1), and Fe 119.6 (14.0-1102.0) µg g(-1), whereas, in soil samples, the average and range for Zn 204.0 (12.0-709.0) µg g(-1), Cd 5.7 (0.2-39.5) µg g(-1), As 3.2 (1.8-5.2) µg g(-1), Cu 22.1 (2.3-77.4) µg g(-1), Pb 0.2 (0.1-0.3) µg g(-1), and Fe 242.4 (25.0-680.0) µg g(-1).

Hereditary angioedema in a Jordanian family with a novel missense mutation in the C1-inhibitor N-terminal domain.

Hereditary angioedema due to C1-inhibitor deficiency (C1-INH-HAE) is an autosomal dominant disease caused by mutations in the SERPING1 gene. A Jordanian family, including 14 individuals with C1-INH-HAE clinical symptoms, was studied. In the propositus and his parents, SERPING1 had four mutations leading to amino acid substitutions. Two are known polymorphic variants (c.167T>C; p.Val34Ala and c.1438G>A; p.Val458Met), the others are newly described. One (c.203C>T; p.Thr46Ile) is located in the N-terminal domain of the C1-inhibitor protein and segregates with angioedema symptoms in the family. The other (c.800C>T; p.Ala245Val) belongs to the serpin domain, and derives from the unaffected father. DNA from additional 24 family members were screened for c.203C>T mutation in the target gene. All individuals heterozygous for the c.203C>T mutation had antigenic and functional plasma levels of C1-inhibitor below 50% of normal, confirming the diagnosis of type I C1-INH-HAE. Angioedema symptoms were present in 14 of 16 subjects carrier for the c.203T allele. Among these subjects, those carrying the c.800T variation had more severe and frequent symptoms than subjects without this mutation. This family-based study provides the first evidence that multiple amino acid substitutions in SERPING1 could influence C1-INH-HAE phenotype.

Seroprevalence and genotyping of hepatitis C virus in multiple transfused Jordanian patients with ß-thalassemia major.

OBJECTIVE: The main objectives of this study are to investigate the prevalence of HCV among patients with ß-thalassemia major and to determine the most prevalent genotype for this virus among them. METHODS: One hundred twenty-two ß-thalassemia major patients who were previously diagnosed at the molecular level were included. All plasma samples were tested for the presence of antibodies by ELISA. Real-time polymerase chain reaction (PCR) was used in the quantitation the HCV RNA viral loads, and consequently, patients with high virus titer were genotyped by the linear array. RESULTS: Forty of the patients were anti-HCV positive. The prevalence of anti-HCV was significantly higher in patients who received blood transfusion before 1993 (83.7%) than in those who received it after 1993 (16.3%) (p=0.000). ß-thalassemia major patients with HCV infection had significantly higher rates of elevated aspartate aminotransferase (54.4% vs 40.5%, p=0.045) and alanine aminotransferase (72.47% vs 37.47%, p=0.00) and of splenectomy (54.8% vs 45.2%, p=0.004) than ß-thalassemia major patients without HCV. CONCLUSION: HCV genotype 4 is the commonest genotype in multi-transfused patients with ß-thalassemia major in Jordan.

Removal of lead and cadmium by halophilic bacteria isolated from the Dead Sea shore, Jordan.

Ten Gram-positive and Gram-negative bacterial cultures were recovered from nine water, mud, and soil samples from the Dead Sea shore at Suwaymah. They were able to grow at 10% NaCl and at 45 degrees C. Bacterial cultures 6 and 8 were able to grow in nutrient media supplemented with 2250 ppm of Pb. Bacterial cultures 1, 3-6, 9, and 10 were able to grow in nutrient medium supplemented with 1000 ppm of Cd. Atomic absorption spectrometry was used to estimate the absorbed Pb and Cd by bacterial cultures from 5-, 25-, 100-, and 500-ppm stock solutions of both elements. After 2 wk, the results showed that the maximum absorption for Pb was achieved by culture 6 in the following percentages: 79.8%, 70.48%, 89.48%, and 83.39%, respectively. The maximum absorption of the same concentration of Cd was achieved by culture 9 with the following percentages: 69.2%, 32.24%, 44.98%, and 60.0%, respectively. After 3 wk of incubation, the estimated absorption of both heavy metals was achieved by the same cultures (6 and 9), respectively, in the following percentages: 86.8%, 76.72%, 96.25%, and 96.0% for Pb and 82.60%, 93.2%, 92.74%, and 89.79% for Cd. The accumulation of the absorbed metals was found to be maximum in the protoplast of all the cultures. The accumulation at the cell wall was maximum in culture 2, and between the cell wall and the plasma membrane, it was maximum in cultures 2 and 8 for Pb and Cd, respectively.