Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide.

Ligand/protein molecular recognition involves a dynamic process, whereby both partners require a degree of structural plasticity to regulate the binding/unbinding event. Here, we present the characterization of the interaction between a highly dynamic G-rich oligonucleotide, M08s-1, and its target protein, human α-thrombin. M08s-1 is the most active anticoagulant aptamer selected thus far. Circular dichroism and gel electrophoresis analyses indicate that both intramolecular and intermolecular G-quadruplex structures are populated in solution. The presence of thrombin stabilises the antiparallel intramolecular chair-like G-quadruplex conformation, that provides by far the main contribution to the biological activity of the aptamer. The crystal structure of the thrombin-oligonucleotide complex reveals that M08s-1 adopts a kinked structural organization formed by a G-quadruplex domain and a long duplex module, linked by a stretch of five purine bases. The quadruplex motif hooks the exosite I region of thrombin and the duplex region is folded towards the surface of the protein. This structural feature, which has never been observed in other anti-exosite I aptamers with a shorter duplex motif, hinders the approach of a protein substrate to the active site region and may well explain the significant increase in the anticoagulant activity of M08s-1 compared to the other anti-exosite I aptamers.

Software Workflows and Infrastructures for Precision Oncology.

Precision oncology mainly relies on genetic and molecular patient profiling from high-throughput sequencing data. The necessity to process and analyze large volumes of data has led to the development of robust computational tools and methods. The most challenging aspect in the implementation of a precision oncology workflow involves proper handling of large volume of data, while ensuring the results are reproducible and replicable. In this chapter, we provide a detailed description of the various tools available for the design and implementation of a precision oncology pipeline along with the technical considerations to make to utilize these tools effectively. We then provide a guide to the development of a precision oncology pipeline, with a specific emphasis on the software workflows and infrastructure needed.

Prognostic significance of serum miR-18a-5p in severe COVID-19 Egyptian patients.

BACKGROUND: The identification of miRNAs as well as characterization of miRNA-mRNA interactions in SARS-CoV-2 infection is important to understand their role in disease pathogenesis. Therefore the aim of the present study was to measure the expression levels of hsa-mir-18a-5p in the sera of severe COVID-19 Egyptian patients admitted to ICU to investigate its roles in the pathogenesis and severity of COVID-19 disease. METHODS: A total of 180 unvaccinated severe COVID-19 patients were enrolled in our study. Besides the routine laboratory work, the expression level of hsa-mir-18a-5p was done using reverse transcription quantitative real-time PCR (RTqPCR) technique. Also, target genes of hsa-mir-18a-5p were explored by using online bioinformatics databases. RESULTS: The expression level of hsa-mir-18a-5p decreased in nonsurvival severe COVID-19 patients (0.38 ± 0.26) when compared to the survival ones (0.84 ± 0.23). While as a prognostic tool for the prediction of bad prognosis and mortality among severe COVID-19 patients, our results showed that the serum hsa-mir-18a-5p expression level is a good sensitive and specific marker. By using bioinformatics tools, our results revealed that the decreased hsa-mir-18a-5p expression level may have a crucial role in COVID-19 pathogenesis and severity through decreased immunological responses (interpreted as lymphopenia) or increased inflammation (interpreted as increased serum levels of IL-6, CRP, LDH). CONCLUSION: Taken together, the decreased expression level of hsa-mir-18a-5p could be a bad prognostic marker and therapeutic overexpression of hsa-mir-18a-5p could be a novel approach in the treatment of COVID-19 disease.

Increased serum interleukin-6 and lactate dehydrogenase levels among nonsurvival severe COVID-19 patients when compared to survival ones.

BACKGROUND: Accurate and rapid laboratory diagnosis of COVID-19 infection and its deterioration is one of the milestones of pandemic control. Therefore, this study aimed to compare the diagnostic and prognostic accuracy of the mainly used laboratory biomarkers (WBCS, neutrophil and lymphocyte percentages, CRP, ferritin, IL-6, D-dimer, procalcitonin, and LDH) in the sera of severe COVID-19 Egyptian patients to assess the most appropriate biomarker used in severe COVID-19 patients. METHODS: A total of 180 unvaccinated severe COVID-19 patients were enrolled in our study. Demographic data, hospitalization time, medical history, oxygen saturation, respiratory rate, oxygen supply, laboratory findings, and thorax tomography of the patients were obtained retrospectively from the hospital's electronic information system. RESULTS: Our results revealed that the levels of neutrophil percentage, CRP, IL-6, PCT, and LDH were significantly increased while lymphocyte percentage was significantly decreased among nonsurvival severe COVID-19 patients when compared with survival ones. By using ROC curve analysis, IL-6, and LDH are the most sensitive and specific markers for the prediction of bad prognosis and mortality among severe COVID-19 patients with 100% and 93% sensitivity and 93.7% specificity; respectively. IL-6 and LDH showed significant correlations with the other parameters, which suggested their association with the severity of COVID-19. CONCLUSION: By using survival severe COVID-19 patients as a control group, our results showed that blood neutrophil percentage, serum CRP, IL-6, PCT, and LDH were significantly increased in non-survivors as compared to survivors. As biomarkers, our results revealed that IL-6 and LDH are good predictors of mortality among severe COVID-19 patients.

Molecular characterization and mutational analysis of recombinant diadenosine 5',5″-P¹,P4-tetraphosphate hydrolase from Plasmodium falciparum.

Asymmetrical diadenosine 5',5"-P¹,P4-tetraphosphate hydrolase (EC 3.6.1.17) from human malaria parasite Plasmodium falciparum was expressed in Escherichia coli, purified to homogeneity, and characterized for the first time as a biological target for chemotherapeutic agents against malaria. Plasmodium falciparum Ap4A (PfAp4A) hydrolase not only catalyzes diadenosine 5',5″-P¹,P4-tetraphosphate (Ap4A) to ATP and AMP, but also diadenosine 5″-P¹,P5-pentaphosphate (Ap5A) to ATP and ADP. Marked enzyme heat stability corresponding to the highest level of activity was observed at 60°C. The recombinant enzyme showed maximal activity in the presence of 5 mM Mg²âº ions. Kinetic analysis revealed the values of K(m) and K(cat) as 0.6 µM and 2.5 min⁻¹, respectively. Comparative protein modeling indicated an additional space in the substrate binding site of the parasitic enzyme compared with that of humans. Mutagenic analysis of the amino acid residue (Pro133) forming the additional space revealed a 5-fold increase in the wild-type Km value when replaced by a smaller (Ala) residue. Furthermore, catalytic activity was markedly affected by introducing a larger residue (Phe), thus creating the potential to develop a specific inhibitor of PfAp4A hydrolase.

Evaluation of serum total sialic acid in moderate COVID-19 patients with and without gastrointestinal tract manifestations.

BACKGROUND: It is known that SARS-CoV-2 mostly infects the respiratory system causing pneumonia; although it can also affect the gastrointestinal tract (GIT), which covered with a bi-layer of mucus rich in glycosylated proteins that terminated by sialic acid. Therefore; this study aimed to evaluate serum total sialic acid (TSA) in moderate COVID-19 patients with and without GIT manifestations. METHODS: A total of 161 moderate COVID-19 patients without and with GIT manifestations and 50 controls were enrolled into our study. Serum electrolytes levels were measured by using colorimetric or turbidmetric commercial assay kits, while the level of serum TSA was measured by using a commercial ELISA kit. RESULTS: Our results showed that serum TSA level was highly significantly increased in moderate COVID-19 patients with GIT manifestations (81.43 ± 8.91) when compared with controls (61.24 ± 6.41) or even moderate COVID-19 patients without GIT manifestations (69.46 ± 7.03). ROC curve analysis showed that AUC for TSA is 0.84 with 76.2 % sensitivity and 73.7 % specificity in discrimination between moderate COVID-19 patients with and without GIT manifestations. Serum potassium and sodium levels were highly significantly decreased in moderate COVID-19 patients with GIT manifestations when compared with controls or even moderate COVID-19 patients without GIT manifestations; while serum calcium level was found to be significantly decreased in moderate COVID-19 patients with GIT manifestations when compared with controls. CONCLUSION: Finally, we can conclude that SA plays a crucial role in the pathogenesis of GIT complications associated with COVID-19 and could be a potential biomarker for the COVID-19 gastrointestinal complications.

Circulating plasma miR-155 is a potential biomarker for the detection of SARS-CoV-2 infection.

Identification of human miRNAs involved in coronavirus-host interplay is important due to the current COVID-19 pandemic. Therefore, this study aimed to measure the circulating plasma miR-155 expression level in COVID-19 patients and healthy controls to investigate its roles in the pathogenesis and severity of COVID-19 disease and to assess its usefulness as a clinical biomarker for the detection of COVID-19 disease and the severity of infection. A total of 150 COVID-19 patients and 50 controls were enrolled into our study. Beside the routine laboratory work and chest computed tomography (CT) scans of COVID-19 patients, plasma miR-155 expression level was measured using reverse transcription quantitative real-time PCR (RT-qPCR) technique. Our results demonstrated increased miR-155 expression level in COVID-19 patients compared to controls, in severe compared to moderate COVID-19 patients, and in non-survival compared to survival COVID-19 patients. miR-155 expression level also had significant correlation with clinicopathological characteristics of COVID-19 patients such as chest CT findings, CRP, ferritin, mortality, D-dimer, WBC count, and lymphocytes and neutrophils percentages. Also, our results showed that the area under the curve (AUC) for miR-155 was 0.986 with 90% sensitivity and 100% specificity when used as a biomarker for the detection of COVID-19 disease; while in detection of severity of COVID-19 disease, AUC for miR-155 was 0.75 with 76% sensitivity and specificity. From these results we can conclude that miR-155 has a crucial role in the pathogenesis and severity of COVID-19; also, it could be a good diagnostic clinical biomarker for the detection of COVID-19 disease and the severity of infection.

Two-dimensional quantum dots for highly efficient heterojunction solar cells.

The electronic and optical properties of finite silicene, graphene, and arsenene heterostructures are investigated using first principles calculations. The optoelectronic properties of these structures are precisely controlled, by chemical functionalization, shape, and size, to produce suitable donor energy gap and minimal conduction band offset that enable the construction of efficient heterojunction solar cells. Heterojunctions with only Van der Waals interactions between layers have been achieved in functionalized silicene/graphene and arsenene/graphene. The distribution of the highest occupied/lowest unoccupied molecular orbital on donor/acceptor layer in addition to the contribution of each layer into the total electronic density of states insure that the only interlayer interaction is the van der Waals one and charge separation is attained. The heterojunctions have donors' energy gaps ranging from 1.2 to 1.8 eV which in conjunction with the very low conduction band offset ∼ 0.002 eV enable the building of type-II solar cells with extremely high power conversion efficiency up to 23.34%. The prominent low energy optical excitations are mainly contributed by a transition from donor molecular orbitals to acceptor ones. Therefore, functionalized 2D heterojunctions are excellent candidates for building ultrathin, stable, and low-cost efficient solar cells.

Interferon-γ-induced protein 10 (IP-10) and serum amyloid A (SAA) are excellent biomarkers for the prediction of COVID-19 progression and severity.

AIMS: Early diagnosis and appropriate treatment are essential in reducing the morbidity and mortality of COVID-19-infected patients. The current study aimed to measure the levels of serum IP-10 and SAA in positive COVID-19 Egyptian patients to explore their clinical values and significance in discrimination between moderate and severe COVID-19 infection and predicting the severity and prognosis of COVID-19 disease. MAIN METHODS: A total of 150 COVID-19 patients and 50 controls were enrolled into our study. Beside the routine lab work of positive COVID-19 patients; IP-10 and SAA were measured using ELISA kit. KEY FINDINGS: Our results revealed that the levels of D-dimer (2.64 ± 3.34), ferritin (494.11 ± 260.96), SAA (171.89 ± 51.96), IP-10 (405.0 ± 85.27), WBCs count (14.38 ± 6.06) and neutrophils count (79.26 ± 5.57) were highly significantly increased in severe to critically severe patients when compared with mild to moderate patients; while lymphocytes count (14.21 ± 5.13) was highly significantly decreased when compared to moderate patients. ROC curve analysis results showed that AUC from high to low was IP-10 Ëƒ SAA Ëƒ Ferritin Ëƒ D-dimer Ëƒ CRP. SIGNIFICANCE: From these results we can conclude that both IP-10 and SAA could be excellent biomarkers in discrimination between moderate and severe COVID-19 infection and predicting the severity and prognosis of COVID-19 disease.

Dengue and hepatitis E virus infection in pregnant women in Eastern Sudan, a challenge for diagnosis in an endemic area.

Dengue fever and hepatitis E virus infection are both a public health problem in developing countries due to poor sanitation. Infection with viral hepatitis and dengue fever can present with similar clinical such and fever, headache and abortion. This study was conducted in Port-Sudan city in the eastern part of the country. ELISA and Real Time PCR tests were used to detect the infection. A total number of 39 pregnant women with a mean age 26 ±7.8 were included in the study. All of them had fever, 32 (92.3%) admitted with headache, 11 (28.2%) of them had vomiting, and abortion was reported in two cases (5.1%). The study showed that 4 (10.3%) of pregnant women were positive for the Hepatitis E virus, 5 (12.8%) positive for Dengue virus IgG, and only one sample (2.6%) was positive for IgM capture ELISA and real time PCR. Death due to hepatitis E infection was reported in one case with 7(th) month of pregnancy. Most of hepatitis cases were reported in the central sector of the Portsudan city. The diagnosis of hepatitis E virus and dengue virus in an endemic area is a great challenge for health care staff working in these areas. Both Dengue virus and Hepatitis E virus infection should be considered in pregnant women especially in similar settings.