Characterization of blue green algae isolated from Egyptian rice field with potential anti-hepatitis C active components

Several species of cyanobacteria has been recognized for its therapeutic value that can be used for treatment of malnutrition, cancer and viral infection. Many natural occurring cyanobacteria are known to produce toxins, for example, species of the genera Microcystis, Nodularia, Nostoc, Anabaena, Aphanizomenon, Cylindrospermopsis, and Planktothrix (Oscillatoria). Cyanotoxins are classified according to their mode of action in vertebrates as hepatotoxins, neurotoxins, cytotoxins, dermatotoxins, and irritants. Microcystin is a hepatotoxin which commonly found in Microcystis and it was found to be produced by other genera, including Anabaena, Nostoc, Nodularia, and Planktothrix. In the present study cyanobacteria strain isolated from Egyptian soil was purified, characterized and identified as Nostoc sp. and named Nostoc EGY. PCR-based techniques targeting the toxin biosynthesis genes were used verifying absence of toxic genes in the newly purified cyanobacteria. Cell lysate was prepared from the purified strain; the efficacy of this lysate to prevent hepatitis C virus (HCV) replication in vitro was proved qualitatively and quantitatively. Lysate prepared from isolated cyanobacteria after 10 and 25 days of cultivation was able to prevent replication of in vitro cultivated HCV.Keywords: Hepatitis C, green algae, cyanobacteria, polymerase chain reactionAfrican Journal of Biotechnology, Vol. 13(9), pp. 1086-1096, 26 February, 201

Diagnostic performance of loop-mediated isothermal amplification (LAMP) and Ultra-sensitive PCR in diagnosis of malaria in western Saudi Arabia

Malaria diagnosis continues to be one of the most important steps in the cycle of control specially in endemic countries with low parasitic load infections. Loop-mediated isothermal amplification (LAMP) and ultrasensitive PCR (Us-PCR) are two promising candidates for malaria diagnosis. A cross sectional study performed at King Faisal Hospital, Taif KSA involved patients suffering from signs and symptoms suggesting of malaria, 35 blood samples diagnosed by Nested Multiplex PCR as a reference method (13 P. falciparum, 17 P. vivax, 3 mixed P. falciparum and P. vivax) plus two negative controls were selected to be included in this study to analyse the performance of two LAMP methods (LAMP OptiGene® and LAMP WarmStart®) and two ultrasensitive PCRs (Us-PCR TARE-2 and Us-PCR Var-ATS). LAMP OptiGene® and LAMP WarmStart® performances were identical and better than the performance of Us PCR TARE 2 and Us-PCR var-ATS for P. falciparum, achieving 93.75% sensitivity, 100% specificity and 97.17% accuracy versus 87.5% sensitivity, 100% specificity and 94.29% accuracy for the Us PCR TARE 2 and 81.25% sensitivity, 94.74% specificity and 88.57% accuracy for the Us PCR var-ATS respectively. In P. vivax diagnosis LAMP OptiGene® performed excellently with 100% sensitivity, specificity, and accuracy while LAMP WarmStart® and Us-PCR Cox1 achieved 100% sensitivity, specificity 93.33% and 97.14% accuracy. The study results highlighted the benefits of using LAMP techniques for field diagnosis of malaria in different settings where the need for a more sensitive and reliable molecular tool is mandatory but at the same time removing the high cost, long turnaround time and the need of highly specialized trained technicians to perform more sophisticated molecular techniques.The authors would like to acknowledge The Deanship of Scientific Research, Taif University, Taif, Saudi Arabia for funding of the resent research.S

High-density SNP-based association mapping of seed traits in fenugreek reveals homology with clover

Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Pityriasis alba: toward an effective treatment

Background Pityriasis alba is a common skin condition that may be challenging to treat, especially in patients with darker skin type where the hypopigmentation may be more noticeable and represents a major cosmetic concern. Objectives This study aims to evaluate the efficacy of three cost-effective treatments of PA in comparison with placebo. Patients/Methods This prospective study was conducted on 80 patients complaining from PA and divided into 4 equal groups according the received topical treatment on the target lesions twice daily for 8 weeks (Calcipotriol 0.005% cream, Tacrolimus 0.03% ointment, topical corticosteroid; Clobetasone butyrate 0.05% cream and Petrolatum as Placebo). Clinical evaluation, Physician Global Assessment, Patient’s satisfaction levels as well as point counting planimetry were done for evaluation of the response. Results Significant improvement of scaling and erythema within 3 weeks after initiation of therapy and hypopigmentation by the 8th week, except for those received placebo. Tarolimus 0.03% ointment showed simple superiority over both Calcipotriol 0.005% cream and topical corticosteroid as regards repigmenation, although, the later received the highest level of patient satisfaction. Conclusion The three treatments were superior to placebo with relative superiority to Tacrolimus 0.03% due to limited side effects

Molecular Identification of <i>Blastocystis hominis</i> Isolates in Patients with Autoimmune Diseases

Background: Blastocystis hominis (B. hominis) is a ubiquitous parasite that has spread worldwide and is commonly present in human stool specimens. It was hypothesized that infection with B. hominis plays a role in the pathogenesis of autoimmune diseases in humans. The aim of this study is to test this hypothesis by investigating patients with autoimmune diseases. Patients with various types of autoimmune diseases with gastrointestinal symptoms were enrolled in this study as cases (n = 72) along with nongastrointestinal symptom patients as controls (n = 58). All participants in this study were subjected to history taking and were investigated for B. hominis infection via wet-mount microscopic stool examinations, staining with trichrome stain, and molecular-based tests applied to their fecal samples. Blood samples were also tested for complete blood counts. B. hominis were identified with specific PCR more in cases (12/72; 16.6%) than in controls (3/58; 5.2%), with a significant difference (p B. hominis when compared to patients with nongastrointestinal symptoms (p-value < 0.05)

Characterization of blue green algae isolated from Egyptian rice field with potential anti-hepatitis C active components

Several species of cyanobacteria has been recognized for its therapeutic value that can be used for treatment of malnutrition, cancer and viral infection. Many natural occurring cyanobacteria are known to produce toxins, for example, species of the genera Microcystis, Nodularia, Nostoc, Anabaena, Aphanizomenon, Cylindrospermopsis, and Planktothrix (Oscillatoria). Cyanotoxins are classified according to their mode of action in vertebrates as hepatotoxins, neurotoxins, cytotoxins, dermatotoxins, and irritants. Microcystin is a hepatotoxin which commonly found in Microcystis and it was found to be produced by other genera, including Anabaena, Nostoc, Nodularia, and Planktothrix. In the present study cyanobacteria strain isolated from Egyptian soil was purified, characterized and identified as Nostoc sp. and named Nostoc EGY. PCR-based techniques targeting the toxin biosynthesis genes were used verifying absence of toxic genes in the newly purified cyanobacteria. Cell lysate was prepared from the purified strain; the efficacy of this lysate to prevent hepatitis C virus (HCV) replication in vitro was proved qualitatively and quantitatively. Lysate prepared from isolated cyanobacteria after 10 and 25 days of cultivation was able to prevent replication of in vitro cultivated HCV

Assessment of serum vitamin D level in patients with systemic lupus erythematosus

Objective To evaluate the serum level of vitamin D in patients with systemic lupus erythematosus (SLE) and its relationship with disease activity. Patients and methods Forty patients suffering from SLE were enrolled in this study (group I). They were further divided into two subgroups according to the SLE disease activity index (SLEDAI) score: group Ia with respect to disease activity and group Ib with respect to disease remission. Another 20 age-matched and sex-matched healthy individuals were chosen as control group II. All patients underwent complete medical history taking and thorough clinical examination; the disease activity was assessed by the use of SLEDAI score. Serum vitamin D level in all patients and controls was measured. Results Vitamin D level was significantly higher in controls than in patients. The vitamin D deficiency was highly prevalent among patients with disease activity than in the remission group. There was highly significant inverse correlation between vitamin D level and SLEDAI score in the patient group. Vitamin D level correlated inversely with C reactive protein (CRP) and anti-dsDNA in the disease activity group, whereas it correlated positively with C3. Conclusion Vitamin D deficiency is prevalent in SLE patients more than in healthy controls; vitamin D deficiency is highly prevalent among patients with disease activity than in the remission group, and vitamin D level correlated inversely with disease activity, which suggest that inadequate vitamin D level, among other factors, probably contributed to the development of active disease in patients with SLE

Identifying SNP markers associated with distinctness, uniformity, and stability testing in Egyptian fenugreek genotypes.

Distinctness, uniformity, and stability (DUS) test is the legal requirement in crop breeding to grant the intellectual property right for new varieties by evaluating their morphological characteristics across environments. On the other hand, molecular markers accurately identify genetic variations and validate the purity of the cultivars. Therefore, genomic DUS can improve the efficiency of traditional DUS testing. In this study, 112 Egyptian fenugreek genotypes were grown in Egypt at two locations: Wadi El-Natrun (Wadi), El-Beheira Governorate, with salty and sandy soil, and Giza, Giza governorate, with loamy clay soil. Twelve traits were measured, of which four showed a high correlation above 0.94 over the two locations. We observed significant genotype-by-location interactions (GxL) for seed yield, as it was superior in Wadi, with few overlapping genotypes with Giza. We attribute this superiority in Wadi to the maternal habitat, as most genotypes grew in governorates with newly reclaimed salty and sandy soil. As a first step toward genomic DUS, we performed an association study, and out of 38,142 SNPs, we identified 39 SNPs demonstrating conditional neutrality and four showing pleiotropic effects. Forty additional SNPs overlapped between both locations, each showing a similar impact on the associated trait. Our findings highlight the importance of GxL in validating the effect of each SNP to make better decisions about its suitability in the marker-assisted breeding program and demonstrate its potential use in registering new plant varieties