Honeybees play a vital role in the world’s food supply by acting as essential pollinators in the ... more Honeybees play a vital role in the world’s food supply by acting as essential pollinators in the agricultural fields. Interestingly, more than one third of the world’s essential crops are honeybee’s dependant. The adult honeybeeworkers harbour a simple specific bacterial spectrum in their guts with vital role in bees’ health. Gut microbial diversity of adult honeybee workerswasstudied through targeting the V3 and V4 regions of the 16S rRNA geneviaIllumina MiSeq. The study identified four phyla of the gut microbiomesinadult workersof the two-honeybee subspecies A.m. jemeniticaandA.m. carnica. The most abundant phylum in microbiome of A.m. jemeniticawasFirmicutes (48%), while Protobacteria and Actinobacteriaphylawere less abundantat figures of31% and 10%, respectively. In microbiome of A.m. carnica,Firmicutes (57%) was also the most dominant phylum, while Protobacteria and Actinobacteria had lower prevalence at figures of 31% and 10%, respectively. At genus level, adult honeybee worke...
Enzymes in the cysteine and methionine metabolic pathways in apical and mature leaves responded d... more Enzymes in the cysteine and methionine metabolic pathways in apical and mature leaves responded differentially to changing environment at two time points (morning, A and midday, G). Upregulated (activated) in apical leaves (blue), upregulated in mature leaves (red), downregulated (repressed) in apical leaves (orange box), downregulated in mature leaves (green box). (DOCX 201Â kb)
Fold change values of assembled transcripts of R. stricta SRA database in different clusters in t... more Fold change values of assembled transcripts of R. stricta SRA database in different clusters in the apical leaves (A1-L4) at different time points of the day (A, morning; F-H, midday & L, dusk). (XLSX 775Â kb)
Fold change values of selected upregulated genes encoding HSPs in apical (A1-L4) and mature (A5-L... more Fold change values of selected upregulated genes encoding HSPs in apical (A1-L4) and mature (A5-L8) leaves during the day (A, morning; F-H, midday & L, dusk) in R. stricta (XLSX 25Â kb)
Table S1. Number of sequence reads generated for each sample. Table S2. List of metabolite signal... more Table S1. Number of sequence reads generated for each sample. Table S2. List of metabolite signals matched to known standards. (DOCX 100 kb)
Tobacco TF IDs in tobacco, their analogues in Arabidopsis and knockout (KO) and over-expression l... more Tobacco TF IDs in tobacco, their analogues in Arabidopsis and knockout (KO) and over-expression lines along with the links to indicate known function in Arabidopsis database (TAIR, http://www.arabidopsis.org/ ). (DOCX 17 kb)
List of TFs (orange box) co-expressed with PCD-related genes in 10 clusters of gene expression in... more List of TFs (orange box) co-expressed with PCD-related genes in 10 clusters of gene expression in tobacco. (DOCX 21 kb)
Tobacco TFs IDs (T1-T31) and primer names and sequences along with the expected amplicon sizes (b... more Tobacco TFs IDs (T1-T31) and primer names and sequences along with the expected amplicon sizes (bp) to be utilized in constructing pTRV2 vectors (blue boxes) for VIGS, in conducting semi-quantitative RT-PCR (orange boxes) or in both (green boxes). Information for amplifying selected tobacco TFs (T14, T15 and T24) via qRT-PCR (purple boxes) and information for amplifying selected tobacco PCD-related genes (G13, G15 and G18) and Arabidopsis TFs ARF109 (AtT14) and TFIID5 (AtTF24), either knocked out or over-expressed, via sqRT-PCR are shown. Gene codes refer to those indicated in Additional file 3: Table S2. (DOCX 28 kb)
Semi-quantitative RT-PCR for tobacco VIGS lines of 13 knocked down TFs induced 2Â h post oxalic a... more Semi-quantitative RT-PCR for tobacco VIGS lines of 13 knocked down TFs induced 2Â h post oxalic acid treatment (20Â mM) as compared to their WT and VIGS line with empty pTRV2 (V2) plants. Amplicon sizes of different genes and primers used are shown in Additional file 5: Table S3. The Nbactin gene was used as the house-keeping control. Gene codes refer to those indicated in Additional file 3: Table S2. (DOCX 684 kb)
Background: Studying human skin-associated bacterial communities is crucial to understanding huma... more Background: Studying human skin-associated bacterial communities is crucial to understanding human diseases, disease progression, and their role in maintaining human health. Objectives: This study aimed to identify normal (healthy) skin microbiome signatures of eight individuals living in Jeddah, Makkah Al-Mukarramah region, Saudi Arabia. Methods: The study involved the analysis of resident skin microbiome in inner elbow of the right arm after ethical approval is issued and an informed consent form is signed by participant individuals. Results: Phylogenetic tree indicated the existence of four phyla, e.g., Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria. Firmicutes were shown to be the highest in abundance, while Bacteroidetes were the lowest. At the genus level, Staphylococcus was the highest in abundance, while Enterococcus was the lowest. At the species level, Bacillus cereus was the highest in abundance, while Roseomonas mucosa was the lowest. The analysis for the high...
Drought tolerance is a complex trait of increasing importance. The present study aims at detectin... more Drought tolerance is a complex trait of increasing importance. The present study aims at detecting molecular markers in eight bread wheat (T. aestivum) cultivars, based on ISSR and AFLP, differing in their performance under drought stress. Wheat is one of the most important cereal crops in the world. Therefore, the identification of molecular markers for drought tolerance is crucial for the future development of tolerant varieties through breeding. Across the two types of markers, a total of 109 cultivar-specific markers were recovered. Most markers were resulted for Sahel 1 cultivar indicating the genetic distance between it and the other wheat cultivars. AFLP analysis resulted in higher level of polymorphism indicating its efficacy in separating closely related germplasm. A number of 49 markers, across both types of markers, for drought tolerance were recovered. A few markers to link cultivars with possible share of a common ancestor were also recovered. The polymorphism informati...
The largest microbial aggregation in the human body exists in the gastrointestinal tract. The mic... more The largest microbial aggregation in the human body exists in the gastrointestinal tract. The microbiota in the host gastrointestinal tract comprises a diverse ecosystem, and the intestinal microbiota plays a vital role in maintaining gut homeostasis. This study aims to examine whether the gut microbiota influences unresponsiveness to anti-TNF-α treatments in primary nonresponder patients, and consequently identify the responsible microbes as biomarkers of unresponsiveness. Stool samples were collected from a cohort of patients with an established diagnosis of IBD, either ulcerative colitis (UC) or Crohn’s disease (CD), following completion of the induction phase of anti TNF therapy. 16S rRNA sequencing analysis was used to examine the pattern of microbiota communities in fecal samples. The quality and quantity of fecal microbiota were compared in responder and primary nonresponder IBD patients following anti-TNF-α therapy. As per our hypothesis, a difference in gut microbiome compo...
Molecular Genetics, Microbiology and Virology, 2019
Objectives of the present study were to evaluate the antibacterial activity of the two types of i... more Objectives of the present study were to evaluate the antibacterial activity of the two types of inorganic magnesium hydroxide [Mg(OH) 2 ] and calcium carbonate [CaCO 3 ] nanoparticles (NPs) on the growth of three Gram-negative bacteria, e.g., Escherichia coli, Pseudomonas aeruginosa and Serratia marcescens and three Gram-positive bacteria, e.g., Streptococcus pyogenes, Staphylococcus aureus and Streptococcus bovis. The synthesis of these NPs was done by a microwave hydrothermal method. The structures and sizes of synthesized nanoparticles were investigated using X-ray diffractometer. Antimicrobial susceptibility of different NPs was determined at 20, 50 and 100 mg/mL by the agar-well diffusion method, growth reduction at the aqueous solution and time-kill assay. The antimicrobial effects across NPs and bacterial species were shown to be dose-dependent. The results of the different experiments indicated that smaller NP sizes have higher antibacterial effects. M29 [Mg(OH) 2-29] nanoparticles followed by silver (Ag) and C1 (CaCO 3-1) showed the highest influence on bacterial growth rates, while similar ability to kill bacteria across treatment time. In addition, Gram-negative bacteria were more affected in terms of the inhibition zone and reduction of growth rates after 24 h as well as in terms of the prolonged treatment of NPs up to 36 h due to the influence of different nanoparticles. We recommend to search the chance of further using M29 and C1 in medicine and industry.
J Pak Med Assoc Abstract Our knowledge of the composition of the vaginal environment in healthy w... more J Pak Med Assoc Abstract Our knowledge of the composition of the vaginal environment in healthy women stands greatly improved. An imbalance in microbial communities is associated with a number of different diseases, disorders and other adverse health outcomes. Cultivation-independent studies have been published indicating that each woman has unique vaginal microbiota. The vaginal microbiome in pregnant women is more stable and associated with high level of Lactobacillus, particularly, Lactobacillus crispatus and low bacterial diversity. The current review was planned to provide a more complete picture of the abundance of various bacteria species in the vagina and how they impact women’s reproductive health and pregnancy outcomes. This should provide a better understanding of what is considered a “healthy” or “unhealthy” vaginal microbiome and how the dysibiosis of the vagina affects the women. Additionally, it was planned to identify factors that influence the structure and / or com...
Fermented soymilk (soymilk yogurt) was made by fermenting soymilk with five probiotic bacterial s... more Fermented soymilk (soymilk yogurt) was made by fermenting soymilk with five probiotic bacterial strains (Lactobacillus plantarum ATCC 14917, Lactobacillus casei DSM 20011, Lactobacillus acidophilus ATCC 20552, Lactococcus thermophilus DSM 20259, and Bifidobacterium longum B41409) that were used as monocultures and combined with them as consortia cultures. Seven pathogenic strains, E. coli O157H7, S. aureus As4, S. typhimurium As3, S. shigae As2, L. monocytogenes As1, P. aeruginosa ATCC 27853, and B. cereus Dsmz 345, were used to study the antibacterial activity of fermented soymilk by agar well diffusion assay. Results indicated that Gram-negative pathogenesis was more sensitive to probiotic cultures than Gram-positive pathogenesis. E. coli O15H7, S. typhimirium As3, and Shigella shigae As2 were more sensitive to probiotic cultures, presenting inhibition zone diameters (IZA) ranging from 10 to 20 mm, 12 to 16 mm, and 10 to 16 mm, respectively. At the same time, P. aeruginosa Atcc 27...
The COVID-19 pandemic has strained healthcare systems. Sensitive, specific, and timely COVID-19 d... more The COVID-19 pandemic has strained healthcare systems. Sensitive, specific, and timely COVID-19 diagnosis is crucial for effective medical intervention and transmission control. RT-PCR is the most sensitive/specific, but requires costly equipment and trained personnel in centralized laboratories, which are inaccessible to resource-limited areas. Antigen rapid tests enable point-of-care (POC) detection but are significantly less sensitive/specific. CRISPR-Cas systems are compatible with isothermal amplification and dipstick readout, enabling sensitive/specific on-site testing. However, improvements in sensitivity and workflow complexity are needed to spur clinical adoption. We outline the mechanisms/strategies of major CRISPR-Cas systems, evaluate their on-site diagnostic capabilities, and discuss future research directions. Current COVID-19 diagnostic platforms The current pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has inflicted~280 million infections and 5.4 million deaths (December 2021). In view of the high human-to-human transmissibility of SARS-CoV-2, and the fact that~20% of infected people are asymptomatic [1,2], rapid and accurate diagnostic tests deployable on-site at the point-of-need will be crucial for timely transmission control and treatment. Such rapid on-site tests can be used for community-level screening at medical facilities, work sites, air/sea customs, or pop-up/mobile testing sites before subsequent confirmatory tests at central clinical laboratories. This will increase diagnostic reach by enabling more tests to be conducted at a faster pace. Reduced testing at clinical laboratories will reduce the strain on healthcare resources, which can be better diverted to medical intervention and patient care. Furthermore, when used at immigration checkpoints, schools, trade and convention centers, such accurate on-site tests will enable safe resumption of travel, education, work, social, and economic activities. Three major biomarkers are employed for the diagnosis of COVID-19 [3]: the genomic RNA of the virus, four major structural and functional proteins/antigensnamely the spike (S), nucleocapsid (N), envelope (E), and membrane (M) proteinsand the neutralizing antibodies (IgM/ IgG) in the infected host produced as part of the humoral immune response against SARS-CoV-2. There are several major testing platforms for diagnosing COVID-19, namely reverse transcription PCR (RT-PCR), lateral flow rapid test kits (RTKs), and sequencing. RT-PCR, which detects the SARS-CoV-2 RNA sequences, is the current gold standard for diagnosing COVID-19 owing to its high sensitivity/specificity. However, it requires instrumentation Highlights CRISPR-based detection systems are poised to emerge as the next-generation point-of-care (POC) diagnostic platform, and have the potential to marry the advantages of RT-PCR (sensitive/specific) and rapid test kits (RTKs) (fast turnaround, user-friendly). These systems also circumvent the deficiencies of both RT-PCR (long turnaround, equipment/trained user requirement) and RTKs (low sensitivity). These POC platforms play a crucial role for effective medical intervention and transmission control of infectious diseases such as COVID-19. For these systems to be widely adopted clinically, developments have been made to enhance the thermal compatibility of CRISPR with isothermal amplification assays, towards a one-step, one-pot platform.
Amebiasis caused by Entamoeba histolytica parasite is among the worst gut diseases worldwide. The... more Amebiasis caused by Entamoeba histolytica parasite is among the worst gut diseases worldwide. The study involved detection of gut mycobiome signature of the infected subjects in a trial to improve ability to diagnose and treat this disease. The results indicated that diversity of samples slightly changed due to infection. Dendrogram indicated that the most common phyla in the human gut are Ascomycota, Basidiomycota and Zygomycota. Species Pichia kudriavzevii, Candida glabrata, Saccharomyces cerevisiae of phylum Ascomycota and Rhodotorula mucilaginosa of phylum Basidiomycota were found highly OTU abundant. Weighted unifrac diversity distances resulted in complete separation of the two groups. Differential abundance analysis indicated that four phyla, six families, nine genera and ten species showed considerable changes in gut mycobiome signatures within and among groups. Unclassified species of genus Malassezia (phylum Basidiomycota) showed high abundance in infected subjects as compared to healthy subjects, while families Saccharomycetaceae and Trichocomaceae, genus Saccharomyces and species S. cerevisiae showed opposite results. Linear discriminant analysis effect size (LEFSE) indicated that family Saccharomycetaceae, of which S. cerevisiae is a downstream taxon, can be a negative biomarker for amebiasis. In conclusion, the study provides new insights into possible use of Saccharomyces as a probiotic against amebiasis.
Objectives: Nonsyndromic orofacial clefts (NSOFCs) are the most common craniofacial malformations... more Objectives: Nonsyndromic orofacial clefts (NSOFCs) are the most common craniofacial malformations observed across the globe. They are classified into three types: (a) cleft palate, (b) cleft lip, and (c) cleft lip and palate. To identify the potential candidate genes contributing to polygenic diseases such as NSOFC, linkage analyses, genome-wide association studies, and genomic rearrangements can be used. Genomic analyses play a vital role in deciphering the genetic basis of the disease based on massively parallel, next-generation sequencing technologies. Materials and Methods: This study identified new genes potentially related to NSOFCs within a consanguineous Saudi family. In this study, whole-exome sequencing was used to detect genes that contribute to the phenotype. Results: The exome analysis revealed NRP1 (rs35320960) as one potential candidate gene that is involved in bone differentiation. The RPL27A gene (rs199996172), which plays a crucial role in ribosome biogenesis, also passed the overall levels of filtration as a candidate gene for NSOFC in this family. Rare variants are situated within the 5' UTR of these two genes. Conclusion: The study suggests that rare variants in NRP1 and RPL27Amay be associated with NSOFC disease etiology.
Enzymes in the flavonoid metabolic pathway in apical and mature leaves responded differentially t... more Enzymes in the flavonoid metabolic pathway in apical and mature leaves responded differentially to changing environments at two time points (morning, A and midday, G). Upregulated (activated) in apical leaves (blue), upregulated in mature leaves (red). (DOCX 193Â kb)
Honeybees play a vital role in the world’s food supply by acting as essential pollinators in the ... more Honeybees play a vital role in the world’s food supply by acting as essential pollinators in the agricultural fields. Interestingly, more than one third of the world’s essential crops are honeybee’s dependant. The adult honeybeeworkers harbour a simple specific bacterial spectrum in their guts with vital role in bees’ health. Gut microbial diversity of adult honeybee workerswasstudied through targeting the V3 and V4 regions of the 16S rRNA geneviaIllumina MiSeq. The study identified four phyla of the gut microbiomesinadult workersof the two-honeybee subspecies A.m. jemeniticaandA.m. carnica. The most abundant phylum in microbiome of A.m. jemeniticawasFirmicutes (48%), while Protobacteria and Actinobacteriaphylawere less abundantat figures of31% and 10%, respectively. In microbiome of A.m. carnica,Firmicutes (57%) was also the most dominant phylum, while Protobacteria and Actinobacteria had lower prevalence at figures of 31% and 10%, respectively. At genus level, adult honeybee worke...
Enzymes in the cysteine and methionine metabolic pathways in apical and mature leaves responded d... more Enzymes in the cysteine and methionine metabolic pathways in apical and mature leaves responded differentially to changing environment at two time points (morning, A and midday, G). Upregulated (activated) in apical leaves (blue), upregulated in mature leaves (red), downregulated (repressed) in apical leaves (orange box), downregulated in mature leaves (green box). (DOCX 201Â kb)
Fold change values of assembled transcripts of R. stricta SRA database in different clusters in t... more Fold change values of assembled transcripts of R. stricta SRA database in different clusters in the apical leaves (A1-L4) at different time points of the day (A, morning; F-H, midday & L, dusk). (XLSX 775Â kb)
Fold change values of selected upregulated genes encoding HSPs in apical (A1-L4) and mature (A5-L... more Fold change values of selected upregulated genes encoding HSPs in apical (A1-L4) and mature (A5-L8) leaves during the day (A, morning; F-H, midday & L, dusk) in R. stricta (XLSX 25Â kb)
Table S1. Number of sequence reads generated for each sample. Table S2. List of metabolite signal... more Table S1. Number of sequence reads generated for each sample. Table S2. List of metabolite signals matched to known standards. (DOCX 100 kb)
Tobacco TF IDs in tobacco, their analogues in Arabidopsis and knockout (KO) and over-expression l... more Tobacco TF IDs in tobacco, their analogues in Arabidopsis and knockout (KO) and over-expression lines along with the links to indicate known function in Arabidopsis database (TAIR, http://www.arabidopsis.org/ ). (DOCX 17 kb)
List of TFs (orange box) co-expressed with PCD-related genes in 10 clusters of gene expression in... more List of TFs (orange box) co-expressed with PCD-related genes in 10 clusters of gene expression in tobacco. (DOCX 21 kb)
Tobacco TFs IDs (T1-T31) and primer names and sequences along with the expected amplicon sizes (b... more Tobacco TFs IDs (T1-T31) and primer names and sequences along with the expected amplicon sizes (bp) to be utilized in constructing pTRV2 vectors (blue boxes) for VIGS, in conducting semi-quantitative RT-PCR (orange boxes) or in both (green boxes). Information for amplifying selected tobacco TFs (T14, T15 and T24) via qRT-PCR (purple boxes) and information for amplifying selected tobacco PCD-related genes (G13, G15 and G18) and Arabidopsis TFs ARF109 (AtT14) and TFIID5 (AtTF24), either knocked out or over-expressed, via sqRT-PCR are shown. Gene codes refer to those indicated in Additional file 3: Table S2. (DOCX 28 kb)
Semi-quantitative RT-PCR for tobacco VIGS lines of 13 knocked down TFs induced 2Â h post oxalic a... more Semi-quantitative RT-PCR for tobacco VIGS lines of 13 knocked down TFs induced 2Â h post oxalic acid treatment (20Â mM) as compared to their WT and VIGS line with empty pTRV2 (V2) plants. Amplicon sizes of different genes and primers used are shown in Additional file 5: Table S3. The Nbactin gene was used as the house-keeping control. Gene codes refer to those indicated in Additional file 3: Table S2. (DOCX 684 kb)
Background: Studying human skin-associated bacterial communities is crucial to understanding huma... more Background: Studying human skin-associated bacterial communities is crucial to understanding human diseases, disease progression, and their role in maintaining human health. Objectives: This study aimed to identify normal (healthy) skin microbiome signatures of eight individuals living in Jeddah, Makkah Al-Mukarramah region, Saudi Arabia. Methods: The study involved the analysis of resident skin microbiome in inner elbow of the right arm after ethical approval is issued and an informed consent form is signed by participant individuals. Results: Phylogenetic tree indicated the existence of four phyla, e.g., Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria. Firmicutes were shown to be the highest in abundance, while Bacteroidetes were the lowest. At the genus level, Staphylococcus was the highest in abundance, while Enterococcus was the lowest. At the species level, Bacillus cereus was the highest in abundance, while Roseomonas mucosa was the lowest. The analysis for the high...
Drought tolerance is a complex trait of increasing importance. The present study aims at detectin... more Drought tolerance is a complex trait of increasing importance. The present study aims at detecting molecular markers in eight bread wheat (T. aestivum) cultivars, based on ISSR and AFLP, differing in their performance under drought stress. Wheat is one of the most important cereal crops in the world. Therefore, the identification of molecular markers for drought tolerance is crucial for the future development of tolerant varieties through breeding. Across the two types of markers, a total of 109 cultivar-specific markers were recovered. Most markers were resulted for Sahel 1 cultivar indicating the genetic distance between it and the other wheat cultivars. AFLP analysis resulted in higher level of polymorphism indicating its efficacy in separating closely related germplasm. A number of 49 markers, across both types of markers, for drought tolerance were recovered. A few markers to link cultivars with possible share of a common ancestor were also recovered. The polymorphism informati...
The largest microbial aggregation in the human body exists in the gastrointestinal tract. The mic... more The largest microbial aggregation in the human body exists in the gastrointestinal tract. The microbiota in the host gastrointestinal tract comprises a diverse ecosystem, and the intestinal microbiota plays a vital role in maintaining gut homeostasis. This study aims to examine whether the gut microbiota influences unresponsiveness to anti-TNF-α treatments in primary nonresponder patients, and consequently identify the responsible microbes as biomarkers of unresponsiveness. Stool samples were collected from a cohort of patients with an established diagnosis of IBD, either ulcerative colitis (UC) or Crohn’s disease (CD), following completion of the induction phase of anti TNF therapy. 16S rRNA sequencing analysis was used to examine the pattern of microbiota communities in fecal samples. The quality and quantity of fecal microbiota were compared in responder and primary nonresponder IBD patients following anti-TNF-α therapy. As per our hypothesis, a difference in gut microbiome compo...
Molecular Genetics, Microbiology and Virology, 2019
Objectives of the present study were to evaluate the antibacterial activity of the two types of i... more Objectives of the present study were to evaluate the antibacterial activity of the two types of inorganic magnesium hydroxide [Mg(OH) 2 ] and calcium carbonate [CaCO 3 ] nanoparticles (NPs) on the growth of three Gram-negative bacteria, e.g., Escherichia coli, Pseudomonas aeruginosa and Serratia marcescens and three Gram-positive bacteria, e.g., Streptococcus pyogenes, Staphylococcus aureus and Streptococcus bovis. The synthesis of these NPs was done by a microwave hydrothermal method. The structures and sizes of synthesized nanoparticles were investigated using X-ray diffractometer. Antimicrobial susceptibility of different NPs was determined at 20, 50 and 100 mg/mL by the agar-well diffusion method, growth reduction at the aqueous solution and time-kill assay. The antimicrobial effects across NPs and bacterial species were shown to be dose-dependent. The results of the different experiments indicated that smaller NP sizes have higher antibacterial effects. M29 [Mg(OH) 2-29] nanoparticles followed by silver (Ag) and C1 (CaCO 3-1) showed the highest influence on bacterial growth rates, while similar ability to kill bacteria across treatment time. In addition, Gram-negative bacteria were more affected in terms of the inhibition zone and reduction of growth rates after 24 h as well as in terms of the prolonged treatment of NPs up to 36 h due to the influence of different nanoparticles. We recommend to search the chance of further using M29 and C1 in medicine and industry.
J Pak Med Assoc Abstract Our knowledge of the composition of the vaginal environment in healthy w... more J Pak Med Assoc Abstract Our knowledge of the composition of the vaginal environment in healthy women stands greatly improved. An imbalance in microbial communities is associated with a number of different diseases, disorders and other adverse health outcomes. Cultivation-independent studies have been published indicating that each woman has unique vaginal microbiota. The vaginal microbiome in pregnant women is more stable and associated with high level of Lactobacillus, particularly, Lactobacillus crispatus and low bacterial diversity. The current review was planned to provide a more complete picture of the abundance of various bacteria species in the vagina and how they impact women’s reproductive health and pregnancy outcomes. This should provide a better understanding of what is considered a “healthy” or “unhealthy” vaginal microbiome and how the dysibiosis of the vagina affects the women. Additionally, it was planned to identify factors that influence the structure and / or com...
Fermented soymilk (soymilk yogurt) was made by fermenting soymilk with five probiotic bacterial s... more Fermented soymilk (soymilk yogurt) was made by fermenting soymilk with five probiotic bacterial strains (Lactobacillus plantarum ATCC 14917, Lactobacillus casei DSM 20011, Lactobacillus acidophilus ATCC 20552, Lactococcus thermophilus DSM 20259, and Bifidobacterium longum B41409) that were used as monocultures and combined with them as consortia cultures. Seven pathogenic strains, E. coli O157H7, S. aureus As4, S. typhimurium As3, S. shigae As2, L. monocytogenes As1, P. aeruginosa ATCC 27853, and B. cereus Dsmz 345, were used to study the antibacterial activity of fermented soymilk by agar well diffusion assay. Results indicated that Gram-negative pathogenesis was more sensitive to probiotic cultures than Gram-positive pathogenesis. E. coli O15H7, S. typhimirium As3, and Shigella shigae As2 were more sensitive to probiotic cultures, presenting inhibition zone diameters (IZA) ranging from 10 to 20 mm, 12 to 16 mm, and 10 to 16 mm, respectively. At the same time, P. aeruginosa Atcc 27...
The COVID-19 pandemic has strained healthcare systems. Sensitive, specific, and timely COVID-19 d... more The COVID-19 pandemic has strained healthcare systems. Sensitive, specific, and timely COVID-19 diagnosis is crucial for effective medical intervention and transmission control. RT-PCR is the most sensitive/specific, but requires costly equipment and trained personnel in centralized laboratories, which are inaccessible to resource-limited areas. Antigen rapid tests enable point-of-care (POC) detection but are significantly less sensitive/specific. CRISPR-Cas systems are compatible with isothermal amplification and dipstick readout, enabling sensitive/specific on-site testing. However, improvements in sensitivity and workflow complexity are needed to spur clinical adoption. We outline the mechanisms/strategies of major CRISPR-Cas systems, evaluate their on-site diagnostic capabilities, and discuss future research directions. Current COVID-19 diagnostic platforms The current pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has inflicted~280 million infections and 5.4 million deaths (December 2021). In view of the high human-to-human transmissibility of SARS-CoV-2, and the fact that~20% of infected people are asymptomatic [1,2], rapid and accurate diagnostic tests deployable on-site at the point-of-need will be crucial for timely transmission control and treatment. Such rapid on-site tests can be used for community-level screening at medical facilities, work sites, air/sea customs, or pop-up/mobile testing sites before subsequent confirmatory tests at central clinical laboratories. This will increase diagnostic reach by enabling more tests to be conducted at a faster pace. Reduced testing at clinical laboratories will reduce the strain on healthcare resources, which can be better diverted to medical intervention and patient care. Furthermore, when used at immigration checkpoints, schools, trade and convention centers, such accurate on-site tests will enable safe resumption of travel, education, work, social, and economic activities. Three major biomarkers are employed for the diagnosis of COVID-19 [3]: the genomic RNA of the virus, four major structural and functional proteins/antigensnamely the spike (S), nucleocapsid (N), envelope (E), and membrane (M) proteinsand the neutralizing antibodies (IgM/ IgG) in the infected host produced as part of the humoral immune response against SARS-CoV-2. There are several major testing platforms for diagnosing COVID-19, namely reverse transcription PCR (RT-PCR), lateral flow rapid test kits (RTKs), and sequencing. RT-PCR, which detects the SARS-CoV-2 RNA sequences, is the current gold standard for diagnosing COVID-19 owing to its high sensitivity/specificity. However, it requires instrumentation Highlights CRISPR-based detection systems are poised to emerge as the next-generation point-of-care (POC) diagnostic platform, and have the potential to marry the advantages of RT-PCR (sensitive/specific) and rapid test kits (RTKs) (fast turnaround, user-friendly). These systems also circumvent the deficiencies of both RT-PCR (long turnaround, equipment/trained user requirement) and RTKs (low sensitivity). These POC platforms play a crucial role for effective medical intervention and transmission control of infectious diseases such as COVID-19. For these systems to be widely adopted clinically, developments have been made to enhance the thermal compatibility of CRISPR with isothermal amplification assays, towards a one-step, one-pot platform.
Amebiasis caused by Entamoeba histolytica parasite is among the worst gut diseases worldwide. The... more Amebiasis caused by Entamoeba histolytica parasite is among the worst gut diseases worldwide. The study involved detection of gut mycobiome signature of the infected subjects in a trial to improve ability to diagnose and treat this disease. The results indicated that diversity of samples slightly changed due to infection. Dendrogram indicated that the most common phyla in the human gut are Ascomycota, Basidiomycota and Zygomycota. Species Pichia kudriavzevii, Candida glabrata, Saccharomyces cerevisiae of phylum Ascomycota and Rhodotorula mucilaginosa of phylum Basidiomycota were found highly OTU abundant. Weighted unifrac diversity distances resulted in complete separation of the two groups. Differential abundance analysis indicated that four phyla, six families, nine genera and ten species showed considerable changes in gut mycobiome signatures within and among groups. Unclassified species of genus Malassezia (phylum Basidiomycota) showed high abundance in infected subjects as compared to healthy subjects, while families Saccharomycetaceae and Trichocomaceae, genus Saccharomyces and species S. cerevisiae showed opposite results. Linear discriminant analysis effect size (LEFSE) indicated that family Saccharomycetaceae, of which S. cerevisiae is a downstream taxon, can be a negative biomarker for amebiasis. In conclusion, the study provides new insights into possible use of Saccharomyces as a probiotic against amebiasis.
Objectives: Nonsyndromic orofacial clefts (NSOFCs) are the most common craniofacial malformations... more Objectives: Nonsyndromic orofacial clefts (NSOFCs) are the most common craniofacial malformations observed across the globe. They are classified into three types: (a) cleft palate, (b) cleft lip, and (c) cleft lip and palate. To identify the potential candidate genes contributing to polygenic diseases such as NSOFC, linkage analyses, genome-wide association studies, and genomic rearrangements can be used. Genomic analyses play a vital role in deciphering the genetic basis of the disease based on massively parallel, next-generation sequencing technologies. Materials and Methods: This study identified new genes potentially related to NSOFCs within a consanguineous Saudi family. In this study, whole-exome sequencing was used to detect genes that contribute to the phenotype. Results: The exome analysis revealed NRP1 (rs35320960) as one potential candidate gene that is involved in bone differentiation. The RPL27A gene (rs199996172), which plays a crucial role in ribosome biogenesis, also passed the overall levels of filtration as a candidate gene for NSOFC in this family. Rare variants are situated within the 5' UTR of these two genes. Conclusion: The study suggests that rare variants in NRP1 and RPL27Amay be associated with NSOFC disease etiology.
Enzymes in the flavonoid metabolic pathway in apical and mature leaves responded differentially t... more Enzymes in the flavonoid metabolic pathway in apical and mature leaves responded differentially to changing environments at two time points (morning, A and midday, G). Upregulated (activated) in apical leaves (blue), upregulated in mature leaves (red). (DOCX 193Â kb)
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Papers by Sherif Edris