Ahmed Moustafa

The American University in Cairo | AUC · Department of Biology

The characterization of the blood virome is important for the safety of blood-derived transfusion products, and for the identification of emerging pathogens. We explored non-human sequence data from whole-genome sequencing of blood from 8,240 individuals, none of whom were ascertained for any infectious disease. Viral sequences were extracted from...

Significance Large-scale initiatives toward personalized medicine are driving a massive expansion in the number of human genomes being sequenced. Therefore, there is an urgent need to define quality standards for clinical use. This includes deep coverage and sequencing accuracy of an individual’s genome. Our work represents the largest effort to da...

Numerous cellular functions including respiration require iron. Plants and phytoplankton must also maintain the iron-rich photosynthetic electron transport chain, which most likely evolved in the iron-replete reducing environments of the Proterozoic ocean. Iron bioavailability has drastically decreased in the contemporary ocean, most likely selecti...

The sea slug Elysia chlorotica acquires plastids by ingestion of its algal food source Vaucheria litorea. Organelles are sequestered in the mollusc's digestive epithelium, where they photosynthesize for months in the absence of algal nucleocytoplasm. This is perplexing because plastid metabolism depends on the nuclear genome for >90% of the needed...

Green for Diatoms Diatoms account for 20% of global carbon fixation and, together with other chromalveolates (e.g., dinoflagellates and coccolithophorids), represent many thousands of eukaryote taxa in the world's oceans and on the tree of life. Moustafa et al. (p. 1724 ; see the Perspective by Dagan and Martin ) have discovered that the genomes of...

Background: Parkinson's disease (PD) has become a global public health challenge as disability and death due to the disease are growing rapidly in comparison to other neurological disorders. There are no up-to-date comprehensive reviews on the epidemiology, environmental and genetic risk factors, phenotypic characterization, and patient-reported ou...

Corals live in a complex, multi-partite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships wi...

Mesenchymal stromal/stem cells (MSCs) are multipotent cells that reside in multiple tissues are capable of self-renewal and differentiation into various cell types. These properties make them promising candidates for regenerative therapies. MSC identification is critical in yielding pure populations for successful therapeutic applications; however,...

Metabolomics research has recently gained popularity because it enables the study of biological traits at the biochemical level and, as a result, can directly reveal what occurs in a cell or a tissue based on health or disease status, complementing other omics such as genomics and transcriptomics. Like other high-throughput biological experiments,...

Stress response helps microorganisms survive extreme environmental conditions and host immunity, making them more virulent or drug resistant. Although both reductionist approaches investigating specific genes and systems approaches analyzing individual stress conditions are being used, less is known about gene networks involved in multiple stress r...

Nearly half of carbon fixation and primary production originates from marine phytoplankton, and much of it occurs in episodic blooms in upwelling regimes. Here, we simulated blooms limited by nitrogen and iron by incubating Monterey Bay surface waters with subnutricline waters and inorganic nutrients and measured the whole-community transcriptomic...

Cardiac valves exhibit highly complex structures and specialized functions that include dynamic interactions between cells, extracellular matrix (ECM) and their hemodynamic environment. Valvular gene expression is tightly regulated by a variety of mechanisms including epigenetic factors such as histone modifications, RNA-based mechanisms and DNA me...

Mesenchymal stromal/stem cells (MSCs) are multipotent cells residing in multiple tissues with the capacity for self-renewal and differentiation into various cell types. These properties make them promising candidates for regenerative therapies. MSC identification is critical in yielding pure populations for successful therapeutic applications; howe...

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third virus that caused coronavirus-related outbreaks over the past 20 years. The outbreak was first reported in December 2019 in Wuhan, China, but rapidly progressed into a pandemic of an unprecedented scale since the 1918 flu pandemic. Besides respiratory complications in pat...

World Microbe Forum, a collaboration between the American Society for Microbiology (ASM), Federation of European Microbiological Societies (FEMS), and several other societies, is breaking barriers to sharing science and addressing the most pressing challenges facing humankind today. That's why this year, ASM Microbe and FEMS Congress 2021 will be p...

Mesenchymal stromal/stem cells (MSCs) are multipotent cells residing in multiple tissues with the capacity for self-renewal and differentiation into various cell types. These properties make them promising candidates for regenerative therapies. MSC identification is critical in yielding pure populations for successful therapeutic applications; howe...

Colorectal cancer (CRC) is the third leading cause of death worldwide, comprising nearly 8% of cancer-related deaths per year. In South Korea, for example, CRC is the second most common cancer in men, and third in women. This study reports on the association of CRC with genetic variations in long noncoding RNAs, activators, and inhibitors of a cell...

Objective: Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that is incurable and ultimately fatal. Few therapeutic options are available to patients. In this study, we explored differences in microbiome composition associated with ALS. Methods: We compared the gut microbiome and inflammatory marker profiles of ALS pat...

Data on molecular characterization of coagulase-negative staphylococci causing neonatal sepsis in low-income countries are highly limited. This report highlights the isolation of three Staphylococcus epidermidis non-genome assembly strains (NGASs) from blood samples from neonates with unknown transmission sources. Pathogenic factors and sources of...

Background: Neonatal sepsis is a global health problem that mainly affects low- and middle-income countries. We have previously shown that early neonatal mortality is high at the Ho Teaching Hospital (HTH) of Ghana. We sought to determine the prevalence of neonatal sepsis, sepsis-related mortality, and bacterial species patterns in neonatal and you...

Background: Colorectal cancer (CRC) incidence is progressively increasing in Egypt. Unfortunately, there is inadequate knowledge of the acquired somatic mutations in Egyptian CRC patients which limit our understanding of its progression. To the best of our knowledge, our study is the first to sequence multiple-gene panel to identify the somatic mut...

Cardiac valves exhibit highly complex structures and specialized functions that include dynamic interactions between cells, extracellular matrix (ECM) and their hemodynamic environment. Valvular gene expression is tightly regulated by a variety of mechanisms including epigenetic factors such as histone modifications, RNA-based mechanisms and DNA me...

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third virus that caused coronavirus-related outbreaks over the past 20 years. The outbreak was first reported in December 2019 in Wuhan, China, but rapidly progressed into a pandemic of an unprecedented scale since the 1918 flu pandemic. Besides respiratory complications in COV...

Humans are host to a multitude of microorganisms that rapidly populate the body at birth, subject to a complex interplay that is dependent on host genetics, lifestyle, and environment. The host-associated microbiome, including the oral microbiome, presents itself in a complex ecosystem important to health and disease. As the most common chronic dis...

The haptophyte Phaeocystis antarctica is endemic to the Southern Ocean, where iron supply is sporadic and its availability limits primary production. In iron fertilization experiments, P. antarctica showed a prompt and steady increase in cell abundance compared to heavily silicified diatoms along with enhanced colony formation. Here we utilized a t...

The incidence of pediatric cancer is lower than that of adult cancer worldwide. However, the former has detrimental side effects on the health of individuals, even after the cancer is cured, due to the impact of treatment on development. Recently, correlations have been made between the gut microbiome and cancer in several studies but only on adult...

Background: Autophagy is a highly conserved lysosomal degradative cellular process implicated in the pathophysiology of wound healing and tissue remodeling. Mammalian autophagy controlled by autophagy associated gene (ATGs); such as ubiquitin activating Enzyme E1 Atg7, hence Atg7 controls the gateway for nascent autophagosome formation. Autophagy-a...

Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report...

Dinoflagellates are microbial eukaryotes that have exceptionally large nuclear genomes; however, their organelle genomes are small and fragmented and contain fewer genes than those of other eukaryotes. The genus Amoebophrya (Syndiniales) comprises endoparasites with high genetic diversity that can infect other dinoflagellates, such as those forming...

Chewing gum containing xylitol may help prevent caries by reducing levels of mutans streptococci (MS) and lactobacilli in saliva and plaque. Very little is known about other species which are possibly beneficial to oral health. In this study, we employed high-throughput sequencing of the 16S rRNA gene to profile microbial communities of saliva and...

Chewing gum containing xylitol may help prevent caries by reducing levels of mutans streptococci (MS) and lactobacilli in saliva and plaque. Very little is known about other species which are possibly beneficial to oral health. In this study, we employed high-throughput sequencing of the 16S rRNA gene to profile microbial communities of saliva and...

Understanding the transcriptional regulatory elements that influence the progression of liver disease in the presence of hepatitis C virus (HCV) infection is critical for the development of diagnostic and therapeutic approaches. Systems biology provides a roadmap by which these elements may be integrated. In this study, a previously published datas...

Urine culture and microscopy techniques are used to profile the bacterial species present in urinary tract infections. To gain insight into the urinary flora, we analyzed clinical laboratory features and the microbial metagenome of 121 clean-catch urine samples. 16S rDNA gene signatures were successfully obtained for 116 participants, while metagen...

Objectives: Inflammatory bowel diseases (IBD), comprised of Crohn’s disease (CD) and ulcerative colitis (UC), are characterized by a complex pathophysiology that is thought to result from an aberrant immune response to a dysbiotic luminal microbiota in genetically susceptible individuals. New technologies support the joint assessment of host-microb...

Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB) in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a...

PCoA plot of Bray–Curtis distances for eukaryotic communities in the sediment. Black = unenriched, orange = P-only, light blue = NP16, dark blue = NP75.

PCoA plot of Bray–Curtis distances for bacterial communities in the sediment. Black = unenriched, orange = P-only, light blue = NP16, dark blue = NP75.

Urine culture and microscopy techniques are used to profile the bacterial species present in urinary tract infections. To gain insight into the urinary flora in infection and health, we analyzed clinical laboratory features and the microbial metagenome of 121 clean-catch urine samples. 16S rDNA gene signatures were successfully obtained for 116 par...

Abundance of EBV in association with use of human reference genome NA12878. The distribution of the abundance of EBV is shown for the EBV B95-8 strain-immortalized the cell line of NA12878, for samples sequenced sharing the same flow cell with human genome NA12878 and for samples sequenced in the absence of human genome NA12878 in the sequencing fl...

Distribution of samples with viruses across the sequencing flow cells. The number of viral reads per samples are shown on the y-axis in relation to the number of samples per flow cell that are positive for the corresponding virus. The presence of multiple positive samples in flow cells that contain one high viral-titer sample is suggestive of conta...

Sequence reads from RNA viruses. Panel A depicts the alignment of 4 reads from one individual to the influenza H1N1 reference sequence M1 and M2, segment seven. Closest match; serotype = H1N1, strain = A/Puerto Rico/8/1934. Panel B depicts the alignment of 18 reads from one individual to a HCV subtype 3 sequence. Closest match, HCV clone FG1-NS3-4a...

Complete listing of viruses putatively identified or contaminating blood DNA of 8,240 individuals. (PDF)

Statistical significant differences for demographic characteristics and viral prevalence or viral load. (PDF)

Assembly of contigs of human viruses. The sensitivity of identification of human viruses differs when using contigs from de novo assembly of reads, versus using individual reads. The upper panel is based on raw counts of the virus reads and the lower panels show the normalized viral abundances. The identification of viruses is improved by several o...

Association of viral presence with demographic characteristics. Panel A-C depict the individual association of viral presence with sex, age and genetic ancestry. Panel D plots the results of the analysis of deviance (variance) for the presence of any human virus in response to the individuals’ gender, ethnicity, age. AFR, African; AMR, Admixed Amer...

Read mapping statistics. Unmapped reads in deep sequencing of the human genome using Illumina HiseqX10 technology. The average percentage of unmapped reads per sample is around 5.23%, and median is 4.91%. (TIF)

Alternative splicing (AS) of precursor RNAs enhances transcriptome plasticity and proteome diversity in response to diverse growth and stress cues. Recent work showed that AS is pervasive across plant species, with more than 60% of intron-containing genes producing different isoforms. Mammalian cell-based assays have discovered various AS inhibitor...

The Amazon River has the largest discharge of all rivers on Earth, and its complex plume system fuels a wide array of biogeochemical processes, across a large area of the western tropical North Atlantic. The plume thus stimulates microbial processes affecting carbon sequestration and nutrient cycles at a global scale. Chromosomal gene expression pa...

Metagenomic profiling of 18S rDNA for Station 10. Nuclear small subunit 18S rDNA maximum likelihood tree with the placement of environmental sequences. Circle sizes are proportion to the normalized taxonomic abundances. (TIF)

Metagenomic profiling of 18S rDNA for Station 27. Nuclear small subunit 18S rDNA maximum likelihood tree with the placement of environmental sequences. Circle sizes are proportion to the normalized taxonomic abundances. (TIF)

Background data for genes analyzed. (TIF)

Log replicate 1 versus log replicate 2 plot of transcript counts at all six stations. The dotted line represents the 1:1 line of identity. The 186 data points represent the 31 genes measured at 6 stations. The average difference between replicate transcripts was 11.43%. (TIF)

Metagenomic profiling of 18S rDNA for Station 2. Nuclear small subunit 18S rDNA maximum likelihood tree with the placement of environmental sequences. Circle sizes are proportion to the normalized taxonomic abundances. (TIF)

Metagenomic profiling of 18S rDNA for Station 3. Nuclear small subunit 18S rDNA maximum likelihood tree with the placement of environmental sequences. Circle sizes are proportion to the normalized taxonomic abundances. (TIF)

Metagenomic profiling of 18S rDNA for Station 25. Nuclear small subunit 18S rDNA maximum likelihood tree with the placement of environmental sequences. Circle sizes are proportion to the normalized taxonomic abundances. (TIF)

Sequencing Data. Compiled data of all the sequences obtained and analyzed at the six stations. Duplicate samples were pooled to account for variations in the data that may occur from only taking one sample. (TIF)

Metagenomic profiling of 18S rDNA for Station 23. Nuclear small subunit 18S rDNA maximum likelihood tree with the placement of environmental sequences. Circle sizes are proportion to the normalized taxonomic abundances. (TIF)

Metatranscriptomic profiling of nitrate transporters (NRT) at the 6 six stations along the ARP. A maximum likelihood tree was used with the placement of metatranscriptomic predicted open-reading frames. Bootstrap support values ? 50% are shown. Circle sizes are proportion to the normalized expression levels. Branch lengths are log10-transformed. (T...