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Article ; Online: Isolation, Characterization, and Comparative Genomic Analysis of Bacteriophage Ec_MI-02 from Pigeon Feces Infecting

Sultan-Alolama, Mohamad Ismail / Amin, Amr / Vijayan, Ranjit / El-Tarabily, Khaled A

International journal of molecular sciences

2023 Volume 24, Issue 11

Abstract: The most significant serotype of Shiga- ... ...

Abstract	The most significant serotype of Shiga-toxigenic
MeSH term(s)	Animals ; Cattle ; Humans ; Escherichia coli O157/genetics ; Escherichia coli O157/metabolism ; Columbidae ; Myoviridae/genetics ; Bacteriophages/genetics ; Genomics ; Feces
Language	English
Publishing date	2023-05-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms24119506
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Article: Revealing the association between vitamin D metabolic pathway gene variants and lung cancer risk: a systematic review and meta-analysis.

Elsalahaty, Mohamed I / Alkafaas, Samar Sami / Bashir, Aya O / El-Tarabily, Khaled A / El-Saadony, Mohamed T / Yousef, Eman H

Frontiers in genetics

2024 Volume 15, Page(s) 1302527

Abstract: Lung cancer is a crucial global issue, with more than one million deaths annually. While smoking is considered the main etiology of the disease, several genetic variants are associated with it. Alterations in vitamin D pathway genes have also been ... ...

Abstract	Lung cancer is a crucial global issue, with more than one million deaths annually. While smoking is considered the main etiology of the disease, several genetic variants are associated with it. Alterations in vitamin D pathway genes have also been studied in regards to lung cancer, but the findings have been inconclusive. We here present a systematic review and meta-analysis of seven genes in this pathway:
Language	English
Publishing date	2024-02-28
Publishing country	Switzerland
Document type	Systematic Review
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2024.1302527
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Article ; Online: Exploiting the role of plant growth promoting rhizobacteria in reducing heavy metal toxicity of pepper (Capsicum annuum L.).

El-Saadony, Mohamed T / Desoky, El-Sayed M / El-Tarabily, Khaled A / AbuQamar, Synan F / Saad, Ahmed M

Environmental science and pollution research international

2024 Volume 31, Issue 18, Page(s) 27465–27484

Abstract: Microorganisms are cost-effective and eco-friendly alternative methods for removing heavy metals (HM) from contaminated agricultural soils. Therefore, this study aims to identify and characterize HM-tolerant (HMT) plant growth-promoting rhizobacteria ( ... ...

Abstract	Microorganisms are cost-effective and eco-friendly alternative methods for removing heavy metals (HM) from contaminated agricultural soils. Therefore, this study aims to identify and characterize HM-tolerant (HMT) plant growth-promoting rhizobacteria (PGPR) isolated from industry-contaminated soils to determine their impact as bioremediators on HM-stressed pepper plants. Four isolates [Pseudomonas azotoformans (Pa), Serratia rubidaea (Sr), Paenibacillus pabuli (Pp) and Bacillus velezensis (Bv)] were identified based on their remarkable levels of HM tolerance in vitro. Field studies were conducted to evaluate the growth promotion and tolerance to HM toxicity of pepper plants grown in HM-polluted soils. Plants exposed to HM stress showed improved growth, physio-biochemistry, and antioxidant defense system components when treated with any of the individual isolates, in contrast to the control group that did not receive PGPR. The combined treatment of the tested HMT PGPR was, however, relatively superior to other treatments. Compared to no or single PGPR treatment, the consortia (Pa+Sr+Pp+Bv) increased the photosynthetic pigment contents, relative water content, and membrane stability index but lowered the electrolyte leakage and contents of malondialdehyde and hydrogen peroxide by suppressing the (non) enzymatic antioxidants in plant tissues. In pepper, Cd, Cu, Pb, and Ni contents decreased by 88.0-88.5, 63.8-66.5, 66.2-67.0, and 90.2-90.9% in leaves, and 87.2-88.1, 69.4-70.0%, 80.0-81.3, and 92.3%% in fruits, respectively. Thus, these PGPR are highly effective at immobilizing HM and reducing translocation in planta. These findings indicate that the application of HMT PGPR could be a promising "bioremediation" strategy to enhance growth and productivity of crops cultivated in soils contaminated with HM for sustainable agricultural practices.
MeSH term(s)	Capsicum/microbiology ; Metals, Heavy/toxicity ; Soil Pollutants/toxicity ; Biodegradation, Environmental ; Bacillus ; Soil Microbiology
Chemical Substances	Metals, Heavy ; Soil Pollutants
Language	English
Publishing date	2024-03-21
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1178791-0
ISSN	1614-7499 ; 0944-1344
ISSN (online)	1614-7499
ISSN	0944-1344
DOI	10.1007/s11356-024-32874-1
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Article ; Online: Enhancement of mangrove growth performance using fish emulsion and halotolerant plant growth-promoting actinobacteria for sustainable management in the UAE.

Alshamsi, Al Anoud A / Sheteiwy, Mohamed S / AbuQamar, Synan F / El-Tarabily, Khaled A

Marine pollution bulletin

2023 Volume 199, Page(s) 115916

Abstract: The combination of fish emulsion (FE) and the actinobacterial isolate, Streptomyces griseorubens UAE1 (Sg) capable of producing plant growth regulators (PGRs) and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, was evaluated on mangrove (Avicennia ...

Abstract	The combination of fish emulsion (FE) and the actinobacterial isolate, Streptomyces griseorubens UAE1 (Sg) capable of producing plant growth regulators (PGRs) and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, was evaluated on mangrove (Avicennia marina) in the United Arab Emirates. Under greenhouse and field conditions, sediments amended with the biostimulant FE effectively enhanced mangrove growth compared to those inoculated with Sg only. Plant growth promotion by Sg was more pronounced in the presence of FE (+FE/+Sg) than in individual applications. Our data showed that Sg appeared to use FE as a source of nutrients and precursors for plant growth promotion. Thus, in planta PGR levels following the combined +FE/+Sg were significantly induced. This is the first report in the field of marine agriculture that uses FE as a nutrient base for soil microorganisms to promote mangrove growth. This study will support mangrove restoration along the Arabian Gulf coastline as a nature-based solution to changing climate and economic activities.
MeSH term(s)	Actinobacteria ; Emulsions ; Plant Development ; Avicennia ; Bacteria ; Plant Roots
Chemical Substances	Emulsions
Language	English
Publishing date	2023-12-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2001296-2
ISSN	1879-3363 ; 0025-326X
ISSN (online)	1879-3363
ISSN	0025-326X
DOI	10.1016/j.marpolbul.2023.115916
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Article ; Online: Complete Genome Sequence of Escherichia coli O157:H7 Phage UAE_MI-01, Isolated from Bird Feces.

Sultan-Alolama, Mohamad Ismail / El-Tarabily, Khaled A / Vijayan, Ranjit

Microbiology resource announcements

2021 Volume 10, Issue 28, Page(s) e0034821

Abstract: Bacteriophage UAE_MI-01 is an Escherichia coli O157:H7 phage that was isolated from the feces of wild pigeons ( ...

Abstract	Bacteriophage UAE_MI-01 is an Escherichia coli O157:H7 phage that was isolated from the feces of wild pigeons (
Language	English
Publishing date	2021-07-15
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.00348-21
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Article ; Online: Co-expression Networks in Predicting Transcriptional Gene Regulation.

AbuQamar, Synan F / El-Tarabily, Khaled A / Sham, Arjun

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2328, Page(s) 1–11

Abstract: Recent progress in transcriptomics and co-expression networks have enabled us to predict the inference of the biological functions of genes with the associated environmental stress. Microarrays and RNA sequencing (RNA-seq) are the most commonly used high- ...

Abstract	Recent progress in transcriptomics and co-expression networks have enabled us to predict the inference of the biological functions of genes with the associated environmental stress. Microarrays and RNA sequencing (RNA-seq) are the most commonly used high-throughput gene expression platforms for detecting differentially expressed genes between two (or more) phenotypes. Gene co-expression networks (GCNs) are a systems biology method for capturing transcriptional patterns and predicting gene interactions into functional and regulatory relationships. Here, we describe the procedures and tools used to construct and analyze GCN and investigate the integration of transcriptional data with GCN to provide reliable information about the underlying biological mechanism.
MeSH term(s)	Algorithms ; Arabidopsis ; Computational Biology/methods ; Gene Expression Profiling/methods ; Gene Expression Regulation/genetics ; Gene Ontology ; Gene Regulatory Networks/genetics ; Microarray Analysis/methods ; Phenotype ; Principal Component Analysis ; Protein Interaction Maps ; Software
Language	English
Publishing date	2021-07-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1534-8_1
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Article ; Online: Characterization and Genomic Analysis of

Sultan-Alolama, Mohamad Ismail / Amin, Amr / El-Tarabily, Khaled A / Vijayan, Ranjit

International journal of molecular sciences

2022 Volume 23, Issue 23

Abstract: Verotoxin- ... ...

Abstract	Verotoxin-producing
Language	English
Publishing date	2022-11-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms232314846
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Article ; Online: Fully resolved assembly of Fusarium proliferatum DSM106835 genome.

Purayil, Gouthaman P / Almarzooqi, Amal Y / El-Tarabily, Khaled A / You, Frank M / AbuQamar, Synan F

Scientific data

2023 Volume 10, Issue 1, Page(s) 705

Abstract: In the United Arab Emirates, sudden decline syndrome (SDS) is a destructive disease of date palm caused by the soil-borne fungal pathogen Fusarium proliferatum (Fp) DSM106835. Here, a high-resolution genome assembly of Fp DSM106835 was generated using ... ...

Abstract	In the United Arab Emirates, sudden decline syndrome (SDS) is a destructive disease of date palm caused by the soil-borne fungal pathogen Fusarium proliferatum (Fp) DSM106835. Here, a high-resolution genome assembly of Fp DSM106835 was generated using PacBio HiFi sequencing with Omni-C data to provide a high-quality chromatin-organised reference genome with 418 scaffolds, totalling 58,468,907 bp in length and an N50 value of 4,383,091 bp from which 15,580 genes and 16,321 transcripts were predicted. The assembly achieved a complete BUSCO score of 99.2% for 758 orthologous genes. Compared to seven other Fp strains, Fp DSM106835 exhibited the highest continuity with a cumulative size of 44.26 Mbp for the first ten scaffolds/contigs, surpassing the assemblies of all examined Fp strains. Our findings of the high-quality genome of Fp DSM106835 provide an important resource to investigate its genetics, biology and evolutionary history. This study also contributes to fulfill the gaps in fungal knowledge, particularly the genes/metabolites associated with pathogenicity during the plant-pathogen interaction responsible for SDS.
MeSH term(s)	Chromosomes ; Fusarium/genetics ; Genome, Fungal
Language	English
Publishing date	2023-10-16
Publishing country	England
Document type	Dataset ; Journal Article
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-023-02610-4
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Article ; Online: Dietary supplementation with a mixture of Dunaliella salina and Spirulina enhances broiler performance by improving growth, immunity, digestive enzymes and gut microbiota.

Alghamdi, Mashail A / Elbaz, Mahmoud I / Ismail, Ismail E / Reda, Fayiz M / Alagawany, Mahmoud / El-Tarabily, Khaled A / Abdelgeliel, Asmaa Sayed

Poultry science

2023 Volume 103, Issue 2, Page(s) 103337

Abstract: The aim of this study is to evaluate the effect of Dunaliella salina and Spirulina (D + S) mixture on performance, carcass yield, kidney and liver markers, lipid profile, and immune responses of fattening chicks. Two hundred broiler chicks at 7 days old ... ...

Abstract	The aim of this study is to evaluate the effect of Dunaliella salina and Spirulina (D + S) mixture on performance, carcass yield, kidney and liver markers, lipid profile, and immune responses of fattening chicks. Two hundred broiler chicks at 7 days old were distributed into 5 experimental groups, 5 replicates each with 8 chicks each. Group 1 was fed on only basal diet; group 2 was fed with basal diet and 0.50 g/kg (D + S); group 3 was fed with basal diet and 1.00 g/kg (D + S); group 4 was fed with basal diet and 1.50 g/kg (D + S); and group 5 was fed with basal diet supplemented with 2.00 g/kg (D + S). The additive mixture (D + S) consisted of (1 D. salina: 1 Spirulina). The experiment lasted for 6 wk. The results demonstrated significantly improved better live body weight, body weight gain, and feed conversion ratio (P<0.01) for groups that received (D + S) at levels of 1.0 and 1.5 g/kg diet compared to other groups at 6 wk of age. There was no significant influence of different levels of dietary feed additives on feed intake or carcass traits. The lipid profile was improved through a reduction of total cholesterol and low-density lipoprotein (LDL) values and increasing high-density lipoprotein (HDL) values, as well as the immune response, which was improved through increasing values of complement 3, immunoglobulin M (IgM), and immunoglobulin G (IgG) in the birds treated with (D + S) compared to the control group. The inclusion of all levels of (D + S)/kg decreased triglyceride, while total protein, albumen, and globulin values (P<0.05 or P<0.01) were higher compared to other groups. The inclusion of the different levels of (D + S)/kg improved liver function, whereas aspartate aminotransferase (AST) and alanine aminotransferase (ALT) values were lower than in other groups (P<0.001). The lowest values of creatinine, urea, and uric acid were noted in birds fed a diet supplemented with 1.50 g (D + S)/kg. Antioxidant levels were improved through increasing values of catalase (CAT) and reduced glutathione (GSH) enzymes in the treated birds with (D + S) compared with the control chicks. Furthermore, digestive enzymes and microbial content were improved in broiler checks fed on diet supplemented with (D + S) compared to the control group. In conclusion, supplementing broiler chicks with a dietary D. salina and Spirulina combination increased their productive performance, immunity, kidney and liver function, lipid profile, and digestive enzymes.
MeSH term(s)	Animals ; Spirulina ; Chickens/physiology ; Gastrointestinal Microbiome ; Dietary Supplements/analysis ; Diet/veterinary ; Body Weight ; Lipids ; Animal Feed/analysis
Chemical Substances	Lipids
Language	English
Publishing date	2023-11-30
Publishing country	England
Document type	Journal Article
ZDB-ID	242586-5
ISSN	1525-3171 ; 0032-5791
ISSN (online)	1525-3171
ISSN	0032-5791
DOI	10.1016/j.psj.2023.103337
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Article ; Online: Molecular detection of highly pathogenic avian influenza H5N8 in commercial broiler chicken farms from 2019 to 2022 [Corrigendum: June 2023, 102(6), p. 102777]

Setta, Ahmed / Yehia, Nahed / Shakak, Amani Osman / Al-Quwaie, Diana A. / Al-Otaibi, Aljohara M. / El-Saadony, Mohamed T. / El-Tarabily, Khaled A. / Salem, Heba

Poultry Science. 2023 June, v. 102, no. 6, p. 102639

2023 , Page(s) 102639

Abstract: Highly pathogenic avian influenza (HPAI) is a serious viral infection that causes massive economic losses in poultry. The current study investigated the HPAI virus prevalence in commercial broiler chicken flocks from 2019 to 2022. Organ samples, ... ...

Abstract	Highly pathogenic avian influenza (HPAI) is a serious viral infection that causes massive economic losses in poultry. The current study investigated the HPAI virus prevalence in commercial broiler chicken flocks from 2019 to 2022. Organ samples, including trachea, cecal tonsils, spleen, brain, as well as tracheal and cloacal swabs, were harvested from 111 problematic broiler chicken flocks that suffered from variable mortalities accompanied with respiratory signs (103 H5-vaccinated and 8 nonvaccinated flocks) in Egypt during the observation duration. Molecular tools were used to analyze the samples, including real-time reverse transcription-polymerase chain reaction (rRT-PCR) and sequence analysis of some PCR positive strains. The results indicated that 24 flocks were positive for HPAI H5N8, representing 21.6%, with 22.3% (23/103) prevalence and 12.5% (1/8) detection in vaccinated and nonvaccinated flocks, respectively, and they were almost detected in the autumn and winter seasons. Phylogenetic evaluation of the hemagglutinin (HA) gene showed that the 6 Egyptian strains were clustered in clade 2.3.4.4b and allocated into 2 groups (I and II). The samples recovered in 2019 were clustered in new subgroup A, and samples recovered in 2020 to 2022 were clustered in new subgroup B with 10 nucleotide mutations (R72S, A83D, T140A). In conclusion, HPAI H5N8 is a serious threat even in vaccinated birds; to control such problems, periodic molecular monitoring with vaccine efficacy evaluation and the use of preventive strategies are recommended.
Keywords	Influenza A virus ; autumn ; avian influenza ; brain ; broiler chickens ; cloaca ; genes ; hemagglutinins ; phylogeny ; reverse transcriptase polymerase chain reaction ; sequence analysis ; spleen ; vaccines ; Egypt ; avian influenza virus ; PCR ; phylogenetic analysis ; poultry ; sequencing
Language	English
Dates of publication	2023-06
Size	p. 102639
Publishing place	Elsevier Inc.
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	242586-5
ISSN	1525-3171 ; 0032-5791
ISSN (online)	1525-3171
ISSN	0032-5791
DOI	10.1016/j.psj.2023.102639
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