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Article ; Online: In Silico Protocol for structure and function prediction of proteins in biological systems

Mohamed Ragab Abdel Gawwad

Network Biology, Vol 13, Iss 4, Pp 186-

2023 Volume 191

Abstract: Proteins carry out the majority of the biological processes of living cells. These macromolecules are almost involved in every cellular process: replication and transcription of DNA, and produce, process, and biosynthesize other proteins. They are ... ...

Abstract	Proteins carry out the majority of the biological processes of living cells. These macromolecules are almost involved in every cellular process: replication and transcription of DNA, and produce, process, and biosynthesize other proteins. They are controlling cell division, metabolism, and materials and information transportation into and out of the cell. The understanding how living cells work requires revealing the structure and function of proteins. Our protocol aim is to analyze protein(s) structure and its function in biological systems. There are 9 steps of the protocol by which the protein(s) is extensively analyzed structurally and functionally. These steps are bioinformatics tools and software: Retrieving sequence of protein(s), Sequence alignment, Phylogenetic tree construction, Protein(s) 3D Structure Prediction and Refinement, Protein(s) 3D structure validation and visualization, Protein(s) Domain Identification, Subcellular Localization of Protein(s) and Interactome Analysis. The protocol links between the structure and function of the protein(s) and a heuristic to predict protein(s) function.
Keywords	proteomics ; 3d structure prediction ; bioinformatics ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	International Academy of Ecology and Environmental Sciences
Document type	Article ; Online
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Article: 1D basin modeling and hydrocarbon generation potential of the Late Carboniferous Limburg Group formations, Northwest European Basin, Netherlands.

Thota, Surya Tejasvi / Shalaby, Mohamed Ragab

Heliyon

2023 Volume 9, Issue 9, Page(s) e19498

Abstract: The Carboniferous rock samples of the Limburg Group formations were studied to investigate the source rock characteristics and the hydrocarbon generative potential. The source rock samples have been collected representing four rock units from three ... ...

Abstract	The Carboniferous rock samples of the Limburg Group formations were studied to investigate the source rock characteristics and the hydrocarbon generative potential. The source rock samples have been collected representing four rock units from three different wells. These samples were analyzed using Rock-Eval pyrolysis results and measured vitrinite reflectance values, and also by generating a one-dimensional basin model of K1 Field. The total organic carbon in these samples varies from 0.31 to 83.56% with a mean of 37.68%, suggesting that Limburg Group formations have excellent potential as a source of hydrocarbons. Kerogen in the Limburg Group formations is type II-III and type III, generate gas prominently. The outcomes of thermal maturation by Tmax and measured vitrinite reflectance reveal that the examined Limburg source rocks are located in the mature zone. The burial and thermal history models show irregular trend patterns due to uplift, erosion, and non-deposition events that took place in the K1 field (where the structural element is Cleaver Bank High). For the Maurits Formation, the oil generation took place at 2011 m at 230.1Ma ago and the top of the gas window was encountered 217.8Ma ago at 2535 m, whereas for the Hospital Ground Formation, the top of the oil window was encountered 186.8Ma ago at 2404 m and the gas generation took place at 2404 m at 161.9Ma ago.
Language	English
Publishing date	2023-08-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e19498
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Article ; Online: Effects of antioxidant vitamins (A, D, E) and trace elements (Cu, Mn, Se, Zn) administration on gene expression, metabolic, antioxidants and immunological profiles during transition period in dromedary camels.

El-Sayed, Ahmed / Ebissy, Eman / Mohamed, Ragab / Ateya, Ahmed

BMC veterinary research

2024 Volume 20, Issue 1, Page(s) 101

Abstract: Background: Nutrition has a primary role for optimum expression of genetic potential, and most of the farmers have limited resources of green fodder. Hence, a fat-soluble vitamin, especially vitamin A and E and trace elements remained most critical in ... ...

Abstract	Background: Nutrition has a primary role for optimum expression of genetic potential, and most of the farmers have limited resources of green fodder. Hence, a fat-soluble vitamin, especially vitamin A and E and trace elements remained most critical in the animal's ration and affects their productive and reproductive performance adversely. Animals cannot be able to produce these vitamins in their bodies; hence, an exogenous regular supply is needed to fulfil the physiological needs and to maintain high production performance. This study elucidated effects of antioxidant vitamins (A, D, E) and trace elements (Cu, Mn, Se, Zn) administration on gene expression, metabolic, antioxidants and immunological parameters in dromedary camels during transition period. Results: At 0 day, there were no appreciable differences in the expression patterns of the metabolic (IGF-I, ACACA, SCD, FASN, LPL, and BTN1A1) genes between the control and treatment groups, despite lower levels. A substantial variation in the mRNA levels of SOD1, SOD3, PRDX2, PRDX3, PRDX4, PRDX6, and AhpC/TSA was observed between the control and treatment groups, according to the antioxidant markers. In comparison to the control group, the treatment group displayed a significant up-regulation at 0 and 21 days. The treatment and control groups exhibited substantial differences in the mRNA values of IL-1α, IL-1β, IL-6, and TNFα, as indicated by immunological markers. In comparison to the control group, there was a noticeable down-regulation in the treatment group at 0 and + 21 days. But IL10 produced the opposite pattern. No significant difference was observed in glucose, cholesterol, triglyceride, HDL, total protein, NEFA, BHBA, cortisol and IGF-1 levels between control and treatment group. The activity of serum GPx, SOD and TAC was significantly affected by time and treatment x time in supplemented groups as compared with control group. IL-1, IL-1, IL-6, and TNF were noticeably greater in the control group and lower in the treatment group. Additionally, in all groups, the concentration of all pro-inflammatory cytokines peaked on the day of delivery and its lowest levels showed on day 21 following calving. The IL-10 level was at its peak 21 days prior to calving and was lowest on calving day. Conclusion: The results demonstrated a beneficial effect of antioxidant vitamins and trace elements on the metabolic, antioxidant and immunological markers in dromedary camels throughout their transition period.
MeSH term(s)	Animals ; Trace Elements/pharmacology ; Antioxidants/metabolism ; Vitamins/pharmacology ; Camelus ; Vitamin A/pharmacology ; Interleukin-6 ; Vitamin K ; Zinc ; RNA, Messenger ; Gene Expression ; Interleukin-1
Chemical Substances	Trace Elements ; Antioxidants ; Vitamins ; Vitamin A (11103-57-4) ; Interleukin-6 ; Vitamin K (12001-79-5) ; Zinc (J41CSQ7QDS) ; RNA, Messenger ; Interleukin-1
Language	English
Publishing date	2024-03-13
Publishing country	England
Document type	Journal Article
ZDB-ID	2191675-5
ISSN	1746-6148 ; 1746-6148
ISSN (online)	1746-6148
ISSN	1746-6148
DOI	10.1186/s12917-024-03959-3
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Article ; Online: Performance of molybdenum vanadate loaded on bentonite for retention of cesium-134 from aqueous solutions.

Ghaly, Mariam / Abass, Mohamed Ragab / Mekawy, Zakaria Ali

Environmental science and pollution research international

2023 Volume 30, Issue 21, Page(s) 60432–60446

Abstract: This article studied the sorption behavior of Cs(I) ions from aqueous solutions onto molybdenum vanadate@bentonite (MoV@bentonite) composite. MoV@bentonite has been fabricated using the precipitation method and was characterized by different analytical ... ...

Abstract	This article studied the sorption behavior of Cs(I) ions from aqueous solutions onto molybdenum vanadate@bentonite (MoV@bentonite) composite. MoV@bentonite has been fabricated using the precipitation method and was characterized by different analytical tools including, FT-IR, XRD, and SEM attached with an EDX unit. The sorption studies applied on Cs(I) ions include the effect of contact time, pH, initial metal concentrations, ionic strength, desorption, and recycling. The experimental results revealed that in the adsorption process carried out after equilibrium time (300 min), saturation capacity has a value of 26.72 mg·g
MeSH term(s)	Bentonite/chemistry ; Molybdenum ; Vanadates ; Spectroscopy, Fourier Transform Infrared ; Hydrogen-Ion Concentration ; Thermodynamics ; Adsorption ; Water/chemistry ; Kinetics ; Solutions
Chemical Substances	Bentonite (1302-78-9) ; Cesium-134 (GWD7N0V43L) ; Molybdenum (81AH48963U) ; Vanadates (3WHH0066W5) ; Water (059QF0KO0R) ; Solutions
Language	English
Publishing date	2023-04-06
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/s11356-023-26607-z
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Article ; Online: Operational and Environmental Assessment of Weaving Section for Urban Roads

Abdelhalim Azam / Fayez Alanazi / Mohamed Ahmed Okail / Mohamed Ragab

Sustainability, Vol 15, Iss 4275, p

Case Study, Aljouf Region, KSA

2023 Volume 4275

Abstract: The urban weaving sections are more complex due to the various disturbing elements within the weaving section, such as lane-change situations. These turbulences reduced road capacity and increased vehicle exhaust emissions. The Highway Capacity Manual ( ... ...

Abstract	The urban weaving sections are more complex due to the various disturbing elements within the weaving section, such as lane-change situations. These turbulences reduced road capacity and increased vehicle exhaust emissions. The Highway Capacity Manual (HCM 2010) has a methodology for the analysis of weaving sections for the free highways; the methodology for the analysis of urban roads is not investigated in the HCM. Therefore, the main objective of this research is to present a systematic analysis of the factors that could potentially affect the capacity and exhaust emissions of urban weaving sections. These factors include the main road traffic volume, the weaving section length (WL), the volume ratio (VR), and the percentage of heavy vehicles (HV%). Two weaving sections were selected in the Aljouf Region, KSA; the Sakakah–Dumat Al-Jandal road. The collected data were used in the development of microsimulation using VISSIM models. The results indicated that increasing the volume ratio and percentage of heavy vehicles caused a decrease in capacity and an increase in exhaust emissions. It was discovered that the increase of weaving length resulted in increasing the capacity. However, increasing the weaving length was not beneficial for reducing exhaust emissions. Finally, regression models were developed for capacity estimation and emissions prediction of urban weaving sections based on weaving length and volume ratio, resulting in relatively high R 2 values.
Keywords	exhaust emissions ; capacity ; VISSIM ; weaving section ; Environmental effects of industries and plants ; TD194-195 ; Renewable energy sources ; TJ807-830 ; Environmental sciences ; GE1-350
Subject code	380
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article: Peripheral Neurectomy for Trigeminal Neuralgia: A Report of Seventeen Cases and Review of the Literature.

Nagy, Mohamed Ragab / Mahmoud, Bokhary

Asian journal of neurosurgery

2021 Volume 16, Issue 2, Page(s) 281–287

Abstract: Background: Surgical intervention for trigeminal neuralgia (TN) is indicated if there is a failure of the medical treatment. Peripheral neurectomy is one of the oldest surgical procedures for TN.: Objective: The aim is to evaluate the clinical ... ...

Abstract	Background: Surgical intervention for trigeminal neuralgia (TN) is indicated if there is a failure of the medical treatment. Peripheral neurectomy is one of the oldest surgical procedures for TN. Objective: The aim is to evaluate the clinical outcome and the recurrence rate following peripheral neurectomy for the management of TN. Patients and methods: This was a retrospective cohort study of 17 patients with classical TN treated by peripheral neurectomy. The visual analogue scale (VAS) was used for pain assessment preoperatively and during the follow-up period. The outcome of surgery was graded as a marked, moderate, or mild improvement. Kaplan-Meier analysis was used for the time to recurrence to predict the probability of recurrence at any given time following the procedure. Results: The mean pain-free interval was 29.3 ± 16.3 months. At 2 and 5 years of the follow-up period, the mean VAS improved significantly ( Conclusion: Peripheral neurectomy provides short to medium-term good pain control for patients with TN. The preoperative severity of pain, anxiety, and depression levels improved markedly after the procedure.
Language	English
Publishing date	2021-05-28
Publishing country	India
Document type	Journal Article
ZDB-ID	2621446-5
ISSN	2248-9614 ; 1793-5482
ISSN (online)	2248-9614
ISSN	1793-5482
DOI	10.4103/ajns.AJNS_361_20
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Article ; Online: Histological, immunohistochemical and serological investigations of the ovary during follicular phase of estrous cycle in Saidi sheep.

Abd-Elkareem, Mahmoud / Khormi, M A / Mohamed, Ragab Hassan / Ali, Fatma / Hassan, Mervat S

BMC veterinary research

2024 Volume 20, Issue 1, Page(s) 98

Abstract: Background: Saidi sheep are the most abundant ruminant livestock species in Upper Egypt, especially in the Assiut governorate. Sheep are one of the most abundant animals raised for food in Egypt. They can convert low-quality roughages into meat and milk ...

Abstract	Background: Saidi sheep are the most abundant ruminant livestock species in Upper Egypt, especially in the Assiut governorate. Sheep are one of the most abundant animals raised for food in Egypt. They can convert low-quality roughages into meat and milk in addition to producing fiber and hides therefore; great opportunity exists to enhance their reproduction. Saidi breed is poorly known in terms of reproduction. So this work was done to give more information on some hormonal, oxidative, and blood metabolites parameters in addition to histological, histochemical and immunohistochemical investigations of the ovary during follicular phase of estrous cycle. The present study was conducted on 25 healthy Saidi ewes for serum analysis and 10 healthy ewes for histological assessment aged 2 to 5 years and weighted (38.5 ± 2.03 kg). Results: The follicular phase of estrous cycle in Saidi sheep was characterized by the presence of ovarian follicles in different stages of development and atresia in addition to regressed corpus luteum. Interestingly, apoptosis and tissue oxidative markers play a crucial role in follicular and corpus luteum regression. The most prominent features of the follicular phase were the presence of mature antral (Graafian) and preovulatory follicles as well as increased level of some blood metabolites and oxidative markers. Here we give a new schematic sequence of ovarian follicles in Saidi sheep and describing the features of different types. We also clarified that these histological pictures of the ovary was influenced by hormonal, oxidative and blood metabolites factors that characterizes the follicular phase of estrous cycle in Saidi sheep. Conclusion: This work helps to understanding the reproduction in Saidi sheep which assist in improving the reproductive outcome of this breed of sheep. These findings are increasingly important for implementation of a genetic improvement program and utilizing the advanced reproductive techniques as estrous synchronization, artificial insemination and embryo transfer.
MeSH term(s)	Female ; Sheep ; Animals ; Ovary/metabolism ; Follicular Phase ; Ovarian Follicle ; Corpus Luteum ; Estrous Cycle
Language	English
Publishing date	2024-03-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2191675-5
ISSN	1746-6148 ; 1746-6148
ISSN (online)	1746-6148
ISSN	1746-6148
DOI	10.1186/s12917-024-03933-z
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Article ; Online: A Study and Assessment of the Status of Energy Efficiency and Conservation at School Buildings

Karim Mohamed Ragab / Mehmet Fatih Orhan / Kenan Saka / Yousef Zurigat

Sustainability, Vol 14, Iss 10625, p

2022 Volume 10625

Abstract: The building sector consumes a significant portion of global energy use. In this regard, this work was undertaken to study the status of energy efficiency and conservation at a large school building in the northern part of United Arab Emirates (UAE). The ...

Abstract	The building sector consumes a significant portion of global energy use. In this regard, this work was undertaken to study the status of energy efficiency and conservation at a large school building in the northern part of United Arab Emirates (UAE). The annual electrical consumption at the school was analyzed and an awareness survey among the students and teachers was conducted to measure the level of awareness as well as to assess the current energy consumption practices. In order to identify energy saving opportunities, an energy audit was carried out wherein the school energy consuming systems, particularly the lighting and air-conditioning systems, were assessed. Furthermore, thermography scanning of the school building envelope was conducted to examine the building insulation and identify air leakage locations. The building electricity supply and distribution systems were assessed using power analyzer and thermography devices. The energy conservation measures identified include removing the extra lighting, installing motion sensors in classrooms and labs, as well as integrating a Networked Optimization Software with the current HVAC (heating, ventilating and air conditioning) system. The methodology consists of seven fundamental steps: (1) case study data collection (analysis of buildings and utility data); (2) survey of real operation conditions; (3) understanding of building behavior; (4) analysis of energy conservation measures; (5) estimation of energy-saving potential; (6) economic assessment; and (7) proposing Energy Conservation Measures (ECMs). In this regard, the school energy consuming systems (lighting, building envelope, and air conditioning (AC)) were examined to identify possible ways to reduce the school energy consumption. The results indicate that the cost of installing motion sensors in classrooms, and labs is approximately AED 20,000 (United Arab Emirates Dirham), which yields an annual energy saving of AED 93,691. Furthermore, with all energy saving measures, a total annual saving of ...
Keywords	energy audit ; energy awareness ; thermography ; energy conservation ; energy management ; energy efficiency ; Environmental effects of industries and plants ; TD194-195 ; Renewable energy sources ; TJ807-830 ; Environmental sciences ; GE1-350
Subject code	690
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: In silico interactome and docking site study of DNA repair proteins (APE1 and APE2) and their role in base excision repair in Arabidopsis thaliana

Esma Kurtanovic / Mohamed Ragab Abdel Gawwad

Network Biology, Vol 11, Iss 3, Pp 241-

2021 Volume 246

Abstract: Flowering time is a life history trait of adaptiveness. Over many generations, phenotypes happen to emerge as mutations or spontaneous damage accumulates in the plastome. Thus, it is of great importance to investigate DNA repair mechanism roles of some ... ...

Abstract	Flowering time is a life history trait of adaptiveness. Over many generations, phenotypes happen to emerge as mutations or spontaneous damage accumulates in the plastome. Thus, it is of great importance to investigate DNA repair mechanism roles of some proteins. Specifically, this study aims to determine potential targets that are part of base excision repair mechanism in Arabidopsis thaliana. To do so, bioinformatic methods are implemented in order to shed light on the functioning of our protein homologs. Their structural and functional similarities are confirmed by multiple sequence alignment, 3D structure prediction, phylogenetic tree construct and interactome analysis. The results indicate that interaction between two proteins is strong evidence that the proteins are involved in the same biological process. This study can be seen as a valuable data resource of predicted cellular functions of proteins and the evolutionary conservation of AP endonuclease families, which again, portrays the divergence of activities and biological contributions.
Keywords	dna damage and repair ; interactome ; docking sites ; ape homologs ; a. thaliana ; base excision repair ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	International Academy of Ecology and Environmental Sciences
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Influence of polymorphisms in candidate genes on carcass and meat quality traits in rabbits.

Hosam M Safaa / Mohamed Ragab / Marwa Ahmed / Belal El-Gammal / Mostafa Helal

PLoS ONE, Vol 18, Iss 11, p e

2023 Volume 0294051

Abstract: Candidate gene is a powerful approach to study gene-trait association and offers valuable information for genetic improvement using marker-assisted selection. The current work aimed to study the polymorphisms of four single nucleotide polymorphism (SNPs) ...

Abstract	Candidate gene is a powerful approach to study gene-trait association and offers valuable information for genetic improvement using marker-assisted selection. The current work aimed to study the polymorphisms of four single nucleotide polymorphism (SNPs) at located growth hormone (GH), insulin-like growth factor-II (IGF-II), fat mass and obesity-associated (FTO), and insulin receptor substrate-1 (IRS-1) genes, and their association with the carcass, and meat quality traits in rabbits. The SNPs were genotyped using RFLP-PCR in New Zealand White and local Baladi rabbits. The results revealed that the heterozygous genotype was the most frequent in all cases, except for the FTO SNP in LB rabbits. There was a significant effect for GH genotypes on meat lightness after slaughter and hind-part weight. While, IGF-II mutation significantly affected slaughter, hot carcass, commercial carcass, and hind-part weights. The FTO SNP was associated with cooking loss and intramuscular fat weight, and the IRS-1 SNP was significantly associated with drip loss and intramuscular fat. Specific-breed effects were obtained for IGF-II SNP on cooking loss, and for the intramuscular fat. Although the results suggested that these mutations are useful candidate genes for selection, more research for detecting more variants associated with carcass and meat quality traits in rabbits are recommended.
Keywords	Medicine ; R ; Science ; Q
Subject code	616
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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