Faculty of Biotechnology Research Paper

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Effects of hypervitaminosis C and D on spermatogenesis through CDKN1B modulation in adult male mice: biochemical and immunohistochemical studies
(Springer Science and Business Media B.V., 2025-06-21) Karima Nasraldin; Ayman A. Diab; Amira S. AbdElkhalek; Selvia N. Talaat; Salma Hossameldin; Fady S. Tawfik; Nada K. Ghaith; Ahmed Said
Background The complex biological process of spermatogenesis produces mature spermatozoa within the testicular environment by terminally differentiating male germ precursor cells. Vitamin C (VC) is a potent water-soluble antioxidant. It has a vital antioxidant role, crucial for maintaining tissue formation and functionality by protecting vital macromolecules from oxidative damage. The essential role of vitamin D (VD) in the male reproductive system has been suggested due to the expression of vitamin D receptor (VDR) and Vitamin D-metabolizing enzymes in the testis and spermatozoa. Aim This study examines the effects of high-dose VC and VD on sperm quality, testosterone levels, and hepatorenal function, focusing on CDKN1B expression during spermatogenesis. Methods Twenty-seven male mice were divided into three groups (n=9/group): (1) saline vehicle control, (2) VC treatment (40 mg/kg, or 800 IU/kg), and (3) VD treatment (25 µg/kg, or 1000 IU/kg). For 15 days, intraperitoneal injections were given every day. Histological and immunohistochemical expression of CDKN1B, as well as biochemical investigations, including liver and kidney biomarkers, testosterone, and sperm parameters, were performed on day 16." Results High-dose vitamin D (VD) treatment significantly reduced sperm count and motility (p<0.01), alongside a marked decline in testosterone levels (p<0.01). Hepatorenal toxicity was evident, with significantly elevated liver enzymes (ALT & AST) and kidney biomarkers (Creatinine & Urea) (p<0.05), with a significant reduction in testis length and weight (p<0.05). In contrast, vitamin C (VC) treatment showed non-significant improvements in sperm motility and testosterone levels, with no adverse hepatorenal effects. Immunohistochemical analysis revealed elevated CDKN1B expression in VDtreated spermatocytes, indicative of cell cycle arrest during spermatogenesis. In contrast, VC downregulated CDKN1B, with no significant reduction in testis weight or length. Conclusion Through hepatorenal toxicity, hormonal suppression, and spermatogenesis disruption mediated by CDKN1B, hypervitaminosis D reduces male fertility. VC, on the other hand, has beneficial antioxidant properties without any adverse effects. These results support cautious VD monitoring and draw attention to the dangers of excessive VD supplementation, especially in clinical settings that employ CYP-inducing drugs. VC might be a safe supplemental treatment for infertility brought on by oxidative stress.
Yttrium oxide nanoparticles induce selective cytotoxicity, genomic instability and ROS mitochondrial P53 mediated apoptosis in human pancreatic cancer cells
(Nature Research, 2025-06-20) Hanan R. H. Mohamed; George M. Hakeem; Yasmin Abdel Latif; Shahd H. Elnawasani; Maria Nagy; Basma A. Mohamed; Rawan Essam; Gehan Safwat
Pancreatic cancer is a hard-to-treat tumor with a poor prognosis. While traditional pancreatic cancer therapies can be effective, issues like cytotoxicity, low selectivity, and drug resistance still pose major challenges. Nanotechnology has shown promise in improving cancer diagnosis and treatment. Yttrium oxide nanoparticles (Y2O3-NPs), for example, have demonstrated potent selective cytotoxicity against triple negative breast cancer cells; but their effects on pancreatic cancer cells have not been explored. This study aimed to explore the impact of Y2O3-NPs on cell proliferation, DNA integrity, and oxidative stress in pancreatic cancer (PANC-1) and human skin fibroblast (HSF) cells. The cytotoxicity of Y2O3-NPs after 72 h were estimated using Sulforhodamine (SRB) cytotoxicity assay, while alkaline Comet assay was done to study genomic DNA integrity. Generation level of reactive oxygen species (ROS) and integrity of mitochondrial membrane potential were also analyzed. Apoptosis induction was investigated using Flow Cytometry and expression level of apoptotic (p53), anti-apoptotic (Bcl2) and mitochondrial (ND3) genes was measured using quantitative RTPCR. Our findings exhibited that Y2O3-NPs had strong selective cytotoxicity against PANC-1 cells with an IC50 value of 31.06 µg/ml, while having minimal effect on normal HSF cells (IC50=319.21 µg/ml). Treatment of PANC-1 cells with Y2O3-NPs at the IC50 concentration for 72 h significantly increased intracellular ROS levels and DNA damage, along with a notable reduction in mitochondrial membrane potential. Additionally, a significant rise in necrotic, early, and late apoptotic cells was observed, accompanied by downregulation of the anti-apoptotic Bcl2 gene and upregulation of the apoptotic p53 and mitochondrial ND3 genes. These findings highlight the selective toxicity of Y2O3-NPs towards cancerous PANC-1 cells, with minimal impact on normal cells. Y2O3-NPs appear to induce apoptosis in cancer cells by increasing ROS generation, damaging DNA, disrupting mitochondrial function, and triggering cell death. This study suggests that Y2O3-NPs may be a promising candidate for pancreatic cancer treatment. Further research is needed to fully explore their therapeutic potential.
Evaluation of the effect of biochar on the metabolic status, oxidative stress, and immune response of Sprague Dawley rats
(Elsevier B.V., 2025-06-20) Salma Mohsen; Mariam Reda; Farah Waleed; Youssef Waleed; Mayar Tarek; Sama Saber; Alyaa Farid; Gehan Safwat
Livestock health is seriously endangered by environmental pollutants in feed, water, and soil, affecting organ health, productivity, and immune system performance. Biochar, a material rich in carbon produced via pyrolysis, attracts interest as an additive to foods for its ability to adsorb toxins, influence gut microbiota, and enhance immune responses. The study aimed to investigate the effects of biochar supplementation (2.5 %, 5 %, and 7.5 %) in animals’ diets on immune response and oxidative stress in male Sprague Dawley rats following immunization with sheep red blood cells (RBCs). Rats were divided into four groups: a control group receiving a standard diet and three groups receiving biochar-supplemented diets. Following six weeks of feeding, the animals were immunized and housed for two more weeks. Liver and kidney function parameters, oxidative stress markers (MDA, SOD, CAT, and GSH), and pro-inflammatory cytokines (IL-6, IL-17, IL-1β, and IFN-γ) were measured before and after immunization. Histopathological changes in the kidney and liver of rats were observed to confirm the biochemical findings. The results demonstrated that liver and kidney function elevated in the control group after immunization; biochar supplementation at 5 % and 7.5 % considerably decreased oxidative stress and inflammation brought on by immunization. Additionally, these groups exhibited improved antioxidant enzyme activity and reduced pro-inflammatory cytokine levels post-immunization. Histopathological analysis confirmed these findings, showing preserved hepatocyte architecture and renal tubular integrity in biochartreated groups compared to controls. According to the results, dietary biochar can be used as a functional feed supplement to help immunized animals mitigate oxidative stress and boost immunological responses
Isolation and Characterization of Zinc Resistant Diazotrophic Bacteria from Assiut Governorate Soils
(Journal of Pure and Applied Microbiology, 2025-05-07) Ahmed Salah; Naemia M. Yousef; Abd El-Latif Hesham; Ingy M. El-Hefny; Asmaa M.M. Mawad
Microorganisms exhibit a complex relationship with heavy metals. While some of these metals are essential for microbial growth and function, others can be detrimental at elevated concentrations, inhibiting or even killing the organisms. In this study, free living diazotrophic bacteria were isolated from contaminated sites. The bacteria were investigated to resist different concentrations of Zn (II); 5-60 mg/L. The results revealed that the bacterial isolate was identified as Bacillus subtilis AUMC-B492 based on 16S rRNA gene sequencing. The bacteria were diazotrophic in nutrition and can fix atmospheric nitrogen for growth and replication in nitrogen free media. B. subtilis AUMC-B492 removed 30% of Zn (II) when initial concentration was 5 mg/L within 48 h in nitrogen free media. It could tolerate up to 100 mg/L of Zn (II) within 24 h. Therefore, strain AUMC-B492 could be used as a promising tool for bioremediation of heavy metals as well as holding potential for agricultural applications.
Induction of potent preferential cell death, severe DNA damage and p53‑independent ROS‑mediated mitochondrial apoptosis by CaTiO3NPs in HNO‑97 tongue cancer cells
(Springer Science and Business Media Deutschland GmbH, 2025-06-04) Hanan R. H. Mohamed; Maivel Michael; Yusuf Elberry; Hagar Magdy; Maryam Ismail; Nourhan Eltayeb; Gehan Safwat; Ayman Diab
The aggressive nature and high recurrence rate of tongue cancer, along with the severe side efects associated with current conventional treatments, underscore the urgent need for alternative therapeutic strategies that ofer improved selectivity and reduced toxicity. Calcium titanate nanoparticles (CaTiO3NPs) have previously demonstrated signifcant cytotoxic efects against MCF-7 breast cancer and A549 non-small cell lung cancer lines. However, their therapeutic potential against tongue cancer remains unexplored. Therefore, this study investigates, for the frst time, the cytotoxic efect of CaTiO3NPs on HNO- 97 tongue cancer cells in comparison to normal human skin fbroblasts (HSF) cells. Using various assays, we assessed their efects on cell viability, reactive oxygen species (ROS) generation, genomic DNA and mitochondrial integrity, and cell death pathways. Cytotoxicity assessment using the sulforhodamine B (SRB) assay demonstrated that CaTiO3NPs signifcantly reduced HNO-97 cell viability in a concentration-dependent manner, with an IC50 of 29.67 µg/ml. In contrast, normal HSF cells exhibited a much higher IC50 of 262.6 µg/ml, indicating strong selectivity for cancer cells (selectivity index=8.85). Mechanistic studies revealed that HNO-97 cell exposure CaTiO3NPs at the IC50 concentration markedly increased ROS production, inducing oxidative stress. This led to signifcant genomic DNA damage, confrmed by the comet assay, and mitochondrial dysfunction, validated through Rhodamine-123 staining. Flow cytometry analysis indicated the induction of both apoptotic and necrotic pathways. At the molecular level, qRT-PCR analysis revealed signifcant downregulation of key genes, including the pro-apoptotic p53, the anti-apoptotic Bcl-2, and the mitochondrial ND3 gene, supporting the involvement of mitochondrial dysfunction and impaired DNA repair mechanisms in the observed cytotoxic efects. Conclusion: Collectively, these fndings demonstrate that CaTiO3NPs elicit strong and selective multi-modal cytotoxic efects against HNO-97 tongue cancer cells and minimal impact on normal HSF cells, supporting their promise as a novel nanotherapeutic agent for tongue cancer. Further in vivo studies are needed to validate their therapeutic efcacy, clinical applicability and biosafety.
Phytochemical Identification Components of Coffee Arabica Extracts and Its Role in Alleviation Alterations of Tetracycline Induced Non-alcoholic Steatohepatitis (NASH) in rats.
(NIDOC (Nat.Inform.Document.Centre), 2025-06-06) Merehan Alaa-ElDin Mohamed; Mustafa M.M. Elbakry; Shaimaa Rihan; Said S. Moselhy
High doses of tetracycline (TET) caused serious health effects, including non-alcoholic steatohepatitis (NASH). We identified the bioactive content of Coffee Arabica extract and its possible role in the alleviation of NASH induced by TET in rats. Sixty male albino rats (150 ± 10 g) were allocated into six groups: Control, TET: it received TET orally (1 g/kg BW) for 8 days; group III (CAME): it received Coffea Arabica methanolic extract (CAME) orally (0.1 g/kg) for 4 weeks; group IV (treated): it received TET then treated with CAME for 4 weeks; group V (preventive): it received CAME for 4 weeks then received TET orally for 8 days, VI (Protected): it received TET and CAME orally for 8 days. The total phenolic in the aqueous, methanolic, and ethanolic extracts were 751.36, 1259.09, and 1146.82 mg GAE/g, respectively. The GC/MS analysis showed the highest content of chlorogenic acid. The CAME ameliorated the liver alterations in TET-intoxicated rats by reducing the indexes of liver function and lipid profile (p<0.001), enhanced antioxidant capacity. CAME preventive is the most effective in liver alteration as portal vein congestion, scattered apoptosis and inflammatory infiltration. The autophagy signals as mTOR and LC3 will be investigated for more explanation its mechanism of action.
Serum miRNA-146 and Cortisol levels in Type 2 Diabetes Mellitus: Novel Biomarkers for Diagnosis and Pathophysiological Insights
(NIDOC (National Information and Documentation Centre), 2025-05-19) Amal A Mohamed; Abbas M Abbas; Rasha Elgamal; Maysa I. Farghly; Hanan A. Hegazy; Mahmoud M Shaheen; Shaimaa A. Fathy; Mohamed El Sherbiny; Ghada Maher Thabet; Karima Nasraldin; Naglaa K. Madkour; Reem Elmahdy; Moamen Abdelfadil Ismail; Noheir Ashraf Ibrahem Fathy Hassan; Ahmed Abdelrahman; Mina Wassef Girgiss; Wael Hafez; Samar S Khalaf
Background: Type 2 Diabetes Mellitus (T2DM) is a chronic condition characterized by hyperglycemia due to defects in insulin action or secretion. Its rising prevalence poses a significant global health challenge. Evidence suggests that T2DM involves non-coding RNA molecules, such as miRNAs, which regulate gene expression. Cortisol, a stress hormone, is also implicated in T2DM by influencing glucose metabolism and contributing to complications. Aim: This study aimed to evaluate the diagnostic and pathophysiological relevance of miRNA-146 and cortisol in T2DM. This study explored their potential as biomarkers for identifying metabolic and inflammatory abnormalities and examined their interactions with glycemic markers (HbA1c and RBG). Methods: This cross-sectional study included 100 T2DM patients and 100 healthy controls from the Suez Canal University outpatient clinic. Biochemical assessments included RBG, fasting insulin, HbA1c, vitamin D, cholesterol, triglycerides (TG), LDL, HDL, cortisol, and miRNA-146. Cortisol and vitamin D levels were measured using ELISA, while miRNA-146 levels were quantified using RT-qPCR. Diagnostic performance was assessed using Receiver Operating Characteristic (ROC) curves, and statistical analyses were performed using IBM SPSS. Results: miRNA-146 levels were significantly lower in T2DM patients than in controls, with a cut-off value of ≤ 6.83, achieving 83.0% sensitivity and 79.0% specificity (AUC = 0.832). This makes miRNA-146 a highly effective diagnostic biomarker for early detection. Cortisol levels were elevated in T2DM patients and positively correlated with HbA1c and RBG, indicating its role in glucose metabolism dysregulation. A cortisol cut-off of ≥ 3.8 nmol/L showed 95.0% sensitivity and 71.0% specificity (AUC = 0.819), suggesting its utility as a secondary screening tool. However, its lower specificity may warrant further confirmatory testing . Conclusion: This study highlights the complementary roles of miRNA-146 and cortisol as T2DM biomarkers. While miRNA-146 demonstrates the highest diagnostic accuracy, cortisol offers additional insights into metabolic disturbances. These findings provide a foundation for improving T2DM diagnosis and monitoring. Further research is needed to validate these biomarkers and to explore their potential as targeted therapeutic strategies.
Nodules-associated Klebsiella oxytoca complex: genomic insights into plant growth promotion and health risk assessment
(BioMed Central Ltd, 2025-05-15) Sameh H. Youseif; Fayrouz H. Abd El‑Megeed; May S. Soliman; Amr Ageez; Akram H. Mohamed; Saher A. Ali; Amani A. El‑Kholy
The swift emergence of antibiotic resistance genes (ARGs) across interconnected One Health compartments poses a signifcant global threat. Although plant growth-promoting (PGP) bacteria possess numerous attributes benefcial to host plants, many of these bacteria also harbor ARGs, necessitating a focused assessment of their negative implica‑ tions. In this context, here we performed whole genome sequencing of 14 PGP endophytic strains isolated from root nodules of faba beans, belonging to three Klebsiella oxytoca species complex (KoSC): K. grimontii (n=5), K. michiganensis (n=5), and K. pasteurii (n=4). We performed comparative genomics, molecular typing, and pangenome analyses on these strains. We identifed signifcant diversity within the KoSC population, classifying the strains into fve sequence types (STs), three of which are novel to this study (ST-542, ST-569, and ST-629). Phylogenomic analysis revealed that the bacterial strains clustered more closely by ST than by their source of isolation. Annotation of gene clusters indi‑ cated that all assembled genomes are enriched with genes involved in PGP activities, alongside a robust array of genes conferring tolerance to abiotic stresses. Importantly, our fndings disclosed that the 14 assembled genomes harbored multiple ARGs, conferring resistance to various antibiotic classes, with 71% of the population classifed as multidrugresistant based on the in vitro antibiotic susceptibility assay. Furthermore, all genomes contained an array of virulence factors critical for survival, pathogenesis, bioflm formation, and root colonization. In conclusion, this study substantiates the hypothesis that certain PGP bacteria may serve as potential reservoirs of multidrug resistance, posing signifcant public health risks. Thus, the future advancement of bacteria-based biofertilizers should integrate environmental con‑ siderations and monitor their impact on antibiotic resistance dissemination in soil ecosystems.
Biological and molecular characterization of Spodoptera littoralis granulovirus with insecticidal activity against the cotton leafworm, Spodoptera littoralis (Boisd.)
(Springer Nature, 2025-05-15) Wael Elmenofy; Norhan Yasser; Lamis Gomaa; Hossam S. El‑Beltagi; Ahmed Mahmoud Ismail
Granuloviruses (GVs) associated to the cotton leafworm Spodoptera littoralis, particularly type I, have been poorly examined. In this study, a field-collected baculovirus isolate, Spodoptera littoralis granulovirus (SpliGV) was characterized. Viral granules with a single rod-shaped virion with a range size of 271–358 in length and 148–171 nm in width, were detected by transmission electron microscopy. The genome pattern of SpliGV was compared to that of the sister strain Spodoptera litura granulovirus (SpltGV) isolate K1 upon restriction endonuclease digestion, and its identity was confirmed. The SpliGV isolate showed to be closed and shares a 99.07% genetic similarity with the Spodoptera litura granulovirus isolate K1, and 95.22% with Spodoptera littoralis granulovirus isolate 66, both classified as Type I granulovirus. The median lethal concentration values (LC50), measured as the concentration of viral occlusion bodied (OBs), for the SpliGV isolate against S. littoralis larvae were 1.76 × 105 OB ml-1 for second instar larvae and 2.92 × 105 OB ml-1 for fourth instar larvae ten days post-infection. Based on its host specificity and virulence traits, the SpliGV isolate is a potential bioagent candidate for the control of S. littoralis.
FokI polymorphism of the vitamin D receptor gene: Linking COVID-19 risk to genetic susceptibility in children
(Academic Press, 2025-05-13) Amal Ahmed Mohamed; Abdullah Taher Alanazi; Hoda H. Ahmed; Samar Elfiky; Muhammad T Abdel Ghafar; Ingy Maher; Sherin A. Taha; Mohammed Zakaria Ali Abu Rahma; Waleed Elagawy; Dina A. Mohareb; Abeer M. Rawy; Heba M. Abostate; Amira AlSayed Youssef; Dalia Saeed Elsayed; Rasha M. Abdel-Hamid
Background Vitamin D receptor (VDR), influenced by gene polymorphisms like FokI, may affect susceptibility to infections, including coronavirus disease 2019 (COVID-19). Since studies in children are limited, we aimed to analyze the correlation between the VDR FokI variant and both the incidence and severity of COVID-19 in Egyptian children. Methods Seventy-seven COVID-19-positive and 107 COVID-19-negative pediatric patients were included. Participants' serum 25(OH)D levels, inflammatory biomarkers, and demographics were evaluated. Real-time polymerase chain reaction (PCR) was used for genotyping the VDR FokI (rs2228570) polymorphism. Results Absolute lymphocyte count (ALC) was significantly lower in COVID-19 patients than in controls, while interleukin-6 (IL-6), erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), procalcitonin, and D-dimer were significantly higher (all p < 0.001). Vitamin D insufficiency was significantly more common in COVID-19 cases (18.2 % versus 3.7 %, p = 0.002). Male sex, increased tumor necrosis factor-alpha (TNF-α), and CRP were significantly associated with severe COVID-19 (p = 0.032, 0.029, < 0.001, respectively). The FokI TT genotype in codominant and recessive models and the T allele in the multiplicative model were significantly correlated with 2.4, 3.0, and 1.8 folds increased COVID-19 risk (p = 0.043, < 0.001, and 0.004, respectively). However, VDR FokI variants did not significantly associate with severe COVID-19. Conclusion The T allele and TT genotype of the FokI variant in the VDR gene increase susceptibility to COVID-19 but not its severity in Egyptian children. Additional research is required to validate the potential role of vitamin D and its receptor polymorphism in COVID-19.
Caffeine-boosted silver nanoparticles target breast cancer cells by triggering oxidative stress, inflammation, and apoptotic pathways
(Elsevier B.V., 2025-05-14) Naief Dahran; Mohamed S. Othman; Farah Mumtaz; Ghada M. Aleid; Mohamed E. Ghoniem; Mai A. Samak; Mohamed T. Elabbasy; Ayman A. Saleh; Sofian T. Obeidat; Ola A. Habotta; Ahmed E. Abdel Moneim
Breast cancer (BC) constitutes a major global health concern and is the second foremost cause of cancer-related mortality among women worldwide. This research investigated the anticancer effectiveness of caffeine-conjugated silver nanoparticles (Caf-AgNPs) against MDA-MB-231 breast cancer cells, utilizing fluorouracil (5-FU) as a reference antitumor drug. The study illustrated that the strategic conjugation of caffeine with AgNPs substantially improved the therapeutic efficacy against breast cancer cell lines and simultaneously attenuated cytotoxicity in normal mouse liver (NBL) cells. Caf-AgNPs significantly increased ROS, malondialdehyde, COX-2, IL-1β, and TNF-α level in BC cells, which was accompanied by a decrease in glutathione levels. The increased levels of cytosolic cytochrome c, caspase-3, and Bax proteins, as well as a significant decrease in Bcl-2 expression and Bcl-2/Bax ratio, were indicative of the significant pro-apoptotic effects of Caf-AgNPs in MDA-MB-231 cells. Cancer cells subjected to Caf-AgNPs demonstrated elevated lactate dehydrogenase (LDH) membrane leakage, signifying cellular membrane disruption. Cell cycle analysis revealed a substantial proportion of early and late stage apoptosis in cancer cells exposed to Caf-AgNPs, accompanied by a notable downregulation of cyclin D1 and cyclin-dependent kinase 2 (CDK2) mRNA expression. Caf-AgNPs utilize several mechanisms for cellular destruction, including cell cycle arrest, oxidative stress induction, modulation of the inflammatory response, and mitochondrial apoptosis. Caf-AgNPs offer a promising and complex strategy for breast cancer intervention. © 2025 American Pharmacists Association
Synthesis of rice husk-loaded chitosan nanoparticles for treatment of amikacin-induced kidney injury in male rats
(Elsevier B.V, 2025-05-10) Alyaa Farid; Aisha Hossam; Malak Waheed; Gehan Safwat
The main causes of amikacin-induced kidney damage are inflammation and oxidative stress. Although rice husks are full of bioactive components that have therapeutic uses, their instability and low bioavailability limit their use. Chitosan nanoparticles improve the stability and bioactivity of phytochemicals by offering an effective drug delivery method. The study aimed to prepare and characterize rice husk-loaded chitosan NPs and evaluate their therapeutic effects against amikacin-induced nephrotoxicity. Ionic gelation was used to create NPs, which were then examined using transmission electron microscopy, zeta potential, and dynamic light scattering. In vitro tests were performed to evaluate their anti-inflammatory and antioxidant properties. Male rats were divided into: negative control, positive control, amikacin-induced kidney injured rats treated with rice husks extract, chitosan NPs or rice husk-loaded chitosan NPs. Gas chromatography verified that rice husks phytochemicals were successfully loaded on chitosan NPs. Rice husk-loaded chitosan NPs had a consistent zeta potential (~58.6 mV) and a nanoscale size (~76.7 nm). When compared to rice husk extract or chitosan NPs, rice husk-loaded chitosan NPs showed better anti-inflammatory and antioxidant properties. In vivo, rice husk-loaded chitosan NPs significantly restored kidney function biomarkers, lowered oxidative stress and inflammation. In conclusion, rice husk-loaded chitosan NPs is a nephroprotective treatment.
A Guide to Basic RNA Sequencing Data Processing and Transcriptomic Analysis
(Bio-protocol LLC, 2025-05-05) Rowayna Shouib; Gary Eitzen; Rineke Steenbergen
RNA sequencing (RNA-Seq) has transformed transcriptomic research, enabling researchers to perform largescale inspection of mRNA levels in living cells. With the growing applicability of this technique to many scientific investigations, the analysis of next-generation sequencing (NGS) data becomes an important yet challenging task, especially for researchers without a bioinformatics background. This protocol offers a beginner-friendly step-by-step guide to analyze NGS data (starting from raw .fastq files), providing the required codes with an explanation of the different steps and software used. We outline a computational workflow that includes quality control, trimming of reads, read alignment to the genome, and gene quantification, ultimately enabling researchers to identify differentially expressed genes and gain insights on mRNA levels. Multiple approaches to visualize this data using statistical and graphical tools in R are also described, allowing the generation of heatmaps and volcano plots to represent genes and gene sets of interest.
Metabolomic analysis reveals key changes in amino acid metabolism in colorectal cancer patients
(Springer, 2025-05-02) Asmaa Ramzy; Taghreed Khaled Abdelmoneim; Menna Arafat; Maha Mokhtar; Ashraf Bakkar; Amany Mokhtar; Wagida Anwar; Sameh Magdeldin; Shymaa Enany
The number of colorectal cancer (CRC) patients is steadily growing worldwide, particularly in developing nations. Nonetheless, recent advances in early detection studies and therapy alternatives have reduced CRC mortality in afuent countries, despite rising incidence. Gut microbiota and their metabolites may contribute to tumor growth and reduced therapeutic efcacy. This preliminary study sought to uncover metabolic fngerprints in colorectal cancer patients. It also emphasizes the correlation between the gut microbiome, microbial metabolism, and altered metabolites in CRC. In this study, stool samples from 20 CRC patients and matched healthy controls were enrolled. Untargeted metabolomics approach based on an ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-MS/MS) were applied. Statistical approaches, pathway enrichment analysis, and network analysis were employed to unleash CRC perturbed metabolic pathways and putative biomarkers. The study identifed a distinct manually curated metabolite profle that is substantially linked to CRC. The steroidogenesis, aspartate, tryptophan (Trp), and urea cycle were the most signifcant pathways that concurrently contributed to CRC.Prominently, among other pathways, Trp metabolism was identifed as a critical pathway, indicating a possible connection between the development of CRC and gut microbiota. In a nutshell the notable resulted metabolites reveal auspicious biomarkers for the initial diagnosis as well as surveilling of CRC progression. This preliminary study highlights the potential involvement that gut bacteria may contribute in CRC patients. Further investigation into the composition of the gut microbiome associated with this metabolic profle may lead to the identifcation of novel biomarkers for early detection and possible targets for treatment.
Freshwater Bivalve Coelatura aegyptiaca as a Sensitive Bioindicator for Zinc Oxide/ Chitosan Nanocomposites Toxicity
(Bentham Science Publishers, 2025-04-11) Mennatallah H. Abdelaziz; Muhammed S. ElRakabawi; Ahmed Mohamed Soliman; Ayman Saber Mohamed
Background: Freshwater bivalves are considered effective biomarkers for pollution in aquatic ecosystems. Despite advances in the use of zinc oxide nanoproducts in several sectors, such as food, industry, and medicine, paying attention to their environmental impacts is crucial. The objective of the study was to investigate the mechanisms of zinc oxide-chitosan nanocomposites (ZnO-CS NCs) ecotoxic in freshwater environments using freshwater bivalves Coelatora aegyptica as a sensitive indicator. Methods: After preparing and characterizing ZnO NPs and ZnO-CS NCs with transmission electron microscopy, ultraviolet spectroscopy, and X-ray diffraction, we exposed the bivalve to three different doses of ZnO NPs and ZnO-CS NCs (12.5, 25, and 50 mg/L) for 7 days. Results: ZnO-CS NCs concentrations significantly increased malondialdehyde and nitric oxide levels, whereas glutathione and catalase levels decreased in investigated organs. Furthermore, histological changes were detected in the tissues of the gills and mantle. Discussion: The bivalve organs had varying quantities of MDA, NO, GSH, and CAT. This could be related to the accumulation pattern of heavy metals in each organ, their close interaction with water, or the removal rates. Conclusion: We concluded from our findings that the toxicity of ZnO-CS NCs on freshwater bivalves causes histological alterations and an oxidative stress response. Moreover, Coelatura aegyptiaca was proposed as a highly sensitive bioindicator to monitor water contamination induced by diverse nanoparticles because it can accumulate and concentrate most pollutants, even at low concentrations. As a result, we recommend conducting additional studies with fresh bivalves to evaluate the aquatic ecosystem well and reduce water contamination at both local and worldwide levels.
Gamma radiation-assisted synthesis of tea tree oil-based chitosan films for active packaging applications
(John Wiley and Sons Ltd, 2025-04-13) Asmaa Sayed; Manar E. Abdel-Raouf; Mikhail Magdy; Ghada A. Mahmoud
Sustainable packaging materials with inherent antimicrobial and antioxidant properties are increasingly demanded for food preservation. In this study, chitosan/polyacrylamide/tea tree oil (CS/PAAm/TTO) films were developed via gamma irradiation, varying both the irradiation dose (10–50 kGy) and the TTO concentration (25–100 μL) to attain an optimized formulation with superior performance. In this regard, the optimization was accomplished via atomic force microscopy (AFM) through assessing the surface morphologies of the films prepared at different irradiation doses, which identified 30 kGy as the optimal irradiation dose for TTO incorporation. On the other hand, comprehensive characterizations using Fourier transfer infrared spectroscopy, x-ray diffraction, thermogravimetric analysis, and contact angle measurements revealed that increasing the irradiation dose and TTO content enhanced hydrophobicity and improved mechanical properties. More specifically, the contact angle increased significantly at higher TTO levels, indicating an increased surface hydrophobicity, while tensile tests demonstrated improved flexibility. In addition, antimicrobial assays confirmed the efficacy of the films against a range of pathogens, and the 1,1-diphenyl-2-picryl hydrazyl assay indicated notable antioxidant activity, with an IC50 value of 111.45 μg/mL for the optimized formulation. These findings underscore the potential of the developed biofilms as advanced, multifunctional packaging materials, offering a promising environmentally friendly alternative to conventional packaging for food preservation.
Synthesis, structural characterization, in vitro biological evaluation and in silico molecular docking of some new 1,2,3-Benzotriazole-based Schiff base derivatives
(Elsevier B.V, 2025-04-09) Shawkat Hayat; Mohamed S. Othman; Hayat Ullah; Amina Qureshi; Fazal Rahim; Sadiqa Begum; Mohsan Nawaz; Abdul Wadood; Amal H. Al-Bagawi; Ahmed M. Aref; Mohamed A. Fareid; Rashid Iqbal
1,2,3-benzotriazole-based Schiff base derivatives were synthesized, characterized through different techniques such as 1 HNMR, 13CNMR, and HREI-MS, and screened against the alpha-glucosidase enzyme. All the synthesized analogues showed good inhibitory potentials with IC50 values ranging from 2.20 ± 0.30 μM to 24.40 ± 0.10 μM as compared to the standard drug acarbose (IC50 = 10.30 ± 0.20 μM). The most potent analogues among the series are 3 (IC50 = 4.30 ± 0.20 μM), 8 (IC50 = 9.40 ± 0.10), 9 (IC50 = 6.20 ± 0.40), 10 (IC50 = 6.60 ± 0.20), 11 (IC50 = 6.10 ± 0.30), 12 (IC50 = 4.70 ± 0.50 μM), 13 (IC50 = 2.20 ± 0.30 μM), 14 (IC50 = 4.30 ± 0.20 μM), and 16 (IC50 = 7.40 ± 0.20), which were found manyfold more active than the standard drug acarbose. A structureactivity relationship study was established that significantly depends on the position, nature, number, and electron-donating/withdrawing effect of the substituent(s) attached to the phenyl ring. We conducted molecular docking studies to investigate the binding interaction of the most potent analogues with the active site of an enzyme.
Modulating Effect of Green Tea and Vitamin C in the Management of “Alzheimer's disease: Oxidative Stress, Cell-Based Anti-Inflammatory and Genotoxic Profiles
(NIDOC (Nat.Inform.Document.Centre), 2025-04-16) Salwa M. El-Hallouty; khaled Mahmoud; Mahmoud Kh. Hanafy; Eman Ayman Abdellatef; Elham M.Youssef
Alzheimer's disease is a progressive brain disorder. Green tea (GT) and vitamin C are known for their antioxidant and anti-inflammatory properties. This study aims to investigate the potential oxidative stress, cell-based anti-inflammatory and genotoxic Profiles for synergistic effect of green tea and vitamin c against to Alzheimer's disease. In vitro assessments included their several antioxidant parameters and ability to inhibit inflammatory markers such as nitric oxide (NO), interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), and matrix metallopeptidase 1(MPP1) in lipopolysaccharide-activated macrophages. In vivo approach evaluated genotoxicity and their potential neurotherapy against Alzheimer's disease using a rat model. Behavioral, biochemical, and histological evaluations were conducted. Green tea methanolic extract (GTME) and vitamin C showed enhanced antioxidant and anti-inflammatory modulator activities. The neurotoxicity rat’s model exhibited cognitive decline and brain injury in contrast to the control group. While treated rats with GTME and vitamin C exhibited improved cognitive function, behavior and reduced AChE levels the combination exerted a significantly more potent effect. Histological analysis confirmed improved brain tissue structure in rats receiving the combined treatment. Crucially, neither compound exhibited genotoxic properties. The combination of GTME and vitamin C demonstrated a promising therapeutic potential for neurodegenerative diseases due to their synergistic effects.
Potent cytotoxicity and induction of ROS‑mediated genomic instability, mitochondrial dysfunction, and apoptosis by Y2O3 NPs in Hep‑G2 hepatic cancer cells
(Springer Science and Business Media Deutschland GmbH, 2025-04-10) Hanan R. H. Mohamed; Rawan Essam; Basma A. Mohamed; George M. Hakeem; Shahd H. Elnawasani; Maria Nagy; Gehan Safwat; Ayman Diab
Hepatic cancer, one of the most prevalent and lethal cancers globally, remains a signifcant health challenge, with limited treatment options underscoring the urgent need for novel, more efective therapies. Yttrium oxide nanoparticles (Y2O3 NPs) have attracted attention in nanomedicine due to their promising properties, including enhanced drug delivery, imaging capabilities, and therapeutic efects. However, the specifc impact of Y2O3 NPs on hepatic cancer is largely unexplored. Therefore, this study was conducted to assess the cytotoxic efects of Y2O3 NPs on cell viability, reactive oxygen species (ROS) generation, genomic stability, mitochondrial integrity, and apoptosis induction in Hep-G2 hepatic cancer cells. The results from the SRB cytotoxicity assay demonstrated a strong concentration-dependent decrease in Hep-G2 cell viability, with a notably low half-maximal inhibitory concentration (IC50) value of 13.15 µg/ml. Exposure to the IC50 concentration of Y2O3 NPs led to increased ROS generation, DNA damage induction, and loss of mitochondrial membrane potential. Furthermore, the expression of pro-apoptotic p53 and mitochondrial ND3 genes was signifcantly upregulated, while the anti-apoptotic Bcl-2 gene was markedly downregulated, triggering apoptosis in Hep-G2 cells after 72 h of exposure to Y2O3 NPs. Collectively, these fndings highlight the therapeutic potential of Y2O3 NPs in hepatic cancer, emphasizing the need for further research to fully explore their efcacy as a treatment option for liver cancer
Towards propagation of epidermal cells for wound repair: glass, as cell culture substrate, enhances proliferation and migration of human keratinocytes
(Frontiers Media SA, 2025-03-20) Hady Shahin; Ingrid Steinvall; Folke Sjöberg; Moustafa Elmasry; Ahmed El-Serafi
Introduction: Human keratinocytes require relatively long propagation time which impedes their availability as autologous cell transplantation within a clinically reasonable timeframe. There is an unmet need for efficient xenofree cell expansion approaches to propagate human keratinocytes as regenerative therapy. Methods: Primary human keratinocytes and HaCaT cells were cultured on glass, plastic, and animal-derived collagen I matrix for 10 days. Proliferation, migration, DNA methylation, as well as gene and protein expression were assessed to characterize the effect of the tested culture substrates on keratinocytes at the molecular and functional levels. Results: Keratinocytes cultured on glass exhibited faster proliferation, global DNA demethylation and upregulation of epidermal differentiation markers. Scratch wound assay revealed that keratinocytes cultured on glass demonstrated enhanced cell migration compared to those on plastic or collagen I. Multiplex immunoassays identified temporal and substrate-dependent variations in a panel of keratinocyte-specific secreted factors, encompassing immunomodulatory cytokines, growth factors, and angiogenic factors. Discussion: Glass, as a culture substrate, promotes epidermal differentiation and enhances keratinocyte migration. The latter is a critical factor in reepithelialization and wound healing. Functional properties suggest that glass may optimize the inflammatory response and promote efficient wound repair, making it a promising candidate for the short-term expansion of keratinocytes for transplantation purposes. Further in-vivo validation is required to definitively establish the efficacy of keratinocytes cultured on glass for clinical applications.

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