Search results for: candidate genes

Authors: Vun Yee Thien, Kenneth Francis Rodrigues, Clemente Michael Vui Ling Wong, Wilson Thau Lym Yong

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Transcriptomes associated with the process of photosynthesis have offered insights into the mechanism of gene regulation in terrestrial plants; however, limited information is available as far as macroalgae are concerned. This investigation aims to decipher the underlying mechanisms associated with photosynthesis in the red alga, Kappaphycus alvarezii, by performing a differential expression analysis on a de novo assembled transcriptomes. Comparative analysis of gene expression was designed to examine the alteration of light qualities and its effect on physiological mechanisms in the red alga. High-throughput paired-end RNA-sequencing was applied to profile the transcriptome of K. alvarezii irradiated with different wavelengths of light (blue 492-455 nm, green 577-492 nm and red 780-622 nm) as compared to the full light spectrum, resulted in more than 60 million reads individually and assembled using Trinity and SOAPdenovo-Trans. The transcripts were annotated in the NCBI non-redundant (nr) protein, SwissProt, KEGG and COG databases with a cutoff E-value of 1e-5 and nearly 30% of transcripts were assigned to functional annotation by Blast searches. Differential expression analysis was performed using edgeR. The DEGs were designated to six categories: BL (blue light) regulated, GL (green light) regulated, RL (red light) regulated, BL or GL regulated, BL or RL regulated, GL or RL regulated, and either BL, GL or RL regulated. These DEGs were mapped to terms in KEGG database and compared with the whole transcriptome background to search for genes that regulated by light quality. The outcomes of this study will enhance our understanding of molecular mechanisms underlying light-induced responses in red algae.

Keywords: de novo transcriptome sequencing, differential gene expression, Kappaphycus alvareziired, red alga

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Authors: Nicholas Bayfield, Mark Newman

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Case Presentation: A 48-year-old male was brought in by ambulance after an out-of-hospital cardiac arrest, with 20 minutes of good-quality cardiopulmonary resuscitation in the community. Return of spontaneous circulation was achieved with defibrillation, revealing an inferior ST-elevation myocardial infarction. He was revascularized emergently in the cath lab and stabilised. Following the procedure, he was noted to have paradoxical respiratory movements of the sternum and high oxygen requirements. CT imaging demonstrated a flail chest with bilateral anterior rib 1-7 fractures as well as a large left-sided extra-pleural haematoma and small haemopneumothorax, secondary to CPR. The patient’s ventilation was stabilised with oxygen via a high-flow humidifier. Pain relief was provided. The anatomy of his rib fractures was not easily amenable to operative fixation. In addition, he was considered to be a high-risk operative candidate due to his recent arrest. He was managed thus non-operatively with an external vacuum dressing applied to the anterior chest wall to minimise respiratory compromise and minimise pain from the motion around the rib fracture sites. Non-operative management was successful, and the patient was reviewed one month later. The paradoxical sternal movement had abated. Discussion: External vacuum dressing has been trialled for non-operative management of rib fractures with varying success. It provides an external brace to minimise fracture site movement during respiration and coughing, thus minimising pain. This modality should be considered a low-cost, high-reward adjunct to non-operative management of bony thoracic trauma.

Keywords: thoracic surgery, thoracic trauma, rib fractures, negative pressure dressing

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Authors: Debjani Ghosh, Goutam Chowdhury, Prosenjit Samanta, Asish Kumar Mukhopadhyay

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Acute diarrhoea caused by diarrheagenic Escherichia coli (DEC) is one of the major public health problem in developing countries, mainly in Asia and Africa. DEC consists of six pathogroups, but the majority of the cases were associated with the three pathogropus, enterotoxigenic E. coli (ETEC), enteroaggregative E. coli (EAEC), and enteropathogenic E. coli (EPEC). Hence, we studied the prevalence and antimicrobial resistance of these three major DEC pathogroups in hospitalized diarrheal patients in Kolkata, India, during 2012-2019 with a large sample size. 8,891 stool samples were processed, and 7.8% of them was identified as DEC infection screened by multiplex PCR, in which ETEC was most common (47.7%) followed by EAEC (38.4%) and EPEC (13.9%). Clinical patient history suggested that children <5 years of age were mostly affected with ETEC and EAEC, whereas people within >5-14 years of age were significantly associated with EPEC and ETEC infections. Antibiogram profile showed a high prevalence of multidrug resistant (MDR) isolates among DEC (56.9%), in which 9% were resistant to antibiotics of six different antimicrobial classes. Screening of the antibiotic resistance conferring genes in DEC showed the presence of blaCTX-M (30.2%) in highest number followed by blaTEM (27.5%), tetB (18%), sul2 (12.6%), strA (11.8%), aadA1 (9.8%), blaOXA-1 (9%), dfrA1 (1.6%) and blaSHV (1.2%) which indicates the existence of mobile genetic elements in those isolates. Therefore, the presence of MDR DEC strains in higher number alarms the public health authorities to take preventive measures before the upsurge of the DEC caused diarrhea cases in near future.

Keywords: diarrheagenic escherichia coli, ETEC, EAEC, EPEC

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Authors: Salina Saddick, Mohamed Afifi, Osama Abuznadah

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This study was carried out to determine the median lethal concentrations (LC50) of Zinc nanoparticles (ZnNPs) on Oreochromis niloticus and Tilapia zillii. The biochemical and molecular potential effects of ZnNPs (500 and 2000 μg L−1) on the antioxidant system in the brain tissue of O. niloticus and T. zillii were investigated. Four hundred fish were used for acute and sub-acute studies. ZnNP LC50 concentrations were investigated in O. niloticus and T. zillii. The effect of 500 and 2000 μg L−1 ZnNPs on brain antioxidants of O. niloticus and T. zillii was investigated. The result indicated that 69 h LC50 was 5.5 ± 0.6 and 5.6 ± 0.4 for O. nilotica and T. zillii, respectively. Fish exposed to 500 μg L−1 ZnNPs showed a significant increase in reduced glutathione (GSH), total glutathione (tGSH) levels, superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), glutathione peroxidase (GPx) and glutathione-S-transferase (GST) activity and gene expression. On the contrary, malondialdehyde (MDA) levels significantly decreased. Meanwhile, fish exposed to 2000 μg L−1 ZnNPs showed a significant decrease of GSH, tGSH levels, SOD, CAT, GR, GPx and GST activity and gene expression. On the contrary, MDA levels significantly increased. It was concluded that, the 96 h LC50 of ZnNPs was 5.5 ± 0.6 and 5.6 ± 0.4 for O. nilotica and T. zillii, respectively. ZnNPs in exposure concentrations of 2000 μg/L induced a deleterious effect on the brain antioxidant system of O. nilotica and T. zillii. In contrast, ZnNPs in exposure concentrations of 500 μg L−1 produced an inductive effect on the brain antioxidant system of O. nilotica and T. zillii.

Keywords: ZnNPs, LC50, antioxidants, O. nilotica

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Authors: Ricardo Chaves, Carlos Vasconcelos

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Candidates to join the Naval Academy have to take a set of physical tests, which is crucial for a high level of physical fitness. Thus, the planning of physical exercises for candidates to the Naval School must take into account the improvement of their physical fitness. The aim of this study was to investigate the impact of a 6-month exercise program to improve the physical fitness of an individual who will apply for the Naval Academy. This was a non-experimental pre-post-evaluation study. The patient was male, had 18 years old, and a body mass index of 21.1 kg.m². The patient participated in a 6-month aerobic and strength exercise program (3 sessions per week, 75 minutes duration each session). Physical fitness tests were performed according to the physical fitness requirements for entry into the Naval academy (muscle strength [maximum number of lifts and maximum number of sit-ups for 1 minute]; aerobic fitness [2.4 km run and 200 m swimming test]) before (baseline) and after the exercise intervention (6 months). Regarding muscle strength, in the abdominal test, the improvements between the pre-test (39 abdominals.) and post-test (61 abdominals) were 56.4%. For elevations, there was an increase in its number by 150% between the pre-test (4 elevations) and post-test (10 elevations). With regard to aerobic fitness, in the 2.4 km race, there was an evolution of 32.0% between the pre-test (16.46 min.) and the post-test (12.42 min.). For the 200-meter swimming test, there was a negative variation of 2% between the pre-test (2.25 min.) and post-test (2.28 min). A 6-month aerobic and strength exercise program leads to a positive evolution in the muscular strength of the patient. Regarding aerobic fitness, opposite results were found, with a positive evolution in the 2.4 km running test and a negative evolution in the swimming test. In future exercise programs for the improvement of the physical fitness of candidates for the Naval Academy, more emphasis has to be done on specific swimming training.

Keywords: case study, exercise program, Naval Academy, physical fitness

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Authors: Tannaz Alimardani, Amirhossein Moghanian, Morteza Elsa

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Bioactive glasses (BGs) are a group of surface-reactive biomaterials used in clinical applications as implants or filler materials in the human body to repair and replace diseased or damaged bone. Sol-gel technique was employed to prepare a SiO₂-CaO-P₂O₅ glass with a nominal composition of 58S BG with the addition of Sr and Li modifiers which imparts special properties to the BG. The effect of simultaneous addition of Sr and Li on bioactivity and biocompatibility, proliferation, alkaline phosphatase (ALP) activity of osteoblast cell line MC3T3-E1 and antibacterial property against methicillin-resistant Staphylococcus aureus (MRSA) bacteria were examined. BGs were characterized by X-ray diffraction, Fourier transform infrared spectroscopy and scanning electron microscopy before and after soaking the samples in the simulated body fluid (SBF) for different time intervals to characterize the formation of hydroxyapatite (HA) formed on the surface of BGs. Structural characterization indicated that the simultaneous presence of 5% Sr and 5% Li in 58S-BG composition not only did not retard HA formation because of the opposite effect of Sr and Li of the dissolution of BG in the SBF, but also stimulated the differentiation and proliferation of MC3T3-E1s. Moreover, the presence of Sr and Li on the dissolution of the ions resulted in an increase in the mean number of DAPI-labeled nuclei which was in good agreement with the live/dead assay. The result of antibacterial tests revealed that Sr and Li-substituted 58S bioactive glass exhibited a potential antibacterial effect against MRSA bacteria. Because of optimal proliferation and ALP activity of MC3T3-E1cells, proper bioactivity and high antibacterial potential against MRSA, BG-5/5 is suggested as a multifunctional candidate for bone tissue engineering.

Keywords: alkaline, alkaline earth, bioglass, co-doping, ion release

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Authors: M. Ntswane, N. Mbuma, M. Labuschagne, A. Mofokeng, M. Rantso

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Cowpea is an essential legume for the nutrition and health of millions of people in different regions. The production and productivity of the crop are very limited in South Africa due to a lack of adapted and stable genotypes. The improvement of nutritional quality is made possible by manipulating the genes of diverse cowpea genotypes available around the world. Assessing the adaptability and stability of the cowpea mutant genotypes for yield and nutritional quality requires examining them in different environments. The objective of the study was to determine the adaptability and stability of cowpea mutant genotypes under South African conditions and to identify the superior genotypes that combine grain yield components, antioxidants, and nutritional quality. Thirty-one cowpea genotypes were obtained from the Agricultural Research Council grain crops (ARC-GC) and were planted in Glen, Mafikeng, Polokwane, Potchefstroom, Taung, and Vaalharts during the 2021/22 summer cropping season. Significant genotype by location interactions indicated the possibility of genetic improvement of these traits. The genotype plus genotype by environment indicated broad adaptability and stability of mutant genotypes. The principal component analysis identified the association of the genotypes with the traits. Phenotypic correlation analysis showed that Zn and protein content were significant and positively correlated and suggested the possibility of indirect selection of these traits. Results from this study could be used to help plant breeders in making informed decisions and developing nutritionally improved cowpea genotypes with the aim of addressing the challenges of poor nutritional quality.

Keywords: cowpea seeds, adaptability, stability, mineral elements, protein content

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Authors: Micheale Yifter Weldemichael

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Sesame (Sesamum indicum L.) is among the most important oilseed crops for its high edible oil quality and quantity. Sesame is grown for food, medicinal, pharmaceutical, and industrial uses. Sesame is also cultivated as a main cash crop in Asia and Africa by smallholder farmers. Despite the global exponential increase in sesame cultivation area, its production and productivity remain low, mainly due to biotic and abiotic constraints. Notwithstanding the efforts to solve these problems, a low level of genetic variation and inadequate genomic resources hinder the progress of sesame improvement. The objective of this paper is, therefore, to review recent advances in the area of molecular breeding and transformation to overcome major production constraints and could result in enhanced and sustained sesame production. This paper reviews various researches conducted to date on molecular breeding and genetic transformation in sesame focusing on molecular markers used in assessing the available online database resources, genes responsible for key agronomic traits as well as transgenic technology and genome editing. The review concentrates on quantitative and semi-quantitative studies on molecular breeding for key agronomic traits such as improvement of yield components, oil and oil-related traits, disease and insect/pest resistance, and drought, waterlogging and salt tolerance, as well as sesame genetic transformation and genome editing techniques. Pitfalls and limitations of existing studies and methodologies used so far are identified and some priorities for future research directions in sesame genetic improvement are identified in this review.

Keywords: abiotic stress, biotic stress, improvement, molecular breeding, oil, sesame, shattering

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Authors: D. W. Mohammed, J. Bowen, S. N. Kukureka

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Successful design and fabrication of flexible devices for electrode components requires a low sheet resistance, high optical transmittance, high mechanical reliability. Indium tin oxide (ITO) film is currently the predominant transparent conductive oxide (TCO) film in potential applications such as flexible organic light- emitting diodes, flat-panel displays, solar cells, and thin film transistors (TFTs). However ITO films are too brittle and their resistivity is rather high in some cases compared with ITO/Ag/ ITO, and they cannot completely meet flexible optoelectronic device requirements. Therefore, in this work the mechanical properties of ITO /Ag/ITO multilayer film that deposited on Polyethylene terephthalate (PET) compared with the single layered ITO sample were investigated using bending fatigue, twisting fatigue and thermal cycling experiments. The electrical resistance was monitored during the application of mechanical and thermal loads to see the pattern of relationship between the load and the electrical continuity as a consequent of failure. Scanning electron microscopy and atomic force microscopy were used to provide surface characterization of the mechanically-tested samples. The effective embedment of the Ag layer between upper and lower ITO films led to metallic conductivity and superior flexibility to the single ITO electrode, due to the high failure strain of the ductile Ag layer. These results indicate that flexible ITO/Ag/ITO multilayer electrodes are a promising candidate for use as transparent conductor in flexible displays. They provided significantly reduced sheet resistance compared to ITO, and improved bending and twisting properties both as a function of radius, angle and thermal cycling.

Keywords: ITO/Ag/ITO multilayer, failure strain, mechanical properties, PET

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Authors: Vinh Duy Cao, Shima Pilehvar, Anna M. Szczotok, Anna-Lena Kjøniksen

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The total energy consumption is dramatically increasing on over the world, especially for building energy consumption where a significant proportion of energy is used for heating and cooling purposes. One of the solutions to reduce the energy consumption for the building is to improve construction techniques and enhance material technology. Recently, microcapsulated phase change materials (MPCM) with high energy storage capacity within the phase transition temperature of the materials is a potential method to conserve and save energy. A new composite materials with high energy storage capacity by mixing MPCM into concrete for passive building technology is the promising candidate to reduce the energy consumption. One of the most untilized building materials for mixing with MPCM is Portland cement concrete. However, the emission of carbon dioxide (CO2) due to producing cement which plays the important role in the global warming is the main drawback of PCC. Accordingly, an environmentally friendly building material, geopolymer, which is synthesized by the reaction between the industrial waste material (aluminosilicate) and a strong alkali activator, is a potential materials to mixing with MPCM. Especially, the effect of MPCM on the thermal and mechanical properties of geopolymer concrete (GPC) is very limited. In this study, high thermal energy storage capacity materials were fabricated by mixing MPCM into geopolymer concrete. This article would investigate the effect of MPCM concentration on thermal and mechanical properties of GPC. The target is to balance the effect of MPCM on improving the thermal performance and maintaining the compressive strength of the geopolymer concrete at an acceptable level for building application.

Keywords: microencapsulated phase change materials, geopolymer concrete, energy storage capacity, thermal performance

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Authors: Shady S. Hassan, Brijesh K. Tiwari, Gwilym A. Williams, Amit K. Jaiswal

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EU is known as the destination with the highest rate of the coffee consumption per capita in the world. Spent coffee grounds (SCG) are the main by-product of coffee brewing. SCG is either disposed as a solid waste or employed as compost, although the polysaccharides from such lignocellulosic biomass might be used as feedstock for fermentation processes. However, SCG as a lignocellulose have a complex structure and pretreatment process is required to facilitate an efficient enzymatic hydrolysis of carbohydrates. However, commonly used pretreatment methods, such as chemical, physico-chemical and biological techniques are still insufficient to meet optimal industrial production requirements in a sustainable way. Ultrasound is a promising candidate as a sustainable green pretreatment solution for lignocellulosic biomass utilization in a large scale biorefinery. Thus, ultrasound pretreatment of SCG without adding harsh chemicals investigated as a green technology to enhance enzyme hydrolysis. In the present work, ultrasound pretreatment experiments were conducted on SCG using different ultrasound frequencies (25, 35, 45, 130, and 950 kHz) for 60 min. Regardless of ultrasound power, low ultrasound frequency is more effective than high ultrasound frequency in pretreatment of biomass. Ultrasound pretreatment of SCG (at ultrasound frequency of 25 kHz for 60 min) followed by enzymatic hydrolysis resulted in total reducing sugars of 56.1 ± 2.8 mg/g of biomass. Fourier transform Infrared Spectroscopy (FTIR) was employed to investigate changes in functional groups of biomass after pretreatment, while high-performance liquid chromatography (HPLC) was employed for determination of glucose. Pretreatment of lignocellulose by low frequency ultrasound in water only was found to be an effective green approach for SCG to improve saccharification and glucose yield compared to native biomass. Pretreatment conditions will be optimized, and the enzyme hydrolysate will be used as media component substitute for the production of ethanol.

Keywords: lignocellulose, ultrasound, pretreatment, spent coffee grounds

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Authors: Samira B. R. Prado, Paulo R. Melfi, Beatriz T. Minguzzi, João P. Fabi

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Fruit softening is the main change that occurs during papaya (Carica papaya L.) ripening. It is characterized by the depolymerization of cell wall polysaccharides, especially the pectic fractions, which causes cell wall disassembling. However, it is uncertain how the modification of the two main pectin polysaccharides fractions (water-soluble – WSF, and oxalate-soluble fractions - OSF) accounts for fruit softening. The aim of this work was to correlate molecular weight changes of WSF and OSF with the gene expression of pectin-solubilizing enzymes (pectinases) during papaya ripening. Papaya fruits obtained from a producer were harvest and storage under specific conditions. The fruits were divided in five groups according to days after harvesting. Cell walls from all groups of papaya pulp were isolated and fractionated (WSF and OSF). Expression profiles of pectinase genes were achieved according to the MIQE guidelines (Minimum Information for publication of Quantitative real-time PCR Experiments). The results showed an increased yield and a decreased molecular weight throughout ripening for WSF and OSF. Gene expression data support that papaya softening is achieved by polygalacturonases (PGs) up-regulation, in which their actions might have been facilitated by the constant action of pectinesterases (PMEs). Moreover, BGAL1 gene was up-regulated during ripening with a simultaneous galactose release, suggesting that galactosidases (GALs) could also account for pulp softening. The data suggest that a solubilization of galacturonans and a depolymerization of cell wall components were caused mainly by the action of PGs and GALs.

Keywords: carica papaya, fruit ripening, galactosidases, plant cell wall, polygalacturonases

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Authors: Abdullah A. Al Qurashi, Hattan A. Hassani, Bader K. Alaslap

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Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy (ARVD/C) is an uncommon, inheritable cardiac disorder characterized by the progressive substitution of cardiac myocytes by fibro-fatty tissues. This pathologic substitution predisposes patients to ventricular arrhythmias and right ventricular failure. The underlying genetic defect predominantly involves genes encoding for desmosome proteins, particularly plakophilin-2 (PKP2). These aberrations lead to impaired cell adhesion, heightening the susceptibility to fibrofatty scarring under conditions of mechanical stress. Primarily, ARVD/C affects the right ventricle, but it can also compromise the left ventricle, potentially leading to biventricular heart failure. Clinical presentations can vary, spanning from asymptomatic individuals to those experiencing palpitations, syncopal episodes, and, in severe instances, sudden cardiac death. The establishment of a diagnostic criterion specifically tailored for ARVD/C significantly aids in its accurate diagnosis. Nevertheless, the task of early diagnosis is complicated by the disease's frequently asymptomatic initial stages, and the overall rarity of ARVD/C cases reported globally. In some cases, as exemplified by the adult female patient in this report, the disease may advance to terminal stages, rendering therapies like Ventricular Tachycardia (VT) ablation ineffective. This case underlines the necessity for increased awareness and understanding of ARVD/C to aid in its early detection and management. Through such efforts, we aim to decrease morbidity and mortality associated with this challenging cardiac disorder.

Keywords: arrhythmogenic right ventricular dysplasia, cardiac disease, interventional cardiology, cardiac electrophysiology

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Authors: Morteza Elsa, Amirhossein Moghanian

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The major aim of this study was to evaluate the effect of CaO content on in vitro hydroxyapatite formation, MC3T3 cells cytotoxicity and proliferation as well as antibacterial efficiency of sol-gel derived SiO₂–CaO–P₂O₅ ternary system. For this purpose, first two grades of bioactive glass (BG); BG-58s (mol%: 60%SiO₂–36%CaO–4%P₂O₅) and BG-68s (mol%: 70%SiO₂–26%CaO–4%P₂O₅)) were synthesized by sol-gel method. Second, the effect of CaO content in their composition on in vitro bioactivity was investigated by soaking the BG-58s and BG-68s powders in simulated body fluid (SBF) for time periods up to 14 days and followed by characterization inductively coupled plasma atomic emission spectrometry (ICP-AES), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), and scanning electron microscopy (SEM) techniques. Additionally, live/dead staining, 3-(4,5dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), and alkaline phosphatase (ALP) activity assays were conducted respectively, as qualitatively and quantitatively assess for cell viability, proliferation and differentiations of MC3T3 cells in presence of 58s and 68s BGs. Results showed that BG-58s with higher CaO content showed higher in vitro bioactivity with respect to BG-68s. Moreover, the dissolution rate was inversely proportional to oxygen density of the BG. Live/dead assay revealed that both 58s and 68s increased the mean number live cells which were in good accordance with MTT assay. Furthermore, BG-58s showed more potential antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) bacteria. Taken together, BG-58s with enhanced MC3T3 cells proliferation and ALP activity, acceptable bioactivity and significant high antibacterial effect against MRSA bacteria is suggested as a suitable candidate in order to further functionalizing for delivery of therapeutic ions and growth factors in bone tissue engineering.

Keywords: antibacterial, bioactive glass, hydroxyapatite, proliferation, sol-gel processes

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Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

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Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max, and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, brassinosteroids, phylogenetic analysis, transcription factor

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Authors: Violina Angelova, Mariana Perifanova-Nemska, Krasimir Ivanov

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The aim of this research was to investigate the potential for the use of Ricinus communis L. (castor oil plant) to remediate metal-polluted sites. This study was performed in industrially polluted soils containing high concentrations of Zn, Pb and Cd, situated at different distances (0.3, 2.0 and 15.0 km) from the source of pollution - the Non-Ferrous Metal Works near Plovdiv, Bulgaria. On reaching commercial ripeness, the castor oil plants were gathered and the contents of heavy metals in their different parts – roots, stems, leaves and seeds, were determined after dry ashing. Physico-chemical characterization, total, DTPA extractable and water-soluble metals in rhizospheric soil samples were carried. Translocation factors (TFs) were also determined. The quantitative measurements were carried out with ICP. A soxhlet extraction was used for the extraction of the oil, using hexane as solvent. The oil was recovered by simple distillation of the solvent. The residual oil obtained was investigated for physicochemical parameters and fatty acid composition. Bioaccumulation factor and translocation factor values (BAF and TF > 1) were greater than one suggesting efficient accumulation in the shoot. The castor oil plant may be preferred as a good candidate for phytoremediation (phytoextraction). These results indicate that R. communis has good potential for removing Pb from contaminated soils attributed to its fast growth, high biomass, strong absorption and accumulation for Pb. The concentrations of heavy metals in the oil were low as seed coats accumulated the highest concentrations of Cd and Pb. In addition, the result of the fatty acid composition analysis confirms the oil to be of good quality and can be used for industrial purposes such as cosmetics, soaps and paint.

Keywords: castor bean, heavy metals, phytoremediation, polluted soils

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Authors: Negar Zaheddoust, Negin Zaheddoust, Abbas Asoudeh-Fard

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Probiotic bacteria have been employed as a novel and less side-effect strategy for anticancer therapy. Since the oral cavity is a host for probiotic and pathogen bacteria to colonize, more investigation is needed to evaluate the effectiveness of this novel adjunctive treatment for oral cancer. We considered Lactobacillus plantarum as a probiotic and Streptococcus mutans as a pathogen bacterium in our study. The aim of this study is to examine the effect of Lactobacillus plantarum and Streptococcus mutans on Casp3, AKT / PTEN, and MAPK signaling pathway, which is involved in apoptosis or survival of oral cancer KB cells. On the other hand, to study the effects of these bacteria on normal cells, we used HUVEC cells. The KB and HUVEC cell lines were co-cultured with Lactobacillus plantarum and Streptococcus mutans isolated from traditional Iranian dairy and dental plaque, respectively. The growth-inhibitory effects of these two bacteria on KB and HUVEC cells were determined by (3-(4, 5-dimethylthiazolyl-2)-2,5diphenyltetrazolium bromide) MTT assay. MTT results demonstrated that the proliferation of KB cells was affected in a time, dose, and strain-dependent manner. In the following, the examination of induced apoptosis or necrosis in co-cultured KB cells with the best IC50 concentration of the Lactobacillus plantarum and Streptococcus mutans will be analyzed by FACS flow cytometry, and the changes in gene expression of Casp3, AKT / PTEN, MAPK genes will be evaluated using real-time polymerase chain reaction.

Keywords: cancer therapy, induced apoptosis, oral cancer, probiotics

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Authors: Samira Khalaji, , Fenneke Klein Jan, Kay-E. Gottschalk, Eugenia Makrantonaki, Karin Scharffetter-Kochanek

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Biological aging is a multi-dimensional process that takes place over a whole range of scales from the nanoscopic alterations within individual cells, over transformations in tissues and organs and to changes of the whole organism. On the single cell level, aging involves mutation of genes, differences in gene expression levels as well as altered posttranslational modifications of proteins. A variety of proteins is affected, including proteins of the cell cytoskeleton and migration machinery. Previous work quantified the expression of cytoskeleton proteins on the gene and protein levels in senescent and young fibroblasts. Their results show that senescent skin fibroblasts have an upregulated expression of the intermediate filament (IF) protein vimentin in contrast to actin and tubulin, which are downregulated. IFs play an important role in providing mechanical stability of cells. However, the mechanical properties of IFs depending on cellular senescence or age of the donor has not been studied so far. Hence, we employed passive microrheology on primary human dermal fibroblasts from female donors with age of 28 years (young) and 86 years (old) as model of in vivo aging and human normal dermal fibroblast from 11-year old male with CPD 17-35 (young) and CPD 58-59 (senescence) as a model of in vitro replicative senescence. In contrast to the expectations, our primary results show no significant differences in the viscoelastic properties of fibroblasts depending on age of the donor or cellular replicative senescence.

Keywords: aging, cytoskeleton, fibroblast, mechanical properties

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Authors: A. Reum Son, Jin Seon Kwon, Seung Hun Park, Hai Bang Lee, Moon Suk Kim

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These days, stem cell therapy is focused on for promising source of treatment in clinical human disease. As a supporter of stem cells, in situ-forming hydrogels with growth factors and cells appear to be a promising approach in tissue engineering. To examine osteogenic differentiation of hTMSCs which is one of mesenchymal stem cells in vivo in an injectable hydrogel, we use a methoxy polyethylene glycol-polycaprolactone blockcopolymer (MPEG-PCL) solution with osteogenic factors. We synthesized MPEG-PCL hydrogel and measured viscosity to check sol-gel transition. In order to demonstrate osteogenic ability of hTMSCs, we conducted in vitro osteogenesis experiment. Then, to confirm the cell cytotoxicity, we performed WST-1 with hTMSCs and MPEG-PCL. As the result of in vitro experiment, we implanted cell and hydrogel mixture into animal model and checked degree of osteogenesis with histological analysis and amount of expression genes. Through these experimental data, MPEG-PCL hydrogel has sol-gel transition in temperature change and is biocompatible with stem cells. In histological analysis and gene expression, hTMSCs are very good source of osteogenesis with hydrogel and will use it to tissue engineering as important treatment method. hTMSCs could be a good adult stem cell source for usability of isolation and high proliferation. When hTMSCs are used as cell therapy method with in situ-formed hydrogel, they may provide various benefits like a noninvasive alternative for bone tissue engineering applications.

Keywords: injectable hydrogel, stem cell, osteogenic differentiation, tissue engineering

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Authors: Naoki Yamamoto, Hidenobu Ozaki, Taiichiro Ookawa, Youming Liu, Kazunori Okada, Aiping Zheng

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Rice sheath blight is one of the destructive fungal diseases in rice. We have thought that rice sheath blight resistance is a polygenic trait. Host-pathogen interactions and secondary metabolites such as lignin and phytoalexins are likely to be involved in defense against R. solani. However, to our knowledge, it is still unknown how sheath blight resistance can be enhanced in rice breeding. To seek for an alternative genetic factor that contribute to sheath blight resistance, we mined relevant allelic variations from rice core collections created in Japan. Based on disease lesion length on detached leaf sheath, we selected 30 varieties of the top tail-end and the bottom tail-end, respectively, from the core collections to perform genome-wide association mapping. Re-sequencing reads for these varieties were used for calling single nucleotide polymorphisms among the 60 varieties to create a SNP panel, which contained 1,137,131 homozygous variant sites after filitering. Association mapping highlighted a locus on the long arm of chromosome 11, which is co-localized with three sheath blight QTLs, qShB11-2-TX, qShB11, and qSBR-11-2. Based on the localization of the trait-associated alleles, we identified an ankyryn repeat-containing protein gene (ANK-M) as an uncharacterized candidate factor for rice sheath blight resistance. Allelic distributions for ANK-M in the whole rice population supported the reliability of trait-allele associations. Gene expression characteristics were checked to evaluiate the functionality of ANK-M. Since an ANK-M homolog (OsPIANK1) in rice seems a basal defense regulator against rice blast and bacterial leaf blight, ANK-M may also play a role in the rice immune system.

Keywords: allele mining, GWAS, QTL, rice sheath blight

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Authors: Muhammad Shahzad Iqbal, Zobia Sarwar, Salah-ud-Din

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Tomato spotted wilt virus (TSWV) belongs to the genus Tospoviruses (family Bunyaviridae). It is one of the most devastating pathogens of tomato (Solanum Lycopersicum) and heavily damages the crop yield each year around the globe. In this study, we retrieved 329 mature miRNA sequences from two microRNA databases (miRBase and miRSoldb) and checked the putative target sites in the downloaded-genome sequence of TSWV. A consensus of three miRNA target prediction tools (RNA22, miRanda and psRNATarget) was used to screen the false-positive microRNAs targeting sites in the TSWV genome. These tools calculated different target sites by calculating minimum free energy (mfe), site-complementarity, minimum folding energy and other microRNA-mRNA binding factors. R language was used to plot the predicted target-site data. All the genes having possible target sites for different miRNAs were screened by building a consensus table. Out of these 329 mature miRNAs predicted by three algorithms, only eight miRNAs met all the criteria/threshold specifications. MC-Fold and MC-Sym were used to predict three-dimensional structures of miRNAs and further analyzed in USCF chimera to visualize the structural and conformational changes before and after microRNA-mRNA interactions. The results of the current study show that the predicted eight miRNAs could further be evaluated by in vitro experiments to develop TSWV-resistant transgenic tomato plants in the future.

Keywords: tomato spotted wild virus (TSWV), Solanum lycopersicum, plant virus, miRNAs, microRNA target prediction, mRNA

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Authors: Arefeh Jafarian, Mohammad Taghikani, Saied Abroun, Amir Allahverdi, Masoud Soleimani

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Introduction: The miRNAs have key roles in control of pancreatic islet development and insulin secretion. In this regards, current study investigated the pancreatic differentiation of human bone marrow mesenchymal stem cells (hBM-MSCs) by up-regulation of miR-375 and down-regulation of miR-9 by lentiviruses containing miR-375 and anti-miR-9. Findings: After 21 days of induction, islet-like clusters containing insulin producing cells (IPCs) were confirmed by dithizone (DTZ) staining. The IPCs and β cell specific related genes and proteins were detected using qRT-PCR and immunofluorescence on days 7, 14 and 21 of differentiation. Glucose challenge test was performed at different concentrations of glucose as well as extracellular and intracellular insulin and C-peptide were assayed using ELISA kit. In derived IPCs by miR-375 alone are capable to express insulin and other endocrine specific transcription factors, the cells lack the machinery to respond to glucose. The differentiated hMSCs by miR-375 and anti-miR-9 lentiviruses could secrete insulin and c-peptide in a glucose-regulated manner. Conclusion: It was found that over-expression of miR-375 led to a reduction in levels of Mtpn protein in derived IPCs, while treatment with anti-miR-9 following miR-375 over-expression had synergistic effects on MSCs differentiation and insulin secretion in a glucose-regulated manner. The researchers reported that silencing of miR-9 increased OC-2 protein in IPCs that may contribute to the observed glucose-regulated insulin secretion. These findings highlight miRNAs functions in stem cells differentiation and suggest that they could be used as therapeutic tools for gene-based therapy in diabetes mellitus.

Keywords: diabetes, differentiation, MSCs, insulin producing cells, miR-375, miR-9

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Authors: Sajjad Jafari

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Background and Aim: The use of herbal medicines has a long history. Today, due to the resistance of microorganisms to antibiotics and antimicrobial substances, herbal medicines have attracted attention due to their significant antimicrobial effects and low toxicity. This study aims to systematically review the antimicrobial effects of different plant extracts (Quercus infectoria) as possible candidates for treating infectious diseases. Material and Methods: The present study is a review study by searching reputable scientific databases such as PubMed, Google Scholar, Scopus, and Web of Science from 2000 to 2023 using the keywords Antimicrobial, Quercus infectoria, Medicinal herbal, Infectious diseases the latest information obtained. Results: In this study, 45 articles were found and reviewed. Quercus infectoria is a small tree native to Greece, Asia Minor, and Iran. Quercus is a plant genus in the family of Fagaceae. This species is generally known under the name ‘‘baloot” in Iran and is commonly used as a medicinal plant. The extracts used included water, hydro-alcoholic, ethanol, methanol. This plant had high inhibition activity and a lethal effect on gram-positive and gram-negative bacteria of ATCC strains, hospital, and resistant strains. Therefore, in addition to antibacterial effects, antiparasitic and antifungal effects. The seed of the plant was the most used and the most effective antimicrobial extract among the ethanol and methanol extracts. Conclusion: The findings of this study suggest that Quercus infectoria has significant antimicrobial effects against a wide range of microorganisms. This makes it a potential candidate for the development of new antimicrobial drugs. Further research is needed to confirm the efficacy and safety of Quercus infectoria in clinical trials.

Keywords: antimicrobial, Quercus infectoria, medicinal herbal, infectious diseases

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Authors: Faraz Zarghami, Elham Anari, Nosratollah Zarghami, Yones Pilehvar-Soltanahmadi, Abolfazl Akbarzadeh, Sepideh Jalilzadeh-Tabrizi

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The development of nanotherapy has presented a new method of drug delivery targeted directly to the neoplasmic tissues, to maximize the action with fewer dose requirements. In the past two decades, poly(lactic-co-glycolic acid) (PLGA) has frequently been investigated by many researchers and is a popular polymeric candidate, due to its biocompatibility and biodegradability, exhibition of a wide range of erosion times, tunable mechanical properties, and most notably, because it is a FDA-approved polymer. Chrysin is a natural flavonoid which has been reported to have some significant biological effects on the processes of chemical defense, nitrogen fixation, inflammation, and oxidation. However, the low solubility in water decreases its bioavailability and consequently disrupts the biomedical benefits. Being loaded with PLGA-PEG increases chrysin solubility and drug tolerance, and decreases the discordant effects of the drug. The well-structured chrysin efficiently accumulates in the breast cancer cell line (T47D). In the present study, the structure and chrysin loading were delineated using proton nuclear magnetic resonance (HNMR), Fourier-transform infrared spectroscopy (FT-IR), and scanning electron microscopy (SEM), and the in vitro cytotoxicity of pure and nanochrysin was studied by the MTT assay. Next, the RNA was exploited and the cytotoxic effects of chrysin were studied by real-time PCR. In conclusion, the nanochrysin therapy developed is a novel method that could increase cytotoxicity to cancer cells without damaging the normal cells, and would be promising in breast cancer therapy.

Keywords: MTT assay, chrysin, flavonoids, nanotherapy

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Authors: Xiaoping Su, Gabriel G. Malouf

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Introduction: Breast cancer is a heterogeneous disease that can be classified in 4 subgroups using transcriptional profiling. The role of lncRNA expression in human breast cancer biology, prognosis, and molecular classification remains unknown. Methods and results: Using an integrative comprehensive analysis of lncRNA, mRNA and DNA methylation in 900 breast cancer patients from The Cancer Genome Atlas (TCGA) project, we unraveled the molecular portraits of 1,700 expressed lncRNA. Some of those lncRNAs (i.e, HOTAIR) are previously reported and others are novel (i.e, HOTAIRM1, MAPT-AS1). The lncRNA classification correlated well with the PAM50 classification for basal-like, Her-2 enriched and luminal B subgroups, in contrast to the luminal A subgroup which behaved differently. Importantly, estrogen receptor (ESR1) expression was associated with distinct lncRNA networks in lncRNA clusters III and IV. Gene set enrichment analysis for cis- and trans-acting lncRNA showed enrichment for breast cancer signatures driven by breast cancer master regulators. Almost two third of those lncRNA were marked by enhancer chromatin modifications (i.e., H3K27ac), suggesting that lncRNA expression may result in increased activity of neighboring genes. Differential analysis of gene expression profiling data showed that lncRNA HOTAIRM1 was significantly down-regulated in basal-like subtype, and DNA methylation profiling data showed that lncRNA HOTAIRM1 was highly methylated in basal-like subtype. Thus, our integrative analysis of gene expression and DNA methylation strongly suggested that lncRNA HOTAIRM1 should be a tumor suppressor in basal-like subtype. Conclusion and significance: Our study depicts the first lncRNA molecular portrait of breast cancer and shows that lncRNA HOTAIRM1 might be a novel tumor suppressor.

Keywords: lncRNA profiling, breast cancer, HOTAIRM1, tumor suppressor

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Authors: Hamzeh Alipour, Masoumeh Bagheri, Tahereh Karamzadeh, Abbasali Raz, Kourosh Azizi

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Netrin-A, a protein identified for conducting commissural axons, has a similar role in angiogenesis. In addition, studies have shown that one of the netrin-A receptors is expressed in the growing cells of small capillaries. It will be interesting to study this new group of molecules because their role in wound healing will become clearer in the future due to angiogenesis. The greenbottle blowfly Luciliasericata (L. sericata) larvae are increasingly used in maggot therapy of chronic wounds. This aim of this was the identification of moleculareatures of Netrin-A in L. sericata larvae. Larvae were reared under standard maggotarium conditions. The nucleic acid sequence of L. sericataNetrin-A (LSN-A) was then identified using Rapid Amplification of cDNA Ends (RACE) and Rapid Amplification of Genomic Ends (RAGE). Parts of the Netrin-A gene, including the middle, 3′-, and 5′-ends were identified, TA cloned in pTG19 plasmid, and transferred into DH5ɑ Escherichia coli. Each part was sequenced and assembled using SeqMan software. This gene structure was further subjected to in silico analysis. The DNA of LSN-A was identified to be 2407 bp, while its mRNA sequence was recognized as 2115 bp by Oligo0.7 software. It translated the Netrin-A protein with 704 amino acid residues. Its molecular weight is estimated to be 78.6 kDa. The 3-D structure ofNetrin-A drawn by SWISS-MODEL revealed its similarity to the Netrin-1 of humans with 66.8% identity. The LSN-A protein conduces to repair the myelin membrane in neuronal cells. Ultimately, it can be an effective candidate in neural regeneration and wound healing. Furthermore, our next attempt is to deplore recombinant proteins for use in medical sciences.

Keywords: maggot therapy, netrin-A, RACE, RAGE, lucilia sericata

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Authors: Taslim Khan, Ray Hua Horng, Rajendra Singh

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This study presents a comprehensive analysis of the design, fabrication, and performance evaluation of a solar-blind Schottky photodetector based on ZnGa₂O₄ grown via MOCVD, utilizing Ni/Au as the Schottky electrode. ZnGa₂O₄, with its wide bandgap of 5.2 eV, is well-suited for high-performance solar-blind photodetection applications. The photodetector demonstrates an impressive responsivity of 280 A/W, indicating its exceptional sensitivity within the solar-blind ultraviolet band. One of the device's notable attributes is its high rejection ratio of 10⁵, which effectively filters out unwanted background signals, enhancing its reliability in various environments. The photodetector also boasts a photodetector responsivity contrast ratio (PDCR) of 10⁷, showcasing its ability to detect even minor changes in incident UV light. Additionally, the device features an outstanding detective of 10¹⁸ Jones, underscoring its capability to precisely detect faint UV signals. It exhibits a fast response time of 80 ms and an ON/OFF ratio of 10⁵, making it suitable for real-time UV sensing applications. The noise-equivalent power (NEP) of 10^-17 W/Hz further highlights its efficiency in detecting low-intensity UV signals. The photodetector also achieves a high forward-to-backward current rejection ratio of 10⁶, ensuring high selectivity. Furthermore, the device maintains an extremely low dark current of approximately 0.1 pA. These findings position the ZnGa₂O₄-based Schottky photodetector as a leading candidate for solar-blind UV detection applications. It offers a compelling combination of sensitivity, selectivity, and operational efficiency, making it a highly promising tool for environments requiring precise and reliable UV detection.

Keywords: wideband gap, solar blind photodetector, MOCVD, zinc gallate

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Authors: Walaa H. Salama, Azza M. Abdel-Aty, Afaf S. Fahmy

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Background: Egyptian Cobra; Naja haje (Elapidae) is one of most common snakes, widely distributed in Egypt and its envenomation causes multi-organ failure leading to rapid death. Thus, Different medicinal plants showed a protective effect against venom toxicity and may complement the conventional antivenom therapy. Aim: The present study was designed to assess both the antioxidant capacity of methanolic extract of rosemary leaves and evaluate the neutralizing ability of the extract against hepatotoxicity induced by Naja haje venom. Methods: The total phenolic and flavonoid contents and the antioxidant capacity of the methanolic rosemary extract were estimated by DPPH and ABTS Scavenging methods. In addition, the rosemary extract were assessed for anti-venom properties under in vitro and in vivo standard assays. Results: The rosemary extract had high total phenolic and flavonoid content as 12 ± 2 g of gallic acid equivalent per 100 gram of dry weight (g GAE/100g dw) and 5.5 ± 0.8 g of catechin equivalent per 100 grams of dry weight (g CE/100g dw), respectively. In addition, the rosemary extract showed high antioxidant capacity. Furthermore, The rosemary extract were inhibited in vitro the enzymatic activities of phospholipase A₂, L-amino acid oxidase, and hyaluronidase of the venom in a dose-dependent manner. Moreover, indirect hemolytic activity, hepatotoxicity induced by venom were completely neutralized as shown by histological studies. Conclusion: The phenolic compounds of rosemary extract with potential antioxidant activity may be considered as a promising candidate for future therapeutics in snakebite therapy.

Keywords: antioxidant activity, neutralization, phospholipase A₂ enzyme, snake venom

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Authors: Alyaa Abdlwahab

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Cutaneous leishmaniasis represents a serious health problem in Syria; this problem has become noticeably aggravated after the civil war in the country. Leishmania tropica parasite is the main cause of cutaneous leishmaniasis in Syria. In order to control the disease, we need an effective vaccine against leishmania parasite. DNA vaccination remains one of the favorable approaches that have been used to face cutaneous leishmaniasis. Ribosomal protein S4 is responsible for important roles in Leishmania parasite life. DNA vaccine based on S4 gene has been used against infections by many species of Leishmania parasite but leishmania tropica parasite, so this gene represents a good candidate for DNA vaccine construction. After proving the existence of ribosomal protein S4 gene in a Syrian strain of Leishmania tropica (LCED Syrian 01), sequencing it and cloning it into pCI plasmid, BALB/C mice were inoculated with pCI-S4 DNA vaccine. The immune response was determined by monitoring the lesion progression in inoculated BALB/C mice for six weeks after challenging mice with Leishmania tropica (LCED Syrian 01) parasites. IL-12, IFN-γ, and IL-4 were quantified in draining lymph nodes (DLNa) of the immunized BALB/C mice by using the RT-qPCR technique. The parasite burden was calculated in the final week for the footpad lesion and the DLNs of the mice. This study proved the existence and the expression of the ribosomal protein S4 gene in Leishmania tropica (LCED Syrian 01) promastigotes. The sequence of ribosomal protein cDNA S4 gene was determined and published in Genbank; the gene size was 822 bp. Expression was also demonstrated at the level of cDNA. Also, this study revealed that pCI-S4 DNA vaccine induces TH1\TH2 response in immunized mice; this response prevents partially developing a dermal lesion of Leishmania.

Keywords: ribosomal protein S4, DNA vaccine, Leishmania tropica, BALB\c

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Authors: Farideh K. Khosroushahi, Serkan Erdal, Mucip Geni̇şel

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Soil salinity is one of the major abiotic stress factors that restricts arable land and reduces crop productivity worldwide. High salt concentration adversely affects plant growth and development inducing water deficit, ionic toxicity, nutrient imbalance, and lead to oxidative stress. Although the stimulating role of mammalian sex hormones on various biological and biochemical processes under normal and stress condition have been proven, there is no study regarding with these hormone's effect on modulation of the alternative respiration pathway and AOX gene expression. In this study, changes in alternative respiration pathway in leaves of maize seedlings under salinity and the possible modulating effect of estrogen on these changes were investigated. Maize seedlings were grown in a hydroponic media for 11 days and then were exposed to salt stress for 3 days after being sprayed estrogen. The data obtained from oxygen consumption revealed that salt stress elevated cellular respiration value in the leaves. In addition, a marked increase was observed at alternative respiration level in salt-stressed seedlings. Compared to salt application alone, supplementation with estrogen resulted in a significant rise in alternative oxidase (AOX) activities. Similarly, while salt stress caused to rise in expressions of AOX gene compared to control seedlings, estrogen application resulted in further activation of these genes’ expression compared to stressed-seedlings alone. These data revealed that mitigating role of estrogen against the detrimental effects of salt stress is linked to modulation of alternative respiration pathway.

Keywords: alternative oxidase, estrogen, Ssalt stress, AOX, maize

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