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BackgroundDNA barcoding have been considered as a tool to facilitate species identification based on its simplicity and high-level accuracy in compression to the complexity and subjective biases linked to morphological identification of taxa. MaturaseK gene (MatK gene)of the chloroplast is very vital in the plant system which is involved in the group II intron splicing. The main objective of this study is to determine the relative utility of the “MatK” chloroplast gene for barcoding in 15 legume as a tool to facilitate species identification based on their simplicity and high-level accuracy linked to morphological identification of taxa.Methods and ResultsMatKgene sequences were submitted to GenBank and the accession numbers were obtained with sequence length ranging from 730 to 1545 nucleotides. These DNA sequences were aligned with database sequence using PROMALS server,Clustal Omega server and Bioedit program. Maximum likelihood and neighbor-joining algorithms were employed for constructing phylogeny. Overall, these results indicated that the phylogenetic tree analysis and the evolutionary distances of an individual dataset of each species were agreed with a phylogenetic tree of all each other consisting of two clades, the first clade comprising(Enterolobium contortisiliquum, Albizia lebbek), Acacia saligna,Leucaena leucocephala, Dichrostachys Cinerea, (Delonix regia, Parkinsonia aculeata), (Senna surattensis, Cassia fistula, Cassia javanica)andSchotia brachypetalawere more closely to each other, respectively. The remaining four species ofErythrina humeana, (Sophora secundiflora, Dalbergia Sissoo, Tipuana Tipu)constituted the second clade.ConclusionMoreover, their sequences could be successfully utilized in single nucleotide polymorphism or as part of the sequence as DNA fragment analysis utilizing polymerase chain reaction in plant systematic. Therefore,MatKgene is considered promising a candidate for DNA barcoding in the plant family Fabaceae and provides a clear relationship between the families.

DNA barcodes have been considered as a tool to facilitate species identification based on their simplicity and high-level accuracy compression to the complexity and subjective biases linked to morphological identification of taxa. MaturaseK gene “MatK” of the chloroplast is very crucial in the plant system which is involved in the group II intron splicing. The main objective of this current study is determining the relative utility of the “MatK” chloroplast gene for barcoding in fifteen legume trees by both single region and multiregional approaches. The chloroplast “MatK” gene sequences were submitted to GenBank and accession numbers (GenBank: LC602060, LC602154, LC602263, LC603347, LC603655, LC603845, LC603846, LC603847, LC604717, LC604718, LC605994, LC604799, LC605995, LC606468, LC606469) were obtained with sequence length ranging from 730 to 1545 nucleotides. These DNA sequences were aligned with database sequence using PROMALS server, Clustal Omega server and Bioedit program. Also, the maximum likelihood and neighbor-joining algorithms for phylogenetic reconstruction using the MEGA-X program were employed. Overall, these results indicated that the phylogenetic tree analysis and the evolutionary distances of an individual dataset of each species were agreed with a phylogenetic tree of all each other consisting of two clades, the first clade comprising (Enterolobium contortisiliquum, Albizia lebbek), Acacia saligna, Leucaena leucocephala, Dichrostachys Cinerea, (Delonix regia, Parkinsonia aculeata), (Senna surattensis, Cassia fistula, Cassia javanica) and Schotia brachypetala were more closely to each other, respectively. The remaining four species of Erythrina humeana, (Sophora secundiflora, Dalbergia Sissoo, Tipuana Tipu) constituted the second clade. Therefore, MatK gene is considered promising a candidate for DNA barcoding in plant family Fabaceae and providing a clear relationship between the families. Moreover, their sequences could be successfully utilized in single nucleotide polymorphism (SNP) or part of the sequence as DNA fragment analysis utilizing polymerase chain reaction (PCR) in plant systematic.

Background:The p7-transactivated protein1 of Hepatitis C virus is a small integral membrane protein of 127 amino acids, which is crucial for assembly and release of infectious virions. Ab initio or comparative modelling, is an essential tool to solve the problem of protein structure prediction and to comprehend the physicochemical fundamental of how proteins fold in nature.Results:Only one domain (1-127) of p7-transactivated protein1 has been predicted using the systematic in silico approach, ThreaDom. I-TASSER was ranked as the best server for full-length 3-D protein structural predictions of p7-transactivated protein1 where the benchmarked scoring system such as C-score, TM-score, RMSD and Z-score are used to obtain quantitative assessments of the I-TASSER models. Scanning protein motif databases, along with secondary and surface accessibility predictions integrated with post translational modification sites (PTMs) prediction revealed functional and protein binding motifs. Three protein binding motifs (two Asp/Glutamnse, CTNNB1- bd_N) with high sequence conservation and two PTMs prediction: Camp_phospho_site and Myristyl site were predicted using BLOCKS and PROSITE scan. These motifs and PTMs were related to the function of p7-transactivated protein1 protein in inducing ion channel/pore and release of infectious virions. Using SCOP, only one hit matched protein sequence at 71-120 was classified as small proteins and FYVE/PHD zinc finger superfamily.Conclusion:Integrating this information about the p7-transactivated protein1 with SCOP and CATH annotations of the templates facilitates the assignment of structure–function/ evolution relationships to the known and the newly determined protein structures.

Introduction Direct-acting antivirals (DAAs) represent a breakthrough in hepatitis C virus (HCV) treatment as they directly inhibit HCV nonstructural (NS) proteins (NS3/4A, NS5A, and NS5B). However, ongoing debates exist regarding their relationship with hepatocellular carcinoma (HCC) whose incidence is widely debated among investigators. This study was conducted to identify host pharmacogenetic factors that may influence HCC incidence upon using HCV DAAs. Materials and methods Details regarding 16 HCV DAAs were collected from literature and DrugBank database. Digital structures of these drugs were fed into the pharmacogenomics/pharmacovigilance in-silico pipeline (PHARMIP) to predict the genetic factors that may underpin HCC development. Results We identified 184 unique genes and 40 unique variants that may have key answers for the DAA/HCC paradox. These findings could be used in different methods to aid in the precise application of HCV DAAs and minimize the proposed risk for HCC. All results could be accessed at: https://doi.org/10.17632/8ws8258hn3.2. Discussion All the identified factors are evidence related to HCC and significantly predicted by PHARMIP as DAA targets. We discuss some examples of the methods of using these results to address the DAA/HCC controversy based on the following three primary levels: 1 - individual DAA drug, 2 - DAA subclass, and 3 - the entire DAA class. Further wet laboratory investigation is required to evaluate these results., Pharmacogenomics; PHARMIP; HCV direct-Acting antivirals; Hepatocellular carcinoma; Personalized medicine, HCV

Graphical abstract, Pharmacovigilance is the pharmacological science that focuses on the safe and appropriate use of drugs.Variability in response to drug therapy in both terms of safety and efficacy is highly related to patient's personal genomics. Hence, pharmacovigilance considers pharmacogenomics methodologies in the evaluation of medicinal products. The aim of this work is to introduce the pharmacovigilance/ pharmacogenomics insilico pipeline (PHARMIP) that uses the drug (or drug candidate) digital structure and the advances in bioinformatics tools and databases to figure-out the genetic factors underlying the drug reported adverse reactions (ADRs).PHARMIP uses user-friendly freely available bioinformatics resources to help pharmacovigilance and pharmacogenomics scientists with minimal bioinformatics experience to retrieve helpful information for their daily basis activities. Also, PHARMIP could help the advances in precision medicine in a drug-centric approach as it can be used to reveal genetic risk factors for certain drug ADRs. Domperidone was used as an example to the application of PHARMIP as the pipeline was initially developed during the insilico exploration of domperidone cardiotoxic ADRs. Method is composed of 3 main steps: • Preparing the drug off-label targets (OLT) list. • Retrieving the related diseases/ adverse reactions (DA) list. • Analysis of DA list to get answers.

Shoot tip and leaf primordial explants of Phoenix dactylifera L. cvs. (Sewi and Oshkingbeel) were cultured in modified MS medium supplemented with various combinations between different growth regulators cytokinins (2iP or BA) and Auxins (2, 4-D or NAA). Friable callus was produced from shoot tip and leaf primordial explants. The highest percentage of callus initiation was achieved on modified MS medium supplemented with 100 mg/L 2,4-D and 3 mg/L 2iP for shoot tip and leaf primordial explants. The highest percentage of embryogenic callus was achieved on modified MS medium supplemented with 10 mg/L 2,4-D, 5 mg/L NAA, 3 mg/L 2iP and 3.0 g/L activated charcoal which gave 87.5% and 75% for Sewi and Oshkingbeel cvs., respectively. Somatic embryos formation were obvious on modified MS medium plus 0.1 mg/L NAA which gave the highest average number (5.16, 4.94) for Sewi and Oshkingbeel, respectively after three subcultures. Greatest embryonic elongation resulted at 0.5 mg/L 2iP + 0.5 mg/L kinetin + 40 g/L sucrose in solid full strength MS medium. Also, the highest value of leaves number was shown on the same medium. The complete plantlets developed from individual embryos (5-10 cm) were transferred to rooting MS medium supplemented with 1 mg/L NAA with good growth in solid and liquid media. Rooted date palm plantlets from both cultivars were transferred to plastic pots (5cm diameter) containing peat-moss, sand and vermiculite at equal volume. Acclimatization percentage decreased gradually during four months in the first acclimatization stage. Date palm plantlets produced from the first acclimatization stage were transferred to plastic pots (20 cm diameter) containing peatmoss, washed sand and vermiculite at equal volume for more growth and development to be ready to cultivate in the field. Although survival percentage was low during the first acclimatization stage, it was very high in the second acclimatization stage and date palm survival percentage became constant after another six months with good growth.

Background Lung cancer is a leading cause of cancer-related death worldwide and is the most commonly diagnosed cancer. Like other cancers, it is a complex and highly heterogeneous disease involving multiple signaling pathways. Identifying potential therapeutic targets is critical for the development of effective treatment strategies. Methods We used a systems biology approach to identify potential key regulatory factors in smoking-induced lung cancer. We first identified genes that were differentially expressed between smokers with normal lungs and those with cancerous lungs, then integrated these differentially expressed genes (DEGs) with data from a protein-protein interaction database to build a network model with functional modules for pathway analysis. We also carried out a gene set enrichment analysis of DEG lists using the Kinase Enrichment Analysis (KEA), Protein-Protein Interaction (PPI) hubs, and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases. Results Twelve transcription factors were identified as having potential significance in lung cancer (CREB1, NUCKS1, HOXB4, MYCN, MYC, PHF8, TRIM28, WT1, CUX1, CRX, GABP, and TCF3); three of these (CRX, GABP, and TCF) have not been previously implicated in lung carcinogenesis. In addition, 11 kinases were found to be potentially related to lung cancer (MAPK1, IGF1R, RPS6KA1, ATR, MAPK14, MAPK3, MAPK4, MAPK8, PRKCZ, and INSR, and PRKAA1). However, PRKAA1 is reported here for the first time. MEPCE, CDK1, PRKCA, COPS5, GSK3B, BRCA1, EP300, and PIN1 were identified as potential hubs in lung cancer-associated signaling. In addition, we found 18 pathways that were potentially related to lung carcinogenesis, of which 12 (mitogen-activated protein kinase, gonadotropin-releasing hormone, Toll-like receptor, ErbB, and insulin signaling; purine and ether lipid metabolism; adherens junctions; regulation of autophagy; snare interactions in vesicular transport; and cell cycle) have been previously identified. Conclusion Our systems-based approach identified potential key molecules in lung carcinogenesis and provides a basis for investigations of tumor development as well as novel drug targets for lung cancer treatment.

Organisms exposed to sub-zero temperatures are at risk of freezing damage. Fingerling channel catfish, Ictalurus punctatus , hybrid catfish (channel catfish female × blue catfish, Ictalurus furcatus , male), channel catfish transgenic for the goldfish glutamate decarboxylase 65 gene driven by the carp β-actin promoter (βA-GAD65), and channel catfish transgenic for the catfish growth hormone gene driven by the antifreeze protein promoter (AFP-ccGH) were compared for survival at different temperatures (9.0 °C, 6.0 °C, 3.0 °C, 1.0 °C, 0.5 °C, 0 °C, and − 0.5 °C) at different salinities (0 ppt, 2.5 ppt, 5 ppt, and 7.5 ppt). The two transgenes were of interest as growth hormone not only affects growth, but also affects osmoregulation, and GAD65 construct could alter gonadotropin with the potential consequence that GnRH affects growth hormone production. Survival was 98–100% for all genetic groups at all salinities between 0 °C and 9.0 °C. However, large differences were observed at − 0.5 °C. At 0 ppt salinity, 100% of AFP-ccGH transgenic (T) fingerlings survived, but survival of all other genetic groups was 0–2%. Raising salinity to 2.5 ppt at sub-zero temperature had a strong positive impact on survival as survival rates of AFP-ccGH (T), AFP-ccGH control (C), channel catfish, βA-GAD65 (T), βA-GAD65 (C) and hybrid catfish were 100, 100, 98, 76, 100 and 18%, respectively. Increasing salinity further to 5 ppt decreased overall survival, although it was still higher than at 0 ppt. Survival rankings were altered, with means for βA-GAD65 (T), βA-GAD65 (C), AFP-ccGH (T), AFP-ccGH (C), channel catfish and hybrid catfish of 69, 0, 15, 22, 0 and 0%, respectively. Mortality was 100% in all genetic groups at − 0.5 °C and 7.5 ppt demonstrating significant interaction between temperature and salinity. Negative heterosis was observed for the hybrids at low temperature at the respective salinities. Statement of relevance We believe that this topic has not been previously addressed. These pleiotropic effects have never been described in GH transgenic or GAD transgenic fish and have relevance for aquaculture/natural resource management for future climate change as well as management and genetic management today. It is the first paper to evaluate the survival of hybrids under freezing, very important for countries that are suffering from freezing weather.

Background and Aim: Interleukin-28B (IL-28B) polymorphism is a predictor of sustained virologic response (SVR), spontaneous clearance and personalizing therapy of hepatitis C virus (HCV). This study aimed to determine IL28B rs12979860 polymorphism among chronic hepatitis C (CHC) Egyptian patients as a step in personalized HCV therapy and pharmacogenomics. Methods: CHC Egyptian patients were received sofosbuvir (SOF) plus pegylated interferon (PEG-IFN) and ribavirin (RBV) for 12 weeks. A total of 82 HCV infected Egyptian patients and 27 healthy individuals were included in the present study. CHC Patients were classified as achieving SVR if plasma HCV-RNA was undetectable (group A) and non-responders if plasma HCV-RNA was detectable (group B). IL28B genotypes were analyzed and their associations with SVR were selected. Results: The end of treatment response (ETR) rate was 100%. However, SVR12 was 76.8% (group A) and 23.2% relapsed (group B). Among studied CHC patients, 50% were IL-28B TT, 40.2% CT, and 9.8% CC. while the percentage of their frequencies in the healthy persons were 18.5%, 51.8%, and 29.6%, respectively. These results showed that the frequencies of TT genotypes were more prevalent in HCV patients. The genotype CC (n=8) achieved higher rates of SVR in group A (87.5%) than relapsed patients in group B (12.5%) and it had the least prevalence in group B compared with the frequencies of CT (21.2%) and TT (26.9%) genotypes. These results showed that CC genotype was associated with SVR. Conclusions: It can be concluded that the individuals with IL28B TT genotype are more susceptible to HCV infection in Egyptian patients and relapse. Moreover, IL-28B CC is useful for pretreatment prediction of the outcome of HCV treatment. Hence, IL28B polymorphism could be considered as a pharmacogenetic predictor in personalized HCV therapy and pharmacogenomics during SOF plus PEG-IFN and RBV therapy for chronic hepatitis C Egyptian patients.

Cistanche phelypea (Fam. Orbanchaceae) is a parasite plant on the root of the host plant. The main natural hosts are the woody species of family chenopodiaceae such as Arthrocnemum macrostachyum and family Zygophyllacea such as Zygophyllum album. It is an obligate parasite which totally depends on its host for water, minerals and organic nutrients. Many species belonging to the same family have the same phenomenon such as orbanche crenata Forsk which attacks legume plants, specially, Vicia faba. Cistanche phelypea L., grows in Egypt in low density but scattered on a large area of the country. It can be recognized in the Nile region including Faiyum, the Oases of the western desert including Siwa, the Red Sea coastal strip, and the entire Sinai Peninsula including the coastal of the Mediterranean. It grows in sandy and alluvial soil, edges of cultivated fields as a parasite on plant roots. In this study the species was surveyed and photographed in Siwa Oasis and in different obliterated Oasis around Siwa Depression. For the first time in Egypt, morphological, chemical study, RAPD molecular markers and biochemical genetic analysis of Peroxidase isozymes were carried out in order to identify the genetical and morphological description of the species including the identification of genetic variation in the studied populations.

Cucumber (Cucumis sativus L. cv. Faris) explants were transformed by LBA4404 strain of Agrobacterium tumefaciens harboring the binary vector pPZPnptCat-WMV. The T-DNA region contains Neomycin Phosphotransferase II (NPT II) as a selectable marker gene and sequences of Watermelon Mosaic Virus-II (WMV-II) fused with Green Fluorcent Protein (GFP) gene under control of 35S promoter. Agrobacterium-mediated transformation was optimized using GFP as a reporter gene. The optimized parameters were Agrobacterium concentration, preculture period, co-cultivation period and immersion time. Results were recorded based on the percentage of green fluorescent protein (GFP) expression. Agrobacterium concentration at (OD 600 nm 0.8), four days of pre-culture, three days of co-cultivation and sixty minutes of immersion time gave the highest percentage of GFP areas (78%, 46%, 82% and 52%, respectively). Cotyledon was the best explants to give the highest percentage of GFP areas in all tested parameters. Following co-cultivation, leaf, cotyledon, callus and shoot-tip explants were cultured on selective and regeneration Murashige and Skoog (MS) medium containing 1mg/L 6-Benzylaminopurine (BA), 200 mg/L kanamycin and 300 mg/L cefotaxime. Kanamycin resistant shoots were induced from these explants after four weeks. Putative transgenic plantlets were produced from leaf, cotyledon and shoot-tip explants at 8 weeks and at 12 weeks from callus. Integration of the transgenes in the cucumber genome was confirmed by PCR analysis. This study showed that the Agrobacterium-mediated gene transfer system and regeneration via organogenesis is an effective method for producing transgenic cucumber plantlets. Cloning construct of Catgfp-WMV-2 into binary vector pPZPnpt was done successfully. Agrobacterium concentration at 0.8, four days of pre-culture, three days of co-cultivation and sixty minutes of immersion time gave the highest number of GFP positive percentage (78%, 46%, 82% and 52%, respectively). Cotyledon was the best explants to give the highest number of GFP positive percentage in all tested parameters. Putative transgenic plantlets were obtained from (leaf, cotyledon and shoot-tip explants after 8 weeks) and after 12 weeks from callus.

Date Palm is one of the most important crops in Egypt. At present, Egypt ranked second in world date production. The objectives of this study are the identification the genetic variance between some local varieties of Date Palm, in line with the establishment of a molecular diagnostic method to study the aetiology and the prevalence of Al Wijam disease. Date palm plantations have been suffering from number of pests and diseases infestation, mainly due to Dubas Bug, Red Palm Weevil, Lesser Date moth, and Al Wijam disease. Genomic DNAs were extracted from 18 Date Palm cultivars collected from Date Palm Research Institute, ARC using three different extraction methods. Nine common cultivars (Zaghlool, Hayani, Oraibi, Samani, Sultan, Bent-Aisha, Amrey, Aglani, and Barhee) and nine Siwi cultivars (Siwi, Fryhee, Taktakt, Quaipe, Karama Ghazally, Helw Ghanem, Gorm Agazal, and Oshbeigel,) were used in this study. In order to determine the genetic polymorphism and discriminate between each of these cultivars, RAPD ...

Hepati tis C is a major healthcare problem that launched the quest and the interest of scientists to search for solutions that allev iate its risks. New groups of drugs are developed and repurposed for this reason. One of the drugs that recently repurposed to be u sed as an anti - HCV drug is Nitazoxanide (NTZ). NTZ is mainly a thiazolide antip arasitic drug that is mainly used for the treatment of cryptosporidiosis and giardiasis . Tizoxanide (TIZ) , which is the active metabolite of NTZ , was recently reported to be act ive against some viruses including hepatitis C virus (HCV) . T he anti - HCV mode of act ion of Nitazoxanide is the overproduction of the hyperphosphorylated HCV non - structural protein 5 A (NS5A). However, the exact mechanism of action is not so clear. S ome pr evious works suggested one member of the CMGC Ser ine /Th re onine protein kinase family to be the primary cellular target of NTZ. A more recent work revealed that NS5A is a direct substrate of casein kinase I α (CKI α ) . However, no direct effect of NTZ or TIZ was reported on CKI α in enzymatic assays. In this work, starting with the chemical structure of NTZ and TIZ, some in - silico approaches were applie d to hypothesize the human primary cellular target for NTZ. Accordingly, glycogen synthase kinase 3 β (GSK3 β ), a member of CMGC Serine/Threonine protein kinase family, was retrieved as a proposed target of NTZ that is likely mediating its anti - HCV effect.

Microsatellite-based DNA fingerprinting has been increasingly applied to cacao (Theobroma cacao L.) genotype identification. However, the accuracy and reliability of using high throughput microsatellite analysis for cacao clone identification have not yet been rigorously assessed. Despite the use of highly robust fingerprinting protocols, cacao genotype identification has been affected by genotyping errors, which potentially mislead the result of clone identification. In this paper, we calculated the probability of identity for 15 selected microsatellite loci. We then quantified the genotyping error rate through repeated genotyping and simulated the impact of the genotyping error on cacao clone identification. Allelic dropout (ADO), or failure to amplify one allele for a heterozygous locus, and false allele (FA), or an amplicon size error by the polymerase, accounted for 48 and 52% of the genotyping inconsistencies, respectively. The result of simulation showed that 99% of the consensus genotype can be generated for the ambiguous loci through a minimum of three polymerase chain reaction (PCR) repetitions. On the basis of the error rate and probability of identity (PID), we designed a genotyping scheme and applied it to the cacao germplasm held in the USDA cacao collection at Mayaguez, Puerto Rico. Out of the 141 samples, we unambiguously identified nine duplicated groups consisting of 34 cacao accessions. This genotyping scheme is being implemented in large scale fingerprinting of cacao germplasm.

A collaborative international program was initiated to identify and describe the genetic diversity of living germplasm collections of Theobroma cacao genotypes that are maintained in several international collections scattered throughout tropical cacao growing countries of the world. Simple sequence repeat (SSR) DNA analysis was identified as the most appropriate molecular tool for DNA fingerprinting these collections during an international forum representing academic, government and industry scientists in the cacao community. Twenty-five SSR primers, which had been previously described, were evaluated as potential candidates to define an efficient, standardized, molecular fingerprinting protocol for T. cacao accessions. These primers have been evaluated for reliability, widespread distribution across the cacao genome, number of alleles produced by the SSR primers in cacao and their ability to discriminate between cacao accessions. Approximately 690 cacao accessions were used to evaluate the utility of these SSR primers as international molecular standards, and a small number of test samples of T. cacao were sent to two other independent laboratories for verification. DNA fragments were selectively amplified by PCR, using the SSR primers labeled with fluorescent dyes, and separated by capillary electrophoresis. Based on this study, the 15 SSR primers that had the highest reproducibility and consistency within a common genotype, while allowing the differentiation of separate divergent genotypes, were selected as international molecular standards for DNA fingerprinting of T. cacao.