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Highlights in BioScience

Journal Papers (14) Details Call for Paper Manuscript submission Publication Ethics Contact Authors' Guide Line
1 Sugar Beet Artificial Seeds an Overview , Wessam M. Rslan
Artificial seed propagation of crops broadens the horizon of plant biotechnology and farming. The technology offers techniques for micropropagulated seed analogs such as axillary leaves, embryogenic calli, somatic embryos, apical shoot tips, and protocorm-like organs. Micropropagules are embedded in gelling medium and carboxyl methyl cellulose active coatings. A variety of plant species, such as mulberry, sandalwood, cardamom, banana, sugar beet, maize, and relative, have recorded encapsulation of micro shoots and somatic embryos and subsequent recovery of full plantlets. This knowledge has shown that artificial seed manufacturing is possibly helpful for the propagation of economically significant species ' inferior hybrids on a big scale. Artificial seed development can only succeed with effective upstream manufacturing of micropropagules and downstream germination procedures for an elevated proportion of plant regeneration as one of the significant value-added plant tissue culture goods. Different micropropagules were regarded for the manufacturing of artificial seeds; however, mostly favored were somatic embryos and axillary stem buds. As micropropagules, somatic embryos were used to create artificial seeds in a wide range of fruit and plant organisms, which include Daucus carota, Picea abies, Arachis hypogaea, Medicago sativa, Psidium guajava, and Vitis vinifera. The review illustrated the concept of synthetic seeds and encapsulation procedure of sugar beet
2 Date Palm Biotechnology: Recent Research an Overview , Wessam M. Rslan
Date palm (Phoenix dactylifera L.) is among the earliest fruit crops cultivated in the arid Arab Peninsula, North Africa, and Middle East territories. Dates are a significant source of food and revenue for the Middle East and North Africa's local communities. It has distinctive features of biology and development that require special methods of reproduction, culture, and governance. In varying date-growing regions, there are thousands of date plant cultivars and varieties. The lengthy life cycle, long juvenile lifespan, and date palm dioecism produce cultivation difficult. Every year, the percentage of crop genomes sequenced has continued to increase. The incredible rate at which DNA samples become accessible is mainly due to the enhancement in cost-and speed-related sequencing techniques. Modern sequencing techniques enable the sequencing at a realistic price of various cultivars of tiny plant genomes. Although many of the published genomes are deemed incomplete, they have nevertheless proven to be useful instruments for understanding significant plant characteristics such as fruit maturation, grain characteristics and adaptation of flowering time, here we review date palm genomic studies and determine its genomics element
3 Sugar Beet Improvement using Agrobacterium-mediated Transformation technology , Abo-Bakr A. Youssef, Wessam M. Rslan
Since discovering Agrobacterium tumefaciens distinctive capacity to incorporate a specified part of their transfer-DNA (T-DNA) into eukaryotic cells, the bacteria were commonly used for crop transformation originally of dicotyledonous crops and subsequently of nearly all organisms. To achieve this, the tumor-inducing (Ti) plasmid was changed to extract phytohormone and opine biosynthetic proteins (cytokinin and auxin) so as not to interfere with ordinary morphological growth. Overall, the conversion mediated by Agrobacterium was easier, more effective and less costly relative to other technologies. It also results in insertions with small copy count. Tumor development in crops has also proved the susceptibility of explants from field-grown sugar beet crops to Agrobacterium tumefaciens. Early efforts by Agrobacterium tumefaciens to transform sugar beet were unsuccessful, primarily owing to an inability to regenerate crops from stably modified callus or suspended cells. A genotype-independent method as defined under which cotyledonary explants of various sugar beet genotypes are inoculated with Agrobacterium tumefaciens comprising whether kanamycin tolerance and GUS activity or kanamycin resistance, GUS activity and glyphosate tolerance. GUS expression, NPT dot blot as well as EPSPS assays verified the presence of transgenes; progeny showed Mendelian genetically modified inheritance and glyphosate tolerance at deadly concentrations to control plants. Unfortunately, there was no publication of technical information about the technique. Here we reviewed the concept Agrobacterium-mediated transformation and how to be applicable
4 Eukaryotic Molecular Biology Databases: An Overview   , Kumar Girish, Singh Dubey
A biological database is a big, structured body of continuous information, generally connected with computerized software intended to update, query, and recover information elements deposited within the framework. A straightforward database could be a single folder comprising several data, each carrying the same number of data. Such famous databases are GenBank from the National Center for Biotechnology Information, SwissProt from the Swiss Institute of Bioinformatics and PIR from the Protein Information Resource. Biological databases are bibliotheques of life science data, gathered from science studies, published literature, high-performance experimental technology, and computational analysis. Here we briefly described some recently published molecular databases.
5 Identification of Genes for Wheat Fungal Resistance Using Bioinformatics Techniques , Ahmed E. Nassar, Khaled H. Mousa, Ahmed A. Madbouly, Shafik D. Ibrahim, Alsamman M. Alsamman
For the majority of world populations, wheat (Triticum aestivum L.) would be the first essential and economic cereal grain crop. Pests and pathogens in both rich and developing countries are constantly threatening wheat production and sustainable development. Multiple gene pathways were recorded to share an association with fungal pathogens with wheat biological resistance. Our aim to use such tools in order to detect and classify fungal resistance genes in wheat through sequence alignment, protein domain identification and phylogenetic analysis. In addition the introduction for restriction fragment length polymorphism (RFLP) for such genes in the new primer database. Approximately 138 sequences of DNA were recovered from the wheat genome by aligning 3845 anti-fungal amino acids through tblastn tool. The NCBI blastn online tool used to detect sequences with functional genes, where 92 genes have been detected. The total number of nucleotides was 48385, where the smallest DNA sequence have 302 bp and the longest contains 977 bp with an average length of 525.9 bp per sequence. The wheat chromosomes 3D, and 4B have the highest number of sequences (9) followed by chromosomes 3B (7) and 3A(6), where wheat genomes A, B and D have 30, 35 and 27 genes, respectively. Five different amino acids motifs have been revealed among studied wheat amino acid sequences. The gene annotation tools used to infer studied amino acid gene annotation. Amino acid sequences belongs to lectin, kinase, tyrosine-protein kinase (STK), thaumatin, and cysteine-rich repeats representing 2, 9, 8, 19, 23 genes respectively, in addition to 31 hypothetical genes. The proteins chemical content have been assessed through 16 different amino acid chemical and physical characteristics
6 Genome-wide identification and comprehensive study of anti-fungal genes in chickpea , Alsamman M Alsamman, Khaled H. Mousa, Ahmed E. Nassar, Ghada A. Shereif, Peter T. Habib, Shafik D. Ibrahim
Chickpea is an important crop that delivers nutritious food to the increasing global community and it will become increasingly popular as a result of climate change. Our objective was to use comprehensive data analysis to locate and identify candidate genes for fungal disease resistance. We used a comprehensive bioinformatics pipeline of sequence alignment, phylogenetic analysis, protein chemical and physical properties assessment and domain structure classification. In order to study gene evolution and genetic diversity, we compared these genes with known anti-fungal genes in different species of plants. A total of 19721 protein sequences belonging to 187 plant species have been downloaded from public databases, including the entire Chickpea genome. We have successfully identified 23 potential anti-fungal genes in 10 different chromosomes and genomic scaffolds using sequence alignment and gene annotation. Ca2 and Ca6 have the highest number of genes followed by Ca3 and Ca4. Anti-fungal chickpea proteins have been identified as cysteine-rich (10), thaumatin (6), pathogenesis (4) and plasmodesmata (3) proteins. Analysis of the chemical and physical correlation of anti-fungal proteins revealed a high correlation between different aspects of anti-fungal proteins. Five different pattern patterns have been detected in the anti-fungal chickpea proteins identified, including domain families associated with fungal resistance. The maximum-likelihood of phylogenetic analysis was successful in distinguishing between anti-fungal chickpea proteins as seen in their protein patterns/domains.
7 Plant Resistance Gene, SNP and Genome Annotation an Overview , Nor S. Zaimah
Plants have developed systems of effective and passive protection to safeguard themselves from pathogens. Active processes include kinds of immune responses that are adaptive and intrinsic. Adaptive immunity is focused on reaction type RNAi and works primarily against viruses. Biological immunity is more general and allows the plant to protect itself against a wide range of pathogens through bacterial and model resistance receptors (PPRs) and forms of resistance (R proteins). PPRs identify molecular models associated with microbes or pathogens that are preserved in a specific category of pathogens. With such big marker amounts, it has become feasible to scan the entire genome for interactions of individual markers with particular quantitatively hereditary traits called whole-genome studies (WGS), genome-wide association trials (GWAS), or association genetics at exceptionally elevated marker densities. Several SNP recognition methods have been used in a specified plant to identify significant amounts of SNPs. These include identification of SNP based on EST feature information; identification of SNP from sequenced genomes; re-sequencing of amplicons; identification of SNP using sequencing techniques of the next generation and identification of SNP based on cluster tests. Pathologic recognizes parts of Genbank completely annotated genome and MetaCyc has been used as a database for the reference pathway. In contrast to sequence similarity information used in other systems, Pathologic uses Genbank annotation information and the EC assignment as evidence of the presence of each pathway in the genome of the interest reference database. When the matching task is finished, pathologic will infer a number of reactions expected to take place in the destination genome and will determine which one of those pathways in the target genome are likely to exist.
8 The Art of Bioinformatics Learning in Our Arabic World , Alsamman M. Alsamman
Bioinformatics became a significant field in life sciences that, draws a number of researchers and extends into a wide range of biological disciplines. Rendering bioinformatics analysis techniques are the most desirable skills in a variety of scholarship programs and academic positions. Teaching bioinformatics is very challenging since it is a multidisciplinary field, where most of the undergraduate programs in colleges provide only one area required for bioinformatics. Besides the regular education system, few bioinformatics training courses are offered and less are affordable to fresh graduates in countries most of which are categorized as developing countries. The high cost of learning, confusing education systems, and the complexity of bioinformatics science has made it very difficult to be taught and more challenging to be studied in Arab countries. This review provides possible solutions to most of these issues and offers the best practice to guide future Arab bioinformaticians to learn bioinformatics in a way that fits our social, financial and academic circumstances. Moreover, it discusses the key aspects that a bioinformatician needs to be aware of and the basic knowledge that must be gained. On the other side, it will illustrate how to start learning, to address some of these challenges and how to deal with some of the related social issues.
9 Plant Molecular Biology Databases , Zubair Awan, Aqib Ali, Abbas Iqbal
Many plant biological database comprises data from study fields including metabolomics, proteomics, genomics, microarray gene expression, and phylogenetic. Information in biological databases involves the role of genes, composition, chromosomal location, clinical impacts of mutations, and similarity of biological sequences and characteristics. We are here targeting to review and rank some of the plant databases according to their use and feature. Hoping that scientists could use this study to pick, combine and correlate distinct databases, based on their study needs and objective specifications.  
10 GeneSyno : Simple tool to extract gene sequence from the human genome despite synonymous gene terms , Alsamman M Alsamman, Peter T. Habib
Extracting gene data from the human genome is a tricky task. Gene name is the key information for harvesting its sequence, annotation, and other related data. Unfortunately, most human genes have different and multiple names, depending on the database and the resource in which they have been published. Such an issue is delaying the ability of researchers to gather the necessary knowledge and to build their opinion on the function of genes. Here we introduce GeneSyno, a simple, versatile, and reliable tool that can be used to extract gene information from human genome data even though it is synonymous gene names. GeneSyno was written using C and Python programming languages and could easily be integrated into another pipeline
11 DNA Variations between Medicago truncatula Symbiotic Mutant Line and Native Variant Using Fluorescence-Based AFLP Marker , Asmaa Hamdy Hassan, Ghada Abu El-Heba, Mohamed A-bouzeid
Genetic mutagenesis is a very efficient tool in studying genes function. Because of the great benefits of legumes as human food and animal feed worldwide, we used a model plant Medicago truncatula for identification gene function related to nitrogen fixation process. Our mutant is a Medicago mutant line contains a tobacco Tnt1 retro-transposon mobile element with the two Long Terminal Repeats (LTR) inserted within the genome. Our mutant is predicted to contain a mutation in gene/s belonging to symbiotic interaction between legume and rhizobia. A novel technique was used based on using fluorescent oligonucleotide primers against oligonucleotide primers for Tnt1-LTRs of our mutant. This novel protocol was very successful in detecting the polymorphism between our mutant line and the wild variant R108 using Biosystems 310 Genetic Analyzer. Electropherograms of the mutant line and wild type gave a total of 561 well- resolved AFLP peaks, 357of which were polymorphic peaks and 204 were monomorphic peaks. This novel technique enables the calculation percentage of polymorphism between the mutant line and the wild type. Additionally, primers combinations amplified more bands from others to detect polymorphism between the plants
12 Characterization of EST‑SSR markers in bread wheat EST related to drought tolerance and functional analysis of SSR‑containing unigenes , Laila Dabab Nahas, Alsamman M. Alsamman, Aladdin Hamwieh, Naim Al-Husein, Ghinwa Lababidi
Bread wheat (Triticum aestivum) is an important staple food around the world. The enormous volume of the genome of wheat makes it quite slow to progress in traditional scientific research. On the other hand, incessant databases and suitable tools on web sites make progress in wheat research quicker and easier. Drought is a major abiotic stress in accordance with weather changes and accelerated increase in drylands. In this study, 9077 ESTs related to drought tolerance in hexaploid wheat were downloaded from NCBI and assembled into 12062 contigs and 4141 singletons. It was found that trinucleotide had the highest frequency 64.71%. Moreover, 53.80% of SSRs found in coding regions in respect of ORFs. The highest amino acids found for tri-and hexanucleotides were Arginine.  In addition, 81% of SSR-containing unigenes had one chromosome location and the highest number of loci was found in chromosomes 1B (69). The distribution of genic SSR loci among the 21 wheat chromosomes, the three subgenomes, and the seven homoeologous groups of wheat chromosomes was significant, with P<0.01 indicating a non-random distribution.  Functional annotation and characterization of SSR-containing unigenes have been performed. Eighty-six sequences were identified and sorted into 25 putative TF families and establish 166 pathways using KEGG.  Primer-BLAST was used to predict the polymorphism, which was 39% of the 63 primer pairs of SSR markers. Our current study attempts to help farmers in wheat breeding programs to have drought-tolerant accessions, particularly in developing countries.
13 Holistic solution to an old "mystery": the global role of antibiotic consumption patterns in the spread of certain non-contagious diseases in EU countries , Gábor Ternák
The discovery and extensive utilization of antibiotics are highly contributed to the considerable lengthening life expectancy of human beings. Antibiotics, mixed with animal fodder, produced considerable growth promoting effect and hence, extended the indications of antibiotics at a much higher level. The indiscriminate use of antibiotics quickly resulted in the emergence of poly-resistant pathogens and the extensive antibiotic pollution of the environment, particularly of the surface water and rivers trough human and animal excreta. Along with extensive and ever increasing antibiotic consumption/pollution, the pandemic-like spreading of certain non-contagious diseases like obesity, diabetes (Type 1-2 T1DM, T2DM), Alzheimer disease (AD), Parkinson disease, multiple sclerosis (MS) etc. started unfolding, which was called as a slow moving disaster, without having any appropriate explanation of the phenomenon. The parallel appearance of those “pandemics”, which appeared simultaneously with the extensive antibiotic consumption, might indicate some kind of association. As far as several publications have reported the crucial role of altered gut flora in the development of metabolic disorders (diabetes, obesity) and neurodegenerative diseases alike (PD, AD, MS), it might be suspected that antibiotics, acting through the modification of microbiome, could influence the morbidity (prevalence) of those, non-infectious diseases. This concept, described below, might serve as a unified explanation, not excluding other, contributing causative factors, for the phenomenon, outlined above.
14 Developing Convolutional Neural Networks-Based System for Predicting Pneumonia Using X-Radiography Image , Peter T Habib, Alsamman M Alsamman, Sameh E. Hassanein, Aladdin Hamwieh
Pneumonia is a respiratory disease caused by Streptococcus Pneumoniae infection. It is a life-threatening disease that causes a high mortality rate for children under 5 years of age every year. Under such circumstances, we have a vital need to develop an appropriate and consistent protocol for the identification and diagnosis of pneumonia. The incorporation of computational approaches into the diagnosis of disease is extremely efficient, promising and reliable. Our goal is to integrate these methods into pneumonia routine diagnosis to save countless lives around the world. We used the machine learning algorithm of Convolutional Neural Networks (CNNs) to identify visual symptoms of pneumonia in X-ray radiographic images and make a diagnostic decision. The dataset used to construct the computational model consists of 5844 X-ray images belonging to the pneumonia affected and normal individuals. Our computational model has been successful in identifying pneumonia patients with a diagnosis accuracy of 84%. Our model may increase the efficiency of the pneumonia diagnosis process and accelerate pathogenicity studies of the disease.