Ahmed Mansour Alzohairy | Zagazig University (original) (raw)

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Papers by Ahmed Mansour Alzohairy

Abstract— One of the main problems for an evolutionary biologist is tracing the modifications of ... more Abstract— One of the main problems for an evolutionary
biologist is tracing the modifications of ancestors in
offspring sequences. The Gene Tracer application was
developed for this function based on a local sequence
alignment algorithm. It takes two ancestors and one
offspring sequence as inputs and locates the similar
regions between offspring and each ancestor. In this
paper, Gene Tracer is further developed to find the origin
of an unknown offspring sequence from a biological
databases based on pairwise local alignment. In addition,
the developed application is sped up by parallelizing the
code on multiprocessors architecture.

Early fruit development is an important trait defining fresh tomato marketability in kingdom of S... more Early fruit development is an important trait defining fresh tomato marketability in kingdom of Saudi Arabia (KSA), which is related to more profit for farmers. Eight commercial cultivars of tomato (Solanumlycopersicum L.) grown in Saudi Arabiaanddiffering in fruit developmentdates were characterized on the molecular genetic basis by inter simple sequence repeats (ISSR) and amplified fragment length polymorphism (AFLP) markers. The results indicated a wide range of molecular variation, in which some markers distinguished among different genotypes. In general, both sets of data allowed for the identification of cultivars by means of pairwise differences, cluster analysis and principal component analysis. AFLP and combined data generated resolved trees with bootstrap support. AFLP and ISSR approaches enabled discrimination among the eight tomato cultivars, which represents a valuable data for improvement of this economic crop in the future. characterization of tomato cultivars grown in Saudi Arabia and differing in earliness of fruit development as revealed by AFLP and ISSR. Life Sci J 2014;11(8s):602-612] (ISSN:1097-8135). http://www.lifesciencesite.com. 122

The discipline of bioinformatics has developed rapidly since the complete sequencing of the first... more The discipline of bioinformatics has developed rapidly since the complete sequencing of the first genomes in the 1990s. The development of many high-throughput techniques during the last decades has ensured that bioinformatics has grown into a discipline that overlaps with, and is required for, the modern practice of virtually every field in the life sciences. This has placed a scientific premium on the availability of skilled bioinformaticians, a qualification that is extremely scarce on the African continent. The reasons for this are numerous, although the absence of a skilled bioinformatician at academic institutions to initiate a training process and build sustained capacity seems to be a common African shortcoming. This dearth of bioinformatics expertise has had a knock-on effect on the establishment of many modern high-throughput projects at African institutes, including the comprehensive and systematic analysis of genomes from African populations, which are among the most genetically diverse anywhere on the planet. Recent funding initiatives from the National Institutes of Health and the Wellcome Trust are aimed at ameliorating this shortcoming. In this paper, we discuss the problems that have limited the establishment of the bioinformatics field in Africa, as well as propose specific actions that will help with the education and training of bioinformaticians on the continent. This is an absolute requirement in anticipation of a boom in high-throughput approaches to human health issues unique to data from African populations.

Retrotransposons (RTs) are major components of most eukaryotic genomes. They are ubiquitous, disp... more Retrotransposons (RTs) are major components of most eukaryotic genomes. They are ubiquitous, dispersed throughout the genome, and their abundance correlates with genome size. Their copy-and-paste lifestyle in the genome consists of three molecular steps involving transcription of an RNA copy from the genomic RT, followed by reverse transcription to generate cDNA, and finally, reintegration into a new location in the genome. This process leads to new genomic insertions without excision of the original element. The target sites of insertions are relatively random and independent for different taxa; however, some elements cluster together in 'repeat seas' or have a tendency to cluster around the centromeres and telomeres. The structure and copy number of retrotransposon families are strongly influenced by the evolutionary history of the host genome. Molecular markers play an essential role in all aspects of genetics and genomics, and RTs represent a powerful tool compared with other molecular and morphological markers. All features of integration activity, persistence, dispersion, conserved structure and sequence motifs, and high copy number suggest that RTs are appropriate genomic features for building molecular marker systems. To detect polymorphisms for RTs, marker systems generally rely on the amplification of sequences between the ends of the RT, such as (long-terminal repeat)-retrotransposons and the flanking genomic DNA. Here, we review the utility of some commonly used PCR retrotransposon-based molecular markers, including inter-primer binding sequence (IPBS), sequence-specific amplified polymorphism (SSAP), retrotransposon-based insertion polymorphism (RBIP), inter retrotransposon amplified polymorphism (IRAP), and retrotransposon-microsatellite amplified polymorphism (REMAP).

Genomic retrotransposons (RTs) are major components of most plant genomes. They spread throughout... more Genomic retrotransposons (RTs) are major components of most plant genomes. They spread throughout the genomes by a process termed retrotransposition, which consists of reverse transcription and reinsertion of the copied element into a new genomic location (a copy-and-paste system). Abiotic and biotic stresses activate long-terminal repeat (LTR) RTs in photosynthetic eukaryotes from algae to angiosperms. LTR RTs could represent a threat to the integrity of host genomes because of their activity and mutagenic potential by epigenetic regulation. Host genomes have developed mechanisms to control the activity of the retroelements and their mutagenic potential. Some LTR RTs escape these defense mechanisms, and maintain their ability to be activated and transpose as a result of biotic or abiotic stress stimuli. These stimuli include pathogen infection, mechanical damage, in vitro tissue culturing, heat, drought and salt stress, generation of doubled haploids, X-ray irradiation and many others. Reactivation of LTR RTs differs between different plant genomes. The expression levels of reactivated RTs are influenced by the transcriptional and post-transcriptional gene silencing mechanisms (e.g. DNA methylation, heterochromatin formation and RNA interference). Moreover, the insertion of RTs (e.g. Triticum aestivum L. Wis2-1A) into or next to coding regions of the host genome can generate changes in the expression of adjacent host genes of the host. In this paper, we review the ways that plant genomic LTR RTs are activated by environmental stimuli to affect restructuring and diversification of the host genome.

The process of modeling and classifications of viruses that belong to a specific family is an imp... more The process of modeling and classifications of viruses that belong to a specific family is an important for biologist and for many biological applications. There are many ways for Viruses families' classification. The degree of similarity or diversity among the structure of the viruses capsid proteins is very useful in studying the Viruses families' classification and their genetic evolution . It also important propose if we construct a mathematical model of the virus life cycle to be able to fully understand the life cycle of Viruses families' activities . In this paper we introduce a proposed mathematical model for some Herpesvirus family viruses simple life cycle and comprehensive study for its classification using sequence alignment algorithms in order to demonstrate their genetic evolution according to the structure of their capsid protein. Herpesvirus family is considered one of the most important family in the families of the enveloped DNA viruses as it contain many dangerous viruses for human health. This family contain one of newly discovered viruses called Epstein-Barr virus (EBV), also called human herpesvirus 4 (HHV-4), which is one of the most common viruses in human. Infection with EBV occurs by the oral transfer of saliva [1] and genital secretions.

Retrotransposons outnumber the genes in large plant genomes, thereby comprising the bulk of the g... more Retrotransposons outnumber the genes in large plant genomes, thereby comprising the bulk of the genome. They are largely quiescent during development, but become more active under stress conditions. These elements spread throughout the genome by a process termed retrotransposition, which includes transcription of an element into RNA, reverse transcription into cDNA, and reinsertion of the copied element into a new genomic location. Biotic and abiotic stresses are regular phenomena facing plants. Likewise, both retrotransposons and retroviruses can be stress-activated. Activation of retrotransposable elements can be induced by various stresses. In particular, long terminal repeat (LTR) retrotransposons, which were found in most plant species, are characterized by a high level of variability in the LTR sequences involved in transcription, and have evolved by gaining new expression patterns mostly associated with responses to diverse stress stimuli. Most of the plant LTR retrotransposons produce larger pools of transcripts in response to biotic and abiotic stress. Recently it was shown that the epigenetic activation of these mobile elements alters the expression of adjacent genes. The new insertions in or next to coding regions generate mutations that can lead to changes in gene expression and reshape the genome, both structurally and functionally. Thus, activation of LTR retrotransposable elements can play an essential role in plant development and evolution.

Phospholipid signaling, frequently associated with rapid responses to environmental stimuli, is w... more Phospholipid signaling, frequently associated with rapid responses to environmental stimuli, is well known in animal and some higher plants. Heat shock is a major component of abiotic stress and stimulates many signaling pathways. Applying heat shock stress to tobacco (Nicotiana tabacum) BY-2 cells activated the phospholipids signaling pathway, including protein kinase C (PKC) and diacylglycerol (DAG) kinase pathways, both of which are associated with the downstream phospholipid pathway. In addition, activation of phospholipase C (PLC) activated heat-activated MAP kinase (HAMK) and caused the accumulation of heat shock protein 70 (HSP70) as an end-point marker. In contrast, chemical inhibition of PLC, PKC or DAG kinase completely or partially inhibited HAMK activation and HSP70 accumulation during heat shock. Moreover, treatment of cells with phosphatidic acid (PA) or PKC activators led to HAMK activation and HSP70 accumulation at 25°C, as did treatment of cells with either IP 3 or cADPR, both of which are known to release Ca 2+ from intracellular stores. We conclude that the heat shock response, as measured by HAMK activation and HSP70 accumulation, requires phospholipid signaling and mobilization of vacuolar Ca 2+ . Thus, the PIP 2 -PLC pathway appears to play a key role in thermotolerance after heat shock treatment.

Genomic retrotransposons are major genomic components in most eukaryotic organisms. Their abundan... more Genomic retrotransposons are major genomic components in most eukaryotic organisms. Their abundance in the genome is generally correlated with genome size. These elements spread throughout the genome by a process termed retro-transposition consisting of transcription, reverse transcription and reinsertion of the copied element into a new genomic location. The target sites are relatively unspecific and independent, thus, integration of the same element into specific site in different taxa is negligible over evolutionary time scales. However, utilization of retrotransposons as cladistic molecular markers represents a particularly interesting complement to other molecular and morphological data. These markers can differentiate between ancestral and derived character state at a respective locus. Retrotransposon content of a given species is strongly influenced by the host evolutionary history, with periods of rapid turnover of retrotransposons sequences. Thus, retrotransposon integration markers are an ideal tool for determining the common ancestry of taxa by a shared derived transpositional event.

Mangoes are an important fruit crop in Egypt and all over the world. Statistics provided by the E... more Mangoes are an important fruit crop in Egypt and all over the world. Statistics provided by the Egyptian Ministry of Agriculture and Land Reclamation indicate that a total of 151,000 Fadden (equiv. 63419.310.464 ha) are planted with mango trees, with a total production of 0.596 million t in Egypt alone. The average yield per Fadden is usually about 5.41 t. For improving the yield and yield attributes, varieties are often produced and evaluated under different conditions. Utilization of molecular marker analysis provided new insights to breeders for molecular assisted selection (MAS). Depending on the marker system used, the genetic similarity analyses varied dramatically. In this report, genomic variation within twelve mango cultivars, widely used in fresh market mango production in Egypt, were investigated using two different molecular marker systems; RAPD (random amplified polymorphic DNA) and ISSR (inter-simple sequence repeat). A new strategy was used to increase RAPD potential in genetic diversity by using three different primer combinations per reaction. Different dendrograms constructed for the RAPD and ISSR results individually and collectively revealed that similarity and clustering is very dependant on the marker system used.

The range of temperature fluctuation which a plant can withstand depends on its genotype and on t... more The range of temperature fluctuation which a plant can withstand depends on its genotype and on the available time to acclimatize to novel temperature. The plant responses are entirely mediated by signaling processes by which the plant can sense the changes in the environment and signal its genes to respond. A family of nuclear-encoded trans-acting transcription factors, termed the heat shock factors (HSFs), governs the expression of heat shock proteins (HSPs), which in turn, protect plant from heat shock effects. The enhanced expression of HSPs is regulated by heat shock factors (HSFs). Plant HSFs are structurally complex and they are typically composed of multiple exons and introns in the encoding region. In the present investigation, a 7-day old tobacco (Nicotiana tabacum cv. 'Bright Yellow 2') cell culture was used to investigate the membrane-based heat activation of HSFs under heat shock. A time course study of HSF1 and HSF2 accumulation using immunoblotting was used to study the synchronization of both HSFs activation in the cells. The effect of membrane fluidity and cytoskeleton reorganization in activating and accumulation of HSF1 and HSF in tobacco cells were demonstrated. In addition, the role of the Heat Activated MAP Kinase (HAMK) in mediating the activation of HSFs was also examined. Comparative analysis of tobacco HSFs and their counterparts in different organisms revealed a high degree of similarities in a corresponding domain, indicating similar function. _____________________________________________________________________________________________________________ Keywords: HAMK, heat shock factor, heat shock, membrane fluidity, tobacco BY-2 cells Abbreviations: ATP, adenosine triphosphate; BSA, bovine serum albumin; BY-2, bright yellow 2; DTT, dithiothreitol; EDTA, ethylene diamine tetraacetic; EGTA, ethylene glycol-bis(b-aminoethyl ether)N',N',N',N'-tetraacetic acid; ERK, extracellular signal regulated protein kinase; HAMK, heat activated MAP kinase; HSE, heat shock elements; HSF, heat shock factor; HSP, heat shock protein; MAPK, mitogen activated protein kinase; PAGE, polyacrylamide gel electrophoresis; SDS, sodium dodecyl sulfate Alessl DR, Cuenda A, Cohen P, Dudley DT, Saltiel AR (1995) PD 098059 is a specific inhibitor of the activation of mitogen-activated protein kinase kinase in vitro and in vivo. The Journal of Biological Chemistry 270, 27489-27494 Baler R, Dahl G, Voellmy R (1993) Activation of human heat shock genes is accompanied by oligomerization, modification, and rapid translocation of heat shock transcription factor HSF1. Molecular Cell Biology 13, 2486-2496 Blom N, Gammeltoft S, Brunak S (1999) Sequence-and structure-based prediction of eukaryotic protein phosphorylation sites. Journal of Molecular Biology 294 (5), 1351-1362 Carratu L, Franceschelli S, Pardini CL, Kobayashi GS, Horvarth I, Vigh L, Maresca B (1996) Membrane lipid perturvation modifies the set point of the temperature of heat shock response in yeast. Molecular cloning and expression of a hexameric Drosophila heat shock factor subject to negative regulation Cell 63, 1085-1097 Coca M A, Almoguera C, Thomas TL, Jordano J (1996) Differential regulation of small heat-shock genes in plants: analysis of a water stress inducible and developmentally activated sunflower promoter. Plant Molecular Biology 31, 863-876 Cotto JJ, Kline M, Morimoto RI (1996) Activation of heat shock factor 1 DNA binding precedes stress-induced serine phosphorylation. The Journal of Biological Chemistry 271, 3355-3358 DeSilva DR, Jones EA, Favata MF, Jaffee BD, Magolda RL, Trzaskos JM, Scherle PA (1998) Inhibition of mitogen-activated protein kinase kinase blocks T cell proliferation but does not induce or prevent energy. Journal of Immunology 160, Scherle PA, Trzaskos JM (1998) Identification of a novel inhibtor of mitogen-activated protein kinase kinase. The Journal Biological Chemistry 273, 18623-18632 Fritsch M, Wu C (1999) Phosphorylation of Drosophila heat shock transcription factor. Cell Stress Chaperones 4, 102-117 Holmberg CI, Hietakangas V, Mikhailov A, Rantanen JO, Kallio M (2001) Phosphorylation of serine 230 promotes inducible transcriptional activity of heat shock factor 1.

في منتصف القرن الثامن عشر قام كل من العالمان (تشارلز دارون) والعالم (الفريد راسل والس ) بان هناك ... more في منتصف القرن الثامن عشر قام كل من العالمان (تشارلز دارون) والعالم (الفريد راسل والس ) بان هناك قوي طبيعية تؤدي الي التطور واطلقوا عليها اسم الانتخاب الطبيعي والتي سوف نتحدث عنها بالتفصيل في الفصل القادم . في منتصف القرن الثامن عشر قام كل من العالمان (تشارلز دارون) والعالم (الفريد راسل والس ) بان هناك قوي طبيعية تؤدي الي التطور واطلقوا عليها اسم الانتخاب الطبيعي والتي سوف نتحدث عنها بالتفصيل في الفصل القادم .

ان نظرية التطور لا تعطي لنا اجابات أكيدة عن كيفية نشأة الارض ولكنها توضح لنا الطرق والميكانكيات ا... more ان نظرية التطور لا تعطي لنا اجابات أكيدة عن كيفية نشأة الارض ولكنها توضح لنا الطرق والميكانكيات التي حدث بها تطور والتنوع البيولوجي علي سطح الارض سواء مما نراة الان او من الاحافير والبقايا الاثرية كما انها لاتوضح لنا كيف ان بعض هذه الكائنات أستطاعت البقاء والتكيف حتي الان وكائنات أخرى أنقرضت. إن تطور الكائنات الحيه هو أمر ملحوظ فى كل الكائنات الحيه مع أختلاف سرعة التغير والتطور بين الكائنات. فمثلا نلاحظ أن تطور الكائنات الغير راقيه والتى تتميز بقصر دورة الحياه هى أكثر سرعه من الكائنات الراقيه ذات دورات الحياه الأطول. كما يمكن ملاحظة أن الكائنات التى تتعرض لضغوط أنتخابيه تكون تكون أكثر سرعة فى حدوث التطور بها. ووقد حدد علماء التطورعدة قوى قد تؤدى الى حدوث التطور منها الأنتخاب الطبيعى والذى سوف نتعرض له بالتفصيل لاحقا.

إن الشكل المظهري للفرد والمعروف باسم phenotype هو في الحقيقة ناتج من التفاعل بين الجينات والبيئة ... more إن الشكل المظهري للفرد والمعروف باسم phenotype هو في الحقيقة ناتج من التفاعل بين الجينات والبيئة المحيطة. هذا التفاعل يبدأ في الرحم ويستمر طيلة حياة الكائن. أن الاختلافات في بعض الصفات المظهرية مثل الطول تحدد غالبا بالجينات فمثلا ان كان لديك اباء واجداد قصار القامة فان من الصعب أن تكون طويل القامة بشكل ملحوظ. وعى الرغم من ذلك فأن العوامل البيئية مثل التغذية ممكن ان يكون لها تاثير في الجسم والطول الى حد ما.

Retrotransposons (RTs) are major components of most eukaryotic genomes; they are ubiquitous, disp... more Retrotransposons (RTs) are major components of most eukaryotic genomes; they are ubiquitous, dispersed throughout the genome, and their abundance correlates with the host genome sizes. Copy-and-paste life style of the RTs consists of three molecular steps, which involve transcription of an RNA copy from the genomic RT, followed by reverse transcription to cDNA, and finally a reintegration event into a new locus of the genome. This process leads to new genomic insertions without excision of the original RT. The target sites of insertions are relatively random and independent for different plant taxa; however, some elements cluster together in ‘repeat seas’ or have a tendency to cluster around the chromosome centromers and telomeres. The structure and copy number of retrotransposon families are strongly influenced by the evolutionary history of the host genome. Molecular barcoding of RTs play an essential role in all fields of genetics and genomics, and represent a powerful tool for molecular barcoding. To detect RT polymorphisms, marker systems generally rely on the amplification of sequences between the ends of the retrotransposon, such as long terminal repeats (LTR) of LTR-retrotransposons (LTR-RT) and the flanking genomic DNA. In this Chapter, we review the utility of some commonly used PCR-based molecular barcoding methods of LTR-RTs, including RBIP(Retrotransposon-Based Insertion Polymorphism), REMAP (Retrotransposon-Microsatellite Amplified Polymorphism), SSAP (Sequence-Specific Amplified Polymorphism), IRAP (Inter Retrotransposon Amplified Polymorphism) and IPBS (Inter Primer Binding Sequence).
Interspersed repetitive DNA sequences comprise a large fraction of the eukaryotic genomes. They predominantly consist of transposable elements (TEs) with two main families, Retrotransposons (Class I) and DNA transposons (Class II) (McClintock, 1984). Retrotransposons (RTs) are the most abundant class of TEs (IHGSC, 2001; Feschotte et al., 2002; Sabot and Schulman, 2006; Kalendar and Schulman, 2006).
There are two major groups of RTs based on the presence vs. absence of long terminal repeats (LTRs), LTR-retrotransposons (LTR-RTs) and non-LTR-retrotransposons. LTR-RTs comprise two main subgroups, copia (with high copy number) and gypsy (with high transposing activity) (Fig. 1). Both, copia and gypsy LTR-RTs, carry regulatory sequences of gene promoters such as CAAT box (e.g., CCATT), TATA box (e.g., TGGCTATAAATAG), transcription start (e.g., CCCATGG), polyadenylation signal (e.g., AATAAG), and polyadenylation start (e.g., TAGT) (Ramallo et al., 2008). All these domains are required for replication and integration of RTs (Sabot and Schulman, 2006; Mansour, 2008). The large internal domain of the LTR-RTs encodes the structural proteins of the virus-like particle, which encapsulate the RNA copy of the RT, and the enzymes Reverse Transcriptase and Integrase (Fig. 1). The process is called transposition.
There are three further non-autonomous, short derivative, recombinant LTR-RTs, LARD (Large Retrotransposon Derivatives), TRIM (Terminal Repeat Retrotransposon in Miniature) and solo-LTR (sequence carrying 5’ and 3’ LTRs only) (Xiong and Eickbush, 1990; Havecker et al., 2004; Jurka et al., 2007). The size of LTR-RTs varies from long (e.g., Bare1 copia LTR-RT at 13,271 bp, NCBI Z17327) to short (e.g., Bare1 copia solo-LTR-RT at 3,130 bp, NCBI AB014756; and the truncated RLC_Lara copia RT; at 735 bp, NCBI EF067844; TREP2298).
In plants, LTR-RTs are more plentiful and active than non-LTR-RTs (AGI, Arabidopsis Genome Initiative, 2000; Rice Chromosome 10 Sequencing Consortium, 2003; Alzohairy et al., 2012; 2013; 2014a,b). Due to the induction of chromosome recombinational processes during the meiotic prophase, active retrotransposons tend to lose their activity due to sequence breakage (Mansour, 2007; 2008; 2009; Alzohairy et al., 2012; 2013; 2014a,b).

Plant DNA Barcoding and Phylogenetics, Pages xx-xx Eds. M. Ajmal Ali, Gábor Gyulai and Fahad Al-H... more Plant DNA Barcoding and Phylogenetics, Pages xx-xx Eds. M. Ajmal Ali, Gábor Gyulai and Fahad Al-Hemaid © 2015 Lambert Academic Publishing, Germany.
Retrotransposons (RTs) are major components of most eukaryotic genomes; they are ubiquitous, dispersed throughout the genome, and their abundance correlates with the host genome sizes. Copy-and-paste life style of the RTs consists of three molecular steps, which involve transcription of an RNA copy from the genomic RT, followed by reverse transcription to cDNA, and finally a reintegration event into a new locus of the genome. This process leads to new genomic insertions without excision of the original RT. The target sites of insertions are relatively random and independent for different plant taxa; however, some elements cluster together in ‘repeat seas’ or have a tendency to cluster around the chromosome centromers and telomeres. The structure and copy number of retrotransposon families are strongly influenced by the evolutionary history of the host genome. Molecular barcoding of RTs play an essential role in all fields of genetics and genomics, and represent a powerful tool for molecular barcoding. To detect RT polymorphisms, marker systems generally rely on the amplification of sequences between the ends of the retrotransposon, such as long terminal repeats (LTR) of LTR-retrotransposons (LTR-RT) and the flanking genomic DNA. In this Chapter, we review the utility of some commonly used PCR-based molecular barcoding methods of LTR-RTs, including RBIP(Retrotransposon-Based Insertion Polymorphism), REMAP (Retrotransposon-Microsatellite Amplified Polymorphism), SSAP (Sequence-Specific Amplified Polymorphism), IRAP (Inter Retrotransposon Amplified Polymorphism) and IPBS (Inter Primer Binding Sequence).
Interspersed repetitive DNA sequences comprise a large fraction of the eukaryotic genomes. They predominantly consist of transposable elements (TEs) with two main families, Retrotransposons (Class I) and DNA transposons (Class II) (McClintock, 1984). Retrotransposons (RTs) are the most abundant class of TEs (IHGSC, 2001; Feschotte et al., 2002; Sabot and Schulman, 2006; Kalendar and Schulman, 2006).
There are two major groups of RTs based on the presence vs. absence of long terminal repeats (LTRs), LTR-retrotransposons (LTR-RTs) and non-LTR-retrotransposons. LTR-RTs comprise two main subgroups, copia (with high copy number) and gypsy (with high transposing activity) (Fig. 1). Both, copia and gypsy LTR-RTs, carry regulatory sequences of gene promoters such as CAAT box (e.g., CCATT), TATA box (e.g., TGGCTATAAATAG), transcription start (e.g., CCCATGG), polyadenylation signal (e.g., AATAAG), and polyadenylation start (e.g., TAGT) (Ramallo et al., 2008). All these domains are required for replication and integration of RTs (Sabot and Schulman, 2006; Mansour, 2008). The large internal domain of the LTR-RTs encodes the structural proteins of the virus-like particle, which encapsulate the RNA copy of the RT, and the enzymes Reverse Transcriptase and Integrase (Fig. 1). The process is called transposition.
There are three further non-autonomous, short derivative, recombinant LTR-RTs, LARD (Large Retrotransposon Derivatives), TRIM (Terminal Repeat Retrotransposon in Miniature) and solo-LTR (sequence carrying 5’ and 3’ LTRs only) (Xiong and Eickbush, 1990; Havecker et al., 2004; Jurka et al., 2007). The size of LTR-RTs varies from long (e.g., Bare1 copia LTR-RT at 13,271 bp, NCBI Z17327) to short (e.g., Bare1 copia solo-LTR-RT at 3,130 bp, NCBI AB014756; and the truncated RLC_Lara copia RT; at 735 bp, NCBI EF067844; TREP2298).
In plants, LTR-RTs are more plentiful and active than non-LTR-RTs (AGI, Arabidopsis Genome Initiative, 2000; Rice Chromosome 10 Sequencing Consortium, 2003; Alzohairy et al., 2012; 2013; 2014a,b). Due to the induction of chromosome recombinational processes during the meiotic prophase, active retrotransposons tend to lose their activity due to sequence breakage (Mansour, 2007; 2008; 2009; Alzohairy et al., 2012; 2013; 2014a,b).

يعتبر تفاعل الـ RAPDاحد تقنيات الـ PCRولكنة يعمل علي تضاعف قطع من الـ DNA(المادة الوراثية) والتي... more يعتبر تفاعل الـ RAPDاحد تقنيات الـ PCRولكنة يعمل علي تضاعف قطع من الـ DNA(المادة الوراثية) والتي بالضرورة تكون غير معروفة (مجهولة) بالنسبة للعلماء (عشوائية).
وفي الغالب يستخدم الـ PCRلعزل و تضاعف قطع معلومة من تتابعات الـ DNA. ولذلك يقوم العلماء باختيار وتحديد قطعة او تتابع الـDNAالمستهدف ثم يقوموا بتصميم بوادئ (Primers) ترتبط بالمنطقة المحيطة للتابع المستهدف للقيام بعملية التضاعف لقطعة الـDNAالمحددة

تحتوى جينومات الكائنات حقيقية النواة على مناطق كبيرة من الدنا المتكرر والتي نشأت عن العناصر المتن... more تحتوى جينومات الكائنات حقيقية النواة على مناطق كبيرة من الدنا المتكرر والتي نشأت عن العناصر المتنقلة، وقد نتج عن السلسلة المتكامله لهذه الجينومات معلومات كبيرة غير مسبوقة عن أصل وطبيعة وتباين هذه العناصر داخل هذه المناطق الجينومية والتي كان من المعتقد فى السابق عدم نشاطها. وقد ساعدت سلسلة الجينوم على التعرف على نوعين جديدين من العناصر الجينومية المتنقلة والمعروفة باسم الـ ((Polintons والـ Helitrons)) إلى جانب عدد كبير من عائلات ومجموعات جديدة من العناصر المتنقلة. ومن الجدير بالذكر أن العناصر المتنقلة هي الأصل التطوري لكثير من الجينات مثل جين RAG1 والذي يلعب دور كبير في جهاز المناعة كما أنها القوى المحركة للتطور والاستقرار الجينومي على المدى الطويل.

1- تمثل كل نقطة علي شريحة المصفوفة الدقيقة قطعة محددة من الDNAوتحتوي كل شريحة علي المجموع الكلي ل... more 1- تمثل كل نقطة علي شريحة المصفوفة الدقيقة قطعة محددة من الDNAوتحتوي كل شريحة علي المجموع الكلي للجينوم الكائن.
2- يضاف الي كل نقطة مجموعة قطع الـcDNA المعلمة.
3- يتم قراءة وتحليل شريحة المصفوفة الدقيقة عن طريق برامج خاصة علي اجهزة الكمبيوتر

لكى نعرف كيف نقرأ نتائج التوازى بين التتابعات الناتجة من برنامج الـ Blast يجب أن نتعرف على بعض ال... more لكى نعرف كيف نقرأ نتائج التوازى بين التتابعات الناتجة من برنامج الـ Blast يجب أن نتعرف على بعض المصطلحات الهامه

أشياء يجب تذكرها عن التتابعات البروتينية: - التتابعات البروتينية هي تتابعات بسيطة يتراوح طولها فى... more أشياء يجب تذكرها عن التتابعات البروتينية:
- التتابعات البروتينية هي تتابعات بسيطة يتراوح طولها فى المتوسط 400 حمض أميني وقد تزيد أو تقل عن ذلك بحوالى 200 حمض. ويستثنى من ذلك بعض التتابعات البروتينية الكبيرة.
- البروتينات الميكروبية أو حقيقيات النواة (النباتات أو الحيوانات) لها نفس الخصائص تقريباً.

أن تركيب الجينات المسئولة عن أنتاج البروتينات تكون أكثر تعقيداً في الحيوانات الراقية حيث تختلف أطوال الجينات في الإنسان عنها في الميكروبات (طولها في الميكروبات بضع مئات أوالاف من القواعد بينما في الأنسان قد تتعدى عشرات أومئات الآلاف من القواعد).
ملحوظة: ليس كل تتابعات الـ DNA ينتج عنها بروتين وداخل الجين نفسه هناك مناطق كثيرة عديمة الفائدة تسمى (junk DNA) ولا تنتج أي بروتين.
وتجدر الأشارة الى أن هناك 3 أنواع من تتابعات الـ DNA تدخل في تركيب الجين:
1- مناطق مشفرة للبروتينات (The protein coding region)
2- مناطق منظمة لعمل الجينات في العادة هي مناطق تسبق المناطق المشفرة للبروتينات (Requlatory region).
3- مناطق غير مشفرة للبروتينات (Untranslated regions)وهى مناطق لاتنتج بروتينات وتسمى (INTRONS) وهي توجد قبل أوبعد المناطق المشفرة للبروتين (EXONS) . وبناءاً على ذلك فالتعامل مع تتابعات الـ DNA تكون أكثر تعقيدا من التعامل مع تتابعات البروتين.

موقع الأكسبسى EXPASY هو قاعدة بيانات بروتينية متميزة تختص بتجميع تراكيب وأشكال ووظائف البروتينات ... more موقع الأكسبسى EXPASY هو قاعدة بيانات بروتينية متميزة تختص بتجميع تراكيب وأشكال ووظائف البروتينات كما يضم مجموعة كبيرة من الروابط لمواقع وبرامج متخصصة فى تحليل التتابعات البروتينية . قد تم إنشاءه وإدارته عن طريق أحد العلماء المشهورين في علم المعلوماتية الحيوية للبروتينات وهو البوفيسور Amos Bairoch. يضم هذا الموقع العديد من الروابط وقواعد بيانات أخرى.
EXPASY اختصارلعبارة Expert Protein Analysis System ويحتوي هذا الموقع المتقدم على قاعدتين هامتان جداً وهاتان القاعدتان هما Swiss port protein و TrEMBI مرتبطتين في قاعدة واحدة تسمى Uniport knowledgebase.

عند محاولة البحث عن تتابع بروتينى عن طريق الأسم فقط فى قاعدة البيانات ستجد العديد من التتابعات ... more عند محاولة البحث عن تتابع بروتينى عن طريق الأسم فقط فى قاعدة البيانات ستجد العديد من التتابعات الببروتينية التى تشبه أوتقارب أسم التتابع المرغوب فى قاعدة البيانات. لذلك يجب أن لاتنزعج أوتحتار فربما تكون هذه هى بداية الطريق لعمل بحث جيد والتوصل لنتائج مزهلة.
فمثلا إن كنت لم تسمع عن كلمة "HSF" قط في حياتك فأين تذهب من هذا؟
كيف يمكن معرفة المزيد عن هذا المصطلح الذي يبدو غامضاً مع هجاء غريب؟
كيف يمكنك أن تقرر بسرعة ما إذا كانت هذا البحث يمكن الأستمرار فيه فى سياق ما سبق لك معرفته عن الجينات الخاصة بك؟
سوف يتم الحصول على الجواب من زيارة الصفحة الرئيسية للمركز الوطنى للبيوتكنولوجى National Center or Biotechnology Information (NCBI)

ولكن ما هي المعلوماتية الحيوية؟ 1- التعريف الضيق: * المعلوماتية الحيوية الكلاسيكية: هو علم يستخدم... more ولكن ما هي المعلوماتية الحيوية؟
1- التعريف الضيق:
* المعلوماتية الحيوية الكلاسيكية: هو علم يستخدم في المقام الأول لتحليل التتابعات سواء بروتينية اوجينومية.
* المعلوماتية الحيوية الحديثة: (ما بعد علوم الجينوم) هوعلم يشتمل على دراسة المقارنة للجينومات المختلفة والحامض النووي وتحليل وظائف الجينومات وتحليل المجموعة البروتينية الكاملة للجينوم بالأضافة الى المعلوماتية الطبية.
2- التعريف الواسع للمعلوماتية الحيوية: هو عبارة عن تحليل كمية كبيرة من المعلومات البيولوجية سواء كانت تتابعات وراثية أو غيرها عن طريق الحاسب الآلي.

علم المعلوماتية الحيوية هو علم يستخدم الحاسب الألى والبرامج وقواعد البيانات لحل وشرح وتفسير العد... more علم المعلوماتية الحيوية هو علم يستخدم الحاسب الألى والبرامج وقواعد البيانات لحل وشرح وتفسير العديد من التساؤلات البيولوجية ويتعامل هذا العلم مع مجموعة البيانات البيولوجية الهائلة الناتجة من المشروعات العلمية الكبيرة مثل مشروع الجينوم البشرى . ويوجد مجالين كبيرين من العلوم البيولوجية يستخدم فيهما علم المعلوماتية الحيوية بشكل أساسى ومتزايد وهما علم الجينومية Genomics (دراسة التركيب والوظيفة للمجموع الكلى لجينات الكائن الحى) وعلم البروتيومية Proteomics (دراسة التركيب والوظيفة للمجموع الكلى لبروتينات الكائن الحى)

- (2012-2013) DAAD fellowship (Biotechnology Program) (100 % research),, Internationales Laborato... more - (2012-2013) DAAD fellowship (Biotechnology Program) (100 % research),, Internationales Laboratorium für Biotechnologie und Consulting, ILBC GmbH  Hermannswerder 14  D-14473 Potsdam, Germany.

(2002-2004) Member or Discovery Grant project A2724 from the Natural Sciences and Engineering Res... more (2002-2004) Member or Discovery Grant project A2724 from the Natural Sciences and Engineering Research Council of Canada NSERC.

(2005- 2008) Selected as a principal investigator to receive a BA/CSSP (The Center for Special St... more (2005- 2008) Selected as a principal investigator to receive a BA/CSSP (The Center for Special Studies and Programs) postdoctoral research grant , No. (050176), for the year 2005 from library of Alexandria to conduct the research titled "Molecular mechanisms of heat-tolerance in tomatoes and production of heat-tolerant t
omatoes by transformation" over a period of 24 months.

(2008-2009) Selected as a principal investigator deputy in the project entitled (Utilization of B... more (2008-2009) Selected as a principal investigator deputy in the project entitled (Utilization of Biotechnology and molecular breeding in the development of stress resistant tomato). Support of Academic Research in Zagazig University project.

(2012-2014). Selected as a principal investigator for establishing an ICTP center at Faculty of ... more (2012-2014). Selected as a principal investigator for establishing an ICTP center at Faculty of Agriculture, Zagazig University

(2012-2017) Principal Investigator of Zagazig University and Egypt in a project entitled " H3ABi... more (2012-2017) Principal Investigator of Zagazig University and Egypt in a project entitled " H3ABioNet: a sustainable African Bioinformatics Network for H3Africa", Funded from: The National Institutes of Health (NIH), USA, Supported by: The National Human Genome Research Institute of the National Institutes of Health under Award Number U41HG006941

In the current work, Different isolates of yeasts were obtained from different ecological habitan... more In the current work, Different isolates of yeasts were obtained from different ecological habitants of Egypt including upper and lower distracts. The genetic variation and genotyping was confirmed using DNA sequence analysis for ITS region (18S to 28S) of each isolates. The phylogenic analysis of each strain was confirmed with its counterpart in GenBank. Some commercially antifungal materials were coated on the surface of Iron oxide nanoparticles mix showed pronounced effect against the yeast isolates under investigations. Usage of combined antifungal materials with nanoparticles enhances the efficiency of such antifungal materials rather than its original form against microbial pathogenic strains.

Callus formation is considered one of the most important aspects for in vitro genetic manipulatio... more Callus formation is considered one of the most important aspects for in vitro genetic manipulation in plants. It has been used extensively during the last few years in many applications in tomatoes. This study aimed to examine the in vitro performance of diverse groups of tomato genotypes and the mode of inheritance of tomato callus induction. To measure the effects of many recommended culture media recipes for callus induction ability. SDS-PAGE and RAPD-PCR were used to find out any biochemical and molecular marker for this trait. Callus induction trait in different genotypes were detected through three catagories of genetically significant markers, morphological marker, protein-based markers and DNA- based Marker (RAPD). Both molecular and biochemical markers associated with this trait offered a promising alternative to morphological marker as they can be analyzed at a very early stage of plant development and mostly display codominant inheritance. Thus, complete information about this trait can be obtained very early to decide the appropriate selection and crosses required for production of plants with good callus induction phenotype to be used in many applications.

Plant tolerance to heat stress proved to be entirely dependent on the signaling flow of informati... more Plant tolerance to heat stress proved to be entirely dependent on the signaling flow of information by which the plant can sense the changes in its surrounding environment and signal its genes to respond by producing special proteins to protect it-self. Any changes or manipulations in this signaling flow of information will presumably lead to a modification in the genetic expression inside the plant cells, consequently, changing plant performance. Understanding these signaling events in response to heat may help us to produce heat tolerant plants capable to stand high temperature stress. In the present investigation, the results showed that a heat activated MAP kinase cascade, involving heat activated MAP kinase (HAMK), played an essential role in heat shock gene expression in tobacco BY-2 cells. In order to determine if heat activation of HAMK involved additional pathways of signaling we studied the upstream regulation of HAMK, including membrane fluidization and reorganization of cytoskeleton. The activation of HAMK and accumulation of heat responsive HSFs, HSP70 and HSP27 proteins were used as end-point markers in these experiments. It is concluded that the heat shock response, as measured by HAMK activation and heat shock proteins accumulation required PKC activation, membrane fluidization and reorganization of the cytoskeleton. A comparative bioinformatic explanation of similarities between tobacco heat shock genes and their counterparts in different organisms revealed a high degree of evolutionary conservation in the corresponding domains, indicating similar function in different species.

Bioinformatics is a pluri-disciplinary science focusing on the applications of computational meth... more Bioinformatics is a pluri-disciplinary science focusing on the applications of computational methods and mathematical statistics to molecular biology. Bioinformatics is also called:

Computational Biology (USA)
Computational Molecular Biology
Computational Genomics
Studying bioinformatics is so important because it is an opportunity to use some of the most interesting computational techniques to understand some of the deep mysteries of life and diseases and hopefully to contribute to cure some of the diseases that affect people. Bioinformatics combines algorithms in computer science and statistics to analyze, understand, and engage in hypothesis about the large repositories of collected biological data and knowledge. One of the most important topics in bioinformatics is sequence alignment or sequence comparison which we are concerned with it in this thesis.
In comparison of bimolecular sequence (i.e., those of DNA, RNA, and protein), regions of high sequence similarity often indicate significant functional or structural similarity as well. The same and related molecular structures and mechanisms are reused and modified during evolution, and thus show up repeatedly within either a single genome or across the genome of a wide variety of species. As a result, sequence comparison is the most commonly used method for inferring structure and biological function. Of course, sequence can have similar structure and function without exhibiting sequence similarity