In Vitro Propagation of Three Date Palm (Phoenix dactylifera L.) Varieties Using Immature Female Inflorescences.

Immature female inflorescences are promising materials for use as explants for the tissue culture of date palm. Four types of MS media were used in this study during the four micropropagation stages-starting media (SM), maturation media (MM), multiplication media (PM) and rooting media (RM)-to micropropagate three elite date palm varieties, Amri, Magdoul and Barhy using the immature female inflorescences as explant. The highest percentage of callus induction in all the varieties studied was obtained on the SM1 (9 µM 2,4-D + 5.7 µM IAA + 10 µM NAA). Culturing on the MM1 (4.5 µM 2,4-D + 9.8 µM 2-iP + 1.5 AC) allowed us to obtain the best value in terms of callus weight. After culturing on the PM1 (4.4 µM BA + 9.8 µM 2-iP) produced the highest numbers of somatic embryos and shoots. The explants on RM2 (0.5 µM NAA + 1.25 µM IBA + 3 g AC) showed the highest root numbers and root lengths, while the highest shoot length was achieved on RM3 (0.5 µM NAA + 0.5 µM IBA + 3 g AC). The Amri variety presented the best response among the three varieties in all parameters, followed by the Magdoul and Barhy varieties. In all the stages of micropropagation, the analysis of variance revealed highly significant variations among varieties and culture media, and a significant difference in the number of roots during the rooting stage. The results also showed non-significant differences in the interaction between varieties and culture media, except for shoot length in the rooting stage. The results also reveal the broad sense heritability ranging from low to high for the measured parameters. It can be concluded that the immature female inflorescences can be used as a productive explant source for successful date palm micropropagation using the SM1, MM1, PM1 and RM2 culture media. It can also be concluded that the success of date palm micropropagation not only depends on the concentrations of growth regulators, but also on their types.

Health-promoting value and food applications of black cumin essential oil: an overview.

Black cumin (Nigella sativa L.) seeds and its essential oil have been widely used in functional foods, nutraceuticals and pharmaceutical products. Analysis of Nigella sativa essential oil using GC and GC-MS resulted in the identification of many bioactive compounds representing ca. 85 % of the total content. The main compounds included p-cymene, thymoquinone, α-thujene, longifolene, ß-pinene, α-pinene and carvacrol. Nigella sativa essential oil exhibited different biological activities including antifungal, antibacterial and antioxidant potentials. Nigella sativa essential oil showed complete inhibition zones against different Gram-negative and Gram-positive bacteria including Penicillium citrinum Bacillus cereus, Bacillus subtilis, Staphylococcus aureus and Pseudomonas aeruginosa. The essential oil showed stronger antioxidant potential in comparison with synthetic antioxidants (i.e., BHA and BHT) in a rapeseed oil model system. The oil exhibited also stronger radical scavenging activity against DPPH·radical in comparison with synthetic antioxidants. The diversity of applications to which Nigella sativa essential oil can be put gives this oil industrial importance.

RNA-Seq analysis of the wild barley (H. spontaneum) leaf transcriptome under salt stress.

Wild salt-tolerant barley (Hordeum spontaneum) is the ancestor of cultivated barley (Hordeum vulgare or H. vulgare). Although the cultivated barley genome is well studied, little is known about genome structure and function of its wild ancestor. In the present study, RNA-Seq analysis was performed on young leaves of wild barley treated with salt (500mM NaCl) at four different time intervals. Transcriptome sequencing yielded 103 to 115 million reads for all replicates of each treatment, corresponding to over 10 billion nucleotides per sample. Of the total reads, between 74.8 and 80.3% could be mapped and 77.4 to 81.7% of the transcripts were found in the H. vulgare unigene database (unigene-mapped). The unmapped wild barley reads for all treatments and replicates were assembled de novo and the resulting contigs were used as a new reference genome. This resulted in 94.3 to 95.3% of the unmapped reads mapping to the new reference. The number of differentially expressed transcripts was 9277, 3861 of which were unigene-mapped. The annotated unigene- and de novo-mapped transcripts (5100) were utilized to generate expression clusters across time of salt stress treatment. Two-dimensional hierarchical clustering classified differential expression profiles into nine expression clusters, four of which were selected for further analysis. Differentially expressed transcripts were assigned to the main functional categories. The most important groups were "response to external stimulus" and "electron-carrier activity". Highly expressed transcripts are involved in several biological processes, including electron transport and exchanger mechanisms, flavonoid biosynthesis, reactive oxygen species (ROS) scavenging, ethylene production, signaling network and protein refolding. The comparisons demonstrated that mRNA-Seq is an efficient method for the analysis of differentially expressed genes and biological processes under salt stress.

Bioinformatics education--perspectives and challenges out of Africa.

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.

Construction of naïve camelids VHH repertoire in phage display-based library.

Camelids have unique antibodies, namely HCAbs (VHH) or commercially named Nanobodies(®) (Nb) that are composed only of a heavy-chain homodimer. As libraries based on immunized camelids are time-consuming, costly and likely redundant for certain antigens, we describe the construction of a naïve camelid VHHs library from blood serum of non-immunized camelids with affinity in the subnanomolar range and suitable for standard immune applications. This approach is rapid and recovers VHH repertoire with the advantages of being more diverse, non-specific and devoid of subpopulations of specific antibodies, which allows the identification of binders for any potential antigen (or pathogen). RNAs from a number of camelids from Saudi Arabia were isolated and cDNAs of the diverse vhh gene were amplified; the resulting amplicons were cloned in the phage display pSEX81 vector. The size of the library was found to be within the required range (10(7)) suitable for subsequent applications in disease diagnosis and treatment. Two hundred clones were randomly selected and the inserted gene library was either estimated for redundancy or sequenced and aligned to the reference camelid vhh gene (acc. No. ADE99145). Results indicated complete non-specificity of this small library in which no single event of redundancy was detected. These results indicate the efficacy of following this approach in order to yield a large and diverse enough gene library to secure the presence of the required version encoding the required antibodies for any target antigen. This work is a first step towards the construction of phage display-based biosensors useful in disease (e.g., TB or tuberculosis) diagnosis and treatment.

Environmental stress activation of plant long-terminal repeat retrotransposons.

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.

Retrotransposon-based molecular markers for assessment of genomic diversity.

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).

Transposable elements domesticated and neofunctionalized by eukaryotic genomes.

Whole genome sequencing has provided a massive amount of information about the origin, diversity and genomic impact of repetitive DNA sequences (repDNA). Among the many classes of repDNA, prokaryotic transposable elements (TEs) replicate, move, amplify and accumulate in invaded genomes and thus represent the major force in restructuring host genes and genomes during evolution. Similar to retroviruses, autonomous TEs became part of the host genomes, and after their molecular domestication, they became functional genes (genomic fossils) in eukaryotic genomes. In this review, examples of the domestication events are discussed, some of which are known to be induced by biotic and abiotic stressors.

Control of glycerol biosynthesis under high salt stress in Arabidopsis.

Loss-of-function and gain-of-function approaches were utilised to detect the physiological importance of glycerol biosynthesis during salt stress and the role of glycerol in conferring salt tolerance in Arabidopsis. The salt stress experiment involved wild type (WT) and transgenic Arabidopsis overexpressing the yeast GPD1 gene (analogue of Arabidopsis GLY1 gene). The experiment also involved the Arabidopsis T-DNA insertion mutants gly1 (for suppression of glycerol 3-phosphate dehydrogenase or G3PDH), gli1 (for suppression of glycerol kinase or GK), and act1 (for suppression of G3P acyltransferase or GPAT). We evaluated salt tolerance levels, in conjunction with glycerol and glycerol 3-phosphate (G3P) levels and activities of six enzymes (G3PDH, ADH (alcohol dehydrogenase), ALDH (aldehyde dehydrogenase), GK, G3PP (G3P phosphatase) and GLYDH (glycerol dehydrogenase)) involved in the glycerol pathway. The GPD1 gene was used to overexpress G3PDH, a cytosolic NAD+-dependent key enzyme of cellular glycerol biosynthesis essential for growth of cells under abiotic stresses. T2 GPD1-transgenic plants and those of the two mutants gli1 and act1 showed enhanced salt tolerance during different growth stages as compared with the WT and gly1 mutant plants. These results indicate that the participation of glycerol, rather than G3P, in salt tolerance in Arabidopsis. The results also indicate that the gradual increase in glycerol levels in T2 GPD1-transgenic, and gli1 and act1 mutant plants as NaCl level increases whereas they dropped at 200mM NaCl. However, the activities of the G3PDH, GK, G3PP and GLYDH at 150 and 200mM NaCl were not significantly different. We hypothesise that mechanism(s) of glycerol retention/efflux in the cell are affected at 200mM NaCl in Arabidopsis.