Basel Khraiwesh

New York University Abu Dhabi · Center for Genomics and Systems Biology

Avicennia marina forests fulfill essential blue carbon and ecosystem services, including halting coastal erosion and supporting fisheries. Genetic studies of A. marina tissues could yield insight into halophyte adaptive strategies, empowering saline agriculture research. We compare transcriptomes from A. marina pneumatophores, stems, leaves, flower...

The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relation...

Poor prognoses remain the most challenging aspect of hepatocellular carcinoma (HCC) therapy. Consequently, alternative therapeutics are essential to control HCC. This study investigated the anticancer effects of safranal against HCC using in vitro, in silico, and network analyses. Cell cycle and immunoblot analyses of key regulators of cell cycle,...

Sodium (Na⁺) accumulation in the cytosol will result in ion homeostasis imbalance and toxicity of transpiring leaves. Studies of salinity tolerance in the diploid wheat ancestor Triticum monococcum showed that HKT1;5-like gene was a major gene in the QTL for salt tolerance, named Nax2. In the present study, we were interested in investigating the m...

Histogram plot of the phenotypic variation of the different traits (grain yield, average flag leaf width, average flag leaf length) measured. Wide dashed line represents the density distribution, while narrow ones represent the normal fitted distribution.

Phenotypic differences between lines carrying different alleles of the four SNPs (11_10610; 12_30476; 11_11186; 11_20272) associated with salt concentration (Na+) showing allelic estimate and directionality. The boxplot shows the differences of Na+ concentration for the four SNPs showing the different alleles of the SNP locus. The box shows the fir...

A midpoint rooted phylogenetic tree showing the relationship between the different lines (tolerant and sensitive) along with the HKT1;5 reference sequence for barley and other species was generated. The accession numbers are as follows: Oryza_indica (HQ162137.1), Oryza_glaberrima (JQ695813.1), Oryza_japonica (AP014957.1), Oryza_rufipogon (JQ695808....

Statistical analysis using the t-student test comparing the range of expression level (means ± SD, n = 3 biological replicates) in tolerant and sensitive lines and tissues (roots, sheaths and leaves) and P-value was reported (<0.05).

A summary of the putative 28 cis-elements along the 1 Kb sequence promoter of the HKT1;5 gene in two tolerant and two sensitive lines using the PlantCARE database.

Statistical analysis using the Dunn (1964) Kruskal-Wallis multiple comparison with p-value adjusted with the false discovery rate method for Na+/K+ ratio in roots, leaf sheaths and leaves at 0, 7, and 15 dSm−1.

Microalgae make up the largest and likely most diverse group of photosynthetic organisms in freshwater and marine systems. As new technologies are emerging for the study of bioactive compounds from microalgae, this group is drawing attention as a promising source of natural products that have wide applications in the food and pharmaceutical industr...

Diatoms, considered as one of the most diverse and largest groups of algae, can provide the means to reach a sustainable production of petrochemical substitutes and bioactive compounds. However, a prerequisite to achieving this goal is to increase the solar-to-biomass conversion efficiency of photosynthesis, which generally remains less than 5% for...

Cell concentration time course measurements.DOI: http://dx.doi.org/10.7554/eLife.25783.006

Phenotype microarray results for plates PM1, PM2, and PM3.DOI: http://dx.doi.org/10.7554/eLife.25783.015

Locations, confidence scores, and accession numbers for PLD and C2 Pfam domains in Chloroidium sp. UTEX 3007.DOI: http://dx.doi.org/10.7554/eLife.25783.018

Models of CDS1-3 in protein data bank (PDB) format.DOI: http://dx.doi.org/10.7554/eLife.25783.025

Cell diameter measurements.DOI: http://dx.doi.org/10.7554/eLife.25783.005

GC-MS results for Chloroidium sp. UTEX 3007 (Cm) and Chlamydomonas reinhardtii (Cre) intracellular polar metabolites.DOI: http://dx.doi.org/10.7554/eLife.25783.016

Table with QUAST results used in (b).DOI: http://dx.doi.org/10.7554/eLife.25783.021

Interactive Venn diagram that can be viewed at interactivenn.net to obtain Pfam sets for numbers displayed in Figure 6.DOI: http://dx.doi.org/10.7554/eLife.25783.022

Flow cytometry measurements.DOI: http://dx.doi.org/10.7554/eLife.25783.007

Amino acid residue alignment of CDS1-3.DOI: http://dx.doi.org/10.7554/eLife.25783.026

GC-FID results for major fatty acid species in Chloroidium sp. UTEX 3007.DOI: http://dx.doi.org/10.7554/eLife.25783.011

Fatty acid profiles of Chloroidium sp. UTEX 3007, Elaeis guineensis (Barcelos et al., 2015), and several other algal isolates (Lang et al., 2011).DOI: http://dx.doi.org/10.7554/eLife.25783.012

HPLC-MS base peak chromatograms (BPCs) for Chloroidium sp. UTEX 3007 and Chlamydomonas reinhardtii extracts.DOI: http://dx.doi.org/10.7554/eLife.25783.013

Predicted Pfam designations for each species in Figure 6.DOI: http://dx.doi.org/10.7554/eLife.25783.020

To investigate the phenomic and genomic traits that allow green algae to survive in deserts, we characterized a ubiquitous species, Chloroidium sp. UTEX 3007, which we isolated from multiple locations in the United Arab Emirates (UAE). Metabolomic analyses of Chloroidium sp. UTEX 3007 indicated that the alga accumulates a broad range of carbon sour...

With the advent of modern biotechnology, microorganisms from diverse lineages have been used to produce bio-based feedstocks and bioactive compounds. Many of these compounds are currently commodities of interest, in a variety of markets and their utility warrants investigation into improving their production through strain development. In this revi...

Metabolic networks are reconstructed to provide computational platforms to guide metabolic engineering experiments and explore fundamental questions on metabolism. Systems level analyses, such as interrogation of phylogenetic relationships within the network, can provide further guidance on modification of metabolic circuitries. Chlamydomonas reinh...

Through iterative cycles of selection, amplification, and mutagenesis, in vitro selection provides the ability to isolate molecules of desired properties and function from large pools (libraries) of random molecules with as many as 1016 distinct species. This review, in recognition of a quarter of century of scientific discoveries made through in v...

We would like to thank all the authors for their excellent contributions to this special issue.

The environmental impacts from consumption of fossil fuels have raised interest in finding renewable energy resources throughout the globe. Much focus has been placed on optimizing microalgae to efficiently produce compounds that can substitute for fossil fuels. However, the path to achieving economical feasibility of this substitution is likely to...

Changes in the environment, such as those caused by climate change, can exert stress on plant growth, diversity and ultimately global food security. Thus, focused efforts to fully understand plant response to stress are urgently needed in order to develop strategies to cope with the effects of climate change. Because Physcomitrella patens holds a k...

BACKGROUND: Oils and bioproducts extracted from cultivated algae can be used as sustainable feedstock for fuels, nutritional supplements, and other bio-based products. Discovery and isolation of new algal species and their subsequent optimization are needed to achieve economical feasibility for industrial applications. Here we describe and validate...

We performed whole-genome resequencing of 12 field isolates and eight commonly studied laboratory strains of the model organism Chlamydomonas reinhardtii to characterize genomic diversity and provide a resource for studies of natural variation. Our data support previous observations that Chlamydomonas is among the most diverse eukaryotic species. N...

http://www.biochemistry.org/Events/tabid/379/MeetingNo/IND122/view/Conference/Default.asp

The uniquely diverse metabolism of algae can make this group of organisms a prime target for biotechnological purposes and applications. To fully reap their biotechnological potential, molecular genetic techniques for manipulating algae must gain track and become more reliable. To this end, this chapter describes the currently available molecular g...

Genomic sequencing is the first step in a systems level study of an algal species, and sequencing studies have grown steadily in recent years. Completed sequences can be tied to algal phenotypes at a systems level through constructing genome-scale metabolic network models. Those models allow the prediction of algal phenotypes and genetic or metabol...

Synthetic Biology is an interdisciplinary approach combining biotechnology, evolutionary biology, molecular biology, systems biology and biophysics. While the exact definition of Synthetic Biology might still be debatable, its focus on design and construction of biological devices that perform useful functions is clear and of great utility to engin...

Sugarcane is an important tropical cash crop meeting 75% of world sugar demand and it is fast becoming an energy crop for the production of bio-fuel ethanol. A considerable area under sugarcane is prone to waterlogging which adversely affects both cane productivity and quality. In an effort to elucidate the genes underlying plant responses to water...

Small, non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. In plants, several classes of small RNAs with specific sizes and dedicated functions have evolved through a series of pathways. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (si...

Blueberry is a widely grown and easily perishable fruit crop. An efficient post-harvest handling is critical, and for that purpose gene technology methods have been part of ongoing programmes to improve crops with high food values such as blueberry. Here we report the isolation, cloning, characterization and differential expression levels of two cD...

Although RNA silencing has been studied primarily in model plants, advances in high-throughput sequencing technologies have enabled profiling of the small RNA components of many more plant species, providing insights into the ubiquity and conservatism of some miRNA-based regulatory mechanisms. Small RNAs of 20 to 24 nucleotides (nt) are important r...

RNA interference (RNAi) is a mechanism that regulates genes by either transcriptional (TGS) or posttranscriptional gene silencing (PTGS), required for genome maintenance and proper development of an organism. Small non-coding RNAs are the key players in RNAi and have been intensively studied in eukaryotes. In plants, several classes of small RNAs w...

Small, non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. In plants, several classes of small RNAs with specific sizes and dedicated functions have evolved through a series of pathways. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (si...

Small RNAs (20-24 nucleotides long and nonprotein coding) have been increasingly investigated. They are responsible for phenomena described as RNA interference (RNAi), cosuppression, gene silencing, or quelling. Major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biosynthesis. MiRNAs con...

MicroRNAs (miRNAs) are ∼21-nt-long small RNAs transcribed from endogenous MIR genes which form precursor RNAs with a characteristic hairpin structure. MiRNAs control the expression of cognate target genes by binding to reverse complementary sequences resulting in cleavage or translational inhibition of the target RNA. Artificial miRNAs (amiRNAs) ca...

Small, non coding RNAs (sRNAs) are a distinct class of regulatory RNAs in plants and animals controlling a variety of biological processes. Given the great impact of sRNAs in biology, recent studies in model seed-plant species, particularly in Arabidopsis thaliana, focused on the identification, biogenesis and functional analysis of sRNAs. In seed...

Dicer proteins are essential components of RNA interference pathways in eukaryotes as they are involved in the processing of endogenous microRNAs (miRNA), short interfering RNAs (siRNA), repeat-associated siRNAs (ra-siRNA) and trans-acting siRNAs (tasi-RNA). In animals, Dicer proteins are part of the RNA-induced silencing complex (RISC). However, s...

Lettuce is one of the most important salad crops grown in worldwide. Nitrogen (N) is the most frequent nutrient in crop production, it is well known that added N is distributed into the plant, the fixed fraction in the soil, leached into the water table or denitrified into the atmosphere. Therefore any technique that improves the N absorption effic...

MicroRNAs (miRNAs) are ~21 nt long small RNAs transcribed from endogenous MIR genes which form precursor RNAs with a characteristic hairpin structure. miRNAs control the expression of cognate target genes by binding to reverse complementary sequences resulting in cleavage or translational inhibition of the target RNA. Artificial miRNAs (amiRNAs) ca...

RNA interference (RNAi) is a mechanism regulating gene transcript levels either by transcriptional gene silencing or by posttranscriptional gene silencing, which act in the genome maintenance and the regulation of gene expression which is typically inferred from measuring transcript abundance. Nuclear "run-on" (or "run-off") transcription assays ha...

RNA interference (RNAi) is a mechanism regulating gene transcript levels by either transcriptional gene silencing (TGS) or by posttranscriptional gene silencing (PTGS), which acts in genome maintenance and the regulation of development. This book show the role of Dicer proteins in the moss Physcomitrella patens, which has four Dicers (DICER-LIKE 1a...

The effects of aminoethoxyvinylglycine (AVG; ReTain®) and 1-methylcyclopropene (1-MCP; SmartFresh™) on the biosynthesis of aroma volatiles and overall quality in 'Delbarde Estivale', an early apple variety, are reported for the first time. Apple fruit were treated with AVG 3 weeks before commercial harvest, following standard procedures. 1-MCP was...

The aim of this study was to assess the effect of AVG- and 1-MCP treatment on the postharvest behaviour of ‘Delbarde Estivale’ apple kept at room temperature, with special emphasis on the biosynthesis of odor volatiles. Fruits were harvested at the proper time, and subjected to AVG (ReTain®) treatment 3 weeks before harvest date. Another lot of fru...

Blueberry (Vaccinium corymbosum) is among the richest fruits in ascorbic acid (AA), which is the most important antioxidant involved in the ascorbate-glutathione cycle. In this cycle monodehydroascorbate reductase (MDAR) is the enzymatic component involved in the regeneration of reduced ascorbate. Here we report on the isolation of a full-length cD...

Blueberry is considered as one of the richest fruit types in ascorbic acid (AA), and is highly recommended for a healthy diet. In plant tissues mono-dehydroascorbate reductase (MDAR) is the enzyme involved in the regeneration of oxidized ascorbate, which is produced after the detoxification of free radicals. Taking into account the importance of th...

MicroRNAs (miRNAs) control gene expression in animals and plants. Like another class of small RNAs, siRNAs, they affect gene expression posttranscriptionally. While siRNAs in addition act in transcriptional gene silencing, a role of miRNAs in transcriptional regulation has been less clear. We show here that in moss Physcomitrella patens mutants wit...

MicroRNAs (miRNAs) are approximately 21-nucleotide-long RNAs processed from nuclear-encoded transcripts, which include a characteristic hairpin-like structure. MiRNAs control the expression of target transcripts by binding to reverse complementary sequences directing cleavage or translational inhibition of the target RNA. Artificial miRNAs (amiRNAs...

A field study was conducted at two locations (Jordan valley and Al-Jubeiha) with different rainfall levels, altitudes and temperature ranges. The study was established to evaluate the optimum planting density, nitrogen (N) form and irrigation level to attain the best quality of lettuce crop in terms of minimum nitrate (NO3) content and to minimise...

A field study was conducted in Jordan Valley and Al-Jubeiha, Jordan, during 2000/2001 to study the optimum planting density, form of nitrogen and irrigation regime for lettuce cv. Amar. Seeds were sown one month before transplanting. A total of 100 kg pure N/ha was applied in the form of Ca(NO3)2, (NH4)2SO4, and CO(NH2)2. The N fertilizer was appli...