Hussien Alameldin

The khmer software package: enabling efficient nucleotide sequence analysis

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/.

Transgene Pyramiding of the HVA1 and mtlD in T3 Maize (Zea mays L.) Plants Confers Drought and Salt Tolerance, along with an Increase in Crop Biomass

The pBY520 containing the Hordeum vulgare  HVA1 regulated by the rice actin promoter (Act1 5′) or the JS101 containing the bacterial mannitol-1-phosphate dehydrogenase (mtlD) also regulated by rice Act1 5′ and a combination of these two plasmids were transferred into the maize genome, and their stable expressions were confirmed through fourth generations. Plants transcribing a combination of the HVA1+mtlD showed higher leaf relative water content (RWC) and greater plant survival as compared with their single transgene transgenic plants and with their control plants under drought stress. When exposed to various salt concentrations, plants transcribing the HVA1+mtlD showed higher fresh and dry shoot and dry root matter as compared with single transgene transgenic plants and with their control plants. Furthermore, the leaves of plants expressing the mtlD accumulated higher levels of mannitol. Plants expressing the HVA1+mtlD improved plant survival rate under drought stress and enhanced shoot and root biomass under salt stress when compared with single transgene transgenic plants and with their wild-type control plants. The research presented here shows the effectiveness of coexpressing of two heterologous abiotic stress tolerance genes in the maize genome. Future field tests are needed to assure the application of this research.

Towards Cellulosic Biofuels Evolution: Using the Petro-Industry Model

While the United States owns only three percent (3%) of the total world petro-oil reserves, it uses over twenty-five percent (25%) of its total global output on an annual basis. Furthermore, the US petro-oil consumption is expected to double by 2050. While the sources for US oil are innumerable, many of the countries which contribute vastly to the US oil supply are economically and politically unstable. This has led to concerns about the security of the US oil supply, since a major political disturbance could be devastating. This article describes a model for the production of affordable and renewable biofuels as well as recombinant high-value industrial co-products from crop residues—waste products in today’s farming environment without competition between commodities critical to global food and feed supplies. This model represents a uniquely attractive business case giving the environmental and economic advantage it would have over petro-oil derived fuels and byproducts. Moreover, it can assist the developed nations to reduce their dependence on imported petro-oil fuels as well as improves the lives of agriculture producers in developed and developing nations around the globe.

Bacterial Mannitol-1-Phophate Dehydrogenase (mtlD) Transgene, Confers Salt Tolerance in the Fourth Generation Transgenic Maize (Zea Mays. L)Plants

About 15% of global agricultural lands are exposed to high salinity, resulting in low crop yields and reduced food supplies. Attempts to develop salinity tolerant crops via selection and breeding have not been sufficient. Bacterial mannitol-1-phophate Dehydrogenase (mtlD) has been known for its tolerance to salinity. Maize is the third cereal crop (after wheat and rice) that is severely affected by soil salinity. We have genetically engineered maize plants with the bacterial mtlD gene, confirmed the integration and expression of this transgene in upto forth progenies, and have confirmed that transgenic plants transcribing the mtlD gene have higher rate of photosynthesis and are more tolerant to different concentrations of NaCl (especially at 200 mM level) as compared with their wild-type nontransgenic control plants.

Developing transgenic wheat to encounter rusts and powdery mildew by overexpressing barley chi26 gene for fungal resistance

BackgroundThe main aim of this study was to improve fungal resistance in bread wheat via transgenesis. Transgenic wheat plants harboring barley chitinase (chi26) gene, driven by maize ubi promoter, were obtained using biolistic bombardment, whereas the herbicide resistance gene, bar, driven by the CaMV 35S promoter was used as a selectable marker.ResultsMolecular analysis confirmed the integration, copy number, and the level of expression of the chi26 gene in four independent transgenic events. Chitinase enzyme activity was detected using a standard enzymatic assay. The expression levels of chi26 gene in the different transgenic lines, compared to their respective controls, were determined using qRT-PCR. The transgene was silenced in some transgenic families across generations. Gene silencing in the present study seemed to be random and irreversible. The homozygous transgenic plants of T4, T5, T6, T8, and T9 generations were tested in the field for five growing seasons to evaluate their resistance against rusts and powdery mildew. The results indicated high chitinase activity at T0 and high transgene expression levels in few transgenic families. This resulted in high resistance against wheat rusts and powdery mildew under field conditions. It was indicated by proximate and chemical analyses that one of the transgenic families and the non-transgenic line were substantially equivalent.ConclusionTransgenic wheat with barley chi26 was found to be resistant even after five generations under artificial fungal infection conditions. One transgenic line was proved to be substantially equivalent as compared to the non-transgenic control.

Isolation, characterization, cloning and bioinformatics analysis of a novel receptor from black cut worm ( Agrotis ipsilon ) of Bacillus thuringiensis vip 3Aa toxins

Black cutworm (BCW) is an economically important lepidopteran insect. The control of this insect by a Bt toxin and the understanding of the interaction between the Bt toxin and its receptor molecule were the objectives of this research work. A gene coding for a Vip3A receptor molecule was identified, characterized, and cloned, from the brush border membrane vesicles (BBMV) of the BCW. The nucleotide sequence analysis of the cloned putative Vip3A-receptor gene revealed that the gene was 1.3-kb long and exhibited no homology with any gene in the gene bank. We succeeded in identifying and characterizing most of the Vip3A-receptor gene sequence; and the nucleotide sequence analysis of the cloned putative Vip3A-receptor gene (accession no. KX858809) revealed about 92% of the expected sequence was recovered, which exhibited no homology with any gene in the GenBank.

Production of the Human Anti-Metastatic Melonoma Interleukin-2 in Maize Vegetative Biomass for Clinical Use

The E.coli produced recombinant human interleukin-2 (rhIL-2) has been approved by the Food and Drug Administration for the immunotherapeutic treatment of the end-stage metastatic melanoma and renal cell cancer. However, the E.coli produced rhIL-2 is very expensive (~

The khmer software package: enabling efficient nucleotide sequence analysis [version 1; referees: 2 approved, 1 approved with reservations]

11,400 USD per treatment). In the present study, we explored the feasibility of producing rhIL-2 in transgenic Zea mays (maize) vegetative biomass instead of its production in E. coli because (1) maize vegetative biomass is abundant, (2) maize can cheaply produce recombinant proteins while obtaining its energy from freely available sun via photosynthesis, has an easy scale-up via reproduction system, can be easily grown by farmers in the field with minimum level of training, and has conserved protein folding machinery including glycosylation similar to that of human. The human hIL-2 gene was codon optimized to maximize its expression in plants. A plasmid construct containing the rhIL-2 regulated by a rubisco green-specific promoter, an endoplasmic reticulum-specific signal peptide, 6-histodin tag was developed and nos terminator The construct was transferred into the maize genome via the gene gun bombardment, and fertile plants developed. Molecular analysis confirmed that the human IL-2 had integrated, transcribed and translated in up to the 4th (T3) generation maize plants. When the same gene construct was transferred into the tobacco genome and the rhIL-2 was purified and its biological activity compared with the FDA approved commercially available E coli- produced version against the marine splenic CD4+ the mice cells, the plant-produced version was as effective as the commercially available E. coli-produced version. Research is needed to test the rhIL-2 producing maize in the field, and to perform preclinical and clinical trial for its potential commercial release.