Publications by authors named "Fozia Saleem"

9 Publications

  • Page 1 of 1

Rewilding crops for climate resilience: economic analysis and de novo domestication strategies.

J Exp Bot 2021 Jun 11. Epub 2021 Jun 11.

International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China.

To match predicted population growth, annual food production should be doubled by 2050. This is not achievable by the current agronomical and breeding practices, due to impact of climate changes and associated abiotic stresses on agricultural production systems. Here, we analyze an impact of global climate trends on crop productivity and show that the overall loss in the crop production from climate-driven abiotic stresses may exceed US$ 170Bln p.a. and represents a major threat to global food security. We also show that abiotic stress tolerance has been present in wild progenitors of modern crops but was lost during their domestication. We argue for a major shift in our paradigm of crop breeding, focusing on the climate resilience, and call for a broader use of wild relatives as a major tool in this process. We argue that, while molecular tools are currently in place to harness a potential of climate-resilient genes present in wild relatives, a complex polygenic nature of tolerance traits remains a major bottleneck in this process. Future research efforts should be focused not only on finding appropriate wild relatives but also on development efficient cell-based high throughput phenotyping platforms allowing to assess in planta operation of key genes.
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http://dx.doi.org/10.1093/jxb/erab276DOI Listing
June 2021

Metabolomics: A Powerful Tool to Study the Complexity of Wheat Metabolome.

Protein Pept Lett 2021 Jan 27. Epub 2021 Jan 27.

Department of Biological Sciences, University of Alberta, Edmonton, AB. Canada.

Wheat is a widely cultivated cereal, consumed by nearly 80% of the total population in the world. Although wheat is growing on 215 million hectares annually, its production is still inadequate to meet the future demand of feeding the 10 billion human population. Global food security is the biggest challenge as climate change is threatening crop production. There is a need to fast-track the wheat breeding by devising modern biotechnological tools. Climate-smart wheat having greater stress resilience, better adaptability and improved agronomic traits are vital to guarantee food security. Substantial understanding and knowledge of vital biochemical pathways and regulatory networks is required for achieving stress resilience in wheat. Metabolomics has emerged as a fascinating technology to speed up the crop improvement programs by deciphering unique metabolic pathways for abiotic/biotic stress tolerance. State-of-the-art metabolomics tools such as nuclear magnetic resonance (NMR) and advanced mass spectrometry (MS) has opened new horizons for detailed analysis of wheat metabolome. The identification of unique metabolic pathways offers various types of stress tolerance and helps to screen the elite wheat cultivars. In this review, we summarize the applications of metabolomics to probe the stressresponsive metabolites and stress-inducive regulatory pathways that govern abiotic/biotic stress tolerance in wheat and highlight the significance of metabolic profiling to characterize wheat agronomics traits. Furthermore, we also describe the potential of metabolomics-assisted speed breeding for wheat improvement and propose future directions.
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http://dx.doi.org/10.2174/0929866528666210127153532DOI Listing
January 2021

Metabolomics: A Way Forward for Crop Improvement.

Metabolites 2019 Dec 14;9(12). Epub 2019 Dec 14.

Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan.

Metabolomics is an emerging branch of "omics" and it involves identification and quantification of metabolites and chemical footprints of cellular regulatory processes in different biological species. The metabolome is the total metabolite pool in an organism, which can be measured to characterize genetic or environmental variations. Metabolomics plays a significant role in exploring environment-gene interactions, mutant characterization, phenotyping, identification of biomarkers, and drug discovery. Metabolomics is a promising approach to decipher various metabolic networks that are linked with biotic and abiotic stress tolerance in plants. In this context, metabolomics-assisted breeding enables efficient screening for yield and stress tolerance of crops at the metabolic level. Advanced metabolomics analytical tools, like non-destructive nuclear magnetic resonance spectroscopy (NMR), liquid chromatography mass-spectroscopy (LC-MS), gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography (HPLC), and direct flow injection (DFI) mass spectrometry, have sped up metabolic profiling. Presently, integrating metabolomics with post-genomics tools has enabled efficient dissection of genetic and phenotypic association in crop plants. This review provides insight into the state-of-the-art plant metabolomics tools for crop improvement. Here, we describe the workflow of plant metabolomics research focusing on the elucidation of biotic and abiotic stress tolerance mechanisms in plants. Furthermore, the potential of metabolomics-assisted breeding for crop improvement and its future applications in speed breeding are also discussed. Mention has also been made of possible bottlenecks and future prospects of plant metabolomics.
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http://dx.doi.org/10.3390/metabo9120303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6969922PMC
December 2019

Modern Trends in Plant Genome Editing: An Inclusive Review of the CRISPR/Cas9 Toolbox.

Int J Mol Sci 2019 Aug 19;20(16). Epub 2019 Aug 19.

Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad 38040, Pakistan.

Increasing agricultural productivity via modern breeding strategies is of prime interest to attain global food security. An array of biotic and abiotic stressors affect productivity as well as the quality of crop plants, and it is a primary need to develop crops with improved adaptability, high productivity, and resilience against these biotic/abiotic stressors. Conventional approaches to genetic engineering involve tedious procedures. State-of-the-art OMICS approaches reinforced with next-generation sequencing and the latest developments in genome editing tools have paved the way for targeted mutagenesis, opening new horizons for precise genome engineering. Various genome editing tools such as transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and meganucleases (MNs) have enabled plant scientists to manipulate desired genes in crop plants. However, these approaches are expensive and laborious involving complex procedures for successful editing. Conversely, CRISPR/Cas9 is an entrancing, easy-to-design, cost-effective, and versatile tool for precise and efficient plant genome editing. In recent years, the CRISPR/Cas9 system has emerged as a powerful tool for targeted mutagenesis, including single base substitution, multiplex gene editing, gene knockouts, and regulation of gene transcription in plants. Thus, CRISPR/Cas9-based genome editing has demonstrated great potential for crop improvement but regulation of genome-edited crops is still in its infancy. Here, we extensively reviewed the availability of CRISPR/Cas9 genome editing tools for plant biotechnologists to target desired genes and its vast applications in crop breeding research.
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http://dx.doi.org/10.3390/ijms20164045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6720679PMC
August 2019

Recombinant mouse prion protein alone or in combination with lipopolysaccharide alters expression of innate immunity genes in the colon of mice.

Prion 2015 ;9(1):59-73

a Department of Agricultural, Food and Nutritional Science ; University of Alberta , Edmonton , AB , Canada ;

The objectives of this study were to test whether recombinant mouse (mo)PrP alone or in combination with LPS or under simulated endotoxemia would affect expression of genes related to host inflammatory and antimicrobial responses. To test our hypotheses colon tissues were collected from 16 male mice (FVB/N strain) and mounted in an Ussing chamber. Application of moPrP to the mucosal side of the colon affected genes related to TLR- and NLR- signaling and antimicrobial responses. When LPS was added on the mucosal side of the colon, genes related to TLR, Nlrp3 inflammasome, and iron transport proteins were over-expressed. Addition of LPS to the serosal side of the colon up-regulated genes related to TLR- and NLR-signaling, Nlrp3 inflammasome, and a chemokine. Treatment with both moPrP and LPS to the mucosal side of the colon upregulated genes associated with TLR, downstream signal transduction (DST), inflammatory response, attraction of dendritic cells to the site of inflammation, and the JNK-apoptosis pathway. Administration of moPrP to the mucosal side and LPS to the serosal side of the colon affected genes related to TLR- and NLR-signaling, DST, apoptosis, inflammatory response, cytokines, chemokines, and antimicrobial peptides. Overall this study suggests a potential role for moPrP as an endogenous 'danger signal' associated with activation of colon genes related to innate immunity and antibacterial responses.
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http://dx.doi.org/10.1080/19336896.2015.1019694DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4601253PMC
February 2016

Lipopolysaccharide induced conversion of recombinant prion protein.

Prion 2014 Mar-Apr;8(2). Epub 2014 May 12.

Department of Biological Sciences; University of Alberta; Edmonton, AB Canada; Department of Computing Science; University of Alberta; Edmonton, AB Canada; National Institute for Nanotechnology; Edmonton, AB Canada.

The conformational conversion of the cellular prion protein (PrP(C)) to the β-rich infectious isoform PrP(Sc) is considered a critical and central feature in prion pathology. Although PrP(Sc) is the critical component of the infectious agent, as proposed in the "protein-only" prion hypothesis, cellular components have been identified as important cofactors in triggering and enhancing the conversion of PrP(C) to proteinase K resistant PrP(Sc). A number of in vitro systems using various chemical and/or physical agents such as guanidine hydrochloride, urea, SDS, high temperature, and low pH, have been developed that cause PrP(C) conversion, their amplification, and amyloid fibril formation often under non-physiological conditions. In our ongoing efforts to look for endogenous and exogenous chemical mediators that might initiate, influence, or result in the natural conversion of PrP(C) to PrP(Sc), we discovered that lipopolysaccharide (LPS), a component of gram-negative bacterial membranes interacts with recombinant prion proteins and induces conversion to an isoform richer in β sheet at near physiological conditions as long as the LPS concentration remains above the critical micelle concentration (CMC). More significant was the LPS mediated conversion that was observed even at sub-molar ratios of LPS to recombinant ShPrP (90-232).
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189894PMC
http://dx.doi.org/10.4161/pri.28939DOI Listing
April 2015

The human urine metabolome.

PLoS One 2013 4;8(9):e73076. Epub 2013 Sep 4.

Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.

Urine has long been a "favored" biofluid among metabolomics researchers. It is sterile, easy-to-obtain in large volumes, largely free from interfering proteins or lipids and chemically complex. However, this chemical complexity has also made urine a particularly difficult substrate to fully understand. As a biological waste material, urine typically contains metabolic breakdown products from a wide range of foods, drinks, drugs, environmental contaminants, endogenous waste metabolites and bacterial by-products. Many of these compounds are poorly characterized and poorly understood. In an effort to improve our understanding of this biofluid we have undertaken a comprehensive, quantitative, metabolome-wide characterization of human urine. This involved both computer-aided literature mining and comprehensive, quantitative experimental assessment/validation. The experimental portion employed NMR spectroscopy, gas chromatography mass spectrometry (GC-MS), direct flow injection mass spectrometry (DFI/LC-MS/MS), inductively coupled plasma mass spectrometry (ICP-MS) and high performance liquid chromatography (HPLC) experiments performed on multiple human urine samples. This multi-platform metabolomic analysis allowed us to identify 445 and quantify 378 unique urine metabolites or metabolite species. The different analytical platforms were able to identify (quantify) a total of: 209 (209) by NMR, 179 (85) by GC-MS, 127 (127) by DFI/LC-MS/MS, 40 (40) by ICP-MS and 10 (10) by HPLC. Our use of multiple metabolomics platforms and technologies allowed us to identify several previously unknown urine metabolites and to substantially enhance the level of metabolome coverage. It also allowed us to critically assess the relative strengths and weaknesses of different platforms or technologies. The literature review led to the identification and annotation of another 2206 urinary compounds and was used to help guide the subsequent experimental studies. An online database containing the complete set of 2651 confirmed human urine metabolite species, their structures (3079 in total), concentrations, related literature references and links to their known disease associations are freely available at http://www.urinemetabolome.ca.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0073076PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762851PMC
April 2014

Detailed biophysical characterization of the acid-induced PrP(c) to PrP(β) conversion process.

Biochemistry 2011 Feb 27;50(7):1162-73. Epub 2011 Jan 27.

Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada T6G 2E8.

Prions are believed to spontaneously convert from a native, monomeric highly helical form (called PrP(c)) to a largely β-sheet-rich, multimeric and insoluble aggregate (called PrP(sc)). Because of its large size and insolubility, biophysical characterization of PrP(sc) has been difficult, and there are several contradictory or incomplete models of the PrP(sc) structure. A β-sheet-rich, soluble intermediate, called PrP(β), exhibits many of the same features as PrP(sc) and can be generated using a combination of low pH and/or mild denaturing conditions. Studies of the PrP(c) to PrP(β) conversion process and of PrP(β) folding intermediates may provide insights into the structure of PrP(sc). Using a truncated, recombinant version of Syrian hamster PrP(β) (shPrP(90-232)), we used NMR spectroscopy, in combination with other biophysical techniques (circular dichroism, dynamic light scattering, electron microscopy, fluorescence spectroscopy, mass spectrometry, and proteinase K digestion), to characterize the pH-driven PrP(c) to PrP(β) conversion process in detail. Our results show that below pH 2.8 the protein oligomerizes and conversion to the β-rich structure is initiated. At pH 1.7 and above, the oligomeric protein can recover its native monomeric state through dialysis to pH 5.2. However, when conversion is completed at pH 1.0, the large oligomer "locks down" irreversibly into a stable, β-rich form. At pH values above 3.0, the protein is amenable to NMR investigation. Chemical shift perturbations, NOE, amide line width, and T(2) measurements implicate the putative "amylome motif" region, "NNQNNF" as the region most involved in the initial helix-to-β conversion phase. We also found that acid-induced PrP(β) oligomers could be converted to fibrils without the use of chaotropic denaturants. The latter finding represents one of the first examples wherein physiologically accessible conditions (i.e., only low pH) were used to achieve PrP conversion and fibril formation.
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http://dx.doi.org/10.1021/bi101435cDOI Listing
February 2011

Palmitoylation gates phosphorylation-dependent regulation of BK potassium channels.

Proc Natl Acad Sci U S A 2008 Dec 19;105(52):21006-11. Epub 2008 Dec 19.

Centre for Integrative Physiology, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh EH89XD, Untied Kingdom.

Large conductance calcium- and voltage-gated potassium (BK) channels are important regulators of physiological homeostasis and their function is potently modulated by protein kinase A (PKA) phosphorylation. PKA regulates the channel through phosphorylation of residues within the intracellular C terminus of the pore-forming alpha-subunits. However, the molecular mechanism(s) by which phosphorylation of the alpha-subunit effects changes in channel activity are unknown. Inhibition of BK channels by PKA depends on phosphorylation of only a single alpha-subunit in the channel tetramer containing an alternatively spliced insert (STREX) suggesting that phosphorylation results in major conformational rearrangements of the C terminus. Here, we define the mechanism of PKA inhibition of BK channels and demonstrate that this regulation is conditional on the palmitoylation status of the channel. We show that the cytosolic C terminus of the STREX BK channel uniquely interacts with the plasma membrane via palmitoylation of evolutionarily conserved cysteine residues in the STREX insert. PKA phosphorylation of the serine residue immediately upstream of the conserved palmitoylated cysteine residues within STREX dissociates the C terminus from the plasma membrane, inhibiting STREX channel activity. Abolition of STREX palmitoylation by site-directed mutagenesis or pharmacological inhibition of palmitoyl transferases prevents PKA-mediated inhibition of BK channels. Thus, palmitoylation gates BK channel regulation by PKA phosphorylation. Palmitoylation and phosphorylation are both dynamically regulated; thus, cross-talk between these 2 major posttranslational signaling cascades provides a mechanism for conditional regulation of BK channels. Interplay of these distinct signaling cascades has important implications for the dynamic regulation of BK channels and physiological homeostasis.
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http://dx.doi.org/10.1073/pnas.0806700106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2605631PMC
December 2008
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