ORCID Profile
0000-0002-8019-4081
Current Organisation
University of Adelaide
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Publisher: Cold Spring Harbor Laboratory
Date: 16-03-2022
DOI: 10.1101/2022.03.14.484309
Abstract: Nitrogen (N) and phosphorus (P) are two essential plant macronutrients that can limit plant growth by different mechanisms. We aimed to shed light on how soybean respond to low nitrogen (LN), low phosphorus (LP) and their combined deficiency (LNP). Generally, these conditions triggered changes in gene expression of the same processes, including cell wall organization, defense response, response to oxidative stress, and photosynthesis, however, response was different in each condition. A typical primary response to LN and LP was detected also in soybean, i.e., the enhanced uptake of N and P, respectively, by upregulation of genes for the corresponding transporters. The regulation of genes involved in cell wall organization showed that in LP roots tended to produce more casparian strip, in LN more secondary wall biosynthesis occurred, and in LNP reduction in expression of genes involved in secondary wall production accompanied by cell wall loosening was observed. Flavonoid biosynthesis also showed distinct pattern of regulation in different conditions: more anthocyanin production in LP, and more isoflavonoid production in LN and LNP, which we confirmed also on the metabolite level. Interestingly, in soybean the nutrient deficiencies reduced defense response by lowering expression of genes involved in defense response, suggesting a role of N and P nutrition in plant disease resistance. In conclusion, we provide detailed information on how LN, LP, and LNP affect different processes in soybean roots on the molecular and physiological levels.
Publisher: Springer Science and Business Media LLC
Date: 18-11-2014
DOI: 10.1007/S11033-014-3837-7
Abstract: Diabetes, a disease caused by excessive blood sugar, is caused by the lack of insulin. For commercial production, insulin is made in bacteria or yeast by protein recombinant technology. The focus of this research is evaluating another resource and producing of recombinant insulin protein in as strawberry as this plant has high potential in production of pharmaceutical proteins. Strawberry is a suitable bioreactor for production of recombinant proteins especially edible vaccines. In this research, human pro-insulin gene was cloned in pCAMBIA1304 vector under CaMV35S promoter and NOS terminator. Agrobacterium tumefaciens LBA4404, AGL1, EHA105, EHA101, C58, C58 (pGV2260) and C58 (pGV3101) strains were used for transformation of pro-insulin gene into strawberry cv. Camarosa, Selva, Sarian Hybrid, Pajaro, Paros, Gaviota, Alpine. Additionally, Agrobacterium rhizogenes K599, R1000, A4 and MSU440 strains were utilized for gene transformation into hairy roots. PCR analysis indicated the presence of transformed human pro-insulin gene in the strawberry and hairy roots. Also, its transcription was confirmed using RT-PCR. Furthermore, the analysis of plants, fruits and hairy roots at the level of proteins using dot blot, ELISA, SDS-PAGE and ECL tests re-confirmed the expression of this protein in the transgenic plants as well as hairy roots. Protein purification of human pro-insulin from transgenic tissues was performed using affinity chromatography. Finally, the bioassay of recombinant pro-insulin was performed. The analysis of second generations of transgenic plants (T1) at DNA and protein levels was also performed as a complementary experiment. This study opens a new avenue in molecular farming of human pro-insulin through its mass production in roots and shoots of strawberry.
Publisher: Springer Science and Business Media LLC
Date: 21-11-2013
Publisher: No publisher found
Publisher: Proceedings of the National Academy of Sciences
Date: 19-03-2014
Abstract: The legume/rhizobia symbiosis involves a root-based exchange of bacterial fixed nitrogen for plant-derived photosynthetic carbon. The exchange takes place within the legume root nodule, which is a specialized root tissue that develops in response to plant and bacterial signal exchange. The bacteria reside within plant cells inside the nodule. In this study, we explore the activity of a membrane-bound soybean transcription factor, Glycine max basic–helix-loop–helix membrane 1, which is important for soybean nodule growth and is linked to the activity of a unique class of ammonium channels and to signaling cascades influencing a nodule circadian clock.
Publisher: No publisher found
Publisher: Wiley
Date: 25-04-2019
DOI: 10.1111/AVJ.12799
Abstract: Koalas in the Mount Lofty Ranges, South Australia, have a high prevalence of oxalate nephrosis, or calcium oxalate kidney crystals. Gastrointestinal tract oxalate-degrading bacteria, particularly Oxalobacter formigenes, have been identified in other animal species and humans, and their absence or low abundance is postulated to increase the risk of renal oxalate diseases. This study aimed to identify oxalate-degrading bacteria in the gastrointestinal tract of koalas and determine their association with oxalate nephrosis. Caecal and faecal s les were collected at necropsy from 22 Mount Lofty Ranges koalas that had been euthanased on welfare grounds, with 8 koalas found to have oxalate nephrosis by renal histopathology. S les were analysed by PCR for the oxc gene, which encodes oxalyl-CoA decarboxylase, and also by Illumina sequencing of the V3-V4 region of the bacterial 16S rRNA gene. The oxc gene was detected in 100% of koala s les, regardless of oxalate nephrosis status. Oxalobacter formigenes was detected in all but one faecal s le, with no difference in abundance between koalas affected and unaffected by oxalate nephrosis. Other species of known oxalate-degrading bacteria were infrequently detected. This is the first study to identify Oxalobacter and other oxalate-degrading bacterial species in koalas, but an association with oxalate nephrosis and absence or low abundance of Oxalobacter was not found. This suggests other mechanisms underlie the risk of oxalate nephrosis in koalas.
Publisher: No publisher found
Publisher: Springer Science and Business Media LLC
Date: 14-03-2022
DOI: 10.1007/S11033-022-07257-9
Abstract: Splice-disrupt genomic variants are one of the causes of cancer-causing errors in gene expression. Little is known about splice-disrupt genomic variants. Here, pattern of splice-disrupt variants was investigated using 21,842,764 genomic variants in different types of prostate cancer. A particular attention was paid to genomic locations of splice-disrupt variants on target genes. HLA-A in prostate cancer, MSR1 in familial prostate cancer, and EGFR in both castration-resistant prostate cancer and metastatic castration-resistant had the highest allele frequencies of splice-disrupt variations. Some splice-disrupt variants, located on coding sequences of NCOR2 , PTPRC , and CRP , were solely present in the advanced metastatic castration-resistant prostate cancer. High-risk splice-disrupt variants were identified based on computationally calculated Polymorphism Phenotyping (PolyPhen), Sorting Intolerant From Tolerant (SIFT), and Genomic Evolutionary Rate Profiling (GERP) + + scores as well as the recorded clinical significance in dbSNP database of NCBI. Functional annotation of damaging splice-disrupt variants highlighted important cancer-associated functions, including endocrine resistance, lipid metabolic process, steroid metabolic process, regulation of mitotic cell cycle, and regulation of metabolic process. This is the first study that profiles the splice-disrupt genomic variants and their target genes in prostate cancer. Literature mining based variant analysis highlighted the importance of rs1800716 variant, located on the CYP2D6 gene, involved in a range of important functions, such as RNA spicing, drug interaction, death, and urotoxicity. This is the first study that profiles the splice-disrupt genomic variants and their target genes in different types of prostate cancer. Unravelling alternative splicing opens a new avenue towards the establishment of new diagnostic and prognostic markers for prostate cancer progression and metastasis.
Publisher: Elsevier BV
Date: 06-2019
Publisher: No publisher found
Publisher: Springer Science and Business Media LLC
Date: 10-2011
Publisher: No publisher found
Publisher: No publisher found
Publisher: Springer Science and Business Media LLC
Date: 07-12-2007
Publisher: Elsevier BV
Date: 04-2010
Publisher: Frontiers Media SA
Date: 12-11-2018
Publisher: Elsevier BV
Date: 11-2014
DOI: 10.1016/J.COMPBIOMED.2014.08.019
Abstract: α-linolenic acid (ALA) is the most frequent omega-3 in plants. The content of ALA is highly variable, ranging from 0 to 1% in rice and corn to >50% in perilla and flax. ALA production is strongly correlated with the enzymatic activity of omega-3 fatty acid desaturase. To unravel the underlying mechanisms of omega-3 ersity, 895 protein features of omega-3 fatty acid desaturase were compared between plants with high and low omega-3. Attribute weighting showed that this enzyme in plants with high omega-3 content has higher amounts of Lys, Lys-Phe, and Pro-Asn but lower Aliphatic index, Gly-His, and Pro-Leu. The Random Forest model with Accuracy criterion when run on the dataset pre-filtered with Info Gain algorithm was the best model in distinguishing high omega-3 content based on the frequency of Lys-Lys in the structure of fatty acid desaturase. Interestingly, the discriminant function algorithm could predict the level of omega-3 only based on the six important selected attributes (out of 895 protein attributes) of fatty acid desaturase with 75% accuracy. We developed "Plant omega3 predictor" to predict the content of α-linolenic acid based on structural features of omega-3 fatty acid desaturase. The software calculates the 6 key structural protein features from imported Fasta sequence of omega-3 fatty acid desaturase or utilizes the imported features and predicts the ALA content using discriminant function formula. This work unravels an underpinning mechanism of omega-3 ersity via discovery of the key protein attributes in the structure of omega-3 desaturase offering a new approach to obtain higher omega-3 content.
Publisher: Springer Science and Business Media LLC
Date: 31-07-2007
Publisher: No publisher found
Publisher: No publisher found
Publisher: IEEE
Date: 05-2009
Publisher: Springer Science and Business Media LLC
Date: 16-11-2016
Publisher: No publisher found
Publisher: Wiley
Date: 31-01-2019
DOI: 10.1002/MC.22975
Abstract: A considerable number of deposited variants has provided new possibilities for knowledge discovery in different types of prostate cancer. Here, we analyzed variants located on 3′UTR, 5′UTR, CDs, Intergenic, and Intronic regions in castration‐resistant prostate cancer (8496 variants), familial prostate cancer (3241 variants), metastatic castration‐resistant prostate cancer (3693 variants), and prostate cancer (16599 variants). Chromosome regions 10p15‐p14 and 2p13 were highly enriched ( P 0.00001) for variants located in 3′UTR, 5′UTR, CDs, intergenic, and intronic regions in castration‐resistant prostate cancer. In contrast, 10p15‐p14, 10q23.3, 12q13.11, 13q12.3, 1q25, and 8p22 regions were enriched ( P 0.001) in familial prostate cancer. In metastatic castration‐resistant prostate cancer, 10p15‐p14, 10q23.3, 11q22‐q23, 14q21.1, and 14q32.13 were highly variant regions ( P 0.001). Chromosome 2 and chromosome 1 hosted many enriched variant regions. AKR1C3 , BRCA1 , BRCA2 , CHGA , CYP19A1 , HOXB13 , KLK3 , and PTEN contained the highest number of 3′UTR, 5′UTR, CDs, Intergenic, and Intronic variants. Network analysis showed that these genes are upstream of important functions including prostate gland development, tumor recurrence, prostate cancer‐specific survival, tumor progression, cancer mortality, long‐term survival, cancer recurrence, angiogenesis, and AR. Interestingly, all of EGFR , JAK2 , NR3C1 , PDZD2 , and SEMA3C genes had single nucleotide polymorphisms (SNP) in castration‐resistant prostate cancer, consistent with high selection pressure on these genes during drug treatment and consequent resistance. High occurrence of variants in 3′UTRs suggests the importance of regulatory variants in different types of prostate cancer an area that has been neglected compared with coding variants. This study provides a comprehensive overview of genomic regions contributing to different types of prostate cancer.
Publisher: Wiley
Date: 23-01-2020
DOI: 10.1111/AVJ.12919
Abstract: In northern Australian koala populations (Queensland and New South Wales), periodontal disease (gingivitis and periodontitis) is common while koala retrovirus subtype A is endogenous, with other subtypes transmitted exogenously. Koala retrovirus has been hypothesised to cause immune suppression and may predispose koalas to diseases caused by concurrent infections. In southern Australia populations (Victoria and South Australia) periodontal disease has not been investigated, and koala retrovirus is presumably exogenously transmitted. This study described oral health in South Australian koalas and investigated if an association between periodontal disease and koala retrovirus exists. Oral health was examined for wild-caught koalas from the Mount Lofty Ranges (n = 75). Koala retrovirus provirus was detected in whole blood using nested PCR and proviral load determined with qPCR. Periodontal disease severity was recorded and used to calculate the Final Oral Health Index (0-normal, 24-severe).Results Periodontal disease was observed in 84% (63/75) of koalas 77% had gingivitis (58/75) and 65% (49/75) had periodontitis. The average Final Oral Health Index was 5.47 (s.d 3.13). Most cases of periodontal disease were associated with the incisors. Koala retrovirus-infected koalas were more likely to present with periodontitis (p = 0.042) and the Final Oral Health Index was negatively correlated with proviral load (ρ = -0.353, p = 0.017). South Australian koalas had a high prevalence of gingivitis and periodontitis. Periodontal disease was more prevalent in the incisors. Exogenous koala retrovirus infection may also facilitate the development of periodontitis by modulation of the immune response to concurrent oral bacterial infections.
Publisher: Elsevier BV
Date: 06-2018
DOI: 10.1016/J.GENE.2018.03.038
Abstract: Exponentially growing scientific knowledge in scientific publications has resulted in the emergence of a new interdisciplinary science of literature mining. In text mining, the machine reads the published literature and transfers the discovered knowledge to mathematical-like formulas. In an integrative approach in this study, we used text mining in combination with network discovery, pathway analysis, and enrichment analysis of genomic regions for better understanding of biomarkers in lung cancer. Particular attention was paid to non-coding biomarkers. In total, 60 MicroRNA biomarkers were reported for lung cancer, including some prognostic biomarkers. MIR21, MIR155, MALAT1, and MIR31 were the top non-coding RNA biomarkers of lung cancer. Text mining identified 447 proteins which have been studied as biomarkers in lung cancer. EGFR (receptor), TP53 (transcription factor), KRAS, CDKN2A, ENO2, KRT19, RASSF1, GRP (ligand), SHOX2 (transcription factor), and ERBB2 (receptor) were the most studied proteins. Within small molecules, thymosin-a1, oestrogen, and 8-OHdG have received more attention. We found some chromosomal bands, such as 7q32.2, 18q12.1, 6p12, 11p15.5, and 3p21.3 that are highly involved in deriving lung cancer biomarkers.
Publisher: No publisher found
No related grants have been discovered for Manijeh Mohammadi Dehcheshmeh.