| 1. |
- Ahmad, Abrar, et al.
(author)
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Alpha 2-macroglobulin 5 bp insertion/deletion polymorphism increases the risk of recurrent venous thromboembolism
- 2018
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In: Gene Reports. - : Elsevier BV. - 2452-0144. ; 13, s. 104-109
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Journal article (peer-reviewed)abstract
- Alpha 2-macroglobulin (A2M) is a protease inhibitor that has been reported to neutralize thrombin, which may decrease the risk of thrombosis. A 5-base pairs (bp) insertion/deletion polymorphism (rs3832852) at the splice acceptor site of exon 18 has been shown to affect the binding of A2M with proteases. However, the role of this important variant in A2M in recurrent VTE is unknown. We investigated the role of 5 bp insertion/deletion polymorphism in VTE recurrence in a follow up study. A2M 5 bp insertion/deletion polymorphism was genotyped in Malmö Thrombophilia Study (MATS, n = 1465, with follow up of ~10 years) by TaqMan Allelic Discrimination assay. Univariate Cox regression analysis showed that A2M polymorphism was significantly associated with higher risk of VTE recurrence (hazard ratio [HR] = 2.61, 95% confidence interval [CI] = 1.06–6.45, P = 0.037). This association remained significant (HR = 2.61, 95% CI = 1.06–6.47, P = 0.038) even after adjusting for sex, family history of VTE, thrombophilia and acquired risk factors for VTE. In conclusion, our results indicate that patients with A2M 5 bp insertion/deletion polymorphism are at significantly higher risk of VTE recurrence and this may predict VTE recurrence.
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| 2. |
- Andersson, Göran
(author)
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Evidence for two protein-coding transcripts at the Igf2as locus
- 2016
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In: Gene Reports. - : Elsevier BV. - 2452-0144. ; 4, s. 60-66
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Journal article (peer-reviewed)abstract
- The insulin-like growth factor 2 antisense (Igf2as) gene is part of the Ins-Igf2-H19 imprinted gene cluster. The function of the paternally expressed Igf2as is still elusive. In our previouswork,we showed that Igf2as transcripts were located in the cytoplasm of C2C12 mouse myoblast cells, associated with polysomes and polyadenylated suggesting that Igf2as is protein coding. In the presentwork, the protein coding capacity of Igf2as was investigated. We demonstrate for the first time the existence of a polypeptide translated froman Igf2as construct. Furthermore, an RNA-Seq analysiswas performed using RNA prepared from skeletal muscles of newborn wild-type and ΔDMR1-U2 mice to further elucidate the function of Igf2as transcripts. We found no evidence for a regulatory role of Igf2as in the imprinted gene cluster. Interestingly, the RNA-Seq analysis indicated that Igf2as plays a role in the energy metabolism, the cell cycle, histone acetylation and muscle contraction pathways. Our Igf2as investigations further elucidated that there are two distinct Igf2as transcripts corresponding to two putative ORFs.
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| 3. |
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| 4. |
- Das, Umi, et al.
(author)
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Computational characterization and expression profile of MTP1 gene associated with zinc homeostasis across dicot plant species
- 2021
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In: Gene Reports. - : Elsevier. - 2452-0144. ; 23, s. 1-13
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Journal article (peer-reviewed)abstract
- This study characterizes different MTP1 (metal tolerance protein)/ZAT (zinc transporter) homologs involved in zinc (Zn) homeostasis in plants. BLAST analysis of AtMTP1 protein against 15 plant species showed 21 MTP1 homologs. These MTP1 protein homologs generally contain ~400 residues, six transmembrane helices and cation transmembrane transporter activity (GO:0008324), which can be utilized in predicting Zn uptake and tolerance mechanisms. These MTP1 genes having 1 exon are located on chromosomes 2, 7, and 14. Motifs contain conserved sequences of 41–50 residues belonging to the cation efflux family, which may help target binding sites and transcription factors. Further, AtMTP1 shows close similarities with Glycine max and Medicago trunculata. Interactome analysis suggests the association of AtMTP1 with cadmium/zinc-transporting ATPase and ZIP metal ion transporter. The AtMTP1 network is predominantly connected to cadmium/zinc-transporting ATPase (heavy metal ATPase 2, HMA2; heavy metal ATPase 3, HMA3; heavy metal ATPase 4, HMA4), cation efflux protein (MTP11), and metal tolerance protein C3 (AT4G58060). The Genevestigator predicts the high expression potential of AtMTP1 in the apical root during senescence, seedling, and bolting stages in an association with 11 co-expressed genes, mainly linked to estradiol toxicity and heat stress. Besides, AtMTP1 protein homologs possess conserved N-glyco motifs and physicochemical properties. The similarity and interactions of AtMTP1 gene with other genes suggest that Zn homeostasis in plants is associated with the regulation of different genes. These findings may advance our understanding to further develop plants capable of maintaining Zn homeostasis under adverse conditions. © 2021 Elsevier Inc.
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| 5. |
- Dey, Subhamoy, et al.
(author)
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Evolutionary and compositional analysis of streptokinase including its interaction with plasminogen: An in silico approach
- 2022
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In: Gene Reports. - : Elsevier. - 2452-0144. ; 29
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Journal article (peer-reviewed)abstract
- Due to the accumulation of cholesterol in arterial wall, clot-forming cascade activated in the blood capillaries lead to conditions like myocardial ischemia and heart failure. These clots are dissolved by the enzyme streptokinase (SK), produced by Streptococcus sp., a normal flora in the human body. In the present study, codon-dependent evolution of twenty-three SK from Streptococcus sp. bacteria, isolated from distinct geographical origins were analyzed. Besides, domain variation, compositional analysis, effective number of codons (ENc) plot, codon adaptation index (CAI), and effect of polymorphism on SK interaction with its substrate plasminogen (Plg) were analyzed. Codon usage bias varied within a tiny range. Studies also reveal that AT ending codons are preferred over GC ending codons. Analyses of the other parameters reveal that the mutational pressure is one of the main factors to shape codon usage biasness. Interfacing and polar contact forming amino acid residues of SK with Plg is identical for all Streptococcus dysgalactiae but not for all Streptococcus pyogenes. Changes of those interfacing amino acid sites exhibit a substantial effect on polar interaction between SK and Plg. The present in silico studies are expected to shed further light to characterize and moreover, to understand the various contributing factors to influence SK adaptation that will be fulfilling to develop efficient thrombolytic therapeutics.
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| 6. |
- Mujtaba, Tahir
(author)
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Development of expressed sequenced tags (EST) to identify some pathogen resistance genes expressed in Gossypium arboreum
- 2019
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In: Gene Reports. - : Elsevier BV. - 2452-0144. ; 15
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Journal article (peer-reviewed)abstract
- Cotton the most important fiber crop is facing a major threat due to a viral disease caused by cotton leaf curl virus (CLCuV). The cotton specie, Gossypium arboreum is resistant to this disease. Cotton scientists are working to find the key genes in G. arboreum that confer resistance against cotton leaf curl disease (CLCuD). Current research work is an effort to find some potential biotic stress related resistance genes from G. arboreum and the their evaluation against CLCuV infection utilizing functional genomics approaches. Leaf cDNA library was constructed from field grown G. arboreum which was further utilized to identify and isolate clones involved in resistance against CLCuD. The clone sequences were exploited to establish expressed sequence tags (EST). The EST represented some important biotic stress resistance genes like lipoxygenase, cytochrome P450, CPMMV like coat protein, serine threonine kinase, a RGA, lipid transfer protein and ubiquitin conjugating enzyme E2. As cotton is a fiber crop so some trichome development genes like aquaporin, arabinogalactans and cellulose synthase were also found. Lipoxygenases are known to be involved in apoptosis and biotic and abiotic stress responses in plants. Here the members of LOX are identified in biotic stress resistant G. arboreum. G. arboreum genome encode 13 LOX proteins. The G. arboreum LOXs are validated based on protein alignment studies. This is the first report wherein number of LOXs are identified in cotton which may help to better understand the apoptosis and responses to biotic and abiotic stresses in naturally resistant G. arboreum.
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