| 1. |
- Aydin, Ebru, et al.
(författare)
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A hypomorphic Cbx3 allele causes prenatal growth restriction and perinatal energy homeostasis defects
- 2015
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Ingår i: Journal of Biosciences. - : Springer Science and Business Media LLC. - 0250-5991 .- 0973-7138. ; 40:2, s. 325-338
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Tidskriftsartikel (refereegranskat)abstract
- Mammals have three HP1 protein isotypes HP1 beta (CBX1), HPl gamma (CBX3) and HP1 alpha (CBX5) that are encoded by the corresponding genes Cbx1, Cbx3 and Cbx5. Recent work has shown that reduction of CBX3 protein in homozygotes for a hypomorphic allele (Cbx3(hypo)) causes a severe postnatal mortality with around 99% of the homozygotes dying before weaning. It is not known what the causes of the postnatal mortality are. Here we show that Cbx3(hypo/hypo) conceptuses are significantly reduced in size and the placentas exhibit a haplo-insufficiency. Late gestation Cbx3(hypo/hypo) placentas have reduced mRNA transcripts for genes involved in growth regulation, amino acid and glucose transport. Blood vessels within the Cbx3(hypo/hypo) placental labyrinth are narrower than wild-type. Newborn Cbx3(hypo/hypo) pups are hypoglycemic, the livers are depleted of glycogen reserves and there is almost complete loss of stored lipid in brown adipose tissue (BAT). There is a 10-fold reduction in expression of the BAT-specific Ucp1 gene, whose product is responsible for non-shivering themogenesis. We suggest that it is the small size of the ChX3(hypo/hypo) neonates, a likely consequence of placental growth and transport defects, combined with a possible inability to thermoregulate that causes the severe postnatal mortality.
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| 2. |
- Das, Sarbashis, et al.
(författare)
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Single-nucleotide variations associated with Mycobacterium tuberculosis KwaZulu-Natal strains.
- 2009
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Ingår i: Journal of Biosciences. - 0250-5991 .- 0973-7138. ; 34:3, s. 397-404
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Tidskriftsartikel (refereegranskat)abstract
- The occurrence of drug resistance in Mycobacterium tuberculosis, the aetiological agent of tuberculosis (TB), is hampering the management and control of TB in the world. Here we present a computational analysis of recently sequenced drug-sensitive (DS), multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains of M. tuberculosis. Single-nucleotide variations (SNVs) were identified in a pair-wise manner using the anchor-based whole genome comparison (ABWGC) tool and its modified version. For this analysis, four fully sequenced genomes of different strains of M. tuberculosis were taken along with three KwaZulu-Natal (KZN) strains isolated from South Africa including one XDR and one MDR strain. KZN strains were compared with other fully sequenced strains and also among each other. The variations were analysed with respect to their biological influence as a result of either altered structure or synthesis. The results suggest that the DR phenotype may be due to changes in a number of genes. The database on KZN strains can be accessed through the website http://mirna.jnu.ac.in/mgdd/.
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| 3. |
- Makowski, Matthew M, et al.
(författare)
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Picking a nucleosome lock : Sequence- and structure-specific recognition of the nucleosome.
- 2020
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Ingår i: Journal of Biosciences. - 0250-5991 .- 0973-7138. ; 45
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Tidskriftsartikel (refereegranskat)abstract
- The nucleosome presents a formidable barrier to DNA-templated transcription by the RNA polymerase II machinery. Overcoming this transcriptional barrier in a locus-specific manner requires sequence-specific recognition of nucleosomal DNA by 'pioneer' transcription factors (TFs). Cell fate decisions, in turn, depend on the coordinated action of pioneer TFs at cell lineage-specific gene regulatory elements. Although it is already appreciated that pioneer factors play a critical role in cell differentiation, our understanding of the structural and biochemical mechanisms by which they act is still rapidly expanding. Recent research has revealed novel insight into modes of nucleosome-TF binding and uncovered kinetic principles by which nucleosomal DNA compaction affects both TF binding and residence time. Here, we review progress and argue that these structural and kinetic studies suggest new models of gene regulation by pioneer TFs.
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| 4. |
- Marathe, Nachiket, et al.
(författare)
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Mossambicus tilapia (Oreochromis mossambicus) collected from water bodies impacted by urban waste carries extended-spectrum beta-lactamases and integron-bearing gut bacteria
- 2016
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Ingår i: Journal of Biosciences. - : Springer Science and Business Media LLC. - 0250-5991 .- 0973-7138. ; 41:3, s. 341-346
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Tidskriftsartikel (refereegranskat)abstract
- Oreochromis mossambicus (Peters 1852) (Tilapia) is one of the most consumed fish globally. Tilapia thrives well in environments polluted by urban waste, which invariably contain antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). Thus, Tilapia surviving in such polluted environments may serve as a potential source for dissemination of ARGs. To investigate this, we isolated bacterial strains from gut of Tilapia found in polluted rivers and lakes near Pune, India, and studied the prevalence of resistance genes by molecular methods. A total of 91 bacterial strains were obtained, which include fish pathogens and human pathogens such as Aeromonas hydrophila, Klebsiella pneumoniae, E. coli, Serratia marcescens, Enterobacter spp. and Shigella spp. Overall the prevalence of class 1 integrons, class 2 integrons, extended-spectrum beta-lactamases (ESBLs) bla(CTX-M), bla(SHV) and aac(6')-Ib-cr gene was 38%, 24%, 38%, 31% and 31% respectively. Forty-two percent of the Enterobacteriaceae strains carried blaCTX-M gene, which is a common ESBL gene in clinics. The study demonstrates that tilapia found in the polluted waters can serve as reservoirs and an alternative route for human exposure to clinically important ARG-carrying bacteria. The consumption and handling of these fish may pose a potential health risk.
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| 5. |
- Mousavifard, A., et al.
(författare)
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Elevated expression of stemness genes in adipose-derived mesenchymal stem cells cultured on fibrin scaffold
- 2020
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Ingår i: Journal of Biosciences. - : Springer Science and Business Media LLC. - 0250-5991 .- 0973-7138. ; 45:1
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Tidskriftsartikel (refereegranskat)abstract
- In regenerative medicine, MSCs need to be pluripotent for better results. In this study, the effect of fibrin scaffold on expression of stemness genes was examined. Adipose-derived MSCs were cultured in tissue culture plates (2D) and 3-dimensional (3D) fibrin scaffolds. The effect of fibrin scaffold on proliferation of adipose-derived MSCs was evaluated by MTT assay. The expression of stemness genes (OCT4andSOX2) were evaluated by qRT-PCR, and flow cytometry was done for Nanog protein level. Cultured MSCs on fibrin scaffold were able to proliferate according to data obtained by MTT assay. Expression ofOCT4andSOX2had a significant increase in cells were cultured in 3D condition compared to 2D condition (P < 0.05). Also, increased expression of Nanog protein in 3D culture was observed (P < 0.05).OCT4andSOX2in 3D condition increased two-fold and three-fold respectively in 2D and 3D conditions. Moreover, expression of Nanog increased 30% more than in 2D condition. Evaluation of important pluripotency regulators such as OCT4, SOX2, and Nanog showed that fibrin scaffolds are useful instruments to maintain stemness of MSCs, which is essential in field of stem cell therapy and regenerative medicine.
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| 6. |
- Richau, Kerstin H., et al.
(författare)
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Structural and gene expression analyses of uptake hydrogenases and other proteins involved in nitrogenase protection in Frankia
- 2013
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Ingår i: Journal of Biosciences. - : Indian Academy of Sciences. - 0250-5991 .- 0973-7138. ; 38:4, s. 703-712
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Tidskriftsartikel (refereegranskat)abstract
- The actinorhizal bacterium Frankia expresses nitrogenase and can therefore convert molecular nitrogen into ammonia and the by-product hydrogen. However, nitrogenase is inhibited by oxygen. Consequently, Frankia and its actinorhizal hosts have developed various mechanisms for excluding oxygen from their nitrogen-containing compartments. These include the expression of oxygen-scavenging uptake hydrogenases, the formation of hopanoid-rich vesicles, enclosed by multi-layered hopanoid structures, the lignification of hyphal cell walls, and the production of haemoglobins in the symbiotic nodule. In this work, we analysed the expression and structure of the so-called uptake hydrogenase (Hup), which catalyses the in vivo dissociation of hydrogen to recycle the energy locked up in this 'waste' product. Two uptake hydrogenase syntons have been identified in Frankia: synton 1 is expressed under free-living conditions while synton 2 is expressed during symbiosis. We used qPCR to determine synton 1 hup gene expression in two Frankia strains under aerobic and anaerobic conditions. We also predicted the 3D structures of the Hup protein subunits based on multiple sequence alignments and remote homology modelling. Finally, we performed BLAST searches of genome and protein databases to identify genes that may contribute to the protection of nitrogenase against oxygen in the two Frankia strains. Our results show that in Frankia strain ACN14a, the expression patterns of the large (HupL1) and small (HupS1) uptake hydrogenase subunits depend on the abundance of oxygen in the external environment. Structural models of the membrane-bound hydrogenase subunits of ACN14a showed that both subunits resemble the structures of known [NiFe] hydrogenases (Volbeda et al. 1995), but contain fewer cysteine residues than the uptake hydrogenase of the Frankia DC12 and Eu1c strains. Moreover, we show that all of the investigated Frankia strains have two squalene hopane cyclase genes (shc1 and shc2). The only exceptions were CcI3 and the symbiont of Datisca glomerata, which possess shc1 but not shc2. Four truncated haemoglobin genes were identified in Frankia ACN14a and Eu1f, three in CcI3, two in EANpec1 and one in the Datisca glomerata symbiont (Dg).
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| 7. |
- Singla, Mamta, et al.
(författare)
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Sub-operon promoter arrangement of disA facilitates c-di-AMP homeostasis and selective stress responses in Mycobacterium smegmatis
- 2023
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Ingår i: Journal of Biosciences. - : Springer Nature. - 0250-5991 .- 0973-7138. ; 48:3
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial second messenger signaling often plays an important role in cellular physiology. In this study, we have attempted to understand how c-di-AMP synthesis and degradation are transcriptionally regulated in Mycobacterium smegmatis. We found that although a c-di-AMP synthesis gene, disA, exists in a multi-gene operon, a sub-operon promoter arrangement facilitates disA gene expression under normal conditions to maintain intracellular c-di-AMP concentration and is induced further during certain stress adaptations. Individual gene-specific promoters also play a key role under various genotoxic stress conditions to shut down c-di-AMP synthesis, which could otherwise be detrimental for cells. Further, we learned that a high c-di-AMP concentration plays a role in the autoregulation of the disA promoter to limit intracellular c-di-AMP concentration. This study was helpful to understand how c-di-AMP synthesis is regulated under normal and stress conditions linked to its physiological relevance in M. smegmatis.
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| 8. |
- Ahmad, Ashraf, 1973
(författare)
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BOXTO as a real-time thermal cycling reporter dye
- 2007
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Ingår i: Journal of Biosciences. - 0250-5991. ; 32:2, s. 229-239
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Tidskriftsartikel (refereegranskat)abstract
- The unsymmetrical cyanine dyes BOXTO (4-[6-(benzoxazole-2-yl-(3-methyl-)-2,3-dihydro-(benzo-1,3-thiazole)-2me thylidene)]-1-methyl-quinolinium chloride) and its positive divalent derivative BOXTO-PRO (4-[(3-methyl-6(benzoxazole-2-yl)-2,3-dihydro-(benzo-1,3-thiazole)-2-met hylidene)]-1-(3-trimethylammonium-propyl)-quinolinium dibromide) were studied as real-time PCR reporting fluorescent dyes and compared to SYBR GREEN I (SG) (2-[N-(3-dimethylaminopropyl)-N-propylamino]-4-[2,3-dihydro-3-methyl-(be nzo-1,3-thiazol-2-yl)-methylidene]-1-phenyl- quinolinium). Unmodified BOXTO showed no inhibitory effects on real-time PCR, while BOXTO-PRO showed complete inhibition. Sufficient fluorescent signal was acquired when 0.5-1.0 mu M BOXTO was used with RotorGene and iCycler platforms. Statistical analysis showed that there is no significant difference between the efficiency and dynamic range of BOXTO and SG. BOXTO stock solution (1.5 mM) was stable at -20 degrees C for more than one year and 40 mu M BOXTO solution was more stable than 5x SG when both were stored at 4 degrees C for 45 days.
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| 9. |
- Gaur, Rahul, et al.
(författare)
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Diet-dependent depletion of queuosine in tRNAs in Caenorhabditis elegans does not lead to a developmental block.
- 2007
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Ingår i: J Biosci. - 0250-5991. ; 32:4, s. 747-54
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Tidskriftsartikel (refereegranskat)abstract
- Queuosine (Q), a hypermodified nucleoside,occurs at the wobble position of transfer RNAs (tRNAs)with GUN anticodons. In eubacteria, absence of Q affects messenger RNA (mRNA) translation and reduces the virulence of certain pathogenic strains. In animal cells,changes in the abundance of Q have been shown to correlate with diverse phenomena including stress tolerance, cell proliferation and tumour growth but the function of Q in animals is poorly understood. Animals are thought to obtain Q (or its analogues) as a micronutrient from dietary sources such as gut micro flora. However,the difficulty of maintaining animals under bacteria-free conditions on Q-deficient diets has severely hampered the study of Q metabolism and function in animals. In this study,we show that as in higher animals, tRNAs in the nematode Caenorhabditis elegans are modified by Q and its sugar derivatives. When the worms were fed on Q-deficient Escherichia coli, Q modification was absent from the worm tRNAs suggesting that C.elegans lacks a de novo pathway of Q biosynthesis. The inherent advantages of C.elegans as a model organism, and the simplicity of conferring a Q-deficient phenotype on it make it an ideal system to investigate the function of Q modification in tRNA.
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