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  • 1
    Publication Date: 2012-06-15
    Description: Background: Single-stranded DNA binding proteins (SSB) are essential for DNA replication, repair, and recombination in all organisms. SSB works in concert with a variety of DNA metabolizing enzymes such as DNA polymerase. Results: We have cloned and purified SSB from Bacillus anthracis (SSBBA). In the absence of DNA, at concentrations [less than or equal to]100 mug/ml, SSBBA did not form a stable tetramer and appeared to resemble bacteriophage T4 gene 32 protein. Fluorescence anisotropy studies demonstrated that SSBBA bound ssDNA with high affinity comparable to other prokaryotic SSBs. Thermodynamic analysis indicated both hydrophobic and ionic contributions to ssDNA binding. FRET analysis of oligo(dT)70 binding suggested that SSBBA forms a tetrameric assembly upon ssDNA binding. This report provides evidence of a bacterial SSB that utilizes a novel mechanism for DNA binding through the formation of a transient tetrameric structure. Conclusions: Unlike other prokaryotic SSB proteins, SSBBA from Bacillus anthracis appeared to be monomeric at concentrations [less than or equal to]100 mug/ml as determined by SE-HPLC. SSBBA retained its ability to bind ssDNA with very high affinity, comparable to SSB proteins which are tetrameric. In the presence of a long ssDNA template, SSBBA appears to form a transient tetrameric structure. Its unique structure appears to be due to the cumulative effect of multiple key amino acid changes in its sequence during evolution, leading to perturbation of stable dimer and tetramer formation. The structural features of SSBBA could promote facile assembly and disassembly of the protein-DNA complex required in processes such as DNA replication.
    Electronic ISSN: 1471-2091
    Topics: Chemistry and Pharmacology
    Published by BioMed Central
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  • 2
    Publication Date: 2018-03-12
    Description: Bamboo is an important member of the family Poaceae and has many inflorescence and flowering features rarely observed in other plant groups. It retains an unusual form of perennialism by having a long vegetati...
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 3
    Publication Date: 2017-01-26
    Description: Plants contain a range of aquaporin (AQP) proteins, which act as transporter of water and nutrient molecules through living membranes. AQPs also participate in water uptake through the roots and contribute to ...
    Electronic ISSN: 1471-2229
    Topics: Biology
    Published by BioMed Central
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  • 4
    Publication Date: 2015-10-31
    Description: Background: In humans, many diseases are associated with the accumulation of free radicals. Antioxidants can scavenge free radicals and minimize their impact. Therefore, the search for naturally occurring antioxidants of plant origin is imperative. Here, we aimed to investigate the antioxidant and free radical scavenging properties of methanolic extracts from Tabebuia pallida (T. pallida) stem bark (TPSB), root bark (TPRB), leaves (TPL), and flowers (TPF). Methods: The antioxidant and free radical scavenging activity were determined by several standard methods using spectrophotomer. Total phenolic and flavonoid contents were estimated using Folin-Ciocalteu reagent and aluminum chloride colorimetric assay methods, respectively. Results: Among the extracts, TPL showed the highest total antioxidant capacity followed by TPRB, TPF, and TPSB. Based on DPPH and hydroxyl radical scavenging activity, TPL showed strong scavenging activity (91.05 ± 1.10 and 62.00 ± 0.57) with IC 50 of 9.20 ± 0.28 and 46.00 ± 2.84 μg/mL, respectively when compared with standard BHT (IC 50 of 7.00 ± 0.25 μg/mL) and CA (75.00 ± 0.14 μg/mL). These results suggest that TPL had the highest radical scavenging activity among the extractives that closely resembled the standard’s. In lipid peroxidation inhibition assay, TPL exhibited the most potent inhibitory activity (83.18 ± 2.12 %) with IC 50 of 12.00 ± 2.12 μg/mL, which closely resembled standard CA (IC 50 of 10.50 ± 0.28 μg/mL). Also, the reducing capacity on ferrous ion was in the following order: TPL 〉 TPRB 〉 TF 〉 TPSB. The phenolic and flavonoid contents of TPL were higher than other extractives. A positive correlation (p value
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 5
    Publication Date: 2013-10-27
    Description: Background: Resveratrol, a naturally occurring stilbene, has been categorized as phytoestrogen due to its capability to compete with natural estrogens for binding to estrogen receptor alpha (ERalpha) and thus modulating the biological responses exerted by the receptor. Biological effects of resveratrol (RES) on estrogen receptor alpha (ERalpha) remain highly controversial, since both estrogenic and anti-estrogenic properties were observed. Results: Here, we provide insight into the structural basis of the agonist/antagonist effects of RES on ERalpha ligand binding domain (LBD). Using atomistic simulation, we found that RES bound ERalpha monomer in antagonist conformation, where Helix 12 moves away from the ligand pocket and orients into the co-activator binding groove of LBD, is more stable than RES bound ERalpha in agonist conformation, where Helix 12 lays over the ligand binding pocket. Upon dimerization, the agonistic conformation of RES-ERalpha dimer becomes more stable compared to the corresponding monomer but still remains less stable compared to the corresponding dimer in antagonist conformation. Interestingly, while the binding pocket and the binding contacts of RES to ERalpha are similar to those of pure agonist diethylstilbestrol (DES), the binding energy is much less and the hydrogen bonding contacts also differ providing clues for the partial agonistic character of RES on ERalpha. Conclusions: Our Molecular Dynamics simulation of RES-ERalpha structures with agonist and antagonist orientations of Helix 12 suggests RES action is more similar to Selective Estrogen Receptor Modulator (SERM) opening up the importance of cellular environment and active roles of co-regulator proteins in a given system. Our study reveals that potential co-activators must compete with the Helix 12 and displace it away from the activator binding groove to enhance the agonistic activity.
    Electronic ISSN: 1472-6807
    Topics: Biology
    Published by BioMed Central
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  • 6
    Publication Date: 2013-04-09
    Description: Background; With an ever-growing ageing population, dementia is fast becoming the chronic disease of the 21stcentury. Elderly people affected with dementia progressively lose their autonomy as they encounterproblems in their Activities of Daily Living (ADLs). Hence, they need supervision and assistancefrom their family members or professional caregivers, which can often lead to underestimated psychologicaland financial stress for all parties. The use of Ambient Assistive Living (AAL) technologiesaims to empower people with dementia and relieve the burden of their caregivers.The aim of this paper is to present the approach we have adopted to develop and deploy a systemfor ambient assistive living in an operating nursing home, and evaluate its performance and usabilityin real conditions. Based on this approach, we emphasise on the importance of deployments in realworld settings as opposed to prototype testing in laboratories.Methods; We chose to conduct this work in close partnership with end-users (dementia patients) and specialistsin dementia care (professional caregivers). Our trial was conducted during a period of 14 monthswithin three rooms in a nursing home in Singapore, and with the participation of eight dementiapatients and two caregivers. A technical ambient assistive living solution, consisting of a set of sensorsand devices controlled by a software platform, was deployed in the collaborating nursing home. Thetrial was preceded by a pre-deployment period to organise several observation sessions with dementiapatients and focus group discussions with professional caregivers. A process of ground truth andsystem's log data gathering was also planned prior to the trial and a system performance evaluationwas realised during the deployment period with the help of caregivers. An ethical approval wasobtained prior to real life deployment of our solution.Results; Patients' observations and discussions allowed us to gather a set of requirements that a system forelders with mild-dementia should fulfil. In fact, our deployment has exposed more concrete requirementsand problems that need to be addressed, and which cannot be identified in laboratory testing.Issues that were neither forecasted during the design phase nor during the laboratory testing surfacedduring deployment, thus affecting the effectiveness of the proposed solution. Results of the systemperformance evaluation show the evolution of system precision and uptime over the deploymentphases, while data analysis demonstrates the ability to provide early detection of the degradation ofpatients' conditions. A qualitative feedback was collected from caregivers and doctors and a set oflessons learned emerged from this deployment experience.Conclusion; Lessons learned from this study were very useful for our research work and can serve as inspirationfor developers and providers of assistive living services. They confirmed the importance of realdeployment to evaluate assistive solutions especially with the involvement of professional caregivers.They also asserted the need for larger deployments. Larger deployments will allow to conduct surveyson assistive solutions social and health impact, even though they are time and manpower consumingduring their first phases.
    Electronic ISSN: 1472-6947
    Topics: Computer Science , Medicine
    Published by BioMed Central
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  • 7
    Publication Date: 2013-05-16
    Description: Background Mutation of amino acid sequences in a protein may have diverse effects on its structure and function. Point mutations ofeven a single amino acid residue in the helices of thenon-redundant database may lead to sequentially identical peptides whichadopt different secondary structures in different proteins. However, variousphysico-chemical factors which govern the formation of these ambivalent helices generated by point mutationsof a sequence are not clearly known.Results Sequences generated by point mutations of helices are mapped on to theirnon-helical counterparts in the SCOP database. The results show thatshort helices are prone to transform into non-helical conformations upon pointmutations. Mutation of amino acid residues by helix breakerspreferentially yield non-helical conformations, while mutation withresidues of intermediate helix propensity display least preferences fornon-helical conformations. Differences in the solvent accessibility of themutating/mutated residues are found to be a major criteria for these sequencesto conform to non-helical conformations. Even with minimal differencesin the amino acid distributions of the sequences flanking the helicaland non-helical conformations, helix-flanking sequences are found bemore solvent accessible.Conclusions All types of mutations from helicalto non-helical conformations are investigated. The primary factorsattributing such changes in conformation can be: i) type/propensity ofthe mutating and mutant residues ii) solvent accessibility of the residue at the mutation siteiii) context/environment dependence of the flanking sequences. Theresults from the present study may be used to design de novoproteins via point mutations.
    Electronic ISSN: 1472-6807
    Topics: Biology
    Published by BioMed Central
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  • 8
    Publication Date: 2013-07-02
    Description: Background: In the progression towards diabetes, glucolipotoxicity is one of the main causes of pancreatic beta cell pathology. The aim of this study was to examine the in vitro effects of chronic glucolipotoxic conditions on cellular responses in pancreatic islets, including glucose and fat metabolism, Calcium mobilization, insulin secretion and insulin content. Results: Exposure of islets to chronic glucolipotoxic conditions decreased glucose stimulated insulin secretion in vitro. Reduced protein levels of Glut2/slc2a2, and decreased glucokinase and pyruvate carboxylase mRNA levels indicated a significant lowering in glucose sensing. Concomitantly, both fatty acid uptake and triglyceride accumulation increased significantly while fatty acid oxidation decreased. This general suppression in glucose metabolism correlated well with a decrease in mitochondrial number and activity, reduction in cellular ATP content and dampening of the TCA cycle. Further, we also observed a decrease in IP3 levels and lower Calcium mobilization in response to glucose. Importantly, chronic glucolipotoxic conditions in vitro decreased insulin gene expression, insulin content, insulin granule docking (to the plasma membrane) and insulin secretion. Conclusions: Our results present an integrated view of the effects of chronic glucolipotoxic conditions on known and novel signaling events, in vitro, that results in reduced glucose responsiveness and insulin secretion.
    Electronic ISSN: 1471-2121
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 9
    Publication Date: 2014-09-04
    Description: Background: Elevated glucose concentrations lead to increased insulin secretion and suppression of glucagon secretion. In fact, insulin is a physiological inhibitor of glucagon secretion. Type 2 diabetes mellitus (T2DM) patients have defects in insulin secretion. In addition to this, lack of suppression of glucagon secretion under elevated glucose concentrations is also observed in T2DM patients. We have earlier shown that GPR40 activation by CNX-011-67 stimulates glucose stimulated insulin secretion (GSIS). Here we extended our studies to examine the impact of GPR40 activation by CNX-011-67 on glucagon secretion from intact islets under both normal and glucolipotoxic conditions.FindingsGlucagon secretion from intact rat islets was suppressed under elevated glucose concentration. Activation of GPR40 by CNX-011-67 further suppressed glucagon secretion. Culturing islets under chronic glucolipotoxic (GL) conditions, we have observed increased high glucose mediated glucagon secretion and content which were reduced with GPR40 activation by CNX-011-67. Interestingly, expression of pre-proglucagon gene (GCG) remained unchanged under glucolipotoxicity in the presence or absence of GPR40 activation. Conclusion: Activation of GPR40 by CNX-011-67 can reduce glucagon secretion from pancreatic islets.
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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  • 10
    Publication Date: 2017-03-23
    Description: Patients’ perspective of diabetes and adherence to its prescribed medications is a significant predictor of glycemic control and overall management of the disease. However, there is a paucity of such informat...
    Electronic ISSN: 1756-0500
    Topics: Biology , Medicine
    Published by BioMed Central
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