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Sökning: WFRF:(Sharma Priyanka)

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1.
  • Beal, Jacob, et al. (författare)
  • Robust estimation of bacterial cell count from optical density
  • 2020
  • Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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2.
  • Mahapatra, Sayanta, et al. (författare)
  • Substoichiometric Hsp104 regulates the genesis and persistence of self-replicable amyloid seeds of Sup35 prion domain
  • 2022
  • Ingår i: Journal of Biological Chemistry. - : Elsevier. - 0021-9258 .- 1083-351X. ; 298:8
  • Tidskriftsartikel (refereegranskat)abstract
    • Prion-like self-perpetuating conformational conversion of proteins is involved in both transmissible neurodegenerative diseases in mammals and non-Mendelian inheritance in yeast. The transmissibility of amyloid-like aggregates is dependent on the stoichiometry of chaperones such as heat shock proteins (Hsps), including disaggregases. To provide the mechanistic underpinnings of the formation and persistence of prefibrillar amyloid seeds, we investigated the role of substoichiometric Hsp104 on the in vitro amyloid aggregation of the prion domain (NM-domain) of Saccharomyces cerevisiae Sup35. At low substoichiometric concentrations, we show Hsp104 exhibits a dual role: it considerably accelerates the formation of prefibrillar species by shortening the lag phase but also prolongs their persistence by introducing unusual kinetic halts and delaying their conversion into mature amyloid fibers. Additionally, Hsp104-modulated amyloid species displayed a better seeding capability compared to NM-only amyloids. Using biochemical and biophysical tools coupled with site-specific dynamic readouts, we characterized the distinct structural and dynamical signatures of these amyloids. We reveal that Hsp104-remodeled amyloidogenic species are compositionally diverse in prefibrillar aggregates and are packed in a more ordered fashion compared to NM-only amyloids. Finally, we show these Hsp104-remodeled, conformationally distinct NM aggregates display an enhanced autocatalytic self-templating ability that might be crucial for phenotypic outcomes. Taken together, our results demonstrate that substoichiometric Hsp104 promotes compositional diversity and conformational modulations during amyloid formation, yielding effective prefibrillar seeds that are capable of driving prion-like Sup35 propagation. Our findings underscore the key functional and pathological roles of substoichiometric chaperones in prion-like propagation.
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3.
  • Wang, Ruifu, et al. (författare)
  • Morphology and Flow Behavior of Cellulose Nanofibers Dispersed in Glycols
  • 2019
  • Ingår i: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 52:15, s. 5499-5509
  • Tidskriftsartikel (refereegranskat)abstract
    • Understanding the morphology and flow behavior of cellulose nanofibers (CNFs) dispersed in organic solvents can improve the process of fabricating new cellulose-based nanocomposites. In this study, jute-based 2,2,6,6-tetramethylpiperidinyl-1-oxyl (TEMPO)-oxidized CNFs with two different charge densities (0.64 and 1.03 mmol/g) were dispersed in ethylene glycol (EG) and propylene glycol (PG) using the solvent exchange method. The morphology and dimensions of CNFs in dry and suspension states were characterized using transmission electron microscopy, atomic force microscopy, and small-angle X-ray scattering techniques. The results showed that the cross-sectional dimensions remained the same in different solvents. Rheological measurements revealed that CNF suspensions in water or glycol (EG and PG) behaved similar to typical polymer solutions with a solvent-independent overlap concentration corresponding to the crowding factor of about 14. Furthermore, a thixotropic behavior was found in the concentrated CNF/glycol systems as observed in typical CNF aqueous suspensions. The fact that TEMPO-oxidized CNFs can be well dispersed in organic solvents opens up new possibilities to improve the CNF–polymer matrix blending, where the use of a viscous solvent can delay the transition to turbulence in processing and improve the control of fiber orientation because of a slower Brownian diffusive motion.
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4.
  • 2019
  • Tidskriftsartikel (refereegranskat)
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5.
  • Couch, Fergus J., et al. (författare)
  • Identification of four novel susceptibility loci for oestrogen receptor negative breast cancer
  • 2016
  • Ingår i: Nature Communications. - : NATURE PUBLISHING GROUP. - 2041-1723. ; 7:11375, s. 1-13
  • Tidskriftsartikel (refereegranskat)abstract
    • Common variants in 94 loci have been associated with breast cancer including 15 loci with genome-wide significant associations (P<5 x 10(-8)) with oestrogen receptor (ER)-negative breast cancer and BRCA1-associated breast cancer risk. In this study, to identify new ER-negative susceptibility loci, we performed a meta-analysis of 11 genome-wide association studies (GWAS) consisting of 4,939 ER-negative cases and 14,352 controls, combined with 7,333 ER-negative cases and 42,468 controls and 15,252 BRCA1 mutation carriers genotyped on the iCOGS array. We identify four previously unidentified loci including two loci at 13q22 near KLF5, a 2p23.2 locus near WDR43 and a 2q33 locus near PPIL3 that display genome-wide significant associations with ER-negative breast cancer. In addition, 19 known breast cancer risk loci have genome-wide significant associations and 40 had moderate associations (P<0.05) with ER-negative disease. Using functional and eQTL studies we implicate TRMT61B and WDR43 at 2p23.2 and PPIL3 at 2q33 in ER-negative breast cancer aetiology. All ER-negative loci combined account for similar to 11% of familial relative risk for ER-negative disease and may contribute to improved ER-negative and BRCA1 breast cancer risk prediction.
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6.
  • Das, Rasel, et al. (författare)
  • Nanocellulose for Sustainable Water Purification
  • 2022
  • Ingår i: Chemical Reviews. - : American Chemical Society (ACS). - 0009-2665 .- 1520-6890. ; 122:9, s. 8936-9031
  • Forskningsöversikt (refereegranskat)abstract
    • Nanocelluloses (NC) are nature-based sustainable biomaterials, which not only possess cellulosic properties but also have the important hallmarks of nanomaterials, such as large surface area, versatile reactive sites or functionalities, and scaffolding stability to host inorganic nanoparticles. This class of nanomaterials offers new opportunities for a broad spectrum of applications for clean water production that were once thought impractical. This Review covers substantial discussions based on evaluative judgments of the recent literature and technical advancements in the fields of coagulation/flocculation, adsorption, photocatalysis, and membrane filtration for water decontamination through proper understanding of fundamental knowledge of NC, such as purity, crystallinity, surface chemistry and charge, suspension rheology, morphology, mechanical properties, and film stability. To supplement these, discussions on low-cost and scalable NC extraction, new characterizations including solution small-angle X-ray scattering evaluation, and structure-property relationships of NC are also reviewed. Identifying knowledge gaps and drawing perspectives could generate guidance to overcome uncertainties associated with the adaptation of NC-enabled water purification technologies. Furthermore, the topics of simultaneous removal of multipollutants disposal and proper handling of post/spent NC are discussed. We believe NC-enabled remediation nanomaterials can be integrated into a broad range of water treatments, greatly improving the cost-effectiveness and sustainability of water purification.
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7.
  • Geng, Lihong, et al. (författare)
  • Structure characterization of cellulose nanofiber hydrogel as functions of concentration and ionic strength
  • 2017
  • Ingår i: Cellulose. - : Springer Netherlands. - 0969-0239 .- 1572-882X. ; 24:12, s. 5417-5429
  • Tidskriftsartikel (refereegranskat)abstract
    • Carboxylated cellulose nanofibers (CNFs), having an average width of 7 nm and thickness of 1.5 nm, were produced by TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl radical)-mediated oxidation method. The fiber cross-sectional dimensions were determined using small-angle X-ray scattering (SAXS), transmission electron microscopy and atomic force microscopy techniques, where the rheological properties under different concentration and ionic strength were also investigated. The formation of hydrogel was evidenced by increasing the CNF concentration or ionic strength of the solvent (water), while the gel structure in ion-induced CNF hydrogels was found to be relatively inhomogeneous. The gelation behavior was closely related to the segmental aggregation of charged CNF, which could be quantitatively characterized by the correlation length (Ο) from the low-angle scattering profile and the scattering invariant (Q) in SAXS.
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8.
  • Geng, Lihong, et al. (författare)
  • Understanding the Mechanistic Behavior of Highly Charged Cellulose Nanofibers in Aqueous Systems
  • 2018
  • Ingår i: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 51:4, s. 1498-1506
  • Tidskriftsartikel (refereegranskat)abstract
    • Mechanistic behavior and flow properties of cellulose nanofibers (CNFs) in aqueous systems can be described by the crowding factor and the concept of contact points, which are functions of the aspect ratio and concentration of CNF in the suspension. In this study, CNFs with a range of aspect ratio and surface charge density (380-1360 mu mol/g) were used to demonstrate this methodology. It was shown that the critical networking point of the CNF suspension, determined by rheological measurements, was consistent with the gel crowding factor, which was 16. Correlated to the crowding factor, both viscosity and modulus of the systems were found to decrease by increasing the charge density of CNF, which also affected the flocculation behavior. Interestingly, an anomalous rheological behavior was observed near the overlap concentration (0.05 wt %) of CNF, at which the crowding factor was below the gel crowding factor, and the storage modulus (G') decreased dramatically at a given frequency threshold. This behavior is discussed in relation to the breakup of the entangled flocs and network in the suspension. The analysis of the mechanistic behavior of CNF aqueous suspensions by the crowding factor provides useful insight for fabricating high-performance nanocellulose-based materials.
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9.
  • Khandelwal, Akanksha, et al. (författare)
  • Discovery of an inflated hot Jupiter around a slightly evolved star TOI-1789
  • 2022
  • Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 509:3, s. 3339-3354
  • Tidskriftsartikel (refereegranskat)abstract
    • We report here the discovery of a hot Jupiter at an orbital period of 3.208664 ± 0.000015 d around TOI-1789 (TYC 1962-00303-1, TESSmag = 9.1) based on the TESS photometry, ground-based photometry, and high-precision radial velocity (RV) observations. The high-precision RV observations were obtained from the high-resolution spectrographs, PARAS at Physical Research Laboratory (PRL), India, and TCES at Thüringer Landessternwarte Tautenburg (TLS), Germany, and the ground-based transit observations were obtained using the 0.43-m telescope at PRL with the Bessel-R filter. The host star is a slightly evolved (log g∗ = 3.943+0.023-0.043), late F-type (Teff= 5991 ± 55 K), metal-rich star ([Fe/H] = 0.373+0.071-0.086 dex) with a radius of R ∗ = 2.168+0.036}-0.034 R located at a distance of 223.53+0.91-0.90} pc. The simultaneous fitting of the multiple light curves and the RV data of TOI-1789 reveals that TOI-1789 b has a mass of MP = 0.70 ± 0.16 MJ, a radius of RP = 1.44+0.24-0.14, RJ, and a bulk density of ρP = 0.28+0.14-0.12 g cm-3 with an orbital separation of a = 0.04882+0.00063-0.0016 au. This puts TOI-1789 b in the category of inflated hot Jupiters. It is one of the few nearby evolved stars with a close-in planet. The detection of such systems will contribute to our understanding of mechanisms responsible for inflation in hot Jupiters and also provide an opportunity to understand the evolution of planets around stars leaving the main-sequence branch.
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10.
  • Lu, Yingchang, et al. (författare)
  • A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk.
  • 2018
  • Ingår i: Cancer Research. - 0008-5472 .- 1538-7445. ; 78:18, s. 5419-5430
  • Tidskriftsartikel (refereegranskat)abstract
    • .AbstractLarge-scale genome-wide association studies (GWAS) have identified approximately 35 loci associated with epithelial ovarian cancer (EOC) risk. The majority of GWAS-identified disease susceptibility variants are located in noncoding regions, and causal genes underlying these associations remain largely unknown. Here, we performed a transcriptome-wide association study to search for novel genetic loci and plausible causal genes at known GWAS loci. We used RNA sequencing data (68 normal ovarian tissue samples from 68 individuals and 6,124 cross-tissue samples from 369 individuals) and high-density genotyping data from European descendants of the Genotype-Tissue Expression (GTEx V6) project to build ovarian and cross-tissue models of genetically regulated expression using elastic net methods. We evaluated 17,121 genes for their cis-predicted gene expression in relation to EOC risk using summary statistics data from GWAS of 97,898 women, including 29,396 EOC cases. With a Bonferroni-corrected significance level of P < 2.2 × 10−6, we identified 35 genes, including FZD4 at 11q14.2 (Z = 5.08, P = 3.83 × 10−7, the cross-tissue model; 1 Mb away from any GWAS-identified EOC risk variant), a potential novel locus for EOC risk. All other 34 significantly associated genes were located within 1 Mb of known GWAS-identified loci, including 23 genes at 6 loci not previously linked to EOC risk. Upon conditioning on nearby known EOC GWAS-identified variants, the associations for 31 genes disappeared and three genes remained (P < 1.47 × 10−3). These data identify one novel locus (FZD4) and 34 genes at 13 known EOC risk loci associated with EOC risk, providing new insights into EOC carcinogenesis.Significance: Transcriptomic analysis of a large cohort confirms earlier GWAS loci and reveals FZD4 as a novel locus associated with EOC risk. Cancer Res; 78(18); 5419–30. ©2018 AACR.
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