| 1. |
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| 2. |
- Kumar, Vimal, et al.
(författare)
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Multiphase fluid flow and heat transfer characteristics in microchannels
- 2017
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Ingår i: Chemical Engineering Science. - : Elsevier BV. - 0009-2509. ; 169, s. 34-66
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Tidskriftsartikel (refereegranskat)abstract
- The boiling flow or condensation is widely encountered in many industrial applications for both cooling as well as heating processes. Compact heat transfer devices, such as micro-heat exchangers and evaporators, are extensively used for both cooling as well as heating processes over conventional heat exchangers, such as microelectronic circuits, automobile and aerospace industries, due to high surface area to volume ratio and heat transfer rates, compactness and easy thermal control. For better design of micro- or mini-heat exchangers, a detailed specific knowledge of the multiphase flow and its properties such as the flow pattern during flow boiling, critical heat flux (CHF) and stable operation are very important. This paper provides a state of art review on boiling flow in microchannels since year 2000 till date. Flow patterns formed and the parameters influencing flow pattern transitions, during multiphase heat transfer in micro- or mini-channels, have been reviewed in detail. The flow regimes and flow pattern maps, and modeling approaches considered for boiling flow in micro-channels/devices with various challenges have been discussed. A lot of contradiction between the experimental data has been observed for the analysis of flow regimes and flow pattern maps. Further, the effect of hydrodynamics during flow boiling and CHF on heat transfer coefficient has been discussed in detail. Recently, with the advancement in measurement techniques, the heat transfer measurement technologies have been synchronized with the visualization techniques, which helped in understanding the boiling flow physics in micro- and mini-channels. Therefore, an in-depth understanding of flow patterns and regimes under boiling flow conditions in mini- and micro-channels can be used to predict the boiling heat transfer mechanism, which can be further used for developing better heat transfer models for boiling flow. Further, enhancement in heat transfer coefficient for boiling flow in microchannels, either by using complex microchannel configurations or nanocoating on the microchannel surface, have received attention recently, which have been discussed and analyzed in the present review. Both micro- and mini-channels have number of applications in aerospace, refrigeration and computational systems; therefore further attention is needed for more robust and precise design.
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| 3. |
- Kushwaha, Naveen, et al.
(författare)
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Impact of mixed convective and radiative heat transfer in spiral-coiled tubes
- 2019
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Ingår i: Transactions - ASME : Journal of Heat Transfer. - : ASME International. - 0022-1481 .- 1528-8943. ; 141:8
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Tidskriftsartikel (refereegranskat)abstract
- Spiral-coiled tube heat exchangers (SCTHE) have higher heat transfer as compared to the conventional heat transfer devices and are extensively used to extract heat from exhaust gases in the chemical processing industries and also from sunlight for domestic applications. However, no attention has been made to predict heat transfer characteristics considering combined convective and radiative heat transfer in spiral-coiled tubes. In the present study, numerical analysis has been performed to predict fluid flow and heat transfer characteristics by combined forced convection and thermal radiation in spiralcoiled tubes. The P-1 radiation and the renormalized group (RNG) k–e turbulence models have been used to study the effect of thermal radiation and turbulent convection heat transfer in the spiral-coiled tube, respectively, over a wide range of Reynolds numbers (10,000–100,000) and curvature ratios (0.02–0.05). The emissivity and optical thickness have been varied from 0.0 to 1.0 and 0.0 to 8.0, respectively, to investigate the effect of thermal radiation on heat transfer characteristics in spiral-coiled tubes. For the considered Reynolds number range, it is found that the heat transfer is enhanced by approximately 10% when radiation is taken into account. It is found that the heat capacity increased with an increase in optical thickness and wall emissivity. Further, the effect of optical thickness on fully developed flow is observed weak and the average heat transfer coefficient is influenced by the wall emissivity over the entire flow.
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| 4. |
- Ravi, Vikash Kumar, et al.
(författare)
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Origin of the Substitution Mechanism for the Binding of Organic Ligands on the Surface of CsPbBr3 Perovskite Nanocubes
- 2017
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Ingår i: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 8:20, s. 4988-4994
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Tidskriftsartikel (refereegranskat)abstract
- Optoelectronic properties of CsPbBr3 perovskite nanocubes (NCs) depend strongly on the interaction of the organic passivating molecules with the inorganic crystal. To understand this interaction, we employed a combination of synchrotron-based X-ray photoelectron spectroscopy (XPS), nuclear magnetic resonance (NMR) spectroscopy, and first-principles density functional theory (DFT)-based calculations. Variable energy XPS elucidated the internal structure of the inorganic part in a layer-by-layer fashion, whereas NMR characterized the organic ligands. Our experimental results confirm that oleylammonium ions act as capping ligands by substituting Cs+ ions from the surface of CsPbBr3 NCs. DFT calculations shows that the substitution mechanism does not require much energy for surface reconstruction and, in contrast, stabilizes the nanocrystal by the formation of three hydrogen bonds between the -NH3(+) moiety of oleylammonium and surrounding Br- on the surface of NCs. This substitution mechanism and its origin are in stark contrast to the usual adsorption of organic ligands on the surface of typical NCs.
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| 5. |
- Rose, Pawan Kumar, et al.
(författare)
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Congo red dye removal using modified banana leaves : Adsorption equilibrium, kinetics, and reusability analysis
- 2023
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Ingår i: Groundwater for Sustainable Development. - : Elsevier BV. - 2352-801X. ; 23
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Tidskriftsartikel (refereegranskat)abstract
- Congo red (CR) dye is a synthetic azo dye expansively used in the textile industry, is discharged to aquatic environments, and is toxic to humans and aquatic flora. The performance of cationic amino-modified banana leaves (CMBL) for CR dye sequestration was evaluated first time in this study. The surface modification of CMBL was analyzed using Scanning electron microscope (SEM) and Fourier transform infrared (FTIR) spectrum and compared with raw banana leaves powder (RBL). The optimum condition for CR dye adsorption using CMBL was optimized using Central Composite Design (CCD) by investigating four critical operating parameters: contact time, pH, RBL/CMBL doses, and initial CR dye concentrations. The proposed model (quadratic) was acceptable due to the high values of correlation coefficients R2 (0.96) and adjusted R2 (0.92). The CMBL exhibited maximum removal efficiency of 76.82% towards CR dye at pH 3 compared to RBL, i.e., 19.63%. Electrostatic interaction and hydrogen bonding were the primary removal mechanisms for the CR dye adsorption process using CMBL. Freundlich isotherm and pseudo-second-order kinetic model exhibited a strong correlation for experimental data and reported a correlation coefficient (R2) of more than 0.99. In addition, CMBL showed excellent reusability for the adsorption of CR dye even after three consecutive adsorption-desorption experiments.
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| 6. |
- Sundell, David, et al.
(författare)
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AspWood : High-Spatial-Resolution Transcriptome Profiles Reveal Uncharacterized Modularity of Wood Formation in Populus tremula
- 2017
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Ingår i: The Plant Cell. - : Oxford University Press (OUP). - 1040-4651 .- 1532-298X. ; 29:7, s. 1585-1604
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Tidskriftsartikel (refereegranskat)abstract
- Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, and efforts to engineer elite varieties will benefit from improved understanding of the transcriptional network underlying cambial growth and wood formation. We generated high-spatial-resolution RNA sequencing data spanning the secondary phloem, vascular cambium, and wood-forming tissues of Populus tremula. The transcriptome comprised 28,294 expressed, annotated genes, 78 novel protein-coding genes, and 567 putative long intergenic noncoding RNAs. Most paralogs originating from the Salicaceae whole-genome duplication had diverged expression, with the exception of those highly expressed during secondary cell wall deposition. Coexpression network analyses revealed that regulation of the transcriptome underlying cambial growth and wood formation comprises numerous modules forming a continuum of active processes across the tissues. A comparative analysis revealed that a majority of these modules are conserved in Picea abies. The high spatial resolution of our data enabled identification of novel roles for characterized genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and lignification. An associated web resource (AspWood, http://aspwood.popgenie.org) provides interactive tools for exploring the expression profiles and coexpression network.
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| 7. |
- Sundell, David, et al.
(författare)
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High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula
- 2016
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, however, efforts to engineer new, elite varieties are constrained by the lack of a comprehensive understanding of the transcriptional network underlying cambial growth and wood formation. We generated RNA Sequencing transcriptome data for four mature, wild-growing aspens (Populus tremula) from high-spatial-resolution tangential cryosection series spanning the secondary phloem, vascular cambium, expanding and secondary cell wall forming xylem cells, cell death zone and the previous years annual ring. The transcriptome comprised 28,294 expressed, previously annotated protein-coding genes, 78 novel protein-coding genes and 567 long intergenic non-coding RNAs. Most paralogs originating from the Salicaceae whole genome duplication had diverged expression, with the notable exception of those with high expression during secondary cell wall deposition. We performed co-expression network analysis to identify central transcriptional modules and associated several of these with known biological processes. This revealed previously uncharacterized complexity underlying the regulation of cambial growth and wood formation, with modules forming a continuum of activated processes across the tissues. The high spatial resolution suggested novel roles for known genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and components of lignification. The associated web resource (AspWood, http://aspwood.popgenie.org) integrates the data within a set of interactive tools for exploring the co-expression network of cambial growth and wood formation.
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| 8. |
- Vikash, Vikash, 1987, et al.
(författare)
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Design and development of high shear mixers: Fundamentals, applications and recent progress
- 2021
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Ingår i: Chemical Engineering Science. - : Elsevier BV. - 0009-2509. ; 232
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Tidskriftsartikel (refereegranskat)abstract
- Dispersion of liquids/particles is a key important requirement in a variety of applications including coatings and paints, cosmetics, healthcare, food, and pharmaceutical processes. In all these industrial processes high intensity of energy is required to overcome the adhesion forces or increasing interfacial surface area per unit volume, which is achieved by high-pressure homogenizers, ultrasonic-assisted devices, and high shear mixers (HSMs). In this paper, HSMs are critically reviewed based on their design and development, and applications (such as dispersion of nanoparticles, emulsification, and mixing) in recent years. HSMs are comprised of rotational (rotor) and stationary (stator) parts with a small gap in between. It is found that there is a significant influence of stator geometry on the uniform size distribution as well as energy dissipation. Though there is extensive work on hydrodynamics and mixing in HSMs are available however, still there is no specific scale-up/down criterion is available for HSMs.
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| 9. |
- Vikash, Vikash, 1987, et al.
(författare)
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Effect of stator geometries on flow fields and mixing performance for viscous fluids
- 2022
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Ingår i: Chemical Engineering and Processing: Process Intensification. - : Elsevier BV. - 0255-2701. ; 180
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Tidskriftsartikel (refereegranskat)abstract
- High shear mixers (HSMs) find wide applications in industrial processes where intense mixing and dispersion of fluids play a vital role. In this work, the flow fields and mixing performance is analyzed in different batch HSMs with varying stator heads, such as disintegrated, slotted, and mesh. Further, the effect of viscosity, flow behavior and rotor speed on hydrodynamics and mixing performance is assessed through numerical investigations. The turbulent flow fields and mixing enhancement are characterized using standard k-ε turbulence model with multiple reference frames approach for various HSMs. The turbulent statistics like turbulent kinetic energy are found to be maximum in the stator hole region and varied with flow behavior. The energy dissipation within the rotor vicinity is found higher for mesh head geometry followed by disintegrated and slotted heads. The effect of tracer injection locations is evaluated to gain comprehensive information on the mixing performance inside the mixing tank. Mixing time (t95) was evaluated and correlated with the existing results. For viscous fluids, complete mixing is hard to achieve due to the presence of cavern effect in smaller stator holes HSM. Moreover, the results provided guidance for further selection, design and development of HSMs for process industries.
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| 10. |
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| 11. |
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| 12. |
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| 13. |
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| 14. |
- Vikash, Vikash, 1987, et al.
(författare)
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Mixing characterization in batch rotor-stator mixer
- 2018
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Mixing characterization of existing batch rotor-stator mixer (RSM) is studied at different rotor speeds (2000, 4000 and 6000 rpm) for two different geometries with different stator heads, such as circular and square. Flow parameters such as mass flow rate, Power number and energy dissipation rate have been investigated in both geometries.
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| 15. |
- Vikash, Vikash, 1987, et al.
(författare)
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Nanoparticle de-agglomeration in viscous fluids using different high shear mixer geometries
- 2022
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Ingår i: Chemical Engineering Science. - : Elsevier BV. - 0009-2509. ; 248:Part A
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Tidskriftsartikel (refereegranskat)abstract
- In the present work, the effect of batch high shear mixer (HSM) geometries is studied on nanoparticles deagglomeration and power draw in water and aqueous glycerol solutions. The kinetics and mechanism of cluster break-up are investigated for disintegrated (less number of larger stator holes), and mesh (higher number of smaller stator holes) heads at different rotor speeds. Mesh head geometry is found to be more efficient for fines generation than disintegrated head. A bi-modal particle size distribution and erosion as dominant break-up mechanism is found. The size of the smallest fines is found to be ≈30 nm for mesh head and ≈50 nm for the disintegrated head. Z-average ranges from 180 to 310 nm for given operating and process conditions. The power draw is more in mesh head and increased with an increase in viscosity. Further, power draw increased with an increase in viscosity of continuous media and rotor speed.
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| 16. |
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| 17. |
- Vikash, Vikash, 1987, et al.
(författare)
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Turbulent statistics of flow fields using large eddy simulations in batch high shear mixers
- 2019
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Ingår i: Chemical Engineering Research and Design. - : Elsevier BV. - 0263-8762 .- 1744-3563. ; 147, s. 561-569
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Tidskriftsartikel (refereegranskat)abstract
- Large eddy simulations (LES) have been carried out for the first time to characterize the flow and turbulent characteristics in three different batch high shear mixers (HSMs) at a constant rotor speed of 4000 rpm. Three HSMs having different stator heads such as circular, square and inclined stator head with 6, 92 and 210 numbers of stator holes, respectively have been investigated. Dynamic Smagorinsky model with sliding mesh method is used for the sub-grid scale stresses at a Reynolds number of 52,000, to overcome the prediction of RANS models. Numerical methodology is validated, in terms of Power number with the available numerical and experimental studies and found in fairly good agreement. The velocity flow patterns and fluctuations at different planes are predicted and vortexes have been observed within the stator holes and bulk fluid. It is observed that velocity magnitude fluctuation isa function of rotor rotations and stator holes size, and fluctuations in one jets emerging from stator holes affect the fluctuations in other plane jets. Further, it is found that smaller the stator holes size, greater is the energy distribution and hence greater will be the drop size distribution in the mixer. Therefore, the inclined stator head HSM can be used for the uniform size distribution in application to de-agglomeration and dispersion. It is found that the energy spectrum of Kolmogorov is followed over the entire length scale for all HSMs and LES provided the richer flow and turbulent information as compared to RANS model.
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| 18. |
- Vikash, Vikash, 1987, et al.
(författare)
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Ultrasonic-assisted de-agglomeration and power draw characterization of silica nanoparticles
- 2020
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Ingår i: Ultrasonics Sonochemistry. - : Elsevier BV. - 1873-2828 .- 1350-4177. ; 65:July
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Tidskriftsartikel (refereegranskat)abstract
- Breakage of nanoparticle cluster require high-intensity devices for stable and uniform distribution of aggregates. The ultra-sonication process is a high energy-intensive technique that produces cavitation effect to break the aggregates. In the present study, ultra-sonication is used for the de-agglomeration of fumed silica nanoparticles in low to high viscosity liquids. Water- and glycerol-based dispersion has been investigated at different solid loadings (up to 10 wt% for water-based dispersion and 5 wt% in glycerol-based dispersion) and viscosity of continuous phase (1–100 mPa.s). Breakup mechanism and kinetics have been studied at optimized operating conditions and no significant effect is found at different solid loadings on breakup mechanism. Particle size measurements are reported and found that volume of fine generation increased with an increase in sonication time. Further, it is observed that the stability of dispersion in the liquid is very high even at high concentration of solid used. Larger agglomerates are found at high viscosity of continuous phase and a lag is also observed for 100 mPa.s glycerol solution even at low solid loading (1 wt%). From, rheological characterizations it is found that the behavior of dispersed solution changed with time, temperature and solid loading. Erosion is found to be the breakup mechanism and further, validated with scattering light characterization. Furthermore, power draw increased with an increase in the viscosity of continuous phase, however, no significant effect of solid loading is observed. It is also observed that process is more energy-efficient at higher solid loading as the volume of fine produced is more as compared to low solid loading. Therefore, it can be concluded that the stable and uniform dispersion of nanoparticles can be achieved using an ultra-sonication device at high solid loading in viscous liquids.
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| 19. |
- Cruciani, Silvia, 1991-, et al.
(författare)
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Benchmarking In-Hand Manipulation
- 2020
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Ingår i: IEEE Robotics and Automation Letters. - : Institute of Electrical and Electronics Engineers (IEEE). - 2377-3766. ; 5:2, s. 588-595
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Tidskriftsartikel (refereegranskat)abstract
- The purpose of this benchmark is to evaluate the planning and control aspects of robotic in-hand manipulation systems. The goal is to assess the systems ability to change the pose of a hand-held object by either using the fingers, environment or a combination of both. Given an object surface mesh from the YCB data-set, we provide examples of initial and goal states (i.e. static object poses and fingertip locations) for various in-hand manipulation tasks. We further propose metrics that measure the error in reaching the goal state from a specific initial state, which, when aggregated across all tasks, also serves as a measure of the systems in-hand manipulation capability. We provide supporting software, task examples, and evaluation results associated with the benchmark.
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| 20. |
- Davey, Norman E., et al.
(författare)
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Discovery of short linear motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome
- 2017
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Ingår i: The FEBS Journal. - : Wiley. - 1742-464X .- 1742-4658. ; 284:3, s. 485-498
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Tidskriftsartikel (refereegranskat)abstract
- The intrinsically disordered regions of eukaryotic proteomes are enriched in short linear motifs (SLiMs), which are of crucial relevance for cellular signaling and protein regulation; many mediate interactions by providing binding sites for peptide-binding domains. The vast majority of SLiMs remain to be discovered highlighting the need for experimental methods for their large-scale identification. We present a novel proteomic peptide phage display (ProP-PD) library that displays peptides representing the disordered regions of the human proteome, allowing direct large-scale interrogation of most potential binding SLiMs in the proteome. The performance of the ProP-PD library was validated through selections against SLiM-binding bait domains with distinct folds and binding preferences. The vast majority of identified binding peptides contained sequences that matched the known SLiM-binding specificities of the bait proteins. For SHANK1 PDZ, we establish a novel consensus TxF motif for its non-C-terminal ligands. The binding peptides mostly represented novel target proteins, however, several previously validated protein-protein interactions (PPIs) were also discovered. We determined the affinities between the VHS domain of GGA1 and three identified ligands to 40-130 mu M through isothermal titration calorimetry, and confirmed interactions through coimmunoprecipitation using full-length proteins. Taken together, we outline a general pipeline for the design and construction of ProP-PD libraries and the analysis of ProP-PD-derived, SLiM-based PPIs. We demonstrated the methods potential to identify low affinity motif-mediated interactions for modular domains with distinct binding preferences. The approach is a highly useful complement to the current toolbox of methods for PPI discovery.
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| 21. |
- Donev, Evgeniy N., et al.
(författare)
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Field testing of transgenic aspen from large greenhouse screening identifies unexpected winners
- 2023
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Ingår i: Plant Biotechnology Journal. - : Wiley. - 1467-7644 .- 1467-7652. ; 21:5, s. 1005-1021
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Tidskriftsartikel (refereegranskat)abstract
- Trees constitute promising renewable feedstocks for biorefinery using biochemical conversion, but their recalcitrance restricts their attractiveness for the industry. To obtain trees with reduced recalcitrance, large-scale genetic engineering experiments were performed in hybrid aspen blindly targeting genes expressed during wood formation and 32 lines representing seven constructs were selected for characterization in the field. Here we report phenotypes of five-year old trees considering 49 traits related to growth and wood properties. The best performing construct considering growth and glucose yield in saccharification with acid pretreatment had suppressed expression of the gene encoding an uncharacterized 2-oxoglutarate-dependent dioxygenase (2OGD). It showed minor changes in wood chemistry but increased nanoporosity and glucose conversion. Suppressed levels of SUCROSE SYNTHASE, (SuSy), CINNAMATE 4-HYDROXYLASE (C4H) and increased levels of GTPase activating protein for ADP-ribosylation factor ZAC led to significant growth reductions and anatomical abnormalities. However, C4H and SuSy constructs greatly improved glucose yields in saccharification without and with pretreatment, respectively. Traits associated with high glucose yields were different for saccharification with and without pretreatment. While carbohydrates, phenolics and tension wood contents positively impacted the yields without pretreatment and growth, lignin content and S/G ratio were negative factors, the yields with pretreatment positively correlated with S lignin and negatively with carbohydrate contents. The genotypes with high glucose yields had increased nanoporosity and mGlcA/Xyl ratio, and some had shorter polymers extractable with subcritical water compared to wild-type. The pilot-scale industrial-like pretreatment of best-performing 2OGD construct confirmed its superior sugar yields, supporting our strategy.
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| 22. |
- Huguet, Carme, et al.
(författare)
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Temperature and Monsoon Tango in a Tropical Stalagmite: Last Glacial-Interglacial Climate Dynamics
- 2018
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Ingår i: Scientific Reports. - : NATURE PUBLISHING GROUP. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- High-resolution paleoclimate data on stable isotopes in a stalagmite were coupled to glycerol dialkyl glycerol tetraethers (GDGTs). The Indian Summer Monsoon (ISM) transitioned from limited rainfall during the Last Glacial Maximum (LGM) to intense precipitation during early Holocene (22 to 6 ka). This was associated with changes in stalagmite growth, abundance of branched (br) and isoprenoid (iso) GDGTs, as well as delta O-18, delta C-13, Sr/Ca and GDGT-derived signals providing both temperature and moisture information. The reconstructed mean annual air temperature (MAAT) of the most modern stalagmite sample at similar to 19 degrees C, matches the surface and cave MAAT, but was similar to 4 degrees C lower during LGM. Warming at the end of LGM occurred before ISM strengthened and indicate 6 ka lag consistent with sea surface temperature records. The isotope records during the Younger Dryas show rapid progressions to dry conditions and weak monsoons, but these shifts are not coupled to TEX86. Moreover, change to wetter and stronger ISM, along with warmer Holocene conditions are not continuous indicating a decoupling of local temperatures from ISM.
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| 23. |
- Kallionpää, Henna, et al.
(författare)
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Early Detection of Peripheral Blood Cell Signature in Children Developing beta-Cell Autoimmunity at a Young Age
- 2019
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Ingår i: Diabetes. - : American Diabetes Association. - 0012-1797 .- 1939-327X. ; 68:10, s. 2024-2034
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Tidskriftsartikel (refereegranskat)abstract
- The appearance of type 1 diabetes (T1D)-associated autoantibodies is the first and only measurable parameter to predict progression toward T1D in genetically susceptible individuals. However, autoantibodies indicate an active autoimmune reaction, wherein the immune tolerance is already broken. Therefore, there is a clear and urgent need for new biomarkers that predict the onset of the autoimmune reaction preceding autoantibody positivity or reflect progressive beta-cell destruction. Here we report the mRNA sequencing-based analysis of 306 samples including fractionated samples of CD4(+) and CD8(+) T cells as well as CD4(-)CD8(-) cell fractions and unfractionated peripheral blood mononuclear cell samples longitudinally collected from seven children who developed beta-cell autoimmunity (case subjects) at a young age and matched control subjects. We identified transcripts, including interleukin 32 (IL32), that were upregulated before T1D-associated autoantibodies appeared. Single-cell RNA sequencing studies revealed that high IL32 in case samples was contributed mainly by activated T cells and NK cells. Further, we showed that IL32 expression can be induced by a virus and cytokines in pancreatic islets and beta-cells, respectively. The results provide a basis for early detection of aberrations in the immune system function before T1D and suggest a potential role for IL32 in the pathogenesis of T1D.
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| 24. |
- Kumar, Vikash, et al.
(författare)
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Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development
- 2020
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Ingår i: Frontiers in Plant Science. - : FRONTIERS MEDIA SA. - 1664-462X. ; 11, s. 1-20
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Tidskriftsartikel (refereegranskat)abstract
- Malectin domain (MD) is a ligand-binding protein motif of pro- and eukaryotes. It is particularly abundant in Viridiplantae, where it occurs as either a single (MD, PF11721) or tandemly duplicated domain (PF12819) called malectin-like domain (MLD). In herbaceous plants, MD- or MLD-containing proteins (MD proteins) are known to regulate development, reproduction, and resistance to various stresses. However, their functions in woody plants have not yet been studied. To unravel their potential role in wood development, we carried out genome-wide identification of MD proteins in the model tree species black cottonwood (Populus trichocarpa), and analyzed their expression and co-expression networks. P. trichocarpa had 146 MD genes assigned to 14 different clades, two of which were specific to the genus Populus. 87% of these genes were located on chromosomes, the rest being associated with scaffolds. Based on their protein domain organization, and in agreement with the exon-intron structures, the MD genes identified here could be classified into five superclades having the following domains: leucine-rich repeat (LRR)-MD-protein kinase (PK), MLD-LRR-PK, MLD-PK (CrRLK1L), MLD-LRR, and MD-Kinesin. Whereas the majority of MD genes were highly expressed in leaves, particularly under stress conditions, eighteen showed a peak of expression during secondary wall formation in the xylem and their co-expression networks suggested signaling functions in cell wall integrity, pathogen-associated molecular patterns, calcium, ROS, and hormone pathways. Thus, P. trichocarpa MD genes having different domain organizations comprise many genes with putative foliar defense functions, some of which could be specific to Populus and related species, as well as genes with potential involvement in signaling pathways in other tissues including developing wood.
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| 25. |
- Kumar, Vikash, et al.
(författare)
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Poplar carbohydrate-active enzymes : whole-genome annotation and functional analyses based on RNA expression data
- 2019
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Ingår i: The Plant Journal. - Hoboken : John Wiley & Sons. - 0960-7412 .- 1365-313X. ; 99:4, s. 589-609
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Tidskriftsartikel (refereegranskat)abstract
- Carbohydrate-active enzymes (CAZymes) catalyze the formation and modification of glycoproteins, glycolipids, starch, secondary metabolites and cell wall biopolymers. They are key enzymes for the biosynthesis of food and renewable biomass. Woody biomass is particularly important for long-term carbon storage and as an abundant renewable natural resource for many industrial applications. This study presents a re-annotation of CAZyme genes in the current Populus trichocarpa genome assembly and in silico functional characterization, based on high-resolution RNA-Seq data sets. Altogether, 1914 CAZyme and expansin genes were annotated in 101 families. About 1797 of these genes were found expressed in at least one Populus organ. We identified genes involved in the biosynthesis of different cell wall polymers and their paralogs. Whereas similar families exist in poplar and Arabidopsis thaliana (with the exception of CBM13 found only in poplar), a few families had significantly different copy numbers between the two species. To identify the transcriptional coordination and functional relatedness within the CAZymes and other proteins, we performed co-expression network analysis of CAZymes in wood-forming tissues using the AspWood database () for Populus tremula. This provided an overview of the transcriptional changes in CAZymes during the transition from primary to secondary wall formation, and the clustering of transcripts into potential regulons. Candidate enzymes involved in the biosynthesis of polysaccharides were identified along with many tissue-specific uncharacterized genes and transcription factors. These collections offer a rich source of targets for the modification of secondary cell wall biosynthesis and other developmental processes in woody plants.
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| 26. |
- Kushwah, Sunita, et al.
(författare)
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Arabidopsis XTH4 and XTH9 Contribute to Wood Cell Expansion and Secondary Wall Formation(1)([OPEN])
- 2020
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Ingår i: Plant Physiology. - : American Society of Plant Science. - 0032-0889 .- 1532-2548. ; 182:4, s. 1946-1965
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Tidskriftsartikel (refereegranskat)abstract
- Xyloglucan is the major hemicellulose of dicotyledon primary cell walls, affecting the load-bearing framework with the participation of xyloglucan endo-transglycosylase/hydrolases (XTHs). We used loss- and gain-of function approaches to study functions of XTH4 and XTH9 abundantly expressed in cambial regions during secondary growth of Arabidopsis (Arabidopsis thaliana). In secondarily thickened hypocotyls, these enzymes had positive effects on vessel element expansion and fiber intrusive growth. They also stimulated secondary wall thickening but reduced secondary xylem production. Cell wall analyses of inflorescence stems revealed changes in lignin, cellulose, and matrix sugar composition indicating an overall increase in secondary versus primary walls in mutants, indicative of higher xylem production compared with the wild type (since secondary walls were thinner). Intriguingly, the number of secondary cell wall layers compared with the wild type was increased in xth9 and reduced in xth4, whereas the double mutant xth4x9 displayed an intermediate number of layers. These changes correlated with specific Raman signals from the walls, indicating changes in lignin and cellulose. Secondary walls were affected also in the interfascicular fibers, where neither XTH4 nor XTH9 was expressed, indicating that these effects were indirect. Transcripts involved in secondary wall biosynthesis and cell wall integrity sensing, including THESEUS1 and WALL ASSOCIATED KINASE2, were highly induced in the mutants, indicating that deficiency in XTH4 and XTH9 triggers cell wall integrity signaling, which, we propose, stimulates xylem cell production and modulates secondary wall thickening. Prominent effects of XTH4 and XTH9 on secondary xylem support the hypothesis that altered xyloglucan affects wood properties both directly and via cell wall integrity sensing.
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| 27. |
- Li, Yitong, et al.
(författare)
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Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition
- 2022
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Ingår i: eLIFE. - : eLife Sciences Publications Ltd. - 2050-084X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Protein phosphatase 2A (PP2A) holoenzymes target broad substrates by recognizing short motifs via regulatory subunits. PP2A methylesterase 1 (PME-1) is a cancer-promoting enzyme and undergoes methylesterase activation upon binding to the PP2A core enzyme. Here, we showed that PME-1 readily demethylates different families of PP2A holoenzymes and blocks substrate recognition in vitro. The high-resolution cryoelectron microscopy structure of a PP2A-B56 holoenzyme-PME-1 complex reveals that PME-1 disordered regions, including a substrate-mimicking motif, tether to the B56 regulatory subunit at remote sites. They occupy the holoenzyme substratebinding groove and allow large structural shifts in both holoenzyme and PME-1 to enable multipartite contacts at structured cores to activate the methylesterase. B56 interface mutations selectively block PME-1 activity toward PP2A-B56 holoenzymes and affect the methylation of a fraction of total cellular PP2A. The B56 interface mutations allow us to uncover B56-specific PME-1 functions in p53 signaling. Our studies reveal multiple mechanisms of PME-1 in suppressing holoenzyme functions and versatile PME-1 activities derived from coupling substrate-mimicking motifs to dynamic structured cores.
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| 28. |
- Moreno Romero, Jordi, et al.
(författare)
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Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm
- 2019
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1474-760X. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundImprinted genes are epigenetically modified during gametogenesis and maintain the established epigenetic signatures after fertilization, causing parental-specific gene expression.ResultsIn this study, we show that imprinted paternally expressed genes (PEGs) in the Arabidopsis endosperm are marked by an epigenetic signature of Polycomb Repressive Complex2 (PRC2)-mediated H3K27me3 together with heterochromatic H3K9me2 and CHG methylation, which specifically mark the silenced maternal alleles of PEGs. The co-occurrence of H3K27me3 and H3K9me2 on defined loci in the endosperm drastically differs from the strict separation of both pathways in vegetative tissues, revealing tissue-specific employment of repressive epigenetic pathways in plants. Based on the presence of this epigenetic signature on maternal alleles, we are able to predict known PEGs at high accuracy and identify several new PEGs that we confirm using INTACT-based transcriptomes generated in this study.ConclusionsThe presence of the three repressive epigenetic marks, H3K27me3, H3K9me2, and CHG methylation on the maternal alleles in the endosperm serves as a specific epigenetic signature that allows prediction of genes with parental-specific gene expression. Our study reveals that there are substantially more PEGs than previously identified, indicating that paternal-specific gene expression is of higher functional relevance than currently estimated. The combined activity of PRC2-mediated H3K27me3 together with the heterochromatic H3K9me3 has also been reported to silence the maternal Xist locus in mammalian preimplantation embryos, suggesting convergent employment of both pathways during the evolution of genomic imprinting.
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| 29. |
- Müller, Niels A., et al.
(författare)
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A single gene underlies the dynamic evolution of poplar sex determination.
- 2020
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Ingår i: Nature Plants. - : Springer Nature. - 2055-0278 .- 2055-026X. ; 6:6, s. 630-637
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Tidskriftsartikel (refereegranskat)abstract
- Although hundreds of plant lineages have independently evolved dioecy (that is, separation of the sexes), the underlying genetic basis remains largely elusive. Here we show that diverse poplar species carry partial duplicates of the ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17) orthologue in the male-specific region of the Y chromosome. These duplicates give rise to small RNAs apparently causing male-specific DNA methylation and silencing of the ARR17 gene. CRISPR–Cas9-induced mutations demonstrate that ARR17 functions as a sex switch, triggering female development when on and male development when off. Despite repeated turnover events, including a transition from the XY system to a ZW system, the sex-specific regulation of ARR17 is conserved across the poplar genus and probably beyond. Our data reveal how a single-gene-based mechanism of dioecy can enable highly dynamic sex-linked regions and contribute to maintaining recombination and integrity of sex chromosomes.
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| 30. |
- Sinha, Vikash Kumar, et al.
(författare)
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Cartography of Liquidity Risk Calculations
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Most accounting studies on the emergence or transformation of risk categories focus on the performative definition of risk categories, i.e., they focus on the specific time-space bound practices of risk management involving different actors and their actions as a source for new risk categories. However, in the last two decades, risk-based regulations in the banking sector have become a prominent source of the transformation of risk categories, representing an ostensive definition of risk categories. However, despite the growing prominence of risk-based regulations and their ostensive definition of the existing risk categories devoid of the time-space of practices, actors and their actions; there is a lack of research on this issue. The few studies that do elaborate on these issues focus on the inherent meaning of control or freedom in the regulations themselves. In the backdrop of this debate, this paper focuses on a central research question: how is the ostensive definition of a risk category established during the enactment of risk-based regulations. Following Foucault's (2005) ideas on discontinuity and the sociological studies on the emergence of conceptual categories, we study the Swedish risk-based regulation of short-term liquidity risk and changes in its meaning over the last two decade. Our findings highlight the three different phases through which the meaning and calculation approaches of the short-term liquidity risk were developed in the ostensive definitions of the regulatory discourses.
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| 31. |
- Sinha, Vikash Kumar, et al.
(författare)
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Manifold Conceptions of the Internal Auditing of Risk Culture in the Financial Sector
- 2020
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Ingår i: Journal of Business Ethics. - : Springer. - 0167-4544 .- 1573-0697. ; 162:1, s. 81-102
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Tidskriftsartikel (refereegranskat)abstract
- This exploratory study investigates the manifold conceptions of the internal auditing (IA) of risk culture prevalent among four influential actors of the financial sector—regulators, normalizers, consultants, and implementers. By inductive analysis of 20 interviews and 295 documents, we illustrate a two-step interpretive scheme utilized by the four actors in their IA approaches of risk culture: defining broad goals and designing visibility schemes. The visibility schemes were tied to the demarcation, measurement, as well as the IA data collection techniques of risk culture. Our results indicate two dichotomous interpretations among the four actors concerning the IA of risk culture. The first interpretation, prevalent among regulators and implementers, promotes the control of risk culture primarily through verification. The second interpretation, adopted by consultants and normalizers, promotes the control of risk culture by IA along with the empowerment of employees through training programs. Our results not only contribute to understanding IA expansions, specifically to non-tangible domains such as risk culture but also enrich the literature exploring the mechanisms different stakeholders utilize to shape weakly professionalized IA practices.
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| 32. |
- Sinha, Vikash Kumar
(författare)
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Reinventing Operational Risk : Distancing Operational Risk from Operations
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Based on 652 archival documents on operational risk (covering a period from 1980 to 2016) from the Basel Committee on Banking Supervision (BCBS) and responses from the lobbyists (banking associations, consultants and banks), this paper inductively examined how the BCBS and the lobbyists contributed to framing of the calculation of operational risk? Following Benford & Snow (2000), Vollmer (2007), and Roussy & Brivot (2016); the paper specifically focused on the framing of meaning (Goffman, 1974) to document the emerging interpretive scheme of the BCBS and the lobbyists. The paper posits two important contributions. First, it demonstrates how the BCBS and the lobbyists framed the operational risk calculations in four different phases. Second, the results of the different approaches on operational risk calculations demonstrate that like other activity-focused accounting instruments (e.g., activity-based costing), the calculation of operational risk allowed a number of different practices leading to non-comparability of operational risks of different banks. The non-comparability led to the withdrawal of activity-focused operational risk calculation by the Basel Committee on Banking Supervision. Based on the analysis of the operational risk case, in the implication section, the paper also discusses ethical questions towards understanding how to balance control and freedom while deploying activity-focused accounting calculations.
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| 33. |
- Sinha, Vikash Kumar
(författare)
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Shaping Risk Management in Banks
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The recent financial crisis of 2007-08 was a watershed moment in the history of banking. The unprecedented event led to severe scrutiny by standard setters and regulators on how the business of banking is run. As a result of this strict scrutiny, a wide variety of reforms aimed at the second line of defense (risk management) ensued globally. These reforms stirred debate among the five actors (regulators, standard setters, normalizers, consultants, and implementers – banks and their interest organizations) that affected not only the shaping of risk management standards but also their implementation in banks. Motivated by these contemporary events, this thesis examines the shaping of risk management in the banking sector.Through the three exploratory field studies in Sweden and Italy, the thesis posits two important contributions. First, the thesis posits a framework, demonstrating how the dynamic shaping of risk management is changing the conceptions of risk management in the banking sector. More specifically, the thesis (in Paper I) demonstrates how the definition of liquidity was changed from its traditional notion of a match between cash inflow and outflow to managing net cash outflow demands by keeping high-quality liquid assets. Furthermore, the thesis (in Paper II) shows how non-convergence of operational risk practices forced regulators to change their activity and detail-oriented advanced approach of risk measurement that (unintentionally) allowed the variation of practices to flourish. In a similar vein, the thesis (in Paper IV) demonstrates how the extension of internal audit to the non-tangible domain of “risk culture” raises doubts about the notion of “verification” and “control” attached to the practices of internal audit in lending credibility to risk management practices.Second, the findings indicate the different participation approaches of various interested actors in the shaping of risk management practices. Here, the thesis (in Paper IV) demonstrates how the five actors (regulators, standard setters, normalizers, consultants, and implementers – banks and their interest organizations) influenced the conception of internal audit of risk culture. On the issue of internal audit of the Basel risk models (in Paper III), the thesisi demonstrates the filtering approaches of multiple institutional demands via the internal organizational conditions that enable full or partial agency of low-level internal auditors in shaping their practices of lending credibility to risk management.Given the findings, the thesis explicates two important implications for practitioners. First, the findings of the thesis indicate that reformulations of risk measurement and internal audit would require standard setters, regulators, normalizers, consultants, and implementers to understand a balance between what to control and whom to empower. Second, banks would need to carefully design the level of freedom to be given to internal audit and risk control teams in managing the complex institutional demands through organizational structure and skilling initiatives.
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| 34. |
- Sinha, Vikash Kumar, et al.
(författare)
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Unfolding the Basel Internal Audit Practices in International Financial Organizations
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Normative and regulative prescriptions present the utopia of independence and objectivity in IA work as governance of other control functions. However, emerging field studies contradict this utopia by raising doubts on the independence and objectivity of IA work in practice. Most of such literature depicts IA members with the full agency by highlighting control over their choices. Some emerging research has started highlighted institutional embeddedness of agency of IA work where institutional prescriptions along with the agency of IA members determines IA practices. Based on three comparative cases, we clarify the nature of agency in IA work by focusing on the availability of institutional prescriptions to IA members due to different internal organizational conditions. Our results provide a theoretical understanding of IA work that has a potential to reconcile our fragmented understandings on how different organizational conditions along with multiple institutional demands lead to compromises on the independence and objectivity of IA work as governance of other control functions.
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| 35. |
- Vashisth, Vikash, et al.
(författare)
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Hydrodynamics and mixing characterization in a novel high shear mixer
- 2017
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Ingår i: Chemical Engineering and Processing: Process Intensification. - : Elsevier BV. - 0255-2701. ; 120, s. 57-67
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Tidskriftsartikel (refereegranskat)abstract
- In the present study hydrodynamics and mixing characteristics in a novel batch rotor-stator mixer (RSM), which is very simple in construction and design, is investigated at different rotor speeds (2000, 4000 and 6000 rpm). The proposed RSM design is comprised of tilted jets/holes in the stator, for the deep penetration in the mixing vessel. For the optimization of operating as well as geometrical parameters of the proposed mixer design, simulations are carried out using transient sliding mesh with k-ε turbulence model at different rotor speeds. It was observed that besides radial and tangential flows jets emerging from stator holes impinge the bulk fluid above and below the stator, which improves mixing and reduces dead zones. Further, the flow parameters such as mass flow rate, Power number, Flow number, pumping efficiency and energy dissipation rate increased with an increase in rotor speed. Further, the energy dissipation rate is found maximum in the rotor swept region. It is observed that the amplitude fluctuations in flowrate and torque, with blade position, increased with the rotor speed. Further, mixing characterization in the novel RSM is studied for the first time in a batch RSM to predict the dead zones in the RSM.
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| 36. |
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| 37. |
- Yadav, Vikash Kumar
(författare)
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Regulation of Gene Expression by Global Methylation Pattern in Plants Development
- 2019
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Ingår i: OMICS‐Based Approaches in Plant Biotechnology. - Hoboken, NJ, USA : John Wiley & Sons, Inc.. - 9781119509936 ; , s. 287-301
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Bokkapitel (refereegranskat)abstract
- Regulation of the copy number of genes through epigenetics is maintained by methylation of nucleic acid, modifications of histones, and change in the structure of chromosome into a high level of packaging. Chromatin modifications are associated with the changes in chromatin states that result from alterations in the histones and modifications in the specific proteins and small RNAs that associate with a genomic region. Methylation of nucleic acid and modifications of histone are considered as the traits concerned mainly with epigenetics. In recent years, regulation of the copy number of genes through methylation of nucleic acid is emerging as a new area of interest in the field of research in plants, which has significant impact on the developmental process and transcriptional regulation. DNA methylation is involved in various aspects in plants like evolution of plant species, defenses, resistance, shoot regeneration, sex determination, and developmental pathways. In genomes, DNA methylation is partitioned into CG and non-CG methylation pattern, where non-CG methylation is known as CHG and CHH. Methylation pattern has been classified into maintenance and de novo DNA methylation, which occur by DNA methyl transferase (DNMtase). DNMtase reported in plants is classified mainly into two categories, that is, maintenance methyl transferase and de novo methyl transferase. Genome-level study of nucleic acid methylation in plants like Arabidopsis, maize, and rice has shown that H3K9me2-dependent pathway, ribonucleic acid directed nucleic acid methylation pathway, and mobile siRNAs are involved in the regulation of the copy number of genes. Recent technological advances have sped up the research in the area of omics-based genomic approaches and high-throughput analysis for the involvement of nucleic acid methylation in plants.
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