Science Collected Works - Research Publications
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ItemSeparation and Paired Proteome Profiling of Plant Chloroplast and Cytoplasmic Ribosomes(MDPI, 2020-07)Conventional preparation methods of plant ribosomes fail to resolve non-translating chloroplast or cytoplasmic ribosome subunits from translating fractions. We established preparation of these ribosome complexes from Arabidopsis thaliana leaf, root, and seed tissues by optimized sucrose density gradient centrifugation of protease protected plant extracts. The method co-purified non-translating 30S and 40S ribosome subunits separated non-translating 50S from 60S subunits, and resolved assembled monosomes from low oligomeric polysomes. Combining ribosome fractionation with microfluidic rRNA analysis and proteomics, we characterized the rRNA and ribosomal protein (RP) composition. The identity of cytoplasmic and chloroplast ribosome complexes and the presence of ribosome biogenesis factors in the 60S-80S sedimentation interval were verified. In vivo cross-linking of leaf tissue stabilized ribosome biogenesis complexes, but induced polysome run-off. Omitting cross-linking, the established paired fractionation and proteome analysis monitored relative abundances of plant chloroplast and cytoplasmic ribosome fractions and enabled analysis of RP composition and ribosome associated proteins including transiently associated biogenesis factors.
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ItemSystematic Review of Plant Ribosome Heterogeneity and Specialization(FRONTIERS MEDIA SA, 2020-06-25)Plants dedicate a high amount of energy and resources to the production of ribosomes. Historically, these multi-protein ribosome complexes have been considered static protein synthesis machines that are not subject to extensive regulation but only read mRNA and produce polypeptides accordingly. New and increasing evidence across various model organisms demonstrated the heterogeneous nature of ribosomes. This heterogeneity can constitute specialized ribosomes that regulate mRNA translation and control protein synthesis. A prominent example of ribosome heterogeneity is seen in the model plant, Arabidopsis thaliana, which, due to genome duplications, has multiple paralogs of each ribosomal protein (RP) gene. We support the notion of plant evolution directing high RP paralog divergence toward functional heterogeneity, underpinned in part by a vast resource of ribosome mutants that suggest specialization extends beyond the pleiotropic effects of single structural RPs or RP paralogs. Thus, Arabidopsis is a highly suitable model to study this phenomenon. Arabidopsis enables reverse genetics approaches that could provide evidence of ribosome specialization. In this review, we critically assess evidence of plant ribosome specialization and highlight steps along ribosome biogenesis in which heterogeneity may arise, filling the knowledge gaps in plant science by providing advanced insights from the human or yeast fields. We propose a data analysis pipeline that infers the heterogeneity of ribosome complexes and deviations from canonical structural compositions linked to stress events. This analysis pipeline can be extrapolated and enhanced by combination with other high-throughput methodologies, such as proteomics. Technologies, such as kinetic mass spectrometry and ribosome profiling, will be necessary to resolve the temporal and spatial aspects of translational regulation while the functional features of ribosomal subpopulations will become clear with the combination of reverse genetics and systems biology approaches.
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ItemInsights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth.(MDPI AG, 2020-08-27)The Earth's oceans are a huge body of water with physicochemical properties and microbial community profiles that change with depth, which in turn influences their biogeochemical cycling potential. The differences between microbial communities and their functional potential in surface to hadopelagic water samples are only beginning to be explored. Here, we used metagenomics to investigate the microbial communities and their potential to drive biogeochemical cycling in seven different water layers down the vertical profile of the Challenger Deep (0-10,500 m) in the Mariana Trench, the deepest natural point in the Earth's oceans. We recovered 726 metagenome-assembled genomes (MAGs) affiliated to 27 phyla. Overall, biodiversity increased in line with increased depth. In addition, the genome size of MAGs at ≥4000 m layers was slightly larger compared to those at 0-2000 m. As expected, surface waters were the main source of primary production, predominantly from Cyanobacteria. Intriguingly, microbes conducting an unusual form of nitrogen metabolism were identified in the deepest waters (>10,000 m), as demonstrated by an enrichment of genes encoding proteins involved in dissimilatory nitrate to ammonia conversion (DNRA), nitrogen fixation and urea transport. These likely facilitate the survival of ammonia-oxidizing archaea α lineage, which are typically present in environments with a high ammonia concentration. In addition, the microbial potential for oxidative phosphorylation and the glyoxylate shunt was enhanced in >10,000 m waters. This study provides novel insights into how microbial communities and their genetic potential for biogeochemical cycling differs through the Challenger deep water column, and into the unique adaptive lifestyle of microbes in the Earth's deepest seawater.
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ItemRapidly assessing cobenefits to advance threat-management alliances.(Wiley, 2020-08)Conservation strategies aimed at reducing threats to biodiversity can have significant implications for multiple sectors in a socioeconomic system, but these cobenefits are often poorly understood. For example, many of the threats to native species also impede agricultural production, yet agriculture is typically perceived as in competition with conservation objectives. Although a comprehensive, multiobjective decision analysis is usually beyond the scope and capacity of conservation decision makers, failing to incorporate key socioeconomic costs and benefits into conservation decision-making processes can result in missed opportunities for diversifying outcomes and creating cost-sharing multisectoral partnerships. We devised a straightforward and readily interpretable approach to incorporate cobenefits into a threat-management prioritization approach. We used it to analyze the agricultural cobenefits of implementing 9 invasive animal management strategies designed to ensure the persistence of 148 threatened species across Australia's Lake Eyre Basin over 50 years. A structured elicitation process with 24 participants (scientists, land managers, agriculturalists, and other stakeholders) was used to collect information on each strategy, including costs, technical and social feasibility, benefits to native threatened species, and cobenefits to agricultural production systems. The costs of targeted invasive animal management to save threatened species across the basin (AU$33 million/year) outweighed the overall benefits to the agricultural industry (estimated AU$226 million/year). The return on investment for these management strategies varied substantially when agricultural cobenefits were considered alongside threatened species benefits and showed synergies and challenges. Our approach demonstrates the value of incorporating cobenefits of conservation actions into cost-effectiveness analyses to guide potential investment and partnerships and to diversify implementation pathways.
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ItemWave Attenuation by Multiple Outer Porous Barriers in the Presence of an Inner Rigid Cylinder(ASCE-AMER SOC CIVIL ENGINEERS, 2020-01-01)The wave forces acting on a rigid cylinder are investigated in the presence of multiple outer porous cylindrical barriers by assuming the linear water wave theory. A Bessel series solution is obtained for the boundary value problem by using the methods of eigenfunction expansion and least-squares approximation. Two configurations of outer porous barriers are considered, namely bottom-standing and surface-piercing. As a special case, the effect of fully extended barriers is studied. The wave loads exerted on the cylinders, free surface elevations, and flow distribution around the structures are computed and analyzed for different physical parameters. The present theory is ratified with the result available in the literature for a single fully extended outer porous barrier. The study reveals that the hydrodynamic forces exerted on the inner impermeable cylinder are reduced significantly as the number of outer porous barriers is increased. Thus, multiple outer fully extended or partial porous barriers can be set up to protect the inner rigid cylinder.
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ItemWave energy dissipation by a floating circular flexible porous membrane in single and two-layer fluids(Elsevier, 2020-06-15)In this study, the impact of gravity wave on a circular elastic floating permeable membrane is investigated using linear water wave theory in both homogeneous and two-layer fluids. The matched eigenfunction expansion technique is employed to obtain an analytic solution of the boundary value problem. Further, the plane wave integral representation of Bessel and Hankel functions are applied to study the influence of porous structure in damping the far-field wave energy. In order to examine the effect of various physical parameters, heave force exerted on the membrane, deflection of the membrane, reflected and transmitted wave amplitudes, flow distribution around the structure and far-field energy dissipation are computed and analyzed for three different edge conditions such as (i) free edge, (ii) moored edge and (iii) clamped edge. The study reveals that the surface wave amplitude on the lee side of the structure decreases significantly in the presence of floating porous elastic membrane. Moreover, the membrane having clamped edge dissipates more wave energy as compared to that for moored and free edge conditions.
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ItemEffect of imposed shear on the dynamics of a contaminated two-layer film flow down a slippery incline(AIP Publishing, 2020-10-01)The linear instability of a surfactant-laden two-layer falling film over an inclined slippery wall is analyzed under the influence of external shear, which is imposed on the top surface of the flow. The free surface of the flow and the interface among the fluids are contaminated by insoluble surfactants. Dynamics of the fluid layers are governed by the Navier–Stokes equations, and the surfactant transport equations regulate the motion of the insoluble surfactants at the interface and free surface. Instability mechanisms are compared by imposing the external shear along and opposite to the flow direction. A coupled Orr–Sommerfeld system of equations is derived using the perturbation technique and normal mode analysis. The eigenmodes corresponding to the Orr–Sommerfeld eigenvalue problem are obtained by employing the spectral collocation method. The numerical results imply that the stronger external shear destabilizes the interface mode instability. However, a stabilizing impact of the external shear on the surface mode is noticed if the shear is imposed in the flow direction, which is in contrast to the role of imposed external shear on the surface mode for a surfactant-laden single layer falling film. Furthermore, in the presence of strong imposed shear, the overall stabilization of the surface mode by wall velocity slip for the stratified two-fluid flow is also contrary to that of the single fluid case. The interface mode behaves differently in the two zones at the moderate Reynolds numbers, and higher external shear magnifies the interfacial instability in both zones. An opposite trend is observed in the case of surface instability. Moreover, the impression of shear mode on the primary instability is analyzed in the high Reynolds number regime with sufficiently low inclination angle. Under such configuration, dominance of the shear mode over the surface mode is observed due to the weaker impact of the gravitational force on the surface instability. The shear mode can also be stabilized by applying the external shear in the counter direction of the streamwise flow. Conclusively, the extra imposed shear on the stratified two-layer falling film plays an active role in the control of the attitude of the instabilities.
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ItemEvisceration of umbilical content with extensive adhesion: A surgical approach(WILEY, 2020-12)With timely recognition and surgical intervention along with administration of an antibiotic, antihistaminic, and anti-inflammatory drugs, evisceration of umbilical content with extensive adhesion can be treated, and the outcome is also good.
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ItemDifferential efficacies of marigold leaves and turmeric paste on the healing of the incised wound in sheep(NETWORK VETERINARIANS BANGLADESH, 2020-12)OBJECTIVE: This study was undertaken to compare the curative efficacy of marigold leaf paste and turmeric paste on healing the incised wound in sheep. The study also determined the antimicrobial effects and histopathological changes in a wound's healing process treated with these medicinal herbs. MATERIALS AND METHODS: Surgical wounds (n = 18) were created aseptically in the skin of the flank region of six healthy sheep dividing them into three experimental groups. Follow-up data were taken up to day 21. Different morphological characteristics of the wound and wound contraction (length and width) were recorded weekly. Samples were collected on days 1, 2, and 3 to test the antimicrobial effects and on days 1, 3, and 7 for histopathological studies. RESULTS: Treatment with marigold leaf paste and turmeric paste resulted in a swelled wound area of 11.78 ± 0.38 mm and 11.52 ± 0.27 mm, respectively. The wound areas were comparatively lower than that of the control group (11.44 ± 0.20 mm). Moreover, the least elevation (2.44 ± 0.12 mm) of the sutured line from the skin surface was noted and compared between the marigold leaf paste and normal saline (2.74 ± 0.13 mm). Bacterial colonies in the nutrient agar medium cultured with swabs from the normal saline-treated group's wound area were found on day 1. On the contrary, bacterial colonies were absent on days 2 and 3 of treatment in the groups treated with both the paste of marigold leaves and turmeric. Less intense tissue reactions and higher keratinization of epithelium were shown in the group treated with marigold leaf paste than turmeric paste and saline-treated groups. CONCLUSION: Marigold leaf paste showed less tissue reaction and healed the wounds effectively. Thus, this paste could be used for the treatment of superficial wounds in sheep.
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ItemPrediction of Epidemics Trend of COVID-19 in Bangladesh(FRONTIERS MEDIA SA, 2020-11-30)Background: Amid a critical and emergent situation like the coronavirus disease (COVID-19) pandemic related to extreme health and economic repercussions, we used and presented the mathematical modeling like susceptible-infectious-recovered (SIR) to have a numerical demonstration that can shed light to decide the fate of the scourge in Bangladesh. To describe the idea about the factors influencing the outbreak data, we presented the current situation of the COVID-19 outbreak with graphical trends. Methods: Primary data were collected and analyzed by using a pre-created Google Survey form having a pre-set questionnaire on the social distancing status of different districts. Secondary data on the total and the daily number of laboratory tests, confirmed positive cases, and death cases were extracted from the publicly available sources to make predictions. We estimated the basic reproduction number (R◦) based on the SIR mathematical model and predicted the probable fate of this pandemic in Bangladesh. Results: Quarantine situations in different regions of Bangladesh were evaluated and presented. We also provided tentative forecasts until 31 May 2020 and found that the predicted curve followed the actual curve approximately. Estimated R◦-values (6.924) indicated that infection rate would be greater than the recovery rate. Furthermore, by calibrating the parameters of the SIR model to fit the reported data, we assume the ultimate ending of the pandemic in Bangladesh by December 2022. Conclusion: We hope that the results of our analysis could contribute to the elucidation of critical aspects of this outbreak and help the concerned authority toward decision making.