scholarly journals The Bacteroidetes Aequorivita sp. and Kaistella jeonii Produce Promiscuous Esterases With PET-Hydrolyzing Activity

2022 ◽  
Vol 12 ◽  
Author(s):  
Hongli Zhang ◽  
Pablo Perez-Garcia ◽  
Robert F. Dierkes ◽  
Violetta Applegate ◽  
Julia Schumacher ◽  
...  
Keyword(s):  
Unique Feature ◽  
Search Algorithm ◽  
Global Climate ◽  
Structural Similarity ◽  
Binding Motif ◽  
High Structural Similarity ◽  
Wide Range ◽  
Cold Active ◽  
Bacteroidetes Phylum ◽  
Binding Residues

Certain members of the Actinobacteria and Proteobacteria are known to degrade polyethylene terephthalate (PET). Here, we describe the first functional PET-active enzymes from the Bacteroidetes phylum. Using a PETase-specific Hidden-Markov-Model- (HMM-) based search algorithm, we identified several PETase candidates from Flavobacteriaceae and Porphyromonadaceae. Among them, two promiscuous and cold-active esterases derived from Aequorivita sp. (PET27) and Kaistella jeonii (PET30) showed depolymerizing activity on polycaprolactone (PCL), amorphous PET foil and on the polyester polyurethane Impranil® DLN. PET27 is a 37.8 kDa enzyme that released an average of 174.4 nmol terephthalic acid (TPA) after 120 h at 30°C from a 7 mg PET foil platelet in a 200 μl reaction volume, 38-times more than PET30 (37.4 kDa) released under the same conditions. The crystal structure of PET30 without its C-terminal Por-domain (PET30ΔPorC) was solved at 2.1 Å and displays high structural similarity to the IsPETase. PET30 shows a Phe-Met-Tyr substrate binding motif, which seems to be a unique feature, as IsPETase, LCC and PET2 all contain Tyr-Met-Trp binding residues, while PET27 possesses a Phe-Met-Trp motif that is identical to Cut190. Microscopic analyses showed that K. jeonii cells are indeed able to bind on and colonize PET surfaces after a few days of incubation. Homologs of PET27 and PET30 were detected in metagenomes, predominantly aquatic habitats, encompassing a wide range of different global climate zones and suggesting a hitherto unknown influence of this bacterial phylum on man-made polymer degradation.

scholarly journals Bacteroidetal cold-active and promiscuous esterases play a significant role in global polyethylene terephthalate (PET) degradation

2021 ◽  
Author(s):  
Hongli Zhang ◽  
Robert Dierkes ◽  
Pablo Pérez-García ◽  
Sebastian Weigert ◽  
Stefanie Sternagel ◽  
...  
Keyword(s):  
Polyethylene Terephthalate ◽  
Significant Role ◽  
Turnover Rate ◽  
Search Algorithm ◽  
Global Climate ◽  
Transcript Abundance ◽  
Wide Range ◽  
Cold Active ◽  
Bacteroidetes Phylum

Abstract Polyethylene terephthalate (PET) is an important synthetic polymer accumulating in nature and recent studies have identified microorganisms capable of degrading PET. While the majority of known PET hydrolases originate from the Actinobacteria and Proteobacteria, here we describe the first functional PET-active enzymes from the Bacteroidetes phylum. Using a PETase-specific Hidden-Markov-Model (HMM)-based search algorithm we identified two promiscuous and cold-active esterases derived from Aequorivita sp. (PET27) and Chryseobacterium jeonii (PET30) acting on PET foil and powder. Notably, one of the enzymes (PET30) was able to hydrolyze PET at temperatures between 4° - 30°C with a similar turnover rate compared to the well-known Ideonella sakaiensis enzyme (IsPETase). PET27 and PET30 homologues were detected in metagenomes encompassing a wide range of different global climate zones. Additional transcript abundance mapping of marine samples imply that these enzymes and source organisms play a significant role in the long-term degradation of microplastic particles and fibers.

scholarly journals The abundance of mRNA transcripts of bacteroidetal polyethylene terephthalate (PET) esterase genes may indicate a role in marine plastic degradation

2021 ◽  
Author(s):  
Hongli Zhang ◽  
Robert Dierkes ◽  
Pablo Pérez-García ◽  
Sebastian Weigert ◽  
Stefanie Sternagel ◽  
...  
Keyword(s):  
Polyethylene Terephthalate ◽  
Turnover Rate ◽  
Search Algorithm ◽  
Global Climate ◽  
Transcript Abundance ◽  
Climate Zones ◽  
Wide Range ◽  
Mrna Transcripts ◽  
Bacteroidetes Phylum

Abstract Polyethylene terephthalate (PET) is an important synthetic polymer accumulating in nature 2 and recent studies have identified microorganisms capable of degrading PET. While the majority of 3 known PET hydrolases originate from the Actinobacteria and Proteobacteria, here we describe the 4 first functional PET-active enzymes from the Bacteroidetes phylum. Using a PETase-specific 5 Hidden-Markov-Model (HMM)-based search algorithm we identified two promiscuous and cold6 active esterases derived from Aequorivita sp. (PET27) and Chryseobacterium jeonii (PET30) acting 7 on PET foil and powder. Notably, one of the enzymes (PET30) was able to hydrolyze PET at 8 temperatures between 4° - 30°C with a similar turnover rate compared to the well-known Ideonella 9 sakaiensis enzyme (IsPETase). 10 PET27 and PET30 homologues were detected in metagenomes encompassing a wide range 11 of different global climate zones. Additional transcript abundance mapping of marine samples imply 12 that these promiscuous enzymes and source organisms may play a role in the long-term 13 degradation of microplastic particles and fibers.

scholarly journals Silicon Effects on the Root System of Diverse Crop Species Using Root Phenotyping Technology

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 885
Author(s):  
Pooja Tripathi ◽  
Sangita Subedi ◽  
Abdul Latif Khan ◽  
Yong-Suk Chung ◽  
Yoonha Kim
Keyword(s):  
Root System ◽  
Root Morphology ◽  
Morphological Traits ◽  
Crop Production ◽  
Spatial Configuration ◽  
Global Climate ◽  
Learning Technologies ◽  
Climate Change Scenarios ◽  
Crop Species ◽  
Wide Range

Roots play an essential function in the plant life cycle, as they utilize water and essential nutrients to promote growth and plant productivity. In particular, root morphology characteristics (such as length, diameter, hairs, and lateral growth) and the architecture of the root system (spatial configuration in soil, shape, and structure) are the key elements that ensure growth and a fine-tuned response to stressful conditions. Silicon (Si) is a ubiquitous element in soil, and it can affect a wide range of physiological processes occurring in the rhizosphere of various crop species. Studies have shown that Si significantly and positively enhances root morphological traits, including root length in rice, soybean, barley, sorghum, mustard, alfalfa, ginseng, and wheat. The analysis of these morphological traits using conventional methods is particularly challenging. Currently, image analysis methods based on advanced machine learning technologies allowed researchers to screen numerous samples at the same time considering multiple features, and to investigate root functions after the application of Si. These methods include root scanning, endoscopy, two-dimensional, and three-dimensional imaging, which can measure Si uptake, translocation and root morphological traits. Small variations in root morphology and architecture can reveal different positive impacts of Si on the root system of crops, with or without exposure to stressful environmental conditions. This review comprehensively illustrates the influences of Si on root morphology and root architecture in various crop species. Furthermore, it includes recommendations in regard to advanced methods and strategies to be employed to maintain sustainable plant growth rates and crop production in the currently predicted global climate change scenarios.

scholarly journals Polymer cyclization for the emergence of hierarchical nanostructures

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chaojian Chen ◽  
Manjesh Kumar Singh ◽  
Katrin Wunderlich ◽  
Sean Harvey ◽  
Colette J. Whitfield ◽  
...  
Keyword(s):  
Self Assembly ◽  
Three Dimensional ◽  
Hierarchical Structures ◽  
Structural Similarity ◽  
Vital Role ◽  
Nanomaterial Synthesis ◽  
Wide Range ◽  
Linear Poly ◽  
Polymer Folding ◽  
Dynamics Simulations

AbstractThe creation of synthetic polymer nanoobjects with well-defined hierarchical structures is important for a wide range of applications such as nanomaterial synthesis, catalysis, and therapeutics. Inspired by the programmability and precise three-dimensional architectures of biomolecules, here we demonstrate the strategy of fabricating controlled hierarchical structures through self-assembly of folded synthetic polymers. Linear poly(2-hydroxyethyl methacrylate) of different lengths are folded into cyclic polymers and their self-assembly into hierarchical structures is elucidated by various experimental techniques and molecular dynamics simulations. Based on their structural similarity, macrocyclic brush polymers with amphiphilic block side chains are synthesized, which can self-assemble into wormlike and higher-ordered structures. Our work points out the vital role of polymer folding in macromolecular self-assembly and establishes a versatile approach for constructing biomimetic hierarchical assemblies.

scholarly journals Microwave Imaging of Breast Skin Utilizing Elliptical UWB Antenna and Reverse Problems Algorithm

Micromachines ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 647
Author(s):  
Sameer Alani ◽  
Zahriladha Zakaria ◽  
Tale Saeidi ◽  
Asmala Ahmad ◽  
Muhammad Ali Imran ◽  
...  
Keyword(s):  
Skin Cancer ◽  
Imaging System ◽  
Signal Transmission ◽  
Similarity Index ◽  
Structural Similarity ◽  
Microwave Imaging ◽  
Ultra Wideband ◽  
Uwb Antenna ◽  
System A ◽  
High Structural Similarity

Skin cancer is one of the most widespread and fast growing of all kinds of cancer since it affects the human body easily due to exposure to the Sun’s rays. Microwave imaging has shown better outcomes with higher resolution, faster processing time, mobility, and less cutter and artifact effects. A miniaturized elliptical ultra-wideband (UWB) antenna and its semi-spherical array arrangement were used for signal transmission and reception from the defected locations in the breast skin. Several conditions such as various arrays of three, six, and nine antenna elements, smaller tumor, multi-tumors, and skin on a larger breast sample of 30 cm were considered. To assess the ability of the system, a breast shape container with a diameter of 130 mm and height of 60 mm was 3D printed and then filled with fabricated skin and breast fat to perform the experimental investigation. An improved modified time-reversal algorithm (IMTR) was used to recreate 2D images of tumors with the smallest radius of 1.75 mm in any location within the breast skin. The reconstructed images using both simulated and experimental data verified that the system can be a reliable imaging system for skin cancer diagnosis having a high structural similarity index and resolution.

scholarly journals Different modes of internalization of apoptotic alkyl-lysophospholipid and cell-rescuing lysophosphatidylcholine

2003 ◽  
Vol 374 (3) ◽  
pp. 747-753 ◽  
Author(s):  
Arnold H. van der LUIT ◽  
Marianne BUDDE ◽  
Marcel VERHEIJ ◽  
Wim J. van BLITTERSWIJK
Keyword(s):  
Lipid Rafts ◽  
De Novo ◽  
Structural Similarity ◽  
Dominant Negative ◽  
Dominant Negative Mutant ◽  
Chemotherapeutic Drugs ◽  
Alternative Substrate ◽  
High Structural Similarity ◽  
Additional Cell ◽  
Cell Membrane Level

The synthetic alkyl-lysophospholipid (ALP), Et-18-OCH3 (1-O-octadecyl-2-O-methyl-rac-glycero-3-phosphocholine), can induce apoptosis in tumour cells. Unlike conventional chemotherapeutic drugs, ALP acts at the cell-membrane level. We have reported previously that ALP is internalized, and interferes with phosphatidylcholine (PC) biosynthesis de novo, which appeared to be essential for survival in lymphoma cells [Van der Luit, Budde, Ruurs, Verheij and Van Blitterswijk (2002) J. Biol. Chem. 277, 39541–39547]. Here, we report that, in HeLa cells, ALP accumulates in lipid rafts, and that internalization is inhibited by low temperature, monensin, disruption of lipid rafts and expression of a dominant-negative mutant of dynamin bearing a replacement of Lys44 with alanine (K44A). Thus ALP is internalized via raft- and dynamin-mediated endocytosis. Dynamin-K44A alleviated the ALP-induced inhibition of PC synthesis and rescued the cells from apoptosis induction. Additional cell rescue was attained by exogenous lysoPC, which after internalization serves as an alternative substrate for PC synthesis (through acylation). Unlike ALP, and despite the high structural similarity to ALP, lysoPC uptake did not occur via lipid rafts and did not depend on functional dynamin, indicating no involvement of endocytosis. Albumin back-extraction experiments suggested that (radiolabelled) lysoPC undergoes transbilayer movement (flipping). We conclude that ALP is internalized by endocytosis via lipid rafts to cause apoptosis, while exogenous cell-rescuing lysoPC traverses the plasma membrane outside rafts by flipping. Additionally, our data imply the importance of ether bonds in lyso-phospholipids, such as in ALP, for partitioning in lipid rafts.

scholarly journals A Classification of Basic Helix-Loop-Helix Transcription Factors of Soybean

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Karen A. Hudson ◽  
Matthew E. Hudson
Keyword(s):  
Transcription Factors ◽  
Genome Sequence ◽  
Search Algorithm ◽  
Soybean Genome ◽  
Binding Potential ◽  
Future Research ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Bhlh Genes ◽  
Wide Range

The complete genome sequence of soybean allows an unprecedented opportunity for the discovery of the genes controlling important traits. In particular, the potential functions of regulatory genes are a priority for analysis. The basic helix-loop-helix (bHLH) family of transcription factors is known to be involved in controlling a wide range of systems critical for crop adaptation and quality, including photosynthesis, light signalling, pigment biosynthesis, and seed pod development. Using a hidden Markov model search algorithm, 319 genes with basic helix-loop-helix transcription factor domains were identified within the soybean genome sequence. These were classified with respect to their predicted DNA binding potential, intron/exon structure, and the phylogeny of the bHLH domain. Evidence is presented that the vast majority (281) of these 319 soybean bHLH genes are expressed at the mRNA level. Of these soybean bHLH genes, 67% were found to exist in two or more homeologous copies. This dataset provides a framework for future studies on bHLH gene function in soybean. The challenge for future research remains to define functions for the bHLH factors encoded in the soybean genome, which may allow greater flexibility for genetic selection of growth and environmental adaptation in this widely grown crop.

Optimal Design of Power System Stabilizer Using a Novel Evolutionary Algorithm

2018 ◽  
Vol 7 (3) ◽  
pp. 24-46
Author(s):  
Sourav Paul ◽  
Provas Roy
Keyword(s):  
Optimal Design ◽  
Power System ◽  
Search Algorithm ◽  
Low Frequency ◽  
Optimal Solution ◽  
Power System Stabilizer ◽  
Low Frequency Oscillation ◽  
Large Power ◽  
Wide Range ◽  
System Stabilizer

In this article, an Oppositional Differential search algorithm (ODSA) is comprehensively developed and successfully applied for the optimal design of power system stabilizer (PSS) parameters which are added to the excitation system to dampen low frequency oscillation as it pertains to large power system. The effectiveness of the proposed method is examined and validated on a single machine infinite bus (SMIB) using the Heffron-Phillips model. The most important advantage of the proposed method is as it reaches toward the optimal solution without the optimal tuning of input parameters of the ODSA algorithm. In order to verify the effectiveness, the simulation was made for a wide range of loading conditions. The simulation results of the proposed ODSA are compared with those obtained by other techniques available in the recent literature to demonstrate the feasibility of the proposed algorithm.

European Forest Management Portfolios Optimized for Uncertain Future Climate

2021 ◽  
Author(s):  
Konstantin Gregor ◽  
Thomas Knoke ◽  
Andreas Krause ◽  
Mats Lindeskog ◽  
Anja Rammig
Keyword(s):  
Forest Management ◽  
Global Climate ◽  
Optimization Techniques ◽  
Wood Products ◽  
Future Climate ◽  
The Other ◽  
Ecosystem Functions ◽  
Northern Europe ◽  
Climate Scenarios ◽  
Wide Range

<p>Forests are considered a major player in climate change mitigation since they influence local and global climate through biogeochemical and biogeophysical feedbacks. However, they are themselves vulnerable to future environmental changes. Thus, forest management needs to focus on both mitigation and adaptation. The special challenge is that decisions on management strategies must be taken today while still a broad range of emission pathways is possible, and a good decision regarding one assumed pathway might turn out to be a bad decision when a different one materializes.</p><p>With our study we try to aid this decision-making process by finding management portfolios that provide relevant ecosystem functions such as local and global climate regulation, water availability, flood protection, and timber production for a wide range of future climate scenarios. To simulate according ecosystem processes and functions, we run the dynamic vegetation model LPJ-GUESS for the most relevant forest types across Europe for four different RCPs and five different management options. We analyze our simulation outputs using robust optimization techniques to determine optimal forest management portfolios for each 0.5° grid cell in Europe that ensure a balanced provision of all considered ecosystem functions in the future under any of the four RCPs.</p><p>Generally, our simulations and optimizations show that diversified management portfolios are most suitable to provide the set of considered ecosystem functions in all climate scenarios everywhere in Europe. While the portfolios show different compositions in different regions, they are quite similar in adjacent grid cells. The suggested future forest composition in Europe tends to be fairly close to present day values except for Northern Europe where a much higher proportion of deciduous types is proposed.</p><p>Management as high forest (trees emerging from seeds) remains the most important form of management. The proposed share of coppice management is much higher in Central and Northern Europe (~20%) than in Southern Europe, where its disadvantages (e.g., high water consumption and its non-suitability to provide long-lived wood products) are more pronounced.</p><p>A succession of ~30% of managed forest to natural forest is proposed by the optimization as it provides highest carbon storage and surface roughness values. However, this infeasibly high share is reduced if the provision of wood harvest is valued higher in the optimization compared to the other ecosystem functions.</p><p>Current public focus on forests lies often on their potential for carbon sequestration, but future forest management must also address the other services that they provide. This work gives insights on how this may be done.</p>

Three Frontiers of the Southern Yucatán Peninsular Region and SYPR Project

2004 ◽  
Author(s):  
B. L. Turner II ◽  
D. R. Foster
Keyword(s):  
Immanuel Kant ◽  
Geographical Information Systems ◽  
Global Climate ◽  
Global Environmental Change ◽  
Geographical Information ◽  
Emergent Properties ◽  
Land Change ◽  
Ecosystem Integrity ◽  
Change Models ◽  
Wide Range

Frontiers advance and retreat, both figuratively and literally. At this moment they are advancing in three ways relevant to the subject of this book and the ongoing project on which it is based. First, after more than a century of reductionist hegemony, various science communities worldwide increasingly recognize the need to improve complementary, synthesis understanding—a way of putting the reductionist pieces of the problem back together again in order to understand how the ‘whole’ system works and to identify the emergent properties that follow from the complex interactions of the pieces. Synthesis understanding is not, of course, new. In the late eighteenth century, Immanuel Kant argued for it as one of the pillars of science in the reorganization of knowledge in the European academy (Turner 2002a) and designated geography as one of the ‘synthesis sciences’. Its contemporary rediscovery, however, rests in the science of global environmental change (Lawton 2001; Steffen et al. 2002), especially efforts to model complex systems, such as those in ocean–atmosphere–land interactions, and has been expanded by emerging research agendas seeking to couple human and environment systems, often registered under the label of ‘sustainability science’ (e.g. Kates et al. 2001; NRC 1999). Second, within these developments landuse and land-cover change (or, simply, land change) is singled out because of its centrality to a wide range of environmental concerns, including global climate change, regional–local hydrological impacts, biodiversity, and, of course, human development and ecosystem integrity (e.g. Brookfield 1995; NRC 2000; Watson et al. 2001). The need to advance an integrated land-change science is also increasingly recognized, one in which human, ecological, and remote sensing and geographical information systems (GIS) sciences are intertwined in problem-solving (Liverman et al. 1998; Klepeis and Turner 2001; Turner 2002b). And central to this effort is the need to advance geographically (spatially) explicit land-change models that can explain and project coupled human-ecological systems, and thus serve a wide range of research and assessment constituencies, from carbon to biodiversity to human vulnerability (IGBP 1999; Irwin and Geoghegan 2001; Kates et al. 2001; Liverman et al. 1998; Veldkamp and Lambin 2001). These two developments—synthesis science and integrated land science directed towards geographically explicit land-change models—constitute the broader intellectual and research frontiers to which this work contributes.

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