scholarly journals New Insights into the Function and Global Distribution of Polyethylene Terephthalate (PET)-Degrading Bacteria and Enzymes in Marine and Terrestrial Metagenomes

2018 ◽  
Vol 84 (8) ◽  
pp. e02773-17 ◽  
Author(s):  
Dominik Danso ◽  
Christel Schmeisser ◽  
Jennifer Chow ◽  
Wolfgang Zimmermann ◽  
Ren Wei ◽  
...  
Keyword(s):  
Polyethylene Terephthalate ◽  
Search Algorithm ◽  
Global Distribution ◽  
Sequence Information ◽  
Microbial Conversion ◽  
Thermostable Enzymes ◽  
Content Type ◽  
Bacterial Phyla ◽  
Degrading Bacteria ◽  
Pet Hydrolase

ABSTRACTPolyethylene terephthalate (PET) is one of the most important synthetic polymers used today. Unfortunately, the polymers accumulate in nature and to date no highly active enzymes are known that can degrade it at high velocity. Enzymes involved in PET degradation are mainly α- and β-hydrolases, like cutinases and related enzymes (EC 3.1.1). Currently, only a small number of such enzymes are well characterized. In this work, a search algorithm was developed that identified 504 possible PET hydrolase candidate genes from various databases. A further global search that comprised more than 16 Gb of sequence information within 108 marine and 25 terrestrial metagenomes obtained from the Integrated Microbial Genome (IMG) database detected 349 putative PET hydrolases. Heterologous expression of four such candidate enzymes verified the function of these enzymes and confirmed the usefulness of the developed search algorithm. In this way, two novel and thermostable enzymes with high potential for downstream application were partially characterized. Clustering of 504 novel enzyme candidates based on amino acid similarities indicated that PET hydrolases mainly occur in the phyla ofActinobacteria,Proteobacteria, andBacteroidetes. Within theProteobacteria, theBetaproteobacteria,Deltaproteobacteria, andGammaproteobacteriawere the main hosts. Remarkably enough, in the marine environment, bacteria affiliated with the phylumBacteroidetesappear to be the main hosts of PET hydrolase genes, rather thanActinobacteriaorProteobacteria, as observed for the terrestrial metagenomes. Our data further imply that PET hydrolases are truly rare enzymes. The highest occurrence of 1.5 hits/Mb was observed in sequences from a sample site containing crude oil.IMPORTANCEPolyethylene terephthalate (PET) accumulates in our environment without significant microbial conversion. Although a few PET hydrolases are already known, it is still unknown how frequently they appear and with which main bacterial phyla they are affiliated. In this study, deep sequence mining of protein databases and metagenomes demonstrated that PET hydrolases indeed occur at very low frequencies in the environment. Furthermore, it was possible to link them to phyla that were previously not known to harbor such enzymes. This work contributes novel knowledge on the phylogenetic relationships, the recent evolution, and the global distribution of PET hydrolases. Finally, we describe the biochemical traits of four novel PET hydrolases.

An improved sparrow search algorithm based on levy flight and opposition-based learning

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Danni Chen ◽  
JianDong Zhao ◽  
Peng Huang ◽  
Xiongna Deng ◽  
Tingting Lu
Keyword(s):  
Parameter Optimization ◽  
Optimization Problem ◽  
Heuristic Algorithms ◽  
Search Algorithm ◽  
Convergence Speed ◽  
Support Vector ◽  
Lévy Flight ◽  
Levy Flight ◽  
Content Type ◽  
Opposition Based Learning

Purpose Sparrow search algorithm (SSA) is a novel global optimization method, but it is easy to fall into local optimization, which leads to its poor search accuracy and stability. The purpose of this study is to propose an improved SSA algorithm, called levy flight and opposition-based learning (LOSSA), based on LOSSA strategy. The LOSSA shows better search accuracy, faster convergence speed and stronger stability. Design/methodology/approach To further enhance the optimization performance of the algorithm, The Levy flight operation is introduced into the producers search process of the original SSA to enhance the ability of the algorithm to jump out of the local optimum. The opposition-based learning strategy generates better solutions for SSA, which is beneficial to accelerate the convergence speed of the algorithm. On the one hand, the performance of the LOSSA is evaluated by a set of numerical experiments based on classical benchmark functions. On the other hand, the hyper-parameter optimization problem of the Support Vector Machine (SVM) is also used to test the ability of LOSSA to solve practical problems. Findings First of all, the effectiveness of the two improved methods is verified by Wilcoxon signed rank test. Second, the statistical results of the numerical experiment show the significant improvement of the LOSSA compared with the original algorithm and other natural heuristic algorithms. Finally, the feasibility and effectiveness of the LOSSA in solving the hyper-parameter optimization problem of machine learning algorithms are demonstrated. Originality/value An improved SSA based on LOSSA is proposed in this paper. The experimental results show that the overall performance of the LOSSA is satisfactory. Compared with the SSA and other natural heuristic algorithms, the LOSSA shows better search accuracy, faster convergence speed and stronger stability. Moreover, the LOSSA also showed great optimization performance in the hyper-parameter optimization of the SVM model.

scholarly journals Efficient Plant Biomass Degradation by Thermophilic Fungus Myceliophthora heterothallica

2012 ◽  
Vol 79 (4) ◽  
pp. 1316-1324 ◽  
Author(s):  
Joost van den Brink ◽  
Gonny C. J. van Muiswinkel ◽  
Bart Theelen ◽  
Sandra W. A. Hinz ◽  
Ronald P. de Vries
Keyword(s):  
Wheat Straw ◽  
Plant Biomass ◽  
Hydrolytic Enzymes ◽  
Reaction Times ◽  
Giant Reed ◽  
Thermophilic Fungi ◽  
Biomass Degradation ◽  
Thermostable Enzymes ◽  
Content Type

ABSTRACTRapid and efficient enzymatic degradation of plant biomass into fermentable sugars is a major challenge for the sustainable production of biochemicals and biofuels. Enzymes that are more thermostable (up to 70°C) use shorter reaction times for the complete saccharification of plant polysaccharides compared to hydrolytic enzymes of mesophilic fungi such asTrichodermaandAspergillusspecies. The genusMyceliophthoracontains four thermophilic fungi producing industrially relevant thermostable enzymes. Within this genus, isolates belonging toM. heterothallicawere recently separated from the well-described speciesM. thermophila. We evaluate here the potential ofM. heterothallicaisolates to produce efficient enzyme mixtures for biomass degradation. Compared to the other thermophilicMyceliophthoraspecies, isolates belonging toM. heterothallicaandM. thermophilagrew faster on pretreated spruce, wheat straw, and giant reed. According to their protein profiles andin vitroassays after growth on wheat straw, (hemi-)cellulolytic activities differed strongly betweenM. thermophilaandM. heterothallicaisolates. Compared toM. thermophila,M. heterothallicaisolates were better in releasing sugars from mildly pretreated wheat straw (with 5% HCl) with a high content of xylan. The high levels of residual xylobiose revealed that enzyme mixtures ofMyceliophthoraspecies lack sufficient β-xylosidase activity. Sexual crossing of twoM. heterothallicashowed that progenies had a large genetic and physiological diversity. In the future, this will allow further improvement of the plant biomass-degrading enzyme mixtures ofM. heterothallica.

scholarly journals Draft Genome Report of Bacillus altitudinis SORB11, Isolated from the Indian Sector of the Southern Ocean

2017 ◽  
Vol 5 (23) ◽  
Author(s):  
Urmi Halder ◽  
Aparna Banerjee ◽  
Vasvi Chaudhry ◽  
Rajeev K. Varshney ◽  
Shrikant Mantri ◽  
...  
Keyword(s):  
Southern Ocean ◽  
Uv Radiation ◽  
Genome Sequence ◽  
Draft Genome ◽  
Resistance Mechanism ◽  
Sequence Information ◽  
Content Type ◽  
Bacillus Altitudinis ◽  
Genome Sequence Information ◽  
Indian Sector

ABSTRACT Here, we present the draft genome sequence of Bacillus altitudinis SORB11, which is tolerant to UV radiation. The strain was isolated from the Indian sector of the Southern Ocean at a depth of 3.8 km. The genome sequence information reported here for B. altitudinis SORB11 gives the basis of its UV resistance mechanism and provides data for further comparative studies with other bacteria resistant to UV radiation.

Obstacle avoidance and path planning of humanoid robot using fuzzy logic controller aided owl search algorithm in complicated workspaces

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Abhishek Kumar Kashyap ◽  
Dayal R. Parhi
Keyword(s):  
Fuzzy Logic ◽  
Fuzzy Logic Controller ◽  
Fuzzy Controller ◽  
Search Algorithm ◽  
Optimal Path ◽  
Humanoid Robots ◽  
Steering Angle ◽  
Content Type ◽  
Hybrid Controller ◽  
Humanoid Nao

Purpose This paper aims to outline and implement a novel hybrid controller in humanoid robots to map an optimal path. The hybrid controller is designed using the Owl search algorithm (OSA) and Fuzzy logic. Design/methodology/approach The optimum steering angle (OS) is used to deal with the obstacle located in the workspace, which is the output of the hybrid OSA Fuzzy controller. It is obtained by feeding OSA's output, i.e. intermediate steering angle (IS), in fuzzy logic. It is obtained by supplying the distance of obstacles from all directions and target distance from the robot's present location. Findings The present research is based on the navigation of humanoid NAO in complicated workspaces. Therefore, various simulations are performed in a 3D simulator in different complicated workspaces. The validation of their outcomes is done using the various experiments in similar workspaces using the proposed controller. The comparison between their outcomes demonstrates an acceptable correlation. Ultimately, evaluating the proposed controller with another existing navigation approach indicates a significant improvement in performance. Originality/value A new framework is developed to guide humanoid NAO in complicated workspaces, which is hardly seen in the available literature. Inspection in simulation and experimental workspaces verifies the robustness of the designed navigational controller. Considering minimum error ranges and near collaboration, the findings from both frameworks are evaluated against each other in respect of specified navigational variables. Finally, concerning other present approaches, the designed controller is also examined, and major modifications in efficiency have been reported.

Croceimicrobium hydrocarbonivorans gen. nov., sp. nov., a novel marine bacterium isolated from a bacterial consortium that degrades polyethylene terephthalate

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Renju Liu ◽  
Qiliang Lai ◽  
Li Gu ◽  
Peisheng Yan ◽  
Zongze Shao
Keyword(s):  
Polyethylene Terephthalate ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
The Family

A novel Gram-stain-negative, aerobic, gliding, rod-shaped and carotenoid-pigmented bacterium, designated A20-9T, was isolated from a microbial consortium of polyethylene terephthalate enriched from a deep-sea sediment sample from the Western Pacific. Growth was observed at salinities of 1–8 %, at pH 6.5–8 and at temperatures of 10–40 °C. The results of phylogenetic analyses based on the genome indicated that A20-9T formed a monophyletic branch affiliated to the family Schleiferiaceae , and the 16S rRNA gene sequences exhibited the maximum sequence similarity of 93.8 % with Owenweeksia hongkongensis DSM 17368T, followed by similarities of 90.4, 90.1 and 88.8 % with Phaeocystidibacter luteus MCCC 1F01079T, Vicingus serpentipes DSM 103558T and Salibacter halophilus MCCC 1K02288T, respectively. Its complete genome size was 4 035 598 bp, the genomic DNA G+C content was 43.2 mol%. Whole genome comparisons indicated that A20-9T and O. hongkongensis DSM 17368T shared 67.8 % average nucleotide identity, 62.7 % average amino acid identity value, 46.6% of conserved proteins and 17.8 % digital DNA–DNA hybridization identity. A20-9T contained MK-7 as the major respiratory quinone. Its major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phospatidylcholine; and the major fatty acids were iso-C15 : 0 (37.5 %), iso-C16 : 0 3-OH (12.4 %), and summed feature 3 (C16 : 1ω7c /C16 : 1ω6c, 11.6 %). Combining the genotypic and phenotypic data, A20-9T could be distinguished from the members of other genera within the family Schleiferiaceae and represents a novel genus, for which the name Croceimicrobium hydrocarbonivorans gen. nov., sp. nov. is proposed. The type strain is A20-9T (=MCCC 1A17358T =KCTC 72878T).

scholarly journals Steroid Degradation in Comamonas testosteroni TA441: Identification of the Entire β-Oxidation Cycle of the Cleaved B Ring

2019 ◽  
Vol 85 (20) ◽  
Author(s):  
Masae Horinouchi ◽  
Hiroyuki Koshino ◽  
Michal Malon ◽  
Hiroshi Hirota ◽  
Toshiaki Hayashi
Keyword(s):  
Gene Clusters ◽  
Degradation Process ◽  
Degradation Pathway ◽  
Ring Cleavage ◽  
Comamonas Testosteroni ◽  
Content Type ◽  
Coa Transferase ◽  
Degrading Bacteria ◽  
Globally Distributed

ABSTRACT Comamonas testosteroni TA441 degrades steroids via aromatization of the A ring, followed by degradation of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, mainly by β-oxidation. In this study, we revealed that 7β,9α-dihydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostanoic acid-coenzyme A (CoA) ester is dehydrogenated by (3S)-3-hydroxylacyl CoA-dehydrogenase, encoded by scdE (ORF27), and then the resultant 9α-hydroxy-7,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid-CoA ester is converted by 3-ketoacyl-CoA transferase, encoded by scdF (ORF23). With these results, the whole cycle of β-oxidation on the side chain at C-8 of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid is clarified; 9-hydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid-CoA ester is dehydrogenated at C-6 by ScdC1C2, followed by hydration by ScdD. 7β,9α-Dihydroxy-17-oxo-1,2,3,4,10,19-hexanorandrostanoic acid-CoA ester then is dehydrogenated by ScdE to be converted to 9α-hydroxy-17-oxo-1,2,3,4,5,6,10,19-octanorandrostan-7-oic acid-CoA ester and acetyl-CoA by ScdF. ScdF is an ortholog of FadA6 in Mycobacterium tuberculosis H37Rv, which was reported as a 3-ketoacyl-CoA transferase involved in C ring cleavage. We also obtained results suggesting that ScdF is also involved in C ring cleavage, but further investigation is required for confirmation. ORF25 and ORF26, located between scdF and scdE, encode enzymes belonging to the amidase superfamily. Disrupting either ORF25 or ORF26 did not affect steroid degradation. Among the bacteria having gene clusters similar to those of tesB to tesR, some have both ORF25- and ORF26-like proteins or only an ORF26-like protein, but others do not have either ORF25- or ORF26-like proteins. ORF25 and ORF26 are not crucial for steroid degradation, yet they might provide clues to elucidate the evolution of bacterial steroid degradation clusters. IMPORTANCE Studies on bacterial steroid degradation were initiated more than 50 years ago primarily to obtain materials for steroid drugs. Steroid-degrading bacteria are globally distributed, and the role of bacterial steroid degradation in the environment as well as in relation to human health is attracting attention. The overall aerobic degradation of the four basic steroidal rings has been proposed; however, there is still much to be revealed to understand the complete degradation pathway. This study aims to uncover the whole steroid degradation process in Comamonas testosteroni TA441 as a model of steroid-degrading bacteria. C. testosteroni is one of the most studied representative steroid-degrading bacteria and is suitable for exploring the degradation pathway, because the involvement of degradation-related genes can be determined by gene disruption. Here, we elucidated the entire β-oxidation cycle of the cleaved B ring. This cycle is essential for the following C and D ring cleavage.

scholarly journals Complete Genome Sequences of Two Mutacin-Producing Streptococcus mutans Strains, T8 and UA140

2020 ◽  
Vol 9 (24) ◽  
Author(s):  
Indranil Biswas
Keyword(s):  
Antimicrobial Peptides ◽  
Streptococcus Mutans ◽  
Genome Sequence ◽  
Complete Genome ◽  
Clinical Isolates ◽  
Sequence Information ◽  
Genome Sequences ◽  
Content Type ◽  
Genome Sequence Information

ABSTRACT Streptococcus mutans is known to produce various antimicrobial peptides called mutacins. Two clinical isolates, T8 and UA140, are well characterized regarding their mutacin production, but genome sequence information was previously unavailable. Complete genome sequences of these two mutacin-producing strains are reported here.

Multimodal biometric system combining left and right palmprints

2019 ◽  
Vol 48 (1) ◽  
pp. 2-13
Author(s):  
Chérif Taouche ◽  
Hacene Belhadef
Keyword(s):  
Feature Vector ◽  
Recognition Accuracy ◽  
Search Algorithm ◽  
Palmprint Recognition ◽  
Multimodal Biometrics ◽  
Chi Square ◽  
Content Type ◽  
Set Size ◽  
Promising Area ◽  
Left And Right

Purpose Palmprint recognition is a very interesting and promising area of research. Much work has already been done in this area, but much more needs to be done to make the systems more efficient. In this paper, a multimodal biometrics system based on fusion of left and right palmprints of a person is proposed to overcome limitations of unimodal systems. Design/methodology/approach Features are extracted using some proposed multi-block local descriptors in addition to MBLBP. Fusion of extracted features is done at feature level by a simple concatenation of feature vectors. Then, feature selection is performed on the resulting global feature vector using evolutionary algorithms such as genetic algorithms and backtracking search algorithm for a comparison purpose. The benefits of such step selecting the relevant features are known in the literature, such as increasing the recognition accuracy and reducing the feature set size, which results in runtime saving. In matching step, Chi-square similarity measure is used. Findings The resulting feature vector length representing a person is compact and the runtime is reduced. Originality/value Intensive experiments were done on the publicly available IITD database. Experimental results show a recognition accuracy of 99.17 which prove the effectiveness and robustness of the proposed multimodal biometrics system than other unimodal and multimodal biometrics systems.

Evolution of conformal antenna design with the aid of probability improved crow search algorithm

2020 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Nama Ajay Nagendra ◽  
Lakshman Pappula
Keyword(s):  
Antenna Arrays ◽  
Search Algorithm ◽  
Fundamental Problem ◽  
Side Lobe ◽  
Side Lobe Level ◽  
Antenna Element ◽  
Content Type ◽  
Conformal Antenna ◽  
Adopted Model ◽  
Better Than

PurposeThe issues of radiating sources in the existence of smooth convex matters by such objects are of huge significance in the modeling of antennas on structures. Conformal antenna arrays are necessary when an antenna has to match to certain platforms. A fundamental problem in the design is that the possible surfaces for a conformal antenna are infinite in number. Furthermore, if there is no symmetry, each element will see a different environment, and this complicates the mathematics. As a consequence, the element factor cannot be factored out from the array factor.Design/methodology/approachThis paper intends to enhance the design of the conformal antenna. Here, the main objective of this task is to maximize the antenna gain and directivity from the first-side lobe and other side-lobes in the two way radiation pattern. Thus the adopted model is designed as a multiobjective concern. In order to attain this multiobjective function, both the element spacing and the radius of each antenna element should be optimized based on the probability of the Crow Search Algorithm (CSA). Thus the proposed method is named Probability Improved CSA (PI-CSA). Here, the First Null Beam Width (FNBW) and Side-Lobe Level (SLL) are minimized. Moreover, the adopted scheme is compared with conventional algorithms, and the results are attained.FindingsFrom the analysis, the gain of the presented PI-CSA scheme in terms of best performance was 52.68% superior to ABC, 25.11% superior to PSO, 13.38% superior to FF and 3.21% superior to CS algorithms. Moreover, the mean performance of the adopted model was 62.94% better than ABC, 13.06% better than PSO, 24.34% better than FF and 10.05% better than CS algorithms. By maximizing the gain and directivity, FNBW and SLL were decreased. Thus, the optimal design of the conformal antenna has been attained by the proposed PI-CSA algorithm in an effective way.Originality/valueThis paper presents a technique for enhancing the design of the conformal antenna using the PI-CSA algorithm. This is the first work that utilizes PI-CSA-based optimization for improving the design of the conformal antenna.

Large-scale economic load dispatch using squirrel search algorithm

2020 ◽  
Vol 14 (6) ◽  
pp. 1351-1380
Author(s):  
Sakthivel V.P. ◽  
Suman M. ◽  
Sathya P.D.
Keyword(s):  
Power Plants ◽  
Large Scale ◽  
Optimization Problems ◽  
Search Algorithm ◽  
Optimization Technique ◽  
Research Work ◽  
Superior Performance ◽  
Economic Load Dispatch ◽  
Fuel Cost ◽  
Content Type

Purpose Economic load dispatch (ELD) is one of the crucial optimization problems in power system planning and operation. The ELD problem with valve point loading (VPL) and multi-fuel options (MFO) is defined as a non-smooth and non-convex optimization problem with equality and inequality constraints, which obliges an efficient heuristic strategy to be addressed. The purpose of this study is to present a new and powerful heuristic optimization technique (HOT) named as squirrel search algorithm (SSA) to solve non-convex ELD problems of large-scale power plants. Design/methodology/approach The suggested SSA approach is aimed to minimize the total fuel cost consumption of power plant considering their generation values as decision variables while satisfying the problem constraints. It confers a solution to the ELD issue by anchoring with foraging behavior of squirrels based on the dynamic jumping and gliding strategies. Furthermore, a heuristic approach and selection rules are used in SSA to handle the constraints appropriately. Findings Empirical results authenticate the superior performance of SSA technique by validating on four different large-scale systems. Comparing SSA with other HOTs, numerical results depict its proficiencies with high-qualitative solution and by its excellent computational efficiency to solve the ELD problems with non-smooth fuel cost function addressing the VPL and MFO. Moreover, the non-parametric tests prove the robustness and efficacy of the suggested SSA and demonstrate that it can be used as a competent optimizer for solving the real-world large-scale non-convex ELD problems. Practical implications This study has compared various HOTs to determine optimal generation scheduling for large-scale ELD problems. Consequently, its comparative analysis will be beneficial to power engineers for accurate generation planning. Originality/value To the best of the authors’ knowledge, this manuscript is the first research work of using SSA approach for solving ELD problems. Consequently, the solution to this problem configures the key contribution of this paper.

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