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Article ; Online: Evaluation of pedotransfer functions to estimate some of soil hydraulic characteristics in North Africa

Adnane Beniaich / Wilfred Otten / Ho-Chul Shin / Hannah V Cooper / Jane Rickson / Aziz Soulaimani / Mohamed El Gharous

Frontiers in Environmental Science, Vol

A case study from Morocco

2023 Volume 11

Abstract: Soil hydraulic properties are an important factor to optimize and adapt water management for a given crop. Pedotransfer functions (PTFs) present a solution to predict soil variables such as hydraulic properties, using fundamental soil properties. In this ...

Abstract	Soil hydraulic properties are an important factor to optimize and adapt water management for a given crop. Pedotransfer functions (PTFs) present a solution to predict soil variables such as hydraulic properties, using fundamental soil properties. In this research, we compared two sources of soil information: iSDAsoil data and field data, in four regions in Morocco. We then used this data to evaluate published data and developed new PTFs using soil information to estimate soil gravimetric moisture content at saturation (w0), field capacity (w330) and permanent wilting point (w15000). A total of 331 samples were collected from four regions: Doukkala, Gharb-Loukous, Moulouya and Tadla. The data was divided into calibration and validation datasets. For development of different PTFs, we used simple linear regression, multiple linear regression, regression tree, Cubist algorithm, and random forest approaches. PTFs developed by Dijkerman (Geoderma, 1988, 42, 29–49) presented the best performance, showing lower RMSE, Bias and MAE compared to other PTFs. Using multiple linear regression to develop PTFs, models based on clay, silt and soil organic matter as input variables showed the best performance after calibration (R2 of 0.590, 0.785, 0.786 for w0, w330, and w15000, respectively). Regarding the techniques based on machine learning, random forest showed the best performance after calibration compared with other algorithms (R2 of 0.930, 0.955, 0.954 for w0, w330, and w15000, respectively). PTFs represent a low cost and easy technique to estimate soil hydraulic properties, to improve water management efficiency for the farmers.
Keywords	soil hydraulic properties ; wilting point ; field capacity ; multiple linear regression ; regression tree ; cubist algorithm ; Environmental sciences ; GE1-350
Subject code	550
Language	English
Publishing date	2023-02-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates

Da Eun Jeong / Hye Seon Lee / Bonsu Ku / Cheol-Hee Kim / Seung Jun Kim / Ho-Chul Shin

Communications Biology, Vol 6, Iss 1, Pp 1-

2023 Volume 14

Abstract: Abstract The N-end rule pathway is a proteolytic system involving the destabilization of N-terminal amino acids, known as N-degrons, which are recognized by N-recognins. Dysregulation of the N-end rule pathway results in the accumulation of undesired ... ...

Abstract	Abstract The N-end rule pathway is a proteolytic system involving the destabilization of N-terminal amino acids, known as N-degrons, which are recognized by N-recognins. Dysregulation of the N-end rule pathway results in the accumulation of undesired proteins, causing various diseases. The E3 ligases of the UBR subfamily recognize and degrade N-degrons through the ubiquitin-proteasome system. Herein, we investigated UBR4, which has a distinct mechanism for recognizing type-2 N-degrons. Structural analysis revealed that the UBR box of UBR4 differs from other UBR boxes in the N-degron binding sites. It recognizes type-2 N-terminal amino acids containing an aromatic ring and type-1 N-terminal arginine through two phenylalanines on its hydrophobic surface. We also characterized the binding mechanism for the second ligand residue. This is the report on the structural basis underlying the recognition of type-2 N-degrons by the UBR box with implications for understanding the N-end rule pathway.
Keywords	Biology (General) ; QH301-705.5
Subject code	570 ; 540
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Structural basis for proapoptotic activation of Bak by the noncanonical BH3-only protein Pxt1.

Dahwan Lim / So-Hui Choe / Sein Jin / Seulgi Lee / Younjin Kim / Ho-Chul Shin / Joon Sig Choi / Doo-Byoung Oh / Seung Jun Kim / Jinho Seo / Bonsu Ku

PLoS Biology, Vol 21, Iss 6, p e

2023 Volume 3002156

Abstract: Bak is a critical executor of apoptosis belonging to the Bcl-2 protein family. Bak contains a hydrophobic groove where the BH3 domain of proapoptotic Bcl-2 family members can be accommodated, which initiates its activation. Once activated, Bak undergoes ... ...

Abstract	Bak is a critical executor of apoptosis belonging to the Bcl-2 protein family. Bak contains a hydrophobic groove where the BH3 domain of proapoptotic Bcl-2 family members can be accommodated, which initiates its activation. Once activated, Bak undergoes a conformational change to oligomerize, which leads to mitochondrial destabilization and the release of cytochrome c into the cytosol and eventual apoptotic cell death. In this study, we investigated the molecular aspects and functional consequences of the interaction between Bak and peroxisomal testis-specific 1 (Pxt1), a noncanonical BH3-only protein exclusively expressed in the testis. Together with various biochemical approaches, this interaction was verified and analyzed at the atomic level by determining the crystal structure of the Bak-Pxt1 BH3 complex. In-depth biochemical and cellular analyses demonstrated that Pxt1 functions as a Bak-activating proapoptotic factor, and its BH3 domain, which mediates direct intermolecular interaction with Bak, plays a critical role in triggering apoptosis. Therefore, this study provides a molecular basis for the Pxt1-mediated novel pathway for the activation of apoptosis and expands our understanding of the cell death signaling coordinated by diverse BH3 domain-containing proteins.
Keywords	Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Quantum Artificial Neural Network Approach to Derive a Highly Predictive 3D-QSAR Model for Blood–Brain Barrier Passage

Taeho Kim / Byoung Hoon You / Songhee Han / Ho Chul Shin / Kee-Choo Chung / Hwangseo Park

International Journal of Molecular Sciences, Vol 22, Iss 10995, p

2021 Volume 10995

Abstract: A successful passage of the blood–brain barrier (BBB) is an essential prerequisite for the drug molecules designed to act on the central nervous system. The logarithm of blood–brain partitioning (LogBB) has served as an effective index of molecular BBB ... ...

Abstract	A successful passage of the blood–brain barrier (BBB) is an essential prerequisite for the drug molecules designed to act on the central nervous system. The logarithm of blood–brain partitioning (LogBB) has served as an effective index of molecular BBB permeability. Using the three-dimensional (3D) distribution of the molecular electrostatic potential (ESP) as the numerical descriptor, a quantitative structure-activity relationship (QSAR) model termed AlphaQ was derived to predict the molecular LogBB values. To obtain the optimal atomic coordinates of the molecules under investigation, the pairwise 3D structural alignments were conducted in such a way to maximize the quantum mechanical cross correlation between the template and a target molecule. This alignment method has the advantage over the conventional atom-by-atom matching protocol in that the structurally diverse molecules can be analyzed as rigorously as the chemical derivatives with the same scaffold. The inaccuracy problem in the 3D structural alignment was alleviated in a large part by categorizing the molecules into the eight subsets according to the molecular weight. By applying the artificial neural network algorithm to associate the fully quantum mechanical ESP descriptors with the extensive experimental LogBB data, a highly predictive 3D-QSAR model was derived for each molecular subset with a squared correlation coefficient larger than 0.8. Due to the simplicity in model building and the high predictability, AlphaQ is anticipated to serve as an effective computational screening tool for molecular BBB permeability.
Keywords	blood–brain barrier ; 3D-QSAR ; structural alignment ; molecular ESP descriptor ; artificial neural network ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	541
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Signaling Pathways Regulated by UBR Box-Containing E3 Ligases

Jung Gi Kim / Ho-Chul Shin / Taewook Seo / Laxman Nawale / Goeun Han / Bo Yeon Kim / Seung Jun Kim / Hyunjoo Cha-Molstad

International Journal of Molecular Sciences, Vol 22, Iss 8323, p

2021 Volume 8323

Abstract: UBR box E3 ligases, also called N-recognins, are integral components of the N-degron pathway. Representative N-recognins include UBR1, UBR2, UBR4, and UBR5, and they bind destabilizing N-terminal residues, termed N-degrons. Understanding the molecular ... ...

Abstract	UBR box E3 ligases, also called N-recognins, are integral components of the N-degron pathway. Representative N-recognins include UBR1, UBR2, UBR4, and UBR5, and they bind destabilizing N-terminal residues, termed N-degrons. Understanding the molecular bases of their substrate recognition and the biological impact of the clearance of their substrates on cellular signaling pathways can provide valuable insights into the regulation of these pathways. This review provides an overview of the current knowledge of the binding mechanism of UBR box N-recognin/N-degron interactions and their roles in signaling pathways linked to G-protein-coupled receptors, apoptosis, mitochondrial quality control, inflammation, and DNA damage. The targeting of these UBR box N-recognins can provide potential therapies to treat diseases such as cancer and neurodegenerative diseases.
Keywords	UBR Box E3 ligases ; N-recognin ; Arg/N-degron pathway ; N-degron ; G-protein signaling ; apoptosis ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	570
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Structural study reveals the temperature-dependent conformational flexibility of Tk-PTP, a protein tyrosine phosphatase from Thermococcus kodakaraensis KOD1.

Hye-Yeoung Yun / Jinhyuk Lee / Hyunmin Kim / Hyojung Ryu / Ho-Chul Shin / Byung-Ha Oh / Bonsu Ku / Seung Jun Kim

PLoS ONE, Vol 13, Iss 5, p e

2018 Volume 0197635

Abstract: Protein tyrosine phosphatases (PTPs) originating from eukaryotes or bacteria have been under intensive structural and biochemical investigation, whereas archaeal PTP proteins have not been investigated extensively; therefore, they are poorly understood. ... ...

Abstract	Protein tyrosine phosphatases (PTPs) originating from eukaryotes or bacteria have been under intensive structural and biochemical investigation, whereas archaeal PTP proteins have not been investigated extensively; therefore, they are poorly understood. Here, we present the crystal structures of Tk-PTP derived from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1, in both the active and inactive forms. Tk-PTP adopts a common dual-specificity phosphatase (DUSP) fold, but it undergoes an atypical temperature-dependent conformational change in its P-loop and α4-α5 loop regions, switching between the inactive and active forms. Through comprehensive analyses of Tk-PTP, including additional structural determination of the G95A mutant form, enzymatic activity assays, and structural comparison with the other archaeal PTP, it was revealed that the presence of the GG motif in the P-loop is necessary but not sufficient for the structural flexibility of Tk-PTP. It was also proven that Tk-PTP contains dual general acid/base residues unlike most of the other DUSP proteins, and that both the residues are critical in its phosphatase activity. This work provides the basis for expanding our understanding of the previously uncharacterized PTP proteins from archaea, the third domain of living organisms.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Method development, matrix effect, and risk assessment of 49 multiclass pesticides in kiwifruit using liquid chromatography coupled to tandem mass spectrometry

Kim, Yool-Ah / A.M. Abd El-Aty / Ho-Chul Shin / Jae-Han Shim / Ji Hoon Jeong / Jing Wang / Md. Musfiqur Rahman / SungShik Shin

Journal of chromatography. 2018 Feb. 15, v. 1076

2018

Abstract: In the present study, a liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) method with a minimal matrix effect (ME) was developed and validated for simultaneous determination of a diverse range of pesticides (49) in kiwifruit. Samples ...

Abstract	In the present study, a liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) method with a minimal matrix effect (ME) was developed and validated for simultaneous determination of a diverse range of pesticides (49) in kiwifruit. Samples extracted by the quick, easy, cheap, effective, rugged, and safe (QuEChERS) citrate-buffered method were analyzed either without purification or following purification (with primary secondary amine (PSA) or PSA + graphitized carbon black (GCB)). With the addition of a clean-up step, the suppression of the ME decreased, with a higher number of pesticides determined by the application of PSA + GCB. The method exhibited good linearity with coefficients of determination (R2) ≥ 0.9972 and satisfactory recoveries (70–120%) with a relative standard deviations (RSDs) <10%. The limits of quantification (LOQ) were lower than the maximum residue limits (MRLs) set by the Korean Ministry of Food and Drug Safety (MFDS) and the CODEX Alimentarius. The developed method was applied to the real samples and the results indicated that the quantitated levels of all pesticides, except for pyraclostrobin and carbendazim, are lower than the MRLs set by the regulatory authorities. The percentage of the acceptable daily intake was <20%, suggesting that there is no risk associated with the intake of residual pesticides through kiwifruit.
Keywords	acceptable daily intake ; carbendazim ; Codex Alimentarius ; drugs ; kiwifruit ; liquid chromatography ; maximum residue limits ; pesticide residues ; pyraclostrobin ; risk ; soot ; statistical analysis ; tandem mass spectrometry
Language	English
Dates of publication	2018-0215
Size	p. 130-138.
Publishing place	Elsevier B.V.
Document type	Article
ISSN	1570-0232
DOI	10.1016/j.jchromb.2018.01.015
Database	NAL-Catalogue (AGRICOLA)

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Article: Quantification of artesunate and its metabolite, dihydroartemisinin, in animal products using liquid chromatography–tandem mass spectrometry

Zheng, Weijia / A. M. Abd El‐Aty / Ahmet Hacımüftüoğlu / Ho‐Chul Shin / Jae‐Han Shim / Jeong‐Min Choi / Seong‐Kwan Kim / Young‐Sun Kang

Journal of separation science. 2018 Sept., v. 41, no. 18

2018

Abstract: An analytical approach using a modified quick, easy, cheap, effective, rugged, and safe extraction method followed by liquid chromatography with electrospray ionization tandem mass spectrometry was developed herein for the determination of artesunate and ...

Abstract	An analytical approach using a modified quick, easy, cheap, effective, rugged, and safe extraction method followed by liquid chromatography with electrospray ionization tandem mass spectrometry was developed herein for the determination of artesunate and its metabolite, dihydroarteminsinin in porcine muscle, egg, eel, flatfish, and shrimp. 10% trichloroacetic acid in acetonitrile mixed with ethyl acetate was used as an extraction solvent. To obtain a good separation, a Phenomenex Kinetex reversed‐phase analytical column was selected with mobile phase consisting of distilled water (A) and acetonitrile (B), both containing 0.05% formic acid. Good linearity was achieved using matrix‐matched calibrations constructed from six concentrations (5–50 μg/kg) with determinant coefficients ≥0.9918. Recoveries estimated from three spiking concentrations (5, 10, and 20 μg/kg) ranged between 71.3 and 104.7% in all matrixes with relative standard deviations ≤8.3%. A variety of samples purchased from markets in Seoul were tested following the protocol described herein. The artesunate and dihydroarteminsinin were not detected in any matrix. The methodology proposed could be used for routine determination of artesunate and its metabolite, dihydroartemisinin in various animal products having variable percentages of fat and protein.
Keywords	acetonitrile ; animal products ; eel ; eggs ; electrospray ionization mass spectrometry ; ethyl acetate ; formic acid ; liquid chromatography ; markets ; metabolites ; muscles ; Pleuronectiformes ; protocols ; shrimp ; solvents ; statistical analysis ; swine ; tandem mass spectrometry ; trichloroacetic acid
Language	English
Dates of publication	2018-09
Size	p. 3538-3546.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2047990-6
ISSN	1615-9314 ; 1615-9306
ISSN (online)	1615-9314
ISSN	1615-9306
DOI	10.1002/jssc.201800499
Database	NAL-Catalogue (AGRICOLA)

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Article: An overview on common aspects influencing the dissipation pattern of pesticides: a review

Farha, Waziha / A. M. Abd El-Aty / Ho-Chul Shin / Jae-Han Shim / Md. Musfiqur Rahman

Environmental monitoring and assessment. 2016 Dec., v. 188, no. 12

2016

Abstract: The common aspects and processes influencing dissipation kinetics of pesticides are determinants of their fate in the environment. Nowadays, with increasing population, the demand for food and fodder crops has also increased. With the development in ... ...

Abstract	The common aspects and processes influencing dissipation kinetics of pesticides are determinants of their fate in the environment. Nowadays, with increasing population, the demand for food and fodder crops has also increased. With the development in science and technology, the methods of controlling pests may improve, but the major role played by the environment cannot be altered, i.e. the environmental factors, climatic conditions, and geology of areas under cultivation. Plants play a crucial role in the dissipation kinetics, as they may vary in species and characteristics. Differences in physico-chemical properties, such as formulation, bioavailability, and efficacy of the pesticide, may result in variable dissipation patterns even under the same environmental conditions. While modelling the dissipation kinetics for any specific pesticide applied to any specific crop, each factor must be considered. This review focusses on the variability observed across common factors, i.e. environmental aspects, plant-associated facts, and observed characteristics of chemical substances, influencing pesticide dissipation.
Keywords	bioavailability ; chemical substances ; climatic factors ; control methods ; forage crops ; geology ; models ; pesticide persistence ; pesticides ; population growth
Language	English
Dates of publication	2016-12
Size	p. 693.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	782621-7
ISSN	1573-2959 ; 0167-6369
ISSN (online)	1573-2959
ISSN	0167-6369
DOI	10.1007/s10661-016-5709-1
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: SMC condensin entraps chromosomal DNA by an ATP hydrolysis dependent loading mechanism in Bacillus subtilis

Larissa Wilhelm / Frank Bürmann / Anita Minnen / Ho-Chul Shin / Christopher P Toseland / Byung-Ha Oh / Stephan Gruber

eLife, Vol

2015 Volume 4

Abstract: Smc–ScpAB forms elongated, annular structures that promote chromosome segregation, presumably by compacting and resolving sister DNA molecules. The mechanistic basis for its action, however, is only poorly understood. Here, we have established a physical ...

Abstract	Smc–ScpAB forms elongated, annular structures that promote chromosome segregation, presumably by compacting and resolving sister DNA molecules. The mechanistic basis for its action, however, is only poorly understood. Here, we have established a physical assay to determine whether the binding of condensin to native chromosomes in Bacillus subtilis involves entrapment of DNA by the Smc–ScpAB ring. To do so, we have chemically cross-linked the three ring interfaces in Smc–ScpAB and thereafter isolated intact chromosomes under protein denaturing conditions. Exclusively species of Smc–ScpA, which were previously cross-linked into covalent rings, remained associated with chromosomal DNA. DNA entrapment is abolished by mutations that interfere with the Smc ATPase cycle and strongly reduced when the recruitment factor ParB is deleted, implying that most Smc–ScpAB is loaded onto the chromosome at parS sites near the replication origin. We furthermore report a physical interaction between native Smc–ScpAB and chromosomal DNA fragments.
Keywords	condensin ; Smc protein ; chromosome segregation ; chromosome condensation ; ParB protein ; sliding clamp ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2015-05-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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