ARTICLE | doi:10.20944/preprints202112.0048.v1
Subject: Biology, Physiology Keywords: Enzyme-constrained model; Escherichia coli; Enzyme kinetics; Protein subunit; Overflow metabolism
Online: 3 December 2021 (10:20:49 CET)
Genome-scale metabolic models (GEMs) have been widely used for phenotypic prediction of microorganisms. However, the lack of other constraints in the stoichiometric model often leads to a large metabolic solution space inaccessible. Inspired by previous studies that take allocation of macromolecule resources into account, we developed a simplified Python-based workflow for constructing enzymatic constrained metabolic network model (ECMpy) and constructed an enzyme-constrained model for Escherichia coli (eciML1515) by directly adding a total enzyme amount constraint in the latest version of GEM for E. coli (iML1515), considering the protein subunit composition in the reaction, and automated calibration of enzyme kinetic parameters. Using eciML1515, we predicted the overflow metabolism of E. coli and revealed that redox balance was the key reason for the difference between E. coli and Saccharomyces cerevisiae in overflow metabolism. The growth rate predictions on 24 single-carbon sources were improved significantly when compared with other enzyme-constrained models of E. coli. Finally, we revealed the tradeoff between enzyme usage efficiency and biomass yield by exploring the metabolic behaviors under different substrate consumption rates. Enzyme-constrained models can improve simulation accuracy and thus can predict cellular phenotypes under various genetic perturbations more precisely, providing reliable guidance for metabolic engineering.
ARTICLE | doi:10.20944/preprints201908.0009.v1
Subject: Biology, Animal Sciences & Zoology Keywords: tea polyphenol; serum hormone; enzyme activity; immune function, enzyme-related genes
Online: 1 August 2019 (05:18:08 CEST)
The present study was conducted to evaluate the effects of dietary supplementation of tea polyphenol （TP） on serum hormone, serum enzyme activity, antioxidant-related and immune-related gene expression of laying hens under heat stress. A total of 288 Chinese yellow chicken (186 days old) were randomly distributed among two treatments, each of which included 6 replicates of 24 hens. Dietary treatments were that the basal diet was supplemented with 200 mg / kg tea polyphenol. The study lasted for 7 weeks, including 1 week of adaptation and 6 weeks of the formal test. The content of high-density lipoprotein cholesterol (HDL-C) and total protein (TP) in serum significantly decreased by dietary supplementation with tea polyphenol. Dietary tea polyphenol supplementation improved serum superoxide dismutase (SOD), glutathione peroxidase (GSH-Px) enzyme activity and decreased serum malondialdehyde (MDA) content in treatments compared to the control. However, supplementation of tea polyphenol did not affect the activity of serum catalase (CAT). The results indicated that long-term feeding of tea polyphenols help to increase the amount of hormones (FSH, E2) associated with reproduction in laying hens and thus improve egg production. It also improved the immune function of laying hens in high temperature environments. Adding tea polyphenols to the diet can significantly increase the serum IgG, IgM content of the laying hens and can upregulate the IgA content. Dietary supplementation of tea polyphenols in the laying hens significantly increased the expression of antioxidant enzyme-related genes (SOD, CAT and GPX1) in the liver. Moreover, the addition of tea polyphenols significantly increased the expression of immune-related genes (Interferon-γ (INF-γ), Interleukin 2 (IL-2) and Interleukin 4 (IL-4)) in the spleen. It is concluded that addition of tea polyphenols has a positive effect on antioxidant activity and immune function of laying hens.
ARTICLE | doi:10.20944/preprints201609.0123.v1
Subject: Life Sciences, Biochemistry Keywords: carbonic anhydrase; acetylcholinesterase; β-Lactam; 2-Azetidinone; enzyme inhibition; enzyme purification
Online: 30 September 2016 (05:38:45 CEST)
β-Lactams are pharmacologically important compounds because of their various biological uses, including antibiotic and so on. β-Lactams were synthesized from benzylidene-inden derivatives and acetoxyacetyl chloride. The inhibitory effect of these compounds was also examined for human carbonic anhydrase I and II (hCA I, and II) and acetylcholinesterase (AChE). The results reveal that β-lactams are inhibitors of hCA I, II and AChE. The Ki values of β-lactams (2a-k) were 0.44-6.29 nM against hCA I, 0.93-8.34 nM against hCA II, and 0.25-1.13 nM against AChE. Our findings indicate that β-lactams (2a-k) inhibit both CA isoenzymes and AChE at low nanomolar concentrations.
REVIEW | doi:10.20944/preprints202211.0147.v1
Subject: Chemistry, Medicinal Chemistry Keywords: topoisomerase; anticancer; cancer; anticancer drugs; enzyme
Online: 8 November 2022 (06:22:07 CET)
Several reviews of inhibitors of topoisomerase II literature have been published covering research before 2018. Therefore, this review is focused primarily on more recent publications with relevant points from the earlier literature. Topoisomerase II is an established target for anticancer drugs, that are further subdivided into poisons and catalytic inhibitors. Whereas most of the topoisomerase II-based drugs in clinical use are mostly topoisomerase II poisons, their mechanism of action has posed severe concern due to DNA damaging potential, including development of multi drug resistance. As a result, we are beginning to see a gradual paradigm shift towards a non-DNA damaging agents, such as the lesser studied topoisomerase II catalytic inhibitors. In addition, this review will describe some novel selective catalytic topoisomerase II inhibitors. The ultimate goal is to bring researchers up to speed by curating and delineating new scaffolds as leads for optimization and development to new potent, safe and selective agents for the treatment of cancer.
ARTICLE | doi:10.20944/preprints202203.0353.v1
Subject: Chemistry, Other Keywords: chlorothalonil; dissipation; enzyme activity; microbial community
Online: 28 March 2022 (03:46:35 CEST)
To get a better knowledge of the effects of residual chlorothalonil on soil characteristics and soil microbial communities, we evaluated the dissipation of chlorothalonil and the effects of different chlorothalonil concentrations on soil respiration, enzyme activities, and microbial community structure in yellow-brown loam soils. Bacterial and fungal soil communities were examined using traditional plate counting and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR–DGGE) methods. Soil properties and the results of DGGE band analysis were both used to estimate the status of the soil microbial ecosystem. The results show that residual chlorothalonil has considerable effects on soil respiration, enzymatic activities, and microbial community structure. In particular, soil respiration and phosphatase activities were increased, while saccharase activity, microbial biomass, and microbial community diversity were decreased by increasing levels of chlorothalonil treatment. Correlation analyses revealed that the application of chlorothalonil was significantly correlated with the change of the soil respiration, urease activity, sucrase activity, soil culturable bacteria and culturable fungi biomass. We conclude that residual chlorothalonil is directly related to soil respiration, enzyme activities, and microbial community structure.
Subject: Materials Science, Biomaterials Keywords: enzyme; bast fibers; enzymatic retting; characterizations
Online: 26 November 2019 (10:27:02 CET)
Natural fibers are a gift from nature that we yet fully utilized until now. It can be classified into several groups and bast fibers are the group having the most promising performance when reinforced in polymer composites. However, numerous factors have been reported that influences mechanical properties of fiber reinforcements in the composite. In this review, bast fiber retting process and the effect of enzymatic retting on fiber and fibers reinforced polymer composites have been discussed and reviewed for the latest researches. Retting precedes mechanical processing (i.e. scutching) of the fiber from the stem and is essential for reduction of fiber breakage. All retting methods except chemical retting process are involving secretes of enzymes by bacteria or fungi under controlled (enzymatic retting) or random conditions (water and dew retting). Besides, enzymatic retting is claimed to have more environmentally friendly wastewater products, shorter retting period and controllable fiber biochemical components under mild incubation conditions. This review comprehensively assesses the enzymatic retting process for producing high-quality bast fiber and will become a reference for future development on bast fiber reinforced polymer composites.
ARTICLE | doi:10.20944/preprints201804.0330.v1
Subject: Biology, Ecology Keywords: nonylphenol; montmorillonite; zebrafish; enrichment; enzyme activity
Online: 26 April 2018 (05:48:32 CEST)
To investigate the effect of montmorillonite on nonylphenol enrichment in a zebrafish model. The AB strain zebrafish were used as the animal subjects and three concentration gradients were set for both nonylphenol and montmorillonite, according to their actual concentrations in aquaculture water in Huzhou city. A group treated with nonylphenol alone was also set, adding up to 12 experimental groups. Concentrations of nonylphenol enriched in the liver, muscle, and gill of zebrafish were detected by solid phase microextraction–high performance liquid chromatography at Day 7, 15, and 30, respectively. Besides, the relative enzymatic activity of Superoxide dismutase (SOD) and the Glutathione S-transferase (GST) were also been detected, and the data were statistically analyzed. The results showed that the concentrations of nonylphenol in zebrafish peaked at Day 7 and gradually decreased afterwards for all the experimental groups. And the montmorillonite reduces short-term accumulation of nonylphenol in gills, and the high concentration of nonylphenol facilitates its enrichment in liver and muscle while the low concentration of nonylphenol doesn’t. Meanwhile, the low concentration of nonylphenol in liver exerts an influence on the inductive effect of SOD and GST while the high concentration of nonylphenol shows the inhibiting effect of SOD and GST.
REVIEW | doi:10.20944/preprints201804.0011.v1
Subject: Materials Science, Nanotechnology Keywords: enzyme; immobilization; organic-inorganic nanoflower; nanobiocatalysts
Online: 2 April 2018 (08:15:44 CEST)
A recent breakthrough in preparation of immobilized enzyme based biocatalysts achieving highly enhanced enzymatic activities and stabilities has become a great alternative to conventional immobilization techniques. The functional hybrid nanobiocatalysts (FHNs) fabricated in this immobilization composed of organic components (amino acid, peptide, protein, enzyme and plant extract) and inorganic components (various metal ions) give flower-like morphology with narrow size distribution and porous structure. The enzyme incorporated FHNs exhibite greatly enhanced catalytic activities and stabilities compared to free and conventionally immobilized enzymes under various experimental conditions. In addition to that, the FHNs consisting of other organic components act as Fenton-like reagents and show peroxidase-like activity owing to presence of metal ions and porous structure in the FHNs. This report basically focuses on preparation, characterization, and bioanalytical applications of the FHNs and explain mechanism of the FHNs formation and thier enhanced activities and stabilities.
ARTICLE | doi:10.20944/preprints202108.0198.v1
Subject: Biology, Animal Sciences & Zoology Keywords: depolymerizing enzyme; debranching enzyme; xylanase; arabinofuranosidase; feruloyl esterase; arabinoxylan; digestion; growth performance; volatile fatty acid; piglet
Online: 9 August 2021 (14:56:56 CEST)
This study was aimed to investigate the effect of xylan depolymerizing enzyme namely endo-xylanase (Xyn) combined with debranching enzymes namely arabinofuranosidase (Afd) and feruloyl esterase (FE) on digestion, growth performance and intestinal volatile fatty acid profile of piglets. The in vitro experiments were firstly conducted to examine the enzymological properties of Xyn, Afd and FE, the synergy among these enzymes, together with the effect of combination of these enzymes on digestion of piglet diet. The in vivo experiment was then implemented by allocating 270 35-d-old postweaning piglets into 3 treatment groups: control group, Xyn group and (Xyn+Afd+FE) group. Each group had 6 replicates (15 piglets/replicate). The results revealed a satisfying thermostability and pH stability of Xyn, Afd and FE. Combination of Xyn, Afd and FE had a superiority (P < 0.05) over Xyn alone and its combination with Afd or FE in promoting degradation of different bran fibers rich in arabinoxylan (Abx). Treatment with combination of Xyn, Afd and FE had advantages over Xyn alone to induce increasing trends (P < 0.10) of in vitro digestibility of dietary nutrients (dry matter, crude protein, crude ash and gross energy) and piglet growth performance (average daily gain, final body weight and feed efficiency), concurrent with a reduction (P < 0.05) of diarrhea rate and increases (P < 0.05) in cecal acetic acid, butyric acid and total volatile fatty acids concentrations as well as pH value of piglets. Collectively, combination of Xyn, Afd and FE was efficient in benefiting degradation of Abx in brans, as well as improving digestion, growth performance and intestinal volatile fatty acid profile of piglets.
ARTICLE | doi:10.20944/preprints202211.0351.v1
Subject: Biology, Other Keywords: enzyme-constrained model; Bacillus subtilis; metabolic engineering
Online: 18 November 2022 (07:09:22 CET)
Genome-scale metabolic models (GEMs) play an important role in the phenotype prediction of microorganisms, and their accuracy can be further improved by integrating other types of biological data such as enzyme concentrations and kinetic coefficients. Enzyme-constrained models (ecModels) have been constructed for several species and were successfully applied to increase the production of commodity chemicals. However, there was still no genome-scale ecModel for the important model organism Bacillus subtilis prior to this study. Here, we integrated enzyme kinetic and proteomic data to construct the first genome-scale ecModel of B. subtilis (ecBSU1) using the ECMpy workflow. We first used ecBSU1 to simulate overflow metabolism and explore the trade-off between biomass yield and enzyme usage efficiency. Then, we simulated the growth rate on eight previously published substrates and found that the simulation results of ecBSU1 were in good agreement with the literature. Finally, we identified target genes that enhance the yield of commodity chemicals using ecBSU1, most of which were consistent with the experimental data, and some of which may be potential novel targets for metabolic engineering. This work demonstrates that the integration of enzymatic constraints is an effective method to improve the performance of GEMs. The ecModel can predict overflow metabolism more precisely and can be used for the identification of target genes to guide the rational design of microbial cell factories.
ARTICLE | doi:10.20944/preprints202209.0019.v1
Subject: Biology, Other Keywords: enzyme-constrained model; Corynebacterium glutamicum; metabolic engineering
Online: 1 September 2022 (09:54:55 CEST)
Genome-scale metabolic model (GEM) is a powerful tool for interpreting and predicting cellular phenotypes under various environmental and genetic perturbations. However, GEM only consid-ers stoichiometric constraints, and the simulated growth and product yield values will show a monotonic linear increase with increasing substrate uptake rate, which deviates from the experi-mentally measured values. Recently, the integration of enzymatic constraints into stoichiometry-based GEMs was proven to be effective in making novel discoveries and predicting new engineer-ing targets. Here we present the first genome-scale enzyme-constrained model (eciCW773) for Corynebacterium glutamicum reconstructed by integrating enzyme kinetic data from various sources using ECMpy workflow based on the high-quality GEM of C. glutamicum (obtained by modifying the iCW773 model). The enzyme-constrained model improved the prediction of pheno-types and simulated overflow metabolism, while also recapitulating the trade-off between biomass yield and enzyme usage efficiency. Finally, we used eciCW773 to identify several gene modifica-tion targets for L-lysine production, most of which agree with previously reported genes. This study shows that incorporating enzyme kinetic information into the GEM enhances the cellular phenotypes prediction of C. glutamicum, which can help identify key enzymes and thus provide reliable guidance for metabolic engineering.
Subject: Chemistry, Analytical Chemistry Keywords: Microfluidic, Conductivity, Mobil-phone, urea, urease enzyme
Online: 22 February 2021 (16:44:31 CET)
In this work, PMMA(Poly methyl methacrylate) microfluidic system was used as a micro-reactor for urea hydrolysis by urease enzyme with use conductivity principle and utilize sound level meter(SLM) App in smartphone as a novel detector by considering the peak height in the App as an indicate for urea concentration. the advantage of use small volume and how the reaction carried on in the microfluidic system with simple and low cost are discussed, and the results were analyzed and statically determine. The linearity, detection limit (3×noise )and Correlation Coefficient, 62.5-500 ppm, 31.25 ppm and 0.992 respectively also, recovery studied were between(98.5-100.13%).
ARTICLE | doi:10.20944/preprints201910.0348.v1
Online: 30 October 2019 (04:59:29 CET)
Immobilization of enzymes is a good field of study to expand the life of enzyme in and lowering the cost of the chemical processes such as separation processes. Urease is an important enzyme with medical and industrial applications. The aim of the present study is to prepare an immobilized urease on a strong cation exchange resin (Amberlite IR120 -Na) and study of its activity and stability. We monitored the liberation of Na ions in the collected fractions and searching for protein in the fractions as an indicators of immobilization by ion exchange phenomenon. Sodium is measured using atomic absorption spectroscopy techniques, while protein tested by Bradford’s method. Immobilized urease activity was evaluated by salicylate-hypochlorite method. The results indicated a complete immobilization of urease enzyme on the resin surface with reserving 92% of the activity of free enzyme. The immobilized urease enzyme on resin showed good stability and it has a 62% of its activity after 154 days of storage at room temperature. It is concluded that a new immobilized urease enzyme system is prepared with good enzyme activity and stability.
COMMUNICATION | doi:10.20944/preprints201906.0001.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: forest soils; soil enzyme aktivity; soil microorganisms
Online: 3 June 2019 (04:45:20 CEST)
Soil proteases are involved in the transformation of organic matter and thus influence the nutrient turnover in the ecosystem. Phytohormones, similarly to proteases, are synthesized and secreted into the soil by fungi and microorganisms and regulating their activity in the rhizosphere. The aim of our work was to find out how the presence of auxins, cytokinins, ethephone and chlorocholine chloride affects the activity of native soil proteases at the spruce tree stand. Auxins stimulated the native proteolytic activity in the spruce tree stand. Synthetic auxins most stimulated the activity of 2-naphthoxyacetic acid and the naturally occurring auxins of indole-3-acetic acid in the organic horizon of the spruce forest. Cytokinins, ethephone and chlorocholine chloride inhibited the activity of native soil proteases in the spruce tree stand. The highest inhibitory effect was found in ethephone and chlorocholine chloride. Overall, the negative effect of phytohormones on the activity of the native proteolytic activity may slow down the decomposition of organic matter and thus make plant nutrition more difficult. The outcomes of our work assist with understanding of the effect of substances produced by the rhizosphere on the activity of soil microorganisms and the soil nitrogen cycle.
ARTICLE | doi:10.20944/preprints201611.0023.v1
Subject: Life Sciences, Other Keywords: anti-yeast; enzyme inhibitors; Terminalia mantaly; Combretaceae
Online: 3 November 2016 (09:35:17 CET)
The chemical investigation of the anti-yeast methanol extract from the stem bark of Terminalia mantaly led to the isolation of seven compounds: 3-O-methyl-4-O-α-rhamnopyranoside ellagic acid (1), 3-O-mehylellagic acid (2), arjungenin or 2,3,19,23-tetrahydroxyolean-12-en-28-oïc acid (3), arjunglucoside or 2,3,19,23-tetrahydroxyolean-12-en-28-oïc acid glucopyranoside (4), 2α,3α,24-trihydroxyolean-11,13(18)-dien-28-oïc acid (5), stigmasterol (6), stigmasterol 3-O-β-D-glucopyranoside (7). Their structures were established by means of spectroscopic analysis and comparison with published data. Compounds 1-5 were tested in vitro for activity against three pathogenic yeast isolates, Candida albicans, Candida parapsilosis and Candida krusei. The activity of compounds 1, 2 and 4 were comparable to that of the reference compound fluconazole (MIC values below 32 µg/ml) against the three tested yeast isolates. They were also tested for inhibitory properties against four enzymes of metabolic significance: Glucose-6-Phosphate Deshydrogenase (G6PD), human erythrocyte Carbonic anhydrase I and II (hCA I and hCA II), Glutathione S-transferase (GST). Compound 4 showed highly potent inhibitory property against the four tested enzymes with overall IC50 values below 4 µM and inhibitory constant (Ki) <3 µM.
REVIEW | doi:10.20944/preprints202110.0197.v1
Subject: Medicine & Pharmacology, Cardiology Keywords: AGING; Age-related comorbidities; Angiotensin-Converting Enzyme; Amyloid-degrading enzyme; Alzheimer’s disease; Dementia; Hypertension; Life extension; Stress resistance
Online: 13 October 2021 (11:04:43 CEST)
A recent report from the American Heart Association in 2018 shows that over 103 million American adults have hypertension. The angiotensin-converting enzyme (ACE) (EC 22.214.171.124) is a dipeptidyl carboxylase that, when inhibited, can reduce blood pressure through the renin-angiotensin system. ACE inhibitors are used as a first-line medication to be prescribed to treat hypertension, chronic kidney disease, heart failure among others. It has been suggested that ACE inhibitors can reduce the symptoms in mouse models. Despite the benefits of ACE inhibitors, previous studies also have suggested that alterations in the ACE gene are risk factors for Alzheimer’s disease (AD) and other neurological diseases. In mice, overexpression of ACE in the brain reduces symptoms of the AD-model systems. Thus, we find opposing effects of ACE on health. To clarify the effects, we dissect the functions of ACE as follows: (1) angiotensin-converting enzyme that hydrolyzes angiotensin I to make angiotensin II in the renin-angiotensin system; (2) amyloid-degrading enzyme that can hydrolyze beta-amyloid and reduce amyloid toxicity. The efficacy of the ACE inhibitors is well established in humans, while the knowledge specific to AD remains to be open for further research. We provide an overview of ACE and inhibitors that link a wide variety of age-related comorbidities from hypertension to Alzheimer’s disease to aging. ACE also serves as an example of the middle-life crisis theory that assumes deleterious events during the midlife, leading to age-related later events.
ARTICLE | doi:10.20944/preprints202001.0261.v1
Subject: Life Sciences, Biochemistry Keywords: sebaleic acid; sapienic acid; positional fatty acid isomer; trans geometrical isomer; extracellular vesicle lipidome; desaturase enzyme; elongase enzyme; lipidomics
Online: 22 January 2020 (16:10:25 CET)
A new pathway leading to the n-10 fatty acid series has been recently evidenced, starting from sapienic acid - a monounsaturated fatty acid (MUFA) resulting from the transformation of palmitic acid by delta-6 desaturase. Sapienic acid attracts attention as novel marker of cancer cell plasticity. Here, we analyzed fatty acids including the n-10 fatty acid contents, and compared for the first time cell membranes and the corresponding extracellular vesicles (EV) of two human prostatic adenocarcinoma cell lines of different aggressiveness (PC3 and LNCaP). The n-10 components were 9-13% of the total fatty acids in both cancer cell lines and EVs, with total MUFA levels significantly higher in EVs of the most aggressive cell type (PC3). High sapienic/palmitoleic ratios indicated the preference for delta-6 vs. delta-9 desaturase enzymatic activity in these cell lines. The expressions analysis of enzymes involved in desaturation and elongation by qRT-PCR showed a higher desaturase activity in PC3 and a higher elongase activity toward polyunsaturated fatty acids than toward saturated fatty acids, compared to LNCaP cells. Our results improve the present knowledge in cancer fatty acid metabolism and lipid phenotypes, highlighting EV lipidomics to monitor positional fatty acid isomer profiles and MUFA levels in cancer.
ARTICLE | doi:10.20944/preprints202108.0059.v1
Subject: Biology, Anatomy & Morphology Keywords: Ballota nigra; salinity; antioxidant; enzyme activity; phytochemical composition
Online: 2 August 2021 (16:31:13 CEST)
Black horehound (Ballota nigra L.) is one of the important medicinal plants, which is a rich source of health-promoting essential oils. Salinity stress affects plant development and alters the quality and quantity of plants extracts and their composition. This study was aimed to investigate the effect of salinity on morphological, physiological characteristics, and secondary metabolites of B. nigra under greenhouse, and in vitro culture conditions. The plants were treated with different concentrations of NaCl (25, 50, 75, 100 mM) and fresh and dry weight of leaf and stem were measured as well as morphological characteristics of the plant. Plant growth was reduced with the increased salinity concentrations. The results showed that all growth-related traits and SPAD were decreased both in vivo and in vitro. Additionally, increased salt concentration affected the cell membrane integrity. Total phenolics content of plants growing in the greenhouse, increased by 21% at 50 mM NaCl, but at higher stress levels (100 mM NaCl), the amounts were decreased significantly. Total flavonoids contents followed similar patterns, with a slight difference. In addition, the maximum and minimum total phenolics contents of plants growing under in vitro condition were observed at 50 mM NaCl and control treatments, respectively. Increasing the salt concentration significantly affected the total flavonoids content, and as a result, the highest amount was observed in 50 and 75 mM NaCl treatments. Antioxidant activity was also measured. Among the NaCl treatments, the highest DPPH scavenging activities (IC50) under greenhouse and in vitro conditions were detected at 50 mM and 25 mM concentrations, respectively. In general, based on the results, with increasing the salinity level to 75 mM, the activities of CAT and APX were significantly upregulated in both greenhouse and in vitro culture conditions. A correlation between total phenolics and flavonoids contents as well as antioxidant activity were obtained. With shifting salinity stress, the type and the amount of the identified essential oil compounds changed. Compounds such as styrene, tridecanol, germacrene-D, beta-Ionone, beta-bisabolene, and caryophyllene oxide increased compared to the controlled treatment.
ARTICLE | doi:10.20944/preprints201809.0372.v2
Subject: Biology, Agricultural Sciences & Agronomy Keywords: biochar; surface area; enzyme activity; immobilization; protein assay
Online: 11 October 2018 (07:49:15 CEST)
Extracellular enzymes catalyze biogeochemical reactions in soil, cycling carbon and nutrients in agricultural systems. Enzymes respond quickly to soil management, including organic amendment inputs, such as biochar, a charcoal-like solid byproduct of bioenergy production. In a previous agricultural field trial, a pine biochar amendment caused an approximately 40% decrease in the enzyme activities of β-glucosidase (BG) and phosphatase (PHOS). The large surface area of the pine biochar has the potential to sorb nutrients and other organic molecules. To test if sorption caused decreased enzyme activity, we used a laboratory assay to quantify the activity of two sorbed enzymes: BG and acid PHOS, involved in the cycling of carbon and phosphorous. The enzymes were incubated with three solid phases: (1) the high surface area pine biochar, (2) the agricultural soil, and (3) a low surface area grass biochar, for an additional comparison. We quantified the sorbed enzymes at pH 6, 7, and 8, using a Bradford protein assay, and measured the immobilized enzyme activities via high-throughput fluorometric analysis. After sorption onto pine biochar, detectable BG and PHOS activity levels dropped by over 95% relative to the soil, supporting direct sorption as one mechanism that reduces enzyme activity in biochar amended soil. This laboratory assay demonstrated that sorption could account for the lack of priming of native soil organic matter and changes in soil phosphorous cycling after pine biochar addition.
ARTICLE | doi:10.20944/preprints201608.0203.v1
Subject: Biology, Entomology Keywords: Sitophilus zeamais; COXⅡ; Soluble proteins; Enzyme activity; AITC
Online: 25 August 2016 (10:11:13 CEST)
COX II containing a dual core CuA active site is one of the three core subunits of mitochondrial Cco, which plays a significant role in the physiological process. In this report, the full-length cDNA of COXⅡ gene was cloned from Sitophilus zeamais, which had an ORF of 684 bp encoding 227 amino acids residues. The predicted COXⅡ protein had a molecular mass of 26.2 kDa with pI value of 6.37, and multiple sequence alignment and phylogenetic analysis indicated that Sitophilus zeamais COXⅡ had high sequence identity 78.51% with the COXⅡ of other insect species, especially similarity to sitophilus oryzae. This gene was subcloned into the prokaryotic expression vector pET-32a, and induced by IPTG in E.coli Transetta (DE3) expression system. Finally the COXⅡ with 6-His tag was purified using affinity chromatography with Ni2+-NTA agarose. WB showed the recombinant COXⅡ was about 44 kD, and the concentration of fusion protein was 50μg/mL. UV-spectrophotometer and infrared spectrometer analysis showed that recombinant COXⅡ could catalyze the oxidation of substrate Cytc, and influenced by AITC. It was found that AITC could form a hydrophobic region with COXⅡ protein via molecular docking, besides, a sulfur atom of AITC structure could form a length of 2.9 Å hydrogen bond with Leu-31. These results will provide valuable information for elucidating the role of COXⅡ in Sitophilus zeamais responses to AITC, meanwhile, it will helpful to carry out a point mutation in AITC binding sites for the future research.
REVIEW | doi:10.20944/preprints202101.0194.v1
Subject: Engineering, Automotive Engineering Keywords: ultrasound; ultrasonic reactors; enzyme kinetic; enzymatic reaction; sonochemical reaction
Online: 11 January 2021 (12:49:39 CET)
The use of low-intensity ultrasound has gotten surprising consideration over the last decade as a method for enhancing the catalytic activity of the enzyme. Ultrasounds have the potential to significantly influence the activity of the enzymatic processes, provided that the energy input is not too high to inactivate the enzyme. By providing the variation in parameters, various physical and chemical effects can be attained that can enhance the enzymatic reaction. Ultrasonic reactors are known for their application in bioprocesses. However, the potential of their applications is still limited broadly due to the lack of proper information about their operational and performance parameters. In this review, the detailed information about ultrasonic reactors is provided by defining the different types of reactors, number and position of ultrasonic transducers. Also, it includes the mechanism of intensification and influence of ultrasonic parameters (intensity, duty cycle and frequency) and enzymatic factors (enzyme concentration, temperature and pH) on the catalytic activity of enzyme during ultrasound treatment.
ARTICLE | doi:10.20944/preprints202003.0409.v2
Subject: Life Sciences, Virology Keywords: angiotensin-converting enzyme 2; SARS-CoV-2; spike protein; COVID-19
Online: 9 April 2020 (09:59:37 CEST)
Objectives Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has high infectivity in humans, attributed to the strong affinity of its spike (S) protein to human angiotensin-converting enzyme 2 (ACE2). Here, we analyzed the structural similarity of the S protein between SARS-CoV-2 and other SARS-related coronaviruses (CoVs). Methods We performed multiple alignment analysis of nine amino acid sequences of CoV S proteins from NCBI with MAFFT web-based software, followed by phylogeny analysis. Three-dimensional structure modeling was performed by SWISS-MODEL. We calculated the template modeling score between the S protein of SARS-CoV-2 and that of other SARS-related CoVs. Results The S1 domain of the unclassified CoV RaTG13 (the host of which is the intermediate horseshoe bat) was structurally very similar to that of SARS-CoV-2, implying that RaTG13 could be the origin of SARS-CoV-2. In addition, the folding property of the entire S protein was nearly the same between SARS-CoV-2 and RaTG13 after the PRRA amino acid insertion was removed from SARS-CoV-2. Conclusions RaTG13 could have a high binding affinity to ACE2, similar to SARS-CoV-2, and it is therefore highly likely to infect other animals. Therefore, massive research and monitoring of CoVs in animals is necessary to prevent future COVID-19-like disasters.
Subject: Life Sciences, Molecular Biology Keywords: icariin; nicotine; sperm density; testosterone; antioxidant enzyme; male mice
Online: 14 October 2019 (09:58:40 CEST)
Nicotine is a pharmacologically active component of tobacco which adversely affects the male reproductive system and fertility and Icariin (ICA) is the main active ingredient of Epimedium herba which has been used to treat several male reproductive problems. This study was aimed at investigating the protective or ameliorative effect of ICA against reproductive toxicity induced by intraperitoneal injection of nicotine in mice. Forty male mice were randomly divided into 4 groups: control, nicotine (0.75 mg/kg intraperitoneally), icariin (ICA, 75 mg/kg), and icariin plus nicotine (ICA + nicotine) group. After 35 days of treatment, the mice were weighed, sacrificed, and their reproductive organs were collected and examined for further studies. In the nicotine-treated group, epididymal sperm density and serum testosterone concentrations significantly decreased relative to the control group. Nicotine also caused oxidative damage as shown by significant reduction in the activities of antioxidant enzymes and an elevation in Malondialdehyde (MDA) levels. Icariin on the other hand, improved the reduction in sperm characteristics, hormone levels, and activities of antioxidant enzymes alterations observed in the nicotine treated mice. These findings indicate that the nicotine-induced reproductive toxicity and oxidative damages on male reproductive tissues can be effectively attenuated by icariin.
ARTICLE | doi:10.20944/preprints201905.0319.v1
Subject: Life Sciences, Microbiology Keywords: cyanobacteria; protease inhibitors; digestive enzyme; daphnia; HPLC; UV/Vis
Online: 27 May 2019 (12:56:49 CEST)
Cyanobacterial mass developments in eutrophic ponds and lakes are a major concern for lake management, as many cyanobacteria produce a huge variety of toxic secondary metabolites, e.g. microcystins. The aim of this research was to culture a strain of the cyanobacterium Microcystis sp strain BM25, to observe its biomass production and to isolate and purify protease inhibitors from this cyanobacterial biomass. Different secondary metabolites were isolated following a standard bioassay-guideline. Isolation was performed, with an enzymatic protease assay as bioassay. High performance liquid chromatography was used to identify different fractions of secondary metabolite from the strain BM25. Moreover, protease homogenates were isolated from Daphnia magna in order to test the inhibitors against naturally occurring major digestive proteases trypsin and chymotrypsin. It was measured that 60% MeOH and the 80% MeOH C18-SPE fraction inhibits chymotrypsin activity 98% (6 nmol pNA min-1 mg-1) and 99 % (4 nmol pNA min-1 mg-1), respectively. In contrast, trypsin activity was not inhibited by methanolic extracts of this cyanobacterium strain.
COMMUNICATION | doi:10.20944/preprints201810.0408.v1
Subject: Chemistry, Other Keywords: Salvia pachyphylla; plant extracts; antioxidant; antimicrobial; antiproliferative; enzyme inhibitory
Online: 18 October 2018 (09:56:26 CEST)
The antioxidant, antimicrobial, antiproliferative, and enzyme inhibitory properties of five extracts from aerial parts of Salvia pachyphylla were examined to assess the prospective of this plant as a source of natural products with therapeutic potential. Those properties were analyzed performing a set of standard assays. The extract obtained with dichloromethane showed the most variety of components, as yielded promising results in all completed assays. Furthermore, the extract obtained with ethyl acetate exhibited that greatest antioxidant activity as well as the best xanthine oxidase inhibitory activity. Remarkably, both extracts obtained with n-hexane or dichloromethane revealed significant antimicrobial activity against the Gram-positive bacteria; also, they showed greater antiproliferative activity against three representative cell lines of the most common types of cancers in women worldwide, and against a cell line that exemplifies cancers that typically develop drug resistance. Despite that other extracts were less active, such as the methanolic or aqueous, their results are promising for the isolation and identification of novel bioactive molecules.
REVIEW | doi:10.20944/preprints201805.0145.v1
Subject: Life Sciences, Biochemistry Keywords: carbonic anhydrase, enzyme inhibition, metalloenzymes, amino acid, glaucoma, tumors
Online: 9 May 2018 (13:55:15 CEST)
Carbonic Anhydrases (CAs) are a superfamily of metalloenzymes widespread in all life kingdoms, classified into seven genetically different families (α-θ). These enzymes catalyse the reversible hydration of carbonic anhydride (CO2), generating bicarbonate (HCO3-) and protons (H+). Fifteen isoforms of human CA (hCA I-XV) have been isolated, their presence being fundamental for the regulation of many physiological processes. In addition, overexpression of some isoforms has been associated with the outbreak or the progression of several diseases. For this reason, for a long time CA inhibitors (CAIs) are used in the control of glaucoma and as diuretics. Furthermore, the search for new potential CAIs for other pharmacological applications is a very active field. Amino acids constitute the smallest fundamental monomers of protein and, due to their useful bivalent chemical properties, are widely used in organic chemistry. Both proteinogenic and non-proteinogenic amino acids have been extensively used to synthesize CAIs. This article provides an overview of the different strategies that have been used to design new CAIs containing amino acids, and how these bivalent molecules influence the properties of the inhibitors.
REVIEW | doi:10.20944/preprints201704.0135.v1
Subject: Life Sciences, Biochemistry Keywords: GPCR; ubiquitination; β-arrestin; deubiquitinating enzyme; E3 ubiquitin ligase
Online: 21 April 2017 (06:23:26 CEST)
G protein-coupled receptors (GPCRs) comprise the largest family of membrane receptors that control many cellular processes and consequently often serve as drug targets. These receptors undergo a strict regulation by mechanisms such as internalization and desensitization, which are strongly influenced by posttranslational modifications. Ubiquitination is a posttranslational modification with a broad range of functions that is currently gaining increased appreciation as a regulator of GPCR activity. The role of ubiquitination in directing GPCRs for lysosomal degradation has already been well-established. Furthermore, this modification can also play a role in targeting membrane and endoplasmic reticulum-associated receptors to the proteasome. Most recently, ubiquitination was also shown to be involved in GPCR signaling. In this review, we present current knowledge on the molecular basis of GPCR regulation by ubiquitination, and highlight the importance of E3 ubiquitin ligases, deubiquitinating enzymes and β-arrestins. Finally, we discuss classical and newly-discovered functions of ubiquitination in controlling GPCR activity.
ARTICLE | doi:10.20944/preprints201701.0053.v2
Subject: Chemistry, Chemical Engineering Keywords: chiral amines; biocatalysis; silica monolith; enzyme immobilization; flow chemistry
Online: 13 February 2017 (09:02:56 CET)
ω-Transaminases have been immobilized on macrocellular silica monoliths and used as heterogeneous biocatalysts in a continuous flow mode enantioselective transamination reaction. The support was prepared by a sol-gel method based on emulsion templating. The enzyme was immobilized on the structured silica monoliths both by adsorption, and by covalent grafting using amino-functionalized silica monoliths and glutaraldehyde as a coupling agent. A simple reactor set-up based on the use of a heat-shrinkable Teflon tube is presented and successfully used for the continuous flow kinetic resolution of a chiral amine, 4-bromo-α-methylbenzylamine. The porous structure of the supports ensures effective mass transfer and the reactor works in the plug flow regime without preferential flow paths. When immobilized in the monolith and used in the flow reactor, transaminases retain their activity and their enantioselectivity. The solid biocatalyst is also shown to be stable both on stream and during storage. These essential features pave the way to the successful development of an environmentally friendly process for chiral amines production.
ARTICLE | doi:10.20944/preprints202012.0002.v1
Subject: Life Sciences, Biochemistry Keywords: 3-ketosteroid Δ1-dehydrogenase; KSTD; KSDH; AcmB; 1,2-dehydrogenation; cholest-4-en-3-one Δ1-dehydrogenase; enzyme immobilization; FAD-dependent enzymes; enzyme immobilization
Online: 1 December 2020 (08:11:00 CET)
Cholest-4-en-3-one Δ1-dehydrogenase (AcmB) from Sterolibacterium denitrificans is successfully immobilized on 3-aminopropyltrimethoysilane functionalized MCF and SBA-15 silica supports using adsorption or covalently with glutaraldehyde or divinyl sulfone linkers. The best catalyst, AcmB on MCF linked covalently with glutaraldehyde, retains the specific activity of the homogenous enzyme while exhibiting a substantial increase of the operational stability. The immobilized enzyme was used continuously in the fed-batch reactor for 27 days, catalyzing 1,2-dehydrogenation of androst-4-en-3-one to androst-1,4-dien-3-one with a final yield of 29.9 mM (8.56 g/L) and 99% conversion. The possibility of reuse of the immobilized catalyst was also demonstrated and resulted with a doubling of the product amount compared to that in the reference homogenous reactor. Finally, it was shown that molecular oxygen from the air can efficiently be used as an electron acceptor either reoxidizing directly the enzyme or the reduced DCPIPH2. Keywords: 3-ketosteroid D1-dehydrogenase; KSTD; KSDH; AcmB; 1,2-dehydrogenation; cholest-4-en-3-one Δ1-dehydrogenase; enzyme immobilization, FAD-dependent enzymes; enzyme immobilization;
BRIEF REPORT | doi:10.20944/preprints202208.0515.v1
Subject: Life Sciences, Other Keywords: angiotensin-converting enzyme 2; BanLec H84T; Cyanovirin; glycosylation; Griffithsin; algorithms
Online: 30 August 2022 (08:31:56 CEST)
The Severe acute respiratory syndrome-Corona virus-2 (SARS-CoV-2) which is responsible for recurring pandemics takes advantage of host-cell processes including the glycosylation pathway. The heavily glycosylated spike protein assists viruses in attachment and penetration. The N-glycans of N-terminal domain N165 and N234 play a significant role in conformational dynamics of the receptor-binding domain (RBD) with angiotensin-converting enzyme 2 (ACE2). In addition, the deletion of N-glycan sites N331 and N334 have been associated with reduced infectivity. This signifies the importance of targeting the N-glycans making them unavailable for interacting with the ACE2 receptor, ultimately leading to reduced infectivity. These glycans can be specifically targeted and can be used for designing SARS specific drugs or neutralizing molecules. In the current study, lectins Griffithsin, Cyanovirin-N, Cyanovirin homolog, and BanLec H84T were used to target the spike protein's N-glycans. Molecular docking programs AutoDock Vina and HADDOCK were used to study lectin-glycan interactions. The interactions look convincible in accordance with the lowest interaction energies best-fit approach but the characteristic feature (scoring functions) of the docking programs are questionable concerning Lectin-Glycan interactions exist in nature. There is a high need of the hour for developing specific algorithms for docking glycans with a preferential selection of terminal residues.
ARTICLE | doi:10.20944/preprints202104.0124.v1
Subject: Keywords: Drinking water; Enzyme-linked immunosorbent assay; Harmful algal blooms; Microcystin
Online: 5 April 2021 (12:25:15 CEST)
Clean, fresh, and safe drinking water is essential to human health and well-being. Occasionally, chemical pollutants taint surface water quality used for consumption. Microcystins (MCs) are toxic heptapeptides produced by freshwater cyanobacteria. These secondary metabolites can reach hazardous concentrations, impairing surface drinking water supplies. Inconsistent screening of MCs is not uncommon in Florida waters as no provisional guidance value is established to protect public health. The occurrence of MCs in Lake Manatee and Lake Washington was monitored over the potential peak algae bloom season (June-August). An indirect competitive enzyme-linked immunosorbent assay (icELISA) quantified total MCs in two drinking water systems. Varied concentrations occurred between June and July, whereas concentrations peaked in August. Overall, MC prevalence was higher in Lake Manatee than Lake Washington. Colorimetric assays measured phosphate and nitrite in environmental water samples. Phosphate and nitrite concentrations strongly correlated with total MCs (p < 0.01). The results indicate the intrinsic nature of environmental MCs in surface drinking water supplies and the need to examine hepatotoxin dynamics to preserve drinking water quality in community served areas.
ARTICLE | doi:10.20944/preprints202102.0004.v1
Subject: Biology, Anatomy & Morphology Keywords: Equine theileriosis; Theileria haneyi; enzyme-linked immunosorbent assay (ELISA), serology
Online: 1 February 2021 (09:41:24 CET)
The apicomplexan parasite Theileria haneyi is one of two known causative agents of equine theileriosis. It causes milder clinical disease than its more virulent counterpart, Theileria equi, in experimentally infected horses, and can superinfect T. equi-positive horses. The current EMA1-based competitive ELISA used in the U.S. to detect equine theileriosis detects T. equi but not T. haneyi, and the complexity of molecular assays precludes widespread use for epidemiologic studies. In order to facilitate urgently needed studies on the prevalence of T. haneyi, the goal of this study was to develop a sensitive and specific serologic assay for the diagnosis of T. haneyi based on the equi mero-zoite antigen 11 (ThEMA11). To achieve this objective, ThEMA11 was recombinantly expressed in eukaryotic cells and its antigenicity assessed using sera from T. haneyi-experimentally infected horses. Confirmation of sera reactiv-ity enabled design and optimization of an indirect ELISA. Specificity of the ELISA for T. haneyi was assessed using a cohort of sera from horses experimentally infected and confirmed PCR-positive for either T. equi or T. haneyi. Data from field samples further demonstrate that the ThEMA11 ELISA is capable of identifying T. haneyi antibodies in horses from multiple continents around the world.
ARTICLE | doi:10.20944/preprints202012.0444.v1
Subject: Biology, Anatomy & Morphology Keywords: novel rumen yeast; screening; isolation; biomass of yeast; cellulase enzyme
Online: 18 December 2020 (07:26:28 CET)
We hypothesized that rumen fluid with yeast producing cellulase enzyme can occur and also produces a high biomass compared to S. cerevisiae. Therefore, the aim of this study was to screen and isolate yeast from rumen fluids with an experimental design method. We optimized a fermentation medium containing sugarcane molasses as a carbon source and urea as a nitrogen source to measure the efficiency of biomass production and cellulase activity. Two fistulated-crossbred Holstein Friesian steers, averaging 350 ± 20 kg body weight, were used to screen and isolate ruminal yeast. The two experiments were designed. A 12 × 3 × 3 factorial was used in a completely randomized design to determine biomass and carboxymethyl cellulase activity. Factor A was isolated yeasts and S. cerevisiae. Factor B was sugarcane molasses (M) concentration. Factor C was urea (U) concentration. Potential yeast was selected for identified and analyzed as a 4 × 3 factorial use in a completely randomized design including. Factor A was incubation times. Factor B was isolated yeast strains including code H-KKU20 (as P. kudriavzevii-KKU20), I-KKU20 (C. tropicalis-KKU20), and C-KKU20 (as Galactomyces sp.-KKU20). Isolation was under aerobic conditions, resulting in a total of 11 different colonies. We noted two appearances of colonies including, asymmetric colonies of isolated yeast (indicated as A, B, C, E, and J) and ovoid colonies (coded as D, F, G, H, I, and K). The highest biomass was observed in three yeasts including codes H, I, and C-KKU20 when inoculated in 25% molasses with 1% urea (M25+U1) (p <0.01). The highest CMCase activity was observed in yeast code H-KKU20 when inoculated in all media solutions (p <0.01). Ruminal yeasts strains H-KKU20, I-KKU20, and C-KKU20 were selected for their ability to produce biomass and their CMCase enzyme synthesis. Identification of isolates H-KKU20 and I-KKU20 revealed that those isolates belonged to Pichia kudriavzevii-KKU20 and Candida tropicalis-KKU20, while C-KKU20 was identified as Galactomyces sp.-KKU20. Two strains provided maximum cell growth: P. kudriavzevii-KKU20 (9.78 and 10.02 Log cell/ml) and C. tropicalis-KKU20 (9.53 and 9.6 Log cells/ml) at 60 and 72 h of incubation time, respectively. The highest ethanol production was observed in S. cerevisiae: 76.4, 77.8, 78.5, and 78.6 g/L at 36, 48, 60, and 72 h of incubation time, respectively (p <0.01). The P. kudriavzevii-KKU20 yielded the least reducing sugar about 30.6 and 29.8 g/L at 60 and 72 h of incubation time, respectively. It could be concluded that screening and isolating yeast from rumen fluids resulted in 11 different characteristics of yeasts. The first novel yeasts discovered in the rumen fluid of cattle were Pichia kudriavzevii-KKU20, Candida tropicalis-KKU20, and Galactomyces sp.- KKU20. P. kudriavzevii-KKU20 had higher results than the other yeasts in terms of biomass production, cellulase enzyme activity, and cell number.
REVIEW | doi:10.20944/preprints202005.0519.v1
Subject: Life Sciences, Molecular Biology Keywords: Angiotensin-Converting Enzyme 2; Spike glycoprotein; TMPRESS2; Furin; Malayan pangolin
Online: 31 May 2020 (21:41:44 CEST)
The outbreak of a novel coronavirus (SARS-CoV2) associated with acute respiratory disease called COVID-19 marked the introduction of the third spillover of an animal CoV to humans in the last 2 decades. The SARS-CoV2 genome analysis with various bioinformatics tools revealed that it belongs to beta CoVs genera, with highly similar genome as bat coronavirus and receptor binding domain (RBD) of spike glycoprotein as Malayan pangolin coronavirus. Based on its genetic proximity, SARS-CoV2 is likely to be originated from bat derived CoV and transmitted to humans via an unknown intermediate mammalian host, probably Malayan pangolin. Further spike protein S1/S2 cleavage site of SARS-CoV2 has acquired polybasic furin cleavage site which is absent in bat and pangolin suggesting natural selection either in an animal host before zoonotic transfer or in humans following zoonotic transfer. In the current review, we recapitulate a preliminary opinion about the disease, origin and life cycle of SARS-CoV2, roles of virus proteins in pathogenesis, commonalities and differences between different corona viruses. We have also highlighted the evidences regarding the potential drugs and vaccine candidates with their modes of action to cope with this viral outbreak. Our review provides comprehensive up-dated information on molecular aspects of the SARS-CoV2.
HYPOTHESIS | doi:10.20944/preprints202005.0039.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: Exercise; Angiotensin-converting enzyme; SARS-CoV-2; COVID-19; Ecology
Online: 3 May 2020 (08:45:12 CEST)
We hypothesize that the reason severe COVID-19 is closely linked to a limited number of conditions such as obesity, hypertension, older age and diabetes is that these conditions are characterized by a pro-inflammatory state in general and an angiotensin converting enzyme-1-bias in particular. We review recent evidence that this pro-inflammatory state can be reversed via regular exercise and a healthy diet. Studies are suggested that could test this hypothesis.
ARTICLE | doi:10.20944/preprints201911.0216.v1
Subject: Life Sciences, Other Keywords: amino acid; digestive enzyme; low protein diet; nitrogen balance; pigs
Online: 19 November 2019 (02:56:38 CET)
This study was conducted to determine the dynamic effects of dietary crude protein (CP) intake on nitrogen (N) balance, ileal amino acid digestibility, and gene expression levels of digestive enzymes at three stages in pigs. In Experiment 1, 18 growing pigs (average body weight (BW) = 9.5 kg) were randomly assigned to one of three treatments (n = 6/treatment group), including normal (20% CP), low (17% CP), and very low (14% CP) protein intake. In Experiment 2, 18 growing pigs (average BW = 30 kg) were allotted randomly to one of three treatments (n = 6/treatment group), including normal (18% CP), low (15% CP), and very low (12% CP) protein intake. In Experiment 3, 18 growing pigs (average BW = 45 kg) were assigned randomly to one of three treatments (n = 6/treatment group), including normal (16% CP), low (13% CP), and very low (10% CP) protein intake. Growing pigs fed the 14% CP and 17% CP diets had lower final BW (P < 0.05) and average daily gain (ADG) (P < 0.05) compared to pigs fed the 20% CP diet. Reducing the dietary CP level from 20 to 14% decreased urinary N excretion by 52.8% (P < 0.001) in Experiment 1. Reducing the dietary CP level from 18 to 12% decreased urinary N excretion by 55.3% (P < 0.001) and reduced fecal N excretion by 34% (P < 0.05) in Experiment 2. Reducing the dietary CP level from 16 to 10% decreased urinary N excretion by 56.4% (P < 0.001) and fecal N excretion by 47.1% (P < 0.001) in Experiment 3. Pigs fed the very low (14%, 12%, and 10% CP) diets showed higher digestibility for CP (P < 0.05), His (P < 0.05), Ile (P < 0.05), Phe (P < 0.05), Thr (P < 0.05), Trp (P < 0.05), Glu (P < 0.05), and Ser (P < 0.05) compared to pigs fed the normal (20%, 18%, and 16% CP) diets among the three experiments. Pigs fed the very low (14%, 12%, and 10% CP) diets showed higher mRNA levels for chymotrypsin C (P < 0.01 in Experiment 1 and 2; P < 0.05 in Experiment 3) compared to pigs fed the normal (20%, 18%, and 16% CP) diets among the three experiments. These results indicated that a reduction in dietary CP by 6% limited the growth performance of growing pigs, and a reduction of dietary CP by 3% supplemented with essential amino acids could reduce the excretion of N into the environment without affecting weight gain.
CASE REPORT | doi:10.20944/preprints201903.0136.v1
Subject: Medicine & Pharmacology, Pharmacology & Toxicology Keywords: cricket glycosaminoglycan; N-glycan; homo db mice; anti-oxidant enzyme
Online: 12 March 2019 (10:28:47 CET)
Field cricket (Gryllus bimaculatus) is newly emerged as an edible insect in several countries. Anti-inflammatory effect of glycosaminoglycan derived this cricket was not fully investigated on chronic disease animal model such as diabetic mouse. For potential therapeutic agents, anti-diabetic activities of field cricket glycosaminoglycan (GbG) was evaluated in diabetic mice based on their abilities to reduce glucose, ALT, AST, LDL-cholesterol, and BUN levels, compared with dung beetle (Catharsius molossus) glycosaminoglycan (CaG) as a positive control glycosaminoglycan. Db mice were orally administered for one month according to their groups: Db Hetero (normal), Db Homo (type-2 diabetic), CaG (5 mg/kg), GbG (5 mg/kg), and metformin (10 mg/kg). Blood glucose level was decreased after 1st week treatment with GbG. It also inhibited LDL-cholesterol and alkaline phosphatase levels. Regarding oxidative damage of diabetic state, levels of hepatocellular biomarkers levels and protein carbonyl content were reduced in db mice treated with GbG. Especially anti-oxidative activities of catalase, superoxide dismutase, and glutathione peroxidase were significantly increased in GbG treated group compared to those in the control. GbG was composed of heparin disaccharides and main N-glycan was identified as Hex9GlcNAc2 (m/z 1905.7) of with neutral mono-sugar mainly comprising of hexose, L (+) rhamnose by mass spectroscopy. These results from sero-biochemical, hepatocellular anti-oxidant assay in db mice data suggest cricket (G. bimaculatus) glycosaminoglycan might play a role in its anti-diabetic action.
ARTICLE | doi:10.20944/preprints201705.0210.v1
Subject: Life Sciences, Other Keywords: pharmacokinetics; tissue distribution; indirect competitive enzyme-linked immunosorbent assay; puerarin
Online: 30 May 2017 (07:47:09 CEST)
Puerarin (PUE) is a compound isolated from the roots of Pueraria lobata. We studied the pharmacokinetics and tissue distribution kinetics of PUE in Sprague-Dawley rats following intraperitoneal administration of three concentrations. Indirect competitive ELISA based on an anti-PUE monoclonal antibody was used to determine the concentration of PUE in the blood, heart, liver, spleen, lung, kidney, hippocampus, cerebral cortex, and striatum. The plasma and tissue distribution kinetic characteristics following a single injection of PUE (20, 40, and 80 mg/kg) were calculated using a non-compartment model. In the high-dose (80 mg/kg) and medium-dose (40 mg/kg) groups, the kinetic profile of PUE in blood and kidney samples showed two absorption peaks, while that of the other tissues showed only one peak. In the low-dose (20 mg/kg) group, there was only one peak, irrespective of the sample type. Pharmacokinetic parameters such as the area under the curve, Cmax, and Tmax varied according to the administered dose. AUC and Cmax values increased dose-dependently. PUE was widely distributed in areas of the brain such as the hippocampus, cerebral cortex, and striatum, providing a foundation for guiding the use of PUE in the treatment of cerebral ischaemic stroke and neurodegenerative diseases.
ARTICLE | doi:10.20944/preprints202301.0366.v1
Subject: Biology, Plant Sciences Keywords: Encephalartos natalensis; microbe-symbiosis; soil nutrition; enzyme activities; soil nutrient cycling
Online: 19 January 2023 (15:29:52 CET)
Encephalartos spp. establish symbioses with nitrogen (N)-fixing bacteria that contribute to soil nutrition and improve plant growth. Despite the Encephalartos mutualistic symbioses with N-fixing bacteria, the identity of other bacteria and their contribution to soil fertility and eco-system functioning are not well understood. This limited information presents a challenge in developing comprehensive conservation and management strategies for these cycad species. Therefore, this study identified the nutrient cycling bacteria in Encephalartos natalensis coral-loid roots, rhizosphere, and non-rhizosphere soils. Additionally, the soil characteristics and soil enzyme activities of the rhizosphere and non-rhizosphere soils were assayed. The coral-loid roots, rhizosphere, and non-rhizosphere soils of E. natalensis were collected from a popu-lation of >500 E. natalensis in a disturbed savanna woodland at Edendale in KwaZulu-Natal (South Africa) for nutrient analysis, bacterial identification, and enzyme activity assays. Nu-trient cycling bacteria such as Lysinibacillus xylanilyticus; Paraburkholderia sabiae, and Novo-sphingobium barchaimii were identified in the coralloid roots, rhizosphere, and non-rhizosphere soils of E. natalensis. Phosphorus (P) cycling (alkaline and acid phosphatase) and N cycling (β-(D)-Glucosaminidase and nitrate reductase) enzyme activities showed a pos-itive correlation with the P and N concentrations in the rhizosphere and non-rhizosphere soils of E. natalensis. Nutrient cycling bacteria identified in E. natalensis coralloid roots, rhizo-sphere, and non-rhizosphere soils and associated enzymes assayed may contribute to soil nu-trient inputs of E. natalensis plants growing in acidic and nutrient-poor savanna woodland ecosystems.
ARTICLE | doi:10.20944/preprints202209.0426.v1
Subject: Medicine & Pharmacology, Psychiatry & Mental Health Studies Keywords: angiotensin-converting enzyme (ACE); antipsychotic medication; polymorphism, insertion/deletion; treatment response
Online: 28 September 2022 (03:12:20 CEST)
We investigated whether a functional insertion/deletion (I/D) polymorphism of angiotensin-converting enzyme (ACE) influenced antipsychotic treatment. At baseline, and after 8 weeks of treatment with various antipsychotic medications, we assessed patients’ Positive and Negative Syndrome Scale (PANSS) scores, PANSS factors, and metabolic syndrome-related parameters (fasting plasma lipid and glucose levels, and body mass index). A total of 186 antipsychotic-naïve first-episode psychosis patients or nonadherent chronic psychosis individuals (99 males and 87 females) were genotyped by polymerase chain reaction analysis. The ACE-I/D polymorphism was significantly associated with changes in PANSS psychopathology only (p < 0.05). Compared to ACE-II homozygous males, ACE-DD homozygous and ACE-ID heterozygous males manifested significantly greater decreases in PANSS positive score, PANSS excitement factor, and PANSS cognitive factor. ACE-DD homozygous females manifested higher decreases in PANSS depression factor compared to ACE-II homozygous and ACE-ID heterozygous females. The polymorphism’s effect size was estimated as moderate to strong, while its contribution to the PANSS psychopathology ranged from ~5.4–8.7%, with the lowest contribution observed for PANSS positive score changes and the highest for PANSS depressive factor changes. Our results indicated that ACE-I/D polymorphism had a statistically significant but weak gender-specific impact on psychopathology data and showed no association between ACE-I/D polymorphism and metabolic syndrome-related parameters.
REVIEW | doi:10.20944/preprints202204.0097.v1
Subject: Biology, Plant Sciences Keywords: Prolyl endoprotease; prolyl oligopeptidase; protease; protein engineering; proteolytic enzyme; proteomics; therapeutics
Online: 11 April 2022 (11:21:44 CEST)
Proteases or peptidases are hydrolases that catalyze the breakdown of polypeptide chains into smaller peptide subunits. Proteases exist in all life forms, including archaea, bacteria, protozoa, insects, animals, and plants, due to their vital functions in cellular processing and regulation. There are several classes of proteases in the MEROPS database based on their catalytic mecha-nisms. This review focuses on the post-proline cleaving enzymes (PPCEs), especially the prolyl endoprotease/oligopeptidase (PEP/POP). To date, most PPCEs studied are of microbial and ani-mal origins. Recently, there are reports of new plant PPCEs. The most common PEP/POP are members of the S9 family that comprise two conserved domains. The substrate-limiting β-propeller domain prevents unwanted digestion, while the α/β hydrolase catalyzes reaction at the carboxyl-terminal of proline residues. PPCEs have diverse applications, are widely used in the beer brewing industry, and have potential as therapeutic agents for Alzheimer’s disease and celiac disease by targeting proline-rich substrates. Protein engineering via mutagenesis has been performed to improve heat resistance, pepsin-resistant capability, specificity, and protein turno-ver of PPCEs for pharmacological applications. This is the first comprehensive review to cover the biotechnological applications of PPCEs and discuss the unique prolyl cleaving activity of dif-ferent enzymes based on the recent structure-function studies from diverse taxa.
ARTICLE | doi:10.20944/preprints202204.0049.v1
Subject: Materials Science, Biomaterials Keywords: L-asparaginase; Enzyme immobilization; Carbon xerogels; Physical adsorption; Central Composite Design
Online: 6 April 2022 (13:49:49 CEST)
L-asparaginase (ASNase) is an aminohydrolase currently used in the pharmaceutical and food industries. Enzyme immobilization is an exciting option for both applications, allowing a more straightforward recovery and increased stability. High surface area and customizable porosity make carbon xerogels (CXs) promising materials for ASNase immobilization. This work describes the influence of contact time, pH, and ASNase concentration on the immobilization yield (IY) and relative recovered activity (RRA) using Central Composite Design methodology. The most promising results were obtained using CX with an average pore size of 4 nm (CX-4), reaching IY and RRA of 100%. At the optimal conditions, the ASNase-CXs biocomposite was characterized and evaluated in terms of kinetic properties and operational, thermal and pH stabilities. The immobilized ASNase onto CX-4 retained 71% of its original activity after six continuous reaction cycles, showed a good thermal stability at 37 °C (RRA of 91% after 90 min) and was able to adapt to both acidic and alkaline environments. Finally, the results indicated a 3.9-fold increase in the immobilized ASNase affinity for the substrate, confirming the potential of CXs as a support for ASNase and as a cost-effective tool for subsequent use in the therapeutic and food sectors.
Subject: Life Sciences, Biochemistry Keywords: web server; rational design; functionalizing enzymes; enzyme discovery; user-friendly tools
Online: 28 January 2021 (07:51:45 CET)
Enzymes are in high demand for very diverse biotechnological applications. However, natural biocatalysts often need to be engineered for fine-tuning their properties towards the end applications, such as the activity, selectivity, stability to temperature or co-solvents, and solubility. Computational methods are increasingly used in this task, providing predictions that narrow down the space of possible mutations significantly and can enormously reduce the experimental burden. Many computational tools are available as web-based platforms, making them accessible to non-expert users. These platforms are typically user-friendly, contain walk-throughs, and do not require deep expertise and installations. Here we describe some of the most recent outstanding web-tools for enzyme engineering and formulate future perspectives in this field.
REVIEW | doi:10.20944/preprints202010.0585.v1
Subject: Medicine & Pharmacology, Allergology Keywords: SARS-CoV-2; Angiotensin-converting enzyme 2; Endothelium dysfunction; Thrombosis; Vasculitis.
Online: 28 October 2020 (11:21:55 CET)
Abstract: SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) infection is associated, alongside with lung infection and respiratory disease, to cardiovascular dysfunction that occurs at any stage of the disease. This includes ischemic heart disease, arrhythmias, and cardiomyopathies. The common pathophysiological link between SARS-CoV-2 infection and the cardiovascular events is represented by coagulation abnormalities and disruption of factors released by endothelial cells which contribute in maintaining the blood vessels into an anti-thrombotic state. Thus, early alteration of the functionality of endothelial cells, which may be found soon after SARS-CoV-2 infection, seems to represent the major target of SARS CoV-2 disease state and accounts for the systemic vascular dysfunction that leads to detrimental effect in terms of hospitalization and death accompanying the disease. In particular, the molecular interaction of SARS-CoV-2 with ACE2 receptor located in endothelial cell surface, either at the pulmonary and systemic level, leads to early impairment of endothelial function which, in turn, is followed by vascular inflammation and thrombosis of peripheral blood vessels. This highlights systemic hypoxia and further aggravates the vicious circle that compromises the development of the disease leading to irreversible tissue damage and death of patients with SARS CoV-2 infection. The review aims to assess some recent advances to define the crucial role of endothelial dysfunction in the pathogenesis of vascular complications accompanying SARS-CoV-2 infection. In particular, the molecular mechanisms associated to the interaction of SARS CoV-2 with ACE2 receptor located on the endothelial cells are highlighted to support its role in compromising endothelial cell functionality. Finally, the consequences of endothelial dysfunction in enhancing pro-inflammatory and pro-thrombotic effects of SARS-CoV-2 infection are assessed in order to identify early therapeutic interventions able to reduce the impact of the disease in high-risk patients.
Subject: Life Sciences, Biotechnology Keywords: NADH cofactor regeneration; ethylene glycol utilization; biocatalysis; atom economy; enzyme kinetics
Online: 2 September 2020 (09:56:19 CEST)
Although cofactor regeneration is an established system in biocatalysis, work remains in developing new and alternative cofactor regeneration systems with greater efficiency, ease of use, and higher atom economy. In addition, cofactor regeneration system only works if the cofactor regeneration reaction operates at similar kinetics compared to the biotransformation reaction. This meant that only specific cofactor regeneration system is capable of coupling with particular biotransformation reaction. This then leaves open the field for the development of a plethora of alternative cofactor regeneration systems each capable of coupling with different biotransformation reaction of different kinetics. This short write-up examines the possibility of tapping on the NADH regenerated from a two-step ethylene glycol utilization pathway. Current knowledge suggests that this angle has not been explored; thereby, opening up possibilities for future experimental investigations into the feasibility of coupling ethylene glycol utilization pathway with biotransformation reaction as a coupled cofactor regeneration system.
ARTICLE | doi:10.20944/preprints202006.0358.v1
Subject: Chemistry, Medicinal Chemistry Keywords: Enzyme inhibition; Secondary Metabolites; In-silico Analysis; Molecular docking; Drug candidates
Online: 30 June 2020 (08:11:28 CEST)
Metabolic enzymes are often targeted for drug development programs of metabolic diseases such as diabetes and its complications. Many secondary metabolites isolated from natural products have shown therapeutic action against these enzymes. However, some commercially available synthetic drugs have shown unfriendly impacts with various side effects. Thus, this research has focused on a comprehensive study of secondary metabolites showing better inhibitory activities towards metabolic enzymes such as α-amylase, α-glucosidase, aldose reductase, and lipase. Further receptor-based virtual screening was performed against the various secondary metabolites database designed in-silico. Using Gold combined with subsequent post-docking analyses, the score was obtained as methyl xestospongic ester (Gold score 65.83), 2,″4″-O-diacetylquercitrin (Gold score 65.15), kaempferol-3-O-neohesperidoside (Gold score 53.37) and isosalvianolic acid C methyl ester (Gold score 53.44) for lipase, aldol reductase, α-amylase, and α-glucosidase, respectively. Besides, vitexin and isovitexin for α-amylase; N-trans-Caffeoyl-tyramin for α-glucosidase; purpurolide F and schaftoside for lipase; acteoside and orientin for aldose reductase could be potential drugs for respective enzymes based on in-silico analyses, supported by experimental IC50 values reported. They could bind to the competitive sites of the various targets of metabolic enzymes, and finally, toxicity analysis using ProTox-II was also performed.
ARTICLE | doi:10.20944/preprints201910.0223.v1
Subject: Life Sciences, Biochemistry Keywords: α-glucosidase; glyceollin; genistein; luteolin; daidzein; phytoalexins; enzyme kinetics; combination index
Online: 19 October 2019 (02:20:45 CEST)
To determine the mode of action of the effects of phytoalexins in soybeans, we analyzed enzyme inhibition kinetics using Michaelis–Menten plots and the Lineweaver–Burk plots. The results showed that glyceollin showed competitive inhibition, genistein showed noncompetitive, daidzein was uncompetitive, and luteolin showed a mixed mode of action. The Ki values were determined using a Dixon plot as: glyceollin, 18.99; genistein, 15.42; luteolin, 16.81; and daidzein, 9.99 μM, respectively. Furthermore, potential synergistic effects between glyceollin and the three designated polyphenols were investigated. A combination of glyceollin and luteolin (the ratio of 3:7 of glyceollin and luteolin) had synergistic effects on α-glucosidase inhibition according to combination index (CI)-isobologram equation. Collectively, these results showed that a combination of glyceollin and luteolin has the potential to inhibit α-glucosidase activity via a synergistic mode of action.
ARTICLE | doi:10.20944/preprints201811.0204.v1
Subject: Biology, Entomology Keywords: Petroselinum crispum; Aedes aegypti; enzyme activity; esterases, mixed-function oxidases; phosphatases
Online: 8 November 2018 (10:41:59 CET)
As part of the ongoing screening research for local edible plants in Thailand, Petroselinum crispum fruit oil was considered as a potential bioinsecticide with proven antimosquito activity against both the pyrethroid susceptible and resistant strains of Aedes aegypti. Due to the comparative mosquitocidal efficacy on these mosquitoes, this plant oil is promoted as a natural alternative and attractive candidate for further study in monitoring resistance of mosquito vectors. Therefore, the aim of this study was to evaluate the impact of P. crispum oil on the biochemical characteristics of the target mosquito larvae of Ae. aegypti, by determining quantitative changes of key enzymes responsible for xenobiotic detoxification, including glutathione-S-transferases (GSTs), α- and β-esterases (α-/β-ESTs), acetylcholinesterase (AChE), acid and alkaline phosphatases (ACP and ALP) and mixed-function oxidases (MFO). Three populations of Ae. aegypti, comprising the pyrethroid susceptible Muang Chiang Mai-susceptible (MCM-S) strain and the pyrethroid resistant Pang Mai Dang-resistant (PMD-R) and Upakut-resistant (UPK-R) strains, were used as test organisms. Biochemical study of Ae. aegypti larvae prior to treatment with P. crispum oil revealed that apart from AChE, the baseline activity of most defensive enzymes, such as GSTs, α-/β-ESTs, ACP, ALP and MFO, in resistant UPK-R or PMD-R, was higher than that determined in susceptible MCM-S. However, after 24-h exposure to P. crispum oil, the pyrethroid susceptible and resistant Ae. aegypti showed similarity in biochemical features, with alterations of enzyme activity in the treated larvae, as compared to the controls. A significant increase in the activity levels of GSTs, α-/β-ESTs, ACP and ALP was recorded in all strains of P. crispum oil-treated Ae. aegypti larvae, whereas MFO and AChE activity in these mosquitoes was decreased. The recognizable larvicidal capability on pyrethroid resistant Ae. aegypti, and the inhibitory effect on AChE and MFO, emphasized the potential of P. crispum oil as an attractive alternative application for management of mosquito resistance in current and future control programs.
ARTICLE | doi:10.20944/preprints201811.0124.v1
Subject: Chemistry, Physical Chemistry Keywords: Lignin, nanoparticle, protein, nanocellulose, fibril, enzyme, heat, self-assembly, cross-link
Online: 5 November 2018 (15:18:23 CET)
Lignin has interesting functionalities to be exploited in adhesives for medicine, foods and textiles. Nanoparticles (NPs) <100 nm coated with poly(L-lysine), PL and poly(L-glutamic acid) PGA were prepared from the laccase treated lignin to coat nanocellulose fibrils (CNF) with heat. NPs ca. 300 nm were prepared, β-casein coated and cross-linked with transglutaminase (Tgase) to agglutinate chamois specimens. Size exclusion chromatography (SEC) and Fourier-transform infrared (FTIR) spectroscopy were used to characterize polymerized lignin, zetapotential and dynamic light scattering (DLS) to ensure coating of colloidal lignin particles (CLPs). Protein adsorption on lignin was studied by quartz crystal microbalance (QCM). Atomic force microscopy (AFM) was exploited to examine interactions between different polymers and to image NPs with transmission electron microscopy (TEM). Tensile testing showed, when using CLPs for the adhesion, the stress improved ca. 10 and strain ca. 6 times compared to polymeric lignin. For the β-casein NPs the values were 20 and 8, respectively, and for the β-casein coated CLPs between these two cases. When NPs were dispersed in adhesive formulation, the Young's moduli confirmed significant improvement in the elasticity of the joints over the adhesive alone. Exploitation lignin in nanoparticulate morphology is a potential method to prepare bionanomaterials for advanced applications.
ARTICLE | doi:10.20944/preprints201810.0133.v2
Subject: Biology, Other Keywords: aging; angiotensin-converting enzyme inhibitors; nutrient metabolism; genetic background; nutritional stress
Online: 29 October 2018 (10:33:59 CET)
The angiotensin-converting enzyme (ACE) is a peptidase that is involved in the synthesis of Angiotensin II, the bioactive component of the renin-angiotensin system. A growing body of literature argues for a beneficial impact of ACE inhibitors (ACEi) on age-associated metabolic disorders, mediated by cellular changes in reactive oxygen species (ROS) that improve mitochondrial function. Yet, our understanding of the relationship between ACEi therapy and metabolic parameters is limited. Here, we used three genetically diverse strains of Drosophila melanogaster to show that Lisinopril treatment reduces thoracic ROS levels and mitochondrial respiration in young flies, and increases mitochondrial content in middle-aged flies. Using untargeted metabolomics analysis, we also showed that Lisinopril perturbs the thoracic metabolic network structure by affecting metabolic pathways involved in glycogen degradation, glycolysis, and mevalonate metabolism. The Lisinopril-induced effects on mitochondrial and metabolic parameters, however, are genotype-specific and likely reflect the drug’s impact on nutrient-dependent fitness traits. Accordingly, we found that Lisinopril negatively affects survival under nutrient starvation, an effect that can be blunted by genotype and age in a manner that partially mirrors the drug-induced changes in mitochondrial respiration. In conclusion, our results provide novel and important insights into the role of ACEi in cellular metabolism.
ARTICLE | doi:10.20944/preprints202212.0189.v1
Subject: Life Sciences, Biochemistry Keywords: mouse CCR9, monoclonal antibody, epitope mapping, alanine scanning, enzyme-linked immunosorbent assay
Online: 12 December 2022 (03:54:29 CET)
C-C chemokine receptor 9 (CCR9) is a receptor for C-C-chemokine ligand 25 (CCL25). CCR9 is crucial in the chemotaxis of immune cells and inflammatory responses. Moreover, CCR9 is highly expressed in tumors including several solid tumors and T-cell acute lymphoblastic leukemia. Several preclinical studies have shown that anti-CCR9 monoclonal antibodies (mAbs) exert antitumor activity. Therefore, CCR9 is an attractive target for tumor therapy. In this study, we conducted the epitope mapping of an anti-mouse CCR9 (mCCR9) mAb, C9Mab-24 (rat IgG2a, kappa), using a 1 × alanine (1 × Ala) and 2 × alanine (2 × Ala)-substitution method via enzyme-linked immunosorbent assay. We first performed the 1 × Ala-substitution method using one alanine-substituted peptides of the mCCR9 N-terminus (amino acids 1-19). C9Mab-24 did not recognize two peptides (F14A and F17A), indicating that Phe14 and Phe17 are critical for C9Mab-24-binding to mCCR9. Furthermore, we conducted the 2 × Ala-substitution method using two consecutive alanine-substituted peptides of the mCCR9 N-terminus, and showed that C9Mab-24 did not react with four peptides (M13A–F14A, F14A–D15A, D16A–F17A, and F17A–S18A), indicating that 13-MFDDFS-18 is involved in C9Mab-24-binding to mCCR9. Overall, combining, the 1 × Ala or 2 × Ala scanning methods could be useful for understanding for target-antibody interaction.
REVIEW | doi:10.20944/preprints202212.0022.v1
Subject: Medicine & Pharmacology, Other Keywords: Fabry disease; globotriaosylceramide; α-galactosidase-A; enzyme replacement therapy; chaperone therapy; migalastat
Online: 1 December 2022 (09:50:49 CET)
Fabry disease is a lysosomal storage disorder caused by the deficiency of the α-galactosidase-A enzyme. Cardiac, renal, and neurological involvement significantly reduces life expectancy. Until a few years ago, treatment options for Fabry disease were limited to enzyme replacement therapy with agalsidase alfa or beta administered by intravenous infusion every 2 weeks. Migalastat (Galafold®) is an oral pharmacological chaperone that increases enzyme activity of “amenable” mutations. The safety and efficacy of migalastat were supported in the phase III FACETS and ATTRACT studies, compared to available enzyme replacement therapies; showing a reduction in left ventricular mass, and stabilization of kidney function and plasma Lyso-Gb3. Similar results were confirmed in subsequent extension publications, both in patients who started migalastat as their first treatment and in patients who were previously on enzyme replacement therapy and switched to migalastat. In this review we describe the safety and efficacy of switching from enzyme replacement therapy to migalastat in patients with Fabry disease and “amenable” mutations, referring to publications available to date.
ARTICLE | doi:10.20944/preprints202209.0156.v1
Subject: Medicine & Pharmacology, Other Keywords: Intervertebral disc; inflammation; degeneration; renin-angiotensin system; therapy; angiotensin-converting enzyme 2
Online: 13 September 2022 (04:29:50 CEST)
Low back pain is a clinically highly relevant musculoskeletal burden and is associated with inflammatory as well as degenerative processes of the intervertebral disc. However, the pathophysiology and cellular pathways contributing to this devastating condition are still poorly understood. Based on previous evidence, we hypothesize that tissue renin-angiotensin system (tRAS) components, including the SARS-CoV-2 entry receptor angiotensin-converting enzyme 2 (ACE2), are present in human nucleus pulposus (NP) cells and associated with inflammatory and degenerative processes. Experiments were performed with NP cells from 4 human donors. The existence of angiotensin II, angiotensin II type 1 receptor (AGTR1), AGTR2, MAS-receptor (MasR), and ACE2 in human NP cells was validated with immunofluorescent staining and gene expression analysis. Hereafter the cell viability was assessed after adding agonists and antagonists of the target receptors as well as angiotensin II in different concentrations for up to 48 hours of exposure. A TNF-α-induced inflammatory in vitro model was employed to assess the impact of angiotensin II addition and the stimulation or inhibition of the tRAS receptors on inflammation, tissue remodeling, expression of tRAS markers, and the release of nitric oxide (NO) into the medium. Further, protein levels of IL-6, IL-8, IL-10, and intracellular as well as secreted angiotensin II were assessed after exposing the cells to the substances, and inducible nitric oxide synthase (iNOS) levels were evaluated utilizing Western Blot. The existence of tRAS receptors and angiotensin II were validated in human NP cells. Cell viability analysis revealed no cytotoxic effects of angiotensin II. The AGTR1 inhibitor Candesartan and the MAS receptors AVE0991 showed cytotoxic effects at high concentrations (100 µM). The addition of angiotensin II only showed a mild impact on gene expression markers. However, there was a significant increase in NO secreted by the cells. The gene expression ratios of pro-inflammatory/anti-inflammatory cytokines IL-6/IL--10, IL-8/IL-10, and TNF-α /IL-10 were positively correlated with the AGTR1/AGTR2 and AGTR1/MAS1 ratios, respectively. The stimulation of the AGTR2 MAS-receptor and the inhibition of the AGTR1 receptor revealed beneficial effects on the gene expression of inflammatory and tissue remodeling markers. This finding was also present at the protein level. We did not find alterations in iNOS protein concentrations after adding the drugs. The current data showed that tRAS components are expressed in human NP cells and are associated with inflammatory and degenerative processes. Further characterization of the associated pathways is warranted. The findings indicate that tRAS modulation might be a novel therapeutic approach to intervertebral disc disease.
REVIEW | doi:10.20944/preprints202202.0187.v1
Subject: Medicine & Pharmacology, Cardiology Keywords: endothelial dysfunction; SARS-CoV-2 infection; thrombosis, angiotensin-converting enzyme-2; angiogenesis
Online: 15 February 2022 (11:05:22 CET)
One of the hallmarks of the SARS-CoV-2 infection has been the inflammatory process that played a role in its pathogenesis, resulting in mortality within susceptible individuals. This uncontrolled inflammatory process leads to severe systemic symptoms via multiple pathways, however, the role of endothelial dysfunction and thrombosis have not been truly explored. This review aims to highlight the pathogenic mechanisms of these inflammatory triggers leading to thrombogenic complications. There are direct and indirect pathogenic pathways of the infection that are examined in detail. We also describe the case of carotid artery thrombosis in a patient following the SARS-CoV-2 infection, while reviewing the literature on the role of ACE2, the endothelium, and the different mechanisms by which SARS-CoV-2 may manifest both acutely and chronically. We also highlight differences from the other coronaviruses that have made this infection pandemic with similarities to the influenza virus.
REVIEW | doi:10.20944/preprints202011.0673.v1
Subject: Keywords: Angiotensin converting enzyme 2 (ACE2); trafficking; localization; SARS-CoV-2; COVID-19
Online: 26 November 2020 (12:10:41 CET)
With the emergence of the novel corona virus SARS-CoV-2 since December 2019, more than 43 million cases have been reported worldwide. This virus has shown high infectivity and severe symptoms in some cases leading to over 1 million deaths globally. Despite the collaborative and concerted research efforts that has been made, no effective treatment for COVID-19 (corona virus disease-2019) is currently available. SARS-CoV-2 uses the angiotensin converting enzyme 2 (ACE2) as an initial mediator for viral attachment and host cell invasion. ACE2 is widely distributed in human tissues including the cell surface of lung cells which represent the primary site of the infection. Inhibiting or reducing cell surface availability of ACE2 represents a promising therapy for tackling COVID-19. In this context, most ACE2–based therapeutic strategies have aimed to achieve this through the use of angiotensin converting enzyme (ACE) inhibitors or neutralizing the virus by exogenous administration of ACE2. However, through this review, we present another perspective focusing on the subcellular localization and trafficking of ACE2. Membrane targeting of ACE2, shedding and its cellular trafficking pathways including internalization are not well elucidated. Therefore, hereby we present an overview on the fate of newly synthesized ACE2, its post translational modifications, what is known of its trafficking pathways. In addition, we highlight the possibility that some of the identified ACE2 missense variants might affect its trafficking efficiency and localization and hence may explain some of the observed variable severity of SARS-CoV-2 infections. Extensive understanding of these processes is necessary to evaluate the potential use of ACE2 as a credible therapeutic target.
ARTICLE | doi:10.20944/preprints202010.0486.v1
Subject: Chemistry, Analytical Chemistry Keywords: COVID-19; carnosine; angiotensin-converting enzyme 2 (ACE2); practitioner; molecular docking; modeling
Online: 23 October 2020 (10:44:07 CEST)
Aims: Angiotensin-converting enzyme 2 (ACE2) plays an important role in the entry of coronaviruses into host cells. This paper described how carnosine, a naturally occurring supplement, can be an effective drug candidate for coronavirus disease (COVID-19) on the basis of molecular docking and modeling to host ACE2 co-crystallized with COVID-19 spike protein. Methods: First, the starting point was ACE2 inhibitors and their structure-activity relationship (SAR). Next, chemical similarity (or diversity) and PubMed searches made it possible to repurpose and assess approved or experimental drugs for COVID-19. In parallel, at all stages, authors performed bioactivity scoring to assess potential repurposed inhibitors at ACE2. Finally, investigators performed molecular docking and modeling of the identified drug candidate to host ACE2 co-crystallized with COVID-19 spike protein. Results: Carnosine emerged as the best known drug candidate to match ACE2 inhibitor structure. Preliminary docking was more optimal to ACE2 than the known typical angiotensin-converting enzyme 1 (ACE1) inhibitor (enalapril) and quite comparable to known or presumed ACE2 inhibitors. Viral spike protein elements binding to ACE2 were retained in the best carnosine pose in SwissDock at 1.75 Angstroms. Out of the three main areas of attachment expected to the co-crystallized protein structure, carnosine bind with higher affinity to two compared to the known ACE2 active site. LibDock score was 92.40 for site 3, 90.88 for site 1, and inside the active site 85.49. Conclusion: Carnosine has promising inhibitory interactions with host ACE2 co-crystallized with COVID-19 spike protein and hence could offer potential mitigating effect against current COVID-19 pandemic.
Subject: Life Sciences, Biotechnology Keywords: pathway optimization; machine learning tools; enzyme activity prediction; promoter classification; expression tuning
Online: 26 August 2020 (04:05:47 CEST)
Successful engineering of a microbial host for efficient production of a target product from a given substrate can be viewed as an extensive optimization task. Such a task involves the selection of high activity enzymes as well as their gene expression regulatory control elements (i.e., promoters and ribosome binding sites). Finally, there is also the need to tune expression of multiple genes along a heterologous pathway to relieve constraints from rate-limiting step and help reduce metabolic burden on cells from unnecessary over-expression of high activity enzymes. While the aforementioned tasks could be performed through combinatorial experiments, such an approach incurs significant cost, time and effort, which is a handicap that can be relieved by application of modern machine learning tools. Such tools could attempt to predict high activity enzymes from sequence, but they are currently most usefully applied in classifying strong promoters from weaker ones as well as combinatorial tuning of expression of multiple genes. This perspective reviews the application of machine learning tools to aid metabolic pathway optimization through identifying challenges in metabolic engineering that could be overcome with the help of machine learning tools.
ARTICLE | doi:10.20944/preprints201704.0122.v1
Subject: Earth Sciences, Environmental Sciences Keywords: crust type; soil depth; physicochemical properties; enzyme; microbial biomass carbon and nitrogen
Online: 19 April 2017 (11:23:58 CEST)
This study investigated the effects of soil crust development on the underlying soil properties. The field sampling work was conducted in June 2016 in the Hobq Desert in Inner Mongolia, North China. Soil crust samples and 0–6, 6–12, 12–18, 18–24, 24–30 cm deep underlying soil samples were taken from five representative areas of different soil crust development stages. All samples were analyzed for physicochemical properties including water content, bulk density, aggregate content, organic matter content, enzyme activities, and microbial biomass carbon and nitrogen. The results showed that the thickness, water content, macroaggregate (>250 μm) content, organic matter content, microbial biomass and enzyme activities of the soil crusts gradually increased along the soil crust development gradient, while the bulk density of the soil crusts decreased. Meanwhile, the physicochemical and biological properties of the soils below the algal and moss crusts were significantly ameliorated when compared with the physical crust. Moreover, the amelioration effects were significant in the upper horizons (approx. 0–12 cm deep) and diminished quickly in the deeper soil layers.
ARTICLE | doi:10.20944/preprints202107.0631.v1
Subject: Chemistry, Analytical Chemistry Keywords: pressurized liquid extraction; enzyme-assisted extraction; non-extractable polyphenols; proanthocyanidins; sweet cherry pomace
Online: 28 July 2021 (12:23:41 CEST)
Sweet cherry pomace is a by-product that can be a source of bioactive phenolic compounds. Usually, polyphenols have been extracted using conventional extraction methodologies. However, a significant fraction, called non-extractable polyphenols (NEPs), remains retained in the conventional extraction residues. Therefore, this work is aimed, for the first time, to investigate the release of NEPs from cherry pomace combining pressurized liquid extraction (PLE) and enzyme-assisted extraction (EAE) using Promod enzyme. A response surface methodology was employed to study the influence of temperature, time, and pH on the NEPs extraction. The response variables were the total phenolic content (TPC) measured by Folin-Ciocalteu method, total proanthocyanidin (PA) content evaluated by vanillin, DMAC, and butanol/HCl assays, and total antioxidant capacity determined by Trolox equivalent antioxidant capacity and inhibition of hydroxyl radical assays. The results indicated that PLE-EAE was more suitable and selective to obtain NEPs from sweet cherry pomace than PLE alone. In fact, the extracts obtained by PLE-EAE displayed higher TPC, PA content, and bioactivity than the extracts obtained by PLE under the same extraction conditions, and those obtained by conventional methods. Moreover, size-exclusion chromatography profiles showed that the combination of PLE and EAE enabled the recovery of NEPs with higher molecular weight than PLE without EAE treatment.
ARTICLE | doi:10.20944/preprints202105.0525.v1
Subject: Medicine & Pharmacology, Allergology Keywords: COVID-19; glycyrrhizin; mineralocorticoid receptor; toll like receptor 4; angiotensin converting enzyme; aldosterone
Online: 21 May 2021 (15:11:30 CEST)
Angiotensin converting enzyme 2 (ACE2) is a key entry point of SARS-CoV-2 virus known to induce COVID-19. We have recently outlined the concept to reduce ACE2 expression by the administration of glycyrrhizin, a component of Glycyrrhiza glabra extract, via its inhibitory activity on 11beta hydroxysteroid dehydrogenase type 2 (11betaHSD2) and resulting activation of mineralocorticoid receptor (MR). We hypothesized that in organs, such as the intestine, which co-express 11betaHSD2, MR and ACE2, the expression of ACE2 would be suppressed. We studied organ tissues from an experiment originally designed to address the effects of Glycyrrhiza glabra extract on the stress response. Male Sprague Dawley rats were left undisturbed or exposed to chronic mild stress for five weeks. For the last two weeks, animals continued with a placebo diet or received a diet containing extract of Glycyrrhiza glabra root at a dose of 150 mg/kg of body weight/day. Quantitative PCR measurements showed a significant decrease in gene expression of ACE2 in the small intestine of rats fed with diet containing Glycyrrhiza glabra extract. This effect was independent of the stress condition and failed to be observed in non-target tissues, namely the heart and the brain cortex. In the small intestine we confirmed the reduction of ACE2 also at the protein level. Present findings provide first evidence to support the hypothesis that Glycyrrhiza glabra extract may reduce an entry point of SARS-CoV-2. Whether this phenomenon, when confirmed in additional studies, is linked to the susceptibility of cells to the virus requires further studies.
Subject: Life Sciences, Genetics Keywords: SARS-CoV-2; COVID-19; Angiotensin-converting enzyme 2; susceptibility; livestock; aquatic mammals
Online: 7 June 2020 (08:18:54 CEST)
SARS-CoV-2, the causal agent of the globally spreading COVID-19, is capable of infecting variable animals besides human being. We evaluated the potential susceptibility of important livestock, pets and aquatic mammals by performing a multi-species sequence analysis of ACE2 based on the reported affected and unaffected animals. We identified a triple amino acid pattern of ACE2, at position 30, 31 and 34, that might be associated with SARS-CoV-2 infection and H34 might be an indicator of the susceptibility to COVID-19.
BRIEF REPORT | doi:10.20944/preprints202003.0091.v1
Subject: Life Sciences, Virology Keywords: SARS-CoV-2; coronavirus; angiotensin converting enzyme 2 (ACE2); receptor utilization; phylogenetic analysis.
Online: 5 March 2020 (12:12:38 CET)
SARS-CoV-2, the newly identified human coronavirus causing severe pneumonia epidemic, was probably originated from Chinese horseshoe bats. However, direct transmission of the virus from bats to humans is unlikely due to lack of direct contact, implying the existence of unknown intermediate hosts. Angiotensin converting enzyme 2 (ACE2) is the receptor of SARS-CoV-2, but only ACE2s of certain species can be utilized by SARS-CoV-2. Here, we evaluated and ranked the receptor-utilizing capability of ACE2s from various species by phylogenetic clustering and sequence alignment with the currently known ACE2s utilized by SARS-CoV-2, predicting potential intermediate hosts of SARS-CoV-2.
REVIEW | doi:10.20944/preprints201810.0175.v1
Subject: Chemistry, Analytical Chemistry Keywords: biosensors; enzyme-based systems; receptor-based systems; toxins; food analysis; environmental monitoring; nanotechnology
Online: 9 October 2018 (05:59:30 CEST)
The exploitation of lipid membranes in biosensors has provided the ability to reconstitute a considerable part of their functionality to detect trace of food toxicants and environmental pollutants. Nanotechnology enabled sensor miniaturization and extended the range of biological moieties that could be immobilized within a lipid bilayer device. This chapter reviews recent progress in biosensor technologies based on lipid membranes suitable for environmental applications and food quality monitoring. Numerous biosensing applications are presented, putting emphasis on novel systems, new sensing techniques and nanotechnology-based transduction schemes. The range of analytes that can be currently detected include, insecticides, pesticides, herbicides, metals, toxins, antibiotics, microorganisms, hormones, dioxins, etc. Technology limitations and future prospects are discussed, focused on the evaluation/ validation and eventually commercialization of the proposed sensors.
REVIEW | doi:10.20944/preprints201808.0069.v1
Subject: Chemistry, Analytical Chemistry Keywords: biosensors, enzyme-based systems, receptor-based systems, toxins, food analysis, environmental monitoring, nanotechnology
Online: 3 August 2018 (14:20:04 CEST)
The exploitation of lipid membranes in biosensors has provided the ability to reconstitute a considerable part of their functionality to detect trace of food toxicants and environmental pollutants. Nanotechnology enabled sensor miniaturization and extended the range of biological moieties that could be immobilized within a lipid bilayer device. This chapter reviews recent progress in biosensor technologies based on lipid membranes suitable for environmental applications and food quality monitoring. Numerous biosensing applications are presented, putting emphasis on novel systems, new sensing techniques and nanotechnology-based transduction schemes. The range of analytes that can be currently detected include, insecticides, pesticides, herbicides, metals, toxins, antibiotics, microorganisms, hormones, dioxins, etc. Technology limitations and future prospects are discussed, focused on the evaluation/ validation and eventually commercialization of the proposed sensors.
ARTICLE | doi:10.20944/preprints202301.0344.v1
Subject: Life Sciences, Biophysics Keywords: microtubule-severing enzyme; tubulin isotypes; tubulin code; post-translational modifications; katanin; microtubule-associated protein
Online: 19 January 2023 (03:16:41 CET)
In celIs, microtubule location, length, and dynamics are regulated by a host of microtubule-associated proteins and enzymes that read where to bind and act based on the microtubule “tubulin code,” which is predominantly encoded in the tubulin carboxy-terminal tail (CTT). Katanin is a highly conserved AAA ATPase enzyme that binds to the tubulin CTTs to remove dimers and sever microtubules. We have previously demonstrated that short CTT peptides are able to inhibit katanin severing. Here, we examine effects of CTT sequences on this inhibition activity. Specifically, we examine CTT sequences found in nature, alpha1A (TUBA1A), detyrosinated alpha1A, Δ2 alpha1A, beta5 (TUBB/TUBB5), beta2a (TUBB2A), beta3 (TUBB3), and beta4b (TUBB4b). We find that these natural CTTs have distinct abilities to inhibit, most noticeably beta3 cannot inhibit katanin. Two non-native CTT tail constructs are also unable to inhibit – despite having 94% sequence identity with alpha1 or beta5 sequences. Surprisingly, we demonstrate that poly-E and poly-D peptides are capable of inhibiting katanin significantly. An analysis of the hydrophobicity of the CTT constructs indicates that more hydrophobic polypeptides are less inhibitory than more polar polypeptides. These experiments not only demonstrate inhibition, but also likely interaction and targeting of katanin to these various CTTs when they are part of a polymerized microtubule filament.
ARTICLE | doi:10.20944/preprints202204.0233.v1
Subject: Medicine & Pharmacology, Cardiology Keywords: chronic kidney disease; gene polymorphism; angiotensin-converting enzyme; cardiovascular disease; cardiovascular mortality risk; genotype
Online: 26 April 2022 (10:05:25 CEST)
The association between angiotensin-converting enzyme insertion/deletion (ACE I/D) polymorphisms and plasma ACE levels may allow for the optimization of a preventive intervention to reduce cardiovascular morbidity and mortality in the chronic kidney disease (CKD) population. In this study, we aimed to analyze the association between ACE I/D polymorphism and cardiovascular mortality risk among non-hemodialyzed chronic kidney disease patients. This cross-sectional study examined 70 patients of Javanese ethnic origin with stable CKD who did not receive hemodialysis. ACE I/D polymorphisms, plasma ACE levels, atherosclerotic cardiovascular disease (ASCVD) risk, and cardiovascular mortality risk were investigated. As per our findings, the I allele was found to be more frequent (78.6) than the D allele (21.4), and the DD genotype was less frequent than the II genotype (4.3 vs. 61.4). The ACE I/D polymorphism had a significant direct positive effect on plasma ACE levels (path coefficient = 0.302, p = 0.021). Similarly, plasma ACE levels had a direct and significant positive effect on the risk of atherosclerotic cardiovascular disease (path coefficient = 0.410, p = 0.000). Moreover, atherosclerotic cardiovascular disease risk had a significant positive effect on cardiovascular mortality risk (path coefficient = 0.918, p = 0.000). The ACE I/D polymorphism had no direct effect on ASCVD and cardiovascular mortality risk. However, our findings show that the indirect effects of high plasma ACE levels may be a factor in the increased risk of ASCVD and cardiovascular mortality in Javanese CKD patients.
ARTICLE | doi:10.20944/preprints202107.0643.v1
Subject: Engineering, Automotive Engineering Keywords: processing waste; Atlantic cod; collagen; red king crab; enzyme preparation; collagen hydrolysate; culture medium
Online: 29 July 2021 (10:25:50 CEST)
The Atlantic cod (Gadus morhua) and red king crab (Paralithodes camtschaticus) processing wastes are massive and unutilized in the Murmansk region of Russia. The samples of skin-containing waste of Atlantic cod fillets production were hydrolyzed using enzyme preparations derived from red king crab hepatopancreases, porcine pancreases and Bacillus subtilis bacteria. The activity of enzymes from crab hepatopancreases was significantly higher than the activity of enzymes derived from other sources. The optimal conditions of the hydrolysis process have been figured out. The samples of cod processing waste hydrolysate were analyzed for amino acid composition and molecular weight distribution. The samples of hydrolysate were used as core components for bacterial culture medium samples. The efficiency of the medium samples was tested for Escherichia coli growth rate; the most efficient sample had efficiency 95.3% of that of a commercially available medium based on fish meal. Substitution of medium components with those derived from industrial by-products is one of the ways to decrease a cost of a culture medium in biopharmaceutical drug production.
ARTICLE | doi:10.20944/preprints202107.0418.v1
Subject: Biology, Anatomy & Morphology Keywords: herbicide efficacy; glutamine synthetase; reactive oxygen species; enzyme turnover; mode of action; Palmer amaranth
Online: 19 July 2021 (16:10:12 CEST)
Glufosinate, a glutamine synthetase (GS) inhibitor, often provides variable weed control depending on environmental conditions such as light, temperature and humidity at the time of application. Midday applications normally provide improved efficacy compared to applications at dawn or dusk. We investigated the physiological, molecular, and biochemical basis for the time-of-day effect on glufosinate efficacy in Amaranthus palmeri. GS1 and GS2 gene expression and protein abundance were assessed in different parts (young leaves, old leaves, and roots) of plants incubated in the dark compared to those in the light. The turnover of GS total activity was also evaluated overtime following glufosinate treatment at midday compared to dusk application. The results suggest that GS in A. palmeri is less expressed and less abundant in the dark compared to in the light. Midday application of glufosinate under intense light conditions in the hours following application provide full control of A. palmeri plants. Consequently, these plants are unable to recover GS activity by de novo protein synthesis. Full activity of GS is required for complete inhibition by the irreversible inhibitor glufosinate. Therefore, glufosinate applications should always be performed in the middle of the day when sunlight is intense, to prevent weed escapes from the herbicide treatment.
ARTICLE | doi:10.20944/preprints202007.0611.v1
Subject: Medicine & Pharmacology, Obstetrics & Gynaecology Keywords: Lysosomal Disorders; Glycogen storage disease Type II; Pompe disease; LOPD; Pregnancy; Enzyme Replacement Therapy
Online: 25 July 2020 (15:48:01 CEST)
There is limited data on pregnancy outcomes in Pompe Disease (PD) resulting from deficiency of the lysosomal enzyme acid alpha-glucosidase. Late-onset PD is characterized by progressive proximal muscle weakness and decline of respiratory function secondary to the involvement of the respiratory muscles. In a cohort of twenty-five females, the effects of both PD on the course of pregnancy and the effects of pregnancy on PD were investigated. Reproductive history, course of pregnancy, use of Enzyme replacement therapy (ERT), PD symptoms, and outcomes of each pregnancy were obtained through a questionnaire. Among 20 subjects that reported one or more pregnancies, one subject conceived while on ERT and continued therapy through two normal pregnancies with worsening of weakness during pregnancy and improvement postpartum. While fertility was not affected, pregnancy may worsen symptoms, or cause initial symptoms to arise. Complications with pregnancy or birth were not higher, except for an increase in the rate of stillbirths (3.8% compared to the national average of 0.2-0.7%). Given small sample size and possible bias of respondents being only women who have been pregnant, further data may be needed to better analyze the effects of pregnancy on PD, and the effects of ERT on pregnancy outcomes.
Subject: Life Sciences, Genetics Keywords: SARS-CoV-2; angiotensin-converting enzyme 2 (ACE2); animal reservoir; cross-species transmission; cats
Online: 8 April 2020 (04:43:14 CEST)
SARS-CoV-2 causes severe pneumonia epidemics and probably originated in horseshoe bats, but the intermediate host is unknown. The interaction of SARS-CoV-2 spike protein and its acceptor protein ACE2 is an important issue in determining viral host range and cross-species infection, while the binding capacity of Spike protein to ACE2 of different species is unknown. Here, we used the atomic structure model of SARS-CoV-2 and human ACE2 to assess the receptor utilization capacity of ACE2s from different species including cats, chimpanzees, dogs, cattles. Our results show, domestic cats (Felis catusc) and dogs (Canis lupus familiaris) are more susceptible to infection by SARS-CoV-2 and that they can efficiently transmit the virus to previously uninfected animals that are housed with them. Especially, cats could be a choice of animal model for screening antiviral drugs or vaccine candidates against SARS-CoV-2.
ARTICLE | doi:10.20944/preprints202002.0265.v1
Subject: Keywords: SARS-CoV; Spike protein; Electrostatic hot spots; Angiotensin-converting enzyme 2 (ACE2); Neutralizing antibody
Online: 18 February 2020 (11:03:10 CET)
The spike protein of SARS coronavirus (SARS-CoV) attaches the virus to its cellular receptor, angiotensin-converting enzyme 2 (ACE2), which is mediated by the receptor binding domain (RBD) of the spike protein. Recently, an analysis based on decade-long structural studies of SARS was reported to illustrate with atomic-level details receptor recognition by the novel coronavirus from Wuhan, i.e., 2019-nCoV. Here, this article reports a comprehensive set of structural electrostatic analysis of all SARS-CoV spike protein RBD-related structures as of February 13, 2020, aiming at identifying the electrostatic hot spots for SARS-CoV spike protein to be complexed with ACE2 and its neutralizing antibodies. First, this article identified a structural action mechanism of the F26G19 antibody (of SARS-CoV spike protein), where its Asp56 residue binds to the Arg426 of the SARS-CoV spike protein RBD against the formation of the interfacial Arg426-Glu329 salt bridges between ACE2 and the SARS-CoV spike protein RBD. Second, a hypothesis is reported that a pair of electrostatic clips exist at the interface between ACE2 and the SARS-CoV spike protein RBD, including both Arg426-Glu329 and His445-Glu23-Lys447 salt bridges. Last, this article reports a structurally identified interfacial Glu35-Arg479 salt bridge which helps stabilize the complex structure of ACE2 and the SARS-CoV spike protein RBD. Overall, the structurally identified electrostatic hot spots reported here may be useful for the design of SARS-CoV-neutralizing antibodies in future.
ARTICLE | doi:10.20944/preprints201907.0064.v1
Subject: Earth Sciences, Environmental Sciences Keywords: microcystins; climatic factors; chronic liver disease and cirrhosis; daily sunlight; enzyme-linked immunosorbent assay
Online: 3 July 2019 (11:46:09 CEST)
Cyanobacteria (blue-green algae) may rapidly propagate under favorable conditions, forming dense blooms. As water blooms deteriorate, blue-green algae can generate potent toxins, potentially harmful to companion animals, wildlife, and even humans. One widely recognized cyanobacterial toxin is microcystin. This algal toxin has been implicated in surface waters globally, increasing liver cancer and/or disease risk amongst those who depend on sources prone to microcystin contamination. Interestingly, no study looked at weather conditions when connecting liver health outcomes to freshwater cyanotoxins. The purpose of this study was to determine if climate was an important determinant of liver mortality and total microcystins at the ecological level. Secondary data was used to evaluate the proposed hypothesis. Environmental data (CDC WONDER) and toxin data (USEPA) were used in multivariate regression analysis. Mean daily sunlight and total microcystins were significant predictors of age-adjusted chronic liver disease and cirrhosis death rates. Mean annual precipitation and mean daily max temperature were non-significant predictors. This study demonstrated how microcystins in combination with climate may increase liver mortality. The results can prompt others to study environmental exposures of terminal liver diseases, guiding environmental health and the water industry of human survival needs.
Subject: Life Sciences, Biochemistry Keywords: enzyme kinetics; Jupyter notebook; kinetic modelling; matplotlib; NMR spectroscopy; optimisation; parametrisation; PySCeS; SciPy; validation
Online: 11 June 2019 (11:15:01 CEST)
Bottom-up systems biology entails the construction of kinetic models of cellular pathways by collecting kinetic information on the pathway components (e.g. enzymes) and collating this into a kinetic model, based for example on ordinary differential equations. This requires integration and data transfer between a variety of tools, ranging from data acquisition in kinetics experiments, to fitting and parameter estimation, to model construction, evaluation and validation. Here, we present a workflow that uses the Python programming language, specifically the modules from the SciPy stack, to facilitate this task. Starting from raw kinetics data, acquired either from spectrophotometric assays with microtitre plates or from NMR spectroscopy time courses, we demonstrate the fitting and construction of a kinetic model using scientific Python tools. The analysis takes place in a Jupyter notebook, which keeps all information related to a particular experiment together in one place and thus serves as an e-labbook, enhancing reproducibility and traceability. The Python programming language serves as an ideal foundation for this framework because it is powerful yet relatively easy to learn for the non-programmer, has a large library of scientific routines and active user community, is open-source and extensible, and many computational systems biology software tools are written in Python or have a Python API. Our workflow thus enables investigators to focus on the scientific problem at hand rather than worrying about data integration between disparate platforms.
ARTICLE | doi:10.20944/preprints201807.0093.v1
Subject: Medicine & Pharmacology, Cardiology Keywords: cardiomyopathy; hemodynamic and biochemical parameters; epidemiological and clinical Parameters; phospholamban angiotensin-1-converting enzyme
Online: 5 July 2018 (10:43:43 CEST)
Background: Cardiomyopathy is commonly observed disease that may occurs due to mutations in either susceptible genes or modifier gene. People with broad age group are affected either attributable to spontaneous or inherited mutations of these genes. Various gene mutations are reported so far but only few of them were studied in detail. Methods: In the current study, we evaluated epidemiological variables like age, sex, familial status, parental consanguinity. We also described specific clinical symptoms associated with the cardiomyopathy condition in Indian population. Results: Our studies on mutation screening of phospholamban gene revealed two transitions (4880 C/T, 4887 T/G) in 5’ flanking region which might cause inherited dilated cardiomyopathy with refractory congestive heart failure are We further deliberated the gene polymorphism of renin angiotensin system gene angiotensin-1-converting enzyme as an associated marker/ modifier in cardiomyopathy patients and their family members. Conclusions: Information on epidemiological, clinical statistics, phospholamban gene mutation analysis and angiotensin-1-converting enzyme gene polymorphism is essential to guide the successful execution for future therapies and benefits us to identify those patients at risk for faster disease progression, congestive heart failure, and arrhythmia.
ARTICLE | doi:10.20944/preprints202203.0008.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: Sustainable dryland farming; clay soil amendment; soil water use; organic matter; enzyme activity; nutrient turnover
Online: 1 March 2022 (08:27:33 CET)
Degraded soils causing from natural and human affects are universal in arid and semi-arid regions all over the world. Bentonite and humic acid (BHA) are increasingly being tested to remediate these degraded lands with potential benefits on crop production and soil health. The objective of this paper was to determine the residual effects four to five years after a one-time BHA application at six rates on (i) dynamic changes in soil properties, and (ii) oat crop productivity parameters, in a dryland farming ecosystem. With increasing rates of one-time BHA application, soil profile water storage displayed a piecewise linear increase plus plateau, whereas soil electrical conductivity, pH and bulk density were all reduced significantly (P < 0.05) in the 0-20 cm and 20-60 cm layers. The improved soil environments gave rise to an increased activity of soil enzymes urease, invertase and catalase that respectively reached the peak values of 97%, 37% and 32% at the rates of 21 to 24 Mg BHA ha-1. These conversely boosted soil nutrient turnover, leading to a 40% higher soil available P. Compared with the control treatment, application of BHA at the estimated optimum rate (roughly 24 Mg ha-1) increased grain yield by 20%, protein yield by 62%, water use efficiency by 41%, and partial factor productivity of N by 20%. Results of this study showed for the first time that a one-time BHA application would be a new and effective strategy to combat land degradation, drought, and promote a sustainable soil micro-ecological environment in dryland agroecosystem under a varying climate scenario.
ARTICLE | doi:10.20944/preprints202112.0371.v1
Subject: Life Sciences, Biochemistry Keywords: Blood Lead levels1; d-aminolevulenic acid dehydratase enzyme activity; d-aminolevulinic acid dehydratase gene polymorphism.
Online: 22 December 2021 (14:36:31 CET)
Rapid industrialization, urbanization, and population explosion in sub-Saharan Africa escalate environmental Lead levels with subsequent elevation of blood Lead levels in children. Nutrition status, age, and genetics govern one’s susceptibility to Lead toxicity. This study expounded this susceptibility by relating blood Lead levels, d-aminolevulinic acid dehydratase enzyme activity (ALAD), and genetic variations of proteins that code for ALAD enzyme in urban children of Uganda. Spectrophotometric analysis for blood Lead (BL), hemoglobin levels, and determination d-levels aminolevulinic acid dehydratase enzyme activity of the blood samples from 198 children were performed prior to a polymerase chain reaction and restriction fragment length digestion for ALAD polymorphism was done. Up to 99.5% of samples coded for the ALAD1 allele whereas 0.05% coded for ALAD2. Genotypes ALAD2-2 members had elevated BLL (mean 14.1 µg/dL) and reduced ALAD enzyme activity compared to others. This, therefore, implies that the majority of children hoard BL which may affect them later in life.
REVIEW | doi:10.20944/preprints202105.0311.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Angiotensin converting enzyme 2; breast feeding; drug therapy; pregnancy; severe acute respiratory syndrome coronavirus 2
Online: 13 May 2021 (15:26:34 CEST)
The coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become the chief concern of the international community in almost no time. As of May 9th, 2021, more than 150 million cases and 3.2 million deaths have been recorded. Considering the early struggle in treating COVID-19 patients, the researchers and clinicians have decided to try the previously available drugs according to their mechanisms of action. Hence, many antivirals, antibiotics, antiparasitics, and antipyretics have been proposed. Pregnant women, fetuses, and infants are known high-risk populations that are threatened during disease outbreaks. Therefore, this article reviews the safety of potential drugs for COVID-19 patients during pregnancy and breastfeeding.
REVIEW | doi:10.20944/preprints202101.0026.v1
Subject: Life Sciences, Biochemistry Keywords: 20S proteasome; protein degradation; intrinsically disordered proteins; enzyme functional cycle; peptides; peptidome; proteome; oxidative stress
Online: 4 January 2021 (12:16:42 CET)
Four decades of proteasome research have yielded extensive information on ubiquitin-dependent proteolysis. The archetype of proteasomes is a 20S barrel-shaped complex that does not rely on ubiquitin as a degradation signal but can degrade substrates with a considerable unstructured stretch. Since roughly half of all proteasomes in most eukaryotic cells are free 20S complexes, ubiquitin-independent protein degradation may coexist with ubiquitin-dependent degradation by the highly regulated 26S proteasome. This article reviews recent advances in our understanding of the biochemical and structural features that underlie the proteolytic mechanism of 20S proteasomes. The two outer α-rings of 20S proteasomes provide a number of potential docking sites for loosely folded polypeptides. The binding of a substrate can induce asymmetric conformational changes, trigger gate opening, and initiate its own degradation through a protease-driven translocation mechanism. Consequently, the substrate translocates through two additional narrow apertures augmented by the β-catalytic active sites. The overall pulling force through the two annuli results in a protease-like unfolding of the substrate and subsequent proteolysis in the catalytic chamber. Although both proteasomes contain identical β-catalytic active sites, the differential translocation mechanisms yield distinct peptide products. Non-overlapping substrate repertoires and product outcomes rationalize cohabitation of both proteasome complexes in cells.
Subject: Medicine & Pharmacology, Cardiology Keywords: COVID-19; SARS-CoV; SARS-CoV-2; Angiotensin-converting enzyme 2; renin-angiotensin-aldosterone system
Online: 25 March 2020 (03:56:27 CET)
The role of the Renin-Angiotensin-Aldosterone System (RAAS) in Corona Virus Disease 2019 (COVID-19) infection has become a controversial topic of discussion. RAAS inhibitors, such as Angiotensin Converting Enzyme (ACE) inhibitors and Angiotensin II receptor blockers (ARBs), which are used to treat cardiovascular diseases, have been implicated in potentially increasing cell surface levels of ACE2. ACE2 is the host receptor for COVID-19 that was discovered in Wuhan, China in December 2019. Since December, COVID-19 has transmitted rapidly across the world and has become a global pandemic. COVID-19 is similar to the Middle East respiratory syndrome coronavirus (MERS-CoV) with the first case reported in Saudi Arabia in September 2012. COVID-19, also known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is also similar to SARS-CoV, which first infected humans in the Guangdong province of southern China in 2002, and caused an epidemic between November 2002 and July 2003. Both SARS-CoV and COVID-19 use ACE2 to enter host cells. ACE2 is primarily expressed in the mouth, lung, heart, esophagus, kidney, bladder, and intestines, and is a component of RAAS, which serves to maintain vascular tone and blood volume. Inhibition or activation of other components of RAAS has been shown to directly increase or decrease the expression and/or activity of ACE2. Furthermore, RAAS-targeting therapeutics, such as ACE inhibitors and ARBs, have also been shown to regulate the expression and/or activity of ACE2, albeit in animal models. Although these changes in ACE2 have been demonstrated only in animal models, there is no evidence that administration of RAAS-targeting therapeutics to humans for the treatment of hypertension, diabetes, and other cardiovascular diseases (e.g., myocardial infarction and heart failure) causes changes in ACE2 expression. Nor is there clinical evidence that RAAS-targeting therapeutics augment COVID-19 infection, morbidity, or mortality. However, clinical evidence does suggest that ACE2 expression may protect against respiratory distress caused by a variety of noxious agents. This review attempts to provide a balanced overview of the potential role of RAAS in regulating ACE2, and the role of ACE2 during COVID-19 infection. Evidence is provided to show that the expression of ACE2 may mediate both positive and negative outcomes, depending on the timing of ACE2 expression.
ARTICLE | doi:10.20944/preprints201811.0246.v1
Subject: Chemistry, Analytical Chemistry Keywords: monoclonal antibodies; polyclonal antibodies; triazines; enzyme immunoassay; quantitative structure-activity relationship analysis; 3D-QSAR; atrazine
Online: 9 November 2018 (11:36:02 CET)
A common task in the immunodetection of structurally close compounds is to analyze the selectivity of immune recognition: it is required to understand the regularities of immune recognition and to elucidate the basic structural elements which provide it. Triazines are compounds of particular interest for such a research due to their high variability and the necessity of their monitoring to provide safety of agricultural products and foodstuffs. We evaluated the binding of 20 triazines with polyclonal (pAb) and monoclonal (mAb) antibodies obtained using atrazine as the immunogenic hapten. A total of >3000 descriptors was used in QSAR analysis of binding activities (pIC50). Comparison of the two enzyme immunoassay systems showed that the system with pAb is much easier to describe using 2D QSAR methodology, while the system with mAb can be described using the 3D QSAR COMFA. Thus, for the 3D QSAR model of the polyclonal antibodies, the main statistical parameter q2 (‘leave-many-out’) is equal 0.498, and for monoclonal antibodies q2 is equal 0.566. Obviously, in the case of pAb, we deal with several targets, while in the case of mAb the target is one, and therefore it is easier to describe it using specific fields of molecular interactions distributed in space.
ARTICLE | doi:10.20944/preprints201808.0548.v1
Subject: Biology, Plant Sciences Keywords: Origanum vulgare; Spodoptera littoralis; terpenoid biosynthesis; larval survival; antioxidant enzyme activity and gene expression; toxicity
Online: 31 August 2018 (13:28:51 CEST)
Terpenoids are toxic compounds produced by plants as a defense strategy against insect herbivores. We tested the effect of Origanum vulgare terpenoids on the generalist herbivore Spodoptera littoralis and the response of the plant to herbivory. Terpenoids were analyzed by GC-FID and GC-MS and quantitative gene expression (qPCR) was evaluated on selected plant genes involved in both terpene biosynthesis. The insect detoxification response to terpenes was evaluated by monitoring antioxidant enzymes activity and expression of insect genes involved in terpene detoxification. O. vulgare terpenoid biosynthesis and gene expression was modulated by S. littoralis feeding. The herbivore-induced increased level of terpenoids (particularly carvacrol and p-cymene) interacted with the herbivore by decreasing larval survival and growth rate. The assimilation by S. littoralis of more than 50% of ingested terpenes correlated with the possible toxic effects of O. vulgare terpenoids. In choice test experiments, carvacrol and γ-terpinene mediated the larval feeding preferences, wherease the prolonged feeding on O. vulgare terpenoids (particularly on γ-terpinene) exerted relevant antinutritional effects on larvae. S. littoralis was found to react to O. vulgare terpenoids by increasing its antioxidant enzymes activities and gene expression, although this was not sufficient to sustain the toxicity of O. vulgare terpenoids.
REVIEW | doi:10.20944/preprints201801.0223.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: abiotic stress; antioxidant defense; enzyme regulations; oxidative stress; plant nutrients; reactive oxygen species; soil fertility
Online: 24 January 2018 (07:01:05 CET)
Among the plant nutrients potassium (K) is one of the vital elements required for plant growth and physiology. Potassium is not only a constituent of plant structure but also plays regulatory function in several biochemical processes related to protein synthesis, carbohydrate metabolism, enzyme activation. There are several physiological processes like stomatal regulation and photosynthesis are dependent on K. In the recent decades K was found to provide abiotic stress tolerance. Under salt stress, K helps in maintaining ion homeostasis and regulation of osmotic balance. Under drought stress condition K regulates the stomatal opening and makes the plants adaptive to water deficit. Many reports provided the notion that K enhances the antioxidant defense in plants and therefore, protects the plants from oxidative stress under various environmental adversities. Also, it provides some cellular signaling alone or in association with other signaling molecules and phytohormones. Although a considerable progress in understanding K-induced abiotic stress tolerance in plants has been achieved the exact molecular mechanisms of such protections are still under research. In this review, we summarized the recent literature on the biological functions of K, its uptake, and translocation and its role in plant abiotic stress tolerance.
REVIEW | doi:10.20944/preprints202301.0420.v1
Subject: Life Sciences, Microbiology Keywords: Cryptococcus; extracellular protease; biofilm, secretory vesicles; hypoxia; hydrolytic enzyme; homeostasis; transcription factors; membrane permeases; membrane transporters
Online: 24 January 2023 (03:08:39 CET)
In this review, we present several extracellular proteases, enzymes, membrane permeases, and transporters as essential accessories proteins for nutrient assimilation, conservation, and transportation as determined by nutrient repletion or depletion. As an obligate aerobic pathogen, it is crucial for invading Cryptococcus (C.) neoformans to negotiate its adaptation to human internal organs like the brain and spinal cord, where the oxygen level is low compared to peripheral organs. Besides, essential metals like copper and iron are important cofactors to functional proteins; however, these metals are not usually freely available to invading human pathogens. Again, the phagolysosome low pH with glucose paucity, internal temperature, immune response, and complex extracellular matrixes are challenging environments that must be circumvented by C. neoformans in the systemic tissues for survival, adaptation, and infection in humans. We review extensive works on several extracellular proteases, enzymes, membrane permeases and transporters orchestrated by different transcription factors and present these proteins as weapons needed to outwit systemic resistance to invading pathogens. Lastly, we examine the extracellular secretory vesicles of C. neoformans as “an exosomal virulence bag” that harbours urease, laccase, phosphatase, and capsular components as additional secretory weapons for tissue invasion and persistence.
REVIEW | doi:10.20944/preprints202107.0271.v1
Subject: Life Sciences, Biochemistry Keywords: bovine colostrum; bacterium; pathogens; probiotic bacteria; cost-effective processing; heat treatment; pasteurization; contamination control; immunoglobulin; enzyme
Online: 12 July 2021 (17:46:44 CEST)
The purpose of bovine colostrum, being the milk secreted by a cow after giving birth, is to transfer passive immunity to the calf. The calves have an insufficient immune system as they lack immunoglobulins (Igs). Subsequently, the supply of good quality bovine colostrum is obligatory. The quality of colostrum is classified by low bacterial counts and adequate Ig concentrations. Bacterial contamination can contain a variety of human pathogens or high counts of spoilage bacteria, which becomes more challenging with emerging use of bovine colostrum as food and food supplements. There is also a growing risk for the spread of zoonotic diseases originating from bovines. For this reason, processing based on heat treatment or other feasible techniques are required. This review provides an overview of literature on the microbial quality of bovine colostrum and processing methods to improve its microbial quality and keep its nutritional values as food. The highlights of this review are: high quality colostrum is a valuable raw material in food products and supplements, the microbial safety of bovine colostrum is increased using appropriate processing, suitable effective heat-treatment, which does not destroy the high nutrition value of colostrum, the heat treatment processes are cost-effective compared to other methods, and heat treatment can be performed in both small- and large-scale production
HYPOTHESIS | doi:10.20944/preprints202008.0607.v2
Subject: Biology, Other Keywords: catalysis; kinetics; time; biological macromolecular enzyme; large biological macro-substrate; catalytic step; catalytic efficiency; turnover number
Online: 16 November 2020 (08:28:55 CET)
Classical enzyme kinetics are summarized and linked with modern discoveries here. The time course of sequential catalytic events by biological macromolecular enzyme is analyzed at the molecular level; the relationships between catalytic efficiency (turnover number), catalytic rate/velocity, the amount of time taken and physical/biochemical conditions of the system are discussed. This writing tries to connect the microscopic molecular behavior of enzyme to kinetic data obtained in experiment, and the hypothesis proposed here provide an interpretation to previous experimental observations and can be testified by future experiments.
ARTICLE | doi:10.20944/preprints202004.0262.v1
Subject: Keywords: angiotensin-converting enzyme; I/D polymorphism; ACE; SARS-CoV-2; COVID-19 mortality rate; testing intensity
Online: 16 April 2020 (08:04:35 CEST)
A literature review was conducted to summarize the frequency of the D-allele of the angiotensin-converting enzyme-1 in all countries with available data. Using an ecological study design limited to high income countries, we found that the country-level frequency of the D-allele was associated with increased COVID-19 incidence and mortality.
HYPOTHESIS | doi:10.20944/preprints202003.0340.v1
Subject: Biology, Other Keywords: coronavirus; SARS-CoV-2; lysosomal storage diseases; lipid rafts; cholesterol; angiotensin-converting enzyme-2 (ACE2); cathepsins
Online: 24 March 2020 (03:07:06 CET)
In the face of the newly emergent COVID-19 pandemic, researchers around the world are racing to identify efficacious drugs capable of preventing or treating its infection. They are doing that by testing already available and approved antimicrobials for their rapid repurposing against COVID-19. Using the data emerging on the comparable efficacy of various compounds having different mechanisms of action and indications, I suggest in this report, their potential mechanistic convergence. Specifically, I highlight the lysosome as a key possible therapeutic target for COVID-19, proposing one of the lysosomal storage disorders, Niemann-Pick type C disease (NPC), as a prototypical condition with inherent resistance or an “unfavorable” host cell environment for viral propagation. The included reasoning evolves from previously generated data in NPC, along with the emerging data on COVID-19. The aim of this report is to suggest that pharmacological induction of a “transient” NPC-like lysosomal dysfunction, could hold answers for targeting the ongoing COVID-19 pandemic.
ARTICLE | doi:10.20944/preprints202201.0226.v1
Subject: Medicine & Pharmacology, Gastroenterology Keywords: Hepatitis C virus (HCV); liver; samples; structure; electrochemiluminescence (ECL); ELISA method (Enzyme-Linked Immunosorbent Assay); antigen-antibodies
Online: 17 January 2022 (12:37:22 CET)
Objective: The study aimed to manage and to analyse the results of the laboratory tests, available nowadays, used from routine clinical practice, for screening of hepatitis C. Methods: comparison of ELISA method results (Enzyme-Linked Immunosorbent Assay) and chemiluminescence methods results. Beside previously mentioned, the study show the structural comparison of normal liver and pathologic liver with hepatic cirrhosis, using permanent samples colored after the technique protocol. Statistical analysis of this study results, was performed using the laboratory informatic system. Results: The results of the study are substantial and intricate. For this purpose, the results of preliminary EСL screening method of patients at risk for HCV who took part in the study, are presented in tables and figures. Results of this study are various and are correlate from different perspectives. Also good to mention that the correlations of results were used in order to identify a possible relationships between indicators of ELISA method and ECL index. More than, correlations antibodies detected in ECL and ELISA are point out. Conclusion: EСL and ELISA method results, are relevant for screening and for diagnostic confirmation in HCV risk patients. Unfotunately in the present study, were impossible to conclude about false-negative results. Good to know our opinion that RT-PCR technique, it is considered proper for the diagnosis of HCV.
REVIEW | doi:10.20944/preprints202104.0602.v2
Subject: Medicine & Pharmacology, Oncology & Oncogenics Keywords: cancer; DNA sequencing; DNA synthesis; enzyme; free-radicals; genome; HPV; oncogenes; retinoblastoma; ribonucleotide reductase; RnR; SMT; TCGA
Online: 6 July 2021 (11:32:47 CEST)
Presence of mutated genes strongly correlates with incidence of cancer. Decades of research, however, has not yielded any specific causative gene or set of genes for the vast majority of cancers. The Cancer Genome Atlas program was supposed to provide clarity but it only gave much more data without any accompanying insight into how the disease begins and progresses. It may be time to notice that epidemiological studies consistently show that the environment, not genes, has the principal role in causing cancer. Since carcinogenic chemicals in our food, drink, air and water are the primary culprit, we need to look at the biochemistry of cancer, with focus on enzymes which carry out any and all transformations in a cell. In particular, attention should be paid to the rate-limiting enzyme in DNA synthesis, ribonucleotide reductase (RnR) which is tightly linked to tumor growth. Beside the circumstantial evidence that cancer is induced at its vulnerable active-site by various carcinogens, there exists experimental proof of its role in initiating retinoblastoma and HPV-related cervical cancers. Blocking the activity of RnR is a certain way to arrest cancer.
Subject: Life Sciences, Biotechnology Keywords: SARS-CoV-2; COVID-19; acute kidney injury; angiotensin converting enzyme II (ACE2); transmembrane serine protease (TMPRSSs)
Online: 23 February 2020 (15:42:24 CET)
Purpose: Acute kidney injury (AKI) is a severe symptom of the 2019 novel coronavirus disease (COVID-19), especially for patients in a critical condition.This study explored the potential mechanism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on AKI at the single-cell level. Methods: 15 normal human kidney samples were collected and analyzed using single-cell RNA sequencing (scRNA-seq). Subsequently, we analyzed the components and proportions of kidney cells expressing the host cellular receptor ACE2 and the key protease TMPRSSs family, and analyzed the expression differences in Occidental and Asian populations. Results: We drafted the currently available world's largest human kidney cell atlas with 42,589 cells and identified 19 clusters through unsupervised hierarchical clustering analysis. ACE2 and TMPRSSs genes were significantly co-expressed in podocytes and proximal convoluted tubules as potential host cells targeted by SARS-CoV-2. Comparative analysis showed that ACE2 expression in kidney cells was no less than that in the lung, esophagus, small intestine and colon, suggesting that the kidney may be an important target organ for SARS-CoV-2. In addition, given the high expression of ACE2 and kidney disease-related genes in Occidental donors relative to Asian donors, Occidental populations with SARS-CoV-2 infection might be a higher risk of of kidney injury.
REVIEW | doi:10.20944/preprints201910.0064.v1
Subject: Biology, Plant Sciences Keywords: cold acclimation; metabolic reprogramming; carbohydrates; subcellular metabolism; sucrose cycling; enzyme activity; arrhenius equation; kinetic modelling; arabidopsis thaliana
Online: 7 October 2019 (11:19:01 CEST)
Plants have evolved tightly regulated strategies to adapt and acclimate to a changing environment to ensure their survival. Various environmental factors affect plant distribution, growth and yield. Low temperature belongs to those abiotic factors which significantly constrain range boundaries of plant species. Exposing plants to low but non-freezing temperature induces a multigenic processes termed cold acclimation, which finally results in an increased freezing tolerance. Cold acclimation comprises reprogramming of the transcriptome, proteome and metabolome and affects communication and signaling between subcellular organelles. Reprogramming of the central carbohydrate metabolism plays a key role in cold acclimation. This review summarizes current knowledge about the role of carbohydrate metabolism in plant cold acclimation. A focus is laid on subcellular metabolic reprogramming, its thermodynamic constraints under low temperature and mathematical modelling of metabolism.
ARTICLE | doi:10.20944/preprints201709.0156.v1
Subject: Biology, Other Keywords: delphinidin; radiation protective agent; proton beam therapy; CCD-18Co cells; reactive oxygen species; antioxidant enzyme; DNA damage
Online: 29 September 2017 (13:49:38 CEST)
Unavoidable exposure to radiosensitive normal tissues around cancerous tumor during the radiotherapy can cause side effects such as self-limited acute toxicities, mild chronic symptoms, or severe organ dysfunction. Nevertheless, clinical use of currently available radiation protective agents is limited because of their generic cytotoxicity. A study on radiation protective effect of delphinidin was conducted with proton-beam-exposed human colon cells (CCD-18Co). The measurement in changes of survival fractions of CCD-18Co with/without delphinidin administration at different radiation doses were measured by 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT) assay. The changes in expression of reactive oxygen species (ROS) and in activities of antioxidant enzymes were measured by colorimetric assays using pertinent assay kits. The measurement of pro-apoptosis/pro-survival protein expressions using Western blot assay and the measurement of DNA damage using comet assay were also fulfilled to evaluate the molecular level of radiation damages in CCD-18Co cells. The experimental results revealed that the pre-administration of delphinidin regulated antioxidant enzymes, reduced ROS, decreased DNA damage, regulated pro-apoptosis/pro-survival proteins, and eventually reduced apoptosis of CCD-18Co cells. In conclusion, it is claimed that delphinidin is nontoxic natural radiation protective compound, and thus delphinidin can be used to protect normal colon tissues during the proton beam therapy.
ARTICLE | doi:10.20944/preprints202101.0227.v1
Subject: Life Sciences, Biochemistry Keywords: tRNAs; tRNA-modifying enzyme; TRMT2A; methyltransferase; tRNA hypomethylation; tRNA-derived small RNAs; tRNA-derived stress-induced RNAs; angiogenin.
Online: 12 January 2021 (15:17:29 CET)
Transfer RNA (tRNA) molecules contain various post-transcriptional modifications that are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation to gene expression control and cellular stress response. Recent evidence indicates that tsRNAs are also modified, however, the impact of tRNA epitranscriptome deregulation on tsRNAs generation is only now beginning to be uncovered. The 5-methyluridine (m5U) modification at position 54 of cytosolic tRNAs is one of the most common and conserved tRNA modifications among species. The tRNA methyltransferase TRMT2A catalyzes this modification, but its biological role remains mostly unexplored. Here, we show that TRMT2A knockdown in human cells induces m5U54 tRNA hypomodification, resulting in angiogenin (ANG) dependent tsRNA formation. More specifically, m5U54 hypomodification is followed by ANG overexpression and tRNA cleavage near the anticodon, resulting in accumulation of 5’tRNA-derived stress-induced RNAs (5’tiRNAs), in particular 5’tiRNA-GlyGCC and 5’tiRNA-GluCTC. Additionally, transcriptomic analysis confirms that down-regulation of TRMT2A and consequently m5U54 hypomodification impacts the cellular stress response and RNA stability, which is often correlated with tsRNA generation. Accordingly, exposure to oxidative stress conditions induces TRMT2A down-regulation and tsRNA formation in mammalian cells. These results establish a link between tRNA demethylation and ANG-dependent tsRNAs formation and unravel m5U54 as a tRNA cleavage protective mark.
REVIEW | doi:10.20944/preprints202001.0315.v1
Subject: Medicine & Pharmacology, Pediatrics Keywords: succinic semialdehyde dehydrogenase deficiency; gamma-amino butyric acid; organic acidurias; enzyme replacement therapy; pharmacological chaperones; clinical trials; autophagy
Online: 26 January 2020 (08:10:19 CET)
Succinic semialdehyde dehydrogenase deficiency (SSADH-D) is a genetic disorder that results from the aberrant metabolism of the neurotransmitter γ-amino butyric acid (GABA). The disease is caused by the impaired activity of the mitochondrial enzyme succinic semialdehyde dehydrogenase. SSADH-D manifests as varying degree of mental retardation, autism, ataxia and epileptic seizures, but the clinical picture is highly heterogeneous. So far, there is no approved therapy for this disease. In this review, we briefly summarize the molecular genetics of SSADH-D, the past and ongoing clinical trials and the emerging features of the molecular pathogenesis, including redox imbalance and mitochondrial dysfunction. The main aim of this review is to discuss the potential use of further therapy approaches that have so far not been tested in SSADH-D, such as pharmacological chaperones, read-through drugs and gene therapy. Special attention will also be paid to elucidating the role of patient advocacy organizations in facilitating research and in the communication between the researchers and the patients.
ARTICLE | doi:10.20944/preprints202301.0583.v2
Subject: Medicine & Pharmacology, Pathology & Pathobiology Keywords: factor XIII; foam cells; macrophages; vascular smooth muscle cells; oxidized LDL; enzyme-modified LDL; transglutaminase; atherosclerotic plaque; cross-linking
Online: 2 February 2023 (11:52:20 CET)
The potentially active A subunit of coagulation factor XIII (FXIII-A) is an intracellular transglutaminase expressed in various cell types including platelets and monocytes/macrophages. It is involved in stabilizing protein structures by cross-linking through Nε-(?-L-glutamyl)-L-lysyl iso-peptide bonds. Macrophages are major cellular constituents of the atherosclerotic plaque and are important in determining its structural/functional features. Two of their important functions are the accumulation of oxidized LDL in the lipid core, and by cross-linking structural proteins they may stabilize the plaque and protect the thrombi of atherogenic origin against fibrinolytic degradation. It is important to know whether these functions operate in parallel utilizing the same cellular compartments. First, we showed that monocyte-derived human macrophages significantly increase their FXIII-A content when up-taking oxidized LDL. This phenomenon is very likely independent of the process of transformation into foam cells, as the transformation of vascular smooth muscle cells into foam cells fails to result in the expression of FXIII-A. FXIII containing macrophage-like cells are abundant in the plaque and FXIII-A is also present in the extracellular core. Several cells co-stained for FXIII-A and for Oil Red O suggest that expression of FXIII-A and lipid up-take are common features of macrophages present in the atherosclerotic plaque.
REVIEW | doi:10.20944/preprints202105.0414.v1
Subject: Medicine & Pharmacology, General Medical Research Keywords: : mineralocorticosteroid receptor antagonist (MRA); angiotensin converting enzyme 2 (ACE2); SARS-CoV-2; transmembrane protease receptor serine 2; furin; plasmin
Online: 18 May 2021 (10:39:03 CEST)
Aims: Spironolactone is a steroidal mineralocoricosteroid receptor antagonist (MRA) used for treatment of resistant hypertension, heart failure and edema. It exerts class specific adverse effects that are shared by other MRAs. Additionally, it exerts unique “off target” steroidal effects that include gynecomastia, impotence and loss of libido in males and menstrual irregularity in females. Together, these have led to a poor tolerability and limited use despite positive results in many randomized, controlled clinical trials. We review the off-target effects of spironolactone that may summate with its MRA action to provide an advantageous profile for prevention or treatment of patients with COVID-19. Methods: Literature review using PubMed Central. Results: The blockade by spironolactone of the androgen receptor should diminish the expression of transmembrane protease serine 2 (TMPRSS2) that has an androgen promoter while its MRA action should enhance the expression of protease nexin1 (PN1) that inhibits furin and plasmin. TMPRSS2, furin and plasmin cooperated to process the SARS-CoV-2 spike protein to increase its high affinity binding to the angiotensin converting enzyme 2 (ACE2) and thereby promote viral cell entry. Its actions as an MRA may reduce inflammation and preserve pulmonary, cardiac and vascular functions. Its anti-plasmin action may combat hemostatic dysfunction. Conclusion: The hypothesis that the off-target effects of spironolactone summate with its MRA actions to provide special benefits for COVID-19 is worthy of direct investigation and clinical trial.
REVIEW | doi:10.20944/preprints202104.0339.v1
Subject: Life Sciences, Biochemistry Keywords: neurodegeneration, glucose metabolism, enzyme catalysis, protein-protein interaction, hydrogen exchange mass spectrometry, protein cross-linking, protein assembly, molecular modeling
Online: 13 April 2021 (10:19:30 CEST)
The 2-oxoglutarate dehydrogenase complex (OGDHc) is a key enzyme in the TCA cycle and represents one of the major regulators of mitochondrial metabolism through NADH and reactive oxygen species levels. The OGDHc impacts cell metabolic and cell signaling pathways through the coupling of 2-oxoglutarate metabolism to gene transcription related to tumor cell proliferation and aging. DHTKD1 is a gene encoding 2-oxoadipate dehydrogenase (E1a), which functions in the L-lysine degradation pathway. The potentially damaging variants in DHTKD1 have been associated to the (neuro) pathogenesis of several diseases. Evidence was obtained for the formation of a hybrid complex between the OGDHc and E1a, suggesting a potential cross talk between the two metabolic pathways and raising fundamental questions about their assembly. Here we reviewed the recent findings and advances in understanding of protein-protein interactions in OGDHc and 2-oxoadipate dehydrogenase complex (OADHc), an understanding that will create a scaffold to help design approaches to mitigate the effects of diseases associated with dysfunction of the TCA cycle or lysine degradation. A combination of biochemical, biophysical and structural approaches such as chemical cross-linking MS and cryo-EM appears particularly promising to provide vital information for the assembly of 2-oxo acid dehydrogenase complexes, their function and regulation.
REVIEW | doi:10.20944/preprints202010.0623.v1
Subject: Medicine & Pharmacology, Allergology Keywords: Glioblastoma; Neural Stem Cells; Mesenchymal Stem Cells; Stem Cell Therapy; Enzyme/Prodrug Therapy; Oncolytic Virotherapy; Nanoparticles; TRAIL; Cytokine Therapy
Online: 29 October 2020 (15:51:04 CET)
The potential of Neural Stem Cells (NSCs) to provide therapeutic benefit for a variety of neurological disorders, including brain malignancies, has been long recognized and has inspired many scientists to design, test and successfully demonstrate that NSCs are efficient and effective therapeutic agents. Glioblastoma, the deadliest form of primary brain tumor, despite extensive and sustained efforts to find better therapies, remains a disease without cure, with a median survival after diagnosis of less than two years. Treatment resistance in glioblastoma is in large part attributed to limitations in the delivery and distribution of therapeutic agents administered either systemically or directly into the tumor due to the highly invasive nature of this cancer and its abnormal intratumoral vasculature. Stem Cells (SCs) have an innate tumor-tropic migratory behavior, can be modified to deliver a variety of therapeutic agents and efficiently distribute their cargo into brain tumors, pursuing invading streams of tumor cells, deep into the brain parenchyma. Over the last twenty years, numerous preclinical trials have demonstrated the feasibility and efficacy of SCs as antiglioma agents, leading to the development of trials to test these therapies in the clinic. In this review we present and analyze these studies and discuss mechanisms underlying their beneficial effect, highlighting experimental progress, limitations and the emergence of promising new therapeutic avenues. We hope to increase awareness of the advantages of using SCs for the treatment of glioblastoma and inspire further studies that will lead to accelerated implementation of effective therapies.
REVIEW | doi:10.20944/preprints202005.0260.v2
Subject: Biology, Other Keywords: COVID-19; SARS-CoV; SARS-like coronavirus; 2019-nCoV; SARS-CoV-2; angiotensin-converting enzyme 2 (ACE2); RdRp; Remdesivir; and neutralizing antibody
Online: 10 July 2020 (16:21:17 CEST)
SARS-CoV-2 is a newly emerging, highly transmissible, and pathogenic coronavirus in humans, which has caused global public health emergency and economic crisis. To date, millions of infections and thousands of deaths have been reported worldwide, and the numbers continue to rise. Currently, there is no specific drug or vaccine against this deadly virus; therefore, there is a pressing need to understand the mechanism through which this virus enters the host cell. Viral entry into the host cell is a multistep process in which SARS-CoV-2 utilizes the receptor binding domain of the spike glycoprotein (S) to recognize ACE2 receptors on the human cells; this initiates host cell entry by promoting viral-host cell membrane fusion through large scale conformational changes in the S protein. Receptor recognition and fusion are critical and essential steps of viral infections and are key determinants of the viral host range and cross-species transmission. In this review, we summarize the current knowledge on the origin and evolution of SARS-CoV-2 and the roles of key viral factors. We discuss the RNA dependent RNA polymerase structure of SARS-CoV-2, its significance in drug discovery, and explain the receptor recognition mechanisms of coronaviruses. We provide a comparative analysis of the SARS-CoV and SARS-CoV-2 S proteins, receptor-binding specificity, and discuss the differences in their antigenicity based on biophysical and structural characteristics.
ARTICLE | doi:10.20944/preprints202003.0161.v1
Subject: Life Sciences, Microbiology Keywords: coronaviruses receptors; angiotensin-converting enzyme 2 (ACE2); COVID-19; SARS-Cov-2; the Red Queen hypothesis; segmented filamentous bacteria
Online: 10 March 2020 (08:45:34 CET)
Understanding how the coronaviruses invade our body is an essential point, and the expression profile of coronaviruses receptor may help us to find where the coronavirus infects our body. We found that the coronavirus receptors, including angiotensin-converting enzyme 2 (ACE2) for SARS-CoV and SARS-Cov-2, are digestion-related enzymes in human enterocytes. Coronaviruses are continually altering the binding receptor and binding modes during their evolution, but the potential target cell in the small intestine is constant when in the lung is inconstant. Enterocytes may act as a conserved cell reservoir for coronaviruses, which may be partially explained by the Red Queen hypothesis. We also found that coronaviruses receptors could be elevated in the presence of both invasive bacteria and their counterpart, probiotics. We demonstrated here that enterocytes act as a conserved cell reservoir for coronaviruses during their evolutions, which should not be ignored in the investigation of coronavirus diagnosis and treatment strategies.