scholarly journals Minimalistic mycoplasmas harbor different functional toxin-antitoxin systems

2021 ◽  
Author(s):  
Virginia Hill ◽  
Hatice Akarsu ◽  
Rubén Sánchez Barbarroja ◽  
Valentina Cippà ◽  
Martin Heller ◽  
...  
Keyword(s):  
Heterologous Expression ◽  
In Silico ◽  
Model Organism ◽  
Future Research ◽  
Phylogenetic Distance ◽  
Minimal Cell ◽  
Unequal Distribution ◽  
Mycoplasma Mycoides ◽  
First Time

AbstractMycoplasmas are minute bacteria controlled by very small genomes ranging from 0.6 to 1.4 Mbp. They lack a cell wall and have been suggested to have progressed through reductive evolution from phylogenetically closely related Clostridia. They are known to colonize the respiratory tract or the urogenital tract among other organs and can cause chronic and subclinical diseases associated with long persistence of the causative agent. Toxin-antitoxin systems (TAS) are genetic elements that have been described for several respiratory and urogenital pathogens as well as for Clostridia, but never for pathogenic mycoplasmas. Here we describe for the first-time different types of TAS in a Mycoplasma pathogen, namely M. mycoides subsp. capri. We identified candidate TAS in silico via TASmania database. Two candidate TAS identified in silico and another candidate TAS suggested in a minimal cell based on transposon mutagenesis were systematically tested for their functionality in hosts with different phylogenetic distance using heterologous expression. Phylogenetic distance of the host used for heterologous expression influenced the outcome of the functional testing. We corroborated functionality of the three candidate TAS in Mycoplasma capricolum subsp. capricolum. Moreover, we confirmed transcription and translation of molecules of the TAS investigated during in vitro growth. We sequence analyzed 15 genomes of M. mycoides subsp. capri and revealed an unequal distribution of the TAS studied pointing towards dynamic gain and loss of TAS within the species.Author summaryMycoplasmas have a minimal genome and have never been shown to possess TAS. In this work we showed the presence of different functional TAS systems in Mycoplasma mycoides subsp. capri, a caprine pathogen for the first time. Sequence analysis of a number of Mycoplasma mycoides subsp. capri strains revealed a plasticity of the genome with respect to TAS carriage. This work paves the way to investigate the biological role of TAS (e.g. persistence, stress tolerance) during infection using mycoplasmas as a simple model organism. Since most mycoplasmas lack classical virulence factors such as exotoxins and go into a kind of stealth mode to evade the immune system, TAS are likely to contribute to the parasitic lifestyle of mycoplasmas and should be investigated in that respect. The availability of synthetic genomics tools to modify a range of Mycoplasma pathogens and well-established challenge models for the latter mycoplasmas will foster future research on TAS in mycoplasmas.

Virtual Screening, Molecular docking and in-silico ADME-Tox analysis for identification of potential main protease (Mpro) enzyme inhibitors

2020 ◽  
Vol 18 ◽  
Author(s):  
Debadash Panigrahi ◽  
Ganesh Prasad Mishra
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
In Silico ◽  
Data Bank ◽  
Future Research ◽  
Reference Compound ◽  
Unexpected Death ◽  
Main Protease ◽  
In Silico Admet

Objective:: Recent pandemic caused by SARS-CoV-2 described in Wuhan China in December-2019 spread widely almost all the countries of the world. Corona virus (COVID-19) is causing the unexpected death of many peoples and severe economic loss in several countries. Virtual screening based on molecular docking, drug-likeness prediction, and in silico ADMET study has become an effective tool for the identification of small molecules as novel antiviral drugs to treat diseases. Methods:: In the current study, virtual screening was performed through molecular docking for identifying potent inhibitors against Mpro enzyme from the ZINC library for the possible treatment of COVID-19 pandemic. Interestingly, some compounds are identified as possible anti-covid-19 agents for future research. 350 compounds were screened based on their similarity score with reference compound X77 from ZINC data bank and were subjected to docking with crystal structure available of Mpro enzyme. These compounds were then filtered by their in silico ADME-Tox and drug-likeness prediction values. Result:: Out of these 350 screened compounds, 10 compounds were selected based on their docking score and best docked pose in comparison to the reference compound X77. In silico ADME-Tox and drug likeliness predictions of the top compounds were performed and found to be excellent results. All the 10 screened compounds showed significant binding pose with the target enzyme main protease (Mpro) enzyme and satisfactory pharmacokinetic and toxicological properties. Conclusion:: Based on results we can suggest that the identified compounds may be considered for therapeutic development against the COVID-19 virus and can be further evaluated for in vitro activity, preclinical, clinical studies and formulated in a suitable dosage form to maximize their bioavailability.

scholarly journals The Influence of Bee Venom Melittin on the Functioning of the Immune System and the Contractile Activity of the Insect Heart—A Preliminary Study

Toxins ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 494 ◽  
Author(s):  
Jan Lubawy ◽  
Arkadiusz Urbański ◽  
Lucyna Mrówczyńska ◽  
Eliza Matuszewska ◽  
Agata Światły-Błaszkiewicz ◽  
...  
Keyword(s):  
Immune System ◽  
Contractile Activity ◽  
Model Organism ◽  
Dependent Manner ◽  
Physiological Studies ◽  
Almost All ◽  
First Time ◽  
Dose Dependent ◽  
Positive Effect

Melittin (MEL) is a basic polypeptide originally purified from honeybee venom. MEL exhibits a broad spectrum of biological activity. However, almost all studies on MEL activity have been carried out on vertebrate models or cell lines. Recently, due to cheap breeding and the possibility of extrapolating the results of the research to vertebrates, insects have been used for various bioassays and comparative physiological studies. For these reasons, it is valuable to examine the influence of melittin on insect physiology. Here, for the first time, we report the immunotropic and cardiotropic effects of melittin on the beetle Tenebrio molitor as a model insect. After melittin injection at 10−7 M and 10−3 M, the number of apoptotic cells in the haemolymph increased in a dose-dependent manner. The pro-apoptotic action of MEL was likely compensated by increasing the total number of haemocytes. However, the injection of MEL did not cause any changes in the percent of phagocytic haemocytes or in the phenoloxidase activity. In an in vitro bioassay with a semi-isolated Tenebrio heart, MEL induced a slight chronotropic-positive effect only at a higher concentration (10−4 M). Preliminary results indicated that melittin exerts pleiotropic effects on the functioning of the immune system and the endogenous contractile activity of the heart. Some of the induced responses in T. molitor resemble the reactions observed in vertebrate models. Therefore, the T. molitor beetle may be a convenient invertebrate model organism for comparative physiological studies and for the identification of new properties and mechanisms of action of melittin and related compounds.

scholarly journals Antioxidant Properties and Reported Ethnomedicinal Use of the Genus Echium (Boraginaceae)

Antioxidants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 722
Author(s):  
Ju Jin ◽  
Mark Boersch ◽  
Akshaya Nagarajan ◽  
Andrew K. Davey ◽  
Matthew Zunk
Keyword(s):  
Traditional Medicine ◽  
Antioxidant Properties ◽  
Future Research ◽  
Antiviral Effects ◽  
Pharmacological Studies ◽  
Phytochemical Components ◽  
Ethnomedicinal Uses ◽  
First Time

The genus Echium L. from the Boraginaceae family consists of 67 recognised species. The genus is widely distributed in the Mediterranean, having been documented in the traditional medicine of the area since 300 B.C. Current pharmacological studies have validated early ethnomedicinal properties showing that Echium spp. possesses antioxidant, analgesic, anxiolytic, anti-inflammatory, antibacterial, and antiviral effects. Nevertheless, only limited papers report specifically on the phytochemistry of this genus. Furthermore, the potential of utilising extracts from Echium species as natural antioxidant preparations has been significantly neglected. For the first time, this review comprehensively describes and discusses the presence of recorded Echium species with ethnomedicinal uses, their antioxidative properties in vitro and in vivo when available, and major phytochemical components recognised as potent antioxidants, as well as the possibilities and opportunities for future research.

scholarly journals Dose-Dependent Beneficial Effects of Tryptophan and Its Derived Metabolites on Akkermansia In Vitro: A Preliminary Prospective Study

2021 ◽  
Vol 9 (7) ◽  
pp. 1511
Author(s):  
Jia Yin ◽  
Yujie Song ◽  
Yaozhong Hu ◽  
Yuanyifei Wang ◽  
Bowei Zhang ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Physiological Function ◽  
Tryptophan Metabolism ◽  
Future Research ◽  
Beneficial Effects ◽  
First Time ◽  
The Relationship ◽  
Dose Dependent ◽  
Indole 3 Acetic Acid

Akkermansia muciniphila, a potential probiotic, has been proven to lessen the effects of several diseases. As established, the relative abundance of Akkermansia is positively correlated with tryptophan metabolism. However, the reciprocal interaction between tryptophan and Akkemansia is still unclear. Herein, for the first time, the possible effects of tryptophan and its derived metabolites on A. muciniphila were preliminarily investigated, including growth, physiological function, and metabolism. Obtained results suggested that 0.4 g/L of tryptophan treatment could significantly promote the growth of A. muciniphila. Notably, when grown in BHI with 0.8 g/L of tryptophan, the hydrophobicity and adhesion of A. muciniphila were significantly improved, potentially due to the increase in the rate of cell division. Furthermore, A. muciniphila metabolized tryptophan to indole, indole-3-acetic acid, indole-3-carboxaldehyde, and indole-3-lactic acid. Indoles produced by gut microbiota could significantly promote the growth of A. muciniphila. These results could provide a valuable reference for future research on the relationship between tryptophan metabolism and A. muciniphila.

scholarly journals A validation scale to determine the readiness of environmental DNA assays for routine species monitoring

2020 ◽  
Author(s):  
Bettina Thalinger ◽  
Kristy Deiner ◽  
Lynsey R. Harper ◽  
Helen C. Rees ◽  
Rosetta C. Blackman ◽  
...  
Keyword(s):  
In Silico ◽  
Meta Analysis ◽  
Environmental Dna ◽  
Single Species ◽  
Future Research ◽  
Individual Species ◽  
General Applicability ◽  
Routine Monitoring ◽  
User Friendly

AbstractThe use of environmental DNA (eDNA) analysis for species monitoring requires rigorous validation - from field sampling to interpretation of PCR-based results - for meaningful application and interpretation. Assays targeting eDNA released by individual species are typically validated with no predefined criteria to answer specific research questions in one ecosystem. Their general applicability, uncertainties and limitations often remain undetermined. The absence of clear guidelines prevents targeted eDNA assays from being incorporated into species monitoring and policy, thus their establishment will be key for the future implementation of eDNA-based surveys. We describe the measures and tests necessary for successful validation of targeted eDNA assays and the associated pitfalls to form the basis of guidelines. A list of 122 variables was compiled, consolidated into 14 thematic blocks, such as “in silico analysis”, and arranged on a 5-level validation scale from “incomplete” to “operational”. Additionally, minimum validation criteria were defined for each level. These variables were evaluated for 546 published single-species assays. The resulting dataset was used to provide an overview of current validation practices and test the applicability of the validation scale for future assay rating. The majority (30%) of investigated assays were classified as Level 1 (incomplete), and 15% did not achieve this first level. These assays were characterised by minimal in silico and in vitro testing, but their share in annually published eDNA assays has declined since 2014. The total number of reported variables ranged from 20% to 76% and deviated both between and within levels. The meta-analysis demonstrates the suitability of the 5-level validation scale for assessing targeted eDNA assays. It is a user-friendly tool to evaluate previously published assays for future research and routine monitoring, while also enabling appropriate interpretation of results. Finally, it provides guidance on validation and reporting standards for newly developed assays.

scholarly journals A Novel Phenylpyrrolidine Derivative: Synthesis and Effect on Cognitive Functions in Rats with Experimental Ishemic Stroke

Molecules ◽  
2021 ◽  
Vol 26 (20) ◽  
pp. 6124
Author(s):  
Denis A. Borozdenko ◽  
Aiarpi A. Ezdoglian ◽  
Tatiana A. Shmigol ◽  
Darya I. Gonchar ◽  
Dmitri N. Lyakhmun ◽  
...  
Keyword(s):  
Neurological Deficit ◽  
Cognitive Functions ◽  
In Silico ◽  
Focal Cerebral Ischemia ◽  
Anxiety Reduction ◽  
Glutamate Excitotoxicity ◽  
Ischemic Brain ◽  
First Time

We performed an in silico, in vitro, and in vivo assessment of a potassium 2-[2-(2-oxo-4-phenylpyrrolidin-1-yl) acetamido]ethanesulfonate (compound 1) as a potential prodrug for cognitive function improvement in ischemic brain injury. Using in silico methods, we predicted the pharmacological efficacy and possible safety in rat models. In addition, in silico data showed neuroprotective features of compound 1, which were further supported by in vitro experiments in a glutamate excitotoxicity-induced model in newborn rat cortical neuron cultures. Next, we checked whether compound 1 is capable of crossing the blood–brain barrier in intact and ischemic animals. Compound 1 improved animal behavior both in intact and ischemic rats and, even though the concentration in intact brains was low, we still observed a significant anxiety reduction and activity escalation. We used molecular docking and molecular dynamics to support our hypothesis that compound 1 could affect the AMPA receptor function. In a rat model of acute focal cerebral ischemia, we studied the effects of compound 1 on the behavior and neurological deficit. An in vivo experiment demonstrated that compound 1 significantly reduced the neurological deficit and improved neurological symptom regression, exploratory behavior, and anxiety. Thus, here, for the first time, we show that compound 1 can be considered as an agent for restoring cognitive functions.

Natural Products as Potential Agents Against SARS-CoV and SARS-CoV-2

2021 ◽  
Vol 28 ◽  
Author(s):  
Joanda Paolla Raimundo e Silva ◽  
Chonny Alexander Herrera Acevedo ◽  
Thalisson Amorim de Souza ◽  
Renata Priscila Barros de Menezes ◽  
Zoe L. Sessions ◽  
...  
Keyword(s):  
Natural Products ◽  
In Silico ◽  
Principal Component ◽  
In Vivo Studies ◽  
In Vitro Assays ◽  
Future Research ◽  
Natural Substances ◽  
Effective Drugs

Background: Natural products are useful agents for the discovery of new lead-compounds and effective drugs to combat coronaviruses (CoV). Objective: The present work provides an overview of natural substances, plant extracts, and essential oils as potential antiSARS-CoV agents. In addition, this work evaluates their drug-like properties which are essential in the selection of compounds in order to accelerate the drug development process. Methods: The search was carried out using PubMed, ScienceDirect and SciFinder. Articles addressing plant-based natural products as potential SARS-CoV or SARS-CoV-2 agents within the last seventeen years were analyzed and selected. The descriptors for Chemometrics analyzes were obtained in alvaDesc and the principal component analyzes (PCA) were carried out in SIMCA version 13.0. Results: Based on in vitro assays and computational analyzes, this review covers twenty nine medicinal plant species and more than 300 isolated substances as potential anti-coronavirus agents. Among them, flavonoids and terpenes were the most promising compound classes. In silico analyses of drug-like properties corroborate these findings and indicate promising candidates for in vitro and in vivo studies to validate their activity. Conclusion: This paper highlights the role of ethnopharmacology in drug discovery and simulates the use of integrative (in silico/ in vitro) and chemocentric approaches to strengthen current studies and guide future research in the field of antivirals agents.

scholarly journals Heterologous Expression of the Pathogen-Specific LIC11711 Gene in the Saprophyte L. biflexa Increases Bacterial Binding to Laminin and Plasminogen

Pathogens ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 599
Author(s):  
Leandro Toshio Kochi ◽  
Luis Guilherme Virgílio Fernandes ◽  
Ana Lucia Tabet Oller Nascimento
Keyword(s):  
Molecular Biology ◽  
Heterologous Expression ◽  
Pathogenic Bacteria ◽  
Bacterial Pathogenesis ◽  
Bacterial Virulence ◽  
Febrile Disease ◽  
Bacterial Binding ◽  
Etiological Agents ◽  
First Time

Leptospirosis is a febrile disease and the etiological agents are pathogenic bacteria of the genus Leptospira. The leptospiral virulence mechanisms are not fully understood and the application of genetic tools is still limited, despite advances in molecular biology techniques. The leptospiral recombinant protein LIC11711 has shown interaction with several host components, indicating a potential function in virulence. This study describes a system for heterologous expression of the L. interrogans gene lic11711 using the saprophyte L. biflexa serovar Patoc as a surrogate, aiming to investigate its possible activity in bacterial virulence. Heterologous expression of LIC11711 was performed using the pMaOri vector under regulation of the lipL32 promoter. The protein was found mainly on the leptospiral outer surface, confirming its location. The lipL32 promoter enhanced the expression of LIC11711 in L. biflexa compared to the pathogenic strain, indicating that this strategy may be used to overexpress low-copy proteins. The presence of LIC11711 enhanced the capacity of L. biflexa to adhere to laminin (Lam) and plasminogen (Plg)/plasmin (Pla) in vitro, suggesting the involvement of this protein in bacterial pathogenesis. We show for the first time that the expression of LIC11711 protein of L. interrogans confers a virulence-associated phenotype on L. biflexa, pointing out possible mechanisms used by pathogenic leptospires.

scholarly journals Removal of a subset of non-essential genes fully attenuates a highly virulentMycoplasmastrain

2019 ◽  
Author(s):  
Joerg Jores ◽  
Li Ma ◽  
Paul Ssajjakambwe ◽  
Elise Schieck ◽  
Anne Liljander ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Mutant Strain ◽  
Parental Strain ◽  
Essential Genes ◽  
Small Scale ◽  
Virulence Traits ◽  
Mycoplasma Mycoides ◽  
First Time

ABSTRACTMycoplasmas are the smallest free-living organisms and cause a number of economically important diseases affecting humans, animals, insects and plants. Here, we demonstrate that highly virulentMycoplasma mycoidessubspeciescapri(Mmc) can be fully attenuatedviatargeted deletion of non-essential genes encoding, among others, potential virulence traits. Five genomic regions, representing approximately ten percent of the originalMmcgenome, were successively deleted usingSaccharomyces cerevisiaeas an engineering platform. Specifically, a total of 68 genes out of the 432 genes verified to be individually nonessential in the JCVI-Syn3.0 minimal cell, were excised from the genome.In vitrocharacterization showed that this mutant was similar to its parental strain in terms of its doubling time, even though ten percent of the genome content were removed. A novelin vivochallenge model in goats revealed that the wild-type parental strain caused marked necrotizing inflammation at the site of inoculation, septicemia and all animals reaching endpoint criteria within seven days after experimental infection. This is in contrast to the mutant strain, which caused no clinical signs nor pathomorphological lesions. These results highlight, for the first time, the rational design, construction and complete attenuation of aMycoplasmastrain via synthetic genomics tools. Trait addition using the yeast-based genome engineering platform and subsequentin vitroorin vivotrials employing theMycoplasmachassis will allow us to dissect the role of individual candidateMycoplasmavirulence factors and lead the way for the development of an attenuated designer vaccine.IMPORTANCEMembers of theMycoplasma mycoidescluster cause important animal plaques in Africa and Asia, which impact animal welfare, provision of food and the life of thousands of small-scale farmers. We applied synthetic biology tools toMycoplasma mycoidesin order to design and create a fully attenuatedMycoplasmastrain that was subsequently confirmedin vivousing a novel caprine infection model. This is the first time that aMycoplasmamutant developed by applying synthetic biology tools has been testedin vivoto pin point candidate virulence traits. The mutant strain is similar to “apathogenicE. coliK12” strains that boosted the research on host-pathogen interactions for the genusEscherichiaand other bacterial genera.

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