Potency of endophytic fungi from Nauclea orientalis L. as antioxidant producer

Nauclea orientalis L. is widely distributed in Indonesia. Secondary metabolites such as flavonoids, polyphenols, and saponins are abundant in the bark of N. orientalis L. These compounds have the potential to act as antioxidants. Endophytic fungi, through genetic transfer and coevolution, can produce the same metabolites as their host plant. As a result, understanding the potential of endophytic fungi from N. orientalis L. to produce antioxidant compounds that can be developed is critical. According to the findings of this study, twelve isolates have the potential to produce secondary metabolites with antioxidant properties. Three isolates had high antioxidant activity: DB2 was identified as Aspergillus minisclerotigenes with an IC50 of 21 g/mL containing tannins, terpenes, and flavonoids, AB3 as Colletotrichum perseae with an IC50 of 31 g/mL containing tannins and terpenoids, and AB1 as Diaporthe tulliensis with an IC50 of 48 g/mL containing tannins. The secondary metabolite group has the potential to be developed into an antioxidant agent

Carbapenem Resistance among Marine Bacteria—An Emerging Threat to the Global Health Sector

The emergence of antibiotic resistance among pathogenic microorganisms is a major issue for global public health, as it results in acute or chronic infections, debilitating diseases, and mortality. Of particular concern is the rapid and common spread of carbapenem resistance in healthcare settings. Carbapenems are a class of critical antibiotics reserved for treatment against multidrug-resistant microorganisms, and resistance to this antibiotic may result in limited treatment against infections. In addition to in clinical facilities, carbapenem resistance has also been identified in aquatic niches, including marine environments. Various carbapenem-resistant genes (CRGs) have been detected in different marine settings, with the majority of the genes incorporated in mobile genetic elements, i.e., transposons or plasmids, which may contribute to efficient genetic transfer. This review highlights the potential of the marine environment as a reservoir for carbapenem resistance and provides a general overview of CRG transmission among marine microbes.

Clarifying the Unique Features of Bacterial Sex

This chapter considers bacterial sex, the details of which turned out to be counter-intuitive, quite different from Joshua Lederberg’s conceptions that were influenced by the ways that higher organisms recombined genes. The contributions of Luca Cavalli, William Hayes, and later, Elie Wollman and Francoise Jacob served to clarify the apparent anomalies, finally to reveal that bacterial sex was very, very different from the modes of genetic recombination of other organisms. The French team clarified the stages of conjugation by interrupting the mating of Hfr x F- at different time points. HGT, can occur by three different processes: transformation, conjugation, and transduction. In every case, HGT is fragmentary and unidirectional, much different than genetic transfer in sexual reproduction in higher organisms, which involves the entire genome in a mutual, two-way recombination of genes.

Strange Genetics

This chapter relates how, in the 1950s, Esther and Joshua Lederberg and their colleagues uncovered a whole new kind of genetic transfer involving plasmids and viruses. In plants and animals, genetic recombination is integrated within the processes of sexual reproduction. Imagine if you could trade genes with strangers at will! That’s what bacteria can do. Esther Lederberg’s discoveries of the F-plasmid and the λ‎ bacteriophage were happy accidents that occurred while she working to complete her dissertation research. Serendipity happens to those who are very attentive, broadly experienced, and open to surprises. Esther Lederberg discovered a transferable factor, the F-factor, that could transform recipients into donors. Then she discovered a lysogenic virus, hiding harmlessly inside the chromosome of its bacterial host. These two surprising discoveries showed that bacteria could transfer genes and pieces of chromosomes horizontally, as opposed to the classical inheritance of plants and animals which pass on genetic traits vertically, down through generations.

Multifidelity Genetic Transfer: An Efficient Framework for Production Optimization

Summary Production optimization led by computing intelligence can greatly improve oilfield economic effectiveness. However, it is confronted with huge computational challenge because of the expensive black-box objective function and the high-dimensional design variables. Many low-fidelity methods based on simplified physical models or data-driven models have been proposed to reduce evaluation costs. These methods can approximate the global fitness landscape to a certain extent, but it is difficult to ensure accuracy and correlation in local areas. Multifidelity methods have been proposed to balance the advantages of the two, but most of the current methods rely on complex computational models. Through a simple but efficient shortcut, our work aims to establish a novel production-optimization framework using genetic transfer learning to accelerate convergence and improve the quality of optimal solution using results from different fidelities. Net present value (NPV) is a widely used standard to comprehensively evaluate the economic value of a strategy in production optimization. On the basis of NPV, we first established a multifidelity optimization model that can synthesize the reference information from high-fidelity tasks and the approximate results from low-fidelity tasks. Then, we introduce the concept of relative fidelity as an indicator for quantifying the dynamic reliability of low-fidelity methods, and further propose a two-mode multifidelity genetic transfer learning framework that balances computing resources for tasks with different fidelity levels. The multitasking mode takes the elite solution as the transfer medium and forms a closed-loop feedback system through the information exchange between low- and high-fidelity tasks in parallel. Sequential transfer mode, a one-way algorithm, transfers the elite solutions archived in the previous mode as the population to high-fidelity domain for further optimization. This framework is suitable for population-based optimization algorithms with variable search direction and step size. The core work of this paper is to realize the framework by means of differential evolution (DE), for which we propose the multifidelity transfer differential evolution (MTDE). Corresponding to multitasking and sequential transfer in the framework, MTDE includes two modes, transfer based on base vector (b-transfer) and transfer based on population (p-transfer). The b-transfer mode incorporates the unique advantages of DE into fidelity switching, whereas the p-transfer mode adaptively conducts population for further high-fidelity local search. Finally, the production-optimization performance of MTDE is validated with the egg model and two real field cases, in which the black-oil and streamline models are used to obtain high- and low-fidelity results, respectively. We also compared the convergence curves and optimization results with the single-fidelity method and the greedy multifidelity method. The results show that the proposed algorithm has a faster convergence rate and a higher-qualitywell-control strategy. The adaptive capacity of p-transfer is also demonstrated in three distinct cases. At the end of the paper, we discuss the generalization potential of the proposed framework.

Longitudinal study of vinyl chloride degrading Dehalococcoides mccartyi-containing cultures to promote horizontal gene transfer

ABSTRACTVinyl chloride (VC) is a human carcinogen that accumulates in soil and groundwater due to incomplete dechlorination of chlorinated ethenes. Some strains of obligate organohalide respiring Dehalococcoides mccartyi can synthesize the VC reductase that catalyzes the dechlorination of VC to ethene. The gene encoding the VC reductase, vcrA, is found on a mobile genetic element called the vcrA-Genomic Island (GI) that may participate in horizontal gene transfer. We designed an experiment to try to induce horizontal gene transfer of the vcrA-GI by mixing two enrichment cultures: one containing the donor D. mccartyi strain with the vcrA-GI that could not fix nitrogen and the second containing the recipient strain devoid of the vcrA-GI that could fix nitrogen. Therefore, mixing the two cultures in medium without ammonium while providing VC as the sole electron acceptor was hypothesized to select for a mutant strain of D. mccartyi that could both fix nitrogen and respire VC. However, after over 4 years of incubation, no evidence for horizontal gene transfer of the vcrA-GI was found. Rather, we observed VC-dechlorinating activity attributed to the TCE reductase, TceA, in the recipient strain. We also observed that D. mccartyi can grow by scavenging low concentrations of fixed nitrogen sources. During this experiment we identified two additional D. mccartyi strains in the KB-1 TCE-enriched culture that could fix nitrogen. The presence of multiple strains of D. mccartyi with distinct phenotypes may enhance bioaugmentation success, but here it may have undermined attempts to force horizontal gene transfer of the vcrA-GI.IMPORTANCEDehalococcoides mccartyi are a powerful bioremediation tool for the degradation of chlorinated solvent contamination in soil and groundwater. Only a few D. mccartyi strains have the ability to dechlorinate toxic chlorinated compounds like vinyl chloride. Interestingly, the genetic ability to dechlorinate vinyl chloride is theorized to be shared among D. mccartyi strains. In this study we attempted to promote the genetic transfer of vinyl chloride degrading ability from one D. mccartyi strain to another. Although we did not observe this exchange, our findings suggest there may be restrictions of genetic transfer between specific clades or sub-groups of D. mccartyi strains. Developing our understanding of genetic transfer among D. mccartyi strains could allow for enhanced degradation of chlorinated solvent contamination in situ.

Development of Biofilms for Antimicrobial Resistance

Biofilms are a unit referred to as assemblage of microbial cells growing as surface-attached microbial communities within the natural surroundings. Their genetic and physiological aspects are widely studied. Biofilm development involves the assembly of extracellular compound substances that forms the most bailiwick network. Quorum sensing is one more crucial development specifically connected with biofilm formation in several microorganism species. In ecological purpose, the biofilm offers protection against unfavorable conditions and provides a platform for the genetic transfer. A biofilm-forming bacterium area unit is medically necessary, as they are resistant to several antibiotics and might spread resistant genes. This chapter provides the summary of microorganism biofilm formation and its significance in ecology.

In vitro conjugation kinetics of ESBL-producing Escherichia coli donors and various Enterobacteriaceae recipients

Background: Extended spectrum beta-lactamase (ESBL)-producing enterobacteria pose a major hazard to public health. Due to the possibility of genetic transfer, ESBL genes might spread to pathogenic enterobacterial strains. Thus, information on possible genetic transfer between enterobacteria is of high interest. It was therefore the aim of this in vitro study to screen the capacity of a wide range of Enterobacteriaceae for time dependent differences in conjugation with five ESBL-producing Escherichia (E.) coli strains. Results: Conjugation frequencies for five potential E. coli donor strains, producing the enzymes CTX-M-1, CTX-M-15, SHV-12, TEM-1, TEM-52 and CMY-2, and six potential recipient strains (E. coli, Serratia marcescens subsp. marcescens, Enterobacter cloacae, Salmonella Typhimurium and Proteus mirabilis) were obtained. Hence, different combinations of donor and recipient strains were co-incubated for between 0 and 22 hours and spread on selective agar. Conjugation frequencies were calculated as transconjugants per donor. Some of the donor and recipient strain combinations did not show plasmid transfer within 22 hours. Hence, the recipient Proteus mirabilis did not accept plasmids from any of the given donors and E. coli ESBL10716 was not able to transfer its plasmid to any recipient. Enterobacter cloacae only accepted the plasmids from the donors E. coli ESBL10708 and E. coli ESBL10716 while E. coli ESBL10708 did not transfer its plasmid to Serratia marcescens subsp. marcescens. E. coli IMT11716 on the other hand did not perform conjugation with the donor E. coli ESBL10689. The remaining mating pairs differed in conjugation frequency, ranging from log -5 to -8.5 transconjugants/donor. The earliest conjugation events were detected after 4 hours. However, some mating pairs turned positive only after 22 hours co-incubation.Conclusion: The results of this study suggest that conjugation is a frequent event in the spread of ESBL genes among commensal and pathogen bacteria. This should be considered when addressing antibiotic resistance issues.

Energy Decay Network

This paper and accompanying Python/C++ Framework is the product of the Authors perceived problems with narrow (Discrimination based) AI. (Artificial Intelligence) The Framework attempts to develop a genetic transfer of experience through potential structural expressions using a common regulation/exchange value (‘energy’) to create a model whereby neural architecture and all unit processes are co-dependently developed . These expressions are born from fractal definition, stochastically tuned and managed by genetic experience; successful routes are maintained through global rules: (Stability of signal propagation/function over cross functional (external state, internal immediate state, and genetic bias towards selection of previous expressions)).These principles are aimed towards creating a diverse and robust network, hopefully reducing the need for transfer learning and computationally expensive translations as demand on compute increases.