Effects of a consortia probiotic inoculant on soil microorganisms and impacts on autoinducers employed in quorum sensing

"December 2013.""A Thesis presented to the Faculty of the Graduate School at the University of Missouri--Columbia In Partial Fulfillment of the Requirements for the Degree Master of Science."Thesis advisor: Dr. Robert J. Kremer.Disease control in plant agriculture is largely achieved through application of various antimicrobials. Manipulation of indigenous soil microbial communities received attention as it promises improved pathogen control and enhanced plant outputs. Another promising tool in disease control is disrupting quorum sensing (QS)-controlled pathogenicity expression. In this work, efficacies of a consortia probiotic soil amendment (CP) were evaluated: (1) impact on soil microbial diversity; (2) capacity to degrade autoinducers involved in QS in soil-borne pathogens. The first efficacy was assayed in Central Missouri during growing season of 2012. Soils under two management situations were studied: cultivated soil and restored grassland. Samples from cultivated soils were also studied under environmentally controlled conditions. Analysis of soil microbial community diversity was carried out with 16s rDNA PCR DGGE. To evaluate the second efficacy, two autoinducers were incubated in a controlled, triplicated study. Pre- and post-incubation autoinducer concentrations were verified using GC-MS. Under field conditions, CP was found to produce no impact (beneficial or adverse) on soil microbial community diversity. Under controlled conditions, depending on particular treatment, CP had no impact on soil microbial diversity or enhanced it. The CP studied was capable of degrading one of two autoinducers, however the capacity varied and it apparently depended on CP batch or storage conditions. Results suggest that CP studied has benign profile against soil microbial communities and under certain circumstances may enhance community diversity. Furthermore, by disrupting QS autoinducers, CP revealed the potential to control pathogenicity. Future studies are required to fully evaluate CP impacts on agricultural produce.Includes bibliographical references (pages 172-206)

Effects of altered TatC proteins on protein secretion efficiency via the twin-arginine translocation pathway of Bacillus subtilis

Protein translocation via the Tat machinery in thylakoids and bacteria occurs through a cooperation between the TatA, TatB and TatC subunits, of which the TatC protein forms the initial Tat substrate-binding site. The Bacillus subtilis Tat machinery lacks TatB and comprises two separate TatAC complexes with distinct substrate specificities: PhoD is secreted by the TatAdCd complex, whereas YwbN is secreted by the TatAyCy complex. To study the role of the Gram-positive TatC proteins in Tat-dependent protein secretion efficiency, we applied several genetic engineering approaches to modify and analyse the B. subtilis TatCd and TatCy proteins. Cytoplasmic and transmembrane domain exchange between TatCd and TatCy resulted in stable chimeric proteins that were unable to secrete both known substrates of the B. subtilis Tat system. Site-directed mutagenesis of conserved residues in the N-terminal part of both TatC proteins revealed significant differences in the degree of importance of these residues between TatCd, TatCy and Escherichia coli TatC. In addition, two small C-terminal deletions in TatCy completely abolished YwbN translocation, indicating that this terminus is essential for Tat translocation activity. Important differences from previous observations for E. coli TatC and implications for substrate binding and translocation are discussed.

Digital standardization of lean manufacturing tools according to Industry 4.0 concept

Standardization is a key element in the effective use of lean manufacturing methodologies and tools for achieving process sustainability. Their combination is conducive to eliminating waste and improving the efficiency of production processes and guarantees the company that employees use the most efficient tools and do not waste time on unnecessary activities. These activities can be further improved by using digital solutions, in accordance with the concept of Industry 4.0. Therefore, the authors have developed the e-Lean system, whose task is to digitize selected lean manufacturing tools. The subject of this work is analysis of the functionality and effectiveness of the essential part of the e-Lean system in the form of specialized TPM (Total Productive Maintenance) software as an application. During implementation in a construction production company, the TPM application was tested by lean manufacturing and maintenance specialists. The research consisted of assessing the functionality and efficiency of processes in relation to conventional TPM solutions. Additional functionalities of the e-Lean system have been confirmed, such as systemic approval of machinery inspection, which requires passing all necessary steps at individual inspection points, direct access for supervisors to the results of inspection activities and their status, direct and easy access to photographic documentation of machines added during inspection both in optimization of working time and its course (e.g., the optimal number of steps taken by the employee during the inspection), as well as an efficient system of motivating employees (collecting points). The improvement in the effectiveness of processes was determined by measuring the control times for three control points (polymerization furnace, packing area, and defibering machines). The average control time was reduced from 16,200 to 13,923 s. Thus, thanks to the use of the application, it was found that the efficiency of using the TPM tool was increased by approx. 15% compared to previously used non-digital solutions.The authors are grateful to FCT (Fundação para a Ciência e Tecnologia, Portugal) who partially financially supported this work through the RD Units Project Scope UIDP/04077/2020 and UIDB/04077/2020

Water properties and bottom water patterns in hadal trench environments

We examine baseline water properties and bottom water patterns in hadal trench environments across the Southern Ocean, Indian Ocean, and western Pacific. Significant differences are identified in the South Fiji Basin and surrounding the Philippine Sea, primarily due to the movement of cold Lower Circumpolar Deep Water along topographic features, highlighting the importance of a trench's geospatial position. We present the first hydrographic profiles in the Java Trench, warranting further research. Salinity increases with increasing depth for profiles over 10 000 dbar, with potential causes including instrumentation error, internal mixing, and saline pore water expulsion. These hadopelagic variations are crucial for assessing climate change impacts, especially regarding Antarctic Bottom Water. The study underscores the importance of incorporating these adiabatic conditions to gain insights into ecological biodiversity, alongside the indispensable baseline conditions presented, which are crucial for future oceanographic research across multiple disciplines.</p

A Greedy Iterative Layered Framework for Training Feed Forward Neural Networks

info:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FCCI-INF%2F29168%2F2017/PT" Custode, L. L., Tecce, C. L., Bakurov, I., Castelli, M., Cioppa, A. D., & Vanneschi, L. (2020). A Greedy Iterative Layered Framework for Training Feed Forward Neural Networks. In P. A. Castillo, J. L. Jiménez Laredo, & F. Fernández de Vega (Eds.), Applications of Evolutionary Computation - 23rd European Conference, EvoApplications 2020, Held as Part of EvoStar 2020, Proceedings (pp. 513-529). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 12104 LNCS). Springer. https://doi.org/10.1007/978-3-030-43722-0_33In recent years neuroevolution has become a dynamic and rapidly growing research field. Interest in this discipline is motivated by the need to create ad-hoc networks, the topology and parameters of which are optimized, according to the particular problem at hand. Although neuroevolution-based techniques can contribute fundamentally to improving the performance of artificial neural networks (ANNs), they present a drawback, related to the massive amount of computational resources needed. This paper proposes a novel population-based framework, aimed at finding the optimal set of synaptic weights for ANNs. The proposed method partitions the weights of a given network and, using an optimization heuristic, trains one layer at each step while “freezing” the remaining weights. In the experimental study, particle swarm optimization (PSO) was used as the underlying optimizer within the framework and its performance was compared against the standard training (i.e., training that considers the whole set of weights) of the network with PSO and the backward propagation of the errors (backpropagation). Results show that the subsequent training of sub-spaces reduces training time, achieves better generalizability, and leads to the exhibition of smaller variance in the architectural aspects of the network.authorsversionpublishe

Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression

Gaining new knowledge through fungal monoculture responses to lignocellulose is a widely used approach that can lead to better cocktails for lignocellulose saccharification (the enzymatic release of sugars which are subsequently used to make biofuels). However, responses in lignocellulose mixed cultures are rarely studied in the same detail even though in nature fungi often degrade lignocellulose as mixed communities. Using a dual RNA-seq approach, we describe the first study of the transcriptional responses of wild-type strains of Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum in two and three mixed species shake-flask cultures with wheat straw. Based on quantification of species-specific rRNA, a set of conditions was identified where mixed cultures could be sampled so as to obtain sufficient RNA-seq reads for analysis from each species. The number of differentially-expressed genes varied from a couple of thousand to fewer than one hundred. The proportion of carbohydrate active enzyme (CAZy) encoding transcripts was lower in the majority of the mixed cultures compared to the respective straw monocultures. A small subset of P. chrysogenum CAZy genes showed five to ten-fold significantly increased transcript abundance in a two-species mixed culture with T. reesei. However, a substantial number of T. reesei CAZy transcripts showed reduced abundance in mixed cultures. The highly induced genes in mixed cultures indicated that fungal antagonism was a major part of the mixed cultures. In line with this, secondary metabolite producing gene clusters showed increased transcript abundance in mixed cultures and also mixed cultures with T. reesei led to a decrease in the mycelial biomass of A. niger. Significantly higher monomeric sugar release from straw was only measured using a minority of the mixed culture filtrates and there was no overall improvement. This study demonstrates fungal interaction with changes in transcripts, enzyme activities and biomass in the mixed cultures and whilst there were minor beneficial effects for CAZy transcripts and activities, the competitive interaction between T. reesei and the other fungi was the most prominent feature of this study