• Microbiology and Biotechnology Letters
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• v.49 no.4
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• pp.478-484
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• 2021

Cellular resources including transcriptional and translational machineries in bacteria are limited, yet microorganisms depend upon them to maximize cellular fitness. Bacteria have evolved strategies for using resources economically. Regulatory networks for the gene expression system enable the cell to synthesize proteins only when necessary. At the same time, regulatory interactions enable the cell to limit losses when the system cannot make a cellular profit due to fake substrates. Also, the architecture of the gene expression flow can be advantageous for clustering functionally related products, thus resulting in effective interactions among molecules. In addition, cellular systems modulate the investment of proteomes, depending upon nutrient qualities, and fast-growing cells spend more resources on the synthesis of ribosomes, whereas nonribosomal proteins are synthesized in nutrient-limited conditions. A deeper understanding of cellular mechanisms underlying the optimal allocation of cellular resources can be used for biotechnological purposes, such as designing complex genetic circuits and constructing microbial cell factories.

• Food Science and Biotechnology
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• v.15 no.5
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• pp.664-671
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• 2006

Modeling the growth kinetics of lactic acid bacteria (LAB), one of the most valuable microbial groups in the food industry, has been actively pursued in order to understand, control, and optimize the relevant fermentation processes. Most modeling approaches have focused on the development of single population models. Primary single population models provide fundamental kinetic information on the proliferation of a primary LAB species, the effects of biological factors on cell inhibition, and the metabolic reactions associated with cell growth. Secondary single population models can evaluate the dependence of primary model parameters, such as the maximum specific growth rate of LAB, on the initial external environmental conditions. This review elucidates some of the most important single population models that are conveniently applicable to the LAB fermentation analyses. Also, a well-defined mixed population model is presented as a valuable tool for assessing potential microbial interactions during fermentation with multiple LAB species.

• Communications for Statistical Applications and Methods
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• v.22 no.6
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• pp.575-587
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• 2015

The development in data collection techniques results in high dimensional data sets, where discrimination is an important and commonly encountered problem that are crucial to resolve when high dimensional data is heterogeneous (non-common variance covariance structure for classes). An example of this is to classify microbial habitat preferences based on codon/bi-codon usage. Habitat preference is important to study for evolutionary genetic relationships and may help industry produce specific enzymes. Most classification procedures assume homogeneity (common variance covariance structure for all classes), which is not guaranteed in most high dimensional data sets. We have introduced regularized elimination in partial least square coupled with QDA (rePLS-QDA) for the parsimonious variable selection and classification of high dimensional heterogeneous data sets based on recently introduced regularized elimination for variable selection in partial least square (rePLS) and heterogeneous classification procedure quadratic discriminant analysis (QDA). A comparison of proposed and existing methods is conducted over the simulated data set; in addition, the proposed procedure is implemented to classify microbial habitat preferences by their codon/bi-codon usage. Five bacterial habitats (Aquatic, Host Associated, Multiple, Specialized and Terrestrial) are modeled. The classification accuracy of each habitat is satisfactory and ranges from 89.1% to 100% on test data. Interesting codon/bi-codons usage, their mutual interactions influential for respective habitat preference are identified. The proposed method also produced results that concurred with known biological characteristics that will help researchers better understand divergence of species.

• BMB Reports
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• v.44 no.1
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• pp.1-10
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• 2011

Inter-cellular communication via diffusible small molecules is a defining character not only of multicellular forms of life but also of single-celled organisms. A large number of bacterial genes are regulated by the change of chemical milieu mediated by the local population density of its own species or others. The cell density-dependent "autoinducer" molecules regulate the expression of those genes involved in genetic competence, biofilm formation and persistence, virulence, sporulation, bioluminescence, antibiotic production, and many others. Recent innovations in recombinant DNA technology and micro-/nano-fluidics systems render the genetic circuitry responsible for cell-to-cell communication feasible to and malleable via synthetic biological approaches. Here we review the current understanding of the molecular biology of bacterial intercellular communication and the novel experimental protocols and platforms used to investigate this phenomenon. A particular emphasis is given to the genetic regulatory circuits that provide the standard building blocks which constitute the syntax of the biochemical communication network. Thus, this review gives focus to the engineering principles necessary for rewiring bacterial chemo-communication for various applications, ranging from population-level gene expression control to the study of host-pathogen interactions.

• Journal of Korean Biological Nursing Science
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• v.21 no.2
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• pp.133-140
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• 2019

Purpose: The purpose of this study was to check the degree of residual microbial contamination after disinfection of reusable suction containers, used in an intensive care unit (ICU) and present basic data for efficient use through cost analysis in comparison to disposable suction containers. Methods: This study was conducted on 32 reusable suction containers used in an ICU on a selected specific day. After disinfection and washing, specimens were collected from the used containers and cultured to check for microbial contamination. Additionally, a comparative narrative study analyzes the cost of using reusable suction containers and disposable suction containers. Data were analyzed with the SPSS WIN 20.0 program using real numbers and percentage ${\chi}^2$-test. Results: As a result of the study, microorganisms were found in all samples where in 30 were gram-positive (62.5%) while 13 were gram-negative (27.1%). Based on level of contamination, microorganisms were less than 10CFU/ml in 18 samples (56.3%); 11-99CFU/ml in six samples (18.8%); and more than 100CFU/ml in eight samples (25%). Cost per day for a reusable suction container was $10,655+{\alpha}$ while cost per day for a disposable suction container was 10,666 won. Conclusion: This study found that reusable suction containers, even after disinfection, accounted for factors of potential infection as well as microbial contamination. So, disposable suction containers are superior in cost-effectiveness and highly efficient for use with infected patients.

• The Plant Pathology Journal
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• v.36 no.6
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• pp.579-590
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• 2020

Botrytis cinerea, which causes gray mold disease in more than 200 plant species, is an economically important pathogen that is mainly controlled by synthetic fungicides. Synergistic fungicide mixtures can help reduce fungicide residues in the environment and mitigate the development of fungicide-resistant strains. In this study, we screened microbial culture extracts on Botrytis cinerea to identify an antifungal synergist for tebuconazole. Among the 4,006 microbial extracts screened in this study, the culture extract from Schizophyllum commune displayed the most enhanced activity with a sub-lethal dosage of tebuconazole, and the active ingredient was identified as schizostatin. In combination with 5 ㎍/ml tebuconazole, schizostatin (1 ㎍/ml) showed disease control efficacy against gray mold on tomato leaf similar to that achieved with 20 ㎍/ml tebuconazole treatment alone. Interestingly, schizostatin showed demethylation inhibitor (DMI)-specific synergistic interactions in the crossed-paper strip assay using commercial fungicides. In a checkerboard assay with schizostatin and DMIs, the fractional inhibitory concentration values were 0.0938-0.375. To assess the molecular mechanisms underlying this synergism, the transcription levels of the ergosterol biosynthetic genes were observed in response to DMIs, schizostatin, and their mixtures. Treatment with DMIs increased the erg11 (the target gene of DMI fungicides) expression level 15.4-56.6-fold. However, treatment with a mixture of schizostatin and DMIs evidently reverted erg11 transcription levels to the pre-DMI treatment levels. These results show the potential of schizostatin as a natural antifungal synergist that can reduce the dose of DMIs applied in the field without compromising the disease control efficacy of the fungicides.

• Asian-Australasian Journal of Animal Sciences
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• v.12 no.1
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• pp.129-138
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• 1999

If rumen bacteria can be manipulated to utilize nutrients (i.e., ammonia and plant cell wall carbohydrates) more completely and efficiently, the need for protein supplementation can be reduced or eliminated and the digestion of fiber in forage or agricultural residue-based diets could be enhanced. However, these approaches require a complete and accurate description of the rumen community, as well as methods for the rapid and accurate detection of microbial density, diversity, phylogeny, and gene expression. Molecular ecology techniques based on small subunit (SSU) rRNA sequences, nucleic acid probes and the polymerase chain reaction (PCR) can potentially provide a complete description of the microbial ecology of the rumen of ruminant animals. The development of these molecular tools will result in greater insights into community structure and activity of gut microbial ecosystems in relation to functional interactions between different bacteria, spatial and temporal relationships between different microorganisms and between microorganisms and reed panicles. Molecular approaches based on SSU rRNA serve to evaluate the presence of specific sequences in the community and provide a link between knowledge obtained from pure cultures and the microbial populations they represent in the rumen. The successful development and application of these methods promises to provide opportunities to link distribution and identity of gastrointestinal microbes in their natural environment with their genetic potential and in situ activities. The use of approaches for assessing pupulation dynamics as well as for assessing community functionality will result in an increased understanding and a complete description of the gastrointestinal communities of production animals fed under different dietary regimes, and lead to new strategies for improving animal growth.

• Journal of Soil and Groundwater Environment
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• v.25 no.2
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• pp.16-23
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• 2020

In this work, ²²²Rn activity, major dissolved ions, and microbial community in ground- and surface waters were investigated to characterize groundwater inflow to the stream located in an urban area, Daejeon, Korea. The measured ²²²Rn activities in groundwater and stream water ranged from 136 to 231 Bq L^-1 and 0.3 to 48.8 Bq L^-1, respectively. The spatial distributions of ²²²Rn activity in the stream strongly suggested groundwater inflow to the stream. The change of geochemical composition of the stream water indicated the effect of groundwater discharge became more pronounced as the stream flows downstream. Furthermore, microbial community composition of the stream water had good similarity to that of groundwater, which is another evidence of groundwater discharge. Although groundwater inflow could not be estimated quantitatively in this study, the results can provide useful information to understand interactions between groundwater and surface water, and determine hydrological processes governing groundwater recharge and hydrogeological cycles of dissolved substances such as nutrients and trace metals.

• Asian-Australasian Journal of Animal Sciences
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• v.27 no.9
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• pp.1285-1292
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• 2014

An in vitro experiment was conducted to evaluate the effects of Aspergillus oryzae culture (AOC) and 2-hydroxy-4-(methylthio)-butanoic acid (HMB) on rumen fermentation and microbial populations between different roughage sources. Two roughage sources (Chinese wild rye [CWR] vs corn silage [CS]) were assigned in a $2{\times}3$ factorial arrangement with HMB (0 or 15 mg) and AOC (0, 3, or 6 mg). Gas production (GP), microbial protein (MCP) and total volatile fatty acid (VFA) were increased in response to addition of HMB and AOC (p<0.01) for the two roughages. The HMB and AOC showed inconsistent effects on ammonia-N with different substrates. For CWR, neither HMB nor AOC had significant effect on molar proportion of individual VFA. For CS, acetate was increased (p = 0.02) and butyrate was decreased (p<0.01) by adding HMB and AOC. Increase of propionate was only occurred with AOC (p<0.01). Populations of protozoa ($p{\leq}0.03$) and fungi ($p{\leq}0.02$) of CWR were differently influenced by HMB and AOC. Percentages of F. succinogenes, R. albus, and R. flavefaciens (p<0.01) increased when AOC was added to CWR. For CS, HMB decreased the protozoa population (p = 0.01) and increased the populations of F. succinogenes and R. albus ($p{\leq}0.03$). Populations of fungi, F. succinogenes (p = 0.02) and R. flavefacien (p = 0.03) were increased by adding AOC. The HMB${\times}$AOC interactions were noted in MCP, fungi and R. flavefacien for CWR and GP, ammonia-N, MCP, total VFA, propionate, acetate/propionate (A/P) and R. albus for CS. It is inferred that addition of HMB and AOC could influence rumen fermentation of forages by increasing the number of rumen microbes.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.7
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• pp.992-997
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• 2002

Two in vivo experiments were conducted to evaluate the effect of novel urease inhibitor hydroquinone (HQ) on ammonia release rate from urea hydrolysis, nitrogen balance, nutrient digestibility and efficiency of microbial protein synthesis. In Exp. 1, twelve crossbred cannulated lambs were randomly assigned within initial body weight block to one of four HQ treatments, which included 0 (control), 30, 60 or 80 mg HQ/kg DM intake. Ammonia concentration and pH of ruminal fluid were immediately measured at 0, 2, 4, 6 and 8 h after feeding. Increasing the dose of HQ tended (p<0.15) to linearly decrease NH3 formation. The ammonia peak concentration (2 h post-feeding) in animals receiving HQ was approximately one-half of that in animals not receiving HQ (p<0.01), and a relatively sustained ammonia release could be obtained at the dose of 30 or 60 mg HQ/kg DM. In Exp. 2, sixteen intact crossbred lambs (weight $40{\pm}0.8kg$) were used in a $2{\times}2$ factorial design experiment. The four rations consisting of soybean meal-based (SBM) or urea-based (Urea) nitrogen source with or without HQ (S1, S0, U1 and U0) were fed in digestion and N balance trials. Apparent digestibility of major nutrients except that of ADF was not affected by either nitrogen source or addition of HQ. Regardless of nitrogen source, supplementation of HQ significantly improved ADF digestibility (p<0.05). The various ration had no effects on N metabolism in the presence of HQ. There was significant difference between total purine derivatives (PD), estimated efficiency of microbial N synthesis (p<0.05) and urea-N excretion (p<0.01) in the urine for the SBM ration and for the Urea ration. However, HQ had little influence on efficiency of microbial N synthesis as proportion of daily intake of total tract digestible OM (p>0.05). No interactions between main nitrogen source and HQ were measured throughout the trial. Results of this study suggest that addition of HQ to ration may improve ADF digestion with having no negative effect on N metabolism and microbial protein production.