A novel repeat sequence-based PCR (rep-PCR) using specific repeat sequences of Mycobacterium intracellulare as a DNA fingerprinting

Repetitive sequence-based PCR (rep-PCR) is a potential epidemiological technique that can provide high-throughput genotype fingerprints of heterogeneous Mycobacterium strains rapidly. Previously published rep-PCR primers, which are based on nucleotide sequences of Gram-negative bacteria may have low specificity for mycobacteria. Moreover, it was difficult to ensure the continuity of the study after the commercial rep-PCR kit was discontinued. Here, we designed a novel rep-PCR for Mycobacterium intracellulare, a major cause of nontuberculous mycobacterial pulmonary disease with frequent recurrence. We screened the 7,645 repeat sequences for 200 fragments from the genome of M. intracellulare ATCC 13950 in silico, finally generating five primers with more than 90% identity for a total of 226 loci in the genome. The five primers could make different band patterns depending on the genome of three different M. intracellulare strains using an in silico test. The novel rep-PCR with the five primers was conducted using 34 bacterial samples of 7 species containing 25 M. intracellulare clinical isolates, compared with previous published rep-PCRs. This shows distinguished patterns depending on species and blotting assay for 6 species implied the sequence specificity of the five primers. The Designed rep-PCR had a 95–98% of similarity value in the reproducibility test and showed 7 groups of fingerprints in M. intracellulare strains. Designed rep-PCR had a correlation value of 0.814 with VNTR, reference epidemiological method. This study provides a promising genotype fingerprinting method for tracing the recurrence of heterogeneous M. intracellulare

Spatially Varying and Scale-Dependent Relationships of Land Use Types with Stream Water Quality

Understanding the complex relationships between land use and stream water quality is critical for water pollution control and watershed management. This study aimed to investigate the relationship between land use types and water quality indicators at multiple spatial scales, namely, the watershed and riparian scales, using the ordinary least squares (OLS) and geographically weighted regression (GWR) models. GWR extended traditional regression models, such as OLS to address the spatial variations among variables. Our results indicated that the water quality indicators were significantly affected by agricultural and forested areas at both scales. We found that extensive agricultural land use had negative effects on water quality indicators, whereas, forested areas had positive effects on these indicators. The results also indicated that the watershed scale is effective for management and regulation of watershed land use, as the predictive power of the models is much greater at the watershed scale. The maps of estimated local parameters and local R2 in GWR models showcased the spatially varying relationships and indicated that the effects of land use on water quality varied over space. The results of this study reinforced the importance of watershed management in the planning, restoration, and management of stream water quality. It is also suggested that planners and managers may need to adopt different strategies, considering watershed characteristics—such as topographic features and meteorological conditions—and the source of pollutants, in managing stream water quality

Evaluating the Relationships between Riparian Land Cover Characteristics and Biological Integrity of Streams Using Random Forest Algorithms

The relationships between land cover characteristics in riparian areas and the biological integrity of rivers and streams are critical in riparian area management decision-making. This study aims to evaluate such relationships using the Trophic Diatom Index (TDI), Benthic Macroinvertebrate Index (BMI), Fish Assessment Index (FAI), and random forest regression, which can capture nonlinear and complex relationships with limited training datasets. Our results indicate that the proportions of land cover types in riparian areas, including urban, agricultural, and forested areas, have greater impacts on the biological communities in streams than those offered by land cover spatial patterns. The proportion of forests in riparian areas has the greatest influence on the biological integrity of streams. Partial dependence plots indicate that the biological integrity of streams gradually improves until the proportion of riparian forest areas reach about 60%; it rapidly decreases until riparian urban areas reach 25%, and declines significantly when the riparian agricultural area ranges from 20% to 40%. Overall, this study highlights the importance of riparian forests in the planning, restoration, and management of streams, and suggests that partial dependence plots may serve to provide insightful quantitative criteria for defining specific objectives that managers and decision-makers can use to improve stream conditions

Assessing the Resilience of Stream Ecosystems to Rainfall Impact

In Republic of Korea, pronounced seasonal precipitation variability poses substantial challenges for stream water quality management and the effective utilization of water resources. Ecologically degraded streams are particularly vulnerable to these fluctuations, which can exacerbate their already fragile condition. We assessed the resilience of reference and impaired streams in response to rainfall through water quality system performance (WQSP). The WQSP is quantified as the concentration of BOD, T-N, and T-P, which represent streams’ eutrophication and anaerobic conditions and respond quickly to disturbances. Reference and impaired streams are classified according to the biological condition and habitat environment of the streams in the Han River watershed of Republic of Korea. The resilience of the stream ecosystem was estimated using WQSP, the linear multiple regression model, and the generalized additive model for rainfall and WQSP. The WQSP reference streams have a lower sensitivity to disturbance and recover more quickly from the influence of rainfall; therefore, they have higher resilience than impaired streams to rainfall events. This study facilitates understanding changes in stream ecosystems of varying conditions in response to rainfall for ensuring long-term stability and adaptability

Numerical Simulation of Wind-Driven Circulation in a Thermally Stratified Flow

The closed water bodies, such as reservoirs and lakes, can be polluted by an inflow of pollutants in the upstream as well as a stratification caused by seasonal natural phenomena. The vertical circulation particularly plays an important role in reducing environmental pollutants. The factors of the vertical circulation are the temperature, wind, thermal diffusivity, sunlight, and so on. The wind is the most significant factor among all possible factors causing the vertical circulation. Thus, it is necessary to describe the validation and application of a three-dimensional numerical model of wind-driven circulation in a thermally stratified flow. In this study, the numerical model is conducted in three steps to calculate the velocity components from the momentum equations in x- and y-directions, the elevations from the free surface equation, and the temperature from the scalar transport equation. The present model was applied to two tests for verification of the numerical accuracy. Numerical results are compared with analytical solutions of the sloshing free surface movement in a rectangular basin and the model is applied to the circulation for the wind-driven flow in a thermal stratification. Consequently, the developed model is validated by two verifications and phenomena of the internal flow

Factors Affecting Lumber Conversion Rate of Sawmill Industry in South Korea

This study is conducted to investigate the factors affecting lumber conversion rate of sawmill industry in South Korea. Data were obtained from the survey of 38 sawmills in all geographic regions of South Korea. The variables examined in this study were region, softwood/hardwood log, domestic1 Imported/both log, the number of power-driven carriages (PDC) installed, the year when and country where PDCs was manufactured, the horse power of PDC, the number of labors required to operate each PDC, the sawing capacity of mill (mill size), and the types of major product and by-products. The lumber recovery factor (LRF) of sawmills were significantly influenced by the origin of logs, level of PDC automation, sawmill size, and size of logs (measured in diameter and length) while not by the location of the mill, types of major product and by-product, log species, and characteristics of PDC. Although these results provide useful information for understanding the technological characteristics of the Korean sawmill industry, further investigation with larger sample is necessary to reveal the more reliable characteristics of sawmill industry in South Korea

Characterization of the complete mitochondrial genome of the false trevally, Lactarius lactarius (Perciformes: Lactariidae)

The complete mitochondrion DNA sequence of Lactarius lactarius was determined by next generation sequencing (NGS) platform as the first mitogenome report in the family. The mitogenome of L. lactarius wa 16,642 bp in length that contains 13 gene-encoded proteins, 2 ribosomal RNA gene (12S and 16S), 22 tRNA gene, and a control region (D-loop). Besides COX1 gene (GTG), all the other protein-coding genes showed typical (ATG) start codon. Incomplete stop condons (TA-/T–) were identified in COX2, COX3, ND2, ND3, ND4 and Cyt B. A phylogenetic analysis with currently reported mitogenomes of its relative species, L. lactarius formed a Lactariidae clade distinct from other families. Two species, Pentaceros japonicus (AB739063) and Banjos banjos (KT345965) were among the most closely related species with 86.61% and 86.33% sequence identity, respectively