Journal of Applied Biosciences最新文献

{"title":"Sequencing, Fast and Slow: Profiling Microbiomes in Human Samples with Nanopore Sequencing","authors":"Yunseol Park, Jeesu Lee, Hyunjin Shim","doi":"10.3390/applbiosci2030028","DOIUrl":"https://doi.org/10.3390/applbiosci2030028","url":null,"abstract":"Rapid and accurate pathogen identification is crucial in effectively combating infectious diseases. However, the current diagnostic tools for bacterial infections predominantly rely on century-old culture-based methods. Furthermore, recent research highlights the significance of host–microbe interactions within the host microbiota in influencing the outcome of infection episodes. As our understanding of science and medicine advances, there is a pressing need for innovative diagnostic methods that can identify pathogens and also rapidly and accurately profile the microbiome landscape in human samples. In clinical settings, such diagnostic tools will become a powerful predictive instrument in directing the diagnosis and prognosis of infectious diseases by providing comprehensive insights into the patient’s microbiota. Here, we explore the potential of long-read sequencing in profiling the microbiome landscape from various human samples in terms of speed and accuracy. Using nanopore sequencers, we generate native DNA sequences from saliva and stool samples rapidly, from which each long-read is basecalled in real-time to provide downstream analyses such as taxonomic classification and antimicrobial resistance through the built-in software (<12 h). Subsequently, we utilize the nanopore sequence data for in-depth analysis of each microbial species in terms of host–microbe interaction types and deep learning-based classification of unidentified reads. We find that the nanopore sequence data encompass complex information regarding the microbiome composition of the host and its microbial communities, and also shed light on the unexplored human mobilome including bacteriophages. In this study, we use two different systems of long-read sequencing to give insights into human microbiome samples in the ‘slow’ and ‘fast’ modes, which raises additional inquiries regarding the precision of this novel technology and the feasibility of extracting native DNA sequences from other human microbiomes.","PeriodicalId":14998,"journal":{"name":"Journal of Applied Biosciences","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136272634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of Adolescents’ Head to Shoulder Region during Tablet Use from Sagittal and Frontal RGB Images","authors":"Ivanna Kramer, S. Bauer","doi":"10.3390/applbiosci2030027","DOIUrl":"https://doi.org/10.3390/applbiosci2030027","url":null,"abstract":"As schools go digital, the use of tablet computers is increasing. Concerns are raised that the extensive use of tablets and the associated bent-over posture may negatively affect the individual’s health. In order to analyse the possible effects of prolonged tablet use on physical health, a detailed analysis of the posture during tablet use is needed so that appropriate preventive measures can be taken to prevent degenerative changes. Therefore, the aim of this study was to measure and report the posture of 56 students while working with a tablet computer and compare it with an upright posture. Sagittal and frontal images were used for measurements of the subjects’ postures while seated, using the tablet, and in a neutral sitting position looking straight ahead. The body position during tablet use was recorded in two different user configurations: tablet flat on the table and tablet in individual freely chosen user configuration. After appropriate annotation of the data, the following parameters were evaluated in different planes. The craniovertebral angle (CVA), head tilt angle (HTA), and forward shoulder angle (FSA) are measurements that describe the extent to which the head bends forward and downward and how the shoulders are aligned in the sagittal plane. On the other hand, the head shoulder angle (HSA), lateral head tilt angle (LHTA), and trunk flexion angle (TFA) are angles measured in the frontal plane, which indicate the degree of head tilt and trunk bending to the right or left side. The measurement results clearly showed that the use of a tablet had a pronounced effect on the positions and rotations of the participants’ head, neck, and shoulders. This was evident through strong deviations observed in the angles measured between the sitting straight posture and the postures while using the tablet. For example, depending on the body posture class, the mean CVA values were 45.76° for straight sitting posture, 28.25° for holding the tablet individually posture, and 26.04° for the posture adopted while using a tablet placed flat on the table.","PeriodicalId":14998,"journal":{"name":"Journal of Applied Biosciences","volume":"33 2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76417196","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of Doxapram, a K2p Channel Blocker, and pH on Heart Rate: Larval Drosophila Model","authors":"Elizabeth R. Elliott, Alaina C. Taul, Maya O. Abul-Khoudoud, Nicole Hensley, R. Cooper","doi":"10.3390/applbiosci2030026","DOIUrl":"https://doi.org/10.3390/applbiosci2030026","url":null,"abstract":"Two-P-domain K+ (K2p) channels are responsible for maintaining the resting membrane potential. K2p channels have varied expression in healthy tissue, but they also change in cancerous or diseased states. The correlation and causation as regards the alteration of K2p channel expression are still being investigated. The compound doxapram seems to block K2p channels and depolarize cells. Using Drosophila, the increased expression of the ORK1 K2p channel in cardiac and skeletal muscle was investigated. The heart rate in larval Drosophila is very sensitive to pH, and since doxapram blocks a subset of the K2p channels that are known to be acid-sensitive, it was postulated that doxapram would affect heart rate. A pH change from 7.1 to 6.5 increased the rate, while that from 7.1 to 7.5 decreased the rate. An amount of 0.1 mM of doxapram had no effect, but 0.5 of mM depressed Drosophila heart rates within five minutes. Exposure to 5 mM of doxapram immediately decreased the rate. Lipopolysaccharides (LPSs) from Gram-negative bacteria acutely increased the rate. LPSs activate K2p channels in the skeletal muscle of larvae and are blocked by doxapram. LPSs slightly reduce depression in the rate induced by doxapram. The overexpression of K2p channels in the heart and skeletal muscle depressed the heart rate and heightened pH sensitivity. At larval neuromuscular junctions, the overexpression in skeletal muscle increases the frequency of spontaneous quantal events and produces a more negative resting membrane potential.","PeriodicalId":14998,"journal":{"name":"Journal of Applied Biosciences","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78177309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Automation of Cluster Extraction in Fundus Autofluorescence Images of Geographic Atrophy","authors":"J. Arslan, K. Benke","doi":"10.3390/applbiosci2030025","DOIUrl":"https://doi.org/10.3390/applbiosci2030025","url":null,"abstract":"The build-up of lipofuscin—an age-associated biomarker referred to as hyperfluorescence—is considered a precursor in the progression of geographic atrophy (GA). Prior studies have attempted to classify hyperfluorescent regions to explain varying rates of GA progression. In this study, digital image processing and unsupervised learning were used to (1) completely automate the extraction of hyperfluorescent regions from images, and (2) evaluate prospective patterns and groupings of hyperfluorescent areas associated with varying levels of GA progression. Patterns were determined by clustering methods, such as k-Means, and performance was evaluated using metrics such as the Silhouette Coefficient (SC), the Davies–Bouldin Index (DBI), and the Calinski–Harabasz Index (CHI). Automated extraction of hyperfluorescent regions was carried out using pseudocoloring techniques. The approach revealed three distinct types of hyperfluorescence based on color intensity changes: early-stage hyperfluorescence, intermediate-stage hyperfluorescence, and late-stage hyperfluorescence, with the early and late stages having three additional subclassifications that could explain varying levels of GA progression. The performance metrics for early-stage hyperfluorescence were SC = 0.597, DBI = 0.915, and CHI = 186.989. For late-stage hyperfluorescence, SC = 0.593, DBI = 1.013, and CHI = 217.325. No meaningful subclusters were identified for the intermediate-stage hyperfluorescence, possibly because it is a transitional phase of hyperfluorescence progression.","PeriodicalId":14998,"journal":{"name":"Journal of Applied Biosciences","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74599227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Review of Partial Hybrids between Herbaceous Medicago sativa and Woody Medicago arborea and Their Potential Role in Alfalfa Improvement","authors":"J. Irwin, E. Bingham","doi":"10.3390/applbiosci2030024","DOIUrl":"https://doi.org/10.3390/applbiosci2030024","url":null,"abstract":"Medicago sativa (2n = 4x = 32) and M. arborea (2n = 4x = 32) were thought to be reproductively isolated until hybrids (Alborea) were produced by sexual reproduction for the first time in 2003 in Wisconsin. The hybrids were asymmetric, at or near 2n = 4x = 32, and with a predominance of the alfalfa genome. Only M. sativa seed parents with reproductive abnormalities, including unreduced eggs, have produced hybrids; where M. arborea has been used as the seed parent, no hybrids have resulted. Pedigree selection within derivatives of the two original M. sativa seed parents (MB and M8) has been successful in increasing the frequency of hybrids produced. While Alborea individuals more closely resemble M. sativa, a number of M. arborea-specific traits have been observed across different hybrid individuals. These include single-coil flat pods, large seeds, yellow flowers, indeterminate growth, a minimal crown, lodging, frost resistance, and anthracnose resistance. These M. arborea traits have the potential to restructure alfalfa to increase its versatility and utilisation. There is emerging evidence from North and South America and Australia that some Alborea selections have the capacity to complement adapted alfalfa cultivars for yield. Work is continuing to introgress M. arborea traits of value into alfalfa.","PeriodicalId":14998,"journal":{"name":"Journal of Applied Biosciences","volume":"58 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89354660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Wine Grapes Ripening: A Review on Climate Effect and Analytical Approach to Increase Wine Quality","authors":"M. Rouxinol, M. Martins, J. M. Barroso, A. Rato","doi":"10.3390/applbiosci2030023","DOIUrl":"https://doi.org/10.3390/applbiosci2030023","url":null,"abstract":"Red wine grapes have an important impact on the economy of many regions, both for wine quality and for their richness in phenolic compounds, which have many health benefits. Climate has been changing substantially in the last years, which affects greatly grape polyphenolic composition and wine quality. In this review, we will unveil the importance of climate in grape development, both physically and chemically, the different methodologies used to evaluate grape quality, the interesting new approaches using NIR spectroscopy, and the functional properties of grapes and red wine, due to their high phenolic content. Climate has an impact in the development of phenolic compounds in grapes, namely in the anthocyanins biosynthesis. The phenolic chemical composition changes during maturation, therefore, it is essential to keep on track the accumulation of these key compounds. This information is crucial to help producers choose the best harvest date since specific compounds like polyphenols are responsible for the color, taste, and mouthfeel of wines, which directly affects wine quality. The usage of different methodologies to assess quality parameters in grapes and wine, can be used to provide essential information to create the chemical profile of each variety to develop calibration methods. NIR spectroscopy seems to be a reliable method to be used in vineyards during grape maturation to provide real time information on quality parameters to producers since many reliable calibration models have been developed over time.","PeriodicalId":14998,"journal":{"name":"Journal of Applied Biosciences","volume":"12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75801612","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring the Synergistic Impacts of Cover Crops and Fertilization on Soil Microbial Metabolic Diversity in Dryland Soybean Production Systems Using Biolog EcoPlates","authors":"Durga P. M. Chinthalapudi, Sapna Pokhrel, W. Kingery, M. Shankle, Shankar Ganapathi Shanmugam","doi":"10.3390/applbiosci2030022","DOIUrl":"https://doi.org/10.3390/applbiosci2030022","url":null,"abstract":"The metabolic diversity of soil microbiota embodies diverse functional capabilities that support ecosystem resilience, driving essential biogeochemical processes and facilitating the optimization of sustainable agricultural systems. Integrating cover crops into agricultural systems cultivates a diverse array of metabolic activities among soil microbes, synergistically enhancing ecosystem services and bolstering soil health for sustainable and productive farming practices. In an effort to gain deeper insights and expand our knowledge, we conducted a study examining the effects of cover crops and fertilizer sources, thereby shedding light on their combined impacts on the metabolic activity dynamics of soil microbial communities. In this investigation, we employed a split-plot design with two factors: (a) cover crop with three solo cover crop species—Cereal rye (Secale cereale), wheat (Triticum aestivum), hairy vetch (Vicia villosa), and one mixture of mustard (Brassica rapa) and cereal rye (Secale cereale) (CC-mix), (b) Fertilizer source includes poultry litter, chemical fertilizer, and no-fertilizer treatments. We assessed the metabolic potential of soil microbiota by using carbon substrates utilizing Biolog EcoPlates. The findings revealed that the plots with CC-mix treatment exhibited greater metabolic diversity compared to the other treatments, while among the fertilizer sources, poultry litter demonstrated higher metabolic activity. Furthermore, both treatment factors predominantly metabolized carbohydrates and polymers compared to other carbon substrate categories. The principal component analysis accounted for 46.4% of the variance, collectively represented by PC1 and PC2, emphasizing the substantial contributions of carbohydrates, amino acids, and carboxylic acids to the observed metabolic diversity. Canonical correspondence analysis revealed that pH had positively correlated with microbial functional diversity, whereas total carbon (TC), total nitrogen (TN), and water-stable aggregates (WSA) showed a negative correlation. In conclusion, cover cropping and type of fertilizer source had a notable impact on soil microbial functional diversity, with the cover crop mixture exhibiting a more pronounced influence than the individual cover crop treatments.","PeriodicalId":14998,"journal":{"name":"Journal of Applied Biosciences","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89059810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Trichoderma species have potential in suppressing Fusarium oxysporum f.sp cubense infecting banana in Kenya","authors":"Samuel Musime Malaka, D. M. Thuranira, M. Mwangi, S. Nchore, Hudson Lubabali, Sylvia W Kuria, Daniel Omingo Omari, C. Gathambiri","doi":"10.35759/jabs.186.10","DOIUrl":"https://doi.org/10.35759/jabs.186.10","url":null,"abstract":"Objectives: This study examined the effectiveness of carbendazim, Trichoderma harzianum, T. asperellum, T. viride, and a combination of the carbendazim and the bio-fungicides for the management of Foc both under in vitro and greenhouse conditions. Methodology and Results: The poisoned food technique was used in the in vitro tests. Fungal radial growth was recorded daily for seven days. In the greenhouse, the test products and Foc were applied directly into the soil, disease severity data was recorded at seven day intervals for 98 days using a scale of 1-5. Data on plant biomass was recorded at the end of the experiment (98 days). ANOVA was used to analyze data on fungal radial growth, disease severity, and plant biomass. The Student-Newman-Keuls (SNK) test was used to compare the results at P≤0.05. For the in vitro test, all treatments significantly (P<0.05) suppressed the growth of Foc compared to the untreated control. In the greenhouse trials a significant difference (P<0.05) in external/yellowing symptoms was observed but vascular discoloration was not different. Conclusions and application of findings: This study provides insights into the performance of bio fungicides and carbendazim in managing Panama disease. Keywords: Banana, Fusarium oxysporum f.sp. cubense, , Panama disease, Trichoderma sp.","PeriodicalId":14998,"journal":{"name":"Journal of Applied Biosciences","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78427794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of Culture Media for In Vitro Expansion of Oral Epithelial Keratinocytes","authors":"Giancarlo A. Cuadra, Abrar Shamim, Raivat Shah, Joey Morgan, D. Palazzolo","doi":"10.3390/applbiosci2020021","DOIUrl":"https://doi.org/10.3390/applbiosci2020021","url":null,"abstract":"Background: Expansion of OKF6/TERT-2 oral epithelial cells in vitro is important for studying the molecular biology of disease and pathology affecting the oral cavity. Keratinocyte serum-free medium (KSFM) is the medium of choice for this cell line. This study compares three media for OKF6/TERT-2 cultures: KSFM, Dulbecco’s Modified Eagle Medium/Nutrient Mixture of Hams F-12 (DMEM/F12), and a composite medium comprised of DMEM/F-12 and KSFM (1:1 v/v), referred to as DFK. The toxicological effects of electronic cigarette liquids (e-liquids) on OKF6/TERT-2 cells cultured in these media were also compared. Methods: Cells were cultured in KSFM, DMEM/F12, or DFK, and cellular morphology, growth, wound healing and the gene expression of mucins and tight junctions were evaluated. Additionally, cytotoxicity was determined after e-liquid exposures. Results: Switching from KSFM to DMEM/F12 or DFK 24 h post-seeding leads to typical cellular morphologies, and these cultures reach confluency faster than those in KSFM. Wound-healing recovery occurred fastest in DFK. Except for claudin-1, there is no difference in expression of the other genes tested. Additionally, e-liquid cytotoxicity appears to be amplified in DFK cultures. Conclusions: DMEM/F12 and DFK are alternative media for OKF6/TERT-2 cell culture to study the molecular biology of disease and pathology, provided cells are initially seeded in KSFM.","PeriodicalId":14998,"journal":{"name":"Journal of Applied Biosciences","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88735435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An Event-Driven Architecture for Genomics-Based Diagnostic Data Processing","authors":"Thomas Krause, Mike Zickfeld, Sebastian Bruchhaus, Thoralf Reis, M. X. Bornschlegl, P. Buono, Michael Kramer, Paul Mc Kevitt, M. Hemmje","doi":"10.3390/applbiosci2020020","DOIUrl":"https://doi.org/10.3390/applbiosci2020020","url":null,"abstract":"Genomics-based diagnostic data (GBDD) are becoming increasingly important for laboratory diagnostics. Due to the large quantity of data and their heterogeneity, GBDD poses a big data challenge. Current analysis tools for GBDD are primarily designed for research and do not meet the requirements of laboratory diagnostics for automation, reliability, transparency, reproducibility, robustness, and accessibility. This makes it difficult for laboratories to use these tools in tests that need to be validated according to regulatory frameworks and to execute tests in a time- and cost-efficient manner. In order to better address these requirements, we propose an event-driven workflow-based architecture as the basis for a processing platform that is highly scalable using container technologies and microservices. A prototype implementation of this approach, called GenomicInsights, has been developed and evaluated to demonstrate its feasibility and suitability for laboratory diagnostics.","PeriodicalId":14998,"journal":{"name":"Journal of Applied Biosciences","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75767820","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}