Growth rates are an important tool in microbiology because they provide high throughput fitness measurements. The release of GrowthRates, a program that uses the output of plate reader files to automatically calculate growth rates, has facilitated experimental procedures in many areas. However, many sources of variation within replicate growth rate data exist and can decrease data reliability. We have developed a new statistical package, CompareGrowthRates (CGR), to enhance the program GrowthRates and accurately measure variation in growth rate data sets. We define a metric, Variability-score (V-score), that can help determine if variation within a data set might result in false interpretations. CGR also uses the bootstrap method to determine the fraction of bootstrap replicates in which a strain will grow the fastest. We illustrate the usage of CGR with growth rate data sets similar to those in Mira, Meza, et al. (Adaptive landscapes of resistance genes change as antibiotic concentrations change. Mol Biol Evol. 32(10): 2707-2715). These statistical methods are compatible with the analytic methods described in Growth Rates Made Easy and can be used with any set of growth rate output from GrowthRates.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850790 | PMC |
| http://dx.doi.org/10.1093/molbev/msx255 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
A comparative study of the genetically improved Abbassa Nile tilapia strain (GIANT-G9) and a commercial strain in Egypt: growth vs. stress response.
Vet Res Commun
January 2025
Genetics and Biotechnology, Department of Aquaculture, Faculty of Fish Resources, Suez University, Suez, 43221, Egypt.
Selective breeding is a potent method for developing strains with enhanced traits. This study compared the growth performance and stress responses of the genetically improved Abbassa Nile tilapia strain (G9; GIANT-G9) with a local commercial strain over 12 weeks, followed by exposure to stressors including high ammonia (10 mg TAN/L), elevated temperature (37 °C), and both for three days. The GIANT-G9 showed superior growth, including greater weight gain, final weight, length gain, specific growth rate, and protein efficiency ratio, as well as a lower feed conversion ratio and condition factor compared to the commercial strain.
View Article and Find Full Text PDFA community-based intervention (the Omama Project) improves neurodevelopment in impoverished 2-year-old Roma children: a quasi-experimental observational study.
Eur J Pediatr
January 2025
CESTA VON, Bratislava, Slovakia.
Unlabelled: High rates of childhood neurodisability are reported among the Roma, Europe's largest ethnic minority community. Interventions targeting early child development (ECD) during the first 2 years of life can improve neurodevelopmental outcomes in vulnerable children; however, evidence from Roma preschoolers is scarce. In a quasi-experimental observational study, we compared neurodevelopmental outcomes at age 2 years, measured on the INTERGROWTH-21st Project Neurodevelopmental Assessment (INTER-NDA), between Roma children receiving a community-based ECD intervention (RI, n = 98), and age- and sex-matched Roma and non-Roma children (RC, n = 99 and NRC, n = 54, respectively) who did not receive the intervention in Eastern Slovakia.
View Article and Find Full Text PDFEvaluation of two MALDI-TOF MS systems and extraction methods for identification of filamentous fungi recovered from clinical specimens.
J Clin Microbiol
January 2025
Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA.
Unlabelled: Rapid and accurate identification of cultured molds is important to determine clinical significance and therapeutic decision-making. Conventional mold identification uses phenotypic macroscopic and microscopic characterization; however, this can take days or weeks for colony maturity and definitive microscopic structure formation, be limited to genus-level identification, and be misidentified due to morphologic mimics or similarities between closely related species. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) revolutionized bacterial and yeast identification but remains uncommon for molds in part because of limited reference libraries.
View Article and Find Full Text PDFImpact of endocrine disorders associated with cleft lip and palate.
Turk J Pediatr
December 2024
Department of Plastic Reconstructive and Aesthetic Surgery, Hacettepe University Faculty of Medicine, Ankara, Türkiye.
Background: Any impediment to the development of midline structures i.e. hypothalamus, pituitary and oral cavity may cause anatomical and functional issues.
View Article and Find Full Text PDFTrends of dental service utilization and expenditure in Taiwan from 2000 to 2020.
J Dent Sci
December 2024
Department of Health Care Administration, Chang Jung Christian University, Tainan, Taiwan.
Background: /purposeSince 1995, Taiwan's National Health Insurance (NHI) has offered a comprehensive dental coverage to over 99 % of the population. This study mainly analyzed the dental service utilization and expenditure trends by the gender, age, and service type and evaluated the resource allocation across different demographics from 2000 to 2020.
Materials And Methods: Nationwide NHI administrative data were used to assess the dental visit rates, average visits per user, and per capita expenditure by the gender, age, and 11 service categories for the years 2000, 2005, 2010, 2015, and 2020.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!