Article
Biochemistry & Molecular Biology
Katrina B. Harris, Kenneth M. Flynn, Vaughn S. Cooper
Summary: Evolution and diversification of Pseudomonas aeruginosa populations in biofilm-promoting environments show that adaptation and genetic variation are maintained without the usual elimination of diversity by fixation events. Multiple mutations are preserved at intermediate frequencies, suggesting that some environments may expose a larger fraction of the genome and select for many adaptations at once. This challenges the conventional idea that strong selection would normally purge genetic and phenotypic diversity.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Genetics & Heredity
Hyein Jung, Hae-Un Jung, Eun Ju Baek, Ju Yeon Chung, Shin Young Kwon, Ji-One Kang, Ji Eun Lim, Bermseok Oh
Summary: Polygenic risk score (PRS) can be used to identify high-risk individuals for diseases and predict complex traits in a population. However, previous studies have shown that PRS models may exhibit a phenomenon known as heteroscedasticity, which can affect the accuracy of PRS-based prediction. This study analyzed the presence of heteroscedasticity in PRS models for various disease-related traits and found that heteroscedasticity was frequently observed in ten out of fifteen quantitative traits. The study suggests that prediction models using PRS should take into account the presence of heteroscedasticity.
FRONTIERS IN GENETICS
(2023)
Article
Multidisciplinary Sciences
Hakeemah Al-nakhle
Summary: The use of virtual laboratory simulations, including scenario-based virtual laboratory simulation (SB-VLS), has increased in various disciplines and has been shown to stimulate cognitive and non-cognitive skills. This study examines the effects of SB-VLS on the development of cognitive skills, specifically scientific report writing skills, in molecular biology courses. Results indicate that SB-VLS has a significant and large effect on intrinsic motivation, self-efficacy, knowledge gain, and lab report scores. SB-VLS is an innovative teaching strategy that effectively develops both cognitive and non-cognitive skills.
Article
Microbiology
Maria Lehmann, Christoph Prohaska, Benjamin Zeldes, Anja Poehlein, Rolf Daniel, Mirko Basen
Summary: Thermophily is an ancient trait among microorganisms. This study explores the evolution of a mesophile from a thermophile and observes a change in phenotype.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Energy & Fuels
Nurafiqah Abdullah, Nurul Hasan
Summary: The Water Alternating Gas (WAG) process involves cyclic injections of water and gas to improve sweep efficiency and reduce gas breakthrough in oil reservoirs. The study found that using the Carlson two-phase hysteresis model with Stone 1 correlation yields the best results, with the optimal WAG ratio being 1:1. Injecting water as the first phase is more efficient compared to CO2 to prevent early breakthrough in the reservoir.
JOURNAL OF PETROLEUM EXPLORATION AND PRODUCTION TECHNOLOGY
(2021)
Article
Geochemistry & Geophysics
Chunting Liu, Mingzhong Li, Guodong Zhang, Yong Zhang
Summary: In this study, the mechanism of bed load proppant transport during slickwater hydraulic fracturing was analyzed using a computational simulation method. A model for calculating the mass flux of the bed load layer was proposed and verified with experimental data. Results revealed that bed load migration plays a crucial role in proppant transport.
Article
Engineering, Environmental
Yalin Li, Xinyi Zhang, Victoria L. Morgan, Hannah A. C. Lohman, Lewis S. Rowles, Smiti Mittal, Anna Kogler, Roland D. Cusick, William A. Tarpeh, Jeremy S. Guest
Summary: This study introduces QSDsan, an open-source tool in Python for the quantitative sustainable design of sanitation and resource recovery systems. QSDsan is capable of handling uncertain technological landscapes while considering critical contextual parameters. Two examples demonstrate the core capabilities of QSDsan and emphasize its advantages in automated design, flexible process modeling, rapid and reproducible simulations, and integrated visualization. The intention is to make QSDsan a community-led platform with online documentation, tutorials, and supporting packages to contribute to the development of safe and affordable sanitation technologies globally.
ENVIRONMENTAL SCIENCE-WATER RESEARCH & TECHNOLOGY
(2022)
Article
Plant Sciences
Lichun Cai, David Comont, Dana MacGregor, Claudia Lowe, Roland Beffa, Paul Neve, Christopher Saski
Summary: Weedy plants, including blackgrass, pose a significant challenge to sustainable crop production globally due to their rapid adaptation to human-mediated management. In this study, we present a chromosome-scale genome assembly of blackgrass and investigate the genetic basis of non-target site herbicide resistance (NTSR). Our findings reveal that NTSR is a polygenic trait that evolves from standing genetic variation.
Article
Acoustics
Yue Li, Onur Atak, Stijn Jonckheere, Wim Desmet
Summary: This paper investigates the challenge of accelerating frequency-domain acoustic simulations using a matrix-free method. It applies rational Krylov projection based model order reduction (MOR) technology to boundary element methods (BEM), avoiding interference with BEM kernels and working with existing fast BEM techniques. The combination of matrix-free MOR and fast BEM techniques achieves significant speed-ups in wideband BEM simulations.
JOURNAL OF SOUND AND VIBRATION
(2022)
Article
Biology
Roger Cropp, John Norbury
Summary: The new eco-evolutionary equations developed provide a better estimation of changes in trait distribution within populations, aiding in understanding the evolutionary process of populations. Through an example of two competing plant populations, the effectiveness of this method in studying the dynamics of evolutionary competition between populations is demonstrated. Simulation results suggest that the new eco-evolutionary equations may offer a good approximation for understanding phenotype changes in populations.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Evolutionary Biology
Austin L. Drury, Jean-Francois Gout, Amy L. Dapper
Summary: Meiotic recombination is a fundamental biological process that affects the genomic landscape. Despite its importance, we lack a clear understanding of the selective pressures that shape its variation in natural populations, including humans. In this study, we simulated the evolution of recombination rates and found that both low and high rates of recombination can have fitness costs in humans. Our findings provide insights into the genetic factors that contribute to the variation in recombination rates.
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Infectious Diseases
Joao S. Rebelo, Celia P. F. Domingues, Francisco Dionisio
Summary: Conjugative plasmids often carry virulence and antibiotic-resistant genes and understanding their behavior can provide insights into their spread. Despite the ubiquity of plasmids in nature, bacteria often replicate slower after plasmid entry, which is inconsistent with their prevalence. Previous research has proposed various hypotheses to explain plasmid maintenance among bacterial communities, but the diverse combinations of bacterial species, strains, plasmids, and environments require a robust explanatory mechanism. This study shows that donor cells benefit from harboring conjugative plasmids even if compensatory mutations occur in the plasmids rather than the chromosomes, providing new insights into the competition between plasmid-containing and plasmid-free cells.
Article
Chemistry, Physical
Mingzhong Hao, Chengjian Wei, Xin Liu, Yun Ge, Jing Cai
Summary: This study introduced the lattice Weaire-Phelan structure to the Ti6Al4V porous scaffold manufactured by SLM technology, and evaluated its microstructure, mechanical properties, and energy absorption capacity. A finite element model was established to simulate the mechanical behaviors during compression tests, confirming the excellent performance of the TC4 biomaterial.
JOURNAL OF ALLOYS AND COMPOUNDS
(2021)
Article
Genetics & Heredity
Troy N. Rowan, Harly J. Durbin, Christopher M. Seabury, Robert D. Schnabel, Jared E. Decker
Summary: This study mapped the recent effects of selection and local adaptation in three cattle populations, identifying 207 genomic loci associated with single-gene and multi-gene traits, as well as hundreds of loci associated with various environments. These findings shed light on mammalian adaptation biology and provide insights for selecting better-adapted cattle in changing environments.
Article
Engineering, Multidisciplinary
M. Vellappandi, Pushpendra Kumar, V Govindaraj, Wedad Albalawi
Summary: This research article investigates the optimal control problem of the mosaic disease model using Caputo fractional derivatives. It explores the roles of spraying and roguing in controlling mosaic spread, and finds that only roguing is an effective control measure in the presence of natural microbial biostimulants.
ALEXANDRIA ENGINEERING JOURNAL
(2022)
Article
Biology
Sheng-Kai Hsu, Ana Marija Jaksic, Viola Nolte, Manolis Lirakis, Robert Kofler, Neda Barghi, Elisabetta Versace, Christian Schloetterer
Article
Evolutionary Biology
Claire Burny, Viola Nolte, Pierre Nouhaud, Marlies Dolezal, Christian Schloetterer
GENOME BIOLOGY AND EVOLUTION
(2020)
Article
Biochemistry & Molecular Biology
Sheng-Kai Hsu, Chaimae Belmouaden, Viola Nolte, Christian Schloetterer
Summary: The study compared expression profiles of replicated Drosophila melanogaster populations exposed to two different temperature regimes in the laboratory for more than 80 generations. It identified genes and gene modules that evolved in the same direction in both temperature regimes, reflecting adaptation to common selection pressures. Additionally, temperature-specific expression changes were observed, with overlap between adaptive genes in experimental evolution and natural Drosophila populations along different temperature clines.
Article
Biochemistry & Molecular Biology
Kathrin A. Otte, Christian Schloetterer
Summary: Shifting from SNP analysis to haplotype reconstruction improves the interpretation of E&R experiments, with haplovalidate allowing for detection of selected haplotypes in Pool-seq data.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Evolutionary Biology
Anna Maria Langmueller, Marlies Dolezal, Christian Schloetterer
Summary: Evolve and Resequence (E&R) studies explore the genomic selection response of populations in Experimental Evolution setups. Secondary E&R, as a promising experimental follow-up procedure, can enhance mapping resolution by allowing for additional recombination events. The crossing scheme and population size are crucial factors determining the power and resolution of secondary E&R, with a minimum population size of 4,800 individuals needed to achieve at least 75% power.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Evolutionary Biology
Claire Burny, Viola Nolte, Marlies Dolezal, Christian Schloetterer
Summary: This study used a modified evolve and resequence (E&R) design to investigate polygenic adaptation in fruit flies, by exposing them to a high-temperature environment. The findings suggest that the X chromosome shows a stronger selection response than autosomes, possibly due to dominance effects, and that adaptive responses were more pronounced in a two-genotype experiment compared to classic E&R studies.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Wei-Yun Lai, Christian Schloetterer
Summary: The study found that after 100 generations of adaptation to a new laboratory environment, the variance of gene expression in Drosophila simulans males was significantly reduced in 125 and 97 genes, suggesting that the drastic loss in environmental complexity may have triggered selection for reduced variance. This observation could have important implications for studies of adaptation processes in natural and experimental populations.
Article
Biology
Rupert Mazzucco, Christian Schloetterer
Summary: The influence of the microbiome on its host is well-documented, but the interplay among members of the microbiome is not yet well-understood. Longitudinal studies provide a promising approach to studying such interactions, and a recent study found that the composition of microbiome changes systematically across different temperature regimes, indicating functional interdependence among different microbiome components.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Genetics & Heredity
Manolis Lirakis, Viola Nolte, Christian Schloetterer
Summary: The genetic basis of adaptation to different environments has long been of interest to evolutionary biologists. This study performed a genome-wide scan on the sibling species of D. melanogaster, D. simulans, to characterize the genetic basis of dormancy. The results suggest that dormancy is a polygenic trait with many loci of small effect.
G3-GENES GENOMES GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Robert Kofler, Viola Nolte, Christian Schlotterer
Summary: The dynamics of transposable element invasions are influenced by multiple factors, and the transposition rate is only one of them. By studying the temperature-dependent activity of the P-element, researchers found that despite differences in transposition rates, the copy numbers of the P-element were very similar at different temperatures. The decrease in insertion rate as the copy number approached a plateau was accompanied by the production of piRNAs. However, fewer P-element insertions were observed in piRNA clusters than expected, indicating that factors other than the trap model influenced the dynamics of TE invasions.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biology
Claire Burny, Viola Nolte, Marlies Dolezal, Christian Schloetterer
Summary: Experimental evolution combined with whole-genome sequencing is a powerful method to study the adaptive architecture of selected traits. This study shows that the presence of a second stressor affects the genomic selection response, and the combination of temperature and laboratory adaptation results in widespread synergistic effects.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Review
Biology
Christian Schloetterer
Summary: Experimental evolution is a useful tool for testing the predictability of evolution without the confounding effects of inaccurate forecasts. Parallel evolution has been studied in both asexual microorganisms and sexual species, but the predictability varies between different aspects. The predictability of genomic selection response for polygenic traits depends on the founder population and the adaptive architecture in the ancestral populations.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Eirini Christodoulaki, Viola Nolte, Wei-Yun Lai, Christian Schloetterer
Summary: This study proposes a new measurement of pleiotropy by integrating information from multiple phenotypes and generations. The results suggest that multiple loci of weak effect contribute to pleiotropy at the genome-wide level. The study also suggests that the modular architecture of gene expression can reduce the costs of pleiotropy.
Article
Biotechnology & Applied Microbiology
Kathrin A. Otte, Viola Nolte, Francois Mallard, Christian Schloetterer
Summary: Understanding the genetic architecture of temperature adaptation is crucial for predicting the impact of climate change on natural populations. Research showed that the adaptive architecture is more dependent on the ancestry of the founder population rather than the specific selection regime, as replicate populations from different environments demonstrated similar responses to cold temperature adaptation.