Article
Microbiology
Kristin Scoggin, Jyotsana Gupta, Rachel Lynch, Aravindh Nagarajan, Manuchehr Aminian, Amy Peterson, L. Garry Adams, Michael Kirby, David W. Threadgill, Helene L. Andrews-Polymenis
Summary: Understanding the molecular mechanisms of resistance and tolerance to pathogen infection can help in developing novel interventions. A study on mice infected with Salmonella Typhimurium found distinct phenotypes of delayed susceptible, tolerant, and resistant strains. Tolerant strains showed lower preinfection core body temperatures, rapid disruption of body temperature postinfection, higher neutrophil levels, and more severe tissue damage compared to resistant strains. Gene analysis identified specific genes associated with tolerance and resistance, particularly fibrinogen genes.
Article
Environmental Sciences
Rafael Alvarado, Brayan Tillaguango, Lizeth Cuesta, Stefania Pinzon, Maria Raquel Alvarado-Lopez, Cem Isik, Vishal Dagar
Summary: Latin America countries show convergence in per capita biocapacity, but with heterogeneous transition pathways. Urban primacy index and economic progress have a negative impact on biocapacity, while the effect of financial globalization index is inconclusive. Adopting common policies can enhance the effectiveness of environmental policies and contribute to the achievement of Sustainable Development Goals related to environmental quality.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2022)
Article
Engineering, Environmental
Ahmed Elbeltagi, Manish Kumar, N. L. Kushwaha, Chaitanya B. Pande, Pakorn Ditthakit, Dinesh Kumar Vishwakarma, A. Subeesh
Summary: This study examines the feasibility and effectiveness of the Random Subspace (RSS) model and its hybridization with M5 Pruning tree (M5P), Random Forest (RF), and Random Tree (RT) to estimate the Standardized Precipitation Index (SPI) for droughts in Rajasthan, India.
STOCHASTIC ENVIRONMENTAL RESEARCH AND RISK ASSESSMENT
(2023)
Review
Environmental Sciences
Dafni Anastasiadi, Francesc Piferrer
Summary: Epigenetic clocks are accurate tools for age prediction in fish, and have great potential for fisheries management and conservation biology. This review discusses the computational steps and tools necessary to build an epigenetic clock in any fish species, with a focus on the recommended bisulfite conversion method for distinguishing methylated and unmethylated cytosines. Machine learning statistical procedures, particularly penalized regressions, are applied to identify a set of CpGs that can accurately predict age, and once validated, only a small number of CpGs are needed for age prediction. The implementation of this molecular resource is expected to increase in the future due to its accuracy and decreasing sequencing costs. Accurate age prediction will greatly contribute to fish population management and conservation efforts.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Peter Grohmann, Michael S. J. Walter
Summary: Utilizing GPU for vector-chain-based statistical tolerance analysis is more efficient with larger sample sizes and can reduce runtime by utilizing array vectorization with NumPy and selecting the proper storage order. These methods, implemented with Python, can improve existing workflows on regular desktop computers for real-time statistical tolerance analysis and synthesis.
APPLIED SCIENCES-BASEL
(2021)
Article
Environmental Sciences
Hossein Norouzi, Asghar Asghari Moghaddam, Fulvio Celico, Jalal Shiri
Summary: By identifying and optimizing the vulnerability of aquifers, utilizing RF and GA methods combined with the BDF framework can effectively evaluate groundwater vulnerability, with high accuracy in the model, which is helpful for groundwater protection and management.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Multidisciplinary Sciences
Beatriz Acuna Hidalgo, Luis M. Silva, Mathias Franz, Roland R. Regoes, Sophie A. O. Armitage
Summary: The relationship between virulence and pathogen clearance in the context of bacterial infections in Drosophila melanogaster is explored. The study demonstrates that variation in infection outcomes is determined by differences in bacterial infection intensity and parasite pathogenicity, while pathogen clearance is influenced by early-phase exploitation. The application of the virulence decomposition framework provides valuable insights into host-pathogen interactions.
NATURE COMMUNICATIONS
(2022)
Article
Agriculture, Dairy & Animal Science
Jian Cheng, KyuSang Lim, Austin M. Putz, Anna Wolc, John C. S. Harding, Michael K. Dyck, Frederic Fortin, Graham S. Plastow, Jack C. M. Dekkers, PigGen Canada
Summary: This study aimed to quantify genetic variation in disease resilience using reaction norm models and identified genotype-by-environment interactions related to disease challenge loads. Results showed that selecting animals based on different levels of CL can improve their resilience, and high-performance animals can be selected at a given CL.
GENETICS SELECTION EVOLUTION
(2022)
Article
Mechanics
R. Sachse, A. K. Pickett, P. Middendorf
Summary: In this paper, a systematic study was conducted on the effect of mechanical design features on fatigue crack growth in adhesive joints. A material model and methodology for fatigue crack growth analysis were presented. The results suggest that a combination of local reinforcement, through-thickness reinforcement, and compression preload are necessary for efficient crack growth arrest, while simply reducing peel stresses is not sufficient. Increasing the effective crack front length and introducing through-thickness stresses can significantly reduce local fatigue crack growth rates.
COMPOSITE STRUCTURES
(2021)
Article
Agronomy
Patricia Ferreira da Silva, Natalia Cassa, Alberto Soares de Melo, Jose Dantas Neto, Luana Aparecida Menegaz Meneghetti, Alisson Silva Costa Custodio, Niclene Ponce Rodrigues de Oliveira, Tonny Jose Araujo da Silva, Edna Maria Bonfim-Silva, Sergio Plens Andrade, Thiago Franco Duarte, Savio da Silva Berilli, Mauricio Novaes Souza, Aparecida de Fatima Madella de Oliveira, Monique Moreira Moulin, Ana Paula Candido Gabriel Berilli
Summary: This study investigated the progress in genetic improvement for drought stress in crops through literature investigation and systematic review. The results showed that research in this area was mainly concentrated in Asian countries. The focus was on the keywords related to drought resistance and stress. The study highlighted the importance of genes and genetically modified organisms in breeding programs, and covered a wide range of crops.
Article
Agronomy
Caijing Li, Baoli Zou, Changsheng Lu, Guiting Song, Qiang Gao, Peng Wang, Guangliang Wu, Wei Jin, Hui Yin, Qin Cheng, Yanning Wang, Qi Zhong, Shiying Huang, Mengmeng Yang, Tao Huang, Haohua He, Jianmin Bian
Summary: This study assessed the low temperature germinability (LTG) of rice using six different indices and conducted a genome-wide association study (GWAS) on a natural population of 211 rice accessions. The researchers identified 18 QTL related to LTG, including 7 novel ones. Additionally, they identified 14 candidate genes that may play a role in cold tolerance. These findings are important for improving cold tolerance in rice cultivars.
Article
Plant Sciences
Ranjita Thapa, Rodante E. Tabien, Michael J. Thomson, Endang M. Septiningsih
Summary: This study evaluated the coleoptile lengths of a geographically diverse rice panel and identified potential candidate genes related to anaerobic germination (AG) tolerance using a combined approach of GWAS and transcriptomics analysis.
Article
Plant Sciences
Linxiao Wang, Kun Yang, Qiuheng Wang, Wei Xiao
Summary: This study reveals a two-branch DNA-damage tolerance mechanism in Arabidopsis, involving Rev3 and Rad5a-Uev1C/D. Mutant analysis shows that Atuev1cd is sensitive to DNA damage, while Atuev1ab is not. Genetic analysis suggests that AtUEV1C/D and AtRAD5a function in the same pathway, while AtREV3 represents a separate pathway for translesion DNA synthesis. This study establishes a two-branch DDT model in plants with similarities and differences from the yeast DDT.
PLANT CELL REPORTS
(2023)
Article
Plant Sciences
Ehsan Rabieyan, Mohammad Reza Bihamta, Mohsen Esmaeilzadeh Moghaddam, Hadi Alipour, Valiollah Mohammadi, Kobra Azizyan, Saeideh Javid
Summary: This study conducted a genome-wide association study on 298 Iranian bread wheat landraces and cultivars, identifying drought-tolerant genotypes, which can contribute to tackling the challenges of diminishing water resources and growing population.
Article
Physics, Multidisciplinary
Przemyslaw Bienias, Igor Boettcher, Ron Belyansky, Alicia J. Kollar, Alexey Gorshkov
Summary: Circuit quantum electrodynamics is a promising platform for efficient quantum simulation and computation. Recent experiments have used superconducting microwave resonators to create hyperbolic lattices that emulate quantum physics in negatively curved space. This study investigates experimental settings where a few superconducting qubits are coupled to a bath of photons on a hyperbolic lattice. The results show good agreement between numerical and analytical descriptions, particularly in the long-wavelength regime. The study also explores the use of qubits as probes of the hyperbolic bath and examines the interactions between qubits mediated by photons along geodesics. Overall, this study presents insights into the possibilities and limitations of using hyperbolic lattices for quantum simulation.
PHYSICAL REVIEW LETTERS
(2022)
Article
Multidisciplinary Sciences
Martin Prchal, Antti Kause, Marc Vandeputte, David Gela, Jean-Michel Allamellou, Girish Kumar, Anastasia Bestin, Jerome Bugeon, Jinfeng Zhao, Martin Kocour
Article
Genetics & Heredity
Pieter W. Knap, Antti Kause
FRONTIERS IN GENETICS
(2018)
Article
Fisheries
Jinfeng Zhao, Martin Prchal, Christos Palaiokostas, Ross D. Houston, Antti Kause, Marc Vandeputte, Alain Vergnet, Jerome Bugeon, Anastasia Bestin, Tomas Vesely, Dagmar Pokorova, Veronika Piackova, Lubomir Pojezdal, Lucie Genestout, David Gela, Hana K. Kroupova, Martin Kocour
Article
Fisheries
Martin Prchal, Martin Kocour, Marc Vandeputte, Antti Kause, Alain Vergnet, Jinfeng Zhao, David Gela, Vojtech Kaspar, Lucie Genestout, Anastasia Bestin, Pierrick Haffray, Jerome Bugeon
Article
Multidisciplinary Sciences
Tuomas Leinonen, Jorma Piironen, Marja-Liisa Koljonen, Jarmo Koskiniemi, Antti Kause
Article
Fisheries
Hanna Kuukka-Anttila, Nina Peuhkuri, Irma Kolari, Antti Kause
AQUACULTURE RESEARCH
(2020)
Article
Fisheries
Anna Maria Eriksson-Kallio, Riikka Holopainen, Perttu Koski, Antti Nousiainen, Heikki Koskinen, Antti Kause, Tuija Gadd
DISEASES OF AQUATIC ORGANISMS
(2020)
Article
Fisheries
Jinfeng Zhao, Martin Prchal, Antti Kause, Marc Vandeputte, David Gela, Hana Kocour Kroupova, Veronika Piackova, Pavel Sauer, Christoph Steinbach, Jean-Michel Allamellou, Christos Palaiokostas, Ross D. Houston, Martin Kocour
Summary: This study investigated the genetic and phenotypic background of energy reserves in Amur mirror carp and their impact on fish performance during the first winter. Results showed most traits related to energy reserves significantly decreased after the first winter, with differing genetic correlations and heritability before and after the winter. Interestingly, genetic correlations between HP glycogen traits and survival in the third growing season were positive, suggesting a genetically based strategy for energy mobilization in common carp. Monitoring FC and HSI could be useful for managing carp stocks.
Article
Fisheries
P. C. Lindholm-Lehto, J. Koskela, H. Leskinen, J. Vielma, A. Kause
Summary: This study investigated the relationships between off-flavor compounds, lipid contents, and fatty acids in rainbow trout reared in a recirculating aquaculture system (RAS). The results showed that fish with high lipid contents accumulated high concentrations of off-flavor compounds, but these compounds were negatively correlated with health-promoting fatty acids. Excessive lipid contents may reduce the nutritional value of the fish.
Article
Fisheries
Silvia Garcia-Ballesteros, Jesus Fernandez, Antti Kause, Beatriz Villanueva
Summary: Carcass and fillet yields are economically important traits in aquaculture, and headless gutted carcass percentage (HC) is a convenient selection criterion. However, HC is a sib trait that cannot be recorded on selection candidates. This study compared different selection strategies for improving HC in rainbow trout breeding programs and found that a combination of genomic and indirect selection is the most effective approach.
Article
Fisheries
Clemence Fraslin, Heikki Koskinen, Antti Nousianen, Ross D. Houston, Antti Kause
Summary: This study demonstrates that selective breeding for improved resistance to columnaris disease in rainbow trout is feasible. A natural outbreak of the disease in a farm environment can be utilized to select fish with greater resistance, and genomic selection is an effective approach to expedite this process.
Article
Agriculture, Dairy & Animal Science
Antti Kause, Antti Nousiainen, Heikki Koskinen
Summary: Improvement in feed conversion ratio (FCR) and reduction in nutrient loading in rainbow trout farming have significantly improved resource efficiency. Selective breeding has contributed to this improvement with an estimated genetic gain of 1.74% per generation in FCR. The use of genetically improved trout reduces feed and production costs.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Genetics & Heredity
Federico C. F. Calboli, Heikki Koskinen, Antti Nousianen, Clemence Fraslin, Ross D. Houston, Antti Kause
Summary: This study conducted a comparative genetic analysis of the quantitative trait loci for resistance to warm water columnaris disease in two farmed rainbow trout populations. The results identified a major quantitative trait loci on chromosome Omy03 and a smaller quantitative trait loci on Omy05. These findings provide insights into the genetic basis of disease resistance and offer potential markers for breeding programs aiming to increase resistance against columnaris disease.
G3-GENES GENOMES GENETICS
(2022)
Article
Agriculture, Multidisciplinary
Luis Gomez-Raya, Wendy M. Rauw, Santiago Cabaleiro, Ruben Caamano, L. Alberto Garcia-Cortes, Antti Kause
SPANISH JOURNAL OF AGRICULTURAL RESEARCH
(2018)
Article
Fisheries
Matti Janhunen, Antti Nousiainen, Heikki Koskinen, Harri Vehvilainen, Antti Kause