Article
Biochemistry & Molecular Biology
Paul Savary, Jean-Christophe Foltete, Herve Moal, Gilles Vuidel, Stephane Garnier
Summary: In this study, the reliability of cost value inference in connectivity models was assessed under different migration rates, population spatial patterns, and degrees of population size heterogeneity. The study also examined whether considering intra-population variables improved the inference when drift was spatially heterogeneous. The results showed that considering intra-population variables can improve the reliability of cost value inference and better identify the true cost scenarios in certain situations.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Biochemistry & Molecular Biology
Nina Marchi, Adamandia Kapopoulou, Laurent Excoffier
Summary: This study examines the impact of sampling heterogeneity of modern and ancient genomes on demographic inference, and introduces a new approach to mitigate this issue. The study shows that the new structured method is efficient and relevant for handling scattered and ancient DNA samples.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Multidisciplinary Sciences
Bart Coppens, Tom E. R. Belpaire, Jiri Pesek, Hans P. Steenackers, Herman Ramon, Bart Smeets
Summary: Biofilms containing extracellular polymeric substances (EPS) can limit the penetration of antimicrobial treatment. To address this issue, functionalized nanoparticles (NPs) have been proposed as carriers for antimicrobial delivery. By using microscopy and modeling, we found that the structure of Salmonella biofilms affects the diffusion and distribution of NPs, with spatial gradients in diffusivity trapping NPs near bacteria. This study suggests that both biofilm structure and EPS level can impact the effectiveness of NP drug delivery, where low EPS levels may enhance delivery and high EPS levels may hinder it.
Article
Biochemistry & Molecular Biology
Guanghao Li, Zuyu Yang, Dafei Wu, Sixue Liu, Xuening Li, Tao Li, Yawei Li, Liji Liang, Weilong Zou, Chung- Wu, Hurng-Yi Wang, Xuemei Lu
Summary: Spatial genetic and phenotypic diversity within solid tumors can have a significant impact on tumor development. The proposed neutral spatial model suggests that mutation accumulation increases towards the periphery and the genealogical relationships are spatially determined, influencing selection efficacy. Testing this model can provide insights into natural selection during tumorigenesis, particularly for small solid tumors.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Drew E. Terasaki Hart, Anusha P. Bishop, Ian J. Wang
Summary: Understanding the drivers of spatial patterns of genomic diversity is crucial in evolutionary genetics. Geonomics, a Python package, allows for complex landscape genomic simulations with full spatial pedigrees, reducing user workload while remaining customizable and extensible. The results of Geonomics are consistent with classic models in population genetics and show efficiency and robustness in capturing complex spatial and evolutionary dynamics.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Dajeong Jeong, Sung-Min Kim, Byung Joo Min, Ju Han Kim, Young Seok Ju, Yong-Oon Ahn, Jiwon Yun, Young Eun Lee, Seok Ryun Kwon, Jae Hyeon Park, Jong Hyun Yoon, Dong Soon Lee
Summary: This study aimed to identify the genetic etiology of congenital neutropenia (CN) patients by studying their bone marrow histology and clinical phenotype. Disease-causing variants were found in genes including ELANE, G6PC3, and CXCR4. BM characteristics associated with these gene variants were summarized. Retrospective analysis also revealed other pathogenic variants related to CN. The results suggest that immunological study and BM exam should be followed by whole-exome sequencing (WES) or an expanded next-generation sequencing panel for CN patient diagnosis.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Johannes Betge, Niklas Rindtorff, Jan Sauer, Benedikt Rauscher, Clara Dingert, Haristi Gaitantzi, Frank Herweck, Kauthar Srour-Mhanna, Thilo Miersch, Erica Valentini, Kim E. Boonekamp, Veronika Hauber, Tobias Gutting, Larissa Frank, Sebastian Belle, Timo Gaiser, Inga Buchholz, Ralf Jesenofsky, Nicolai Haertel, Tianzuo Zhan, Bernd Fischer, Katja Breitkopf-Heinlein, Elke Burgermeister, Matthias P. Ebert, Michael Boutros
Summary: Patient-derived organoids can be used to model human diseases and tumors, and understanding their morphology can provide insights into treatment response. This study uses high-throughput imaging analysis to quantify the phenotypes of colorectal cancer organoids after treatment with small molecules, and identifies the underlying biological mechanisms and drug interventions that can influence their morphology.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Warren S. D. Tennant, Eric Cardinale, Catherine Cetre-Sossah, Youssouf Moutroifi, Gilles Le Godais, Davide Colombi, Simon E. F. Spencer, Mike J. Tildesley, Matt J. Keeling, Onzade Charafouddine, Vittoria Colizza, W. John Edmunds, Raphaelle Metras
Summary: A mathematical metapopulation model was developed to study Rift Valley fever virus transmission in the Comoros archipelago, and Bayesian framework was used to fit the model to surveillance data. The study found that coordinated within-island control measures are more effective than between-island animal movement restrictions in reducing disease burden.
NATURE COMMUNICATIONS
(2021)
Article
Mathematics, Applied
Mengxin Chen, Ranchao Wu
Summary: This paper formulates a diffusive nutrient-microorganism model in a spatially heterogeneous environment with zero-flux boundary conditions, showing more complex and realistic dynamical behaviors. Fundamental properties are established using various methods, profiles of positive solutions are described, and existence results of non-constant steady states are given.
JOURNAL OF MATHEMATICAL ANALYSIS AND APPLICATIONS
(2022)
Article
Environmental Studies
Shuang Liu, Xuefei Li, Long Chen, Qing Zhao, Chaohui Zhao, Xisheng Hu, Jian Li
Summary: This study investigated the spatial heterogeneity of cooling effects of urban landscape by comprehensively considering the composition and configuration of different landscapes. The results revealed that water patches had a more significant cooling effect on the surrounding environment, and the cooling effect of landscape pattern was more important in the urban center. The findings provide valuable insights for landscape planning strategies at specific locations.
Article
Plant Sciences
Moses C. Wambulwa, Ya-Huang Luo, Guang-Fu Zhu, Richard Milne, Francis N. Wachira, Zeng-Yuan Wu, Hong Wang, Lian-Ming Gao, De-Zhu Li, Jie Liu
Summary: Intra-specific genetic diversity is crucial for species adaptation and survival. This study analyzed the patterns of plastid genetic diversity within 15 plant species in southwest China and identified the highest genetic diversity in the Yulong Mountain region. The study also found that climatic, topographic, and anthropogenic factors influenced genetic diversity.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Mathematics, Applied
Jinliang Wang, Wenjing Wu, Chunyang Li
Summary: In this article, a strict analysis is conducted on a reaction-diffusion mosquito-borne disease model in a spatially heterogeneous environment, where the total human populations stabilize. By utilizing fundamental theories of the dynamical system, threshold-type results are established based on the basic reproduction number. The mutual impacts of spatial heterogeneity and diffusion coefficients on the basic reproduction number are explored, and the existence, uniqueness, and global attractivity of the nontrivial steady state are investigated using arguments of asymptotically autonomous semiflows. The global attractivity of the nontrivial steady state is achieved through the Lyapunov function when all parameters are independent of space.
ADVANCES IN NONLINEAR ANALYSIS
(2023)
Article
Genetics & Heredity
Tatiana Souza do Amaral, Juliana Silveira dos Santos, Fernanda Fraga Rosa, Marcelo Bruno Pessoa, Lazaro Jose Chaves, Milton Cezar Ribeiro, Rosane Garcia Collevatti
Summary: This study investigated the effects of landscape features on genetic diversity and adaptive quantitative traits of plants, finding that landscapes with higher compositional heterogeneity may lead to lower evolutionary potential and higher genetic diversity. Additionally, agricultural landscapes with low quality mosaic may be more stressful for plant species.
FRONTIERS IN GENETICS
(2021)
Review
Oncology
Nabih Maslah, Lina Benajiba, Stephane Giraudier, Jean-Jacques Kiladjian, Bruno Cassinat
Summary: Myeloproliferative neoplasms are characterized by driver mutations targeting the JAK/STAT pathway and often display additional mutations targeting various pathways. The disease progression typically involves a chronic phase followed by an accelerated phase or transformation into more aggressive diseases. Recent studies have shed light on the rates and mechanisms of mutation acquisition and selection in hematopoietic cells, using novel techniques to decipher clonal architecture and mutation-induced cell modifications at the single cell level.
Article
Microbiology
Frederic Bigey, Emilie Pasteur, Xymena Polomska, Stephane Thomas, Anne-Marie Crutz-Le Coq, Hugo Devillers, Cecile Neuveglise
Summary: This study investigates the genomic and phenotypic diversity of 56 natural isolates of Yarrowia lipolytica. The results show that Y. lipolytica is a recently evolving species with low genetic diversity and its huge diversity in lipid metabolism is likely due to complex regulations.
