Article
Biology
Ranjeet Kumar Rout, Sk Sarif Hassan, Sabha H. Sheikh, Saiyed Umer, Kshira Sagar Sahoo, Amir Gandomi
Summary: This study examined the spatial distribution of amino acids in the primary protein sequences of SARS-CoV-2 and compared them with SARS-CoV proteins. The differences in amino acid spatial distribution between SARS-CoV-2 and SARS-CoV proteins were identified, enabling researchers to differentiate between the two types of coronavirus. The study also revealed similarities and differences among important structural proteins, E, M, N, and S, which are crucial for establishing an evolutionary tree with other coronavirus strains.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Julieann Puleo, Kornelia Polyak
Summary: Evading immune-mediated destruction is a critical step in tumor evolution, and the immune system is a strong selective pressure in tumorigenesis. Analyzing tumor immune evasion from a Darwinian perspective can provide important insights into the mechanisms of primary immune escape and acquired resistance to immunotherapy.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2022)
Article
Multidisciplinary Sciences
Taylorlyn Stephan, Shawn M. Burgess, Hans Cheng, Charles G. Danko, Clare A. Gill, Erich D. Jarvis, Klaus-Peter Koepfli, James E. Koltes, Eric Lyons, Pamela Ronald, Oliver A. Ryder, Lynn M. Schriml, Pamela Soltis, Sue VandeWoude, Huaijun Zhou, Elaine A. Ostrander, Elinor K. Karlsson
Summary: Genomics research has primarily focused on humans and a limited number of species, resulting in a lack of understanding about the genomes of the majority of species. However, a broad view that encompasses the vast diversity of life is necessary to comprehend how genomes function and how genetic variation shapes phenotypes. Integrating comparative genomics with other fields is crucial for scientific discovery and the protection of ourselves and our world.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Zhe Zhang, Miaomiao Zhu, Qi Xie, Robert M. Larkin, Xueping Shi, Bo Zheng
Summary: The study introduces a new R package called CProtMEDIAS for protein phylogenetic analysis, which utilizes dimensionality reduction algorithms for fast analysis of amino acid sequences. It was applied to the plant homeobox superfamily for clustering, pseudotime analysis, and evolutionary trajectory analysis.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Dimitrii O. Kostenko, Eugene Korotkov
Summary: The aim of this study was to compare the performance of multiple alignment methods in aligning highly divergent amino acid sequences. The results showed that although MAHDS had slightly lower quality alignments compared to other algorithms, it compensated with greater statistical significance. Additionally, MAHDS outperformed other methods in constructing statistically significant alignments for highly divergent protein sequences.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Astronomy & Astrophysics
Milan Pesta, Ondrej Pejcha
Summary: The mass ratio of a contact binary star evolves through various processes and undergoes tidal Darwin instability when it crosses a critical threshold q(min), resulting in rapid coalescence and observable brightening. The distribution of q for contact binary stars has not been well-measured due to the requirement of spectroscopy. However, it is possible to infer the mass-ratio distribution using Bayesian inference and light-curve amplitudes. Through this method, a sample of contact binary candidates was obtained and their mass-ratio distribution was modeled. The results show a dependence of q(min) on the structure of the components and are consistent with previous theoretical predictions.
ASTRONOMY & ASTROPHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Pawel Blazej, Konrad Pawlak, Dorota Mackiewicz, Pawel Mackiewicz
Summary: This study investigates the evolutionary mechanisms of codon block structure in the genetic code through computer simulations. The results demonstrate that the reading system similar to that present in the standard genetic code (SGC) quickly dominates during evolution and possesses similar characteristics to the SGC.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Feng Zhou, Ruojie Sha, Heng Ni, Nadrian Seeman, Paul Chaikin
Summary: Artificial self-replication and exponential growth have the potential to aid in better understanding fundamental processes in nature and developing new materials and devices. By introducing mutation and growth advantages in a system of DNA origami dimers, researchers have demonstrated a Darwinian-like evolution. Through controlled mutation rates and growth advantages, a new species can take over the system in a relatively short amount of time.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
H. Bonnefond, Y. Lie, T. Lacour, B. Saint-Jean, G. Carrier, E. Pruvost, A. Talec, O. Bernard, A. Sciandra
Summary: Species domestication and improvement are important for increasing agricultural production. The microalgae industry can follow the same path by selecting and improving microalgal strains. The use of competition in a dynamic environment can drive the evolution and emergence of new adapted populations with enhanced properties. By selecting microalgae strains under variable light intensity, we successfully increased biomass productivity and observed the appearance of new alleles.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Article
Multidisciplinary Sciences
Yoojeong Seo, Joyeon Kang, Tae Il Kim, Chan Gyu Joo
Summary: This study used MRI to investigate the correlation between glutamine uptake and the distribution of glutamine transporters, glutaminase, and CSC markers. The results showed a positive correlation between glutamine uptake and the distribution of ASCT2 and certain CSC markers.
SCIENTIFIC REPORTS
(2022)
Article
Mathematics, Applied
Luca Courte, Patrick Dondl, Michael Ortiz
Summary: In this study, we prove the Taylor scaling law for dislocation lines moving by curvature and characterized by line-tension under the influence of applied shear stress in a plane with a random array of obstacles. We demonstrate, in terms of optimal scaling, that the critical applied shear stress for yielding or unbounded motion of the dislocation scales proportionally to the square root of the obstacle density. Taylor scaling dominates the linear-scaling based on purely energetic considerations for sufficiently small obstacle densities, and thus characterizes the dominant rate-limiting mechanism in that regime.
ARCHIVE FOR RATIONAL MECHANICS AND ANALYSIS
(2022)
Article
Biochemical Research Methods
Zengchao Mu, Ting Yu, Xiaoping Liu, Hongyu Zheng, Leyi Wei, Juntao Liu
Summary: The FEGS method is a novel model for extracting features of protein sequences, which effectively combines graphical and statistical features to transform protein sequences into numerical vectors. It outperforms other compared methods in phylogenetic analysis of protein sequence data sets.
BMC BIOINFORMATICS
(2021)
Article
Evolutionary Biology
Paschalia Kapli, Ioanna Kotari, Maximilian J. Telford, Nick Goldman, Ziheng Yang
Summary: Inference of deep phylogenies has primarily used protein sequences, but our analysis shows that DNA sequences may be just as useful and should not be excluded. We conducted a simulation study and analyzed empirical data, which suggest that DNA sequences can recover the correct tree as often as protein sequences. Using DNA data has computational advantages and allows for advanced models that account for heterogeneity in the nucleotide-substitution process.
SYSTEMATIC BIOLOGY
(2023)
Review
Oncology
Sophia Belkhir, Frederic Thomas, Benjamin Roche
Summary: The article discusses how mathematical models can help design alternative treatment strategies that take into account the ecology and evolution of tumors to avoid the emergence of resistance. Adaptive therapy is a promising anti-cancer treatment strategy that adjusts treatment cycles to control the population of treatment-resistant cells. Mathematical modeling is essential to understand cancer dynamics in response to treatments and to improve treatment outcomes with adaptive therapy strategies.
Article
Quantum Science & Technology
Nicolas Lori
Summary: The physics-cell approach, based on a Darwinian perspective, proposes an explanation for the standard model of physics, allowing for the violation of charge-parity-time symmetry. It uses the concept of physics cells to contain quantum fields and explains phenomena such as dark matter, dark energy, and black holes.
QUANTUM INFORMATION PROCESSING
(2022)
Article
Chemistry, Multidisciplinary
Michal Andrzejewski, Jedrzej Marciniak, Kacper W. Rajewski, Andrzej Katrusiak
CRYSTAL GROWTH & DESIGN
(2015)
Article
Chemistry, Multidisciplinary
Jedrzej Marciniak, Michal Kazmierczak, Kacper W. Rajewski, Andrzej Katrusiak
CRYSTAL GROWTH & DESIGN
(2016)
Article
Chemistry, Multidisciplinary
Jedrzej Marciniak, Julia Bakowicz, Michal A. Dobrowolski, Kamil F. Dziubek, Michal Kazmierczak, Damian Paliwoda, Kacper W. Rajewski, Szymon Sobczak, Marcin Stachowicz, Andrzej Katrusiak
CRYSTAL GROWTH & DESIGN
(2016)
Article
Chemistry, Physical
Jedrzej Marciniak, Andrzej Katrusiak
JOURNAL OF PHYSICAL CHEMISTRY C
(2017)
Article
Biochemistry & Molecular Biology
Bogumil Brycki, Anna Kozirog, Iwona Kowalczyk, Tomasz Pospieszny, Paulina Materna, Jedrzej Marciniak
Article
Chemistry, Physical
Weizhao Cai, Jedrzej Marciniak, Michal Andrzejewski, Andrzej Katrusiak
JOURNAL OF PHYSICAL CHEMISTRY C
(2013)
Article
Chemistry, Physical
Jedrzej Marciniak, Michal Andrzejewski, Weizhao Cai, Andrzej Katrusiak
JOURNAL OF PHYSICAL CHEMISTRY C
(2014)
Article
Chemistry, Multidisciplinary
Ewa Patyk, Jedrzej Marciniak, Hanna Tomkowiak, Andrzej Katrusiak, Klaus Merz
ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS
(2014)
