Article
Oncology
J. Gempt, F. Withake, A. K. Aftahy, H. S. Meyer, M. Barz, C. Delbridge, F. Liesche-Starnecker, G. Prokop, N. Pfarr, J. Schlegel, B. Meyer, C. Zimmer, B. H. Menze, B. Wiestler
Summary: The study revealed that nearly half of glioblastoma patients have tumors composed of heterogeneous methylation subtypes. Some patients' tumors consist of subvolumes with both methylated and unmethylated MGMT promoter. Analysis of gene copy number variations and phylogeny showed a common pattern in early stages of tumor development.
Article
Ecology
Thales A. Pereira, Simone A. Vieira, Rafael S. Oliveira, Pablo A. P. Antiqueira, Gustavo H. Migliorini, Gustavo Q. Romero
Summary: Environmental heterogeneity is an important factor in explaining the biodiversity of tropical forests. In this study, the authors investigated the effects of epiphytic tank bromeliads on soil chemistry and seedling community structure in a Brazilian coastal sandy forest. They found that the presence of bromeliads increased nitrogen and phosphorus concentrations in the soil, altered pH and calcium levels, and reduced light availability. These changes in soil conditions indirectly affected the structure of seedling communities, decreasing their diversity, density, and biomass.
Article
Plant Sciences
Muhammad Saeed Akhtar, Shahid Ullah Khan, Ebraheem Abdu Musad Saleh, Said Muhammad, Mohammad Islam, Umber Zaman, Khalil ur Rehman, Gul Nawab, Muhammad Naveed Akhtar, Nabil A. Alhakamy, M. K. Rasha Ibrahim, Ehab A. Abdelrahman
Summary: In this study, DNA of 16 Pyrus plants from Pakistan was extracted and analyzed, revealing varying levels of similarity and query coverage with different species. Phylogenetic analysis showed slight genetic variation among the genotypes, suggesting potential for the development of new sub-species and varieties.
SOUTH AFRICAN JOURNAL OF BOTANY
(2023)
Article
Biochemistry & Molecular Biology
Xiaobo Zheng, Jinen Song, Chune Yu, Zongguang Zhou, Xiaowei Liu, Jing Yu, Guangchao Xu, Jiqiao Yang, Xiujing He, Xin Bai, Ya Luo, Yu Bao, Huifang Li, Lie Yang, Mingqing Xu, Nan Song, Xiaodong Su, Jie Xu, Xuelei Ma, Hubing Shi
Summary: The study characterized cell types, transcriptional signatures, and differentially expressed genes at each stage of colorectal cancer development using single-cell RNA sequencing, identifying adenoma and carcinoma precursor cell populations and potential drivers of adenoma initiation. The overexpression of these drivers promoted colorectal epithelial cell proliferation and resulted in the formation of polyp-like buds. These findings enhance our understanding of colorectal cancer and may contribute to improved diagnosis and treatment.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Article
Multidisciplinary Sciences
Dan Wu, Xueling Ma, Yuanyan Meng, Rongjin Cai, Xiaolong Zhang, Li Liu, Lianping Deng, Changjing Chen, Fang Wang, Qingbiao Xu, Bin He, Mingzhu He, Rensheng Hu, Jinjing Zhen, Yan Han, Shaoshen He, Liuxing Xu
Summary: This study examined the impact of nitrogen fertilization on phyllosphere microorganisms in silage maize to enhance the production of high-quality silage. The results showed that nitrogen application rates did not significantly affect the abundance of lactic acid bacteria, aerobic bacteria, yeasts, or molds on the leaf surfaces. However, these microbes were more abundant during the flowering stage compared to the dough stage. Furthermore, the nitrogen application rate had no significant impact on the chemical properties of the leaf surfaces. Notably, the abundance of Pantoea decreased with higher nitrogen application rates, while that of other microorganisms did not change significantly.
Article
Multidisciplinary Sciences
Mads S. Thomsen, Andrew H. Altieri, Christine Angelini, Melanie J. Bishop, Fabio Bulleri, Roxanne Farhan, Viktoria M. M. Fruhling, Paul E. Gribben, Seamus B. Harrison, Qiang He, Moritz Klinghardt, Joachim Langeneck, Brendan S. Lanham, Luca Mondardini, Yannick Mulders, Semonn Oleksyn, Aaron P. Ramus, David R. Schiel, Tristan Schneider, Alfonso Siciliano, Brian R. Silliman, Dan A. Smale, Paul M. South, Thomas Wernberg, Stacy Zhang, Gerhard Zotz
Summary: Habitat heterogeneity is a primary driver of biodiversity patterns, but its universal role has not been fully understood due to a lack of coordinated experiments. This study conducted 22 experiments to assess the impact of habitat heterogeneity on biodiversity across different ecosystems and regions, and found that positive and additive effects were common across the three axes of heterogeneity. These findings provide mechanistic insights into the importance of habitat heterogeneity in promoting biodiversity through facilitative interactions.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Wei Wang, Zequn Dong, Zhong Du, Pengxiang Wu
Summary: Psyllids are a challenging clade in taxonomy and phylogenetics. This study reveals conflicts between nucleotide-based and amino-acid-based phylogenetic trees in this group. Compositional heterogeneity in nucleotide sequences is identified as a cause of this conflict. Using the RY-coding strategy helps reconcile the nucleotide-based phylogeny with the amino-acid-based one. In addition, variations in evolutionary rate can lead to errors in nucleotide-based phylogeny.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2023)
Article
Evolutionary Biology
Danila S. Kostin, Aleksey A. Martynov, Vladimir S. Lebedev, Elena D. Zemlemerova, Anton R. Gromov, Leonid A. Lavrenchenko
Summary: Gerbillinae is the second largest subfamily in the Muridae family, consisting of approximately 16 genera and more than 100 species. Through genetic analysis, the phylogenetic placement of Ammodillus, a monotypic genus, has been elucidated for the first time, providing the most complete tribal phylogeny of Gerbillinae to date. The results support Ammodillus as a sister taxon to all other gerbillines and suggest its separation dates back to approximately 11.7 million years ago. The subfamily is divided into four tribes.
Article
Biochemical Research Methods
Linda K. Sundermann, Jeff Wintersinger, Gunnar Ratsch, Jens Stoye, Quaid Morris
Summary: Tumors are composed of multiple subpopulations of genetically distinct cancer cells. A new method called partial clone tree captures uncertainty in the data more efficiently and can handle large-scale clone trees. SubMARine, an algorithm based on partial clone trees, provides accurate reconstruction of clone trees in a polynomial time and space.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Teiji Sota, Yasuoki Takami, Hiroshi Ikeda, Hongbin Liang, Gayane Karagyan, Clarke Scholtz, Michio Hori
Summary: Carabinae beetles, a group of flightless underground insects, are widely distributed on all continents except Antarctica. Through DNA analysis, researchers have found that Carabinae originated in the Americas and diversified into four tribes. The ancestral Carabinae had wings, but three of the tribes lost their wings and flight capability during evolution. The study also revealed a higher speciation rate of Carabinae in Eurasia.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Seema Khadirnaikar, Sudhanshu Shukla, S. R. M. Prasanna
Summary: This study identified novel subgroups in cancer using multi-omics data, showing that patients with different tumor types may be similar molecularly. Classification models for subgroup identification were proposed and validated.
Article
Genetics & Heredity
Shiwen Xu, Yunfei Wu, Yingqi Liu, Ping Zhao, Zhuo Chen, Fan Song, Hu Li, Wanzhi Cai
Summary: This study focused on the comparative mitogenomic analysis of 55 species from eight common families of Pentatomoidea, revealing heterogeneity in base composition and contrasting evolutionary rates, especially in Urostylididae. Phylogenetic analyses under site-homogenous models showed more stable tree topologies with exclusion of Urostylididae or removal of third codon positions of protein coding genes, while analyses under the site-heterogeneous mixture model consistently recovered the relationships between families within Pentatomoidea.
Article
Multidisciplinary Sciences
Takuma Shibahara, Chisa Wada, Yasuho Yamashita, Kazuhiro Fujita, Masamichi Sato, Junichi Kuwata, Atsushi Okamoto, Yoshimasa Ono
Summary: Deep learning can accurately predict the intrinsic subtypes of breast cancer, but it has not been used directly to study the genes associated with each subtype. We developed an explainable deep learning model, the point-wise linear (PWL) model, to analyze the importance of feature variables. Our study demonstrates the clinical benefits of analyzing breast cancer subtypes and validates the capability of the PWL model.
Article
Biology
Lucie A. Bergeron, Soren Besenbacher, Jaco Bakker, Jiao Zheng, Panyi Li, George Pacheco, Mikkel-Holger S. Sinding, Maria Kamilari, M. Thomas P. Gilbert, Mikkel H. Schierup, Guojie Zhang
Summary: The study revealed that the rate of de novo mutations in rhesus macaques is positively correlated with paternal age, with the paternal lineage contributing most of the mutations. Approximately 3.5% of de novo mutations were shared between siblings, likely arising from early developmental stages. The estimated yearly mutation rate in rhesus macaques also provided insights into primate evolution when compared to traditional molecular clock methods.
Article
Evolutionary Biology
Vladimir Smirnov, Tandy Warnow
Summary: The study compared two basic approaches for estimating trees on large datasets, finding that using UPP to align sequences and RAxML to compute a tree on the alignment provided the best accuracy, outperforming trees computed using phylogenetic placement methods, particularly in cases of substantial sequence length heterogeneity and high rates of evolution. Additionally, it was found that FastTree had poor accuracy on alignments containing fragmentary sequences.
SYSTEMATIC BIOLOGY
(2021)
Article
Plant Sciences
De-Kui Chen, Xin-Mao Zhou, Carl J. Rothfels, Lara D. Shepherd, Ralf Knapp, Liang Zhang, Ngan Thi Lu, Xue-Ping Fan, Xia Wan, Xin-Fen Gao, Hai He, Li-Bing Zhang
Summary: Lycopodiaceae, one of the oldest lineages of vascular plants, has over 400 species distributed across continents, with the highest diversity in tropical regions. Through various analysis methods, this study inferred a global phylogeny of 155 species in the family, revealing three primary clades and 17 major clades within the family.
Article
Biodiversity Conservation
Manuela Dal Forno, James D. Lawrey, Bibiana Moncada, Frank Bungartz, Martin Grube, Eric Schuettpelz, Robert Luecking
Summary: The large number of lichen specimens collected worldwide and deposited in herbaria offer the potential for assessing species boundaries and diversity. This study demonstrates the successful use of high-throughput sequencing to overcome the limitations of DNA fragmentation in historical collections. The integration of molecular and phenotypic approaches provides a comprehensive understanding of diversity in lichenized Basidiomycota.
Editorial Material
Plant Sciences
Luz A. Triana-Moreno, Pedro B. Schwartsburd, Agustina Yanez, Nelson Tulio L. Pena, Li-Yaung Kuo, Carl Rothfels, Michael Sundue
Article
Plant Sciences
Jarmila Pittermann, Alex Baer, Courtney Campany, Steven Jansen, Helen Holmlund, Eric Schuettpelz, Klaus Mehltreter, James E. E. Watkins Jr
Summary: The Cretaceous-Cenozoic expansion of tropical forests created canopy space for diverse epiphytic communities, including Eupolypod ferns. Eupolypods proliferated in this niche, and the transition to the canopy was associated with reduced xylem content and smaller tracheid diameters. However, no differences were found in species vulnerability to embolism and pit membrane thickness. In Eupolypod epiphytes, traits associated with water conservation, such as thicker leaves and lower stomatal density, favored water retention and may have contributed to the radiation in the canopy.
Article
Evolutionary Biology
Carrie M. Tribble, Michael R. May, Abigail Jackson-Gain, Rosana Zenil-Ferguson, Chelsea D. Specht, Carl J. Rothfels
Summary: Testing adaptive hypotheses about the evolution of continuous traits in association with developmentally structured discrete traits, while considering other hidden evolutionary forces, is a challenge in evolutionary biology. This study expands existing phylogenetic comparative methods and finds that plants with different underground storage organs (USOs) do not differ in their climatic niche, except for root morphology, where modified roots are associated with lower temperature seasonality. These findings question the generalization of ecological patterns across geophytic taxa, as different USO types may reflect adaptations to different climatic conditions.
SYSTEMATIC BIOLOGY
(2023)
Article
Plant Sciences
Luz A. Triana-Moreno, Agustina Yanez, Li-Yaung Kuo, Carl J. Rothfels, Nelson Tulio L. Pena, Pedro B. Schwartsburd, Michael Sundue
Summary: In this study, a molecular phylogenetic revision of hayscented ferns was conducted. The results showed that hayscented ferns are polyphyletic and a new classification was proposed. Three morphologically distinct clades were identified and a new type species was suggested. Additionally, three new genera were discovered: Microlepia, Mucura, and Sitobolium.
Article
Plant Sciences
Michael D. Windham, Kathryn T. Picard, Kathleen M. Pryer
Summary: Previously published evidence suggests that Draba maguirei may represent a species complex rather than a single species. A systematic study reveals the existence of three distinct lineages within D. maguirei, with each lineage having different chromosome numbers and occupying different geographic ranges. The clarification of the diversity and distribution of these taxa is important for conservation efforts.
AMERICAN JOURNAL OF BOTANY
(2023)
Article
Multidisciplinary Sciences
Shivesh Kumar, Yan Wang, Ye Zhou, Lucas Dillard, Fay-Wei Li, Carly A. Sciandra, Ning Sui, Rodolfo Zentella, Emily Zahn, Jeffrey Shabanowitz, Donald F. Hunt, Mario J. Borgnia, Alberto Bartesaghi, Tai-ping Sun, Pei Zhou
Summary: Kumar and colleagues have revealed the distinct features of Arabidopsis O-fucosyltransferase SPINDLY (SPY) through cryo-EM structures. They found that SPY has unique active-site features and dynamic conformations that regulate its enzymatic activity. The study also showed that the N-terminal peptide and TPRs in SPY play important roles in inhibiting and regulating its activity.
NATURE COMMUNICATIONS
(2023)
Article
Ecology
William A. Freyman, Matthew G. Johnson, Carl J. Rothfels
Summary: In this paper, we introduce homologizer, a flexible Bayesian method that uses a phylogenetic framework to infer the separation of gene copies into their respective subgenomes across different loci. Through simulation tests, we demonstrate the robustness of homologizer to factors such as incomplete lineage sorting and the phylogenetic informativeness of loci. Furthermore, we establish the utility of homologizer on real data by analyzing a multilocus dataset from the fern family Cystopteridaceae. Lastly, we discuss the potential use of homologizer beyond its core phasing functionality to identify non-homologous sequences.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Plant Sciences
Gisel Y. de la Cerda, Jacob B. Landis, Evan Eifler, Adriana I. Hernandez, Fay-Wei Li, Jing Zhang, Carrie M. Tribble, Nisa Karimi, Patricia Chan, Thomas Givnish, Susan R. Strickler, Chelsea D. Specht
Summary: This article presents methods used to generate long-read Nanopore sequencing reads for the Liliales and demonstrates how modifications to standard protocols directly impact read length and total output. The goal is to assist those interested in generating long-read sequencing data in determining the necessary steps for optimizing output and results.
APPLICATIONS IN PLANT SCIENCES
(2023)
Article
Plant Sciences
Nikolai M. Hay, Michael D. Windham, Terezie Mandakova, Martin A. Lysak, Kasper P. Hendriks, Klaus Mummenhoff, Frederic Lens, Kathleen M. Pryer, C. Donovan Bailey
Summary: This study successfully resolved the phylogeny of the Boechera tribe using sequence data from target enrichment approaches. The results provide a foundation for a new taxonomy and further research on Boechera as a model system.
AMERICAN JOURNAL OF BOTANY
(2023)
Editorial Material
Genetics & Heredity
Fay-Wei Li
Summary: Fay-Wei Li recalls a 1966 paper by Klekowski and Baker, where they noted that homosporous pteridophytes had more chromosomes than heterosporous lineages, and proposed hypotheses on the evolutionary impact of polyploidy.
NATURE REVIEWS GENETICS
(2023)
Article
Plant Sciences
Tetsuya Hisanaga, Shuangyang Wu, Peter Schafran, Elin Axelsson, Svetlana Akimcheva, Liam Dolan, Fay-Wei Li, Frederic Berger
Summary: Recent studies have shown variations in the correlation between chromatin modifications and transcription among different eukaryotes. In this study, the chromatin of the hornwort Anthoceros agrestis was investigated to establish similarities across bryophytes and determine the ancestral chromatin organization of land plants. The results suggest that the ancestral genome of bryophytes had a combination of different types of chromatin, including facultative heterochromatin, euchromatin, and constitutive heterochromatin.
Article
Microbiology
Warren Shou Leong Ang, Olivia Burleigh, Sarah Frail, Yago V. S. Santos, Bhavyaa Tyagi, Fay-Wei Li
Summary: Metagenomic analysis of symbiotic cyanobacteria colonies within Gunnera tinctoria stems identified a new strain of Nostoc, and its genome sequence is reported here.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Plant Sciences
Nikolai M. Hay, Jadesola V. Akinwuntan, Victor Cai, Michael D. Windham, Kathleen M. Pryer
Summary: Anthropogenic climate change poses a threat to the survival of Gymnocarpium appalachianum, a narrowly endemic fern. Understanding the species' distribution and potential relocation for conservation purposes is crucial. Ecological niche modeling was used to project the future distribution of G. appalachianum and suggests the importance of human-mediated population relocation to cooler areas.
AMERICAN FERN JOURNAL
(2023)