Article
Biochemistry & Molecular Biology
Alan Garcia-Elfring, Antoine Paccard, Timothy J. Thurman, Ben A. Wasserman, Eric P. Palkovacs, Andrew P. Hendry, Rowan D. H. Barrett
Summary: This study investigates parallel selection in six populations of threespine stickleback inhabiting bar-built estuaries undergoing seasonal environmental changes. Consistent allele frequency changes across estuaries indicate a potential role for parallel selection, with genomic changes related to osmoregulation and ion balance providing insight into early stages of adaptation in marine to freshwater transitions.
Article
Ecology
Ellen L. White, Holger Klinck, Jonathan M. Bull, Paul R. White, Denise Risch
Summary: This study demonstrates the transferability of pre-trained CNN models to new acoustic environments. By fine-tuning the models with limited site-specific data, the performance of the CNN in the new environment is significantly improved.
ECOLOGICAL INFORMATICS
(2023)
Article
Agronomy
Richard Snowball, Harmohinder S. Dhammu, Mario Francesco D'Antuono, David Troldahl, Ian Biggs, Callen Thompson, Mark Warmington, Amanda Pearce, Darshan L. Sharma
Summary: Quinoa is being evaluated for its potential as a crop in Australia, with trials conducted in different climate conditions. The study found that winter and spring rain-fed conditions in Geraldton and spring and summer irrigation at Bool Lagoon yielded the highest seed yield. Genetic diversity and suitable management practices can further enhance the yield potential of quinoa in Australia.
Article
Telecommunications
Ouya Wang, Jiabao Gao, Geoffrey Ye Li
Summary: In recent years, deep learning has been widely used in communications and achieved remarkable performance improvement. Most existing works rely on data-driven deep learning, which requires a large amount of training data and computing resources. This paper introduces few-shot learning to reduce the training data requirement for new environments by leveraging the learning experience from known environments. By embedding an attention network into the deep learning-based communication model, different environments can be learned together, allowing the communication model to perform well in new environments with only a few pilot blocks. Through an example of deep-learning-based channel estimation, this novel design method achieves better performance than the existing data-driven approach for few-shot learning.
IEEE TRANSACTIONS ON COGNITIVE COMMUNICATIONS AND NETWORKING
(2023)
Article
Plant Sciences
Xin Xu, Lixin Zhang, Xiaoning Cao, Lifeng Liu, Bingjun Jiang, Chunlei Zhang, Hongchang Jia, Xiangguang Lyu, Yumei Su, Yupeng Cai, Luping Liu, Shengrui Zhang, Fulu Chen, Cunxiang Wu, Bin Liu, Wensheng Hou, Shi Sun, Jinsheng Lai, Tianfu Han
Summary: Soybean, a short-day plant, utilizes cotyledons to accelerate flowering by perceiving photoperiod and upregulating the flowering promoting gene GmFT2a. Cotyledons can support the entire life cycle and play a substantial role in the flowering process, proposing a new 'cotyledon-based self-reliance' model for rapid flowering in soybeans and other dicots grown in long-day environments at high latitudes.
PLANT CELL AND ENVIRONMENT
(2021)
Article
Biology
Sarah E. Diamond, Eric G. Prileson, Ryan A. Martin
Summary: This article reviews different lines of evidence used to assess urban adaptation and provides a synthesis of local adaptation to urban and rural environments. While there is support for local adaptation to both urban and rural environments, there is an asymmetry, with urban adaptation being less prevalent. There is also considerable variation among study systems.
CURRENT OPINION IN INSECT SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Meng-Meng Wang, Fu-Jie Xu, Yan Su, Yun Geng, Xiao-Ting Qian, Xu-Ling Xue, Ya-Qiong Kong, Zheng-Hong Yu, Hong-Ke Liu, Zhi Su
Summary: A new cyclometalated Ir-III complex, Ir-Rhein, based on rhein, is reported to specifically target mitochondria and effectively inhibit metabolic adaptations. The complex induces severe mitochondrial damage and initiates mitophagy, leading to reduction in both mitochondrial and glycolytic bioenergetics and eventually causing ATP starvation death. Moreover, Ir-Rhein overcomes cisplatin resistance and shows promising antiproliferation performance for cisplatin-resistant cancer cells.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biology
Xingwen Peng, Jilong Cheng, Hong Li, Anderson Feijo, Lin Xia, Deyan Ge, Zhixin Wen, Qisen Yang
Summary: This study sequenced the genomes of hairy-footed jerboas from different desert zones in China and discovered different genetic adaptations to different desert environments. Jerboas in high-altitude deserts selected ATR and HIF1AN genes, which are associated with intense UV radiation and hypoxia in high-altitude environments. In arid deserts, jerboas showed stronger genetic selection in energy and water homeostasis, indicating that water scarcity may be the main driver of desert adaptation in these animals.
Article
Biochemistry & Molecular Biology
Ling-Yun Chen, Bei Lu, Diego F. Morales-Briones, Michael L. Moody, Fan Liu, Guang-Wan Hu, Chien-Hsun Huang, Jin-Ming Chen, Qing-Feng Wang
Summary: The study explored the adaptations of plants in the Alismatales order to aquatic environments and the occurrence of whole-genome duplication events during evolution. The results indicate that different evolutionary patterns are closely related to lineage and life form.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Danwen Liu, Zhenkui Qin, Maokai Wei, Dexu Kong, Qiaojun Zheng, Shumiao Bai, Siyu Lin, Zhifeng Zhang, Yubin Ma
Summary: This study systematically analyzed the composition and expression of heat shock proteins (HSPs) in Urechis unicinctus, a species thriving in the intertidal zone. The results showed that HSPs, especially the sHSP and HSP70 families, may play significant roles in response to sulfide stress in U. unicinctus.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Engineering, Marine
Gabriele De Falco, Chiara Lauritano, Sabrina Carrella
Summary: Extreme environments have unique conditions, including hypoxia/anoxia, freezing/heat temperatures, and desiccation. Species are adapting to these conditions through miRNA-mediated responses. miRNAs regulate gene expression and can directly or indirectly influence pathways, leading to specific responses. Understanding these miRNA-mediated responses can have applications in developing biomarkers of stress and genetic engineering of algal species.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Green & Sustainable Science & Technology
Lyla Mehta, Shilpi Srivastava, Synne Movik, Hans Nicolai Adam, Rohan D'Souza, Devanathan Parthasarathy, Lars Otto Naess, Nobuhito Ohte
Summary: This paper discusses how transformation can be conceptualized from the bottom up in marginal environments with high levels of climate-related uncertainties, focusing on bottom-up change, identities, wellbeing, and the recovery of agency by marginalized people. It concludes by examining potential challenges of such engagements and emphasizes a normative and political approach to Transformations to Sustainability.
CURRENT OPINION IN ENVIRONMENTAL SUSTAINABILITY
(2021)
Article
Evolutionary Biology
Dragan Stajic, Claudia Bank, Isabel Gordo
Summary: Epigenetic regulation of gene expression allows for the emergence of distinct phenotypic states within the clonal population, and these states can switch in a stochastic manner between generations. This study shows that under fluctuating environmental conditions, rapid epigenetic switching provides an advantage, while genetic mutations are favored in stable environments.
GENOME BIOLOGY AND EVOLUTION
(2022)
Review
Biology
Ermenegilda Parrilli, Pietro Tedesco, Marco Fondi, Maria Luisa Tutino, Angelina Lo Giudice, Donatella de Pascale, Renato Fani
Summary: Extremophilic microbes have adapted to survive in harsh conditions, such as low/high temperatures. Pseudoalteromonas species, especially P. haloplanktis TAC125, are important marine bacteria known for their ability to thrive in extreme environments, particularly in cold temperatures. Their unique adaptations make them valuable for both basic research and biotechnological applications.
PHYSICS OF LIFE REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Zuyao Liu, Marius Roesti, David Marques, Melanie Hiltbrunner, Verena Saladin, Catherine L. Peichel
Summary: Chromosomal fusions play an important role in facilitating adaptation to different environments by enabling the linkage of adaptive alleles and creating regions of low recombination. Through the study of stickleback fish, researchers have found independent chromosomal fusion events in marine and freshwater lineages, which are associated with adaptive traits. Comparisons of the genomes of different stickleback populations also show enriched regions of divergent selection on these fused chromosomes. Gene flow between marine and freshwater populations can increase genetic diversity within these selection regions, supporting the formation of adaptive clusters. This study highlights the significance of chromosomal fusions in facilitating freshwater adaptation in stickleback fish.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Maxwell L. Neal, Ling Wei, Eliza Peterson, Mario L. Arrieta-Ortiz, Samuel A. Danziger, Nitin S. Baliga, Alexis Kaushansky, John D. Aitchison
Summary: Researchers developed a gene regulatory network model for Plasmodium falciparum using machine learning, which accurately predicted gene expression levels across diverse datasets. By investigating gene expression coherence, they found that artemisinin resistance in the parasite is associated with incoherent expression across multiple regulatory programs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Vivek Srinivas, Mario L. Arrieta-Ortiz, Amardeep Kaur, Eliza J. R. Peterson, Nitin S. Baliga
Article
Environmental Sciences
Jacob J. Valenzuela, Justin Ashworth, Allison Cusick, Raffaela M. Abbriano, E. Virginia Armbrust, Mark Hildebrand, Monica Orellana, Nitin S. Baliga
Summary: This study identified a potential bioindicator for the resilience shift of diatoms under ocean acidification conditions, which is a putative Na+(K+)/H+ antiporter localized in plastid membrane that may play an important role in maintaining pH homeostasis. The differential in transcript levels of this antiporter between nighttime and daytime could serve as an indicator for the resilience shift of diatoms in response to high CO2 conditions in marine environments.
FRONTIERS IN MARINE SCIENCE
(2021)
Correction
Cell Biology
Eliza J. R. Peterson, Abrar A. Abidi, Mario L. Arrieta-Ortiz, Boris Aguilar, James T. Yurkovich, Amardeep Kaur, Min Pan, Vivek Srinivas, Ilya Shmulevich, Nitin S. Baliga
Review
Oncology
James H. Park, Adrian Lopez Garcia de Lomana, Diego M. Marzese, Tiffany Juarez, Abdullah Feroze, Parvinder Hothi, Charles Cobbs, Anoop P. Patel, Santosh Kesari, Sui Huang, Nitin S. Baliga
Summary: Pronounced differences between individuals and cell-cell heterogeneity within tumors are major obstacles in effective brain tumor treatment, necessitating a personalized precision medicine approach. A systems biology approach is crucial for developing a multiscale understanding of disease mechanisms. Integrating patient tumor analysis with clinical medicine can optimize treatment strategies.
Article
Multidisciplinary Sciences
Charlotte Cooper, Eliza J. R. Peterson, Rebeca Bailo, Min Pan, Albel Singh, Patrick Moynihan, Makoto Nakaya, Nagatoshi Fujiwara, Nitin Baliga, Apoorva Bhatt
Summary: This study reveals that the mycolic acid desaturase regulator (MadR) controls mycolic acid desaturation and biosynthesis in response to cell envelope stress. This unique regulation mechanism is distinct to other regulators and MadR acts as a key regulatory checkpoint during infection to coordinate mycolic acid remodeling.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Mathematical & Computational Biology
Selva Rupa Christinal Immanuel, Mario L. Arrieta-Ortiz, Rene A. Ruiz, Min Pan, Adrian Lopez Garcia de Lomana, Eliza J. R. Peterson, Nitin S. Baliga
Summary: The ability of Mycobacterium tuberculosis to adopt heterogeneous physiological states is crucial for its immune system evasion and antibiotic resistance. Developing new TB therapeutics requires a systems-level approach to understand the complexity of network-based adaptations of Mtb.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2021)
Article
Multidisciplinary Sciences
Aaron N. Brooks, Amanda L. Hughes, Sandra Clauder-Muenster, Leslie A. Mitchell, Jef D. Boeke, Lars M. Steinmetz
Summary: This study investigates the effects of sequence features and transcriptional context on RNA transcript isoform expression. Using synthetic yeast strains with rearranged genes, the researchers discovered that neighboring transcription also influences gene expression levels and transcript isoform boundaries. They identified features of transcriptional context that can predict these alterations and successfully engineered a synthetic circuit where transcript length is controlled by neighboring transcription.
Article
Multidisciplinary Sciences
Liselot Dewachter, Aaron N. N. Brooks, Katherine Noon, Charlotte Cialek, Alia Clark-ElSayed, Thomas Schalck, Nandini Krishnamurthy, Wim Versees, Wim Vranken, Jan Michiels
Summary: Deep mutational scanning is a powerful method for investigating protein function and stability. In this study, the researchers perform deep mutational scanning on three essential E. coli proteins and study the effects of mutations in their original genomic context. They use over 17,000 protein variants to explore protein function and the importance of individual amino acids. The study also evaluates resistance development against antimicrobial compounds and identifies potential targets for drug development.
NATURE COMMUNICATIONS
(2023)
Correction
Multidisciplinary Sciences
Liselot Dewachter, Aaron N. Brooks, Katherine Noon, Charlotte Cialek, Alia Clark-ElSayed, Thomas Schalck, Nandini Krishnamurthy, Wim Versees, Wim Vranken, Jan Michiels
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Mario L. Arrieta-Ortiz, Min Pan, Amardeep Kaur, Evan Pepper-Tunick, Vivek Srinivas, Ananya Dash, Selva Rupa Christinal Immanuel, Aaron N. Brooks, Tyson R. Shepherd, Nitin S. Baliga
Summary: There is an urgent need for strategies to discover secondary drugs to prevent or disrupt antimicrobial resistance (AMR), which is causing >700,000 deaths annually. Researchers found that tetracycline-resistant Escherichia coli undergo metabolic and transcriptional remodeling to support antibiotic resistance. They also discovered that sertraline, a drug, can resensitize tetracycline-resistant E. coli to the antibiotic.
Article
Microbiology
Alan P. R. Lorenzetti, Ulrike Kusebauch, Livia S. Zaramela, Wei-Ju Wu, Joao P. P. de Almeida, Serdar Turkarslan, Adrian L. G. de Lomana, Jose V. Gomes-Filho, Ricardo Z. N. Vencio, Robert L. Moritz, Tie Koide, Nitin S. Baliga
Summary: In this study, we investigated the scale of post-transcriptional regulation in the halophilic archaeon Halobacterium salinarum NRC-1. Our integrated analysis revealed that a large number of protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for post-transcriptional processing and regulation. Additionally, we found evidence for the conditional post-transcriptional regulation of a subset of genes involved in stressful environment acclimation. These findings provide valuable insights into the role of post-transcriptional regulation in environmental adaptation and are made available as an interactive atlas for further research.
Article
Multidisciplinary Sciences
Ulrike Kusebauch, Alan P. R. Lorenzetti, David S. Campbell, Min Pan, David Shteynberg, Charu Kapil, Mukul K. Midha, Adrian Lopez Garcia de Lomana, Nitin S. Baliga, Robert L. Moritz
Summary: Researchers have reported a comprehensive spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, which enables the measurement of a large fraction of its proteome. This library provides a valuable resource for confidently measuring and quantifying any protein of this archaeon.
Article
Biochemical Research Methods
Vivek Srinivas, Rene A. Ruiz, Min Pan, Selva Rupa Christinal Immanuel, Eliza J. R. Peterson, Nitin S. Baliga
Summary: The study presents a method named DRonA and MLSynergy, which uses transcriptome signature to detect drug responses of Mycobacterium tuberculosis and predict their cell killing effects, providing a new framework for rapid monitoring of drug effects and discovery of effective drug combinations.
CELL REPORTS METHODS
(2021)
Article
Oncology
Matthew A. Wall, Serdar Turkarslan, Wei-Ju Wu, Samuel A. Danziger, David J. Reiss, Mike J. Mason, Andrew P. Dervan, Matthew W. B. Trotter, Douglas Bassett, Robert M. Hershberg, Adrian Lopez Garcia de Lomana, Alexander V. Ratushny, Nitin S. Baliga
Summary: This study reports a transcriptional regulatory network inferred from multi-omics data that accurately predicts disease progression risk in multiple myeloma patients and provides insights into possible mechanisms and therapeutic vulnerabilities.
NPJ PRECISION ONCOLOGY
(2021)
