Article
Genetics & Heredity
Selina Jansky, Ashwini Kumar Sharma, Verena Koerber, Andres Quintero, Umut H. Toprak, Elisa M. Wecht, Moritz Gartlgruber, Alessandro Greco, Elad Chomsky, Thomas G. P. Gruenewald, Kai-Oliver Henrich, Amos Tanay, Carl Herrmann, Thomas Hoefer, Frank Westermann
Summary: Single-cell transcriptomic analysis reveals cell types and lineage trajectories during different developmental stages in neuroblastomas and healthy adrenal glands. The transcriptomes of neuroblastoma cells closely resemble developing neuroblasts of the adrenal gland.
Article
Plant Sciences
Nan Sun, Can Li, Xiangning Jiang, Ying Gai
Summary: ATP-binding cassette transporters (ABC transporters) are crucial for plant physiology, including organ development, nutrient acquisition, stress response, disease resistance, and environmental interaction. This study investigated the transcriptomic changes in transgenic tobacco with overexpression of LkABCG36 and LkABCG40 transporters. The results showed enrichment in cell wall biogenesis and hormone signal transduction for LkABCG36, and metabolic and biosynthetic processes related to environmental adaptation for LkABCG40. These findings suggest that LkABCG36 promotes plant organ growth and development by increasing auxin transport, while LkABCG40 enhances resistance in transgenic tobacco.
Article
Biotechnology & Applied Microbiology
Melissa K. Drown, Douglas L. Crawford, Marjorie F. Oleksiak
Summary: Physiological trait variation plays a crucial role in health, responses to global climate change, and ecological performance. However, we still have limited knowledge about the genes and genomic architectures that define this variation. By studying the relationship between physiological traits and mRNA expression, we can gain insights into the genetic architecture of physiological processes and understand how mRNA expression is related to heritable fitness-related traits.
Article
Ecology
Kun Zhou, Tin Yan Wong, Lexin Long, Karthik Anantharaman, Weipeng Zhang, Wai Chuen Wong, Rui Zhang, Pei-Yuan Qian
Summary: Marine biofilms are complex communities of microorganisms that play a crucial ecological role in oceans. Our study unveiled active viruses in natural biofilms and their complex interplay with prokaryotes. Biofilm prokaryotes have more abundant defence genes than seawater prokaryotes, and the defence gene composition differs between biofilms and the surrounding seawater.
Article
Fisheries
Chuankun Zhu, Zhengjun Pan, Guoliang Chang, Nan Wu, Hui Wang, Huaiyu Ding, Xiaogang Qiang, Lei Zhang, Jun Qiang, Ji Zhang, Tingwu Liu
Summary: This study identified Aeromonas veronii as the pathogen causing ulcerative syndrome in Pseudobagrus ussuriensis for the first time, and revealed differential gene expressions in the liver, head kidney, and spleen of infected fish. The immune-related DEGs involved in both innate and adaptive immunity responses against ulcerative syndrome were identified, providing valuable information for future genetic studies and genetic improvement of P. ussuriensis against ulcerative syndrome.
Article
Environmental Sciences
Lufang Su, Dandan Guo, Heping Wan, Ping Wang, Lan Cao, Yanmin Long, Chaohui Chen, Yangyang Song, Yonghong Zhang, Changli Zeng, Rui Guo, Xiaoyun Liu
Summary: This study revealed the effects of flame retardants on Arabidopsis by transcriptome and metabolome analysis. The findings showed that these compounds had different inhibitory effects on seed germination and plant growth, and influenced various pathways and channels. Additionally, different types of flame retardants had variant characteristics on plants. Arabidopsis exhibited a response to biotic stress, including immune mechanisms, after exposure to these compounds. Overall, this research provided vital insights into the molecular perspective of Arabidopsis response to flame retardant stress through transcriptome and metabolome analysis.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Genetics & Heredity
Yu-Fang Tang, Pu-Gen An, Bao-Xin Gu, Shu Yi, Xiao Hu, Wen-Jie Wu, Jie Zhang
Summary: This study investigated the underlying mechanisms of adenoid cystic carcinoma (ACC) at the transcriptome level. A new gene fusion, TVP23C-CDRT4, was found to be highly expressed in ACC. PRAME may serve as a potential target for ACC immunotherapy.
FRONTIERS IN GENETICS
(2023)
Article
Plant Sciences
Mingming Dong, Shudan Xue, Ezra S. Bartholomew, Xuling Zhai, Lei Sun, Shuo Xu, Yaqi Zhang, Shuai Yin, Wenyue Ma, Shuying Chen, Zhongxuan Feng, Chao Geng, Xiangdong Li, Xingwang Liu, Huazhong Ren
Summary: This study provides insights into the molecular processes involved in multicellular trichome formation in cucumber and presents a framework for understanding the regulatory network of multicellular trichome formation.
Review
Genetics & Heredity
Ioannis Eleftherianos, Christa Heryanto
Summary: Insects in nature interact with a wide variety of microbial enemies, including entomopathogenic and filarial nematodes, which are crucial for devising strategies to reduce disease transmission in humans. Transcriptomic approaches are key in identifying insect molecules with anti-nematode activity and understanding conserved pathways of anti-nematode immunity in humans.
Article
Horticulture
Rongli Mo, Na Zhang, Jinxin Li, Qiang Jin, Zhixian Zhu, Zhaoxia Dong, Yong Li, Cheng Zhang, Cui Yu
Summary: This study identified differentially expressed genes associated with anthocyanin accumulation in mulberries through transcriptome analysis, and found that ethylene enhances anthocyanin accumulation in mulberry fruits.
Article
Environmental Sciences
Li Xia, Ma Xiaodong, Cheng Yunhe, Liu Junxiang, Zou Junzhu, Zhai Feifei, Sun Zhenyuan, Han Lei
Summary: The study utilized transcriptomics and metabolomics to analyze changes in gene expression and metabolites in Salix viminalis roots under phenanthrene stress. The results demonstrated that the plant had a positive defense strategy in response to phenanthrene challenge and may have initiated defense-related reactions within a short period of time.
Article
Plant Sciences
Thais R. Boufleur, Nelson S. S. Massola Jr, Sioly Becerra, Elena Baraldi, Lillian B. J. Bibiano, Serenella A. A. Sukno, Michael R. R. Thon, Riccardo Baroncelli
Summary: This study investigates the response of soybean to different strains of C. truncatum and reveals that different soybean cultivars exhibit varying levels of susceptibility. The study also identifies genes related to the plant immune system that play important roles in defense against soybean anthracnose.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Xin Li, Chenying Duan, Ruyi Li, Dong Wang
Summary: The study revealed that differentially expressed genes and epigenetic regulatory networks play important roles in sperm head and tail formation. The ART3 protein is crucial for sperm deformation and its localization was investigated, providing new insights into male infertility research. Investigating the localization of ART3 protein in seminiferous tubules and epididymal sperm sheds light on the process of spermiogenesis, offering potential for the development of new strategies for male infertility treatment.
Article
Food Science & Technology
Yuchang Wang, Yuyang Song, Dawei Wang
Summary: The metabolome and transcriptome profiles of different variations of Docynia delavayi fruit were analyzed to understand the mechanism of fruit color formation. Flavonoid metabolites were identified as the major coloring substances, and the expression of certain genes in the anthocyanin synthesis pathway was found to be significantly upregulated. This study provides important insights for breeding and nutritional research in D. delavayi.
Article
Plant Sciences
Sunjeet Kumar, Xinfang Huang, Gaojie Li, Qun Ji, Kai Zhou, Guopeng Zhu, Weidong Ke, Hongwei Hou, Honglian Zhu, Jingjing Yang
Summary: Blanching significantly affects gene expression and pathways in the stems of water dropwort, impacting photosynthesis and plant hormone signal transduction pathways.
Article
Biochemistry & Molecular Biology
Carla Hurt, Kristin Hultgren, Arthur Anker, Alan R. Lemmon, Emily Moriarty Lemmon, Heather Bracken-Grissom
Summary: The snapping shrimp genus Alpheus, with its hyperdiverse nature, presents challenges in understanding evolutionary relationships and mechanisms behind its diversification. The use of AHE method in this study showed a lack of monophyly in traditionally defined species groups and the independent evolution of symbiotic associations in multiple lineages within the genus.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Joanna M. Wolfe, Javier Luque, Heather D. Bracken-Grissom
Summary: The article discusses the evolutionary history of the crab body plan and the degree of phenotypic variation within crabs, proposing ecological advantages of the crab body and a hypothesis of phenotypic integration. This provides a foundation for future research on the genomic and developmental basis of the crab-like body form.
Editorial Material
Biochemistry & Molecular Biology
Danielle M. DeLeo, Heather D. Bracken-Grissom
Summary: Understanding the drivers of biodiversity requires consideration of various factors, including genetics, selective pressures, and neutral processes. This study uses an integrative approach to explore the drivers behind the diversification of bioluminescent signaling in cypridinid ostracods, tracing the molecular evolution of luciferase to decipher the link between genotype and phenotype.
Article
Ecology
Laura E. Timm, Thomas L. Jackson, Joan A. Browder, Heather D. Bracken-Grissom
Summary: The Gulf of Mexico pink shrimp, Farfantepenaeus duorarum, plays a crucial role in fisheries in the United States and Mexico, with management efforts focused on understanding the impact of early life history on genetic diversity and population structure. Recent research in the Gulf has revealed differentiated populations and highlighted the importance of genetic diversity in management decisions for this commercially important species.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Biodiversity Conservation
Carlos Varela, Heather Bracken-Grissom
Summary: By combining morphological and molecular techniques, this study successfully identified 12 unknown larval and two juvenile species from the infraorder Caridea and suborder Dendrobranchiata in the northern Gulf of Mexico. This research fills the gap in missing or non-existent larval descriptions for many taxa, serving as a crucial first step in advancing the understanding of deep-sea larval diversity.
Article
Evolutionary Biology
Charles Golightly, Danielle M. DeLeo, Nicole Perez, Tin-Yam Chan, Jose M. Landeira, Heather D. Bracken-Grissom
Summary: Deep-sea shrimp of the family Sergestidae Dana, 1852 provide a unique system for studying the evolution of bioluminescence. The present study used molecular data to construct an updated genus-level phylogeny of sergestid shrimp, compared with previous morphological trees, and identified preliminary patterns across light organ type and species' depth distributions.
INVERTEBRATE SYSTEMATICS
(2022)
Article
Marine & Freshwater Biology
Connor O'Brien, Heather D. Bracken-Grissom, J. Antonio Baeza
Summary: The semi-terrestrial Atlantic ghost crab Ocypode quadrata is a medium-sized species found in sandy temperate and tropical beaches of the western Atlantic Ocean. Despite its ecological importance and use as a bio-indicator, there are limited genetic and genomic resources available for this species. This study successfully assembled and characterized the complete mitochondrial genome of O. quadrata, revealing its gene content and organization, and providing valuable genomic resources for further research on this species. An analysis of selective pressure on protein-coding genes showed purifying selection across all genes, with variations observed in different regions.
JOURNAL OF CRUSTACEAN BIOLOGY
(2022)
Article
Marine & Freshwater Biology
Stormie B. Collins, Heather D. Bracken-Grissom, J. Antonio Baeza
Summary: This study reports the complete mitochondrial genome of Farfantepenaeus duorarum and reveals its conserved gene order with congeners. The analysis of K-A/K-S ratios suggests that purifying selection is acting on all coding genes in F. duorarum's mitochondrial genome. This research provides valuable insights into the genomic features and evolutionary adaptations of F. duorarum.
JOURNAL OF CRUSTACEAN BIOLOGY
(2022)
Article
Ecology
Lorian E. Schweikert, Kate N. Thomas, Vanessa M. Moreno, Anchita Casaubon, Charles Golightly, Heather D. Bracken-Grissom
Summary: Constraints on energy resources and available light in the deep sea lead to differences in eye size among deep-sea sergestid shrimps, with eye size related to visual performance and ecology. Light organ type is a significant correlate of eye size, suggesting the importance of bioluminescence in sergestid vision. The study reveals that eye size increases with depth before 1,000 m and then decreases in the aphotic zone, and sighting distance thresholds of bioluminescence vary between species.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Genetics & Heredity
Angelica Colin, Carolina Galvan-Tirado, Laura Carreon-Palau, Heather D. Bracken-Grissom, J. Antonio Baeza
Summary: This study characterized the complete mitochondrial genomes of two anomuran species and found that their genome structures and codon usage profiles are similar to other congeneric species. The selective pressure analysis on protein-coding genes revealed that these genes have undergone purifying selection. Furthermore, the phylogenomic analysis based on translated protein-coding genes confirmed the monophyly of the infraorder Anomura and provided more detailed relationships at the genus level.
Article
Genetics & Heredity
Pedro A. Peres, Heather Bracken-Grissom, Laura E. Timm, Fernando L. Mantelatto
Summary: This study used mtDNA data and ddRAD-seq technology to explore the diversification patterns and processes within the swimming crab C. ornatus. The results showed significant genetic differentiation between groups on the north and south sides of the AOP, but also signs of hybridization. Demographic modeling indicated that divergence started around 8 million years ago following the formation of the AOP. The study suggested that speciation with gene flow was explained by the interplay among the AOP, oceanographic currents, and long larval dispersal.
Article
Multidisciplinary Sciences
Lorian E. Schweikert, Laura E. Bagge, Lydia F. Naughton, Jacob R. Bolin, Benjamin R. Wheeler, Michael S. Grace, Heather D. Bracken-Grissom, Soenke Johnsen
Summary: By studying hogfish, the authors describe a cellular mechanism in which chromatophore pigment activity alters the light hitting the SWS1 receptors in the skin, providing insight into the significance of dermal photoreception. One possible function of dermal photoreception in hogfish is to monitor chromatophores and detect information about color change performance.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Tamara Frank, Jamie Sickles, Danielle Deleo, Patricia Blackwelder, Heather Bracken-Grissom
Summary: Many marine species use bioluminescence to counterilluminate, and recent studies have shown that deep-sea shrimps have light-sensitive photophores. Our experiments on Pesta shrimps also demonstrated photosensitivity in their internal organs, suggesting a dual functionality of light detection and emission in these photophores.
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Jorge L. Perez-Moreno, Mihika T. Kozma, Danielle M. DeLeo, Heather D. Bracken-Grissom, David S. Durica, Donald L. Mykles
Summary: Transcriptomes from nontraditional model organisms often contain unexplored data that can provide insights in traditional systems and other fields. However, access to genomic and transcriptomic resources for these organisms is limited.
G3-GENES GENOMES GENETICS
(2023)
Meeting Abstract
Zoology
H. D. Bracken-Grissom, C. Golightly, L. Schweikert, D. M. Deleo
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2023)