Article
Multidisciplinary Sciences
Peijie Zhou, Shuxiong Wang, Tiejun Li, Qing Nie
Summary: MuTrans is a method based on multiscale reduction technique that can identify the underlying stochastic dynamics governing cell-fate transitions, construct cell-fate dynamical manifold, distinguish stable and transition cells, and quantify transition probabilities between cell states. The method is consistent with Langevin equation and transition rate theory, and has been shown to robustly unravel complex cell fate dynamics induced by transition cells in various systems. It bridges data-driven and model-based approaches for single-cell resolution analysis of cell-fate transitions.
NATURE COMMUNICATIONS
(2021)
Article
Fisheries
Fengqin Shang, Mingxiu Bao, Fujun Liu, Ziwen Hu, Shengnan Wang, Xiao Yang, Yundeng Yu, Hongbin Zhang, Chihang Jiang, Xuemei Qiu, Yang Liu, Xiuli Wang
Summary: Through transcriptomic analysis, this study revealed the biological processes and molecular mechanisms of hypoxia in Takifugu rubripes. Hypoxia downregulated genes associated with the immune system and inflammation, but promoted dissolved oxygen uptake through angiogenesis and altered the expression patterns of genes involved in the inhibition of cell growth and proliferation.
Article
Agronomy
Yujie Lin, Jian Ma, Nan Wu, Fan Qi, Zhanwu Peng, Dandan Nie, Rongrong Yao, Xin Qi, Jan Slaski, Fu Yang, Ningning Wang, Jian Zhang
Summary: Alkaline stress affects plant growth and development by altering endogenous ionic concentration and osmotic pressure, and triggering gene expression. In this study, we analyzed the changes in gene expression of a salt-alkali stress tolerance rice cultivar subjected to extreme high pH alkaline stress. The differentially expressed genes (DEGs) were mainly enriched in apoptotic process, metabolic pathways, and hormone synthesis. We also identified 125 genes specifically expressed during alkaline stress for the first time.
Article
Biochemistry & Molecular Biology
Matin Miryeganeh, Hidetoshi Saze
Summary: Mangrove trees, with their high adaptability to difficult coastal conditions, serve as an interesting model system for understanding stress tolerance in plants. This study utilized RNA-Seq to characterize the leaf transcriptome of the Bruguiera gymnorhiza species and compared gene expression profiles between populations growing under different levels of stress, providing valuable insights into plant adaptations. Genes related to salt and osmotic stress showed elevated expression levels in trees growing in high salinity conditions, suggesting potential targets for future research on salt resistance in mangroves and other woody plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Hiroki Ura, Sumihito Togi, Yo Niida
Summary: This study compared the advantages and disadvantages of three RNA-Seq library preparation methods and found that TruSeq detected transcripts and splicing events better than the other methods, accurately measuring gene expression levels and splicing events. TeloPrime had higher coverage at the transcription start site, while SMARTer performed better than TeloPrime in terms of the number of detected transcripts and splicing events among the studied full-length double-stranded cDNA methods.
Article
Horticulture
Yanli Yao, Mingwei Li, Wenqiu Lin, Shenghui Liu, Qingsong Wu, Qiong Fu, Zhuying Zhu, Yuyao Gao, Xiumei Zhang
Summary: Watercore is a physiological disorder in pineapples that affects fruit quality and storage life. This study, using transcriptome analysis, revealed the molecular mechanism of watercore for the first time and identified key genes related to this disorder.
Article
Multidisciplinary Sciences
Yuki Yoshioka, Hiroshi Yamashita, Go Suzuki, Chuya Shinzato
Summary: Research found that Acropora corals tend to select a single species of symbiont, Symbiodinium microadriaticum, in early life stages, even though this species is rarely found in mature colonies. When coral larvae were exposed to native symbionts, the gene expression gradually changed, with upregulation of pattern recognition receptor-like and transporter genes, and suppression of cellular function genes related to immunity and apoptosis.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Matin Miryeganeh, Hidetoshi Saze
Summary: This study presents the transcriptome of the widely distributed mangrove Rhizophora stylosa and examines its response to salt stress, providing insights into the molecular mechanisms underlying stress response in mangroves and other plants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Keyvan Esmaeilzadeh-Salestani, Masoud Tohidfar, Rahele Ghanbari Moheb Seraj, Banafsheh Khaleghdoust, Indrek Keres, Hashem Marawne, Evelin Loit
Summary: This study compares the effects of organic and mineral nitrogen fertilizers on gene activity in barley. The results show that mineral nitrogen fertilizer treatment leads to a higher number of differentially expressed genes compared to organic nitrogen fertilizer treatment. Pathways related to amino acid synthesis and ribosomal activities are upregulated in mineral fertilizer treatment, while pathways related to starch and sucrose metabolism and carotenoid biosynthesis are downregulated. Organic nitrogen fertilizer treatment enriches pathways related to phenylpropanoid biosynthesis and plant-pathogen interaction. These findings provide insights into the genetic regulation of barley growth in field conditions and can guide the development of sustainable cropping practices and low nitrogen input varieties.
Article
Biochemistry & Molecular Biology
Desalegn D. Serba, Xiaoxi Meng, James Schnable, Elfadil Bashir, J. P. Michaud, P. V. Vara Prasad, Ramasamy Perumal
Summary: The study used RNA-Seq technology to analyze the effects of sugarcane aphid on moderately resistant and susceptible genotypes, revealing transcriptome differences between the two genotypes at multiple time points after infestation by SCA. The resistant genotype exhibited differential expression of several gene clusters during SCA infestation, while the susceptible genotype showed a series of down-regulated genes on the basis of the resistant genotype.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Octavio Martinez, Magda L. Arce-Rodriguez, Fernando Hernandez-Godinez, Christian Escoto-Sandoval, Felipe Cervantes-Hernandez, Corina Hayano-Kanashiro, Jose J. Ordaz-Ortiz, M. Humberto Reyes-Valdes, Fernando G. Razo-Mendivil, Ana Garces-Claver, Neftali Ochoa-Alejo
Summary: This study compared the gene expression profiles of domesticated and wild chili pepper ancestors during fruit development, revealing significant differences in cell cycle gene expression between them, possibly driven by selection pressures during domestication. Domesticated genotypes showed higher gene expression levels and earlier peaks.
Article
Agriculture, Dairy & Animal Science
Jitka Kyselova, Ladislav Tichy, Zuzana Sztankoova, Jirina Markova, Katerina Kavanova, Monika Beinhauerova, Michala Muskova
Summary: This study explores the potential role of immune genes in the fight against caseous lymphadenitis (CL) in sheep. By investigating the blood transcriptome, the study provides new insights into the disease course and host-pathogen interaction, which can help prevent the spread of incurable diseases and improve animal breeding for bacterial resistance.
Article
Plant Sciences
Pawandeep Singh Kohli, Lekha T. Pazhamala, Balaji Mani, Jitendra Kumar Thakur, Jitender Giri
Summary: Root hairs are extensions of root epidermal cells that increase in length and density under low phosphorus availability. This study explores the genes involved in root hair development and response to low phosphorus in chickpea, an important leguminous crop. The findings reveal that genes related to root hair initiation and cellular differentiation are upregulated, and genes involved in cell wall synthesis, cytoskeleton/vesicle transport, and ethylene biosynthesis are also upregulated in root hairs. In addition, genes related to low phosphorus responses, such as lipid and/or pectin P remobilization and acid phosphatases, are induced in root hairs. The study also highlights the preferential enrichment of processes involved in symbiotic interactions in root hairs. Overall, root hairs exhibit a multifaceted response to low phosphorus, involving molecular changes in epidermal cell differentiation and root hair initiation, as well as tip growth and various low phosphorus responses in elongated root hairs.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Zongchang Xu, Meng Wang, Tingting Ren, Keyang Li, Yiqiang Li, Prince Marowa, Chengsheng Zhang
Summary: The study revealed that the accumulation of Na+ in leaves of Apocynum venetum under salt stress led to a decrease in flavonoid concentration, resulting in reduced salt tolerance. Overexpressing flavonoid synthesis pathway genes in Arabidopsis improved salt tolerance due to increased total flavonoid accumulation. The findings provide a foundation for understanding the molecular mechanisms underlying salt tolerance in plants.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Vasiliy V. Reshetnikov, Polina E. Kisaretova, Natalia P. Bondar
Summary: Research on the molecular causes of stress-associated psychopathologies is crucial for understanding the development mechanisms of depression, generalized anxiety disorder, and posttraumatic stress disorders. This study conducted a meta-analysis of transcriptome changes in mice and human patients, finding the most reliable molecular alterations associated with different durations of stress.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Emma F. Camp, Tim Kahlke, Matthew R. Nitschke, Deepa Varkey, Nerissa L. Fisher, Lisa Fujise, Samantha Goyen, David J. Hughes, Caitlin A. Lawson, Mickael Ros, Stephen Woodcock, Kun Xiao, William Leggat, David J. Suggett
ENVIRONMENTAL MICROBIOLOGY
(2020)
Article
Ecology
Kate M. Quigley, Carlos Alvarez Roa, Victor H. Beltran, Bill Leggat, Bette L. Willis
Summary: The research shows that experimental selection of heat-tolerant symbionts can improve coral heat tolerance, but this tolerance may not directly translate to enhanced growth and survival of the coral.
RESTORATION ECOLOGY
(2021)
Article
Marine & Freshwater Biology
Francesco Ricci, Alexander Fordyce, William Leggat, Linda L. Blackall, Tracy Ainsworth, Heroen Verbruggen
Summary: The study characterized the endolithic microbial community of the common coral Isopora palifera in the Great Barrier Reef, revealing the abundance of oxygenic photosynthetic endolithic microbes, including chlorophyll a. The bacterial community was mainly composed of Proteobacteria, Bacteroidetes, Actinobacteria, and Spirochaetes, while the micro-eukaryotic community was dominated by endolithic green algae and the protist Labyrynthula at high relative abundance.
Article
Microbiology
A. J. Fordyce, T. D. Ainsworth, W. Leggat
Summary: This study reveals correlations between coral interspecific skeletal morphology and endolithic microbial biomass, largely influenced by skeleton density and light capture capacity. Different coral species show significant differences in endolithic microbial biomass, with skeletal structure being a predictor of these interspecific variations.
Article
Biochemistry & Molecular Biology
Tracy D. Ainsworth, William Leggat, Brian R. Silliman, Coulson A. Lantz, Jessica L. Bergman, Alexander J. Fordyce, Charlotte E. Page, Juliana J. Renzi, Joseph Morton, C. Mark Eakin, Scott F. Heron
Summary: Coral bleaching has had a significant impact on reefs worldwide, with the realization of near-annual bleaching events in recent years. While technology allows for the prediction of large-scale bleaching, the ability to predict reef-scale and within-reef patterns in real-time for all reef users is limited.
Article
Marine & Freshwater Biology
Clinton A. Oakley, Stefanie Pontasch, Paul L. Fisher, Shaun P. Wilkinson, Robert A. Keyzers, Thomas Krueger, Sophie Dove, Ove Hoegh-Guldberg, William Leggat, Simon K. Davy
Summary: This study investigated the composition and response of thylakoid fatty acids of dinoflagellate symbionts to high- and low-temperature stress in the southernmost coral reef. The results showed genotype-specific differences in fatty acid quality and a similar fatty acid adjustment response to temperature changes. However, fatty acid saturation was not a reliable predictor of photosystem efficiency under thermal stress in dinoflagellate symbionts.
Article
Environmental Sciences
William Leggat, Scott F. Heron, Alexander Fordyce, David J. Suggett, Tracy D. Ainsworth
Summary: Despite decades of research into coral bleaching, a standardized metric for comparing ecological observations and experimental simulations is still lacking. The introduction of the experimental Degree Heating Week (eDHW) metric aims to standardize the variable thermal conditions employed in experimental studies of coral bleaching.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2022)
Article
Environmental Sciences
Jessica L. Bergman, William Leggat, Tracy D. Ainsworth
Summary: The study shows that Pocillopora damicornis responds to thermal stress by experiencing a decline in symbiont densities and photophysiological parameters, while the microbial community remains stable regardless of the degree of thermal stress. This suggests that generalist species like P. damicornis may play a role in shaping coral reef ecosystems following disturbances.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Multidisciplinary Sciences
Emma F. Camp, Tim Kahlke, Brandon Signal, Clinton A. Oakley, Adrian Lutz, Simon K. Davy, David J. Suggett, William P. Leggat
Summary: The Symbiodiniaceae are a diverse family of marine dinoflagellates that have a symbiotic relationship with invertebrates. They are sensitive to thermal stress, and research shows that this sensitivity is influenced by both phylogenetic dependent and independent traits. To understand the drivers of Symbiodiniaceae heat stress tolerance, researchers have provided a dataset that includes transcriptome, metabolome, and proteome data.
Review
Biochemistry & Molecular Biology
Francesco Ricci, William Leggat, Charlotte E. Page, Tracy D. Ainsworth
Summary: GAs, characterized by anomalous growth formations in stony corals, are a widespread coral disease linked to human activities. The biological functions of GA tissue include limited reproduction, reduced access to resources, and weakened ability to defend against predators. Studies have shown that disease progression may involve host genes related to oncogenesis.
TRENDS IN MICROBIOLOGY
(2022)
Article
Marine & Freshwater Biology
Stephanie Grace Gardner, William Leggat, Tracy Danielle Ainsworth
Summary: The coral reef crisis has influenced research for over two decades, during which time the capacity of corals to withstand and respond to environmental stress has been documented from the cellular to ecosystem level. Over the past decade, research is increasingly working towards uncovering the extent of coral-bacterial interactions, finding that diverse and stable microbial interactions can be indicative of the health of the coral host.
Article
Biology
Christopher R. J. Kavazos, Francesco Ricci, William Leggat, Jordan M. Casey, J. Howard Choat, Tracy D. Ainsworth
Summary: The study investigates the intestinal microbiome of planktivorous and algae-farming damselfish species using 16S rRNA gene sequencing. The results show that the richness of the intestinal bacterial communities of damselfish reflects the host species' diet and trophic guilds. Algae-farming damselfish have a more diverse core microbiome and are enriched in Actinobacillus and Pasteurellaceae, while planktivorous damselfish are enriched in Vibrionaceae.
INTEGRATIVE ORGANISMAL BIOLOGY
(2022)
Article
Ecology
Coulson A. Lantz, William Leggat, Jessica L. Bergman, Alexander Fordyce, Charlotte Page, Thomas Mesaglio, Tracy D. Ainsworth
Summary: Coral bleaching events continue to degrade coral reefs worldwide, causing a shift in the ecosystem from coral to algae dominance. This study found that during a bleaching event, a degraded coral reef community was still able to maintain positive net ecosystem calcification and production, despite declining coral health. Elevated temperatures may have enhanced calcification in non-hermatypic calcifiers. However, the study highlights that positive net ecosystem calcification on degraded reefs may not equate to net positive accretion of a complex reef structure in the future.
Article
Biodiversity Conservation
C. E. Page, W. Leggat, S. F. Heron, A. J. Fordyce, T. D. Ainsworth
Summary: The study found that high water flow conditions can delay coral responses to thermal stress, but do not provide long-term protection; sustained exposure to thermal stress will eventually affect coral health.
CONSERVATION PHYSIOLOGY
(2021)
Article
Fisheries
A. J. Fordyce, T. D. Ainsworth, C. E. Page, J. L. Bergman, C. A. Lantz, W. Leggat
Summary: Climate change is leading to more frequent marine heatwaves globally, resulting in widespread coral reef degradation. Endolithic microalgae reproduce abundantly during marine heatwaves, potentially delaying coral starvation while accelerating the dissolution of coral skeletons, affecting the structural complexity of coral reefs. The high frequency of these blooms underscores the importance of further research to understand the role of these microorganisms during coral bleaching events.
MARINE AND FRESHWATER RESEARCH
(2021)