Article
Biotechnology & Applied Microbiology
Jingxian Zhang, Jiping Shi, Chenyang Yuan, Xiangcen Liu, Guilin Du, Ruimei Fan, Baoguo Zhang
Summary: This study investigated the role of miRNAs in lipid accumulation induced by nitrogen deprivation in Chlamydomonas reinhardtii. It identified a set of miRNAs that showed differential expression after nitrogen deprivation, suggesting their involvement in lipid transport and metabolism. The findings highlight the importance of miRNAs in microalgae lipid accumulation and provide theoretical guidance for bio-oil engineering production.
BIOENGINEERING-BASEL
(2022)
Article
Biotechnology & Applied Microbiology
Yufei Zhang, Zipeng Gu, Yudong Ren, Lu Wang, Jian Zhang, Chengwei Liang, Shanying Tong, Yitao Wang, Dong Xu, Xiaowen Zhang, Naihao Ye
Summary: The study revealed that Chlamydomonas reinhardtii exhibits specific adaptive evolution to elevated CO2, especially under long-term conditions, where although the nutritional constituents decrease, the growth and photosynthesis of algal cells significantly increase.
MARINE BIOTECHNOLOGY
(2021)
Review
Biochemical Research Methods
Mohammad Reza Karimi, Amir Hossein Karimi, Shamsozoha Abolmaali, Mehdi Sadeghi, Ulf Schmitz
Summary: Holistic perspectives are crucial in understanding the complexity of tumors and current single-layer analysis has limitations. Integrative multilayer approaches are emerging as effective tools in achieving systemic views on cancer biology.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Chemistry, Physical
V Grechanik, I Naidov, M. Bolshakov, A. Tsygankov
Summary: This study demonstrates the possibility of phototrophic hydrogen production in C. reinhardtii under N-deprived conditions, indicating a potential strategy for sustainable hydrogen production. The implementation of a two-step illumination protocol can significantly enhance hydrogen production, and the relationship between PSII activity and hydrogen production in C. reinhardtii was investigated.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2021)
Article
Environmental Sciences
Zhongquan Jiang, Yutong Sun, Huize Guan, Danqing Sun, Shu Fang, Xuening Ma, Zhongyang Wang, Zhen Li, Chunhua Zhang, Ying Ge
Summary: The study found that when exposed to low concentrations of As(V), Chlamydomonas reinhardtii accumulated starch and produced more extracellular polysaccharides, while under high concentrations of As(V), the cells redirected carbon flux and transformed lipids into polysaccharides, indicating the critical involvement of polysaccharides in As(V) resistance in C. reinhardtii.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Article
Environmental Sciences
Yan Huang, Jinlong Lai, Yang Huang, Xuegang Luo, Xu Yang, Zewei Liu, Yue Duan, Chen Li
Summary: This study investigated the effects of nano-BiOI on freshwater microalgae and its toxicological mechanisms. The results showed that nano-BiOI stimulated algal growth at low concentrations but inhibited growth at higher concentrations. Nano-BiOI induced the generation of intracellular reactive oxygen species and interfered with the mineral nutrient metabolism of the algae. Metabolomics analysis revealed significant alterations in metabolic pathways under high concentrations of nano-BiOI.
JOURNAL OF ENVIRONMENTAL SCIENCES
(2022)
Article
Clinical Neurology
Dominique F. Leitner, Yik Siu, Aryeh Korman, Ziyan Lin, Evgeny Kanshin, Daniel Friedman, Sasha Devore, Beatrix Ueberheide, Aristotelis Tsirigos, Drew R. Jones, Thomas Wisniewski, Orrin Devinsky
Summary: High-fat and low-carbohydrate diets, such as the modified Atkins diet (MAD), can reduce seizure frequency in treatment-resistant epilepsy patients. These diets mimic fasting and induce high levels of ketone bodies, potentially shifting brain energy production and impacting neuronal and astrocyte metabolism.
Article
Multidisciplinary Sciences
Lei Li, Lin Huang, Chenyang Huang, Jia Xu, Yukai Huang, Haihua Luo, Xinya Lu, Shuyue He, Gang Yuan, Li Chen, Xue Han, Xusong Cao, Aolin Jiang, Cuiting Liu, Junmin Shi, Hong Yang, Yong Jiang
Summary: This study focused on the molecular dynamics profiles of exosomes in serum during the development of sepsis. High-performance liquid chromatography-tandem mass spectrometry and RNA-seq were used to detect the dynamic profiles of exosome proteins and RNAs. Integrative multiomics analyses revealed the association of exosome components with various biological processes and molecular pathways. Importantly, exosomes derived from septic serum showed potential therapeutic effects in septic mice.
JOURNAL OF ADVANCED RESEARCH
(2022)
Review
Plant Sciences
Xiangyu Xu, Cassio Flavio Fonseca de Lima, Lam Dai Vu, Ive De Smet
Summary: Changes in weather patterns, drought risks, and rising global temperature negatively impact crop growth and productivity. Plants are exposed to multiple stresses simultaneously, but most studies focus on individual stress conditions. This mini-review focuses on the combination of drought and heat, summarizing current research results, identifying knowledge gaps, and suggesting potential future focus areas.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Quentin Nicoud, Florian Lamouche, Anais Chaumeret, Thierry Balliau, Romain Le Bars, Mickael Bourge, Fabienne Pierre, Florence Guerard, Erika Sallet, Solenn Tuffigo, Olivier Pierre, Yves Dessaux, Francoise Gilard, Bertrand Gakiere, Istvan Nagy, Attila Kereszt, Michel Zivy, Peter Mergaert, Benjamin Gourion, Benoit Alunni
Summary: The study reveals a low symbiotic efficiency between Bradyrhizobium diazoefficiens USDA110 and Aeschynomene afraspera, with a disconnection of terminal bacteroid differentiation features. This unique symbiotic relationship results in reduced bacterial viability under high stress conditions.
Review
Biotechnology & Applied Microbiology
Bashar Amer, Edward E. K. Baidoo
Summary: Biomanufacturing, a key component of biotechnology, utilizes biological systems to produce commercial bioproducts which are of interest to various industries. Technologies like synthetic biology and metabolic engineering heavily rely on omics driven systems biology for research and development, aiding in the establishment of industrial biomanufacturing platforms. These technologies have a significant impact on the production of biofuels, bioproducts, agricultural and food biotechnology, as well as current COVID-19 research.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Review
Oncology
Miaomiao Ye, Yibin Lin, Shuya Pan, Zhi-wei Wang, Xueqiong Zhu
Summary: Ovarian cancer ranks as the fifth most common cause of cancer-related death in females. Multi-omics approaches have been applied to determine the mechanisms of ovarian oncogenesis at different levels and have identified potential diagnostic and prognostic biomarkers and therapeutic targets. The discovery of molecular signatures and targeted therapy strategies could significantly improve the prognosis of ovarian cancer patients.
FRONTIERS IN ONCOLOGY
(2021)
Review
Microbiology
Juan Jose Gonzalez-Plaza, Cristina Furlan, Tomaz Rijavec, Ales Lapanje, Rocio Barros, Juan Antonio Tamayo-Ramos, Maria Suarez-Diez
Summary: The study of microbial cells interacting with natural and synthetic interfaces has been enriched by the development of advanced omics technologies, allowing for the isolation and analysis of nucleic acids, proteins, and metabolites from complex samples. This review discusses the challenges in analyzing microbial cells at genomic, transcriptomic, proteomic, and metabolomic levels, and describes both experimental and computational approaches to address them. The integration of multi omics datasets is presented as a means to achieve a systems level understanding of these complex interactions.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Christina Skodra, Vaia Styliani Titeli, Michail Michailidis, Christos Bazakos, Ioannis Ganopoulos, Athanassios Molassiotis, Georgia Tanou
Summary: The olive tree is the most important perennial crop in the Mediterranean region, but olive drupe research has received less attention. Olive drupe ripening is a complex process involving numerous physiological and molecular changes. The application of -omics techniques provides a systematic description of olive fruit development and ripening.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
David I. Gonzalez, Ruby A. Ynalvez
Summary: This study compared the effects of nitrogen-, sulfur-, and nitrogen and sulfur-deprivations on the C. reinhardtii starchless mutant cc5373-sta6. Nutrient-deprived cells showed higher total chlorophyll, cell density, and protein content. Lipid bodies in cells subjected to nutrient deprivation increased in number and size, with variations in expression levels of ACC and PEPC under different deprivation conditions.
Article
Plant Sciences
Tessa B. Moyer, Jessie L. Allen, Lindsey N. Shaw, Leslie M. Hicks
Summary: Traditional medicinal plants are a rich source of antimicrobial agents, including antimicrobial peptides (AMPs). Advances in genomic sequencing, in silico AMP predictions, and mass spectrometry-based peptidomics have enabled high-throughput discovery of bioactive peptides. This study profiled Amaranthus tricolor aerial tissue using MS-based proteomics/peptidomics, identifying AMPs predicted in silico and uncovering novel peptides within three AMP classes. Bioactivity screening of isolated Atr-LTP1 showed efficacy against ESKAPE bacterial pathogens.
JOURNAL OF NATURAL PRODUCTS
(2021)
Article
Biochemistry & Molecular Biology
Thualfeqar Al-Mohanna, Najmeh Nejat, Anthony A. Iannetta, Leslie M. Hicks, George Popescu, Sorina C. Popescu
Summary: Upon pathogen infection, receptors in plants trigger localized and systemic immune responses, with oscillations in the redox environment altering protein function. Arabidopsis thaliana thimet oligopeptidases TOP1 and TOP2 play crucial roles in plant defense against pathogens and oxidative stress, with increased activity under oxidative regulation contributing to immune signaling. TOP1 and TOP2 are involved in ROS-induced gene expression and can cleave immune component peptides, suggesting a role in redox-mediated signaling of local and systemic immunity.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Mike Pollard, Yair Shachar-Hill
Summary: Quantitative flux maps describing glycerolipid synthesis are important for engineering lipid content and composition in oilseeds. This study investigated the kinetic complexity of glycerolipid flux network in cultured embryos of Camelina sativa. The results showed that there were two distinct synthesis components for triacylglycerol (TAG), with the major component associated with the intermediate pool dominated by diacylglycerol (DAG) and phosphatidylcholine (PC), and the minor component localized to surface cells across the whole embryo.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Yuan Xu, Thomas Wieloch, Joshua A. M. Kaste, Yair Shachar-Hill, Thomas D. Sharkey
Summary: This study presents a carbon-13 washout model for leaf metabolism and identifies three processes that contribute to the labeling of Calvin-Benson cycle (CBC) metabolites. The model integrates CBC, cytosolic sugar pools, the glucose-6-phosphate shunt, and vacuolar sugars into a single system, providing a more complete understanding of carbon movement in photosynthetic metabolism.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Tingting Li, Na Pang, Lian He, Yuan Xu, Xinyu Fu, Yinjie Tang, Yair Shachar-Hill, Shulin Chen
Summary: The microalga Chlorella sorokiniana adjusts metabolic flux and biomass synthesis to adapt to light conditions. Under light conditions, the microalga reduces fluxes in glucose catabolism, the tricarboxylic acid cycle, and anaplerotic reaction, while activating the RuBisCO reaction.
Article
Biochemical Research Methods
Kathryne C. Ford, Joshua A. M. Kaste, Yair Shachar-Hill, Michaela A. TerAvest
Summary: This study demonstrates the potential of genetic engineering in the bacterium S. oneidensis for carbon-neutral production. By using Flux Balance Analysis (FBA) and gene knockdown experiments, the researchers successfully deleted a conditionally essential gene and paved the way for future electricity-driven CO2 conversion.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Plant Sciences
Danielle Yvonne Hoffmann, Yair Shachar-Hill
Summary: Acyl editing refers to a cycle of deacylation and reacylation on a lipid, which plays a crucial role in fatty acid desaturation and modification prior to incorporation into other pools. This review focuses on the comparison of acyl editing in land plants and algae, particularly the evidence for acyl editing on phosphatidylcholine (PC) and betaine lipids such as diacylglyceryltrimethylhomoserine (DGTS). The review also discusses the contribution of DGTS to lipid synthesis in microalgae and proposes future analyses to study the role of betaine lipids in acyl editing.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Anne K. Steensma, Yair Shachar-Hill, Berkley J. Walker
Summary: This study investigates the growth mechanism of Cyanidioschyzonmerolae, an extremophilic red microalga, in low-pH and high-temperature environments. The findings suggest that this alga may use a novel carbon-concentrating mechanism (CCM).
PHOTOSYNTHESIS RESEARCH
(2023)
Article
Plant Sciences
Samia Daldoul, Mahmoud Gargouri, Christoph Weinert, Ali Jarrar, Bjoern Egert, Ahmed Mliki, Peter Nick
Summary: This study compared the physiological and metabolic responses of a salt-tolerant accession of Vitis sylvestris, Tebaba, from Tunisia, with the widely used 1103 Paulsen rootstock in the Mediterranean. It was found that Tebaba can cope with salinity through robust redox homeostasis, rechanneling metabolic pathways towards antioxidants and compatible osmolytes, and buffering photosynthesis to avoid cell-wall breakdown. It is suggested that introgression of Tebaba into commercial grapevine varieties is preferred over using Tebaba as a rootstock for improving salt tolerance.
Article
Biochemistry & Molecular Biology
Joshua A. M. Kaste, Antwan Green, Yair Shachar-Hill
Summary: The modeling of biochemical reaction rates, or fluxes, in metabolic networks is commonly used in both basic biological research and biotechnological applications. Different modeling methods, such as kinetic and constraint-based approaches, have been developed to estimate and predict fluxes. However, there is a lack of resources that teach these approaches in an integrated way. We have developed a series of modeling simulations in Python to teach various metabolic modeling techniques and have seen improvements in learners' competence and confidence after attending a metabolic modeling workshop that utilized these simulations.
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION
(2023)
Article
Plant Sciences
Yuan Xu, Abubakarr A. Koroma, Sean E. Weise, Xinyu Fu, Thomas D. Sharkey, Yair Shachar-Hill
Summary: Plants employ various adaptive strategies to respond to daylength variation, including adjustments in growth, photosynthesis, carbon utilization, and metabolic flux. Under short-day conditions, plants compensate for reduced CO2 fixation by enhancing photosynthetic rates and reducing respiration in the light, while also reducing the partitioning of glucose and increasing starch accumulation to sustain carbon availability during the longer night. Isotopic labeling results demonstrate substantial changes in the partitioning of amino acids and TCA cycle intermediates between rapidly and slowly turning over pools in response to different daylengths.
Article
Biochemical Research Methods
Joshua A. M. Kaste, Yair Shachar-Hill
Summary: The study demonstrates that integrating relative gene expression levels into metabolic flux predictions improves the accuracy of the predictions in a multi-tissue system.
Review
Biotechnology & Applied Microbiology
Joshua A. M. Kaste, Yair Shachar-Hill
Summary: This article reviews the history and state-of-the-art in constraint-based metabolic model validation and model selection. It proposes a combined model validation and selection framework that incorporates metabolite pool size information.
BIOTECHNOLOGY PROGRESS
(2023)
Article
Biochemical Research Methods
Kathryne C. Ford, Joshua A. M. Kaste, Yair Shachar-Hill, Michaela A. TerAvest
Summary: This study presents a pipeline for deleting a conditional essential gene from the genome of Shewanella oneidensis bacteria. The effects of gene deletions on cell growth and survival were analyzed using Flux Balance Analysis and gene knockdown experiments. The results indicate that the deleted gene is not essential for survival, providing a foundation for further genetic engineering.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Plant Sciences
Danielle Yvonne Young, Na Pang, Yair Shachar-Hill
Summary: Isotopic labeling research reveals that a major chloroplast membrane lipid in Chlamydomonas cells contributes glyceryl backbones and fatty acids for oil accumulation through the removal of its headgroup. This finding is significant for the potential utilization of microalgae lipids as feedstocks for biofuels, nutraceuticals, and other high-value compounds.
