Article
Chemistry, Multidisciplinary
Nico Fricke, Krishnan Raghunathan, Ajit Tiwari, Katherine M. Stefanski, Muthuraj Balakrishnan, Alex G. Waterson, Ricardo Capone, Hui Huang, Charles R. Sanders, Joshua A. Bauer, Anne K. Kenworthy
Summary: Plasma membrane organization greatly affects cellular functionality. Clustering of specific lipids and proteins in nanoscale membrane rafts is a well-known mechanism for this organization. However, the study of rafts is challenging due to the lack of chemical tools and therapeutic targeting methods. In this study, a high-throughput screen and image analysis pipeline were developed to identify small molecules that enhance or inhibit raft formation. The platform proved to be effective in validating known raft modulators and discovering new ones.
ACS CENTRAL SCIENCE
(2022)
Article
Chemistry, Applied
Dong-Shin Kim, Qui Woung Kim, Hoon Kim, Hyun-Jin Kim
Summary: This study found that the germination rate of rice samples is associated with their physicochemical properties, sensory quality, and seed viability. A lower germination rate leads to increased lipid oxidation, hardness, and most pasting properties of rice, while reducing seed viability, moisture content, and adhesiveness. Changes in germination rate also affect the cellular structure and metabolites related to the sensory quality of rice.
Article
Biotechnology & Applied Microbiology
Preeti Mehta, Rekha Rani, Ravi Gupta, Anshu Mathur, Sankara Sri Venkata Ramakumar
Summary: This study investigates the potential stimulatory effects of three different biochemical modulators on the biomass, lipid, and DHA production of Schizochytrium sp. MTCC 5890. Among the tested modulators, individual supplementation of 6-BAP and Ses significantly improved the biomass, lipid, and DHA accumulation. Additionally, the combined supplementation of 6-BAP and Ses further increased the productivities of biomass, lipid, and DHA.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Review
Chemistry, Multidisciplinary
Jeffrey Y. W. Mak, Ligong Liu, David P. Fairlie
Summary: Researchers have made significant contributions in the field of microbial natural products and synthetic ligands over the past decade, particularly focusing on compounds related to riboflavin and uracils that modulate immune cells. Through collaboration, they discovered a naturally occurring compound synthesized by bacteria that activates MAIT cells, leading to its use in detecting and characterizing MAIT cells in tissues.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Computer Science, Artificial Intelligence
Samuel Goldman, Jeremy Wohlwend, Martin Strazar, Guy Haroush, Ramnik J. Xavier, Connor W. Coley
Summary: MIST is a neural network-driven workflow that annotates tandem mass spectra peaks with chemical structures. It incorporates domain insights into its architecture by encoding peaks with their chemical formula representations, and outperforms standard neural architectures and the state-of-the-art kernel method.
NATURE MACHINE INTELLIGENCE
(2023)
Article
Biotechnology & Applied Microbiology
Mario Birkholz, Danai Eleni Malti, Stephan Hartmann, Peter Neubauer
Summary: This study demonstrates an electrical approach for separating lipid-producing microalgae using dielectrophoresis in a microfluidic flow cell. The method is not only suitable for process analysis, but also for strain selection of the most productive cell lines.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Gastroenterology & Hepatology
Henrik M. Roager, Catherine Stanton, Lindsay J. Hall
Summary: The development of the infant gut microbiome is crucial for the microbiome ecology, function, and host health. Technological advancements now allow for better profiling of metabolites in the infant gut, providing insights into the roles of microbial-derived metabolites in shaping the microbiome community and influencing host-microbial interactions during early life. This review summarizes the current knowledge on the development of the infant gut microbiota and metabolism within the first year of life, emphasizing the importance of microbial metabolites in enhancing our understanding of early life interactions.
Article
Chemistry, Medicinal
Samuel Goldman, Jiayi Xin, Joules Provenzano, Connor W. Coley
Summary: This study proposes an energy-based modeling framework, MIST-CF, for ranking chemical formula and adduct assignments in unannotated MS/MS spectra. The method utilizes a Formula Transformer neural network architecture for data-driven learning and eliminates the need for time-intensive fragmentation tree construction. The results demonstrate the superior performance of MIST-CF on multiple experimental datasets.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemistry & Molecular Biology
Gabriele Rocchetti, Alessandra Scansani, Giulia Leni, Samantha Sigolo, Terenzio Bertuzzi, Aldo Prandini
Summary: This study investigated the chemical changes of Coppa Piacentina, an Italian PDO meat product, during ripening and their correlation with sensory quality. The ripening time significantly altered the chemical composition, including decreased moisture content and changes in fatty acid profile. Metabolomics analysis revealed the impact of lipid oxidation during ripening, with specific metabolites being discriminant in predicting the changes observed. Sensory analysis showed the highest degree of ripening resulted in enhanced color intensity, slice firmness, and chewing consistency.
Article
Engineering, Environmental
Shweta Tripathi, Manikyaprabhu Kairamkonda, Payal Gupta, Krishna Mohan Poluri
Summary: Microalgae can mitigate the effects of environmental pollution by conserving carbon footprint and generating green energy. This study focused on the Cd-tolerant algal strain Scenedesmus sp. IITRIND2 and investigated the molecular mechanisms underlying Cd tolerance and carbon flux channelization for enhanced lipid/EPS production. The study revealed metabolic rewiring and the activation of defense networks in the algal cells, resulting in the production of biodiesel quality lipids and soluble EPS. These findings provide insight into the potential of algal-based biorefinery approaches for Cd remediation and sustainable production.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Chemistry, Analytical
Evan A. Larson, Trevor T. Forsman, Lachlan Stuart, Theodore Alexandrov, Young Jin Lee
Summary: In this study, a pipeline for rigorous annotation of on-tissue derivatized MSI data using Metaspace was presented and validated. The pipeline enabled fast and accurate annotations of metabolites, and a method to remove false derivatized annotations was developed. This pipeline facilitates broadly targeted spatial metabolomics using multiple derivatization reagents.
ANALYTICAL CHEMISTRY
(2022)
Article
Food Science & Technology
Jinhyuk Na, Hye-Jeong Hwang, Mal-Soon Shin, Mingyu Kang, Jihye Lee, Geul Bang, Young Jun Kim, Yu-Jin Hwang, Kyung-A. Hwang, Youngja H. Park
Summary: White radish extract has the most beneficial effects on reducing triglycerides, while purple radish extract significantly reduces low-density lipoprotein cholesterol. Purple radish extract improves total cholesterol and high-density lipoprotein cholesterol levels, leading to a significant decrease in the atherogenic index and cardiac risk factor.
JOURNAL OF FUNCTIONAL FOODS
(2021)
Article
Biochemical Research Methods
Sadjad Fakouri Baygi, Yashwant Kumar, Dinesh Kumar Barupal
Summary: Researchers have developed a new data processing pipeline called IDSL.IPA to generate comprehensive and high-fidelity metabolomics data matrices from large-scale population studies. The pipeline includes features such as ion pair identification, peak detection and characterization, retention time correction, peak annotation, and parallel computation for faster data processing.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Nutrition & Dietetics
Hengxian Qu, Lina Zong, Jian Sang, Yunchao Wa, Dawei Chen, Yujun Huang, Xia Chen, Ruixia Gu
Summary: In this study, transcriptomic and metabolomic analyses were used to explore the mechanism of probiotics in alleviating lipid metabolism disorders. It was found that Lactobacillus rhamnosus hsryfm 1301 fermented milk could directly regulate lipid metabolism through the modulation of metabolic pathways and indirectly regulate it through pathways such as amino acid metabolism, the nervous system, and the endocrine system. This multi-target synergy of the fermented milk helped alleviate lipid metabolism disorders caused by a high-fat diet.
Article
Pharmacology & Pharmacy
Yu Dong, Xu-Xu Zhuang, Yi-Ting Wang, Jieqiong Tan, Du Feng, Min Li, Qing Zhong, Zhiyin Song, Han-Ming Shen, Evandro F. Fang, Jia-Hong Lu
Summary: Maintaining mitochondrial homeostasis is crucial for treating various diseases, and mitophagy, the selective degradation of mitochondria, has shown promising therapeutic potential. However, there are frequent methodological flaws in studies on chemical mitophagy modulators, leading to unreliable conclusions. This review aims to summarize the molecular mechanisms of mitophagy, propose a characterization system for mitophagy modulators, analyze the methods used in previous studies, and provide novel targets for pharmacological intervention.
PHARMACOLOGICAL RESEARCH
(2023)
Article
Biochemical Research Methods
Ruifeng Hu, Guangsheng Pei, Peilin Jia, Zhongming Zhao
Summary: The study introduced and implemented a VAE model to explore large-scale epigenomics data for classification of histone modifications, tissue/cell specificity, and classification of new data with unknown sources.
Article
Biochemistry & Molecular Biology
Guangsheng Pei, Yin-Ying Wang, Lukas M. Simon, Yulin Dai, Zhongming Zhao, Peilin Jia
Summary: This study developed a tensor-based method to impute gene expression data on a transcriptome-wide level, applied it to the BrainSpan resource, and conducted deconvolutional analyses to characterize major cell-type dynamics. Integration with GWAS summary statistics revealed novel trait-cell-type associations and trait-spatio-temporal relationships. Overall, the imputed BrainSpan transcriptomic data provide a valuable resource for further studies on the transcriptional and cellular dynamics of the human brain.
Article
Biochemistry & Molecular Biology
Guangsheng Pei, Ruifeng Hu, Yulin Dai, Astrid Marilyn Manuel, Zhongming Zhao, Peilin Jia
Summary: The authors used a deep learning convolutional neural network model, DeepFun, to predict the regulatory effects of genetic variants based on epigenomic data, and prioritized trait-associated loci in GWAS studies. By applying this model, they refined important GWAS associations and provided novel insights into understanding the molecular basis of human complex diseases.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Nathaniel K. Berg, Jiwen Li, Boyun Kim, Tingting Mills, Guangsheng Pei, Zhongming Zhao, Xiangyun Li, Xu Zhang, Wei Ruan, Holger K. Eltzschig, Xiaoyi Yuan
Summary: The study revealed the crucial role of the neuronal guidance protein netrin-1 in controlling lung inflammation by modulating CCL2-dependent infiltration of NK cells during LPS-induced lung injury. Deletion of netrin-1 in the myeloid compartment led to exacerbated lung inflammation and increased mortality rates.
Article
Multidisciplinary Sciences
Peilin Jia, Ruifeng Hu, Guangsheng Pei, Yulin Dai, Yin-Ying Wang, Zhongming Zhao
Summary: Drug response in cancer patients varies significantly due to tumor heterogeneity, with transcriptome context playing a key role. Researchers developed a deep variational autoencoder model to compress gene signatures into latent vectors and accurately impute drug response.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Xinyu Song, Jinjin Diao, Jiaqi Yao, Jinyu Cui, Tao Sun, Lei Chen, Weiwen Zhang
Summary: The study introduced a synthetic NOG pathway to increase acetyl-CoA pool in Synechocystis 6803, leading to enhanced productivity by eliminating native competing pathways. The integrated approach demonstrated an increase in acetyl-CoA concentration and production of value-added chemicals in cyanobacteria.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Mengfan Tang, Guangsheng Pei, Dan Su, Chao Wang, Xu Feng, Mrinal Srivastava, Zhen Chen, Zhongming Zhao, Junjie Chen
Summary: The study identified that CCNC is a critical survival target in cells with BRCA2 loss, potentially contributing to PARPi resistance.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Guangsheng Pei, Ruifeng Hu, Peilin Jia, Zhongming Zhao
Summary: The Deep-Fun web server utilizes a convolutional neural network framework and chromatin profiles from ENCODE and Roadmap projects to assess the functional activity of non-coding genetic variants. It expands the functionality of existing non-coding variant prioritizing tools by providing specific functional assessments in a tissue- and cell type-specific manner. The server has been validated with datasets from various GWAS studies and is expected to be widely used in genetics, functional genomics, and disease studies.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Bingrui Li, Guangsheng Pei, Jun Yao, Qingqing Ding, Peilin Jia, Zhongming Zhao
Summary: This study comprehensively characterized cell-type alterations across 18 cancer types and identified myofibroblastic CAF (myCAF) composition as a poor prognostic factor in nine cancer types. Furthermore, genes associated with the differentiation degree of myCAF and inflammatory CAF (iCAF) were identified, highlighting their roles in fibroblast and extracellular matrix-related pathways. These findings provide therapeutic perspectives for targeting CAF subtypes in the tumor microenvironment and arranging treatment schemes based on CAF compositions in different cancer types.
Article
Biochemical Research Methods
Xuyang Sun, Shubin Li, Fenfang Zhang, Tao Sun, Lei Chen, Weiwen Zhang
Summary: In this study, a genetic switch repressed by NanR and induced by N-acetylneuraminic acid (Neu5Ac) was developed in fast-growing cyanobacteria. The switch achieved high induction with minimal leakage through optimization of NanR expression level and introduction of Neu5Ac transporter. The orthogonality between the NanR/Neu5Ac switch and theophylline-responsive riboregulator was also investigated, showing potential for coordinated or binary regulation of target genes.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Oncology
Divya Ravirala, Brandon Mistretta, Preethi H. Gunaratne, Guangsheng Pei, Zhongming Zhao, Xiaoliu Zhang
Summary: Novel chimeric molecules, BiCEP and TriCEP, were constructed and evaluated in this study for their ability to engage both NK and T cells, enhancing antitumor activities. Both molecules showed promising results in engaging immune cells to kill tumor cells, suggesting their potential in oncolytic virotherapy for cancer treatment.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2021)
Article
Biochemical Research Methods
Jiaqi Yao, Jin Wang, Yue Ju, Zhengxin Dong, Xinyu Song, Lei Chen, Weiwen Zhang
Summary: This study engineered a xylose utilization pathway from Escherichia coli into fast-growing cyanobacteria, enabling photomixotrophic cultivation based on xylose. By rewiring the metabolism and driving more carbon flux from xylose to acetyl-CoA, the biosynthesis of 3-hydroxypropionic acid was significantly improved.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Xu Feng, Mengfan Tang, Merve Dede, Dan Su, Guangsheng Pei, Dadi Jiang, Chao Wang, Zhen Chen, Mi Li, Litong Nie, Yun Xiong, Siting Li, Jeong-Min Park, Huimin Zhang, Min Huang, Klaudia Szymonowicz, Zhongming Zhao, Traver Hart, Junjie Chen
Summary: Exploiting cancer vulnerabilities is crucial for finding anticancer drugs. This study used CRISPR screens to uncover genetic interactions between tumor suppressor genes and protein-coding genes, leading to the discovery of high-confidence synthetic lethal interactions and essential paralog gene pairs. It also suggests that targeting certain tumor suppressors could suppress the proliferation of cells lacking other tumor suppressors, providing valuable information for targeted cancer therapy.
Article
Genetics & Heredity
Guangsheng Pei, Fangfang Yan, Lukas M. Simon, Yulin Dai, Peilin Jia, Zhongming Zhao
Summary: Single-cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex and dynamic cellular mechanisms. In this study, the researchers present deCS, an automatic cell type annotation method that enhances annotation accuracy using comprehensive human cell type expression profiles and marker genes. The results show that expanding the references is critical for improving annotation accuracy, and deCS significantly reduces computation time and increases accuracy compared to existing tools. The researchers also demonstrate the broad utility of deCS in identifying trait-cell type associations in human complex traits, providing deep insights into disease pathogenesis.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Danesh H. Sopariwala, Andrea S. Rios, Guangsheng Pei, Anirban Roy, Meiricris Tomaz da Silva, Hao Thi Thu Nguyen, Addison Saley, Rachel Van Drunen, Anastasia Kralli, Kristin Mahan, Zhongming Zhao, Ashok Kumar, Vihang A. Narkar
Summary: In this study, the role of nuclear receptor ERR alpha/gamma in regulating skeletal muscle composition, contractility, and exercise capacity was elucidated. The deletion of ERR alpha/gamma led to decreased expression of genes associated with mitochondrial and oxidative metabolism, resulting in impaired mitochondrial function, angiogenesis, and exercise capacity.
Article
Agricultural Engineering
Yinping Xiang, Meiying Jia, Rui Xu, Jialu Xu, Lele He, Haihao Peng, Weimin Sun, Dongbo Wang, Weiping Xiong, Zhaohui Yang
Summary: This study investigated the impact of the non-antibiotic pharmaceutical carbamazepine on antibiotic resistance genes (ARGs) during anaerobic digestion. The results showed that carbamazepine induced the enrichment of ARGs and increased the abundance of bacteria carrying these genes. It also facilitated microbial aggregation and intercellular communication, leading to an increased frequency of ARGs transmission. Moreover, carbamazepine promoted the acquisition of ARGs by pathogens and elevated their overall abundance.
BIORESOURCE TECHNOLOGY
(2024)
Review
Agricultural Engineering
Weixin Zhao, Tianyi Hu, Hao Ma, Dan Li, Qingliang Zhao, Junqiu Jiang, Liangliang Wei
Summary: This review summarizes the effects and potential mechanisms of biochar on microbial behavior in AD systems. The addition of biochar has been found to promote microbial colonization, alleviate stress, provide nutrients, and enhance enzyme activity. Future research directions include targeted design of biochar, in-depth study of microbial mechanisms, and improved models.
BIORESOURCE TECHNOLOGY
(2024)
Review
Agricultural Engineering
Christina Karmann, Anna Magrova, Pavel Jenicek, Jan Bartacek, Vojtech Kouba
Summary: This review assesses nitrogen removal technologies in reject water treatment, highlighting the differences in environmental impacts and economic benefits. Partial nitritation-anammox shows potential for economic benefits and positive environmental outcomes when operated and controlled properly.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Wei-Hao Huang, Ying-Ju Chang, Duu-Jong Lee
Summary: This study modified pinecone biochar with layered double hydroxide (LDH) to enhance its adsorption capacity for heavy metal and phosphate ions. The LDH-biochar showed significantly improved adsorption capacities for Pb2+ and phosphate, and a slight increase for Cu2+ and Co2+. The LDH layer enhanced the adsorption through various mechanisms.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Chao Song, Fanfan Cai, Shuang Yang, Ligong Wang, Guangqing Liu, Chang Chen
Summary: This paper developed a machine learning model to predict the biochemical methane potential during anaerobic digestion. Model analysis identified lignin content, organic loading, and nitrogen content as key attributes for methane production prediction. For feedstocks with high cellulose content, early methane production is lower but can be improved by prolonging digestion time. Moreover, lignin content exceeding a certain value significantly inhibits methane production.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Sang Min Lee, Ju Young Lee, Ji-Sook Hahn, Seung-Ho Baek
Summary: This study successfully developed an efficient platform strain using Yarrowia lipolytica for the bioconversion of renewable resources into adipic acid, achieving a remarkable increase in production level.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Sefkan Kendir, Matthias Franzreb
Summary: This study presents a novel approach using magnetic separation to efficiently harvest freshwater microalgae, Chlorella vulgaris. By combining pH-induced calcium phosphate precipitation with cheap natural magnetite microparticles, harvesting efficiencies up to 98% were achieved in the model medium.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Ishaq Kariim, Ji-Yeon Park, Wajahat Waheed Kazmi, Hulda Swai, In-Gu Lee, Thomas Kivevele
Summary: The impact of reaction temperature, residence time, and ethanol: acetone on the energy compositions and yield enhancement of biocrudes was investigated. The results showed that under appropriate conditions, biocrudes with high energy and low oxygen content can be obtained, indicating a high potential for utilization.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Xiyue Zhang, Xiyao Li, Liang Zhang, Yongzhen Peng
Summary: Intermittent aeration is an innovative approach to enhance nitrogen removal in low carbon-to-nitrogen ratio municipal sewage, providing an efficient strategy for the continuous plug-flow AOA process.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Xu Yang, Mahmoud Mazarji, Mengtong Li, Aohua Li, Ronghua Li, Zengqiang Zhang, Junting Pan
Summary: This study investigated the impact of magnetite on the nitrogen cycle of pig manure biostabilisation. The addition of magnetite increased N2O emissions and decreased NH3 emissions during composting. It also increased the total nitrogen content but should be considered for its significant increase in N2O emissions in engineering practice.
BIORESOURCE TECHNOLOGY
(2024)
Review
Agricultural Engineering
Ty Shitanaka, Haylee Fujioka, Muzammil Khan, Manpreet Kaur, Zhi-Yan Du, Samir Kumar Khanal
Summary: The market value of microalgae has exponentially increased in the past two decades, thanks to their applications in various industries. However, the supply of high-value microalgal bioproducts is limited due to several factors, and strategies are being explored to overcome these limitations and improve microalgae production, thus increasing the availability of algal-derived bioproducts in the market.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Martin Kerner, Thorsten Wolff, Torsten Brinkmann
Summary: The efficiency of using enriched CO2 from flue gas for large-scale production of green microalgae has been studied. The results show that the use of membrane devices and static mixers can effectively improve the CO2 recovery rate and maintain the suitable pH and temperature during cultivation, achieving a more economical and sustainable microalgae production.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Rui Ma, Ji Li, Rd Tyagi, Xiaolei Zhang
Summary: This review summarizes the microorganisms capable of using CO2 and CH4 to produce PHAs, illustrating the production process, factors influencing it, and discussing optimization techniques. It identifies the challenges and future prospects for developing economically viable PHAs production using GHGs as a carbon source.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Bing Wang, Peng Zhang, Xu Guo, Xu Bao, Junjie Tian, Guomin Li, Jian Zhang
Summary: The addition of zeolite in the co-composting of chicken manure and straw significantly reduced the emissions of ammonia and N2O, and increased the nitrate content. Zeolite also promoted the abundance of nitrification genes and inhibited the expression of denitrification genes.
BIORESOURCE TECHNOLOGY
(2024)
Article
Agricultural Engineering
Rohit Dey, Franziska Ortiz Tena, Song Wang, Josef Martin Messmann, Christian Steinweg, Claudia Thomsen, Clemens Posten, Stefan Leu, Matthias S. Ullrich, Laurenz Thomsen
Summary: This study investigated the operation of a 1000L microalgae-based membrane photobioreactor system for continuous secondary wastewater treatment. The research focused on a green microalgae strain called Desmodesmus sp. The study aimed to understand key trends and optimization strategies by conducting experiments in both summer and winter seasons. The findings showed that maintaining low cell concentrations during periods of light inhibition was beneficial for nutrient uptake rates. Effective strategies for enhancing algae-based wastewater treatment included cell mass recycling and adjusting dilution rates based on light availability.
BIORESOURCE TECHNOLOGY
(2024)
