Article
Chemistry, Medicinal
Maxim S. Kokoulin, Lyudmila A. Romanenko, Aleksandra S. Kuzmich, Oleg Chernikov
Summary: Two cell-wall-associated polysaccharides were isolated and purified from a deep-sea marine bacterium, with the first one containing d-arabinose and the second one consisting of d-galactose and a rare component of bacterial glycans, d-xylulose.
Article
Multidisciplinary Sciences
Dragana Despotovic, Einav Aharon, Olena Trofimyuk, Artem Dubovetskyi, Kesava Phaneendra Cherukuri, Yacov Ashani, Or Eliason, Martin Sperfeld, Haim Leader, Andrea Castelli, Laura Fumagalli, Alon Savidor, Yishai Levin, Liam M. Longo, Einat Segev, Dan S. Tawfik
Summary: Anthropogenic organophosphorus compounds (AOPCs) are widely used synthetic organic phosphorus compounds. Only a few bacteria have been found to possess the key enzyme for AOPC degradation. This study reveals the utilization of diverse AOPCs by marine bacteria, indicating their capability to adapt to phosphorus limitation and pollution. The discovery offers potential for the bioremediation of anthropogenic pollutants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Zeng-Hui Zhang, Rui-Lian Lin, Xiang-Yun Yu, Li-Xia Chen, Zhu Tao, Xin Xiao, Gang Wei, Carl Redshaw, Jing-Xin Liu
Summary: The study showed that Q[8] can encapsulate l-valine, d-leucine, and d-methionine in aqueous solution. X-ray crystallography revealed the structural details of the inclusion complexes formed between Q[8] and the amino acids, with the deformation degree of the Q[8] host being related to the molecular size of the encapsulated guests.
Article
Multidisciplinary Sciences
Jianan Li, Wenxia Yu, Shisheng Huang, Susu Wu, Liping Li, Jiankui Zhou, Yu Cao, Xingxu Huang, Yunbo Qiao
Summary: Both ABEs and CBEs can induce transcriptome-wide RNA off-target editing independent of gRNA. Engineering ABEmax variants has successfully achieved minimized RNA off-target activities as the goal.
NATURE COMMUNICATIONS
(2021)
Article
Engineering, Marine
Rosario Calogero, Carmen Rizzo, Erika Arcadi, Maria Giulia Stipa, Pierpaolo Consoli, Teresa Romeo, Pietro Battaglia
Summary: In this study, luminescent bacteria were isolated from two deep sea organisms, and the luxAB gene was used as a molecular approach to detect bioluminescence. Physiological tests and screening of extracellular polymeric substances were conducted. The majority of the isolates were related to species of Photobacterium, with one exception of a Vibrio isolate from the teleost Chlorophthalmus agassizi.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2022)
Article
Agriculture, Dairy & Animal Science
C. W. Maynard, S. Y. Liu, J. T. Lee, J. Caldas, J. J. E. Diehl, S. J. Rochell, S. Dridi, M. T. Kidd
Summary: This study investigated the dietary valine requirements for female broilers through three experiments, with a conclusion that the requirement is 78 Val/Lys for males and 77 Val/Lys for females based on feed conversion responses. No significant linear or quadratic responses were found in experiments 1 through 3, while some responses were observed in experiments 4 and 5, suggesting a potential need for further investigation.
ANIMAL FEED SCIENCE AND TECHNOLOGY
(2021)
Article
Food Science & Technology
Yusa Nakamura, Takanori Sato, Muneshige Takatori, Toshihiko Hirama, Kazuhito Oshima, Kigen Takahashi
Summary: This study provides the first report on the effective utilization of the deep sea for improving food quality. The results suggest that deep-sea aging can promote proteolysis and enhance the quality of fish such as greater amberjack, while its effectiveness may vary depending on fish species and depths.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Linda Armbrecht, Michael E. Weber, Maureen E. Raymo, Victoria L. Peck, Trevor Williams, Jonathan Warnock, Yuji Kato, Ivan Hernandez-Almeida, Frida Hoem, Brendan Reilly, Sidney Hemming, Ian Bailey, Yasmina M. Martos, Marcus Gutjahr, Vincent Percuoco, Claire Allen, Stefanie Brachfeld, Fabricio G. Cardillo, Zhiheng Du, Gerson Fauth, Chris Fogwill, Marga Garcia, Anna Glueder, Michelle Guitard, Ji-Hwan Hwang, Mutsumi Iizuka, Bridget Kenlee, Suzanne O'Connell, Lara F. Perez, Thomas A. Ronge, Osamu Seki, Lisa Tauxe, Shubham Tripathi, Xufeng Zheng
Summary: Antarctica is susceptible to climate change, and it is crucial to study the responses of the polar marine ecosystem to ensure urgent action. Sedimentary ancient DNA analysis provides insights into ecosystem-wide changes, as demonstrated in this study of the Scotia Sea region.
NATURE COMMUNICATIONS
(2022)
Article
Environmental Sciences
Hongyi Li, Zhengyan Kang, Kaixin Zhang, Shichu Gong, Xinxin Zhao, Zhen Yan, Shuguang Wang, Chao Song
Summary: Microbiologically influenced corrosion (MIC) caused by biofilm is a serious problem in many industries. D-amino acids could enhance traditional corrosion inhibitors by reducing biofilm formation. This study investigated the synergistic corrosion inhibition mechanism of D-Phenylalanine (D-Phe) and 1-hydroxyethane-1,1-diphosphonic acid (HEDP) on Desulfovibrio vulgaris-induced corrosion. The combination of HEDP and D-Phe effectively reduced corrosion, inhibited biofilm formation, and altered gene expression related to cell structure, electron transfer, and quorum sensing.
ENVIRONMENTAL RESEARCH
(2023)
Article
Food Science & Technology
Sirinapa Sasanam, Vilai Rungsardthong, Benjawan Thumthanaruk, Sombat Wijuntamook, Vasan Rattananupap, Savitri Vatanyoopaisarn, Chureerat Puttanlek, Dudsadee Uttapap, Solange Mussatto
Summary: This study investigated the production of process flavorings by direct extrusion method using a model system consisted of D-xylose and different amino acids, and analyzed the aroma compounds, solubility, and water absorption index. The properties and odor characteristics of the flavorings varied significantly depending on the amino acids used.
Article
Environmental Sciences
Ying Liu, Yi-Rong Liu, Ya-Juan Feng, Teng Huang, Shuai Jiang, Zi-Hang Wang, Hui Cao, Wei Huang
Summary: New Particle Formation (NPF) is a crucial source of aerosol particles and has significant impacts on the environment and human health. Recent field detections have shown the presence of valine (VAL) in urban areas, suggesting its potential role in atmospheric nucleation. However, there is still a lack of comprehensive reports on how VAL interacts with precursor Sulfuric Acid (SA) and atmospheric organic amine Dimethylamine (DMA) in multi-component nucleation. This paper uses quantum chemical calculation and cluster kinetic simulation to investigate the nucleation mechanism of (SA)x(DMA)y(VAL)z (0
ATMOSPHERIC ENVIRONMENT
(2021)
Article
Ecology
Dalton J. Leprich, Beverly E. Flood, Peter R. Schroedl, Elizabeth Ricci, Jeffery J. Marlow, Peter R. Girguis, Jake V. Bailey
Summary: The study demonstrates the presence of sulfur-oxidizing bacteria on carbonate rocks at marine methane seeps, and their ability to induce carbonate dissolution. Experimental results show that sulfur-oxidizing bacteria can dissolve carbonate at different rates in bioreactors simulating seep conditions, indicating that the acidic microenvironments produced by these bacteria can dissolve carbonate rocks.
Article
Biotechnology & Applied Microbiology
Lian Wang, Huijing Wang, Jianbin Chen, Zhijie Qin, Shiqin Yu, Jingwen Zhou
Summary: A new biosynthetic pathway was constructed by introducing caffeic acid synthesis modules into Escherichia coli, leading to an increased titer of rosmarinic acid and reduced synthesis of analogues. L-amino acid deaminase was introduced to balance metabolic flux, and the stability of caffeoyl-CoA was improved by knocking out the menI gene. The final strain achieved the highest reported production of rosmarinic acid in fed-batch fermentation. The strategies applied in this study provide a foundation for the synthesis of other caffeic acid and rosmarinic acid derivatives.
METABOLIC ENGINEERING
(2023)
Article
Environmental Sciences
Ananya Ashok, Susana Agusti
Summary: Oligotrophic areas in the oceans are important, but little is known about the sensitivity of microbial communities to pollutants in such areas. This study found that when exposed to polycyclic aromatic hydrocarbons (PAHs), some microbial populations in the oligotrophic Red Sea decreased, and chlorophyll-a levels also decreased substantially. However, certain bacteria and Synechococcus sp. showed high tolerance, indicating adaptation to chronic pollution.
Article
Biophysics
Da-xia Zhang, Rui Wang, Haichao Cao, Jian Luo, Tong-fang Jing, Bei-xing Li, Wei Mu, Feng Liu, Youming Hou
Summary: A study was conducted to synthesize an ecofriendly polymer for nanogel delivery system of pesticide, which showed favorable stability and efficient pest control under various conditions. The nanogel demonstrated prolonged pest control period and effective bioactivity against pests, indicating a promising future for pesticide delivery.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2022)
Article
Chemistry, Physical
Ryuju Suzuki, Kazuma Yasuhara, Shigeru Deguchi
Summary: This study demonstrates the significant impact of molecular distortion on the optical properties of carotenoids, suggesting the potential for creating new materials by actively controlling the conformation of flexible molecules.
JOURNAL OF PHYSICAL CHEMISTRY C
(2022)
Article
Biotechnology & Applied Microbiology
Junya Hirai, Syun-ichi Urayama, Yoshiro Takaki, Miho Hirai, Keizo Nagasaki, Takuro Nunoura
Summary: This study investigated the diversity of viruses associated with zooplankton collected from the subtropical western North Pacific using sequencing methods. The results showed that zooplankton function as a reservoir of diverse RNA viruses and that studying zooplankton viruses can provide a better understanding of the role of viruses in marine ecosystems.
MICROBES AND ENVIRONMENTS
(2022)
Article
Biochemistry & Molecular Biology
Satoshi Hiraoka, Tomomi Sumida, Miho Hirai, Atsushi Toyoda, Shinsuke Kawagucci, Taichi Yokokawa, Takuro Nunoura
Summary: In this study, culture-independent "metaepigenomic" analysis using single-molecule real-time sequencing was conducted on marine microbial communities, revealing diverse unexplored DNA modifications and novel alternative specificities in MTases. These findings are significant for understanding the co-evolutionary history of methylation systems and genomes.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Mikiko Tsudome, Mikako Tachioka, Masayuki Miyazaki, Kohsuke Uchimura, Miwako Tsuda, Yoshihiro Takaki, Shigeru Deguchi
Summary: This study developed a nanofiber-based assay for the enzymatic hydrolysis of cellulose, enabling quantification of enzymatic degradation of <1 ng crystalline cellulose and revealing genetic diversity in cellulase-producing microorganisms. This highlights the importance of interdisciplinary collaboration in addressing sustainability challenges.
Review
Biochemical Research Methods
So Fujiyoshi, Kyoko Yarimizu, Ishara Perera, Michel Abanto, Milko Jorquera, Fumito Maruyama
Summary: The cause of harmful algal blooms has been a mystery, but research using genetic technologies has made progress in understanding its mechanism. A long-term monitoring of toxic algae and its associated bacteria as a community, known as 'holobiont', in Chilean coastal waters has been conducted from the perspective of bacteria as the driver of algal blooms. This review discusses the challenges of holobiont monitoring, particularly in standardization and compliance with monitoring protocols, to ensure reliable and sustainable data collection. It suggests adopting the high-throughput sequencing (HTS) standard operating procedure (SOP) by the International Human Microbiome to enhance the quality and consistency of holobiont monitoring in the harmful algal world.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)
Article
Microbiology
Mikiko Tsudome, Mikako Tachioka, Masayuki Miyazaki, Miwako Tsuda, Yoshihiro Takaki, Shigeru Deguchi
Summary: Cell strain GE09T was isolated from a nanofibrous cellulose plate immersed in the deep sea. It is a Gram-stain-negative, motile, aerobic cell that can grow with cellulose as its sole nutrient. The closest relative of strain GE09T is Marinagarivorans algicola Z1T, with a similarity of 97.4%. The difference in carbohydrate-active enzymes and major cellular fatty acids between GE09T and M. algicola Z1T reflects their differences in energy sources and isolation environments. Based on these taxonomic characteristics, strain GE09T represents a new species in the genus Marinagarivorans, named Marinagarivorans cellulosilyticus sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Shigeru Deguchi, Hiroki Degaki, Ikuo Taniguchi, Tsuyoshi Koga
Summary: The deep sea, characterized by high pressure, low temperature, and no sunlight, provides unique physicochemical processes and specialized biochemical mechanisms that can inspire scientific and technological advances. This Perspective discusses three examples of deep-sea-inspired chemistry: soft materials that respond to high pressures, molecular self-assembly inspired by the chemistry of deep-sea hydrothermal vents, and nanobiotechnology and biomimetics inspired by survival strategies of deep-sea organisms. The Perspective aims to promote the sustainable utilization of the ocean based on knowledge and inspire chemists to harness their inspiration from the deep sea.
Article
Multidisciplinary Sciences
Kunal Dutta, Sergey Shityakov, Fumito Maruyama
Summary: Under low iron conditions, fadD and irr genes were upregulated in Bradyrhizobium japonicum. FadD showed similarity to Xcc's RpfB in protein folding and functional domains, and exhibited similar molecular docking and dynamics simulation results. The upregulation of fadD in response to low iron conditions may lead to the inhibition of DSF's iron uptake and virulence.
SCIENTIFIC REPORTS
(2023)
Review
Multidisciplinary Sciences
Jianjian Hou, So Fujiyoshi, Ishara Uhanie Perera, Yukiko Nishiuchi, Makiko Nakajima, Daisuke Ogura, Kyoko Yarimizu, Fumito Maruyama
Summary: Bioaerosols are important in the atmosphere and can impact human health. Most bioaerosol samples have low biomass, including those from indoor and outdoor environments. High-volume filter-based or liquid-based samplers compatible with NGS analysis are needed to improve bioaerosol detection limits for microorganisms.
JOURNAL OF THE INDIAN INSTITUTE OF SCIENCE
(2023)
Article
Biochemical Research Methods
Mikako Tachioka, Mikiko Tsudome, Shigeru Deguchi
Summary: This paper presents a surface pitting observation technology (SPOT) for quantitatively analyzing enzymatic hydrolysis of cellulose. By using a porous substrate to accelerate the hydrolysis rate and combining inkjet patterning and optical profilometry, the volume loss during hydrolysis can be analyzed.
Review
Microbiology
Yi Zhang, Yoshihiro Takaki, Yukari Yoshida-Takashima, Satoshi Hiraoka, Kanako Kurosawa, Takuro Nunoura, Ken Takai
Summary: With the advance of high-throughput sequencing, the molecular basis of coevolutionary interaction between viruses and host microorganisms is predominantly elucidated by in silico genomic analyses. This article proposes a one-day workflow using in vitro protein synthesis and enzymatic assays to confirm the function of putative R-M genes. The approach allows for preliminary characterizations of putative R-M systems with minimal equipment and time costs.
Review
Biotechnology & Applied Microbiology
Syun-ichi Urayama, Yoshihiro Takaki, Yuto Chiba, Yanjie Zhao, Misa Kuroki, Daisuke Hagiwara, Takuro Nunoura
Summary: This review summarizes the host-virus relationships of eukaryotic microbial RNA viruses. By analyzing the classification and environmental distribution of different virus families, it is found that persistent-type viruses play an important role in viral diversity and host relationships.
MICROBES AND ENVIRONMENTS
(2022)
Article
Biotechnology & Applied Microbiology
Mamoru Oshiki, Yoshihiro Takaki, Miho Hirai, Takuro Nunoura, Atsushi Kamigaito, Satoshi Okabe
Summary: This study performed a metagenomic analysis of anammox bacterial enrichment cultures and obtained 14 high-quality metagenome-assembled genomes. It revealed the genome composition of anammox bacteria and identified the involvement of Bacteroidota and Chloroflexota MAGs in the degradation of polymeric substances.
MICROBES AND ENVIRONMENTS
(2022)
Article
Biotechnology & Applied Microbiology
Shoichi Sakaguchi, Syun-ichi Urayama, Yoshihiro Takaki, Kensuke Hirosuna, Hong Wu, Youichi Suzuki, Takuro Nunoura, Takashi Nakano, So Nakagawa
Summary: A dataset called NeoRdRp was created in this study for the detection of various RNA viruses from metatranscriptome data. Through clustering and sequence alignment, 1,182 HMM profiles were successfully generated, which can effectively detect the majority of RNA viruses.
MICROBES AND ENVIRONMENTS
(2022)
Article
Chemistry, Applied
Noriyuki Isobe, Hanna Massaad, Revaz Chachanidze, Francois Caton, Denis C. D. Roux, Shigeru Deguchi
Summary: The long-term self-association of gum arabic in water was investigated by studying its aggregation process with or without an oil/water interface. The results showed that the presence of oil at the interface led to continuous structuration of gum arabic molecules. The degree of structuration of gum arabic aggregates was influenced by the type of oil. The rheological properties of the aqueous gum arabic solution were strongly affected by the interfacial conditions.
CARBOHYDRATE POLYMER TECHNOLOGIES AND APPLICATIONS
(2022)
