Article
Biochemical Research Methods
Alienke van Pijkeren, Anna-Sophia Egger, Madlen Hotze, Elisabeth Zimmermann, Tobias Kipura, Julia Grander, Andre Gollowitzer, Andreas Koeberle, Rainer Bischoff, Kathrin Thedieck, Marcel Kwiatkowski
Summary: Proteomics and metabolomics play vital roles in systems biology, and the simultaneous extraction of proteome and metabolome from the same sample is important. This study compared the performance of different surfactants and urea for proteome extraction and found that urea showed the best efficiency for simultaneous proteo-metabolome analysis.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Biochemical Research Methods
Ahmed Serag, Zaynab Shakkour, Abdulsalam M. Halboup, Firas Kobeissy, Mohamed A. Farag
Summary: Despite being readily available, sweat metabolomics and proteomics research lags behind, while the role of skin host-microbiome interactions in shaping sweat characteristics is highlighted. The review discusses the current state and future applications of sweat omics, emphasizing the need for a better understanding of sweat chemicals and their functions. Overall, the potential of sweat as an information-rich biofluid complementing skin metabolome/proteome exploration is underscored.
JOURNAL OF PROTEOMICS
(2021)
Review
Multidisciplinary Sciences
Lloyd M. Smith, Jeffrey N. Agar, Julia Chamot-Rooke, Paul O. Danis, Ying Ge, Joseph A. Loo, Ljiljana Pasa-Tolic, Yury O. Tsybin, Neil L. Kelleher
Summary: Understanding the structure and properties of proteins is crucial in deciphering biological functions. The concept of defining the human proteome as a reference set of proteoforms is proposed, with a call for improved technologies in a two-pronged strategy.
Article
Plant Sciences
Joana Figueiredo, Ana Rita Cavaco, Leonor Guerra-Guimaraes, Celine Leclercq, Jenny Renaut, Jorge Cunha, Jose Eiras-Dias, Carlos Cordeiro, Ana Rita Matos, Marta Sousa Silva, Andreia Figueiredo
Summary: The analysis of complex biological systems challenges researchers, especially in understanding interactions within plant cellular compartments such as the apoplast. Despite knowledge on the involvement of apoplast in various processes, its dynamics remain poorly understood due to lack of efficient extraction methods.
PHYSIOLOGIA PLANTARUM
(2021)
Review
Agricultural Engineering
Nam Kyu Kang, Kwangryul Baek, Hyun Gi Koh, Christine Anne Atkinson, Donald R. Ort, Yong-Su Jin
Summary: Microalgae are promising sustainable resources that can convert CO2 into biofuels and chemicals directly, but their industrial production and economic feasibility are still limited. Metabolic engineering approaches have been used to enhance the productivity of microalgal bioproducts, with impressive advances in the last decade. Challenges remain in achieving effective production of chemicals and fuels via microalgal metabolic engineering.
BIORESOURCE TECHNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Bilal Moiz, Andrew Li, Surya Padmanabhan, Ganesh Sriram, Alisa Morss Clyne
Summary: Cell metabolism represents the coordinated changes in genes, proteins, and metabolites that occur in health and disease; quantifying metabolic fluxes requires sophisticated mathematical and computational analysis of data from isotope labeling experiments; isotope-assisted metabolic flux analysis (iMFA) is a rigorous computational approach for fluxome quantification.
Article
Dentistry, Oral Surgery & Medicine
Zi-yun Chen, Tian-tian Xu, Zhao-jia Liang, Li Zhao, Xiao-qin Xiong, Kun-ke Xie, Wan-xin Yu, Xiao-wen Zeng, Jie Gao, Ying-hong Zhou, Gang Luo, Ting Yu
Summary: The study characterized the gingival metabolome in mice with obesity induced by high-fat diet and with/without periodontitis. The results showed distinct effects of periodontitis and HFD on gingival metabolome, with a greater impact in HFD mice. Specific metabolic pathways were enriched in each condition, and targeted validation confirmed additive effects between HFD and periodontitis. Overall, obese population consuming excessive HFD displayed amplified metabolic response to periodontitis.
JOURNAL OF CLINICAL PERIODONTOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Maria Pilar Giner, Stefan Christen, Simona Bartova, Mikhail Makarov, Marie E. Migaud, Carles Canto, Sofia Moco
Summary: NAD(+) and its reduced form NADH are essential coenzymes in hundreds of metabolic reactions, serving as substrates for key enzymes. Analyzing the NAD(+) metabolome using liquid chromatography-tandem mass spectrometry can provide insights into NAD(+) biology and its implications for health and disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Analytical
Yuming Jiang, Alexandre Hutton, Caleb W. Cranney, Jesse G. Meyer
Summary: This article introduces an improved direct infusion and ion mobility method for proteome analysis, and proposes a label-free quantification method DISPA-LFQ, which can rapidly identify and quantify proteins in complex mixtures. This technology has important applications in drug screening, biomarker discovery, and clinical analysis.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Wei-Sheng Wu, Hsin-Yi Wu, Pin-Hsuan Wang, Ting-Yu Chen, Kuan-Ru Chen, Chih-Wei Chang, Dong-En Lee, Bo-Heng Lin, William Chih-Wei Chang, Pao-Chi Liao
Summary: Lung cancer is a major cause of cancer-related death worldwide, and research is needed to dissect its pathogenic mechanisms and discover specific biomarkers. LCMD is the first database to provide information on lung cancer-related metabolites, aiming to promote the discovery of biomarkers for lung cancer.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Vijaykumar Patra, Natalie Bordag, Yohann Clement, Harald Koefeler, Jean-Francois Nicolas, Marc Vocanson, Sophie Ayciriex, Peter Wolf
Summary: Skin metabolites (< 1500 Da) are crucial for various skin functions and their interactions with microbiome and UV exposure were investigated in this study. Germ-free, disinfected, and control mice were exposed to immunosuppressive doses of UVB radiation, and lipidome and metabolome profiling of their skin tissue were performed. UV differentially regulated metabolites and membrane lipid species, showing a microbiome-dependent effect. These findings provide insights into the dynamics of skin metabolome, microbiome, and UV exposure, and have implications for the development of skin health applications based on metabolites or lipids.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Medicinal
Changshui Wang, Shuzhen Zhao, Yuan Xu, Wenxue Sun, Yuanyuan Feng, Deshuai Liang, Yun Guan
Summary: This study investigated the correlations between gut microbiota compositions and hepatic metabolomic disorders in mice with methotrexate-induced hepatoxicity. The results showed that methotrexate alters the gut microbiota and hepatic metabolite profiles, leading to liver injury.
DRUG DESIGN DEVELOPMENT AND THERAPY
(2022)
Review
Plant Sciences
Julia Mergner, Bernhard Kuster
Summary: Proteins play essential roles in cellular processes, and studying protein expression, interactions, and modifications is crucial for understanding the molecular mechanisms underlying plant phenotypes. Mass spectrometry technology allows for the global identification and quantification of thousands of proteins, revealing dynamic changes in the plant proteome.
ANNUAL REVIEW OF PLANT BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Zdenka Bartosova, Helga Ertesvag, Eirin Lishaugen Nyflot, Kristoffer Kampe, Inga Marie Aasen, Per Bruheim
Summary: Thraustochytrids are marine microorganisms known for accumulating DHA-rich lipids. Current bioprocesses based on thraustochytrids are not commercially competitive for DHA production, leading to the need for genetic and metabolic engineering strategies. Metabolite profiling data suggest that lipid accumulation may be limited by the availability of glycerol-3-phosphate rather than acetyl-CoA or NADPH.
Article
Biochemical Research Methods
Roger Gine, Jordi CapeHades, Josep M. Badia, Dennis Vughs, Michaela Schwaiger-Haber, Theodore Alexandrov, Maria Vinaixa, Andrea M. Brunner, Gary J. Patti, Oscar Yanes
Summary: HERMES is a molecular-formula-oriented and peak-detection-free method that uses LC/MS1 information to optimize MS2 acquisition, improving the identification rate and biological specificity of metabolites.
Article
Environmental Sciences
Mohneesh Kalwani, Hillol Chakdar, Amit Srivastava, Sunil Pabbi, Pratyoosh Shukla
Summary: Modern agriculture relies heavily on synthetic fertilizers, but nanofertilizers provide an innovative, efficient, and eco-friendly alternative. They release nutrients slowly to support plant growth and conserve beneficial microbiome diversity, although there are still challenges related to production, transportation, and dosage sensitivity.
Review
Biotechnology & Applied Microbiology
Niwas Kumar, Chiranjib Banerjee, Sangeeta Negi, Pratyoosh Shukla
Summary: This review provides an overview on the key challenges, technological advancements, and economic and technical aspects of microalgal biomass harvesting techniques. It explores the potential of bioharvesting mediated by microbial, animal, and plant-based polymeric flocculants, highlighting their higher dewatering potential, lower toxicity, and eco-friendly properties.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2023)
Article
Microbiology
Meenal Rastogi, Smriti Shrivastava, Pratyoosh Shukla
Summary: This study identified four potential xylanase-producing fungi from soil and vegetable wastes, revealing their genetic analysis and enzyme activity. The xylanolytic fungi, belonging to Aspergillus species, showed promising xylanase activities under certain conditions, suggesting their potential industrial applications in lignocellulose saccharification.
JOURNAL OF BASIC MICROBIOLOGY
(2022)
Article
Engineering, Environmental
Hillol Chakdar, Shobit Thapa, Amit Srivastava, Pratyoosh Shukla
Summary: Cyanobacteria have emerged as a potential option for bioremediation of heavy metals due to their unique adaptations and robust metabolic machineries. Understanding their physiological responses and regulation at the molecular level is necessary to identify candidate genes and proteins for improving bioremediation efficiency. These approaches might pave new possibilities of implementing genetic engineering strategies in the future.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Review
Biochemistry & Molecular Biology
Guddu Kumar Gupta, Mandeep Dixit, Rajeev Kumar Kapoor, Pratyoosh Shukla
Summary: The pulp and paper industry releases a significant amount of wastewater containing hazardous organochlorine compounds, prompting the need for cost-effective and nonpolluting practices to mitigate environmental impact. Enzymatic treatments, particularly using xylanolytic enzymes, show potential for enhancing paper quality through hydrolysing raw materials and can be used for bio-deinking and bio-bleaching.
MOLECULAR BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Monika Yadav, Sunita, Pratyoosh Shukla
Summary: This study focused on isolating potential probiotic strains from dairy products. Among the isolated strains, strain MYPS5.1 of Weissella paramesenteroides was identified as the best candidate with potential therapeutic properties. This strain exhibited antibiotic resistance and produced a high concentration of exopolysaccharide. It also showed interaction with cyclin-dependent kinase, which is thought to play a role in cancer pathogenesis.
Article
Agricultural Engineering
Mandeep Dixit, Guddu Kumar Gupta, Monika Yadav, Deepak Chhabra, Rajeev Kumar Kapoor, Puneet Pathak, Nishi K. Bhardwaj, Pratyoosh Shukla
Summary: The present study demonstrates the efficient enzymatic production and improved deinking efficiency of thermophilic fungus Thermomyces lanuginosus VAPS25. The combinatory artificial intelligence-based tool increased the activity of endoglucanase, amylase, and lipase. Metal ions also enhanced the activity of these enzymes. Furthermore, the enzymes improved the deinking efficiency and paper strength parameters, suggesting their potential for an economical paper recycling process.
BIORESOURCE TECHNOLOGY
(2022)
Review
Agricultural Engineering
Amit Srivastava, Mohneesh Kalwani, Hillol Chakdar, Sunil Pabbi, Pratyoosh Shukla
Summary: Microalgae pigments, as eco-friendly alternatives to synthetic dyes, have significant value in nutrition and pharmaceutical industries. However, expensive cultivation methods and microbial contamination remain major obstacles to large-scale production.
BIORESOURCE TECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Ishu Khangwal, Pratyoosh Shukla
Summary: In this study, xylooligosaccharides were extracted and produced from sugarcane bagasse and coconut coir by enzymatic treatment. The results revealed that sugarcane bagasse was more suitable as a source for xylooligosaccharide production compared to coconut coir, and can be used at an industrial level.
INDIAN JOURNAL OF MICROBIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
L. Paikhomba Singha, Pratyoosh Shukla
Summary: This review emphasizes the importance of using mixed microbial cultures and their interactions with the microbiome in the open environment for sustainable functions in harsh conditions. It explores the possibility of using microbiome engineering and microbial communication through quorum sensing. The review also discusses the challenges and potential solutions for implementing microbiome engineering in real environments.
BIOPROCESS AND BIOSYSTEMS ENGINEERING
(2023)
Article
Agricultural Engineering
Mandeep Dixit, Deepak Chhabra, Pratyoosh Shukla
Summary: In this study, an enzyme consortium containing endoglucanase, lipase, and amylase was obtained and optimized using artificial intelligence-based tools. The highest enzyme activity achieved for each enzyme was 8.8 IU/g, 153.68 U/g, and 19.2 IU/g, respectively, using Thermomyces lanuginosus VAPS25. The optimized enzyme consortium showed reliable catalytic activity at 50-80 degrees C and pH 6.0-9.0.
BIORESOURCE TECHNOLOGY
(2023)
Article
Environmental Sciences
Mandeep Dixit, Pratyoosh Shukla
Summary: This study reports the optimization of endoglucanase production from the newly isolated fungus Aspergillus niger MPS25. The enzyme showed maximum activity at 60 degrees C and was stimulated by Co2+ ions and inhibited by Mn2+ ions. The enzymatic hydrolysis of wheat straw produced a significant amount of reducing sugars, indicating its potential in the biofuel industry. The enzyme also improved the deinking efficiency of mixed office waste and old newspapers, as well as the physical strength properties of the handmade paper sheets. Additionally, FTIR and XRD analysis provided insights into the changes in functional groups and cellulose crystallinity.
Article
Biochemistry & Molecular Biology
Sunita, Nirjara Singhvi, Vipin Gupta, Yogendra Singh, Pratyoosh Shukla
Summary: Implementation of computational tools in identifying drug targets for Tuberculosis has shown promise. Nucleoid-Associated Proteins have been found to play a significant role in regulating cellular processes of Mycobacterium tuberculosis, making them potential targets for new drugs. This study used computational methods to identify potential inhibitors for eight Nucleoid-Associated Proteins, and found several FDA-approved drugs as novel targets with therapeutic potential for TB.
MOLECULAR BIOTECHNOLOGY
(2023)
Review
Agricultural Engineering
Riya Bongirwar, Pratyoosh Shukla
Summary: Recent advances in metabolic engineering have made cyanobacteria a promising option for sustainable production, thanks to their natural ability to produce metabolites. However, the source-sink balance in cyanobacteria needs to be optimized for enhanced photosynthetic efficiency. This review discusses approaches for achieving source-sink balance and engineering metabolic sinks in cyanobacteria, as well as the importance of understanding cyanobacterial strains for valuable metabolites.
BIORESOURCE TECHNOLOGY
(2023)
Review
Environmental Sciences
Niwas Kumar, Pratyoosh Shukla
Summary: Emerging contaminants (ECs) are a global issue due to their toxicity, impacts on human health, and potential role in antimicrobial resistance. Current wastewater treatment systems are not effective in removing ECs, but microalgae-based processes offer cost and energy-efficient solutions. Microalgae can transform ECs into less toxic compounds, and the resulting microalgal biomass can be used for biofuel production.
ENVIRONMENTAL POLLUTION
(2023)
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)