Yuan Yao, Kai Lan, Thomas E Graedel, Narasimha D Rao
{"title":"Models for Decarbonization in the Chemical Industry.","authors":"Yuan Yao, Kai Lan, Thomas E Graedel, Narasimha D Rao","doi":"10.1146/annurev-chembioeng-100522-114115","DOIUrl":"10.1146/annurev-chembioeng-100522-114115","url":null,"abstract":"<p><p>Various technologies and strategies have been proposed to decarbonize the chemical industry. Assessing the decarbonization, environmental, and economic implications of these technologies and strategies is critical to identifying pathways to a more sustainable industrial future. This study reviews recent advancements and integration of systems analysis models, including process analysis, material flow analysis, life cycle assessment, techno-economic analysis, and machine learning. These models are categorized based on analytical methods and application scales (i.e., micro-, meso-, and macroscale) for promising decarbonization technologies (e.g., carbon capture, storage, and utilization, biomass feedstock, and electrification) and circular economy strategies. Incorporating forward-looking, data-driven approaches into existing models allows for optimizing complex industrial systems and assessing future impacts. Although advances in industrial ecology-, economic-, and planetary boundary-based modeling support a more holistic systems-level assessment, more efforts are needed to consider impacts on ecosystems. Effective applications of these advanced, integrated models require cross-disciplinary collaborations across chemical engineering, industrial ecology, and economics.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":" ","pages":"139-161"},"PeriodicalIF":7.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139563267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Introduction.","authors":"Michael F Doherty, Rachel A Segalman, Ravi S Kane","doi":"10.1146/annurev-ch-15-040824-100001","DOIUrl":"https://doi.org/10.1146/annurev-ch-15-040824-100001","url":null,"abstract":"","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":"15 1","pages":"i"},"PeriodicalIF":7.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141756799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jyot D Antani, Aakansha Shaji, Rachit Gupta, Pushkar P Lele
{"title":"Reassessing the Standard Chemotaxis Framework for Understanding Biased Migration in <i>Helicobacter pylori</i>.","authors":"Jyot D Antani, Aakansha Shaji, Rachit Gupta, Pushkar P Lele","doi":"10.1146/annurev-chembioeng-100722-114625","DOIUrl":"10.1146/annurev-chembioeng-100722-114625","url":null,"abstract":"<p><p><i>Helicobacter pylori</i> infections are a major cause of peptic ulcers and gastric cancers. The development of robust inflammation in response to these flagellated, motile bacteria is correlated with poor prognosis. Chemotaxis plays a crucial role in <i>H. pylori</i> colonization, enabling the bacteria to swim toward favorable chemical environments. Unlike the model species of bacterial chemotaxis, <i>Escherichia coli</i>, <i>H. pylori</i> cells possess polar flagella. They run forward by rotating their flagella counterclockwise, whereas backward runs are achieved by rotating their flagella clockwise. We delve into the implications of certain features of the canonical model of chemotaxis on our understanding of biased migration in polarly flagellated bacteria such as <i>H. pylori</i>. In particular, we predict how the translational displacement of <i>H. pylori</i> cells during a backward run could give rise to chemotaxis errors within the canonical framework. Also, <i>H. pylori</i> lack key chemotaxis enzymes found in <i>E. coli</i>, without which sensitive detection of ligands with a wide dynamic range seems unlikely. Despite these problems, <i>H. pylori</i> exhibit robust ability to migrate toward urea-rich sources. We emphasize various unresolved questions regarding the biophysical mechanisms of chemotaxis in <i>H. pylori</i>, shedding light on potential directions for future research. Understanding the intricacies of biased migration in <i>H. pylori</i> could offer valuable insights into how pathogens breach various protective barriers in the human host.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":" ","pages":"51-62"},"PeriodicalIF":7.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138481848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Will Hydrogen Be a New Natural Gas? Hydrogen Integration in Natural Gas Grids.","authors":"Gerald Linke","doi":"10.1146/annurev-chembioeng-100522-110306","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-100522-110306","url":null,"abstract":"<p><p>Hydrogen is similar to natural gas in terms of its physical and chemical properties but does not release carbon dioxide when burnt. This makes hydrogen an energy carrier of great importance in climate policy, especially as an enabler of increasing integration of volatile renewable energy, progressive electrification, and effective emission reductions in the hard-to-decarbonize sectors. Leaving aside the problems of transporting hydrogen as a liquid, technological challenges along the entire supply chain can be considered as solved in principle, as shown in the experimental findings of the Hydrogen Innovation Program of the German Technical and Scientific Association for Gas and Water. By scaling up production and end-use capacities and, most importantly, producing hydrogen in regions with abundant renewable energy, hydrogen and its applications can displace natural gas at affordable prices in the medium term. However, this substitution will take place at different rates in different regions and with different levels of added value, all of which must be understood for hydrogen uptake to be successful.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":"15 1","pages":"63-80"},"PeriodicalIF":7.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141756800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Masoud Ghasemi, Michael Geitner, Agatha O'Connell, Enrique D Gomez
{"title":"Three-Dimensional Morphology of Polymeric Membranes from Electron Tomography.","authors":"Masoud Ghasemi, Michael Geitner, Agatha O'Connell, Enrique D Gomez","doi":"10.1146/annurev-chembioeng-100722-104623","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-100722-104623","url":null,"abstract":"<p><p>Recent advances in the water-energy landscape hinge upon our improved understanding of the complex morphology of materials involved in water treatment and energy production. Due to their versatility and tunability for applications ranging from drug delivery to fuel cells, polymeric systems will play a crucial role in shaping the future of water-energy nexus applications. Electron tomography (ET) stands as a transformative approach for elucidating the intricate structures inherent to polymers, offering unparalleled insights into their nanoscale architectures and functional properties in three dimensions. In particular, the various morphological and chemical characteristics of polymer membranes provide opportunities for perturbations to standard ET for the study of these systems. We discuss the applications of transmission electron microscopy in establishing structure-function relationships in polymeric membranes with an emphasis on traditional ET and cryogenic ET (cryo-ET). The synergy between ET and cryo-ET to unravel structural complexities and dynamic behaviors of polymer membranes holds immense potential in driving progress and innovation across frontiers related to water-energy nexus applications. Expected final online publication date for the <i>Annual Review of Chemical and Biomolecular Engineering</i> , Volume 15 is June 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":" ","pages":""},"PeriodicalIF":8.4,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139995420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Justyn Fine, Bunyarit Meksiriporn, Jiacheng Tan, Jamie B Spangler
{"title":"Mechanism-Driven Design of Multispecific Antibodies for Targeted Disease Treatment.","authors":"Justyn Fine, Bunyarit Meksiriporn, Jiacheng Tan, Jamie B Spangler","doi":"10.1146/annurev-chembioeng-100522-102155","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-100522-102155","url":null,"abstract":"<p><p>Antibody-based therapeutics constitute a rapidly growing class of pharmaceutical compounds. However, monoclonal antibodies, which specifically engage only one target, often lack the mechanistic intricacy to treat complex diseases. To expand the utility of antibody therapies, significant efforts have been invested in designing multispecific antibodies, which engage multiple targets using a single molecule. These efforts have culminated in remarkable translational progress, including nine US Food and Drug Administration-approved multispecific antibodies, with countless others in various stages of preclinical or clinical development. In this review, we discuss several categories of multispecific antibodies that have achieved clinical approval or shown promise in earlier stages of development. We focus on the molecular mechanisms used by multispecific antibodies and how these mechanisms inform their customized design and formulation. In particular, we discuss multispecific antibodies that target multiple disease markers, multiparatopic antibodies, and immune-interfacing antibodies. Overall, these innovative multispecific antibody designs are fueling exciting advances across the immunotherapeutic landscape. Expected final online publication date for the <i>Annual Review of Chemical and Biomolecular Engineering</i> , Volume 15 is June 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":" ","pages":""},"PeriodicalIF":8.4,"publicationDate":"2024-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139566303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Designing Multivalent and Multispecific Biologics","authors":"Jennifer J. Kang, Ayako Ohoka, Casim A. Sarkar","doi":"10.1146/annurev-chembioeng-100722-112440","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-100722-112440","url":null,"abstract":"In the era of precision medicine, multivalent and multispecific therapeutics present a promising approach for targeted disease intervention. These therapeutics are designed to interact with multiple targets simultaneously, promising enhanced efficacy, reduced side effects, and resilience against drug resistance. We dissect the principles guiding the design of multivalent biologics, highlighting challenges and strategies that must be considered to maximize therapeutic effect. Engineerable elements in multivalent and multispecific biologic design—domain affinities, valency, and spatial presentation—must be considered in the context of the molecular targets as well as the balance of important properties such as target avidity and specificity. We illuminate recent applications of these principles in designing protein and cell therapies and identify exciting future directions in this field, underscored by advances in biomolecular and cellular engineering and computational approaches.Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering , Volume 15 is June 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":"60 3 1","pages":""},"PeriodicalIF":8.4,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138563717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alison J Shapiro, Robert M O'Dea, Sonia C Li, Jamael C Ajah, Garrett F Bass, Thomas H Epps
{"title":"Engineering Innovations, Challenges, and Opportunities for Lignocellulosic Biorefineries: Leveraging Biobased Polymer Production.","authors":"Alison J Shapiro, Robert M O'Dea, Sonia C Li, Jamael C Ajah, Garrett F Bass, Thomas H Epps","doi":"10.1146/annurev-chembioeng-101121-084152","DOIUrl":"10.1146/annurev-chembioeng-101121-084152","url":null,"abstract":"<p><p>Alternative polymer feedstocks are highly desirable to address environmental, social, and security concerns associated with petrochemical-based materials. Lignocellulosic biomass (LCB) has emerged as one critical feedstock in this regard because it is an abundant and ubiquitous renewable resource. LCB can be deconstructed to generate valuable fuels, chemicals, and small molecules/oligomers that are amenable to modification and polymerization. However, the diversity of LCB complicates the evaluation of biorefinery concepts in areas including process scale-up, production outputs, plant economics, and life-cycle management. We discuss aspects of current LCB biorefinery research with a focus on the major process stages, including feedstock selection, fractionation/deconstruction, and characterization, along with product purification, functionalization, and polymerization to manufacture valuable macromolecular materials. We highlight opportunities to valorize underutilized and complex feedstocks, leverage advanced characterization techniques to predict and manage biorefinery outputs, and increase the fraction of biomass converted into valuable products.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":"14 ","pages":"109-140"},"PeriodicalIF":8.4,"publicationDate":"2023-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9960331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Everything You Wanted to Know about Deep Eutectic Solvents but Were Afraid to Be Told.","authors":"Dinis O Abranches, João A P Coutinho","doi":"10.1146/annurev-chembioeng-101121-085323","DOIUrl":"10.1146/annurev-chembioeng-101121-085323","url":null,"abstract":"<p><p>Are deep eutectic solvents (DESs) a promising alternative to conventional solvents? Perhaps, but their development is hindered by a plethora of misconceptions. These are carefully analyzed here, beginning with the very meaning of DESs, which has strayed far beyond its original scope of eutectic mixtures of Lewis or Brønsted acids and bases. Instead, a definition that is grounded on thermodynamic principles and distinguishes between eutectic and deep eutectic is encouraged, and the types of precursors that can be used to prepare DESs are reviewed. Landmark works surrounding the sustainability, stability, toxicity, and biodegradability of these solvents are also discussed, revealing piling evidence that numerous DESs reported thus far, particularly those that are choline based, lack sufficient sustainability-related traits to be considered green solvents. Finally, emerging DES applications are reviewed, emphasizing their most remarkable feature: the ability to liquefy a solid compound with a target property, allowing its use as a liquid solvent.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":"14 ","pages":"141-163"},"PeriodicalIF":8.4,"publicationDate":"2023-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9603994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ryan Buchser, Phillip Sweet, Aparna Anantharaman, Lydia Contreras
{"title":"RNAs as Sensors of Oxidative Stress in Bacteria.","authors":"Ryan Buchser, Phillip Sweet, Aparna Anantharaman, Lydia Contreras","doi":"10.1146/annurev-chembioeng-101121-070250","DOIUrl":"10.1146/annurev-chembioeng-101121-070250","url":null,"abstract":"<p><p>Oxidative stress is an important and pervasive physical stress encountered by all kingdoms of life, including bacteria. In this review, we briefly describe the nature of oxidative stress, highlight well-characterized protein-based sensors (transcription factors) of reactive oxygen species that serve as standards for molecular sensors in oxidative stress, and describe molecular studies that have explored the potential of direct RNA sensitivity to oxidative stress. Finally, we describe the gaps in knowledge of RNA sensors-particularly regarding the chemical modification of RNA nucleobases. RNA sensors are poised to emerge as an essential layer of understanding and regulating dynamic biological pathways in oxidative stress responses in bacteria and, thus, also represent an important frontier of synthetic biology.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":"14 ","pages":"265-281"},"PeriodicalIF":8.4,"publicationDate":"2023-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9606167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}