scholarly journals In vivo interactome profiling by enzyme‐catalyzed proximity labeling

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yangfan Xu ◽  
Xianqun Fan ◽  
Yang Hu
Keyword(s):  
State Of The Art ◽  
Catalytic Efficiency ◽  
Biological Processes ◽  
Protein Protein Interaction ◽  
Current State ◽  
Protein Interactome ◽  
Potential Applications ◽  
Protein Protein Interaction Networks ◽  
Temporal And Spatial

AbstractEnzyme-catalyzed proximity labeling (PL) combined with mass spectrometry (MS) has emerged as a revolutionary approach to reveal the protein-protein interaction networks, dissect complex biological processes, and characterize the subcellular proteome in a more physiological setting than before. The enzymatic tags are being upgraded to improve temporal and spatial resolution and obtain faster catalytic dynamics and higher catalytic efficiency. In vivo application of PL integrated with other state of the art techniques has recently been adapted in live animals and plants, allowing questions to be addressed that were previously inaccessible. It is timely to summarize the current state of PL-dependent interactome studies and their potential applications. We will focus on in vivo uses of newer versions of PL and highlight critical considerations for successful in vivo PL experiments that will provide novel insights into the protein interactome in the context of human diseases.

scholarly journals Electro-Quasistatic Animal Body Communication for Untethered Rodent Biopotential Recording

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shreeya Sriram ◽  
Shitij Avlani ◽  
Matthew P. Ward ◽  
Shreyas Sen
Keyword(s):  
Lower Energy ◽  
Sensor Node ◽  
State Of The Art ◽  
The Body ◽  
Animal Body ◽  
Current State ◽  
Communication Modalities ◽  
First Time ◽  
Biopotential Recording

AbstractContinuous multi-channel monitoring of biopotential signals is vital in understanding the body as a whole, facilitating accurate models and predictions in neural research. The current state of the art in wireless technologies for untethered biopotential recordings rely on radiative electromagnetic (EM) fields. In such transmissions, only a small fraction of this energy is received since the EM fields are widely radiated resulting in lossy inefficient systems. Using the body as a communication medium (similar to a ’wire’) allows for the containment of the energy within the body, yielding order(s) of magnitude lower energy than radiative EM communication. In this work, we introduce Animal Body Communication (ABC), which utilizes the concept of using the body as a medium into the domain of untethered animal biopotential recording. This work, for the first time, develops the theory and models for animal body communication circuitry and channel loss. Using this theoretical model, a sub-inch$$^3$$ 3 [1″ × 1″ × 0.4″], custom-designed sensor node is built using off the shelf components which is capable of sensing and transmitting biopotential signals, through the body of the rat at significantly lower powers compared to traditional wireless transmissions. In-vivo experimental analysis proves that ABC successfully transmits acquired electrocardiogram (EKG) signals through the body with correlation $$>99\%$$ > 99 % when compared to traditional wireless communication modalities, with a 50$$\times$$ × reduction in power consumption.

scholarly journals Annotating proteins with generalized functional linkages

2008 ◽  
Vol 105 (46) ◽  
pp. 17700-17705 ◽  
Author(s):  
Richard Llewellyn ◽  
David S. Eisenberg
Keyword(s):  
Protein Function ◽  
Biological Process ◽  
Computational Method ◽  
Majority Voting ◽  
Target Protein ◽  
Biological Processes ◽  
Gene Products ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Networks

As genome sequencing outstrips the rate of high-quality, low-throughput biochemical and genetic experimentation, accurate annotation of protein function becomes a bottleneck in the progress of the biomolecular sciences. Most gene products are now annotated by homology, in which an experimentally determined function is applied to a similar sequence. This procedure becomes error-prone between more divergent sequences and can contaminate biomolecular databases. Here, we propose a computational method of assignment of function, termed Generalized Functional Linkages (GFL), that combines nonhomology-based methods with other types of data. Functional linkages describe pairwise relationships between proteins that work together to perform a biological task. GFL provides a Bayesian framework that improves annotation by arbitrating a competition among biological process annotations to best describe the target protein. GFL addresses the unequal strengths of functional linkages among proteins, the quality of existing annotations, and the similarity among them while incorporating available knowledge about the cellular location or individual molecular function of the target protein. We demonstrate GFL with functional linkages defined by an algorithm known as zorch that quantifies connectivity in protein–protein interaction networks. Even when using proteins linked only by indirect or high-throughput interactions, GFL predicts the biological processes of many proteins in Saccharomyces cerevisiae, improving the accuracy of annotation by 20% over majority voting.

scholarly journals Hydrothermal Carbonization of Organic Waste and Biomass: A Review on Process, Reactor, and Plant Modeling

2020 ◽  
Author(s):  
Giulia Ischia ◽  
Luca Fiori
Keyword(s):  
Organic Waste ◽  
Review Paper ◽  
Recent Literature ◽  
State Of The Art ◽  
Hydrothermal Carbonization ◽  
Residual Biomass ◽  
Current State ◽  
Potential Applications ◽  
Intrinsic Complexity ◽  
Context Models

Abstract Hydrothermal carbonization (HTC) is an emerging path to give a new life to organic waste and residual biomass. Fulfilling the principles of the circular economy, through HTC “unpleasant” organics can be transformed into useful materials and possibly energy carriers. The potential applications of HTC are tremendous and the recent literature is full of investigations. In this context, models capable to predict, simulate and optimize the HTC process, reactors, and plants are engineering tools that can significantly shift HTC research towards innovation by boosting the development of novel enterprises based on HTC technology. This review paper addresses such key-issue: where do we stand regarding the development of these tools? The literature presents many and simplified models to describe the reaction kinetics, some dealing with the process simulation, while few focused on the heart of an HTC system, the reactor. Statistical investigations and some life cycle assessment analyses also appear in the current state of the art. This work examines and analyzes these predicting tools, highlighting their potentialities and limits. Overall, the current models suffer from many aspects, from the lack of data to the intrinsic complexity of HTC reactions and HTC systems. Therefore, the emphasis is given to what is still necessary to make the HTC process duly simulated and therefore implementable on an industrial scale with sufficient predictive margins. Graphic Abstract

scholarly journals Photoacoustic reporter genes for noninvasive molecular imaging and theranostics

2020 ◽  
Vol 13 (03) ◽  
pp. 2030005
Author(s):  
Zhao Lei ◽  
Yun Zeng ◽  
Xiaofen Zhang ◽  
Xiaoyong Wang ◽  
Gang Liu
Keyword(s):  
Molecular Imaging ◽  
Fluorescent Proteins ◽  
Photoacoustic Imaging ◽  
High Sensitivity ◽  
Reporter Genes ◽  
Biological Processes ◽  
Deep Tissue ◽  
Potential Applications ◽  
Improved Performance

Noninvasive molecular imaging makes the observation and comprehensive understanding of complex biological processes possible. Photoacoustic imaging (PAI) is a fast evolving hybrid imaging technology enabling in vivo imaging with high sensitivity and spatial resolution in deep tissue. Among the various probes developed for PAI, genetically encoded reporters attracted increasing attention of researchers, which provide improved performance by acquiring images of a PAI reporter gene’s expression driven by disease-specific enhancers/promoters. Here, we present a brief overview of recent studies about the existing photoacoustic reporter genes (RGs) for noninvasive molecular imaging, such as the pigment enzyme reporters, fluorescent proteins and chromoproteins, photoswitchable proteins, including their properties and potential applications in theranostics. Furthermore, the challenges that PAI RGs face when applied to the clinical studies are also examined.

scholarly journals Exosome: A New Player in Translational Nanomedicine

2020 ◽  
Vol 9 (8) ◽  
pp. 2380 ◽  
Author(s):  
Houssam Aheget ◽  
María Tristán-Manzano ◽  
Loubna Mazini ◽  
Marina Cortijo-Gutierrez ◽  
Pablo Galindo-Moreno ◽  
...  
Keyword(s):  
Ex Vivo ◽  
Cell Types ◽  
Structural Features ◽  
Biologically Active ◽  
Biological Processes ◽  
New Approach ◽  
Current State ◽  
Exosome Biogenesis ◽  
Production Techniques

Summary: Exosomes are extracellular vesicles released by the vast majority of cell types both in vivo and ex vivo, upon the fusion of multivesicular bodies (MVBs) with the cellular plasma membrane. Two main functions have been attributed to exosomes: their capacity to transport proteins, lipids and nucleic acids between cells and organs, as well as their potential to act as natural intercellular communicators in normal biological processes and in pathologies. From a clinical perspective, the majority of applications use exosomes as biomarkers of disease. A new approach uses exosomes as biologically active carriers to provide a platform for the enhanced delivery of cargo in vivo. One of the major limitations in developing exosome-based therapies is the difficulty of producing sufficient amounts of safe and efficient exosomes. The identification of potential proteins involved in exosome biogenesis is expected to directly cause a deliberate increase in exosome production. In this review, we summarize the current state of knowledge regarding exosomes, with particular emphasis on their structural features, biosynthesis pathways, production techniques and potential clinical applications.

scholarly journals In vitro and in vivo trematode models for chemotherapeutic studies

Parasitology ◽  
2009 ◽  
Vol 137 (3) ◽  
pp. 589-603 ◽  
Author(s):  
J. KEISER
Keyword(s):  
Liver Fluke ◽  
Fasciola Hepatica ◽  
State Of The Art ◽  
Parasitic Diseases ◽  
Current State ◽  
Food Borne ◽  
Essential Components ◽  
Discovery Pipeline

SUMMARYSchistosomiasis and food-borne trematodiases are chronic parasitic diseases affecting millions of people mostly in the developing world. Additional drugs should be developed as only few drugs are available for treatment and drug resistance might emerge. In vitro and in vivo whole parasite screens represent essential components of the trematodicidal drug discovery cascade. This review describes the current state-of-the-art of in vitro and in vivo screening systems of the blood fluke Schistosoma mansoni, the liver fluke Fasciola hepatica and the intestinal fluke Echinostoma caproni. Examples of in vitro and in vivo evaluation of compounds for activity are presented. To boost the discovery pipeline for these diseases there is a need to develop validated, robust high-throughput in vitro systems with simple readouts.

An Empirical Examination of the Current State of Publically Available Nanotechnology Guidance Materials

2012 ◽  
Vol 40 (4) ◽  
pp. 751-762 ◽  
Author(s):  
Laura Fleege ◽  
Frances Lawrenz
Keyword(s):  
Environmental Science ◽  
Technology Development ◽  
Atomic Scale ◽  
One Dimension ◽  
New Materials ◽  
Empirical Examination ◽  
Current State ◽  
Potential Applications ◽  
The U.S

Nanotechnology not only offers the promise of new enhancements to existing materials but also allows for the development of new materials and devices. The potential applications of nanotechnology range from medicine to agriculture to health and environmental science and beyond. Nanotechnology is growing at such a rate that Lux Research in 2007 estimated that nanotechnology will be incorporated into 15% of global manufactured goods by 2014. The U.S. National Nanotechnology Initiative defines nanotechnology as the following: “(1) Research and technology development involving structures with at least one dimension in the range of 1-100 nanometers (nm), frequently with atomic/molecular precision; (2) Creating and using structures, devices, and systems that have unique properties and functions because of their nanoscale dimensions; (3) The ability to control or manipulate on the atomic scale.” Nanomedicine and its subcategories of nanotherapeutics and in vivo nanodiagnostics incorporate nanoscale materials with unique properties that can enable new or improved treatments and diagnostics for many diseases and disorders.

scholarly journals Hepatocyte organoids and cell transplantation: What the future holds

2021 ◽  
Author(s):  
Weng Chuan Peng ◽  
Lianne J. Kraaier ◽  
Thomas A. Kluiver
Keyword(s):  
Cell Transplantation ◽  
Liver Diseases ◽  
Large Scale ◽  
Fetal Liver ◽  
Culture Conditions ◽  
Current State ◽  
Metabolic Gene Expression ◽  
Potential Applications

AbstractHistorically, primary hepatocytes have been difficult to expand or maintain in vitro. In this review, we will focus on recent advances in establishing hepatocyte organoids and their potential applications in regenerative medicine. First, we provide a background on the renewal of hepatocytes in the homeostatic as well as the injured liver. Next, we describe strategies for establishing primary hepatocyte organoids derived from either adult or fetal liver based on insights from signaling pathways regulating hepatocyte renewal in vivo. The characteristics of these organoids will be described herein. Notably, hepatocyte organoids can adopt either a proliferative or a metabolic state, depending on the culture conditions. Furthermore, the metabolic gene expression profile can be modulated based on the principles that govern liver zonation. Finally, we discuss the suitability of cell replacement therapy to treat different types of liver diseases and the current state of cell transplantation of in vitro-expanded hepatocytes in mouse models. In addition, we provide insights into how the regenerative microenvironment in the injured host liver may facilitate donor hepatocyte repopulation. In summary, transplantation of in vitro-expanded hepatocytes holds great potential for large-scale clinical application to treat liver diseases.

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