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Annual Review of Biophysics May 2020Many enzymes appear to diffuse faster in the presence of substrate and to drift either up or down a concentration gradient of their substrate. Observations of these... (Review)
Review
Many enzymes appear to diffuse faster in the presence of substrate and to drift either up or down a concentration gradient of their substrate. Observations of these phenomena, termed enhanced enzyme diffusion (EED) and enzyme chemotaxis, respectively, lead to a novel view of enzymes as active matter. Enzyme chemotaxis and EED may be important in biology and could have practical applications in biotechnology and nanotechnology. They are also of considerable biophysical interest; indeed, their physical mechanisms are still quite uncertain. This review provides an analytic summary of experimental studies of these phenomena and of the mechanisms that have been proposed to explain them and offers a perspective on future directions for the field.
Topics: Chemotaxis; Diffusion; Enzymes
PubMed: 31986056
DOI: 10.1146/annurev-biophys-121219-081535 -
Expert Review of Proteomics 2023Investigating the taxonomic and functional composition of human microbiomes can aid in the understanding of disease etiologies, diagnosis, and therapy monitoring for... (Review)
Review
INTRODUCTION
Investigating the taxonomic and functional composition of human microbiomes can aid in the understanding of disease etiologies, diagnosis, and therapy monitoring for several diseases, including inflammatory bowel disease or obesity. One method for microbiome monitoring is metaproteomics, which assesses human and microbial proteins and thus enables the study of host-microbiome interactions. This advantage led to increased interest in metaproteome analyses and significant developments to introduce this method into a clinical context.
AREAS COVERED
This review summarizes the recent progress from a technical side and an application-related point of view.
EXPERT OPINION
Numerous publications imply the massive potential of metaproteomics to impact human health care. However, the key challenges of standardization and validation of experimental and bioinformatic workflows and accurate quantification methods must be overcome.
Topics: Humans; Proteomics; Microbiota; Bacterial Proteins; Computational Biology; Obesity
PubMed: 37249060
DOI: 10.1080/14789450.2023.2215440 -
Rheumatology (Oxford, England) Jan 2024Calprotectin (CLP) is a calcium-binding protein produced by neutrophils and monocytes in the course of inflammation. Today, the role of faecal CLP in chronic IBD is well... (Review)
Review
Calprotectin (CLP) is a calcium-binding protein produced by neutrophils and monocytes in the course of inflammation. Today, the role of faecal CLP in chronic IBD is well known, but in recent years attention has shifted towards circulating CLP. In fact, this molecule can be measured in different biological fluids: blood, saliva and urine, using different analytic methods that are described in this review. Furthermore, different data confirm the relevant role of serum CLP in autoimmune diseases. In this review we will highlight the correlation between high levels of circulating CLP and specific autoantibodies of major autoimmune pathologies paving the way to the employment of CLP measurement as useful biomarker for monitoring outcome in different pathologies.
Topics: Humans; Leukocyte L1 Antigen Complex; Inflammation; Biomarkers; Feces; Neutrophils; Inflammatory Bowel Diseases
PubMed: 37603715
DOI: 10.1093/rheumatology/kead405 -
Sensors (Basel, Switzerland) Dec 2022Sucrose is a primary metabolite in plants, a source of energy, a source of carbon atoms for growth and development, and a regulator of biochemical processes. Most of the... (Review)
Review
Sucrose is a primary metabolite in plants, a source of energy, a source of carbon atoms for growth and development, and a regulator of biochemical processes. Most of the traditional analytical chemistry methods for sucrose quantification in plants require sample treatment (with consequent tissue destruction) and complex facilities, that do not allow real-time sucrose quantification at ultra-low concentrations (nM to pM range) under in vivo conditions, limiting our understanding of sucrose roles in plant physiology across different plant tissues and cellular compartments. Some of the above-mentioned problems may be circumvented with the use of bio-compatible ligands for molecular recognition of sucrose. Nevertheless, problems such as the signal-noise ratio, stability, and selectivity are some of the main challenges limiting the use of molecular recognition methods for the in vivo quantification of sucrose. In this review, we provide a critical analysis of the existing analytical chemistry tools, biosensors, and synthetic ligands, for sucrose quantification and discuss the most promising paths to improve upon its limits of detection. Our goal is to highlight the criteria design need for real-time, in vivo, highly sensitive and selective sucrose sensing capabilities to enable further our understanding of living organisms, the development of new plant breeding strategies for increased crop productivity and sustainability, and ultimately to contribute to the overarching need for food security.
Topics: Sucrose; Carbon; Chemistry, Analytic; Crop Production; Recognition, Psychology
PubMed: 36502213
DOI: 10.3390/s22239511 -
Scientific Reports Jan 2023In this article, we demonstrate the viability of highly monochromatic full-field X-ray absorption near edge structure based tomography using a laboratory-scale...
In this article, we demonstrate the viability of highly monochromatic full-field X-ray absorption near edge structure based tomography using a laboratory-scale Johann-type X-ray absorption spectrometer utilising a conventional X-ray tube source. In this proof-of-concept, by using a phantom embedded with elemental Se, Na[Formula: see text]SeO[Formula: see text], and Na[Formula: see text]SeO[Formula: see text], we show that the three-dimensional distributions of Se in different oxidation states can be mapped and distinguished from the phantom matrix and each other with absorption edge contrast tomography. The presented method allows for volumetric analyses of chemical speciation in mm-scale samples using low-brilliance X-ray sources, and represents a new analytic tool for materials engineering and research in many fields including biology and chemistry.
Topics: Tomography, X-Ray Computed; Radiography; Phantoms, Imaging; X-Rays
PubMed: 36611113
DOI: 10.1038/s41598-023-27409-6 -
Critical Reviews in Food Science and... 2024Neural network (i.e. deep learning, NN)-based data analysis techniques have been listed as a pivotal opportunity to protect the integrity and safety of the global food... (Review)
Review
Neural network (i.e. deep learning, NN)-based data analysis techniques have been listed as a pivotal opportunity to protect the integrity and safety of the global food supply chain and forecast $11.2 billion in agriculture markets. As a general-purpose data analytic tool, NN has been applied in several areas of food science, such as food recognition, food supply chain security and omics analysis, and so on. Therefore, given the rapid emergence of NN applications in food safety, this review aims to provide a comprehensive overview of the NN application in food analysis for the first time, focusing on domain-specific applications in food analysis by introducing fundamental methodology, reviewing recent and notable progress, and discussing challenges and potential pitfalls. NN demonstrated that it has a bright future through effective collaboration between food specialist and the broader community in the food field, for example, superiority in food recognition, sensory evaluation, pattern recognition of spectroscopy and chromatography. However, major challenges impeded NN extension including void in the food scientist-friendly interface software package, incomprehensible model behavior, multi-source heterogeneous data, and so on. The breakthrough from other fields proved NN has the potential to offer a revolution in the immediate future.
Topics: Neural Networks, Computer; Humans; Food Analysis; Food Safety; Food Technology; Food Supply; Deep Learning
PubMed: 36322538
DOI: 10.1080/10408398.2022.2139217 -
Biosensors Mar 2022Rapid, on-site diagnostics allow for timely intervention and response for warfighter support, environmental monitoring, and global health needs. Portable optical...
Rapid, on-site diagnostics allow for timely intervention and response for warfighter support, environmental monitoring, and global health needs. Portable optical biosensors are being widely pursued as a means of achieving fieldable biosensing due to the potential speed and accuracy of optical detection. We recently developed the portable engineered analytic sensor with automated sampling (PEGASUS) with the goal of developing a fieldable, generalizable biosensing platform. Here, we detail the development of PEGASUS's sensing hardware and use a test-bed system of identical sensing hardware and software to demonstrate detection of a fluorescent conjugate at 1 nM through biotin-streptavidin chemistry.
Topics: Biosensing Techniques; Environmental Monitoring; Streptavidin
PubMed: 35448255
DOI: 10.3390/bios12040195 -
Annual Review of Biophysics May 2023Synthetic biology seeks to probe fundamental aspects of biological form and function by construction [i.e., (re)synthesis] rather than deconstruction (analysis). In this... (Review)
Review
Synthetic biology seeks to probe fundamental aspects of biological form and function by construction [i.e., (re)synthesis] rather than deconstruction (analysis). In this sense, biological sciences now follow the lead given by the chemical sciences. Synthesis can complement analytic studies but also allows novel approaches to answering fundamental biological questions and opens up vast opportunities for the exploitation of biological processes to provide solutions for global problems. In this review, we explore aspects of this synthesis paradigm as applied to the chemistry and function of nucleic acids in biological systems and beyond, specifically, in genome resynthesis, synthetic genetics (i.e., the expansion of the genetic alphabet, of the genetic code, and of the chemical make-up of genetic systems), and the elaboration of orthogonal biosystems and components.
Topics: Genetic Code; Nucleic Acids; Synthetic Biology
PubMed: 37159296
DOI: 10.1146/annurev-biophys-111622-091203 -
Chemical Communications (Cambridge,... Apr 2022Electronic resonances are states that are unstable towards loss of electrons. They play critical roles in high-energy environments across chemistry, physics, and biology... (Review)
Review
Electronic resonances are states that are unstable towards loss of electrons. They play critical roles in high-energy environments across chemistry, physics, and biology but are also relevant to processes under ambient conditions that involve unbound electrons. This feature article focuses on complex-variable techniques such as complex scaling and complex absorbing potentials that afford a treatment of electronic resonances in terms of discrete square-integrable eigenstates of non-Hermitian Hamiltonians with complex energy. Fundamental aspects of these techniques as well as their integration into molecular electronic-structure theory are discussed and an overview of some recent developments is given: analytic gradient theory for electronic resonances, the application of rank-reduction techniques and quantum embedding to them, as well as approaches for evaluating partial decay widths.
PubMed: 35395664
DOI: 10.1039/d1cc07090h -
Nature Communications May 2022Facile geometric-structural response of liquid crystalline colloids to external fields enables many technological advances. However, the relaxation mechanisms for liquid...
Facile geometric-structural response of liquid crystalline colloids to external fields enables many technological advances. However, the relaxation mechanisms for liquid crystalline colloids under mobile boundaries remain still unexplored. Here, by combining experiments, numerical simulations and theory, we describe the shape and structural relaxation of colloidal liquid crystalline micro-droplets, called tactoids, where amyloid fibrils and cellulose nanocrystals are used as model systems. We show that tactoids shape relaxation bears a universal single exponential decay signature and derive an analytic expression to predict this out of equilibrium process, which is governed by liquid crystalline anisotropic and isotropic contributions. The tactoids structural relaxation shows fundamentally different paths, with first- and second-order exponential decays, depending on the existence of splay/bend/twist orientation structures in the ground state. Our findings offer a comprehensive understanding on dynamic confinement effects in liquid crystalline colloidal systems and may set unexplored directions in the development of novel responsive materials.
Topics: Amyloid; Anisotropy; Colloids; Liquid Crystals; Nanoparticles
PubMed: 35589676
DOI: 10.1038/s41467-022-30123-y