scholarly journals Analytical Technologies for Liquid Biopsy of Subcellular Materials

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Camila D.M. Campos ◽  
Katie Childers ◽  
Sachindra S.T. Gamage ◽  
Harshani Wijerathne ◽  
Zheng Zhao ◽  
...  
Keyword(s):  
Liquid Biopsy ◽  
Viral Infections ◽  
Mixed Population ◽  
Annual Review ◽  
Publication Date ◽  
Blood Draw ◽  
Sample Matrix ◽  
Figures Of Merit ◽  
Viral Particles ◽  
Different Types

Liquid biopsy markers, which can be secured from a simple blood draw or other biological samples, are used to manage a variety of diseases and even monitor for bacterial or viral infections. Although there are several different types of liquid biopsy markers, the subcellular ones, including cell-free DNA, microRNA, extracellular vesicles, and viral particles, are evolving in terms of their utility. A challenge with liquid biopsy markers is that they must be enriched from the biological sample prior to analysis because they are a vast minority in a mixed population, and potential interferences may be present in the sample matrix that can inhibit profiling the molecular cargo from the subcellular marker. In this article, we discuss existing and developing analytical enrichment platforms used to isolate subcellular liquid biopsy markers, and discuss their figures of merit such as recovery, throughput, and purity. Expected final online publication date for the Annual Review of Analytical Chemistry, Volume 14 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Endogenous Retroviruses Drive Resistance and Promotion of Exogenous Retroviral Homologs

2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Elliott S. Chiu ◽  
Sue VandeWoude
Keyword(s):  
Immune Modulation ◽  
Viral Infections ◽  
Viral Evolution ◽  
Endogenous Retroviruses ◽  
Annual Review ◽  
Publication Date ◽  
Biological Functions ◽  
Self Tolerance ◽  
Vertebrate Hosts ◽  
Insight Into

Endogenous retroviruses (ERVs) serve as markers of ancient viral infections and provide invaluable insight into host and viral evolution. ERVs have been exapted to assist in performing basic biological functions, including placentation, immune modulation, and oncogenesis. A subset of ERVs share high nucleotide similarity to circulating horizontally transmitted exogenous retrovirus (XRV) progenitors. In these cases, ERV–XRV interactions have been documented and include ( a) recombination to result in ERV–XRV chimeras, ( b) ERV induction of immune self-tolerance to XRV antigens, ( c) ERV antigen interference with XRV receptor binding, and ( d) interactions resulting in both enhancement and restriction of XRV infections. Whereas the mechanisms governing recombination and immune self-tolerance have been partially determined, enhancement and restriction of XRV infection are virus specific and only partially understood. This review summarizes interactions between six unique ERV–XRV pairs, highlighting important ERV biological functions and potential evolutionary histories in vertebrate hosts. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 9 is February 16, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Role of the Inflammasome in Liver Disease

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Marcelle de Carvalho Ribeiro ◽  
Gyongyi Szabo
Keyword(s):  
Liver Disease ◽  
Liver Diseases ◽  
Annual Review ◽  
Publication Date ◽  
Inflammasome Activation ◽  
Proinflammatory Response ◽  
Nonalcoholic Fatty Liver ◽  
Pyrin Domain ◽  
Different Types

The involvement of inflammasomes in the proinflammatory response observed in chronic liver diseases, such as alcohol-associated liver disease (ALD) and nonalcoholic fatty liver disease (NAFLD), is widely recognized. Although there are different types of inflammasomes, most studies to date have given attention to NLRP3 (nucleotide-binding oligomerization domain-like receptor family, pyrin domain containing 3) in the pathogenesis of ALD, NAFLD/nonalcoholic steatohepatitis, and fibrosis. Canonical inflammasomes are intracellular multiprotein complexes that are assembled after the sensing of danger signals and activate caspase-1, which matures interleukin (IL)-1β, IL-18, and IL-37 and also induces a form of cell death called pyroptosis. Noncanonical inflammasomes activate caspase-11 to induce pyroptosis. We discuss the different types of inflammasomes involved in liver diseases with a focus on ( a) signals and mechanisms of inflammasome activation, ( b) the role of different types of inflammasomes and their products in the pathogenesis of liver diseases, and ( c) potential therapeutic strategies targeting components of the inflammasomes or cytokines produced upon inflammasome activation. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Feruloylated Arabinoxylan and Oligosaccharides: Chemistry, Nutritional Functions, and Options for Enzymatic Modification

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shang Lin ◽  
Jane W. Agger ◽  
Casper Wilkens ◽  
Anne S. Meyer
Keyword(s):  
Cell Walls ◽  
Annual Review ◽  
Publication Date ◽  
Food Ingredients ◽  
Structural Modifications ◽  
Grain Processing ◽  
Cereal Grain ◽  
Different Types ◽  
Cereal Brans ◽  
Antioxidant Effects

Cereal brans and grain endosperm cell walls are key dietary sources of different types of arabinoxylan. Arabinoxylan is the main group of hemicellulosic polysaccharides that are present in the cell walls of monocot grass crops and hence in cereal grains. The arabinoxylan polysaccharides consist of a backbone of β-(1→4)-linked xylopyranosyl residues, which carry arabinofuranosyl moieties, hence the term arabinoxylan. Moreover, the xylopyranosyl residues can be acetylated or substituted by methyl-glucuronic acid. The arabinofuranosyls may be esterified with a feruloyl group. Feruloylated arabinoxylo-oligosaccharides exert beneficial bioactivities via prebiotic, immunomodulatory, and/or antioxidant effects. New knowledge on microbial enzymes that catalyze specific structural modifications of arabinoxylans can help us understand how these complex fibers are converted in the gut and provide a foundation for the production of feruloylated arabinoxylo-oligosaccharides from brans or other cereal grain processing sidestreams as functional food ingredients. There is a gap between the structural knowledge, bioactivity data, and enzymology insight. Our goal with this review is to present an overview of the structures and bioactivities of feruloylated arabinoxylo-oligosaccharides and review the enzyme reactions that catalyze specific changes in differentially substituted arabinoxylans. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 12 is March 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Genetics of Thoroughbred Racehorse Performance

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Ernest Bailey ◽  
Jessica L. Petersen ◽  
Theodore S. Kalbfleisch
Keyword(s):  
Genetic Variation ◽  
Annual Review ◽  
Publication Date ◽  
The Past ◽  
Racing Performance ◽  
Thoroughbred Horses ◽  
Genomic Tools ◽  
Dna Variants ◽  
Different Types ◽  
Genomic Regions

Thoroughbred horses have been selected for racing performance for more than 400 years. Despite continued selection, race times have not improved significantly during the past 60 years, raising the question of whether genetic variation for racing performance still exists. Studies using phenotypes such as race time, money earned, and handicapping, however, demonstrate that there is extensive variation within these traits and that they are heritable. Even so, these are poor measures of racing success since Thoroughbreds race at different ages and distances and on different types of tracks, and some may not race at all. With the advent of genomic tools, DNA variants are being identified that contribute to racing success. Aside from strong associations for myostatin variants with best racing distance, weak to modest associations with racing phenotypes are reported for other genomic regions. These data suggest that diverse genetic strategies have contributed to producing a successful racehorse, and genetic variation contributing to athleticism remains important. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Hostile Takeover: How Viruses Reprogram Prokaryotic Metabolism

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Tyler B. Jacobson ◽  
Melanie M. Callaghan ◽  
Daniel Amador-Noguez
Keyword(s):  
Essential Feature ◽  
Annual Review ◽  
Publication Date ◽  
Primary Metabolism ◽  
Virion Production ◽  
Viral Particles ◽  
Metabolic Remodeling ◽  
Holistic Understanding ◽  
Cellular Machinery ◽  
Widespread Phenomenon

To reproduce, prokaryotic viruses must hijack the cellular machinery of their hosts and redirect it toward the production of viral particles. While takeover of the host replication and protein synthesis apparatus has long been considered an essential feature of infection, recent studies indicate that extensive reprogramming of host primary metabolism is a widespread phenomenon among prokaryotic viruses that is required to fulfill the biosynthetic needs of virion production. In this review we provide an overview of the most significant recent findings regarding virus-induced reprogramming of prokaryotic metabolism and suggest how quantitative systems biology approaches may be used to provide a holistic understanding of metabolic remodeling during lytic viral infection. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Motivation for Roots in Distributed Morphology

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
David Embick
Keyword(s):  
Online Publication ◽  
Distributed Morphology ◽  
Annual Review ◽  
Publication Date ◽  
Phase Theory ◽  
Lexical Categories ◽  
Different Types ◽  
Minimalist Syntax ◽  
Domain Differences

Within Distributed Morphology, it has been proposed that the lexical vocabulary consists of Roots: category-less primitives. The motivation for Roots is connected with a line of argument reaching back to Chomsky concerning the representation of lexical categories and their role in syntax. At the center of the theory of Roots is the Two Domains Intuition: the idea that there are two different types of domains in which grammatical interactions (form: allomorphy; meaning: allosemy) occur. Roots are posited as part of an argument against lexicalist approaches to the Two Domains Intuition that reduce it to a modular distinction between the lexicon and the syntax. In place of the modular distinction, Root-based approaches hypothesize that domain differences are derivative of syntactic locality effects in a way that connects with the phase theory of Minimalist syntax. This review examines developments leading to current versions of a Roots-and-contexts theory. A particular focus is on the idea that separating lexical Roots from the morphemes that categorize them is essential to defining the distinct locality domains that are posited to explain the effects subsumed under the Two Domains Intuition. Expected final online publication date for the Annual Review of Linguistics, Volume 7 is January 14, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Detection and Monitoring of Viral Infections via Wearable Devices and Biometric Data

2021 ◽  
Vol 24 (1) ◽  
Author(s):  
Craig J. Goergen ◽  
MacKenzie J. Tweardy ◽  
Steven R. Steinhubl ◽  
Stephan W. Wegerich ◽  
Karnika Singh ◽  
...  
Keyword(s):  
Viral Infections ◽  
Wearable Devices ◽  
Lessons Learned ◽  
Warning Signs ◽  
Machine Learning Techniques ◽  
Annual Review ◽  
Publication Date ◽  
Biometric Data ◽  
Asymptomatic Individuals ◽  
Monitoring Technologies

Mounting clinical evidence suggests that viral infections can lead to detectable changes in an individual's normal physiologic and behavioral metrics, including heart and respiration rates, heart rate variability, temperature, activity, and sleep prior to symptom onset, potentially even in asymptomatic individuals. While the ability of wearable devices to detect viral infections in a real-world setting has yet to be proven, multiple recent studies have established that individual, continuous data from a range of biometric monitoring technologies can be easily acquired and that through the use of machine learning techniques, physiological signals and warning signs can be identified. In this review, we highlight the existing knowledge base supporting the potential for widespread implementation of biometric data to address existing gaps in the diagnosis and treatment of viral illnesses, with a particular focus on the many important lessons learned from the coronavirus disease 2019 pandemic. Expected final online publication date for the Annual Review of Biomedical Engineeing, Volume 24 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Culturing Human Gut Microbiomes in the Laboratory

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Simone Renwick ◽  
Caroline M. Ganobis ◽  
Riley A. Elder ◽  
Connor Gianetto-Hill ◽  
Gregory Higgins ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Axenic Culture ◽  
Model Systems ◽  
Annual Review ◽  
Publication Date ◽  
Human Gut ◽  
Complex Interactions ◽  
Viral Particles ◽  
Eukaryotic Microbes

The human gut microbiota is a complex community of prokaryotic and eukaryotic microbes and viral particles that is increasingly associated with many aspects of host physiology and health. However, the classical microbiology approach of axenic culture cannot provide a complete picture of the complex interactions between microbes and their hosts in vivo. As such, recently there has been much interest in the culture of gut microbial ecosystems in the laboratory as a strategy to better understand their compositions and functions. In this review, we discuss the model platforms and methods available in the contemporary microbiology laboratory to study human gut microbiomes, as well as current knowledge surrounding the isolation of human gut microbes for the potential construction of defined communities for use in model systems. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Sex Differences in Respiratory Viral Pathogenesis and Treatments

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Rebecca L. Ursin ◽  
Sabra L. Klein
Keyword(s):  
Sex Differences ◽  
Viral Infections ◽  
Respiratory Infections ◽  
Influenza Viruses ◽  
Annual Review ◽  
Publication Date ◽  
Biological Sex ◽  
Respiratory Viral Infections ◽  
Syncytial Virus ◽  
The Life Course

Biological sex affects the outcome of diverse respiratory viral infections. The pathogenesis of respiratory infections caused by viruses ranging from respiratory syncytial virus to influenza viruses and severe acute respiratory syndrome coronavirus 2 differs between the sexes across the life course. Generally, males are more susceptible to severe outcomes from respiratory viral infections at younger and older ages. During reproductive years (i.e., after puberty and prior to menopause), females are often at greater risk than males for severe outcomes. Pregnancy and biological sex affect the pathogenesis of respiratory viral infections. In addition to sex differences in the pathogenesis of disease, there are consistent sex differences in responses to treatments, with females often developing greater immune responses but experiencing more adverse reactions than males. Animal models provide mechanistic insights into the causes of sex differences in respiratory virus pathogenesis and treatment outcomes, where available. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Systemic Risk in Financial Networks: A Survey

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Matthew O. Jackson ◽  
Agathe Pernoud
Keyword(s):  
Systemic Risk ◽  
Online Publication ◽  
Financial Networks ◽  
Annual Review ◽  
Publication Date ◽  
Feedback Effects ◽  
Optimal Regulation ◽  
Fire Sales ◽  
Different Types ◽  
The Relationship

We provide an overview of the relationship between financial networks and systemic risk. We present a taxonomy of different types of systemic risk, differentiating between direct externalities between financial organizations (e.g., defaults, correlated portfolios, fire sales), and perceptions and feedback effects (e.g., bank runs, credit freezes). We also discuss optimal regulation and bailouts, measurements of systemic risk and financial centrality, choices by banks regarding their portfolios and partnerships, and the changing nature of financial networks. Expected final online publication date for the Annual Review of Economics, Volume 13 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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