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.

PI(4,5)P2 Clustering and Its Impact on Biological Functions

2021 ◽  
Vol 90 (1) ◽  
Author(s):  
Yi Wen ◽  
Volker M. Vogt ◽  
Gerald W. Feigenson
Keyword(s):  
Plasma Membrane ◽  
Cell Biology ◽  
Cellular Proteins ◽  
Annual Review ◽  
Publication Date ◽  
Biological Functions ◽  
Cellular Functions ◽  
Dynamic Distribution ◽  
Multivalent Cation ◽  
Lipid Environment

Located at the inner leaflet of the plasma membrane, phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] comprises only 1–2 mol% of total PM lipids. With its synthesis and turnover both spatially and temporally regulated, PI(4,5)P2 recruits and interacts with hundreds of cellular proteins to support a broad spectrum of cellular functions. Several factors contribute to the versatile and dynamic distribution of PI(4,5)P2 in membranes. Physiological multivalent cations such as Ca2+ and Mg2+ can bridge between PI(4,5)P2 headgroups, forming nanoscopic PI(4,5)P2–cation clusters. The distinct lipid environment surrounding PI(4,5)P2 affects the degree of PI(4,5)P2 clustering. In addition, diverse cellular proteins interacting with PI(4,5)P2 can further regulate PI(4,5)P2 lateral distribution and accessibility. This review summarizes the current understanding of PI(4,5)P2 behavior in both cells and model membranes, with emphasis on both multivalent cation– and protein-induced PI(4,5)P2 clustering. Understanding the nature of spatially separated pools of PI(4,5)P2 is fundamental to cell biology. Expected final online publication date for the Annual Review of Biochemistry, Volume 90 is June 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Regulation of Mitochondrial Ca2+ Uptake

2020 ◽  
Vol 83 (1) ◽  
Author(s):  
Elizabeth Murphy ◽  
Charles Steenbergen
Keyword(s):  
Cell Death ◽  
Genetic Alterations ◽  
Annual Review ◽  
Publication Date ◽  
Mitochondrial Matrix ◽  
Atp Production ◽  
The Past ◽  
Specific Manner ◽  
Insight Into ◽  
Disease Specific

Mitochondria are responsible for ATP production but are also known as regulators of cell death, and mitochondrial matrix Ca2+ is a key modulator of both ATP production and cell death. Although mitochondrial Ca2+ uptake and efflux have been studied for over 50 years, it is only in the past decade that the proteins responsible for mitochondrial Ca2+ uptake and efflux have been identified. The identification of the mitochondrial Ca2+ uniporter (MCU) led to an explosion of studies identifying regulators of the MCU. The levels of these regulators vary in a tissue- and disease-specific manner, providing new insight into how mitochondrial Ca2+ is regulated. This review focuses on the proteins responsible for mitochondrial transport and what we have learned from mouse studies with genetic alterations in these proteins. Expected final online publication date for the Annual Review of Physiology, Volume 83 is February 10, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Evolution and Physiology of Amphibious Yeasts

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Fouad El Baidouri ◽  
Polona Zalar ◽  
Timothy Y. James ◽  
Amy S. Gladfelter ◽  
Anthony Amend
Keyword(s):  
Online Publication ◽  
Convergent Evolution ◽  
Annual Review ◽  
Publication Date ◽  
Ecological Diversity ◽  
Aquatic Habitats ◽  
Evolutionary Mechanisms ◽  
Unicellular Organisms ◽  
Extreme Habitats ◽  
Insight Into

Since the emergence of the first fungi some 700 million years ago, unicellular yeast-like forms have emerged multiple times in independent lineages via convergent evolution. While tens to hundreds of millions of years separate the independent evolution of these unicellular organisms, they share remarkable phenotypic and metabolic similarities, and all have streamlined genomes. Yeasts occur in every aquatic environment yet examined. Many species are aquatic; perhaps most are amphibious. How these species have evolved to thrive in aquatic habitats is fundamental to understanding functions and evolutionary mechanisms in this unique group of fungi. Here we review the state of knowledge of the physiological and ecological diversity of amphibious yeasts and their key evolutionary adaptations enabling survival in aquatic habitats. We emphasize some genera previously thought to be exclusively terrestrial. Finally, we discuss the ability of many yeasts to survive in extreme habitats and how this might lend insight into ecological plasticity, including amphibious lifestyles. 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.

Designing Relevant Preclinical Rodent Models for Studying Links Between Nutrition, Obesity, Metabolism, and Cancer

2021 ◽  
Vol 41 (1) ◽  
Author(s):  
Elaine M. Glenny ◽  
Michael F. Coleman ◽  
Erin D. Giles ◽  
Elizabeth A. Wellberg ◽  
Stephen D. Hursting
Keyword(s):  
Treatment Options ◽  
Annual Review ◽  
Publication Date ◽  
Rodent Models ◽  
Cancer Model ◽  
Preclinical Models ◽  
Cancer Models ◽  
The Impact ◽  
The Relationship ◽  
Insight Into

Diet and nutrition are intricately related to cancer prevention, growth, and treatment response. Preclinical rodent models are a cornerstone to biomedical research and remain instrumental in our understanding of the relationship between cancer and diet and in the development of effective therapeutics. However, the success rate of translating promising findings from the bench to the bedside is suboptimal. Well-designed rodent models will be crucial to improving the impact basic science has on clinical treatment options. This review discusses essential experimental factors to consider when designing a preclinical cancer model with an emphasis on incorporating these models into studies interrogating diet, nutrition, and metabolism. The aims of this review are to ( a) provide insight into relevant considerations when designing cancer models for obesity, nutrition, and metabolism research; ( b) identify common pitfalls when selecting a rodent model; and ( c) discuss strengths and limitations of available preclinical models. Expected final online publication date for the Annual Review of Nutrition, Volume 41 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Bayesian Inference: The Comprehensive Approach to Analyzing Single-Molecule Experiments

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Colin D. Kinz-Thompson ◽  
Korak Kumar Ray ◽  
Ruben L. Gonzalez
Keyword(s):  
Probability Theory ◽  
Bayesian Inference ◽  
Single Molecule ◽  
Biophysical Model ◽  
Annual Review ◽  
Publication Date ◽  
Structural Details ◽  
Self Consistent ◽  
Insight Into ◽  
Data Analysis Methods

Biophysics experiments performed at single-molecule resolution provide exceptional insight into the structural details and dynamic behavior of biological systems. However, extracting this information from the corresponding experimental data unequivocally requires applying a biophysical model. In this review, we discuss how to use probability theory to apply these models to single-molecule data. Many current single-molecule data analysis methods apply parts of probability theory, sometimes unknowingly, and thus miss out on the full set of benefits provided by this self-consistent framework. The full application of probability theory involves a process called Bayesian inference that fully accounts for the uncertainties inherent to single-molecule experiments. Additionally, using Bayesian inference provides a scientifically rigorous method of incorporating information from multiple experiments into a single analysis and finding the best biophysical model for an experiment without the risk of overfitting the data. These benefits make the Bayesian approach ideal for analyzing any type of single-molecule experiment. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Convergent Co-option of the Retroviral gag Gene during the Early Evolution of Mammals

2019 ◽  
Vol 93 (14) ◽  
Author(s):  
Jianhua Wang ◽  
Zhen Gong ◽  
Guan-Zhu Han
Keyword(s):  
Transcriptome Sequencing ◽  
Negative Selection ◽  
Endogenous Retroviruses ◽  
Rna Seq ◽  
Biological Functions ◽  
Conserved Synteny ◽  
Wide Range ◽  
Vertebrate Hosts ◽  
Evolution Of Mammals ◽  
Retroviral Infections

ABSTRACT Endogenous retroviruses, records of past retroviral infections, are ubiquitous in vertebrate genomes. On occasion, vertebrate hosts have co-opted retroviral genes for their own biological functions. Here, we perform a phylogenomic survey of retroviral gag gene homologs within vertebrate genomes and identify two ancient co-opted retroviral gag genes, designated wucaishi1 (wcs1) and wucaishi2 (wcs2), in mammals. Conserved synteny and evolutionary analyses suggest that the wcs1 and wcs2 co-options occurred before the origin of modern placental mammals (∼100 million years ago) and before the origin of modern marsupials (∼80 million years ago), respectively. We found that the wcs genes were lost or pseudogenized multiple times during the evolutionary course of mammals. While the wcs1 gene is mainly subject to negative selection in placental mammals (except in Perissodactyla), the wcs2 gene underwent positive selection in marsupials. Moreover, analyses of transcriptome-sequencing (RNA-seq) data suggest that the wcs1 and the wcs2 genes are expressed in a wide range of tissues. The convergent wcs co-option in mammals implies the retroviral gag gene might have been repurposed more frequently than previously thought. IMPORTANCE Retroviruses occasionally can infect host germ lines, forming endogenous retroviruses. Vertebrates, in turn, recruited retroviral genes for their own biological functions, a process formally known as co-option or exaptation. To date, co-opted retroviral gag genes have rarely been reported. In this study, we identified two co-opted retroviral gag genes, designated wucaishi1 (wcs1) and wucaishi2 (wcs2), in mammals. The co-option of wcs1 and wcs2 occurred before the origin of modern placentals and before the origin of modern marsupials, respectively. Our study indicates that retroviral gag gene co-option might have occurred more frequently than previously thought during the evolutionary course of vertebrates.

How Cortical Circuits Implement Cortical Computations: Mouse Visual Cortex as a Model

2021 ◽  
Vol 44 (1) ◽  
Author(s):  
Cristopher M. Niell ◽  
Massimo Scanziani
Keyword(s):  
Visual Cortex ◽  
Cortical Neurons ◽  
Model Organism ◽  
Annual Review ◽  
Publication Date ◽  
Cortical Circuits ◽  
Cortical Function ◽  
Mouse Visual Cortex ◽  
The Brain ◽  
Insight Into

The mouse, as a model organism to study the brain, gives us unprecedented experimental access to the mammalian cerebral cortex. By determining the cortex's cellular composition, revealing the interaction between its different components, and systematically perturbing these components, we are obtaining mechanistic insight into some of the most basic properties of cortical function. In this review, we describe recent advances in our understanding of how circuits of cortical neurons implement computations, as revealed by the study of mouse primary visual cortex. Further, we discuss how studying the mouse has broadened our understanding of the range of computations performed by visual cortex. Finally, we address how future approaches will fulfill the promise of the mouse in elucidating fundamental operations of cortex. Expected final online publication date for the Annual Review of Neuroscience, Volume 44 is July 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.

Chiral Induced Spin Selectivity and Its Implications for Biological Functions

2021 ◽  
Vol 51 (1) ◽  
Author(s):  
Ron Naaman ◽  
Yossi Paltiel ◽  
David H. Waldeck
Keyword(s):  
Structural Effect ◽  
Annual Review ◽  
Publication Date ◽  
Main Function ◽  
Chiral Molecule ◽  
Biological Functions ◽  
Chiral Molecules ◽  
The Past ◽  
Pass Through ◽  
Do So

Chirality in life has been preserved throughout evolution. It has been assumed that the main function of chirality is its contribution to structural properties. In the past two decades, however, it has been established that chiral molecules possess unique electronic properties. Electrons that pass through chiral molecules, or even charge displacements within a chiral molecule, do so in a manner that depends on the electron's spin and the molecule's enantiomeric form. This effect, referred to as chiral induced spin selectivity (CISS), has several important implications for the properties of biosystems. Among these implications, CISS facilitates long-range electron transfer, enhances bio-affinities and enantioselectivity, and enables efficient and selective multi-electron redox processes. In this article, we review the CISS effect and some of its manifestations in biological systems. We argue that chirality is preserved so persistently in biology not only because of its structural effect, but also because of its important function in spin polarizing electrons. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Increasingly Intelligent Micromachines

2022 ◽  
Vol 5 (1) ◽  
Author(s):  
Tian-Yun Huang ◽  
Hongri Gu ◽  
Bradley J. Nelson
Keyword(s):  
State Of The Art ◽  
Autonomous Systems ◽  
Annual Review ◽  
Publication Date ◽  
Significant Progress ◽  
The Past ◽  
Water Cleaning ◽  
Information Media ◽  
Insight Into ◽  
Made In

Intelligent micromachines, with dimensions ranging from a few millimeters down to hundreds of nanometers, are miniature systems capable of performing specific tasks autonomously at small scales. Enhancing the intelligence of micromachines to tackle the uncertainty and variability in complex microenvironments has applications in minimally invasive medicine, bioengineering, water cleaning, analytical chemistry, and more. Over the past decade, significant progress has been made in the construction of intelligent micromachines, evolving from simple micromachines to soft, compound, reconfigurable, encodable, multifunctional, and integrated micromachines, as well as from individual to multiagent, multiscale, hierarchical, self-organizing, and swarm micromachines. The field leverages two important trends in robotics research—the miniaturization and intelligentization of machines—but a compelling combination of these two features has yet to be realized. The core technologies required to make such tiny machines intelligent include information media, transduction, processing, exchange, and energy supply, but embedding all of these functions into a system at the micro- or nanoscale is challenging. This article offers a comprehensive introduction to the state-of-the-art technologies used to create intelligence for micromachines and provides insight into the construction of next-generation intelligent micromachines that can adapt to diverse scenarios for use in emerging fields. Expected final online publication date for the Annual Review of Control, Robotics, and Autonomous Systems, Volume 5 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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