Causative Microbes in Host-Microbiome Interactions

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Graham J. Britton ◽  
Jeremiah J. Faith
Keyword(s):  
Immune System ◽  
Human Microbiome ◽  
Individual Species ◽  
Annual Review ◽  
Publication Date ◽  
Sequencing Technology ◽  
Specific Effects ◽  
Therapeutic Benefits ◽  
Experimental Approaches

Despite identification of numerous associations between microbiomes and diseases, the complexity of the human microbiome has hindered identification of individual species and strains that are causative in host phenotype or disease. Uncovering causative microbes is vital to fully understand disease processes and to harness the potential therapeutic benefits of microbiota manipulation. Developments in sequencing technology, animal models, and bacterial culturing have facilitated the discovery of specific microbes that impact the host and are beginning to advance the characterization of host-microbiome interaction mechanisms. We summarize the historical and contemporary experimental approaches taken to uncover microbes from the microbiota that affect host biology and describe examples of commensals that have specific effects on the immune system, inflammation, and metabolism. There is still much to learn, and we lay out challenges faced by the field and suggest potential remedies for common pitfalls encountered in the hunt for causative commensal microbes. 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.

Learning Through Processing: Toward an Integrated Approach to Early Word Learning

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Stephan C. Meylan ◽  
Elika Bergelson
Keyword(s):  
Word Learning ◽  
Empirical Work ◽  
Integrated Approach ◽  
Linguistic Knowledge ◽  
Annual Review ◽  
Publication Date ◽  
Learning Mechanisms ◽  
Lexical Knowledge ◽  
Novel Word Learning

Children's linguistic knowledge and the learning mechanisms by which they acquire it grow substantially in infancy and toddlerhood, yet theories of word learning largely fail to incorporate these shifts. Moreover, researchers’ often-siloed focus on either familiar word recognition or novel word learning limits the critical consideration of how these two relate. As a step toward a mechanistic theory of language acquisition, we present a framework of “learning through processing” and relate it to the prevailing methods used to assess children's early knowledge of words. Incorporating recent empirical work, we posit a specific, testable timeline of qualitative changes in the learning process in this interval. We conclude with several challenges and avenues for building a comprehensive theory of early word learning: better characterization of the input, reconciling results across approaches, and treating lexical knowledge in the nascent grammar with sufficient sophistication to ensure generalizability across languages and development. Expected final online publication date for the Annual Review of Linguistics, Volume 8 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Immunosensation: Neuroimmune Cross Talk in the Skin

2021 ◽  
Vol 39 (1) ◽  
Author(s):  
Masato Tamari ◽  
Aaron M. Ver Heul ◽  
Brian S. Kim
Keyword(s):  
Immune System ◽  
Host Immunity ◽  
The Body ◽  
Annual Review ◽  
Publication Date ◽  
Protective Behaviors ◽  
Evolutionarily Conserved ◽  
Structural Barrier ◽  
Thermal Stimuli ◽  
Antimicrobial Immunity

Classically, skin was considered a mere structural barrier protecting organisms from a diversity of environmental insults. In recent decades, the cutaneous immune system has become recognized as a complex immunologic barrier involved in both antimicrobial immunity and homeostatic processes like wound healing. To sense a variety of chemical, mechanical, and thermal stimuli, the skin harbors one of the most sophisticated sensory networks in the body. However, recent studies suggest that the cutaneous nervous system is highly integrated with the immune system to encode specific sensations into evolutionarily conserved protective behaviors. In addition to directly sensing pathogens, neurons employ novel neuroimmune mechanisms to provide host immunity. Therefore, given that sensation underlies various physiologies through increasingly complex reflex arcs, a much more dynamic picture is emerging of the skin as a truly systemic organ with highly coordinated physical, immunologic, and neural functions in barrier immunology. Expected final online publication date for the Annual Review of Immunology, Volume 39 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Bacteriophage-Bacteria Interactions in the Gut: From Invertebrates to Mammals

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Joshua M. Kirsch ◽  
Robert S. Brzozowski ◽  
Dominick Faith ◽  
June L. Round ◽  
Patrick R. Secor ◽  
...  
Keyword(s):  
Immune System ◽  
Environmental Conditions ◽  
Online Publication ◽  
Annual Review ◽  
Publication Date ◽  
Microbiota Composition ◽  
Complex Environment ◽  
Health And Disease ◽  
Polymicrobial Communities ◽  
Diverse Interactions

Bacteria and their viruses (bacteriophages or phages) interact antagonistically and beneficially in polymicrobial communities such as the guts of animals. These interactions are multifaceted and are influenced by environmental conditions. In this review, we discuss phage-bacteria interactions as they relate to the complex environment of the gut. Within the mammalian and invertebrate guts, phages and bacteria engage in diverse interactions including genetic coexistence through lysogeny, and phages directly modulate microbiota composition and the immune system with consequences that are becoming recognized as potential drivers of health and disease. With greater depth of understanding of phage-bacteria interactions in the gut and the outcomes, future phage therapies become possible. 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 Perspective on Data Science

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Roger D. Peng ◽  
Hilary S. Parker
Keyword(s):  
Iterative Process ◽  
Data Science ◽  
Annual Review ◽  
Publication Date ◽  
Broad Definition ◽  
The Core ◽  
Fields Of Study ◽  
Points Of Interest ◽  
New Knowledge

The field of data science currently enjoys a broad definition that includes a wide array of activities which borrow from many other established fields of study. Having such a vague characterization of a field in the early stages might be natural, but over time maintaining such a broad definition becomes unwieldy and impedes progress. In particular, the teaching of data science is hampered by the seeming need to cover many different points of interest. Data scientists must ultimately identify the core of the field by determining what makes the field unique and what it means to develop new knowledge in data science. In this review we attempt to distill some core ideas from data science by focusing on the iterative process of data analysis and develop some generalizations from past experience. Generalizations of this nature could form the basis of a theory of data science and would serve to unify and scale the teaching of data science to large audiences. Expected final online publication date for the Annual Review of Statistics, Volume 9 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Mycotoxin Production in Fusarium According to Contemporary Species Concepts

2021 ◽  
Vol 59 (1) ◽  
Author(s):  
Gary P. Munkvold ◽  
Robert H. Proctor ◽  
Antonio Moretti
Keyword(s):  
Fusarium Species ◽  
Pathogenic Fungi ◽  
Species Concepts ◽  
Classification Systems ◽  
Individual Species ◽  
Annual Review ◽  
Publication Date ◽  
Mycotoxin Production ◽  
Depth Of Knowledge ◽  
Genus Fusarium

Fusarium is one of the most important genera of plant-pathogenic fungi in the world and arguably the world's most important mycotoxin-producing genus. Fusarium species produce a staggering array of toxic metabolites that contribute to plant disease and mycotoxicoses in humans and other animals. A thorough understanding of the mycotoxin potential of individual species is crucial for assessing the toxicological risks associated with Fusarium diseases. There are thousands of reports of mycotoxin production by various species, and there have been numerous attempts to summarize them. These efforts have been complicated by competing classification systems based on morphology, sexual compatibility, and phylogenetic relationships. The current depth of knowledge of Fusarium genomes and mycotoxin biosynthetic pathways provides insights into how mycotoxin production is distributed among species and multispecies lineages (species complexes) in the genus as well as opportunities to clarify and predict mycotoxin risks connected with known and newly described species. Here, we summarize mycotoxin production in the genus Fusarium and how mycotoxin risk aligns with current phylogenetic species concepts. Expected final online publication date for the Annual Review of Phytopathology, Volume 59 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Molecules from the Microbiome

2021 ◽  
Vol 90 (1) ◽  
Author(s):  
Emilee E. Shine ◽  
Jason M. Crawford
Keyword(s):  
Small Molecules ◽  
Molecular Mechanisms ◽  
System Development ◽  
Human Microbiome ◽  
Host Responses ◽  
Annual Review ◽  
Publication Date ◽  
Mechanistic Studies ◽  
Immune System Development ◽  
Interdisciplinary Approaches

The human microbiome encodes a second genome that dwarfs the genetic capacity of the host. Microbiota-derived small molecules can directly target human cells and their receptors or indirectly modulate host responses through functional interactions with other microbes in their ecological niche. Their biochemical complexity has profound implications for nutrition, immune system development, disease progression, and drug metabolism, as well as the variation in these processes that exists between individuals. While the species composition of the human microbiome has been deeply explored, detailed mechanistic studies linking specific microbial molecules to host phenotypes are still nascent. In this review, we discuss challenges in decoding these interaction networks, which require interdisciplinary approaches that combine chemical biology, microbiology, immunology, genetics, analytical chemistry, bioinformatics, and synthetic biology. We highlight important classes of microbiota-derived small molecules and notable examples. An understanding of these molecular mechanisms is central to realizing the potential of precision microbiome editing in health, disease, and therapeutic responses. 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.

Quantum-State Control and Manipulation of Paramagnetic Molecules with Magnetic Fields

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Brianna R. Heazlewood
Keyword(s):  
Magnetic Fields ◽  
Chemical Reactivity ◽  
Paramagnetic Species ◽  
Annual Review ◽  
Publication Date ◽  
State Control ◽  
Magnetic Traps ◽  
Paramagnetic Molecules ◽  
Experimental Approaches ◽  
And Control

Since external magnetic fields were first employed to deflect paramagnetic atoms in 1921, a range of magnetic field–based methods have been introduced to state-selectively manipulate paramagnetic species. These methods include magnetic guides, which selectively filter paramagnetic species from all other components of a beam, and magnetic traps, where paramagnetic species can be spatially confined for extended periods of time. However, many of these techniques were developed for atomic—rather than molecular—paramagnetic species. It has proven challenging to apply some of these experimental methods developed for atoms to paramagnetic molecules. Thanks to the emergence of new experimental approaches and new combinations of existing techniques, the past decade has seen significant progress toward the manipulation and control of paramagnetic molecules. This review identifies the key methods that have been implemented for the state-selective manipulation of paramagnetic molecules—discussing the motivation, state of the art, and future prospects of the field. Key applications include the ability to control chemical interactions, undertake precise spectroscopic measurements, and challenge our understanding of chemical reactivity at a fundamental level. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 72 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Somatic Mosaicism in Biology and Disease

2021 ◽  
Vol 84 (1) ◽  
Author(s):  
Hayato Ogawa ◽  
Keita Horitani ◽  
Yasuhiro Izumiya ◽  
Soichi Sano
Keyword(s):  
Genome Sequencing ◽  
Somatic Mutations ◽  
Somatic Mosaicism ◽  
Clinical Information ◽  
Annual Review ◽  
Clinical Implications ◽  
Publication Date ◽  
Sequencing Data ◽  
Sequencing Technology ◽  
The Individual

Contrary to earlier beliefs, every cell in the individual is genetically different due to somatic mutations. Consequently, tissues become a mixture of cells with distinct genomes, a phenomenon termed somatic mosaicism. Recent advances in genome sequencing technology have unveiled possible causes of mutations and how they shape the unique mutational landscape of the tissues. Moreover, the analysis of sequencing data in combination with clinical information has revealed the impacts of somatic mosaicism on disease processes. In this review, we discuss somatic mosaicism in various tissues and its clinical implications for human disease. Expected final online publication date for the Annual Review of Physiology, Volume 84 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

A Tale of Two Checkpoints: ATR Inhibition and PD-(L)1 Blockade

2021 ◽  
Vol 73 (1) ◽  
Author(s):  
Natalie Y.L. Ngoi ◽  
Guang Peng ◽  
Timothy A. Yap
Keyword(s):  
Ataxia Telangiectasia ◽  
Innate Immune ◽  
Annual Review ◽  
Publication Date ◽  
Checkpoint Activation ◽  
Cycle Arrest ◽  
Specific Effects ◽  
Damage Response ◽  
Shed Light

Innate immunity and the DNA damage response (DDR) pathway are inextricably linked. Within the DDR, ataxia telangiectasia and Rad3-related (ATR) is a key kinase responsible for sensing replication stress and facilitating DNA repair through checkpoint activation, cell cycle arrest, and promotion of fork recovery. Recent studies have shed light on the immunomodulatory role of the ATR-CHK1 pathway in the tumor microenvironment and the specific effects of ATR inhibition in stimulating an innate immune response. With several potent and selective ATR inhibitors in developmental pipelines, the combination of dual ATR and PD-(L)1 blockade has attracted increasing interest in cancer therapy. In this review, we summarize the clinical and preclinical data supporting the combined inhibition of ATR and PD-(L)1, discuss the potential challenges surrounding this approach, and highlight biomarkers relevant for selected patients who are most likely to benefit from the blockade of these two checkpoints. Expected final online publication date for the Annual Review of Medicine, Volume 73 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals A Genetic Perspective on Cetacean Evolution

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Andrea A. Cabrera ◽  
Martine Bérubé ◽  
Xênia M. Lopes ◽  
Marie Louis ◽  
Tom Oosting ◽  
...  
Keyword(s):  
Online Publication ◽  
Nuclear Dna ◽  
Population Change ◽  
Annual Review ◽  
Publication Date ◽  
The Past ◽  
Nuclear Genomes ◽  
Past Population

Studies of cetacean evolution using genetics and other biomolecules have come a long way—from the use of allozymes and short sequences of mitochondrial or nuclear DNA to the assembly of full nuclear genomes and characterization of proteins and lipids. Cetacean research has also advanced from using only contemporary samples to analyzing samples dating back thousands of years, and to retrieving data from indirect environmental sources, including water or sediments. Combined, these studies have profoundly deepened our understanding of the origin of cetaceans; their adaptation and speciation processes; and of the past population change, migration, and admixture events that gave rise to the diversity of cetaceans found today. Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics, Volume 52 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Sign in / Sign up

Export Citation Format

Share Document