Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
E. Maggie Sogin ◽  
Manuel Kleiner ◽  
Christian Borowski ◽  
Harald R. Gruber-Vodicka ◽  
Nicole Dubilier
Keyword(s):  
Hydrothermal Vents ◽  
Annual Review ◽  
Publication Date ◽  
Metabolic Diversity ◽  
Research Directions ◽  
Physiological Diversity ◽  
Living Together ◽  
Gain Energy ◽  
Chemosynthetic Bacteria ◽  
Ecological Success

Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between chemosynthetic bacteria and eukaryotes and that these chemosymbioses are ubiquitous in both deep-sea and shallow-water environments. The symbionts are primary producers that gain energy from the oxidation of reduced compounds, such as sulfide and methane, to fix carbon dioxide or methane into biomass to feed their hosts. This review outlines how the symbiotic partners have adapted to living together. We first focus on the phylogenetic and metabolic diversity of these symbioses and then highlight selected research directions that could advance our understanding of the processes that shaped the evolutionary and ecological success of these associations. 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.

New Developments in Social Network Analysis

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Daniel J. Brass
Keyword(s):  
Social Networks ◽  
Social Network ◽  
Social Network Analysis ◽  
Network Analysis ◽  
Organizational Behavior ◽  
Annual Review ◽  
Publication Date ◽  
Research Directions ◽  
New Research ◽  
Conceptual Foundations

This review of social network analysis focuses on identifying recent trends in interpersonal social networks research in organizations, and generating new research directions, with an emphasis on conceptual foundations. It is organized around two broad social network topics: structural holes and brokerage and the nature of ties. New research directions include adding affect, behavior, and cognition to the traditional structural analysis of social networks, adopting an alter-centric perspective including a relational approach to ego and alters, moving beyond the triad in structural hole and brokerage research to consider alters as brokers, expanding the nature of ties to include negative, multiplex/dissonant, and dormant ties, and exploring the value of redundant ties. The challenge is to answer the question “What's next in social network analysis?” Expected final online publication date for the Annual Review of Organizational Psychology and Organizational Behavior, Volume 9 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Evolution in Cities

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Sarah E. Diamond ◽  
Ryan A. Martin
Keyword(s):  
Online Publication ◽  
Evolutionary Biology ◽  
Urban Environments ◽  
Annual Review ◽  
Publication Date ◽  
Evolutionary Mechanisms ◽  
Research Directions ◽  
Evolutionary Forces ◽  
Research Questions ◽  
Biology Research

Although research performed in cities will not uncover new evolutionary mechanisms, it could provide unprecedented opportunities to examine the interplay of evolutionary forces in new ways and new avenues to address classic questions. However, while the variation within and among cities affords many opportunities to advance evolutionary biology research, careful alignment between how cities are used and the research questions being asked is necessary to maximize the insights that can be gained. In this review, we develop a framework to help guide alignment between urban evolution research approaches and questions. Using this framework, we highlight what has been accomplished to date in the field of urban evolution and identify several up-and-coming research directions for further expansion. We conclude that urban environments can be used as evolutionary test beds to tackle both new and long-standing questions in evolutionary biology. 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.

Tensors in Statistics

2020 ◽  
Vol 8 (1) ◽  
Author(s):  
Xuan Bi ◽  
Xiwei Tang ◽  
Yubai Yuan ◽  
Yanqing Zhang ◽  
Annie Qu
Keyword(s):  
Data Representation ◽  
Future Research ◽  
Annual Review ◽  
Publication Date ◽  
Network System ◽  
Imaging Analysis ◽  
Research Directions ◽  
Tensor Decompositions ◽  
Software Libraries ◽  
Future Research Directions

This article provides an overview of tensors, their properties, and their applications in statistics. Tensors, also known as multidimensional arrays, are generalizations of matrices to higher orders and are useful data representation architectures. We first review basic tensor concepts and decompositions, and then we elaborate traditional and recent applications of tensors in the fields of recommender systems and imaging analysis. We also illustrate tensors for network data and explore the relations among interacting units in a complex network system. Some canonical tensor computational algorithms and available software libraries are provided for various tensor decompositions. Future research directions, including tensors in deep learning, are also discussed. Expected final online publication date for the Annual Review of Statistics, Volume 8 is March 7, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Machine Learning for Sustainable Energy Systems

2021 ◽  
Vol 46 (1) ◽  
Author(s):  
Priya L. Donti ◽  
J. Zico Kolter
Keyword(s):  
Machine Learning ◽  
Sustainable Energy ◽  
Energy Systems ◽  
Future Research ◽  
Annual Review ◽  
Publication Date ◽  
Research Directions ◽  
Sustainable Energy Systems ◽  
Future Research Directions ◽  
And Storage

In recent years, machine learning has proven to be a powerful tool for deriving insights from data. In this review, we describe ways in which machine learning has been leveraged to facilitate the development and operation of sustainable energy systems. We first provide a taxonomy of machine learning paradigms and techniques, along with a discussion of their strengths and limitations. We then provide an overview of existing research using machine learning for sustainable energy production, delivery, and storage. Finally, we identify gaps in this literature, propose future research directions, and discuss important considerations for deployment. Expected final online publication date for the Annual Review of Environment and Resources, Volume 46 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Next-Generation Mass Spectrometry Metabolomics Revives the Functional Analysis of Plant Metabolic Diversity

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Dapeng Li ◽  
Emmanuel Gaquerel
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
Test Theory ◽  
Annual Review ◽  
Publication Date ◽  
Next Generation ◽  
Metabolic Diversity ◽  
Ecological Functions ◽  
Metabolome Data ◽  
Generation Sequencing

The remarkable diversity of specialized metabolites produced by plants has inspired several decades of research and nucleated a long list of theories to guide empirical ecological studies. However, analytical constraints and the lack of untargeted processing workflows have long precluded comprehensive metabolite profiling and, consequently, the collection of the critical currencies to test theory predictions for the ecological functions of plant metabolic diversity. Developments in mass spectrometry (MS) metabolomics have revolutionized the large-scale inventory and annotation of chemicals from biospecimens. Hence, the next generation of MS metabolomics propelled by new bioinformatics developments provides a long-awaited framework to revisit metabolism-centered ecological questions, much like the advances in next-generation sequencing of the last two decades impacted all research horizons in genomics. Here, we review advances in plant (computational) metabolomics to foster hypothesis formulation from complex metabolome data. Additionally, we reflect on how next-generation metabolomics could reinvigorate the testing of long-standing theories on plant metabolic diversity. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Physiology and Biogeochemistry of SUP05

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Robert M. Morris ◽  
Rachel L. Spietz
Keyword(s):  
Hydrothermal Vents ◽  
Heterotrophic Bacteria ◽  
Primary Source ◽  
Annual Review ◽  
Publication Date ◽  
Community Studies ◽  
Oxygen Minimum Zones ◽  
Anoxic Waters ◽  
Total Bacterial Community ◽  
Oxygen Minimum

The SUP05 clade of gammaproteobacteria (Thioglobaceae) comprises both primary producers and primary consumers of organic carbon in the oceans. Host-associated autotrophs are a principal source of carbon and other nutrients for deep-sea eukaryotes at hydrothermal vents, and their free-living relatives are a primary source of organic matter in seawater at vents and in marine oxygen minimum zones. Similar to other abundant marine heterotrophs, such as SAR11 and Roseobacter, heterotrophic Thioglobaceae use the dilute pool of osmolytes produced by phytoplankton for growth, including methylated amines and sulfonates. Heterotrophic members are common throughout the ocean, and autotrophic members are abundant at hydrothermal vents and in anoxic waters; combined, they can account for more than 50% of the total bacterial community. Studies of both cultured and uncultured representatives from this diverse family are providing novel insights into the shifting biogeochemical roles of autotrophic and heterotrophic bacteria that cross oxic–anoxic boundary layers in the ocean. Expected final online publication date for the Annual Review of Marine Science, Volume 14 is January 2022. 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.

Advancing Socioeconomic Rights Through Interdisciplinary Factfinding: Opportunities and Challenges

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Sarah Knuckey ◽  
Joshua D. Fisher ◽  
Amanda M. Klasing ◽  
Tess Russo ◽  
Margaret L. Satterthwaite
Keyword(s):  
Human Rights ◽  
Mixed Methods ◽  
Social Science ◽  
Science Volume ◽  
Lessons Learned ◽  
Limited Resources ◽  
Annual Review ◽  
Publication Date ◽  
Socioeconomic Rights ◽  
Human Rights Movement

The human rights movement is increasingly using interdisciplinary, multidisciplinary, mixed-methods, and quantitative factfinding. There has been too little analysis of these shifts. This article examines some of the opportunities and challenges of these methods, focusing on the investigation of socioeconomic human rights. By potentially expanding the amount and types of evidence available, factfinding's accuracy and persuasiveness can be strengthened, bolstering rights claims. However, such methods can also present significant challenges and may pose risks in individual cases and to the human rights movement generally. Interdisciplinary methods can be costly in human, financial, and technical resources; are sometimes challenging to implement; may divert limited resources from other work; can reify inequalities; may produce “expertise” that disempowers rightsholders; and could raise investigation standards to an infeasible or counterproductive level. This article includes lessons learned and questions to guide researchers and human rights advocates considering mixed-methods human rights factfinding. Expected final online publication date for the Annual Review of Law and Social Science, Volume 17 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Conversation and Culture

2021 ◽  
Vol 50 (1) ◽  
Author(s):  
Simeon Floyd
Keyword(s):  
Conversation Analysis ◽  
Quantitative Methods ◽  
Sequential Analysis ◽  
Contemporary Literature ◽  
Annual Review ◽  
Publication Date ◽  
Face To Face ◽  
Qualitative And Quantitative Methods ◽  
Language Studies ◽  
Speech Communities

Conversation analysis is a method for the systematic study of interaction in terms of a sequential turn-taking system. Research in conversation analysis has traditionally focused on speakers of English, and it is still unclear to what extent the system observed in that research applies to conversation more generally around the world. However, as this method is now being applied to conversation in a broader range of languages, it is increasingly possible to address questions about the nature of interactional diversity across different speech communities. The approach of pragmatic typology first applies sequential analysis to conversation from different speech communities and then compares interactional patterns in ways analogous to how traditional linguistic typology compares morphosyntax. This article discusses contemporary literature in pragmatic typology, including single-language studies and multilanguage comparisons reflecting both qualitative and quantitative methods. This research finds that microanalysis of face-to-face interaction can identify both universal trends and culture-specific interactional tendencies. Expected final online publication date for the Annual Review of Anthropology, Volume 50 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Mechanical Patterning in Animal Morphogenesis

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Yonit Maroudas-Sacks ◽  
Kinneret Keren
Keyword(s):  
Pattern Formation ◽  
Large Scale ◽  
Coarse Grained ◽  
Annual Review ◽  
Publication Date ◽  
Biochemical Processes ◽  
Substantial Progress ◽  
Biological Pattern Formation ◽  
Effective Theories ◽  
Biochemical Signals

Morphogenesis is one of the most remarkable examples of biological pattern formation. Despite substantial progress in the field, we still do not understand the organizational principles responsible for the robust convergence of the morphogenesis process across scales to form viable organisms under variable conditions. Achieving large-scale coordination requires feedback between mechanical and biochemical processes, spanning all levels of organization and relating the emerging patterns with the mechanisms driving their formation. In this review, we highlight the role of mechanics in the patterning process, emphasizing the active and synergistic manner in which mechanical processes participate in developmental patterning rather than merely following a program set by biochemical signals. We discuss the value of applying a coarse-grained approach toward understanding this complex interplay, which considers the large-scale dynamics and feedback as well as complementing the reductionist approach focused on molecular detail. A central challenge in this approach is identifying relevant coarse-grained variables and developing effective theories that can serve as a basis for an integrated framework for understanding this remarkable pattern-formation process. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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