Drosophila sechellia: A Genetic Model for Behavioral Evolution and Neuroecology

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Thomas O. Auer ◽  
Michael P. Shahandeh ◽  
Richard Benton
Keyword(s):  
Genetic Model ◽  
Morinda Citrifolia ◽  
Host Specialization ◽  
Annual Review ◽  
Publication Date ◽  
Behavioral Evolution ◽  
Island Endemic ◽  
Drosophila Sechellia ◽  
Open Questions ◽  
Morphological Adaptations

Defining the mechanisms by which animals adapt to their ecological niche is an important problem bridging evolution, genetics, and neurobiology. We review the establishment of a powerful genetic model for comparative behavioral analysis and neuroecology, Drosophila sechellia. This island-endemic fly species is closely related to several cosmopolitan generalists, including Drosophila melanogaster, but has evolved extreme specialism, feeding and reproducing exclusively on the noni fruit of the tropical shrub Morinda citrifolia. We first describe the development and use of genetic approaches to facilitate genotype/phenotype associations in these drosophilids. Next, we survey the behavioral, physiological, and morphological adaptations of D. sechellia throughout its life cycle and outline our current understanding of the genetic and cellular basis of these traits. Finally, we discuss the principles this knowledge begins to establish in the context of host specialization, speciation, and the neurobiology of behavioral evolution and consider open questions and challenges in the field. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

The Ecology and Evolution of Model Microbial Mutualisms

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Jeremy M. Chacón ◽  
Sarah P. Hammarlund ◽  
Jonathan N.V. Martinson ◽  
Leno B. Smith ◽  
William R. Harcombe
Keyword(s):  
Future Study ◽  
Evolutionary Dynamics ◽  
Interspecific Interactions ◽  
Natural World ◽  
Annual Review ◽  
Publication Date ◽  
Controlled Experiments ◽  
Evolutionary Origins ◽  
Ecological Features ◽  
Open Questions

Mutually beneficial interspecific interactions are abundant throughout the natural world, including between microbes. Mutualisms between microbes are critical for everything from human health to global nutrient cycling. Studying model microbial mutualisms in the laboratory enables highly controlled experiments for developing and testing evolutionary and ecological hypotheses. In this review, we begin by describing the tools available for studying model microbial mutualisms. We then outline recent insights that laboratory systems have shed on the evolutionary origins, evolutionary dynamics, and ecological features of microbial mutualism. We touch on gaps in our current understanding of microbial mutualisms, note connections to mutualism in nonmicrobial systems, and call attention to open questions ripe for future study. 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.

scholarly journals Influenza Virus RNA-Dependent RNA Polymerase and the Host Transcriptional Apparatus

2021 ◽  
Vol 90 (1) ◽  
Author(s):  
Tim Krischuns ◽  
Maria Lukarska ◽  
Nadia Naffakh ◽  
Stephen Cusack
Keyword(s):  
Influenza Virus ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Annual Review ◽  
Publication Date ◽  
Rna Dependent Rna Polymerase ◽  
Open Questions ◽  
Virus Rna ◽  
Cap Binding Complex ◽  
Rnap Ii

Influenza virus RNA-dependent RNA polymerase (FluPol) transcribes the viral RNA genome in the infected cell nucleus. In the 1970s, researchers showed that viral transcription depends on host RNA polymerase II (RNAP II) activity and subsequently that FluPol snatches capped oligomers from nascent RNAP II transcripts to prime its own transcription. Exactly how this occurs remains elusive. Here, we review recent advances in the mechanistic understanding of FluPol transcription and early events in RNAP II transcription that are relevant to cap-snatching. We describe the known direct interactions between FluPol and the RNAP II C-terminal domain and summarize the transcription-related host factors that have been found to interact with FluPol. We also discuss open questions regarding how FluPol may be targeted to actively transcribing RNAP II and the exact context and timing of cap-snatching, which is presumed to occur after cap completion but before the cap is sequestered by the nuclear cap-binding complex. 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.

Quantitative Control for Stoichiometric Protein Synthesis

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
James C. Taggart ◽  
Jean-Benoît Lalanne ◽  
Gene-Wei Li
Keyword(s):  
Protein Synthesis ◽  
Protein Production ◽  
Protein Complexes ◽  
Annual Review ◽  
Publication Date ◽  
Rna Turnover ◽  
Regulatory Strategies ◽  
Open Questions ◽  
Genome Wide ◽  
Bacterial Protein Synthesis

Bacterial protein synthesis rates have evolved to maintain preferred stoichiometries at striking precision, from the components of protein complexes to constituents of entire pathways. Setting relative protein production rates to be well within a factor of two requires concerted tuning of transcription, RNA turnover, and translation, allowing many potential regulatory strategies to achieve the preferred output. The last decade has seen a greatly expanded capacity for precise interrogation of each step of the central dogma genome-wide. Here, we summarize how these technologies have shaped the current understanding of diverse bacterial regulatory architectures underpinning stoichiometric protein synthesis. We focus on the emerging expanded view of bacterial operons, which encode diverse primary and secondary mRNA structures for tuning protein stoichiometry. Emphasis is placed on how quantitative tuning is achieved. We discuss the challenges and open questions in the application of quantitative, genome-wide methodologies to the problem of precise protein production. 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.

On the Role of Competing Interactions in Charged Colloids with Short-Range Attraction

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
José Ruiz-Franco ◽  
Emanuela Zaccarelli
Keyword(s):  
Short Range ◽  
Condensed Matter ◽  
Annual Review ◽  
Publication Date ◽  
Colloidal Systems ◽  
Competing Interactions ◽  
Charged Colloids ◽  
Open Questions ◽  
Cluster Phase

In this review, we discuss recent advances in the investigation of colloidal systems interacting via a combination of short-range attraction and long-range repulsion. The prototypical examples of this phenomenology are charged colloids with depletion interactions, but the results apply, to a large extent, also to suspensions of globular proteins, clays, and, in general, to systems with competing attractive (hydrophobic) and repulsive (polar) contributions. After a brief introduction to the problem, we focus on the three disordered states that characterize these systems: equilibrium cluster phase, equilibrium gel, and Wigner glass of clusters. We provide a comparison of their static and dynamic observables, mainly by means of numerical simulations. Next, we discuss the few available studies on their viscoelastic properties and on their response to an external shear. Finally, we provide a summary of the current findings and also raise the main open questions and challenges for the future in this topic. Expected final online publication date for the Annual Review of Condensed Matter Physics, Volume 12 is March 10, 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals The Future of Solar Neutrinos

2021 ◽  
Vol 71 (1) ◽  
Author(s):  
Gabriel D. Orebi Gann ◽  
Kai Zuber ◽  
Daniel Bemmerer ◽  
Aldo Serenelli
Keyword(s):  
Current Knowledge ◽  
Solar Neutrinos ◽  
Experimental Program ◽  
Annual Review ◽  
Publication Date ◽  
Proton Proton ◽  
Flavor Oscillations ◽  
Current State ◽  
Open Questions ◽  
Neutrino Fluxes

In this article we review the current state of the field of solar neutrinos, including flavor oscillations, nonstandard effects, solar models, cross section measurements, and the broad experimental program thus motivated and enabled. We describe the historical discoveries that contributed to current knowledge, and define critical open questions to be addressed in the next decade. We discuss standard solar models, including uncertainties and problems related to the solar composition, and review experimental and model solar neutrino fluxes, including future prospects. We review the state of the art of the nuclear reaction data relevant for solar fusion in the proton–proton chain and carbon–nitrogen–oxygen cycle. Finally, we review the current and future experimental programs that can address outstanding questions in this field. Expected final online publication date for the Annual Review of Nuclear and Particle Science, Volume 71 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals The Fertilization Enigma: How Sperm and Egg Fuse

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Victoria E. Deneke ◽  
Andrea Pauli
Keyword(s):  
Viral Entry ◽  
Molecular Mechanisms ◽  
Muscle Development ◽  
Annual Review ◽  
Publication Date ◽  
Open Questions ◽  
Singular Event ◽  
Multistep Process ◽  
Mammalian Fertilization ◽  
Emerging Themes

Fertilization is a multistep process that culminates in the fusion of sperm and egg, thus marking the beginning of a new organism in sexually reproducing species. Despite its importance for reproduction, the molecular mechanisms that regulate this singular event, particularly sperm–egg fusion, have remained mysterious for many decades. Here, we summarize our current molecular understanding of sperm–egg interaction, focusing mainly on mammalian fertilization. Given the fundamental importance of sperm–egg fusion yet the lack of knowledge of this process in vertebrates, we discuss hallmarks and emerging themes of cell fusion by drawing from well-studied examples such as viral entry, placenta formation, and muscle development. We conclude by identifying open questions and exciting avenues for future studies in gamete fusion. 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.

scholarly journals Algorithms and Decision-Making in the Public Sector

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Karen Levy ◽  
Kyla E. Chasalow ◽  
Sarah Riley
Keyword(s):  
Decision Making ◽  
Public Sector ◽  
Problem Formulation ◽  
Annual Review ◽  
Publication Date ◽  
Criminal Justice Education ◽  
The Public ◽  
Technology Acquisition ◽  
Open Questions ◽  
The Social

This article surveys the use of algorithmic systems to support decision-making in the public sector. Governments adopt, procure, and use algorithmic systems to support their functions within several contexts—including criminal justice, education, and benefits provision—with important consequences for accountability, privacy, social inequity, and public participation in decision-making. We explore the social implications of municipal algorithmic systems across a variety of stages, including problem formulation, technology acquisition, deployment, and evaluation. We highlight several open questions that require further empirical research. 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.

The Hubbard Model

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Daniel P. Arovas ◽  
Erez Berg ◽  
Steven A. Kivelson ◽  
Srinivas Raghu
Keyword(s):  
Hubbard Model ◽  
Approximate Solutions ◽  
Annual Review ◽  
Publication Date ◽  
Strongly Correlated Electron ◽  
Correlated Electron Systems ◽  
Correlated Electron ◽  
Open Questions ◽  
Spatial Dimensions ◽  
Primary Focus

The repulsive Hubbard model has been immensely useful in understanding strongly correlated electron systems and serves as the paradigmatic model of the field. Despite its simplicity, it exhibits a strikingly rich phenomenology reminiscent of that observed in quantum materials. Nevertheless, much of its phase diagram remains controversial. Here, we review a subset of what is known about the Hubbard model based on exact results or controlled approximate solutions in various limits, for which there is a suitable small parameter. Our primary focus is on the ground state properties of the system on various lattices in two spatial dimensions, although both lower and higher dimensions are discussed as well. Finally, we highlight some of the important outstanding open questions. Expected final online publication date for the Annual Review of Condensed Matter Physics, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Genomics analysis of Drosophila sechellia response to Morinda citrifolia fruit diet

2021 ◽  
Author(s):  
Joseph D. Coolon ◽  
Zachary Drum ◽  
Stephen Lanno ◽  
Sadie Gregory ◽  
Serena Shimshak ◽  
...  
Keyword(s):  
Gene Expression ◽  
Regulatory Networks ◽  
Morinda Citrifolia ◽  
Individual Compound ◽  
General Role ◽  
Toxin Resistance ◽  
Island Endemic ◽  
Drosophila Sechellia ◽  
Genome Wide ◽  
Genetic Mechanisms

Drosophila sechellia is an island endemic host specialist that has evolved to consume the toxic fruit of Morinda citrifolia, also known as noni fruit. Recent studies by our group and others have examined genome-wide gene expression responses of fruit flies to individual highly abundant compounds found in noni responsible for the fruits unique chemistry and toxicity. In order to relate these reductionist experiments to the gene expression responses to feeding on noni fruit itself, we fed rotten noni fruit to adult female D. sechellia and performed RNA-sequencing. Combining the reductionist and more wholistic approaches, we have identified candidate genes that may contribute to each individual compound and those that play a more general role in response to the fruit as a whole. Using the compound specific and general responses, we used transcription factor prediction analyses to identify the regulatory networks and specific regulators involved in the responses to each compound and the fruit itself. The identified genes and regulators represent the possible genetic mechanisms and biochemical pathways that contribute to toxin resistance and noni specialization in D. sechellia

Long-Distance Transported RNAs: From Identity to Function

2021 ◽  
Vol 73 (1) ◽  
Author(s):  
Julia Kehr ◽  
Richard J. Morris ◽  
Friedrich Kragler
Keyword(s):  
Biological Function ◽  
Plant Biology ◽  
Annual Review ◽  
Publication Date ◽  
Messenger Rnas ◽  
Biological Functions ◽  
Long Distance ◽  
Rna Molecules ◽  
Open Questions ◽  
Different Types

There is now a wealth of data, from different plants and labs and spanning more than two decades, which unequivocally demonstrates that RNAs can be transported over long distances, from the cell where they are transcribed to distal cells in other tissues. Different types of RNA molecules are transported, including micro- and messenger RNAs. Whether these RNAs are selected for transport and, if so, how they are selected and transported remain, in general, open questions. This aspect is likely not independent of the biological function and relevance of the transported RNAs, which are in most cases still unclear. In this review, we summarize the experimental data supporting selectivity or nonselectivity of RNA translocation and review the evidence for biological functions. After discussing potential issues regarding the comparability between experiments, we propose criteria that need to be critically evaluated to identify important signaling RNAs. Expected final online publication date for the Annual Review of Plant Biology, Volume 73 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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