Bacterial Multicellularity: The Biology of Escherichia coli Building Large-Scale Biofilm Communities

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Diego O. Serra ◽  
Regine Hengge
Keyword(s):  
Escherichia Coli ◽  
Large Scale ◽  
Second Messengers ◽  
Emergent Properties ◽  
Annual Review ◽  
Publication Date ◽  
Growth And Survival ◽  
Chemical Gradients ◽  
Life Itself ◽  
Scale Matrix

Biofilms are a widespread multicellular form of bacterial life. The spatial structure and emergent properties of these communities depend on a polymeric extracellular matrix architecture that is orders of magnitude larger than the cells that build it. Using as a model the wrinkly macrocolony biofilms of Escherichia coli, which contain amyloid curli fibers and phosphoethanolamine (pEtN)-modified cellulose as matrix components, we summarize here the structure, building, and function of this large-scale matrix architecture. Based on different sigma and other transcription factors as well as second messengers, the underlying regulatory network reflects the fundamental trade-off between growth and survival. It controls matrix production spatially in response to long-range chemical gradients, but it also generates distinct patterns of short-range matrix heterogeneity that are crucial for tissue-like elasticity and macroscopic morphogenesis. Overall, these biofilms confer protection and a potential for homeostasis, thereby reducing maintenance energy, which makes multicellularity an emergent property of life itself. 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.

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.

Gang Research in the Twenty-First Century

2021 ◽  
Vol 5 (1) ◽  
Author(s):  
Caylin Louis Moore ◽  
Forrest Stuart
Keyword(s):  
Large Scale ◽  
Criminological Theory ◽  
First Century ◽  
Annual Review ◽  
Publication Date ◽  
Theoretical Frameworks ◽  
Twenty First Century ◽  
State Interventions ◽  
And Behavior ◽  
Analytical Approaches

For nearly a century, gang scholarship has remained foundational to criminological theory and method. Twenty-first-century scholarship continues to refine and, in some cases, supplant long-held axioms about gang formation, organization, and behavior. Recent advances can be traced to shifts in the empirical social reality and conditions within which gangs exist and act. We draw out this relationship—between the ontological and epistemological—by identifying key macrostructural shifts that have transformed gang composition and behavior and, in turn, forced scholars to revise dominant theoretical frameworks and analytical approaches. These shifts include large-scale economic transformations, the expansion of punitive state interventions, the proliferation of the Internet and social media, intensified globalization, and the increasing presence of women and LGBTQ individuals in gangs and gang research. By introducing historically unprecedented conditions and actors, these developments provide novel opportunities to reconsider previous analyses of gang structure, violence, and other related objects of inquiry. Expected final online publication date for the Annual Review of Criminology, Volume 5 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Origin and Early Evolution of the Eukaryotic Cell

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Toni Gabaldón
Keyword(s):  
Current Knowledge ◽  
Eukaryotic Cell ◽  
Early Evolution ◽  
Annual Review ◽  
Publication Date ◽  
Eukaryotic Evolution ◽  
Life Itself ◽  
Metabolic Interactions ◽  
Phylogenomic Analyses ◽  
Origin Of Eukaryotes

The origin of eukaryotes has been defined as the major evolutionary transition since the origin of life itself. Most hallmark traits of eukaryotes, such as their intricate intracellular organization, can be traced back to a putative common ancestor that predated the broad diversity of extant eukaryotes. However, little is known about the nature and relative order of events that occurred in the path from preexisting prokaryotes to this already sophisticated ancestor. The origin of mitochondria from the endosymbiosis of an alphaproteobacterium is one of the few robustly established events to which most hypotheses on the origin of eukaryotes are anchored, but the debate is still open regarding the time of this acquisition, the nature of the host, and the ecological and metabolic interactions between the symbiotic partners. After the acquisition of mitochondria, eukaryotes underwent a fast radiation into several major clades whose phylogenetic relationships have been largely elusive. Recent progress in the comparative analyses of a growing number of genomes is shedding light on the early events of eukaryotic evolution as well as on the root and branching patterns of the tree of eukaryotes. Here I discuss current knowledge and debates on the origin and early evolution of eukaryotes. I focus particularly on how phylogenomic analyses have challenged some of the early assumptions about eukaryotic evolution, including the widespread idea that mitochondrial symbiosis in an archaeal host was the earliest event in eukaryogenesis. 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.

Dog Models of Aging

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Audrey Ruple ◽  
Evan MacLean ◽  
Noah Snyder-Mackler ◽  
Kate E. Creevy ◽  
Daniel Promislow
Keyword(s):  
Large Scale ◽  
Mammalian Species ◽  
Annual Review ◽  
Publication Date ◽  
Companion Dogs ◽  
Age Related ◽  
Key Concepts ◽  
Similarities And Differences ◽  
Laboratory Models ◽  
Unique Potential

As the most phenotypically diverse mammalian species that shares human environments and access to sophisticated healthcare, domestic dogs have unique potential to inform our understanding of the determinants of aging. Here we outline key concepts in the study of aging and illustrate the value of research with dogs, which can improve dog health and support translational discoveries. We consider similarities and differences in aging and age-related diseases in dogs and humans and summarize key advances in our understanding of genetic and environmental risk factors for morbidity and mortality in dogs. We address health outcomes ranging from cancer to cognitive function and highlight emerging research opportunities from large-scale cohort studies in companion dogs. We conclude that studying aging in dogs could overcome many limitations of laboratory models, most notably, the ability to assess how aging-associated pathways influence aging in real-world environments similar to those experienced by humans. 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.

Accumulating Knowledge in the Organizational Sciences

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Frank A. Bosco
Keyword(s):  
Organizational Behavior ◽  
Cognitive Neuroscience ◽  
Large Scale ◽  
Scientific Progress ◽  
Science Research ◽  
Annual Review ◽  
Publication Date ◽  
Organizational Research ◽  
Research Findings ◽  
Meta Analyses

In some fields, research findings are rigorously curated in a common language and made available to enable future use and large-scale, robust insights. Organizational researchers have begun such efforts [e.g., metaBUS ( http://metabus.org/ )] but are far from the efficient, comprehensive curation seen in areas such as cognitive neuroscience or genetics. This review provides a sample of insights from research curation efforts in organizational research, psychology, and beyond—insights not possible by even large-scale, substantive meta-analyses. Efforts are classified as either science-of-science research or large-scale, substantive research. The various methods used for information extraction (e.g., from PDF files) and classification (e.g., using consensus ontologies) is reviewed. The review concludes with a series of recommendations for developing and leveraging the available corpus of organizational research to speed scientific progress. 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.

The Basis of Navigation Across Species

2021 ◽  
Vol 73 (1) ◽  
Author(s):  
Cody A. Freas ◽  
Ken Cheng
Keyword(s):  
Large Scale ◽  
Error Reduction ◽  
Annual Review ◽  
Publication Date ◽  
Additional Component ◽  
Oscillatory Systems ◽  
Neural Architecture ◽  
Wide Range ◽  
Reduction Strategies ◽  
Cycling Behavior

Animals navigate a wide range of distances, from a few millimeters to globe-spanning journeys of thousands of kilometers. Despite this array of navigational challenges, similar principles underlie these behaviors across species. Here, we focus on the navigational strategies and supporting mechanisms in four well-known systems: the large-scale migratory behaviors of sea turtles and lepidopterans as well as navigation on a smaller scale by rats and solitarily foraging ants. In lepidopterans, rats, and ants we also discuss the current understanding of the neural architecture which supports navigation. The orientation and navigational behaviors of these animals are defined in terms of behavioral error-reduction strategies reliant on multiple goal-directed servomechanisms. We conclude by proposing to incorporate an additional component into this system: the observation that servomechanisms operate on oscillatory systems of cycling behavior. These oscillators and servomechanisms comprise the basis for directed orientation and navigational behaviors. Expected final online publication date for the Annual Review of Psychology, Volume 73 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Systems Biology of the Vasopressin V2 Receptor: New Tools for Discovery of Molecular Actions of a GPCR

2021 ◽  
Vol 62 (1) ◽  
Author(s):  
Lihe Chen ◽  
Hyun Jun Jung ◽  
Arnab Datta ◽  
Euijung Park ◽  
Brian G. Poll ◽  
...  
Keyword(s):  
Systems Biology ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Water Channel ◽  
Peptide Hormone ◽  
Annual Review ◽  
Publication Date ◽  
Large Scale Data ◽  
V2 Receptor ◽  
Scale Data

Systems biology can be defined as the study of a biological process in which all of the relevant components are investigated together in parallel to discover the mechanism. Although the approach is not new, it has come to the forefront as a result of genome sequencing projects completed in the first few years of the current century. It has elements of large-scale data acquisition (chiefly next-generation sequencing–based methods and protein mass spectrometry) and large-scale data analysis (big data integration and Bayesian modeling). Here we discuss these methodologies and show how they can be applied to understand the downstream effects of GPCR signaling, specifically looking at how the neurohypophyseal peptide hormone vasopressin, working through the V2 receptor and PKA activation, regulates the water channel aquaporin-2. The emerging picture provides a detailed framework for understanding the molecular mechanisms involved in water balance disorders, pointing the way to improved treatment of both polyuric disorders and water-retention disorders causing dilutional hyponatremia. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Neural Network Potentials: A Concise Overview of Methods

2022 ◽  
Vol 73 (1) ◽  
Author(s):  
Emir Kocer ◽  
Tsz Wai Ko ◽  
Jörg Behler
Keyword(s):  
Machine Learning ◽  
Atomic Structure ◽  
Electrostatic Interactions ◽  
Large Scale ◽  
Machine Learning Algorithms ◽  
Annual Review ◽  
Publication Date ◽  
Great Success ◽  
Concise Overview ◽  
Wide Range

In the past two decades, machine learning potentials (MLPs) have reached a level of maturity that now enables applications to large-scale atomistic simulations of a wide range of systems in chemistry, physics, and materials science. Different machine learning algorithms have been used with great success in the construction of these MLPs. In this review, we discuss an important group of MLPs relying on artificial neural networks to establish a mapping from the atomic structure to the potential energy. In spite of this common feature, there are important conceptual differences among MLPs, which concern the dimensionality of the systems, the inclusion of long-range electrostatic interactions, global phenomena like nonlocal charge transfer, and the type of descriptor used to represent the atomic structure, which can be either predefined or learnable. A concise overview is given along with a discussion of the open challenges in the field. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Wild Meat Is Still on the Menu: Progress in Wild Meat Research, Policy, and Practice from 2002 to 2020

2021 ◽  
Vol 46 (1) ◽  
Author(s):  
Daniel J. Ingram ◽  
Lauren Coad ◽  
E.J. Milner-Gulland ◽  
Luke Parry ◽  
David Wilkie ◽  
...  
Keyword(s):  
Large Scale ◽  
Research Policy ◽  
Monitoring And Evaluation ◽  
Annual Review ◽  
Publication Date ◽  
Policy And Practice ◽  
Major Barrier ◽  
Regulatory Frameworks ◽  
Emerging Issues ◽  
Wild Meat

Several hundred species are hunted for wild meat in the tropics, supporting the diets, customs, and livelihoods of millions of people. However, unsustainable hunting is one of the most urgent threats to wildlife and ecosystems worldwide and has serious ramifications for people whose subsistence and income are tied to wild meat. Over the past 18 years, although research efforts have increased, scientific knowledge has largely not translated into action. One major barrier to progress has been insufficient monitoring and evaluation, meaning that the effectiveness of interventions cannot be ascertained. Emerging issues include the difficulty of designing regulatory frameworks that disentangle the different purposes of hunting, the large scale of urban consumption, and the implications of wild meat consumption for human health. To address these intractable challenges, we propose eight new recommendations for research and action for sustainable wild meat use, which would support the achievement of the United Nations Sustainable Development Goals. 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.

Two P or Not Two P: Understanding Regulation by the Bacterial Second Messengers (p)ppGpp

2021 ◽  
Vol 75 (1) ◽  
Author(s):  
Gert Bange ◽  
Ditlev E. Brodersen ◽  
Anastasia Liuzzi ◽  
Wieland Steinchen
Keyword(s):  
Second Messengers ◽  
Stringent Response ◽  
Direct Interaction ◽  
Growth Conditions ◽  
Annual Review ◽  
Publication Date ◽  
Cellular Processes ◽  
Gram Positive Bacteria ◽  
Downstream Effects ◽  
Structural Aspects

Under stressful growth conditions and nutrient starvation, bacteria adapt by synthesizing signaling molecules that profoundly reprogram cellular physiology. At the onset of this process, called the stringent response, members of the RelA/SpoT homolog (RSH) protein superfamily are activated by specific stress stimuli to produce several hyperphosphorylated forms of guanine nucleotides, commonly referred to as (p)ppGpp. Some bifunctional RSH enzymes also harbor domains that allow for degradation of (p)ppGpp by hydrolysis. (p)ppGpp synthesis or hydrolysis may further be executed by single-domain alarmone synthetases or hydrolases, respectively. The downstream effects of (p)ppGpp rely mainly on direct interaction with specific intracellular effectors, which are widely used throughout most cellular processes. The growing number of identified (p)ppGpp targets allows us to deduce both common features of and differences between gram-negative and gram-positive bacteria. In this review, we give an overview of (p)ppGpp metabolism with a focus on the functional and structural aspects of the enzymes involved and discuss recent findings on alarmone-regulated cellular effectors. 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.

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