The Making of Plant Armor: The Periderm

2022 ◽  
Vol 73 (1) ◽  
Author(s):  
Olga Serra ◽  
Ari Pekka Mähönen ◽  
Alexander J. Hetherington ◽  
Laura Ragni
Keyword(s):  
Regulatory Networks ◽  
Plant Biology ◽  
Raw Material ◽  
Industrial Processes ◽  
Annual Review ◽  
Publication Date ◽  
Biotic And Abiotic Stress ◽  
Meristematic Tissue ◽  
Future Challenges ◽  
Periderm Formation

The periderm acts as armor protecting the plant's inner tissues from biotic and abiotic stress. It forms during the radial thickening of plant organs such as stems and roots and replaces the function of primary protective tissues such as the epidermis and the endodermis. A wound periderm also forms to heal and protect injured tissues. The periderm comprises a meristematic tissue called the phellogen, or cork cambium, and its derivatives: the lignosuberized phellem and the phelloderm. Research on the periderm has mainly focused on the chemical composition of the phellem due to its relevance as a raw material for industrial processes. Today, there is increasing interest in the regulatory network underlying periderm development as a novel breeding trait to improve plant resilience and to sequester CO2. Here, we discuss our current understanding of periderm formation, focusing on aspects of periderm evolution, mechanisms of periderm ontogenesis, regulatory networks underlying phellogen initiation and cork differentiation, and future challenges of periderm research. 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.

A Comparative Overview of the Intracellular Guardians of Plants and Animals: NLRs in Innate Immunity and Beyond

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Zane Duxbury ◽  
Chih-hang Wu ◽  
Pingtao Ding
Keyword(s):  
Immune Responses ◽  
Genetic Architecture ◽  
Pathogen Detection ◽  
Current Knowledge ◽  
Plant Immunity ◽  
Innate Immune ◽  
Plant Biology ◽  
Annual Review ◽  
Publication Date ◽  
Nucleotide Binding Domain

Nucleotide-binding domain leucine-rich repeat receptors (NLRs) play important roles in the innate immune systems of both plants and animals. Recent breakthroughs in NLR biochemistry and biophysics have revolutionized our understanding of how NLR proteins function in plant immunity. In this review, we summarize the latest findings in plant NLR biology and draw direct comparisons to NLRs of animals. We discuss different mechanisms by which NLRs recognize their ligands in plants and animals. The discovery of plant NLR resistosomes that assemble in a comparable way to animal inflammasomes reinforces the striking similarities between the formation of plant and animal NLR complexes. Furthermore, we discuss the mechanisms by which plant NLRs mediate immune responses and draw comparisons to similar mechanisms identified in animals. Finally, we summarize the current knowledge of the complex genetic architecture formed by NLRs in plants and animals and the roles of NLRs beyond pathogen detection. 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.

Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Nikhil Mishra ◽  
Carl-Philipp Heisenberg
Keyword(s):  
Cell Fate ◽  
Regulatory Networks ◽  
Annual Review ◽  
Publication Date ◽  
Technological Advances ◽  
Complex Shapes ◽  
Gene Regulatory ◽  
And Mathematics ◽  
Multicellular Organisms ◽  
Shape Changes

Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future. 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.

Sepsis-Induced Immunosuppression

2021 ◽  
Vol 84 (1) ◽  
Author(s):  
Lisa K. Torres ◽  
Peter Pickkers ◽  
Tom van der Poll
Keyword(s):  
Organ Transplant ◽  
Annual Review ◽  
Publication Date ◽  
Predisposing Factor ◽  
Substantial Impact ◽  
Immunomodulatory Agents ◽  
Secondary Infections ◽  
Future Challenges ◽  
Treatment Paradigm ◽  
New Treatment

Sepsis is expected to have a substantial impact on public health and cost as its prevalence increases. Factors contributing to increased prevalence include a progressively aging population, advances in the use of immunomodulatory agents to treat a rising number of diseases, and immune-suppressing therapies in organ transplant recipients and cancer patients. It is now recognized that sepsis is associated with profound and sustained immunosuppression, which has been implicated as a predisposing factor in the increased susceptibility of patients to secondary infections and mortality. In this review, we discuss mechanisms of sepsis-induced immunosuppression and biomarkers that identify a state of impaired immunity. We also highlight immune-enhancing strategies that have been evaluated in patients with sepsis, as well as therapeutics under current investigation. Finally, we describe future challenges and the need for a new treatment paradigm, integrating predictive enrichment with patient factors that may guide the future selection of tailored immunotherapy. 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.

scholarly journals Physiologically Based Modeling of Food Digestion and Intestinal Microbiota: State of the Art and Future Challenges. An INFOGEST Review

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Steven Le Feunteun ◽  
Ahmed Al-Razaz ◽  
Matthijs Dekker ◽  
Erwin George ◽  
Beatrice Laroche ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Historical Background ◽  
Annual Review ◽  
Publication Date ◽  
Physiologically Based ◽  
The Future ◽  
Future Challenges ◽  
Full Picture ◽  
Food Digestion

This review focuses on modeling methodologies of the gastrointestinal tract during digestion that have adopted a systems-view approach and, more particularly, on physiologically based compartmental models of food digestion and host–diet–microbiota interactions. This type of modeling appears very promising for integrating the complex stream of mechanisms that must be considered and retrieving a full picture of the digestion process from mouth to colon. We may expect these approaches to become more and more accurate in the future and to serve as a useful means of understanding the physicochemical processes occurring in the gastrointestinal tract, interpreting postprandial in vivo data, making relevant predictions, and designing healthier foods. This review intends to provide a scientific and historical background of this field of research, before discussing the future challenges and potential benefits of the establishment of such a model to study and predict food digestion and absorption in humans. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 12 is March 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Molecular Simulation of Electrode-Solution Interfaces

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Laura Scalfi ◽  
Mathieu Salanne ◽  
Benjamin Rotenberg
Keyword(s):  
Electrostatic Interactions ◽  
Statistical Physics ◽  
Electricity Production ◽  
Industrial Processes ◽  
Annual Review ◽  
Publication Date ◽  
Metallic Electrode ◽  
Physical Mechanisms ◽  
Pure Solvent ◽  
And Storage

Many key industrial processes, from electricity production, conversion, and storage to electrocatalysis or electrochemistry in general, rely on physical mechanisms occurring at the interface between a metallic electrode and an electrolyte solution, summarized by the concept of an electric double layer, with the accumulation/depletion of electrons on the metal side and of ions on the liquid side. While electrostatic interactions play an essential role in the structure, thermodynamics, dynamics, and reactivity of electrode-electrolyte interfaces, these properties also crucially depend on the nature of the ions and solvent, as well as that of the metal itself. Such interfaces pose many challenges for modeling because they are a place where quantum chemistry meets statistical physics. In the present review, we explore the recent advances in the description and understanding of electrode-electrolyte interfaces with classical molecular simulations, with a focus on planar interfaces and solvent-based liquids, from pure solvent to water-in-salt-electrolytes. 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.

Plant Pan-Genomics Comes of Age

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Li Lei ◽  
Eugene Goltsman ◽  
David Goodstein ◽  
Guohong Albert Wu ◽  
Daniel S. Rokhsar ◽  
...  
Keyword(s):  
High Resolution ◽  
Dna Sequences ◽  
Repetitive Sequences ◽  
Plant Biology ◽  
Annual Review ◽  
Publication Date ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Large Size ◽  
Sizable Fraction

A pan-genome is the nonredundant collection of genes and/or DNA sequences in a species. Numerous studies have shown that plant pan-genomes are typically much larger than the genome of any individual and that a sizable fraction of the genes in any individual are present in only some genomes. The construction and interpretation of plant pan-genomes are challenging due to the large size and repetitive content of plant genomes. Most pan-genomes are largely focused on nontransposable element protein coding genes because they are more easily analyzed and defined than noncoding and repetitive sequences. Nevertheless, noncoding and repetitive DNA play important roles in determining the phenotype and genome evolution. Fortunately, it is now feasible to make multiple high-quality genomes that can be used to construct high-resolution pan-genomes that capture all the variation. However, assembling, displaying, and interacting with such high-resolution pan-genomes will require the development of new tools. 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.

Beyond Casual Resemblances: Rigorous Frameworks for Comparing Regeneration Across Species

2021 ◽  
Vol 37 (1) ◽  
Author(s):  
Mansi Srivastava
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Evolutionary History ◽  
Adult Stem Cells ◽  
Annual Review ◽  
Publication Date ◽  
Animal Phyla ◽  
History Of ◽  
Gene Regulatory ◽  
Unifying Principles

The majority of animal phyla have species that can regenerate. Comparing regeneration across animals can reconstruct the molecular and cellular evolutionary history of this process. Recent studies have revealed some similarity in regeneration mechanisms, but rigorous comparative methods are needed to assess whether these resemblances are ancestral pathways (homology) or are the result of convergent evolution (homoplasy). This review aims to provide a framework for comparing regeneration across animals, focusing on gene regulatory networks (GRNs), which are substrates for assessing process homology. The homology of the wound-induced activation of Wnt signaling and of adult stem cells are discussed as examples of ongoing studies of regeneration that enable comparisons in a GRN framework. Expanding the study of regeneration GRNs in currently studied species and broadening taxonomic sampling for these approaches will identify processes that are unifying principles of regeneration biology across animals. These insights are important both for evolutionary studies of regeneration and for human regenerative medicine. 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.

Phytochrome Signaling Networks

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Mei-Chun Cheng ◽  
Praveen Kumar Kathare ◽  
Inyup Paik ◽  
Enamul Huq
Keyword(s):  
Protein Interactions ◽  
Translational Regulation ◽  
Regulatory Networks ◽  
Annual Review ◽  
Publication Date ◽  
Protein Protein Interactions ◽  
Conformational Switching ◽  
E3 Ligases ◽  
Almost All

The perception of light signals by the phytochrome family of photoreceptors has a crucial influence on almost all aspects of growth and development throughout a plant's life cycle. The holistic regulatory networks orchestrated by phytochromes, including conformational switching, subcellular localization, direct protein-protein interactions, transcriptional and posttranscriptional regulations, and translational and posttranslational controls to promote photomorphogenesis, are highly coordinated and regulated at multiple levels. During the past decade, advances using innovative approaches have substantially broadened our understanding of the sophisticated mechanisms underlying the phytochrome-mediated light signaling pathways. This review discusses and summarizes these discoveries of the role of the modular structure of phytochromes, phytochrome-interacting proteins, and their functions; the reciprocal modulation of both positive and negative regulators in phytochrome signaling; the regulatory roles of phytochromes in transcriptional activities, alternative splicing, and translational regulation; and the kinases and E3 ligases that modulate PHYTOCHROME INTERACTING FACTORs to optimize photomorphogenesis. 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.

scholarly journals Tuber and Tuberous Root Development

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Wolfgang Zierer ◽  
David Rüscher ◽  
Uwe Sonnewald ◽  
Sophia Sonnewald
Keyword(s):  
Tuberous Root ◽  
Plant Biology ◽  
Annual Review ◽  
Publication Date ◽  
Storage Organ ◽  
Tuber Development ◽  
Crop Species ◽  
The World ◽  
Potato Tuberization ◽  
And Storage

Root and tuber crops have been an important part of human nutrition since the early days of humanity, providing us with essential carbohydrates, proteins, and vitamins. Today, they are especially important in tropical and subtropical regions of the world, where they help to feed an ever-growing population. Early induction and storage organ size are important agricultural traits, as they determine yield over time. During potato tuberization, environmental and metabolic status are sensed, ensuring proper timing of tuberization mediated by phloem-mobile signals. Coordinated cellular restructuring and expansion growth, as well as controlled storage metabolism in the tuber, are executed. This review summarizes our current understanding of potato tuber development and highlights similarities and differences to important tuberous root crop species like sweetpotato and cassava. Finally, we point out knowledge gaps that need to be filled before a complete picture of storage organ development can emerge. 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.

Genetics of Shoot Meristem and Shoot Regeneration

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Leor Eshed Williams
Keyword(s):  
Shoot Regeneration ◽  
Developmental Plasticity ◽  
Genetic Network ◽  
Shoot Meristem ◽  
Annual Review ◽  
Publication Date ◽  
Cell Specification ◽  
Future Challenges ◽  
Gene Regulatory ◽  
Stochastic Events

Plants exhibit remarkable lineage plasticity, allowing them to regenerate organs that differ from their respective origins. Such developmental plasticity is dependent on the activity of pluripotent founder cells or stem cells residing in meristems. At the shoot apical meristem (SAM), the constant flow of cells requires continuing cell specification governed by a complex genetic network, with the WUSCHEL transcription factor and phytohormone cytokinin at its core. In this review, I discuss some intriguing recent discoveries that expose new principles and mechanisms of patterning and cell specification acting both at the SAM and, prior to meristem organogenesis during shoot regeneration. I also highlight unanswered questions and future challenges in the study of SAM and meristem regeneration. Finally, I put forward a model describing stochastic events mediated by epigenetic factors to explain how the gene regulatory network might be initiated at the onset of shoot regeneration. 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.

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