Fifteen compelling open questions in plant cell biology

As scientists, we are at least as excited about the open questions—the things we do not know—as the discoveries. Here, we asked 15 experts to describe the most compelling open questions in plant cell biology. These are their questions: How are organelle identity, domains, and boundaries maintained under the continuous flux of vesicle trafficking and membrane remodeling? Is the plant cortical microtubule cytoskeleton a mechanosensory apparatus? How are the cellular pathways of cell wall synthesis, assembly, modification, and integrity sensing linked in plants? Why do plasmodesmata open and close? Is there retrograde signaling from vacuoles to the nucleus? How do root cells accommodate fungal endosymbionts? What is the role of cell edges in plant morphogenesis? How is the cell division site determined? What are the emergent effects of polyploidy on the biology of the cell, and how are any such “rules” conditioned by cell type? Can mechanical forces trigger new cell fates in plants? How does a single differentiated somatic cell reprogram and gain pluripotency? How does polarity develop de-novo in isolated plant cells? What is the spectrum of cellular functions for membraneless organelles and intrinsically disordered proteins? How do plants deal with internal noise? How does order emerge in cells and propagate to organs and organisms from complex dynamical processes? We hope you find the discussions of these questions thought provoking and inspiring.

We asked 15 experts to address what they consider to be the most compelling open questions in plant cell biology and these are their questions.     

The molecular architecture of protein-protein binding sites

The formation of specific protein interactions plays a crucial role in most, if not all, biological processes, including signal transduction, cell regulation, the immune response and others. Recent advances in our understanding of the molecular architecture of protein-protein binding sites, which facilitates such diversity in binding affinity and specificity, are enabling us to address key questions. What is the amino acid composition of binding sites? What are interface hotspots? How are binding sites organized? What are the differences between tight and weak interacting complexes? How does water contribute to binding? Can the knowledge gained be translated into protein design? And does a universal code for binding exist, or is it the architecture and chemistry of the interface that enable diverse but specific binding solutions?     

The role of DNA fragmentation in apoptosis

The formation of distinct DNA fragments of oligonucleosomal size (180-200 bp lengths) is a biochemical hallmark of apoptosis in many cells. Recent observations also suggest large DNA fragments and even single-strand cleavage events occur during cell death. These observations have raised many questions. What are the types of DNA cleavage observed during apoptosis? What are the nucleases involved? And what is the role of these nucleolytic events in apoptosis?     

Cell wall proteins: a new insight through proteomics

Cell wall proteins are essential constituents of plant cell walls; they are involved in modifications of cell wall components, wall structure, signaling and interactions with plasma membrane proteins at the cell surface. The application of proteomic approaches to the cell wall compartment raises important questions: are there technical problems specific to cell wall proteomics? What kinds of proteins can be found in Arabidopsis walls? Are some of them unexpected? What sort of post-translational modifications have been characterized in cell wall proteins to date? The purpose of this review is to discuss the experimental results obtained to date using proteomics, as well as some of the new questions challenging future research.     

Physiology and biophysics of chloride and cation cotransport across cell membranes

Many important questions remain to be answered about the mechanism that mediates coupled Na,K,Cl cotransport. We still do not know what the ATP requirement involves. Is ATP the direct energy source? Such an energy source does not seem to be necessary, inasmuch as the net free energy in the combined transmembrane chemical gradients of Na, K, and Cl is quite sufficient to maintain the observed high Cl(i). Could a protein kinase-mediated mechanism be responsible for the ATP requirement? How does reducing Cl(i) stimulate the transporter? What are the kinetic relationships for the co-ions at the outward- and inward-facing transport sites? Are they symmetrical? Can the squid axon regulate its cell volume? If so, is the Na,K,Cl transporter directly involved? Thus, the squid axon remains a fruitful preparation to study a transport mechanism similar to that found in a variety of cells. Its large size confers unique experimental advantages that should help us in our quest to understand this widely distributed transport mechanism.     

Perspective on architecture and assembly of membrane contact sites

Membrane contact sites (MCS) are platforms of physical contact between different organelles. They are formed through interactions involving lipids and proteins, and function in processes such as calcium and lipid exchange, metabolism and organelle biogenesis. In this article, we discuss emerging questions regarding the architecture, organisation and assembly of MCS, such as: What is the contribution of different components to the interaction between organelles? How is the specific composition of different types of membrane contacts sites established and maintained? How are proteins and lipids spatially organised at MCS and how does that influence their function? How dynamic are MCS on the molecular and ultrastructural level? We highlight current state of research and point out experimental approaches that promise to contribute to a spatiomechanistic understanding of MCS functions.     

Introduction: Who's at the bottom? Examining claims about racial hierarchy

Why do claims about racial hierarchy matter? The question whether some groups are worse off than others is highly pertinent at a time when there is growing recognition of multiple forms of racisms and racial oppression. It is widely accepted that racial hierarchies are still with us today, and this concept is peppered throughout writings on “race” and racisms, but, what, exactly, are racial hierarchies, how do racial hierarchies continue to matter, and in what ways do they operate? This special issue, which focuses on the USA and Britain, also addresses the following questions: Does the concept of racial hierarchy aid us in illuminating racial inequalities and the differential experiences of groups in Western multi-ethnic societies such as the USA and Britain? What sorts of criteria are used in arguments about the place of groups along racial hierarchies? What are the political implications of claims made about racial hierarchies?     

Teaching and Research at Marine Stations: Present Priorities, Future Directions

SYNOPSIS. A conflict exists at many universities today betweenthe demand to maintain a competitive position as a researchinstitution, contributing to the rapidly advancing scholarshipin science, and the need to provide available and sympatheticcommunication between undergraduate students and the most vigorousfaculty. This conflict is especially apparent at marine stations.A marine station is usually geographically and politically isolatedfrom the main campus with its advantage of size and opportunitiesto obtain and share sophisticated equipment used in today'sscience. There is also a historical trend of smaller teachinglaboratories evolving into larger research-oriented facilities.And, financial support is not as readily available for researchand education in natural history and whole animal biology, idealsubjects for study at marine stations, as it is for some otherfields. In this presentation I examine the following questions:1. What is the role of teaching at marine stations today? 2.What are some of the current pressures that conflict with thisrole? and 3. What are some solutions to these conflicts? I approachthese questions from my experience as a teacher and researchscientist at a small marine station which has been concernedwith undergraduate teaching. I propose that marine field stationsof diverse sizes and roles, both teaching and research, canbe and should be supported financially and that this supportof diversity will return strong health to marine science nationallyand internationally.     

Signaling pathway of autophagy associated with innate immunity

Autophagy has recently been shown to be an important component of the innate immune response. The signaling pathways leading to activation of autophagy in innate immunity are not well studied. Our recent study shows that Toll-like receptor 4 (TLR 4) serves as an environmental sensor for autophagy. We define a new molecular pathway in which lipopolysaccharide (LPS) induces autophagy in human and murine macrophages by a pathway regulated through Toll-interleukin 1 receptor domain-containing adaptor-inducing interferon-beta (TRIF)-dependent, myeloid differentiation factor 88 (MyD88)-independent TLR4 signaling. Receptor-interacting protein (RIP1) and p38 mitogen-activated protein-kinase (MAPK) are downstream components of this pathway. This signaling pathway does not affect cell viability, indicating that it is distinct from an autophagic death signaling pathway. We further show that LPS-induced autophagy can enhance mycobacterial co-localization with the autophagosomes. The above study raises important questions. (1) What is the complete signaling pathway for LPS-induced autophagy? (2) Does TLR3 mediate autophagy? (3) What are the mechanisms that determine whether autophagy acts as a pro-death or pro-survival pathway? (4) What are the physiological functions of LPS-induced autophagosomes? Future studies examining the above questions should provide us with important clues as to how autophagy is regulated in innate immunity, and how autophagy can be utilized in pathogen clearance.     

Transition from academia to industry: a personal account

A career in industry has become a widely accepted alternative for those of us trained in medicine and/or science who have traditionally focused on careers in academia. Like any career decision, consideration of a position in industry should include asking yourself a series of fundamental questions. A few of the key questions should include: 1) What kind of work environment do you find most enjoyable? (e.g., patient care setting, basic research lab, team-oriented setting); 2) What are you focused on accomplishing in your career? (basic research discoveries, contributions to clinical medicine, compensation); 3) Are you team oriented in your interactions or are you more of an individual contributor? A successful career in any endeavor, including industry, starts with a careful and honest examination of what you are best suited for and inspired to do.     

Spatial patterning of the spruce budworm

The spatial and temporal distribution of the spruce budworm is modelled by a nonlinear diffusion equation. Two questions are considered:

1. What is the critical size of a patch of forest which can support an outbreak?
2. What is the width of an effective barrier to spread of an outbreak?

Answers to these questions are obtained with the aid of comparison methods for nonlinear diffusion equations.     

Forty Years of Prcs-What Have We Learned?

What are phase-response curves (PRCs)? How can they be measured? How should they be plotted? These questions and many other fascinating facets of PRCs are addressed in this review, including research topics in which phase-resetting data have provided crucial insights: entrainment, phototransduction, pacemaker mechanism, phase markers of the pacemaker, and gauges of oscillator amplitude. PRCs have enlightened us and will continue to be a valuable tool in clock research.     

Timeline: AIDS pathogenesis: what have two decades of HIV research taught us?

22 years ago, the first cases of an acquired immunodeficiency syndrome afflicting young, homosexual American men were reported, heralding what we now know to be the beginning of the HIV epidemic. Since then, billions of US dollars have been invested in HIV research in the hope of gaining a better understanding of this infection and how to prevent and treat it. What are the landmarks in HIV research over the past two decades, and what questions still remain to be answered? What has the intense study of HIV infection taught us about other virus infections and how our immune system responds to them?     

Forty years of PRCs--what have we learned?

What are phase-response curves (PRCs)? How can they be measured? How should they be plotted? These questions and many other fascinating facets of PRCs are addressed in this review, including research topics in which phase-resetting data have provided crucial insights: entrainment, phototransduction, pacemaker mechanism, phase markers of the pacemaker, and gauges of oscillator amplitude. PRCs have enlightened us and will continue to be a valuable tool in clock research.     

Cellular engineering in a minimal microbe: structure and assembly of the terminal organelle of Mycoplasma pneumoniae

Mycoplasma pneumoniae is a minimal microbe with respect to cell envelope composition, biosynthetic and regulatory capabilities and genome size, yet it possesses a remarkably complex, multifunctional terminal organelle. This membrane-bound extension of the mycoplasma cell is defined by the presence of an electron-dense core that appears as paired, parallel bars oriented longitudinally and enlarging at the distal end to form a terminal button. Most non-cytadhering mutants of M. pneumoniae isolated to date exhibit defects in the architecture of the terminal organelle. Detailed characterization of those mutants has revealed the identities of many component proteins of the terminal organelle as well as the likely order in which some of those components are required. Additional questions regarding the composition of the electron-dense core, the means by which the terminal organelle is duplicated during cell division and the manner in which this process is regulated remain to be answered. Thus, it seems that there is much to be learned about cellular engineering and spatial regulation in these 'simple' cell wall-less bacteria.     

Cell death: questions for histochemists concerning the causes of the various cytological changes

Summary The question of cell death is accessible to study by histochemists and many questions remain to be resolved. From a physiological point of view, the most important are the causal relationships. (1) At what phase in cell death is the synthesis of RNA disrupted and at what phase is the rate of degradation of RNA increased? (2) Does the disruption of synthesis result from a direct genetic command, or does it result indirectly from gradual deterioration of energy resources or optimal ionic conditions? (3) What properties, presumably of the substrate organelles, marks them for specific absorption into autophagic vacuoles? (4) What proteases and other hydrolases operate currently undetected in the cytoplasm? How are they controlled and regulated? (5) Why does the physiologically dying cell shrink and appear more dense? To what extent is a cell in this state able to regulate any metabolic parameter? The advent of newer, more sensitive and quantitative techniques, and greater attention to the controls and causes as opposed to the phenomena, should help to resolve these questions.     

Similar binding sites and different partners: implications to shared proteins in cellular pathways

We studied a data set of structurally similar interfaces that bind to proteins with different binding-site structures and different functions. Our multipartner protein interface clusters enable us to address questions like: What makes a given site bind different proteins? How similar/different are the interactions? And, what drives the apparently less-specific association? We find that proteins with common binding-site motifs preferentially use conserved interactions at similar interface locations, despite the different partners. Helices are major vehicles for binding different partners, allowing alternate ways to achieve favorable association. The binding sites are characterized by imperfect packing, planar architectures, bridging water molecules, and, on average, smaller size. Interestingly, analysis of the connectivity of these proteins illustrates that they have more interactions with other proteins. These findings are important in predicting "date hubs," if we assume that "date hubs" are shared proteins with binding sites capable of transient binding to multipartners, linking higher-order networks.     

Artophagy: The art of autophagy—Macroautophagy

Many of us have sketched (by hand or on the computer) depictions of macroautophagy; however, how often have we considered which elements in the drawing are key to illustrating the process? These types of illustrations are easily modified and/or discarded. On the other hand, if you plan to depict the process of macroautophagy in a more permanent medium you need to be more thoughtful about the composition. What items must be included? How should they be situated? What should be the size of each component? Here, we consider one example of an artist’s approach to depicting macroautophagy in a mixed-medium sculpture.     

Normal and pathological oscillatory communication in the brain

The huge number of neurons in the human brain are connected to form functionally specialized assemblies. The brain's amazing processing capabilities rest on local communication within and long-range communication between these assemblies. Even simple sensory, motor and cognitive tasks depend on the precise coordination of many brain areas. Recent improvements in the methods of studying long-range communication have allowed us to address several important questions. What are the common mechanisms that govern local and long-range communication and how do they relate to the structure of the brain? How does oscillatory synchronization subserve neural communication? And what are the consequences of abnormal synchronization?     

Nitrogen- or phosphorus-limited growth in herbaceous, wet vegetation: relations with atmospheric inputs and management regimes

Herbaceous vegetation under temperate climatic conditions generally shows nitrogen- or phosphorus-limited plant growth, which creates conditions for a high botanical diversity. Is nitrogen (N) or phosphorus (P) the most important limiting factor, or are both generally in short supply? What are the consequences of Increased N and P inputs that result from anthropogenic disturbances? A new indicator of N or P limitation, that is, the vegetation N:P ratio, allows us to address these questions for a range of mires, dune slacks and moist grasslands.