Mother trees, altruistic fungi, and the perils of plant personification.

There are growing doubts about the true role of the common mycorrhizal networks (CMN or wood wide web) connecting the roots of trees in forests. We question the claims of a substantial carbon transfer from 'mother trees' to their offspring and nearby seedlings through the CMN. Recent reviews show that evidence for the 'mother tree concept' is inconclusive or absent. The origin of this concept seems to stem from a desire to humanize plant life but can lead to misunderstandings and false interpretations and may eventually harm rather than help the commendable cause of preserving forests. Two recent books serve as examples: The Hidden Life of Trees and Finding the Mother Tree.

A rich and bountiful harvest: Key discoveries in plant cell biology.

The field of plant cell biology has a rich history of discovery, going back to Robert Hooke's discovery of cells themselves. The development of microscopes and preparation techniques has allowed for the visualization of subcellular structures, and the use of protein biochemistry, genetics, and molecular biology has enabled the identification of proteins and mechanisms that regulate key cellular processes. In this review, seven senior plant cell biologists reflect on the development of this research field in the past decades, including the foundational contributions that their teams have made to our rich, current insights into cell biology. Topics covered include signaling and cell morphogenesis, membrane trafficking, cytokinesis, cytoskeletal regulation, and cell wall biology. In addition, these scientists illustrate the pathways to discovery in this exciting research field.

Morphological description of Laevicaulisstuhlmanni (Simroth, 1895) (Pulmonata, Veronicellidae) from Egypt.

Background: Terrestrial slugs and snails are increasingly becoming serious pests of agricultural, horticultural and ornamental plants in Egypt, resulting in major economic losses. New information: This paper provides a detailed morphological and anatomical description of the veronicellid slug Laevicaulisstuhlmanni (Simroth, 1895) that has been recently recorded from Egypt. This population from Egypt is compared with Laevicaulis populations recently reported and described from Libya as L.striatus (Simroth, 1896) and with available data in literature. Some notes and a distribution map of the veronicellids introduced in north-eastern Africa are provided.

Plants have neither synapses nor a nervous system.

The alleged existence of so-called synapses or equivalent structures in plants provided the basis for the concept of Plant Neurobiology (Baluska et al., 2005; Brenner et al., 2006). More recently, supporters of this controversial theory have even speculated that the phloem acts as a kind of nerve system serving long distance electrical signaling (Mediano et al., 2021; Baluska and Mancuso, 2021). In this review we have critically examined the literature cited by these authors and arrive at a completely different conclusion. Plants do not have any structures resembling animal synapses (neither chemical nor electrical). While they certainly do have complex cell contacts and signaling mechanisms, none of these structures provides a basis for neuronal-like synaptic transmission. Likewise, the phloem is undoubtedly a conduit for the propagation of electrical signaling, but the characteristics of this process are in no way comparable to the events underlying information processing in neuronal networks. This has obvious implications in regard to far-going speculations into the realms of cognition, sentience and consciousness.

Integrated information theory does not make plant consciousness more convincing.

It has been proposed by some plant scientists that plants are cognitive and conscious organisms, although this is a minority view. Here we present a brief summary of some of the arguments against this view, followed by a critique of an article in this same issue of Biochemical and Biophysical Research Communications by Calvo, Baluska, and Trewavas (2020) that cites Integrated Information Theory (IIT) as providing additional support for plant consciousness. The authors base their argument on the assumptions that all cells are conscious and that consciousness is confined to life. However, IIT allows for consciousness in various nonliving systems, and thus does not restrict consciousness to living organisms. Therefore, IIT cannot be used to prove plant consciousness, for which there is neither empirical evidence nor support from other, neuron-based, theories of consciousness.

The functional false discovery rate with applications to genomics.

The false discovery rate (FDR) measures the proportion of false discoveries among a set of hypothesis tests called significant. This quantity is typically estimated based on p-values or test statistics. In some scenarios, there is additional information available that may be used to more accurately estimate the FDR. We develop a new framework for formulating and estimating FDRs and q-values when an additional piece of information, which we call an "informative variable", is available. For a given test, the informative variable provides information about the prior probability a null hypothesis is true or the power of that particular test. The FDR is then treated as a function of this informative variable. We consider two applications in genomics. Our first application is a genetics of gene expression (eQTL) experiment in yeast where every genetic marker and gene expression trait pair are tested for associations. The informative variable in this case is the distance between each genetic marker and gene. Our second application is to detect differentially expressed genes in an RNA-seq study carried out in mice. The informative variable in this study is the per-gene read depth. The framework we develop is quite general, and it should be useful in a broad range of scientific applications.

Anesthetics and plants: no pain, no brain, and therefore no consciousness.

Plants have a rich variety of interactions with their environment, including adaptive responses mediated by electrical signaling. This has prompted claims that information processing in plants is similar to that in animals and, hence, that plants are conscious, intelligent organisms. In several recent reports, the facts that general anesthetics cause plants to lose their sensory responses and behaviors have been taken as support for such beliefs. These lipophilic substances, however, alter multiple molecular, cellular, and systemic functions in almost every organism. In humans and other animals with complex brains, they eliminate the experience of pain and disrupt consciousness. The question therefore arises: do plants feel pain and have consciousness? In this review, we discuss what can be learned from the effects of anesthetics in plants. For this, we describe the mechanisms and structural prerequisites for pain sensations in animals and show that plants lack the neural anatomy and all behaviors that would indicate pain. By explaining the ubiquitous and diverse effects of anesthetics, we discuss whether these substances provide any empirical or logical evidence for "plant consciousness" and whether it makes sense to study the effects of anesthetics on plants for this purpose. In both cases, the answer is a resounding no.

Modeling molecular development of breast cancer in canine mammary tumors.

Understanding the changes in diverse molecular pathways underlying the development of breast tumors is critical for improving diagnosis, treatment, and drug development. Here, we used RNA-profiling of canine mammary tumors (CMTs) coupled with a robust analysis framework to model molecular changes in human breast cancer. Our study leveraged a key advantage of the canine model, the frequent presence of multiple naturally occurring tumors at diagnosis, thus providing samples spanning normal tissue and benign and malignant tumors from each patient. We showed human breast cancer signals, at both expression and mutation level, are evident in CMTs. Profiling multiple tumors per patient enabled by the CMT model allowed us to resolve statistically robust transcription patterns and biological pathways specific to malignant tumors versus those arising in benign tumors or shared with normal tissues. We showed that multiple histological samples per patient is necessary to effectively capture these progression-related signatures, and that carcinoma-specific signatures are predictive of survival for human breast cancer patients. To catalyze and support similar analyses and use of the CMT model by other biomedical researchers, we provide FREYA, a robust data processing pipeline and statistical analyses framework.

Debunking a myth: plant consciousness.

Claims that plants have conscious experiences have increased in recent years and have received wide coverage, from the popular media to scientific journals. Such claims are misleading and have the potential to misdirect funding and governmental policy decisions. After defining basic, primary consciousness, we provide new arguments against 12 core claims made by the proponents of plant consciousness. Three important new conclusions of our study are (1) plants have not been shown to perform the proactive, anticipatory behaviors associated with consciousness, but only to sense and follow stimulus trails reactively; (2) electrophysiological signaling in plants serves immediate physiological functions rather than integrative-information processing as in nervous systems of animals, giving no indication of plant consciousness; (3) the controversial claim of classical Pavlovian learning in plants, even if correct, is irrelevant because this type of learning does not require consciousness. Finally, we present our own hypothesis, based on two logical assumptions, concerning which organisms possess consciousness. Our first assumption is that affective (emotional) consciousness is marked by an advanced capacity for operant learning about rewards and punishments. Our second assumption is that image-based conscious experience is marked by demonstrably mapped representations of the external environment within the body. Certain animals fit both of these criteria, but plants fit neither. We conclude that claims for plant consciousness are highly speculative and lack sound scientific support.

EMAC, Retromer, and VSRs: do they connect?

Eukaryotic organisms share many common features in terms of endomembrane trafficking. This fact has helped plant scientists to propose testable hypotheses on how plant intracellular membrane trafficking is achieved and regulated based on knowledge from yeast and mammals. However, when a new compartment has been identified in a plant cell that has a vesicle tethering complex located at a position which is completely different to its counterpart in yeast and mammalian cells, caution is demanded when interpreting possible interactions with other trafficking elements. This is exemplified by the recently discovered EMAC (ER and microtubule-associated compartment). It has been postulated that this compartment is the recipient of vacuolar sorting receptors (VSRs) transported retrogradely via "retromer vesicles" from a post-Golgi location. Unfortunately, this suggestion was based entirely on our knowledge of retromer from yeast and mammalian cells, and did not take into account the available literature on the composition, localization, and function of the plant retromer. It also lacked reference to recent contradictory findings on VSR trafficking. In this short article, we have tried to rectify this situation, pointing out that plant retromer may not function as a pentameric complex of two subunits: the retromer core and the sorting nexins.

Plant Golgi ultrastructure.

The plant Golgi apparatus (sensu lato: Golgi stack + Trans Golgi Network, TGN) is a highly polar and mobile key organelle lying at the junction of the secretory and endocytic pathways. Unlike its counterpart in animal cells it does not disassemble during mitosis. It modifies glycoproteins sent to it from the endoplasmic reticulum (ER), it recycles ER resident proteins, it sorts proteins destined for the vacuole from secretory proteins, it receives proteins internalised from the plasma membrane and either recycles them to the plasma membrane or retargets them to the vacuole for degradation. In functional terms the Golgi apparatus can be likened to a car factory, with incoming (COPII traffic) and returning (COPI traffic) railway lines at the entry gate, and a distribution centre (the TGN) at the exit gate of the assembly hall. In the assembly hall we have a conveyor belt system where the incoming car parts are initially assembled (in the cis-area) then gradually modified into different models (processing of secretory cargo) as the cars pass along the production line (cisternal maturation). After being released the trans-area, the cars (secretory cargos) are moved out of the assembly hall and passed on to the distribution centre (TGN), where the various models are placed onto different trains (cargo sorting into carrier vesicles) for transport to the car dealers. Cars with motor problems are returned to the factory for repairs (endocytosis to the TGN). This simple analogy also incorporates features of quality control at the COPII entry gate with defective parts being returned to the manufacturing center (the ER) via the COPI trains (vesicles). In recent years, numerous studies have contributed to our knowledge on Golgi function and structure in both animals, yeast and plants. This review, rather than giving a balanced account of the structure as well as of the function of the Golgi apparatus has purposely a marked slant towards plant Golgi ultrastructure integrating findings from the mammalian/animal field.

A Model for ERD2 Function in Higher Plants.

ER lumenal proteins have a K(H)DEL motif at their C-terminus. This is recognized by the ERD2 receptor (KDEL receptor in animals), which localizes to the Golgi apparatus and serves to capture escaped ER lumenal proteins. ERD2-ligand complexes are then transported back to the ER via COPI coated vesicles. The neutral pH of the ER causes the ligands to dissociate with the receptor being returned to the Golgi. According to this generally accepted scenario, ERD2 cycles between the ER and the Golgi, although it has been found to have a predominant Golgi localization. In this short article, we present a model for the functioning of ERD2 receptors in higher plants that explains why it is difficult to detect fluorescently tagged ERD2 proteins in the ER. The model assumes that the residence time for ERD2 in the ER is very brief and restricted to a specific domain of the ER. This is the small disc of ER immediately subjacent to the first cis-cisterna of the Golgi stack, representing specialized ER export and import sites and therefore constituting part of what is known as the "secretory unit", a mobile aggregate of ER domain plus Golgi stack. ERD2 molecules in the ER domain of the secretory unit may be small in number, transient and optically difficult to differentiate from the larger population of ERD2 molecules in the overlying Golgi stack in the confocal microscope.

Plants Neither Possess nor Require Consciousness.

In claiming that plants have consciousness, 'plant neurobiologists' have consistently glossed over the remarkable degree of structural and functional complexity that the brain had to evolve for consciousness to emerge. Here, we outline a new hypothesis proposed by Feinberg and Mallat for the evolution of consciousness in animals. Based on a survey of the brain anatomy, functional complexity, and behaviors of a broad spectrum of animals, criteria were established for the emergence of consciousness. The only animals that satisfied these criteria were the vertebrates (including fish), arthropods (e.g., insects, crabs), and cephalopods (e.g., octopuses, squids). In light of Feinberg and Mallat's analysis, we consider the likelihood that plants, with their relative organizational simplicity and lack of neurons and brains, have consciousness to be effectively nil.