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Two recent studies have addressed the long-term consequences of whole genome duplications (WGD). Specifically, they analyzed transcriptomes of the plant Arabidopsis thaliana and of four salmonids to assess the impact of WGD on gene expression. These studies point to commonalities in gene expression adjustments after polyploidization that we outline and discuss below., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

In 1997, the first in vivo bisphenol A (BPA) study by endocrinologists reported that feeding BPA to pregnant mice induced adverse reproductive effects in male offspring at the low dose of 2 µg/kg/day. Since then, thousands of studies have reported adverse effects in animals administered low doses of BPA. Despite more than 100 epidemiological studies suggesting associations between BPA and disease/dysfunction also reported in animal studies, regulatory agencies continue to assert that BPA exposures are safe. To address this disagreement, the CLARITY-BPA study was designed to evaluate traditional endpoints of toxicity and modern hypothesis-driven, disease-relevant outcomes in the same set of animals. A wide range of adverse effects was reported in both the toxicity and the mechanistic endpoints at the lowest dose tested (2.5 µg/kg/day), leading independent experts to call for the lowest observed adverse effect level (LOAEL) to be dropped 20 000-fold from the current outdated LOAEL of 50 000 µg/kg/day. Despite criticism by members of the Endocrine Society that the Food and Drug Administration (FDA)'s assumptions violate basic principles of endocrinology, the FDA rejected all low-dose data as not biologically plausible. Their decisions rely on 4 incorrect assumptions: dose responses must be monotonic, there exists a threshold below which there are no effects, both sexes must respond similarly, and only toxicological guideline studies are valid. This review details more than 20 years of BPA studies and addresses the divide that exists between regulatory approaches and endocrine science. Ultimately, CLARITY-BPA has shed light on why traditional methods of evaluating toxicity are insufficient to evaluate endocrine disrupting chemicals., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Endocrine Society. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

How organisms control organ size is not fully understood. We found that Syd/JIP3 is required for proper wing size in Drosophila. JIP3 mutations are associated with organ size defects in mammals. The underlying mechanisms are not well understood. We discovered that Syd/JIP3 inhibition results in a downregulation of the inhibitor of apoptosis protein 1 (Diap1) in the Drosophila wing. Correspondingly, Syd/JIP3 deficient tissues exhibit ectopic cell death and yield smaller wings. Syd/JIP3 inhibition generated similar effects in mammalian cells, indicating a conserved mechanism. We found that Yorkie/YAP stimulates Syd/JIP3 in Drosophila and mammalian cells. Notably, Syd/JIP3 is required for the full effect of Yorkie-mediated tissue growth. Thus Syd/JIP3 regulation of Diap1 functions downstream of Yorkie/YAP to control growth. This study provides mechanistic insights into the recent and perplexing link between JIP3 mutations and organ size defects in mammals, including in humans where de novo JIP3 variants are associated with microcephaly., Competing Interests: Declaration of competing interest None., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Anticoagulant rodenticides (ARs) are used in rat eradication efforts on island wildlife refuges. AR bait pellets can get into coral reef areas during broadcasting and lead to exposure of non-target organisms, such as marine fishes. The objective of this study was to determine the sensitivity of representative saltwater fishes, Red-toothed triggerfish (Odonus niger) and Black triggerfish (Melichthys niger), and common freshwater fishes, fathead minnow (Pimephales promelas), and largemouth bass (Micropterus salmoides) to first generation ARs, diphacinone (DPN) and chlorophacinone (CPN), as well as a second-generation AR, brodifacoum (BROD). Acute toxicity of ARs was evaluated by single dose, intraperitoneal injections. The median lethal dose (LD50) ranges were 137-175 μg DPN/g, 155-182 μg CPN/g, and 36-48 μg BROD/g for Red-toothed triggerfish and 90-122 μg DPN/g, 125-164 μg CPN/g, and 50-75 μg BROD/g for black triggerfish. Laboratory surrogate test fish species fathead minnow and largemouth bass were of similar sensitivity toward AR-induced toxicity compared to triggerfish based on LD50 values. Sublethal effects on elevated clotting time occurred in dose-dependent fashion in all fish tested. Fish appear to have low sensitivity to AR chemicals as compared to other taxa, in particular mammals and birds, based on across-taxa comparisons of species sensitivity distributions of whole body, single dose acute lethality (LD50 values). The sensitivity of fish to waterborne exposures of ARs has yet to be fully evaluated and indeed may prove more hazardous to fish., Competing Interests: Declaration of Competing Interest The authors have no conflicts of interest., (Published by Elsevier B.V.)

The number and type of ion channels present in the membrane determines the electrophysiological function of every neuron. In many species, stereotyped output of neurons often persists for years [1], and ion channel dysregulation can change these properties to cause severe neurological disorders [2-4]. Thus, a fundamental question is how do neurons coordinate channel expression to uphold their firing patterns over long timescales [1, 5]? One major hypothesis purports that neurons homeostatically regulate their ongoing activity through mechanisms that link membrane voltage to expression relationships among ion channels [6-10]. However, experimentally establishing this feedback loop for the control of expression relationships has been a challenge: manipulations that aim to test for voltage feedback invariably disrupt trophic signaling from synaptic transmission and neuromodulation in addition to activity [9, 11, 12]. Further, neuronal activity often relies critically on these chemical mediators, obscuring the contribution of voltage activity of the membrane per se in forming the channel relationships that determine neuronal output [6, 13]. To resolve this, we isolated an identifiable neuron in crustaceans and then either kept this neuron silent or used a long-term voltage clamp protocol to artificially maintain activity. We found that physiological voltage activity-independent of all known forms of synaptic and neuromodulatory feedback-maintains most channel mRNA relationships, while metabotropic influences may play a relatively smaller role. Thus, ion channel relationships likely needed to maintain neuronal identity are actively and continually regulated at least in part at the level of channel mRNAs through feedback by membrane voltage., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Misiones, Argentina, contains the largest remaining tract of Upper Paraná Atlantic Forest ecoregion; however, ~50% of native forest is unprotected and located in a mosaic of plantations, agriculture, and pastures. Existing protected areas are becoming increasingly isolated due to ongoing habitat modification. These factors, combined with lower than expected regional carnivore densities, emphasize the need to understand the effect of fragmentation on animal movement and connectivity between protected areas. Using detection dogs and genetic analyses of scat, we collected data on jaguars (Panthera onca), pumas (Puma concolor), ocelots (Leopardus pardalis), oncillas (Leopardus tigrinus), and bush dogs (Speothos venaticus) across habitats that varied in vegetation, disturbance, human proximity, and protective status. With MaxEnt we evaluated habitat use, habitat suitability, and potential species richness for the five carnivores across northern-central Misiones, Argentina. Through a multifaceted cost analysis that included unique requirements of each carnivore and varying degrees of overlap among them, we determined the optimal location for primary/secondary corridors that would link the northern-central zones of the Green Corridor in Misiones and identified areas within these corridors needing priority management. A secondary analysis, comparing these multispecies corridors with the jaguar's unique requirements, demonstrated that this multispecies approach balanced the preferences of all five species and effectively captured areas required by this highly restricted and endangered carnivore. We emphasize the potential importance of expanding beyond a single umbrella or focal species when developing biological corridors that aim to capture the varied ecological requirements of coexisting species and ecological processes across the landscape. Detection dogs and genetic analyses of scat allow data on multiple species to be collected efficiently across multiple habitat types independent of the degree of legal protection. These data used with multifocal GIS analyses balance the varying degree of overlap and unique properties among them allowing for comprehensive conservation strategies to be developed relatively rapidly. Our comprehensive approach serves as a model to other regions faced with habitat loss and lack of data. The five carnivores focused on in our study have wide ranges, so the results from this study can be expanded and combined with surrounding countries, with analyses at the species or community level.

This article presents protocols for fluorescence in situ hybridization (FISH) in the cultivated soybean, Glycine max. The protocols represent soybean-optimized versions developed for maize. We describe the use of two different probes types: genomic-repeat-based fluorescently-tagged oligonucleotides and bacterial artificial chromosomes (BACs). The two probe types can be used either individually or together, depending on the experimental questions. The article also includes starting points for executing FISH in additional legume species. © 2017 by John Wiley & Sons, Inc., (Copyright © 2017 John Wiley & Sons, Inc.)

This unit presents a highly reliable protocol to produce and screen metaphase chromosome spreads from root tip cell suspensions of soybean (Glycine max), or other legumes. The procedures represent soybean-optimized versions of protocols developed for maize. The use of pressurized nitrous oxide to reliably generate metaphase-arrested chromosomes is crucial to overcoming one of the challenges of working with tiny and numerous soybean chromosomes. © 2017 by John Wiley & Sons, Inc., (Copyright © 2017 John Wiley & Sons, Inc.)

Charcot-Marie-Tooth (CMT) is the most common inherited peripheral neuropathy, affecting approximately 2.8 million people. The CMT leads to distal neuropathy that is characterized by reduced motor nerve conduction velocity, ataxia, muscle atrophy and sensory loss. We generated a mouse model of CMT type 2E (CMT2E) expressing human neurofilament light E396K (hNF-L E396K ), which develops decreased motor nerve conduction velocity, ataxia and muscle atrophy by 4 months of age. Symptomatic hNF-L E396K mice developed phenotypes that were consistent with proprioceptive sensory defects as well as reduced sensitivity to mechanical stimulation, while thermal sensitivity and auditory brainstem responses were unaltered. Progression from presymptomatic to symptomatic included a 50% loss of large diameter sensory axons within the fifth lumbar dorsal root of hNF-L E396K mice. Owing to proprioceptive deficits and loss of large diameter sensory axons, we analyzed muscle spindle morphology in presymptomatic and symptomatic hNF-L E396K and hNF-L control mice. Muscle spindle cross-sectional area and volume were reduced in all hNF-L E396K mice analyzed, suggesting that alterations in muscle spindle morphology occurred prior to the onset of typical CMT pathology. These data suggested that CMT2E pathology initiated in the muscle spindles altering the proprioceptive sensory system. Early sensory pathology in CMT2E could provide a unifying hypothesis for the convergence of pathology observed in CMT., (© 2016 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.)

Fluorescence In Situ Hybridization (FISH) is the annealing of fluorescent DNA probes to their complementary sequences on prepared chromosomes and subsequent visualization with a fluorescent microscope. In maize, FISH is useful for distinguishing each of the ten chromosomes in different accessions (karyotyping), roughly mapping single genes, transposable elements, transgene insertions, and identifying various chromosomal alterations. FISH can also be used to distinguish chromosomes between different Zea species in interspecific hybrids by use of retroelement painting. © 2016 by John Wiley & Sons, Inc., (Copyright © 2016 John Wiley & Sons, Inc.)

High-quality preparations of chromosomes are useful for many purposes. To prepare metaphase chromosome spreads in maize, root tips are harvested and treated with nitrous oxide to stop cell division at metaphase before being fixed in acetic acid. This process allows a high number of condensed chromosome spreads to be obtained at the end of the procedure. To prepare chromosome spreads from various stages of meiosis, anthers are first fixed before being examined for developmental stage. Cells are digested with a mixture of enzymes before the chromosomes are dropped onto glass sides and fixed under UV light. © 2016 by John Wiley & Sons, Inc., (Copyright © 2016 John Wiley & Sons, Inc.)

Few gating-modifier toxins have been reported to target low-voltage-activated (LVA) calcium channels, and the structural basis of toxin sensitivity remains incompletely understood. Studies of voltage-gated potassium (Kv) channels have identified the S3b-S4 "paddle motif," which moves at the protein-lipid interface to drive channel opening, as the target for these amphipathic neurotoxins. Voltage-gated calcium (Cav) channels contain four homologous voltage sensor domains, suggesting multiple toxin binding sites. We show here that the S3-S4 segments within Cav3.1 can be transplanted into Kv2.1 to examine their individual contributions to voltage sensing and pharmacology. With these results, we now have a more complete picture of the conserved nature of the paddle motif in all three major voltage-gated ion channel types (Kv, Nav, and Cav). When screened with tarantula toxins, the four paddle sequences display distinct toxin binding properties, demonstrating that gating-modifier toxins can bind to Cav channels in a domain specific fashion. Domain III was the most commonly and strongly targeted, and mutagenesis revealed an acidic residue that is important for toxin binding. We also measured the lipid partitioning strength of all toxins tested and observed a positive correlation with their inhibition of Cav3.1, suggesting a key role for membrane partitioning.

Background: Stoichiometric imbalances in macromolecular complexes can lead to altered function. Such imbalances stem from under- or over-expression of a subunit of a complex consequent to a deletion, duplication or regulatory mutation of an allele encoding the relevant protein. In some cases, the phenotypic perturbations induced by such alterations can be subtle or be lacking because nonlinearities in the process of protein complex assembly can provide some degree of buffering., Results: We explore with biochemical models of increasing plausibility how buffering can be elicited. Specifically, we analyze the formation of a dimer AB and show that there are particular sets of parameters so that decreasing/increasing the input amount of either A or B translates into a non proportional (buffered) change of AB. The buffer effect also appears in higher-order structures provided that there are intermediate subcomplexes in the assembly process., Conclusions: We highlight the importance of protein degradation and/or conformational inactivation for buffering to appear. The models sketched here have experimental support but can be further tested with existing biological resources.

We present data on amphibian density, species richness, and diversity from a 7140-ha area consisting of 200 ponds in the Midwestern U.S. that represents most of the possible lentic aquatic breeding habitats common in this region. Our study includes all possible breeding sites with natural and anthropogenic disturbance processes that can be missing from studies where sampling intensity is low, sample area is small, or partial disturbance gradients are sampled. We tested whether pond area was a significant predictor of density, species richness, and diversity of amphibians and if values peaked at intermediate pond areas. We found that in all cases a quadratic model fit our data significantly better than a linear model. Because small ponds have a high probability of pond drying and large ponds have a high probability of fish colonization and accumulation of invertebrate predators, drying and predation may be two mechanisms driving the peak of density and diversity towards intermediate values of pond size. We also found that not all intermediate sized ponds produced many larvae; in fact, some had low amphibian density, richness, and diversity. Further analyses of the subset of ponds represented in the peak of the area distribution showed that fish, hydroperiod, invertebrate density, and canopy are additional factors that drive density, richness and diversity of ponds up or down, when extremely small or large ponds are eliminated. Our results indicate that fishless ponds at intermediate sizes are more diverse, produce more larvae, and have greater potential to recruit juveniles into adult populations of most species sampled. Further, hylid and chorus frogs are found predictably more often in ephemeral ponds whereas bullfrogs, green frogs, and cricket frogs are found most often in permanent ponds with fish. Our data increase understanding of what factors structure and maintain amphibian diversity across large landscapes.

Environmental gradients are instrumental in shaping the distribution and local abundance of species because at the most fundamental level, an organism's performance is constrained by the environment it inhabits. In topographically complex landscapes, slope, aspect, and vegetative cover interact to affect solar exposure, creating temperature-moisture gradients and unique microclimates. The significance of the interaction of abiotic gradients and biotic factors such as competition, movement, or physiology has long been recognized, but the scale at which these factors vary on the landscape has generally precluded their inclusion in spatial abundance models. We used fine-scale spatial data relating to surface-soil moisture, temperature, and canopy cover to describe the spatial distribution of abundance of a terrestrial salamander, Plethodon albagula, across the landscape. Abundance was greatest in dense-canopy ravine habitats with high moisture and low solar exposure, resulting in a patchy distribution of abundance. We hypothesize that these patterns reflect the physiological constraints of Plethodontid salamanders. Furthermore, demographic cohorts were not uniformly distributed among occupied plots on the landscape. The probability of gravid female occurrence was nearly uniform among occupied plots, but juveniles were much more likely to occur on plots with lower surface temperatures. The disconnect between reproductive effort and recruitment suggests that survival differs across the landscape and that local population dynamics vary spatially. Our study demonstrates a connection between abundance, fine-scale environmental gradients, and population dynamics, providing a foundation for future research concerning movement, population connectivity, and physiology.

Mitochondrial DNA (mtDNA) insertions into nuclear chromosomes have been documented in a number of eukaryotes. We used fluorescence in situ hybridization (FISH) to examine the variation of mtDNA insertions in maize. Twenty overlapping cosmids, representing the 570-kb maize mitochondrial genome, were individually labeled and hybridized to root tip metaphase chromosomes from the B73 inbred line. A minimum of 15 mtDNA insertion sites on nine chromosomes were detectable using this method. One site near the centromere on chromosome arm 9L was identified by a majority of the cosmids. To examine variation in nuclear mitochondrial DNA sequences (NUMTs), a mixture of labeled cosmids was applied to chromosome spreads of ten diverse inbred lines: A188, A632, B37, B73, BMS, KYS, Mo17, Oh43, W22, and W23. The number of detectable NUMTs varied dramatically among the lines. None of the tested inbred lines other than B73 showed the strong hybridization signal on 9L, suggesting that there is a recent mtDNA insertion at this site in B73. Different sources of B73 and W23 were examined for NUMT variation within inbred lines. Differences were detectable, suggesting either that mtDNA is being incorporated or lost from the maize nuclear genome continuously. The results indicate that mtDNA insertions represent a major source of nuclear chromosomal variation.

Memories can have different strengths, largely dependent on the intensity of reinforcers encountered. The relationship between reinforcement and memory strength is evident in asymptotic memory curves, with the level of the asymptote related to the intensity of the reinforcer. Although this is likely a fundamental property of memory formation, relatively little is known of how memory strength is determined. Memory performance at different levels in Drosophila can be measured in an operant heat-box conditioning paradigm. In this spatial learning paradigm, flies learn and remember to avoid one-half of a dark chamber associated with a temperature outside of the preferred range. The reinforcement temperature has a strong effect on the level of learning in wild-type flies, with higher temperatures inducing stronger memories. Additionally, two mutations alter memory-acquisition curves, either changing acquisition rate or asymptotic memory level. The rutabaga mutation, affecting a type-1 adenylyl cyclase, decreases the acquisition rate. In contrast, the white mutation, modifying an ABC transporter, limits asymptotic memory. The white mutation does not negatively affect classical olfactory conditioning but actually improves performance at low reinforcement levels. Thus, memory acquisition/memory strength and classical olfactory/operant spatial memories can be genetically dissociated. A conceptual model of operant conditioning and the levels at which rutabaga and white influence conditioning is proposed.

In an attempt to compensate for their sessile nature, plants have developed growth responses to deal with the copious and rapid changes in their environment. These responses are known as tropisms and they are marked by a directional growth response that is the result of differential cellular growth and development in response to an external stimulation such as light, gravity or touch. While the mechanics of tropic growth and subsequent development have been the topic of debate for more than a hundred years, only recently have researchers been able to make strides in understanding how plants perceive and respond to tropic stimulations, thanks in large part to mutant analysis and recent advances in genomics. This paper focuses on the recent advances in four of the best-understood tropic responses and how each affects plant growth and development: phototropism, gravitropism, thigmotropism and hydrotropism. While progress has been made in deciphering the events between tropic stimulation signal perception and each characteristic growth response, there are many areas that remain unclear, some of which will be discussed herein. As has become evident, each tropic response pathway exhibits distinguishing characteristics. However, these pathways of tropic perception and response also have overlapping components - a fact that is certainly related to the necessity for pathway integration given the ever-changing environment that surrounds every plant.

Centromeres are key to the correct segregation and inheritance of genetic information. Eukaryotic centromeres, which are located in large blocks of highly repetitive DNA, have been notoriously difficult to sequence. Several groups have recently succeeded in analyzing centromeric sequences in human, Drosophila and Arabidopsis, providing new insights into the importance of DNA sequence for centromere function.

A cDNA encoding a nuclear-encoded chloroplast nucleic acid-binding protein (NBP) has been isolated from maize. Identified as an in vitro DNA-binding activity, NBP belongs to a family of nuclear-encoded chloroplast proteins which share a common domain structure and are thought to be involved in posttranscriptional regulation of chloroplast gene expression. NBP contains an N-terminal chloroplast transit peptide, a highly acidic domain and a pair of ribonucleoprotein consensus sequence domains. NBP is expressed in a light-dependent, organ-specific manner which is consistent with its involvement in chloroplast biogenesis. The relationship of NBP to the other members of this protein family and their possible regulatory functions are discussed.