Where Are We Now? Bergmann's Rule Sensu Lato in Insects

Abstract Bergmann's rule states that individuals of a species/clade at higher altitudes or latitudes will be larger than those at lower ones. A systemic review of the known literature on inter- and intraspecific variation in insect size along latitudinal or altitudinal clines was done to see how often such clines appeared and whether they reflected classwide, species-specific, or experimentally biased tendencies. Nearly even numbers of studies showed Bergmann clines and converse-Bergmann clines, where insects get smaller as latitude/altitude increases. In fact, the majority of studies suggested no clines at all. Small ranges may have obscured certain clines, while giant ranges may have introduced artifacts. Researchers examining interspecific patterns found clines less frequently than those examining intraspecific patterns because of variation among species within the clades, which renders interspecific studies unhelpful. Bergmann's rule does not apply to hexapods with nearly the same consistency as it does to endothermic vertebrates. The validity of Bergmann's rule for any group and range of insects is highly idiosyncratic and partially depends on the study design. I conclude that studies of Bergmann's rule should focus within species and look at widespread but contiguous populations to account for all sources of variation while minimizing error.     

High fertigation frequency and phosphorus level: Effects on summer-grown bell pepper growth and blossom-end rot incidence

The objective was to examine the effects of fertigation frequency and P application rate on bell pepper growth and blossom-end rot (BER) incidence, under hot conditions. The experiment comprised six treatments: two concentrations of phosphorus (3 and 30 mg L^–1) combined with three fertigation frequencies (two and eight events per day, and for 1.5 min every 25 min throughout the day). Increasing the fertigation frequency significantly increased the plants acquisition of nutrients, especially phosphorus and manganese. A significant linear regression was obtained between aboveground biomass, and leaf P concentration in the early vegetative stage. Based on the linear regression, 96% of the dry weight variations could be explained by differences in leaf P concentration, indicating that the main effect of fertigation frequency was related to improved P mobilization and uptake. Increasing the daily fertigation frequency from two to eight and to 30 applications reduced the number of BER fruits from 7 to 3 and to 2 per plant, respectively, and accordingly, increased the yield of export-quality fruits from 6.5 to 10 and to 10.5 per plant, respectively. The Mn concentration in plants exposed to low fertigation frequency were low, probably in the deficiency range, but they increased with increasing fertigation frequency. A negative correlation was found between the accumulated number of BER-affected fruits throughout the experiment and fruit-Mn concentrations. In light of recent findings that BER effects in the fruit tissue include the production of oxygen free-radicals and diminution of anti-oxidative compounds and enzymatic activities, and the known crucial role of manganese in enzyme activities and in detoxification of oxygen free-radicals, the relationships between BER incidence and fruit-Mn concentration may indicate that BER is related to Mn deficiency. Future researches are needed to validate this hypothesis.     

Drag of the Cytosol as a Transport Mechanism in Neurons

Axonal transport is typically divided into two components, which can be distinguished by their mean velocity. The fast component includes steady trafficking of different organelles and vesicles actively transported by motor proteins. The slow component comprises nonmembranous materials that undergo infrequent bidirectional motion. The underlying mechanism of slow axonal transport has been under debate during the past three decades. We propose a simple displacement mechanism that may be central for the distribution of molecules not carried by vesicles. It relies on the cytoplasmic drag induced by organelle movement and readily accounts for key experimental observations pertaining to slow-component transport. The induced cytoplasmic drag is predicted to depend mainly on the distribution of microtubules in the axon and the organelle transport rate.     

Mathematical Conditions for Induced Cell Differentiation and Trans-differentiation in Adult Cells

We present a theoretical framework for the analysis of the effect of a fully differentiated cell population on a neighboring stem cell population in Multi-Cellular Organisms (MCOs). Such an organism is constituted by a set of different cell populations, each set of which converges to a different cycle from all possible options, of the same Boolean network. Cells communicate via a subset of the nodes called signals. We show that generic dynamic properties of cycles and nodes in random Boolean networks can induce cell differentiation. Specifically we propose algorithms, conditions and methods to examine if a set of signaling nodes enabling these conversions can be found. Surprisingly we find that robust conversions can be obtained even with a very small number of signals. The proposed conversions can occur in multiple spatial organizations and can be used as a model for regeneration in MCOs, where an islet of cells of one type (representing stem cells) is surrounded by cells of another type (representing differentiated cells). The cells at the outer layer of the islet function like progenitor cells (i.e. dividing asymmetrically and differentiating). To the best of our knowledge, this is the first work showing a tissue-like regeneration in MCO simulations based on random Boolean networks. We show that the probability to obtain a conversion decreases with the log of the node number in the network, showing that the model is relevant for large networks as well. We have further checked that the conversions are not trivial, i.e. conversions do not occur due to irregular structures of the Boolean network, and the converting cycle undergoes a respectable change in its behavior. Finally we show that the model can also be applied to a realistic genetic regulatory network, showing that the basic mathematical insight from regular networks holds in more complex experiment-based networks.     

Antifungal activities of essential oils applied by dip-treatment on areca palm (Areca catechu) leaf sheath and persistence of their potency upon storage

The antifungal activities of cinnamon oil, clove oil, anise oil, and peppermint oil, and their main components (cinnamaldehyde, eugenol, trans-anethole, and menthol, respectively) against molds identified from areca palm leaf sheath (Mucor dimorphosporus, Penicillium sp., Aspergillus niger, and Rhizopus sp.) were investigated. An agar dilution method was employed to determine the minimum inhibitory concentration (MIC) of essential oils and their main components. Zone inhibition tests and the inhibitory effect of the leaf sheath dip-treated with essential oils against those molds were examined. Major components of essential oils on the leaf sheath during storage were quantified by gas chromatography analysis. The MIC values of essential oils on agar and on the leaf sheath were identical. With an MIC of 50 ??g ml⁻¹, cinnamon oil had the strongest inhibitory effect. At their MICs the oils were capable of providing protection against mold growth on the leaf sheath for at least 12 weeks during storage at 25 °C and 100% RH. Scanning electron microscope examination showed that essential oils prevented spore germination. Except for menthol in peppermint oil, the main components of the essential oils, which were fairly stable over the storage period, largely contributed to the antifungal activity.     

Differentiation agents increase the potential AraC therapy of AML by reactivating cell death pathways without enhancing ROS generation

Acute myeloid leukemia (AML) has a poor prognosis and requires new approaches for treatment. We have reported that a combination of vitamin D-based cell differentiation agents (doxercalciferol/carnosic acid [D2/CA]) added following the cytotoxic drug arabinocytosine (AraC) increases AML cell death (CD), a model for improved therapy of this disease. Because AraC-induced CD is known to involve reactive oxygen species (ROS) generation, here we investigated if the modulation of cellular REDOX status plays a role in the enhancement of cell death (ECD) by D2/CA. Using thiol antioxidants, such as N-acetyl cysteine (NAC), we found a significant inhibition of ECD, yet this occurred in the absence of any detectable change in cellular ROS levels. In contrast, NAC reduced the vitamin D receptor (VDR) abundance and its signaling of ECD. Importantly, VDR knockdown and NAC similarly inhibited ECD without producing an additive effect. Thus, the proposed post-AraC therapy may be compromised by agents that reduce VDR levels in AML blasts.     

Direct consumptive interactions between mammalian herbivores and plant-dwelling invertebrates: prevalence,significance, and prospectus

Mammalian herbivores induce changes in the chemical composition, phenology, distribution, and abundance of the plants they feed on. Consequently, invertebrate herbivores (predominantly insects) that depend on those plants, and the predators and parasitoids that are associated with them, may be affected. This plant-mediated indirect interaction between mammals and invertebrates has been extensively studied, but mammalian herbivores may also directly affect plant-dwelling invertebrates (PDI) by incidentally ingesting them while feeding. The ubiquity and small size of PDI render them highly susceptible to incidental ingestion, but as common as this interaction may intuitively seem, very little is known about its prevalence and ecological consequences. Nevertheless, cases of incidental ingestion of PDI and associated adaptations for avoiding it that have been sporadically documented in several invertebrate groups and life stages allow us to carefully extrapolate and conclude that it should be common in nature. Incidental ingestion may, therefore, bear significant consequences for PDI, but it may also affect the mammalian herbivores and the shared plants. Future research on incidental ingestion of PDI would have to overcome several technical difficulties to gain better insight into this understudied ecological interaction.     

A structural EM algorithm for phylogenetic inference.

A central task in the study of molecular evolution is the reconstruction of a phylogenetic tree from sequences of current-day taxa. The most established approach to tree reconstruction is maximum likelihood (ML) analysis. Unfortunately, searching for the maximum likelihood phylogenetic tree is computationally prohibitive for large data sets. In this paper, we describe a new algorithm that uses Structural Expectation Maximization (EM) for learning maximum likelihood phylogenetic trees. This algorithm is similar to the standard EM method for edge-length estimation, except that during iterations of the Structural EM algorithm the topology is improved as well as the edge length. Our algorithm performs iterations of two steps. In the E-step, we use the current tree topology and edge lengths to compute expected sufficient statistics, which summarize the data. In the M-Step, we search for a topology that maximizes the likelihood with respect to these expected sufficient statistics. We show that searching for better topologies inside the M-step can be done efficiently, as opposed to standard methods for topology search. We prove that each iteration of this procedure increases the likelihood of the topology, and thus the procedure must converge. This convergence point, however, can be a suboptimal one. To escape from such "local optima," we further enhance our basic EM procedure by incorporating moves in the flavor of simulated annealing. We evaluate these new algorithms on both synthetic and real sequence data and show that for protein sequences even our basic algorithm finds more plausible trees than existing methods for searching maximum likelihood phylogenies. Furthermore, our algorithms are dramatically faster than such methods, enabling, for the first time, phylogenetic analysis of large protein data sets in the maximum likelihood framework.     

Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates

Distance-based methods for phylogeny reconstruction are the fastest and easiest to use, and their popularity is accordingly high. They are also the only known methods that can cope with huge datasets of thousands of sequences. These methods rely on evolutionary distance estimation and are sensitive to errors in such estimations. In this study, a novel Bayesian method for estimation of evolutionary distances is developed. The proposed method enables the use of a sophisticated evolutionary model that better accounts for among-site rate variation (ASRV), thereby improving the accuracy of distance estimation. Rate variations are estimated within a Bayesian framework by extracting information from the entire dataset of sequences, unlike standard methods that can only use one pair of sequences at a time. We compare the accuracy of a cascade of distance estimation methods, starting from commonly used methods and moving towards the more sophisticated novel method. Simulation studies show significant improvements in the accuracy of distance estimation by the novel method over the commonly used ones. We demonstrate the effect of the improved accuracy on tree reconstruction using both real and simulated protein sequence alignments. An implementation of this method is available as part of the SEMPHY package.