Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions

Bacteria often face complex environments. We asked how gene expression in complex conditions relates to expression in simpler conditions. To address this, we obtained accurate promoter activity dynamical measurements on 94 genes in E. coli in environments made up of all possible combinations of four nutrients and stresses. We find that the dynamics across conditions is well described by two principal component curves specific to each promoter. As a result, the promoter activity dynamics in a combination of conditions is a weighted average of the dynamics in each condition alone. The weights tend to sum up to approximately one. This weighted-average property, called linear superposition, allows predicting the promoter activity dynamics in a combination of conditions based on measurements of pairs of conditions. If these findings apply more generally, they can vastly reduce the number of experiments needed to understand how E. coli responds to the combinatorially huge space of possible environments.     

Evaluating the Synergistic Neutralizing Effect of Anti-Botulinum Oligoclonal Antibody Preparations

Botulinum neurotoxins (BoNT) are considered some of the most lethal known substances. There are seven botulinum serotypes, of which types A, B and E cause most human botulism cases. Anti-botulinum polyclonal antibodies (PAbs) are currently used for both detection and treatment of the disease. However, significant improvements in immunoassay specificity and treatment safety may be made using monoclonal antibodies (MAbs). In this study, we present an approach for the simultaneous generation of highly specific and neutralizing MAbs against botulinum serotypes A, B, and E in a single process. The approach relies on immunization of mice with a trivalent mixture of recombinant C-terminal fragment (Hc) of each of the three neurotoxins, followed by a parallel differential robotic hybridoma screening. This strategy enabled the cloning of seven to nine MAbs against each serotype. The majority of the MAbs possessed higher anti-botulinum ELISA titers than anti-botulinum PAbs and had up to five orders of magnitude greater specificity. When tested for their potency in mice, neutralizing MAbs were obtained for all three serotypes and protected against toxin doses of 10 MsLD₅₀–500 MsLD₅₀. A strong synergistic effect of up to 400-fold enhancement in the neutralizing activity was observed when serotype-specific MAbs were combined. Furthermore, the highly protective oligoclonal combinations were as potent as a horse-derived PAb pharmaceutical preparation. Interestingly, MAbs that failed to demonstrate individual neutralizing activity were observed to make a significant contribution to the synergistic effect in the oligoclonal preparation. Together, the trivalent immunization strategy and differential screening approach enabled us to generate highly specific MAbs against each of the A, B, and E BoNTs. These new MAbs may possess diagnostic and therapeutic potential.     

Interactive effects of salinity and a predator on mosquito oviposition and larval performance

Oviposition habitat selection (OHS) is increasingly being recognized as playing a large role in explaining mosquito distributions and community assemblages. Most studies have assessed the role of single factors affecting OHS, while in nature, oviposition patterns are most likely explained by multiple, interacting biotic and abiotic factors. Determining how various factors interact to affect OHS is important for understanding metapopulation and metacommunity dynamics. We investigated the individual and interactive effects of three water salinities (0, 15 and 30 p.p.t. NaCl added) and the aquatic predator Anisops debilis Perplexa (Hemiptera: Notonectidae) on OHS and larval performance of the mosquitoes Ochlerotatus caspius Pallas and Culiseta longiareolata Macquart (Diptera: Culicidae) in outdoor-artificial-pool and laboratory experiments. C. longiareolata inhabited only freshwater pools, strongly avoided pools containing A. debilis, and larvae experienced lower survival in the presence of A. debilis. Salinity concentration interacted strongly with the predator in affecting OHS and larval survival of O. caspius; oviposition increased with increasing salinity in the absence of the predator and decreased with increasing salinity in the presence of the predator. O. caspius larval survival in predator-free pools was lowest in freshwater and highest at intermediate salinity. In predator pools, survival was highest at high salinity, where predation rate was shown to be lowest in the laboratory. Our results highlight that assessing the role of single factors in affecting mosquito distributions can be misleading. Instead, multiple factors may interact to affect oviposition patterns and larval performance.     

Anatomical funneling, sparse connectivity and redundancy reduction in the neural networks of the basal ganglia

The major anatomical characteristics of the main axis of the basal ganglia are: (1) Numerical reduction in the number of neurons across layers of the feed-forward network, (2) lateral inhibitory connections within the layers, and (3) neuro-modulatory effects of dopamine and acetylcholine, both on the basal ganglia neurons and on the efficacy of information transmission along the basal ganglia axis. We recorded the simultaneous activity of neurons in the output stages of the basal ganglia as well as the activity of dopaminergic and cholinergic neurons during the performance of a probability decision-making task. We found that the functional messages of the cholinergic and dopaminergic neurons differ, and that the cholinergic message is less specific than that of the dopaminergic neurons. The output stage of the basal ganglia showed uncorrelated neuronal activity. We conclude that despite the huge numerical reduction from the cortex to the output nuclei of the basal ganglia, the activity of these nuclei represents an optimally compressed (uncorrelated) version of distinctive features of cortical information.     

Optimal gene partition into operons correlates with gene functional order

Gene arrangement into operons varies between bacterial species. Genes in a given system can be on one operon in some organisms and on several operons in other organisms. Existing theories explain why genes that work together should be on the same operon, since this allows for advantageous lateral gene transfer and accurate stoichiometry. But what causes the frequent separation into multiple operons of co-regulated genes that act together in a pathway? Here we suggest that separation is due to benefits made possible by differential regulation of each operon. We present a simple mathematical model for the optimal distribution of genes into operons based on a balance of the cost of operons and the benefit of regulation that provides 'just-when-needed' temporal order. The analysis predicts that genes are arranged such that genes on the same operon do not skip functional steps in the pathway. This prediction is supported by genomic data from 137 bacterial genomes. Our work suggests that gene arrangement is not only the result of random historical drift, genome re-arrangement and gene transfer, but has elements that are solutions of an evolutionary optimization problem. Thus gene functional order may be inferred by analyzing the operon structure across different genomes.     

Yield, transpiration and growth of tomatoes under combined excess boron and salinity stress

Boron is essential to growth at low concentrations and limits growth and yield when in excess. Little is known regarding plant response to excess boron (B) and salinity occurring simultaneously. The influences of B and salinity on tomatoes (Lycopersicon esculentum Mill. Cv `5656') were investigated in lysimeters. Salinity levels were 1, 3, 6 and 9 dSm^–1 and B levels were 0.028, 0.185, 0.37, 0.74, 1.11, 1.48 mol m^–3. Excess boron was found to decrease yield and transpiration of tomatoes. This effect was inhibited when plants were exposed to simultaneous B and salinity stresses. Both irrigation water salinity and boron concentration influenced water use of the plants in the same manner as they influenced yield. While yield was found to decrease with increased boron concentration in leaf tissue, increased salinity led to decreased boron accumulation. Yield response was found to correlate better to B concentration in irrigation water and soil solution than to plant tissue B content. A dominant-stress-factor model was assumed and validated. The model applies the principle that when a plant is submitted to conditions of stress caused by B in conjunction with salinity, the more severe stress determines yield. The results of this study have significance in modeling and management of high salinity high boron conditions. Under saline conditions, differences in crop yield and in water use may not be experienced over a significant range of boron concentrations.     

A highly conductive drainage extension to control the lower boundary condition of lysimeters

Lysimeters are used to study and monitor water, fertilizers, salts and other contaminants and are particularly valuable in transpiration and evapotranspiration research. Saturation at the soil bottom boundary in a lysimeter is inherent to its design. A drainage extension made of porous media with high hydraulic conductivity and substantial water holding capacity was devised to extend the lysimeter in order to produce soil moisture conditions mimicking those in the field. Design criteria that assure equal discharge in the soil and in the highly conductive drain (HCD) were established and formulated. Desired matric head at the lysimeter base is determined by HCD extension length. Its value can be manipulated and can range between saturation and the soil's field capacity. Conditions where the HCD is not limiting to flow are obtained through selection of the appropriate cross sectional area ratio between the soil in the lysimeter and the HCD. The validity of these criteria was confirmed with 200 l working lysimeters in the field, with and without plants, and with detailed flow tests utilizing smaller (15 l) lysimeters. Comparison of computed and measured matric head and leachate volume indicates that the proposed method can serve to maintain conditions similar to those in the field.     

A possible role for flowering locus T‐encoding genes in interpreting environmental and internal cues affecting olive (Olea europaea L.) flower induction

Olive (Olea europaea L.) inflorescences, formed in lateral buds, flower in spring. However, there is some debate regarding time of flower induction and inflorescence initiation. Olive juvenility and seasonality of flowering were altered by overexpressing genes encoding flowering locus T (FT). OeFT1 and OeFT2 caused early flowering under short days when expressed in Arabidopsis. Expression of OeFT1/2 in olive leaves and OeFT2 in buds increased in winter, while initiation of inflorescences occurred i n late winter. Trees exposed to an artificial warm winter expressed low levels of OeFT1/2 in leaves and did not flower. Olive flower induction thus seems to be mediated by an increase in FT levels in response to cold winters. Olive flowering is dependent on additional internal factors. It was severely reduced in trees that carried a heavy fruit load the previous season (harvested in November) and in trees without fruit to which cold temperatures were artificially applied in summer. Expression analysis suggested that these internal factors work either by reducing the increase in OeFT1/2 expression or through putative flowering repressors such as TFL1. With expected warmer winters, future consumption of olive oil, as part of a healthy Mediterranean diet, should benefit from better understanding these factors.     

Biphasic response as a mechanism against mutant takeover in tissue homeostasis circuits

Tissues use feedback circuits in which cells send signals to each other to control their growth and survival. We show that such feedback circuits are inherently unstable to mutants that misread the signal level: Mutants have a growth advantage to take over the tissue, and cannot be eliminated by known cell‐intrinsic mechanisms. To resolve this, we propose that tissues have biphasic responses in which the signal is toxic at both high and low levels, such as glucotoxicity of beta cells, excitotoxicity in neurons, and toxicity of growth factors to T cells. This gives most of these mutants a frequency‐dependent selective disadvantage, which leads to their elimination. However, the biphasic mechanisms create a new unstable fixed point in the feedback circuit beyond which runaway processes can occur, leading to risk of diseases such as diabetes and neurodegenerative disease. Hence, glucotoxicity, which is a dangerous cause of diabetes, may have a protective anti‐mutant effect. Biphasic responses in tissues may provide an evolutionary stable strategy that avoids invasion by commonly occurring mutants, but at the same time cause vulnerability to disease.