Delayed maturation of nodules reduces symbiotic effectiveness of the Lotus japonicus-Rhizobium sp. NGR234 interaction

Lotus japonicus, a model legume, develops an efficient, nitrogen-fixing symbiosis with Mesorhizobium loti that promotes plant growth. Lotus japonicus also forms functional nodules with Rhizobium sp. NGR234 and R. etli. Yet, in a plant defence-like reaction, nodules induced by R. etli quickly degenerate, thus limiting plant growth. In contrast, nodules containing NGR234 are long-lasting. It was found that NGR234 initiates nodule formation in a similar way to M. loti MAFF303099, but that the nodules which develop on eleven L. japonicus ecotypes are less efficient in fixing nitrogen. Detailed examination of nodulation of L. japonicus cultivar MG-20 revealed that symbiosomes formed four weeks after inoculation by NGR234 are enlarged in comparison with MAFF303099 and contain multiple bacteroids. Nevertheless, nodules formed by NGR234 fix sufficient nitrogen to avoid rejection by the plant. With time, these nodules develop into fully efficient organs containing bacteroids tightly enclosed in symbiosome membranes, just like those formed by M. loti MAFF303099. This work demonstrates the usefulness of using the well-characterized micro-symbiont NGR234 to study symbiotic signal exchange in the later stages of rhizobia-legume symbioses, especially given the large range of bacterial (NGR234) and plant (L. japonicus) mutants that are availabl

Role of BacA in Lipopolysaccharide Synthesis, Peptide Transport, and Nodulation by \u3cem\u3eRhizobium\u3c/em\u3e sp. Strain NGR234

BacA of Sinorhizobium meliloti plays an essential role in the establishment of nitrogen-fixing symbioses with Medicago plants, where it is involved in peptide import and in the addition of very-long-chain fatty acids (VLCFA) to lipid A of lipopolysaccharide (LPS). We investigated the role of BacA in Rhizobium species strain NGR234 by mutating the bacA gene. In the NGR234 bacA mutant, peptide import was impaired, but no effect on VLCFA addition was observed. More importantly, the symbiotic ability of the mutant was comparable to that of the wild type for a variety of legume species. Concurrently, an acpXL mutant of NGR234 was created and assayed. In rhizobia, AcpXL is a dedicated acyl carrier protein necessary for the addition of VLCFA to lipid A. LPS extracted from the NGR234 mutant lacked VLCFA, and this mutant was severely impaired in the ability to form functional nodules with the majority of legumes tested. Our work demonstrates the importance of VLCFA in the NGR234-legume symbiosis and also shows that the necessity of BacA for bacteroid differentiation is restricted to specific legume-Rhizobium interactions

Cyclic-β-glucans of Rhizobium (Sinorhizobium) sp. strain NGR234 are required for hypo-osmotic adaptation, motility, and efficient symbiosis with host plants

Cyclic-β-glucans (CβG) consist of cyclic homo-polymers of glucose that are present in the periplasmic space of many Gram-negative bacteria. A number of studies have demonstrated their importance for bacterial infection of plant and animal cells. In this study, a mutant of Rhizobium (Sinorhizobium) sp. strain NGR234 (NGR234) was generated in the cyclic glucan synthase (ndvB)-encoding gene. The great majority of CβG produced by wild-type NGR234 are negatively charged and substituted. The ndvB mutation abolished CβG biosynthesis. We found that, in NGR234, a functional ndvB gene is essential for hypo-osmotic adaptation and swimming, attachment to the roots, and efficient infection of Vigna unguiculata and Leucaena leucocephal

A Screen-Peck Task for Investigating Cognitive Bias in Laying Hens

Affect-induced cognitive judgement biases occur in both humans and animals. Animals in a more negative affective state tend to interpret ambiguous cues more negatively than animals in a more positive state and vice versa. Investigating animals' responses to ambiguous cues can therefore be used as a proxy measure of affective state. We investigated laying hens' responses to ambiguous stimuli using a novel cognitive bias task. In the 'screen-peck' task, hens were trained to peck a high/low saturation orange circle presented on a computer screen (positive cue-P) to obtain a mealworm reward, and to not peck when the oppositely saturated orange circle was presented (negative cue-N) to avoid a one second air puff. Ambiguous cues were orange circles of intermediate saturation between the P and N cue (near-positive-NP; middle-M; near-negative-NN), and were unrewarded. Cue pecking showed a clear generalisation curve from P through NP, M, NN to N suggesting that hens were able to associate colour saturation with reward or punishment, and could discriminate between stimuli that were more or less similar to learnt cues. Across six test sessions, there was no evidence for extinction of pecking responses to ambiguous cues. We manipulated affective state by changing temperature during testing to either ~20°C or ~29°C in a repeated measures cross-over design. Hens have been shown to prefer temperatures in the higher range and hence we assumed that exposure to the higher temperature would induce a relatively positive affective state. Hens tested under warmer conditions were significantly more likely to peck the M probe than those tested at cooler temperatures suggesting that increased temperature in the ranges tested here may have some positive effect on hens, inducing a positive cognitive bias

Characterising particulate random media from near-surface backscattering: A machine learning approach to predict particle size and concentration

To what extent can particulate random media be characterised using direct wave backscattering from a single receiver/source? Here, in a two-dimensional setting, we show using a machine learning approach that both the particle radius and concentration can be accurately measured when the boundary condition on the particles is of Dirichlet type. Although the methods we introduce could be applied to any particle type. In general backscattering is challenging to interpret for a wide range of particle concentrations, because multiple scattering cannot be ignored, except in the very dilute range. Across the concentration range from 1% to 20% we find that the mean backscattered wave field is sufficient to accurately determine the concentration of particles. However, to accurately determine the particle radius, the second moment, or average intensity, of the backscattering is necessary. We are also able to determine what is the ideal frequency range to measure a broad range of particles sizes. To get rigorous results with supervised machine learning requires a large, highly precise, dataset of backscattered waves from an infinite half-space filled with particles. We are able to create this dataset by introducing a numerical approach which accurately approximates the backscattering from an infinite half-space.EPSRC Grant EP/K033208/I and EP/R014604/

Comorbidities in the diseasome are more apparent than real: What Bayesian filtering reveals about the comorbidities of depression

Comorbidity patterns have become a major source of information to explore shared mechanisms of pathogenesis between disorders. In hypothesis-free exploration of comorbid conditions, disease-disease networks are usually identified by pairwise methods. However, interpretation of the results is hindered by several confounders. In particular a very large number of pairwise associations can arise indirectly through other comorbidity associations and they increase exponentially with the increasing breadth of the investigated diseases. To investigate and filter this effect, we computed and compared pairwise approaches with a systems-based method, which constructs a sparse Bayesian direct multimorbidity map (BDMM) by systematically eliminating disease-mediated comorbidity relations. Additionally, focusing on depression-related parts of the BDMM, we evaluated correspondence with results from logistic regression, text-mining and molecular-level measures for comorbidities such as genetic overlap and the interactome-based association score. We used a subset of the UK Biobank Resource, a cross-sectional dataset including 247 diseases and 117,392 participants who filled out a detailed questionnaire about mental health. The sparse comorbidity map confirmed that depressed patients frequently suffer from both psychiatric and somatic comorbid disorders. Notably, anxiety and obesity show strong and direct relationships with depression. The BDMM identified further directly co-morbid somatic disorders, e.g. irritable bowel syndrome, fibromyalgia, or migraine. Using the subnetwork of depression and metabolic disorders for functional analysis, the interactome-based system-level score showed the best agreement with the sparse disease network. This indicates that these epidemiologically strong disease-disease relations have improved correspondence with expected molecular-level mechanisms. The substantially fewer number of comorbidity relations in the BDMM compared to pairwise methods implies that biologically meaningful comorbid relations may be less frequent than earlier pairwise methods suggested. The computed interactive comprehensive multimorbidity views over the diseasome are available on the web at Co=MorNet: bioinformatics.mit.bme.hu/UKBNetworks

Increasing morphological disparity and decreasing optimality for jaw speed and strength during the radiation of jawed vertebrates

The Siluro-Devonian adaptive radiation of jawed vertebrates, which underpins almost all living vertebrate biodiversity, is characterized by the evolutionary innovation of the lower jaw. Multiple lines of evidence have suggested that the jaw evolved from a rostral gill arch, but when the jaw took on a feeding function remains unclear. We quantified the variety of form in the earliest jaws in the fossil record from which we generated a theoretical morphospace that we then tested for functional optimality. By drawing comparisons with the real jaw data and reconstructed jaw morphologies from phylogenetically inferred ancestors, our results show that the earliest jaw shapes were optimized for fast closure and stress resistance, inferring a predatory feeding function. Jaw shapes became less optimal for these functions during the later radiation of jawed vertebrates. Thus, the evolution of jaw morphology has continually explored previously unoccupied morphospace and accumulated disparity through time, laying the foundation for diverse feeding strategies and the success of jawed vertebrates

Regional default mode network connectivity in major depressive disorder

The relationship between altered default mode network (DMN) connectivity and abnormal serotonin function in major depressive disorder (MDD) has not been investigated. Using intravenous citalopram and resting-state fMRI, we investigated DMN intra-network connectivity and serotonin function in 77 healthy controls and patients with MDD. There were no significant main effects of MDD or citalopram on DMN intra-network connectivity; however, significant interactions indicated that group differences under saline were modified by citalopram. In MDD patients during saline infusion, in contrast with controls, the DMN (i) did not include the precuneus that was instead part of an anti-correlated network but (ii) did include amygdala that was part of the anti-correlated network in controls. Citalopram infusion in MDD patients restored the pattern seen in controls under saline. In healthy controls, citalopram infusion disengaged the precuneus from the DMN and engaged the amygdala, partially reproducing the abnormalities seen under saline in MDD. In exploratory analyses within the MDD group, greater rumination self-ratings were associated with greater intra-network connectivity of the anterior cingulate cortex with the DMN. We hypothesise that, in MDD, disengagement of the precuneus from the DMN relates to overgeneral memory bias in rumination. The opposite effect, with greater engagement of the amygdala in the DMN, reflects the negative valence of rumination. Reversal of these abnormalities by citalopram suggests that they may be related to impaired serotonin function. That citalopram engaged the amygdala in the DMN in controls may relate to the paradoxical effects on aversive processing seen with acute SSRIs in healthy subjects

Reversed Frontotemporal Connectivity During Emotional Face Processing in Remitted Depression

BackgroundVulnerability to relapse persists after remission of an acute episode of major depressive disorder. This has been attributed to abnormal biases in the processing of emotional stimuli in limbic circuits. However, neuroimaging studies have not so far revealed consistent evidence of abnormal responses to emotional stimuli in limbic structures, such as the amygdala, in remitted depression. This suggests the problem might lie in the integrated functioning of emotion processing circuits.MethodsWe recruited 22 unmedicated patients in remission from major depressive disorder (rMDD) and 21 age-matched healthy control subjects. Functional magnetic resonance imaging was performed during a face emotion processing task. Dynamic causal modeling was used with Bayesian model selection to determine the most likely brain networks and valence-specific modulation of connectivity in healthy control subjects and rMDD.ResultsIn healthy volunteers, sad faces modulated bi-directional connections between amygdala and orbitofrontal cortex and between fusiform gyrus and orbitofrontal cortex. Happy faces modulated unidirectional connections from fusiform gyrus to orbitofrontal cortex. In rMDD, the opposite pattern was observed, with evidence of happy faces modulating bidirectional frontotemporal connections and sad faces modulating unidirectional fusiform–orbitofrontal connections.ConclusionsParticipants with rMDD have abnormal modulation of frontotemporal effective connectivity in response to happy and sad face emotions, despite normal activations within each region. Specifically, processing of mood incongruent happy information was associated with a more richly modulated frontotemporal brain network, whereas mood congruent sad information was associated with less network modulation. This supports a hypothesis of dysfunction within cortico–limbic connections in individuals vulnerable to depression