Comparative genome analysis of Lactobacillus casei strains isolated from Actimel and Yakult products reveals marked similarities and points to a common origin

Corrigendum: Douillard, F. P., Kant, R., Ritari, J., Paulin, L., Palva, A. & de Vos, W. M. Microbial Biotechnology 2014, 7, 1, p. 85, DOI: 10.1111/1751-7915.12095Peer reviewe

Improved algorithm for neuronal ensemble inference by Monte Carlo method

Neuronal ensemble inference is one of the significant problems in the study of biological neural networks. Various methods have been proposed for ensemble inference from their activity data taken experimentally. Here we focus on Bayesian inference approach for ensembles with generative model, which was proposed in recent work. However, this method requires large computational cost, and the result sometimes gets stuck in bad local maximum solution of Bayesian inference. In this work, we give improved Bayesian inference algorithm for these problems. We modify ensemble generation rule in Markov chain Monte Carlo method, and introduce the idea of simulated annealing for hyperparameter control. We also compare the performance of ensemble inference between our algorithm and the original one.Comment: 14 pages, 3 figure

Characterization of Highly Mucus-Adherent Non-GMO Derivatives of Lacticaseibacillus rhamnosus GG

Lacticaseibacillus rhamnosusGG is one of the best studied lactic acid bacteria in the context of probiotic effects.L. rhamnosusGG has been shown to prevent diarrhea in children and adults and has been implicated to have mitigating or preventive effects in several disorders connected to microbiota dysbiosis. The probiotic effects are largely attributed to its adhesive heterotrimeric sortase-dependent pili, encoded by thespaCBA-srtC1gene cluster. Indeed, the strain-specific SpaCBA pili have been shown to contribute to adherence, biofilm formation and host signaling. In this work we set out to generate non-GMO derivatives ofL. rhamnosusGG that adhere stronger to mucus compared to the wild-type strain using chemical mutagenesis. We selected 13 derivatives that showed an increased mucus-adherent phenotype. Deep shotgun resequencing of the strains enabled division of the strains into three classes, two of which revealed SNPs (single nucleotide polymorphisms) in thespaAandspaCgenes encoding the shaft and tip adhesive pilins, respectively. Strikingly, the other class derivatives demonstrated less clear genotype - phenotype relationships, illustrating that pili biogenesis and structure is also affected by other processes. Further characterization of the different classes of derivatives was performed by PacBio SMRT sequencing and RNAseq analysis, which resulted in the identification of molecular candidates driving pilin biosynthesis and functionality. In conclusion, we report on the generation and characterization of three classes of strongly adherentL. rhamnosusGG derivatives that show an increase in adhesion to mucus. These are of special interest as they provide a window on processes and genes driving piliation and its control inL. rhamnosusGG and offer a variety of non-GMO derivatives of this key probiotic strain that are applicable in food products.Peer reviewe

Whole-brain computation of cognitive versus acoustic errors in music : A mismatch negativity study

Previous studies have evidenced how the local prediction of physical stimulus features may affect the neural processing of incoming stimuli. Less known are the effects of cognitive priors on predictive processes, and how the brain computes local versus cognitive predictions and their errors. Here, we determined the differential brain mechanisms underlying prediction errors related to high-level, cognitive priors for melody (rhythm, contour) versus low-level, local acoustic priors (tuning, timbre). We measured with magnetoencephalography the mismatch negativity (MMN) prediction error signal in 104 adults having varying levels of musical expertise. We discovered that the brain regions involved in early predictive processes for local priors were primary and secondary auditory cortex and insula, whereas cognitive brain regions such as cingulate and orbitofrontal cortices were recruited for early melodic errors in cognitive priors. The involvement of higher-level brain regions for computing early cognitive errors was enhanced in musicians, especially in cingulate cortex, inferior frontal gyrus, and supplementary motor area. Overall, the findings expand knowledge on whole-brain mechanisms of predictive processing and the related MMN generators, previously mainly confined to the auditory cortex, to a frontal network that strictly depends on the type of priors that are to be computed by the brain.Peer reviewe

The N-Terminal GYPSY Motif Is Required for Pilin-Specific Sortase SrtC1 Functionality in Lactobacillus rhamnosus Strain GG

Predominantly identified in pathogenic Gram-positive bacteria, sortase-dependent pili are also found in commensal species, such as the probiotic-marketed strain Lactobacillus rhamnosus strain GG. Pili are typically associated with host colonization, immune signalling and biofilm formation. Comparative analysis of the N-terminal domains of pilin-specific sortases from various piliated Gram-positive bacteria identified a conserved motif, called GYPSY, within the signal sequence. We investigated the function and role of the GYPSY residues by directed mutagenesis in homologous (rod-shaped) and heterologous (coccoid-shaped) expression systems for pilus formation. Substitutions of some of the GYPSY residues, and more specifically the proline residue, were found to have a direct impact on the degree of piliation of Lb. rhamnosus GG. The present findings uncover a new signalling element involved in the functionality of pilin-specific sortases controlling the pilus biogenesis of Lb. rhamnosus GG and related piliated Gram-positive species.Peer reviewe

A computational study on altered theta-gamma coupling during learning and phase coding

There is considerable interest in the role of coupling between theta and gamma oscillations in the brain in the context of learning and memory. Here we have used a neural network model which is capable of producing coupling of theta phase to gamma amplitude firstly to explore its ability to reproduce reported learning changes and secondly to memory-span and phase coding effects. The spiking neural network incorporates two kinetically different GABAA receptor-mediated currents to generate both theta and gamma rhythms and we have found that by selective alteration of both NMDA receptors and GABAA,slow receptors it can reproduce learning-related changes in the strength of coupling between theta and gamma either with or without coincident changes in theta amplitude. When the model was used to explore the relationship between theta and gamma oscillations, working memory capacity and phase coding it showed that the potential storage capacity of short term memories, in terms of nested gamma-subcycles, coincides with the maximal theta power. Increasing theta power is also related to the precision of theta phase which functions as a potential timing clock for neuronal firing in the cortex or hippocampus

Low-cost irradiance sensors for irradiation assessments inside tree canopies.

The solar irradiation that a crop receives is directly related to the physical and biological processes that affect the crop. However, the assessment of solar irradiation poses certain problems when it must be measured through fruit inside the canopy of a tree. In such cases, it is necessary to check many test points, which usually requires an expensive data acquisition system. The use of conventional irradiance sensors increases the cost of the experiment, making them unsuitable. Nevertheless, it is still possible to perform a precise irradiance test with a reduced price by using low-cost sensors based on the photovoltaic effect. The aim of this work is to develop a low-cost sensor that permits the measurement of the irradiance inside the tree canopy. Two different technologies of solar cells were analyzed for their use in the measurement of solar irradiation levels inside tree canopies. Two data acquisition system setups were also tested and compared. Experiments were performed in Ademuz (Valencia, Spain) in September 2011 and September 2012 to check the validity of low-cost sensors based on solar cells and their associated data acquisition systems. The observed difference between solar irradiation at high and low positions was of 18.5% ± 2.58% at a 95% confidence interval. Large differences were observed between the operations of the two tested sensors. In the case of a-Si cells based mini-modules, an effect of partial shadowing was detected due to the larger size of the devices, the use of individual c-Si cells is recommended over a-Si cells based mini-modules

Obliteration of radical cavities with autogenous cortical bone; long-term results

<p>Abstract</p> <p>Background</p> <p>To evaluate the long-term surgical outcome(s) in patients who have undergone canal-wall-down operation with mastoid and epitympanic obliteration using autologous cortical bone chips, bone pate and meatally-based musculoperiosteal flap technique.</p> <p>Method</p> <p>Retrospective evaluation of seventy patients operated during 1986–1991 due to a cholesteatoma. An otomicroscopy was performed to evaluate the postoperative outer ear canal configuration with a modified Likert scale (1 – 4). The outer ear canal physical volume was assessed by tympanometry. The hearing outcome and a patient-filled questionnaire were also analyzed.</p> <p>Results</p> <p>The posterior wall results were 1.8 (± 0.9 SD) and the attic region 1.8 (± 0.9 SD) (ns., p > 0.05). These values show either no cavity formation or minor formation of a cavity, with a good functional result. The mean volume of the operated ear canal was 1.7 (± 0.5 SD) ml. The volume of the contralateral ear canal was 1.2 (± 0.3 SD) ml (*** p < 0.0001). A comparison of the current mean ABG to the preoperative mean ABG and to the ABG at one-year postoperatively, 5-years postoperatively or 10-years postoperatively showed no statistical significance (p > 0.05).</p> <p>Conclusion</p> <p>ABG does not significantly change in the long-term. The configuration of the cavity tends to change, however, the obliteration material is stable in the long-term and clinically significant cavitation rarely occurs.</p

Representation of Time-Varying Stimuli by a Network Exhibiting Oscillations on a Faster Time Scale

Sensory processing is associated with gamma frequency oscillations (30–80 Hz) in sensory cortices. This raises the question whether gamma oscillations can be directly involved in the representation of time-varying stimuli, including stimuli whose time scale is longer than a gamma cycle. We are interested in the ability of the system to reliably distinguish different stimuli while being robust to stimulus variations such as uniform time-warp. We address this issue with a dynamical model of spiking neurons and study the response to an asymmetric sawtooth input current over a range of shape parameters. These parameters describe how fast the input current rises and falls in time. Our network consists of inhibitory and excitatory populations that are sufficient for generating oscillations in the gamma range. The oscillations period is about one-third of the stimulus duration. Embedded in this network is a subpopulation of excitatory cells that respond to the sawtooth stimulus and a subpopulation of cells that respond to an onset cue. The intrinsic gamma oscillations generate a temporally sparse code for the external stimuli. In this code, an excitatory cell may fire a single spike during a gamma cycle, depending on its tuning properties and on the temporal structure of the specific input; the identity of the stimulus is coded by the list of excitatory cells that fire during each cycle. We quantify the properties of this representation in a series of simulations and show that the sparseness of the code makes it robust to uniform warping of the time scale. We find that resetting of the oscillation phase at stimulus onset is important for a reliable representation of the stimulus and that there is a tradeoff between the resolution of the neural representation of the stimulus and robustness to time-warp. Author Summary Sensory processing of time-varying stimuli, such as speech, is associated with high-frequency oscillatory cortical activity, the functional significance of which is still unknown. One possibility is that the oscillations are part of a stimulus-encoding mechanism. Here, we investigate a computational model of such a mechanism, a spiking neuronal network whose intrinsic oscillations interact with external input (waveforms simulating short speech segments in a single acoustic frequency band) to encode stimuli that extend over a time interval longer than the oscillation's period. The network implements a temporally sparse encoding, whose robustness to time warping and neuronal noise we quantify. To our knowledge, this study is the first to demonstrate that a biophysically plausible model of oscillations occurring in the processing of auditory input may generate a representation of signals that span multiple oscillation cycles.National Science Foundation (DMS-0211505); Burroughs Wellcome Fund; U.S. Air Force Office of Scientific Researc

Explicit processing of verbal and spatial features during letter-location binding modulates oscillatory activity of a fronto-parietal network.

The present study investigated the binding of verbal and spatial features in immediate memory. In a recent study, we demonstrated incidental and asymmetrical letter-location binding effects when participants attended to letter features (but not when they attended to location features) that were associated with greater oscillatory activity over prefrontal and posterior regions during the retention period. We were interested to investigate whether the patterns of brain activity associated with the incidental binding of letters and locations observed when only the verbal feature is attended differ from those reflecting the binding resulting from the controlled/explicit processing of both verbal and spatial features. To achieve this, neural activity was recorded using magnetoencephalography (MEG) while participants performed two working memory tasks. Both tasks were identical in terms of their perceptual characteristics and only differed with respect to the task instructions. One of the tasks required participants to process both letters and locations. In the other, participants were instructed to memorize only the letters, regardless of their location. Time–frequency representation of MEG data based on the wavelet transform of the signals was calculated on a single trial basis during the maintenance period of both tasks. Critically, despite equivalent behavioural binding effects in both tasks, single and dual feature encoding relied on different neuroanatomical and neural oscillatory correlates. We propose that enhanced activation of an anterior–posterior dorsal network observed in the task requiring the processing of both features reflects the necessity for allocating greater resources to intentionally process verbal and spatial features in this task